VictorJuiz/thesis huggingface dataset:
X-ray studies concerning the structure of 6-phosphogluconate dehydrogenase

This thesis is concerned with the structure determination of 6-phosphogluconate dehydrogenase (6-phospho-D-gluconate:NADP+ oxidoreductase (decarboxylating), E.C.1.1.1.44) from sheep liver. This protein is the second enzyme in the pentose phosphate pathway and catalyses the conversion of 6-phosphogluconate to ribulose-5-phosphate and CO2.
Chapter 1 gives an introduction to the chemical properties of 6-phosphogluconate dehydrogenase (6PGDH) and compares these properties for the enzyme from a variety of sources. The common structural features of the NAD+-dependent dehydrogenases are discussed in terms of divergent and convergent evolution. Details of an NADP+-dependent enzyme, E.coli dihydrofolate reductase are also given. This is the only published high resolution structure of an NADP+-dependent enzyme to date (Matthews et al. (1977)).
The crystallographic techniques used in the course of this work are discussed in Chapter 2. Particular attention is paid to the application of synchrotron radiation in protein crystallography in optimising heavy atom anomalous scattering. Appendix I also gives some experimental details relevant to this.
Chapters 3, 4, and 5 give details of the structural results. In Chapter 3 the low resolution (6 Å) structure is presented with a full analysis of the derivatives (KAu(CN)2 and K2Pt(CN)4) used in the double derivative phase determination. The 6 Å electron density map could be interpreted. It showed the overall shape of the monomer and enabled the dimer axis to be identified. It also yielded the structurally interesting features of several long columns of density of the correct cross section for α-helix and also a cleft region. Chapter 4 is concerned with the determination of the coenzyme (NADP+) binding position at 6 Å resolution. Difference electron density maps calculated from X-ray measurements on crystals soaked in the oxidised coenzyme indicated the binding of NADP+ in the cleft region. Also, by using an iodinated derivative of the coenzyme, iodopyridine adenine dinucleotide phosphate (IADP+), it was possible to identify the nicotinamide moiety of the coenzyme and thus orient the coenzyme with respect to the enzyme. Chapter 5 describes the screenless rotation method and its application to the 2.6 Å crystallographic study of 6PGDH. In particular, the collection of the data for the native enzyme crystals and the K2Pt(CN)4 derivative. The phases calculated at 6 Å with two derivatives (as described in §3) were extended to 2.7 Å by calculating phases, using the photographic data, by the method of single isomorphous replacement with anomalous scattering. This enabled an electron density map to be calculated to 2.7 Å. Preliminary details of the quality of this electron density map are given.

Advisor: Adams, M
The role of histone modification in DNA double-strand break repair in Schizosaccharomyces pombe

DNA double-strand breaks (DSBs) are highly genotoxic lesions, which when incorrectly repaired can lead to gross chromosomal rearrangements and tumourigenesis through oncogene activation or loss of heterozygosity at tumour suppressor loci. Chromatin structure and therefore histone modification can play a key role in the repair of these lesions through affecting the access of repair machinery to the break. To identify novel histone-modifying enzymes involved in DSB repair, nineteen histone-modifying mutants from an S. pombe deletion library were screened for altered DSB repair. Eleven genes were identified as required for normal DSB repair: set1⁺, set2⁺, mst2⁺, sir2⁺, set3⁺, set11⁺, hat1⁺, set13⁺, clr4⁺, gcn5⁺ and elp3⁺. Two genes, hat1⁺ and set13⁺ are required for efficient homologous recombination (HR). In addition, four genes set1⁺, set2⁺, set3⁺ and mst2⁺ are required for non-homologous end-joining (NHEJ). Analysis of set1Δ, set2Δ, set3Δ and mst2Δ deletion mutants showed impaired NHEJ was associated with significantly increased levels of repair by HR, supporting the existence of a competitive relationship between these mechanisms of repair.
Further work focused on Set2, a H3K36 methyltransferase. In addition to a role for Set2 in NHEJ, a role for Set2 in promoting efficient DNA replication was identified. This is likely through regulation of MBF-dependent genes. However, this altered progression of DNA replication was not responsible for the repair phenotype seen. The methyltransferase activity of Set2 was required for its role in NHEJ and DNA replication. Further analysis of a H3K36R mutant identified an additional role for H3K36 in DSB repair. Results indicate that H3K36 is also acetylated by Gcn5; quantitative analysis of DSB repair in a gcn5Δ mutant, identified a role for Gcn5 in promoting HR repair. Modification of H3K36 by methylation and acetylation is mutually exclusive, and preliminary analysis of the levels of these modifications suggests that they are cell cycle controlled. The findings presented here support a model whereby differential modification of H3K36 by Gcn5 and Set2 defines the DNA repair mechanism utilised. Methylation of H3K36 by Set2, which peaks in G1, promotes NHEJ whereas acetylation of H3K36 by Gcn5, which peaks in S phase, promotes HR.

Keywords: DNA repair
Advisor: Humphrey, T
Multiple sequence analysis in the presence of alignment uncertainty

Sequence alignment is one of the most intensely studied problems in bioinformatics, and is an important step in a wide range of analyses. An issue that has gained much attention in recent years is the fact that downstream analyses are often highly sensitive to the specific choice of alignment.
One way to address this is to jointly sample alignments along with other parameters of interest. In order to extend the range of applicability of this approach, the first chapter of this thesis introduces a probabilistic evolutionary model for protein structures on a phylogenetic tree; since protein structures typically diverge much more slowly than sequences, this allows for more reliable detection of remote homologies, improving the accuracy of the resulting alignments and trees, and reducing sensitivity of the results to the choice of dataset. In order to carry out inference under such a model, a number of new Markov chain Monte Carlo approaches are developed, allowing for more efficient convergence and mixing on the high-dimensional parameter space.
The second part of the thesis presents a directed acyclic graph (DAG)-based approach for representing a collection of sampled alignments. This DAG representation allows the initial collection of samples to be used to generate a larger set of alignments under the same approximate distribution, enabling posterior alignment probabilities to be estimated reliably from a reasonable number of samples. If desired, summary alignments can then be generated as maximum-weight paths through the DAG, under various types of loss or scoring functions.
The acyclic nature of the graph also permits various other types of algorithms to be easily adapted to operate on the entire set of alignments in the DAG. In the final part of this work, methodology is introduced for alignment-DAG-based sequence annotation using hidden Markov models, and RNA secondary structure prediction using stochastic context-free grammars. Results on test datasets indicate that the additional information contained within the DAG allows for improved predictions, resulting in substantial gains over simply analysing a set of alignments one by one.

Keywords: Markov chain Monte Carlo
structural alignment
stochastic context-free grammars
graphical models
globin evolution
multiple sequence alignment
statistical alignment
sequence annotation
Bayesian phylogenetics
alignment uncertainty
directed acyclic graphs
hidden Markov models
RNA secondary structure
Advisor: Hein, J
The Role of Hypoxia-Regulated MicroRNA in Cancer

MicroRNAs (miRNAs) are short, non-coding RNA sequences which regulate gene expression. Regulation is mediated primarily through binding to complementary sites in their un-translated regions which leads to mRNA degradation or translational repression. Hypoxia is a known feature of many tumours, and increased hypoxia is associated with poor prognosis. Hypoxia leads to the up-regulation of many genes involved in a variety of functions including angiogenesis, a shift to glycolytic metabolism, and cell proliferation. This is mediated by the heterodimeric transcription factor HIF (hypoxia inducible factor), which is stabilised in hypoxia. In normoxia, the von-Hippel Lindau protein (VHL) targets HIF for degradation. Mutation in the VHL gene, as is frequently seen in clear cell renal cell cancer (CCRCC), results in constitutive over-expression of HIF and its gene targets, leading to a pro-angiogenic and pro-tumourigenic state.
This thesis examined the expression of hypoxia-regulated miRNAs in cancer. The principal aims were to determine gene targets of miR-210, and to explore the effects of its over-expression and knock-down, both in vitro and in vivo. The expression of hypoxia-regulated miRNAs was examined in clinical renal tumour samples with matched normal tissue controls, and correlated with VHL mutation status.
It was found that miR-210 targeted the iron sulphur cluster homologue (ISCU) gene, and was responsible for much of its down-regulation in hypoxia. Knock-down of ISCU had consequences on cell metabolism, in particular involving mitochondrial function and iron metabolism. miR-210 was found to be highly over-expressed in clear cell renal tumours (CCRCC), with greater expression seen in tumours with VHL mutations. miR-210 over-expression was also observed in papillary renal tumours, but to a lesser extent than in CCRCCs. miR-210 expression appeared to be correlated with reduced stage and grade, and improved survival. ISCU protein expression in CCRCCs was determined by immunohistochemistry, which showed that its expression correlated negatively with miR-210 expression, suggesting a functional role of miR-210 in vivo.

Keywords: microRNA
hypoxia
renal cancer
Advisor: Harris, A
The morphology and semantics of expressive affixes

This dissertation focuses on two aspects of expressive affixes: their morphological/typological properties and their semantics. With regard to the former, it shows that the expressive morphology of many languages (including Bantu, West Atlantic, Walman, Sanskrit, English, Romance, Slavic, and others), has the following properties: 1) it is systematically anomalous when compared to plain morphology, or the ordinary processes of word-formation and inflection. From this, it follows that many familiar morphological arguments that adduce the data of expressive morphology ought to be reconsidered; and 2) it is far more pervasive than has been traditionally thought. For example, the Sanskrit preverb, and the Indo-European aspectual prefix/particle generally, are shown to have systematically expressive functions.
With respect to the semantics of expressive affixes, it develops a novel multidimensional account, in the sense of Potts (2005, 2007), of Spanish "connotative affixes," which can simultaneously convey descriptive and expressive meaning. It shows that their descriptive meaning is that of a gradable adjective, viewed as a degree relation which includes a measure function, in the sense of Kennedy (1997). The expressive meanings of connotative affixes, and expressives generally, arise as they manipulate the middle coordinate, I, of expressive indices which, it is proposed, is inherently specified on all lexical items and canonically set to "neutral." It introduces a new mechanism, AFF, which is an algebraic operation for manipulating I, and which accounts for the well-known, and seemingly "contradictory," range of meanings that expressive affixes can express. Whereas prior work assumes that expressive affixes are inherently polysemous, this approach derives their many attested meanings and functions (e.g., "small," "young," "bad," deprecation, appreciation, hypocorism, intensification/exactness, and attenuation/approximation, as well as pragmatic effects like illocutionary mitigation) compositionally, from the interactions of their multidimensionality with the meanings of the roots to which they attach.

Keywords: semantics
typology
morphology
pragmatics
expressives
Advisor: Maiden, M
Asudeh, A
Nervous system metabolism

The aim of this thesis was to investigate the cellular biochemistry and metabolism of the human brain in vivo using magnetic resonance as the basic technique. Magnetic resonance imaging (MRI) can provide images of human structure and has already proved to be diagnostically useful in Neurology. Magnetic resonance spectroscopy (MRS) has the potential for measuring the tissue metabolite concentrations and metabolic rates of intracellular reactions in vivo. The great advantage of MRS is that many elements already present in abundance can be used to follow these intracellular reactions; no alien compounds need to be injected into the subject in the hope that they will eventually enter the tissue under investigation. However there are still considerable problems in receiving signal from the region of interest. No single approach in MRS has proved to be suitable for all investigations.
An existing technique in MRS, phase modulated rotating frame imaging (PMRFI) was extended to measure absolute tissue concentration and enzyme flux rates of intracellular compounds containing phosphorus nuclei at above 1mmol/L tissue concentration in tissue volumes greater than 10ml. These technical limitations restricted the work of this thesis to the human cerebral hemispheres.
Adenosine triphosphate (ATP) and phosphocreatine (PCr) are essential cytoplasmic compounds, providing energy for transport and biosynthetic pathways within the cell. Phosphorus MRS can also measure intracellular pH (pHi), providing an insight into ion metabolism within the cell. Finally 31P MRS can also measure the concentration of certain phospholipid groups and their precursors, phosphoethanolamine (PE) and phosphocholine (PC).
The initial work carried out involved the construction, testing and modification of a probe suitable for clinical work. Studies were performed on subjects to establish a normal range for absolute tissue concentrations and enzyme flux rates through creatine phosphokinase. Studies on patients with primary brain tumours, acromegaly, herpes simplex encephalitis, HIV infections and those recovering following severe head injury were studied. Consistent changes in pHi, high energy phosphate and phospholipid metabolism were found in these conditions. The probable mechanisms underlying these changes are discussed and further investigations suggested.

Advisor: Ledingham, J
The thinning of the liquid layer over a probe in two-phase flow

The draining of the thin water film that is formed between a two dimensional, infinite, initially flat oil-water interface and a smooth, symmetric probe, as the interface is advected by a steady and uniform flow parallel to the probe axis, is modelled using classical fluid dynamics. The governing equations are nondimensionalised using values appropriate to the oil extraction industry. The bulk flow is driven by inertia and, in some extremes, surface tension while the viscous effects are initially confined to thin boundary layers on the probe and the interface. The flow in the thin water film is dominated by surface tension, and passes through a series of asymptotic regimes in which inertial forces are gradually overtaken by viscous forces. For each of these regimes, and for those concerning the earlier stages of approach, possible solution strategies are discussed and relevant literature reviewed. Consideration is given to the drainage mechanism around a probe which protrudes a fixed specified distance into the oil. A lubrication analysis of the thin water film may be matched into a capillary-static solution for the outer geometry using a slender transition region if, and only if, the pressure gradient in the film is negative as it meets the static meniscus. The remarkable result is that, in practice, there is a race between rupture in the transition region and rupture at the tip. The analysis is applicable to the case of a very slow far field flow and offers significant insight into the non-static case. Finally, a similar approach is applied to study the motion of the thin water film in the fully inviscid approximation, with surface tension and a density contrast between the fluids.
Materialising kinship, constructing relatedness: kin group display and commemoration in First Intermediate Period and Middle Kingdom Egypt (ca 2150–1650 BCE)

The aim of this thesis is to contribute to the understanding of ancient Egyptian kinship in the First Intermediate Period and Middle Kingdom (ca 2150–1650 BCE) by exploring how forms of relatedness were displayed in the monumental record. Kinship and marriage are contextually driven sociocultural phenomena that should be approached from the actors' perspective; such an approach can achieve some insight into emic notions of kinship, because monuments were integral to society and contributed to perpetuating and sustaining its fabric.
The introduction (chapter 1) presents the theoretical background on which the thesis is based, namely the notion of kinship as process, where relationships can be constructed and reconstructed throughout one’s life. In addition, it provides a working definition of 'kin group', an analytical category that is taken as the primary unit of social analysis that can encompass several ways of being related. Chapter 2 offers a discussion of kinship terminology in the First Intermediate Period and Middle Kingdom. The focus is less on basic kinship terms than on the little understood terminology for kin groups and how these were presented in the written record. Chapter 3 treats stelae, which constitute the core corpus of material for the thesis. Stelae present a variety of images of kin groups and, moreover, they should be considered within the larger units of which they were part. Many of these stelae are unprovenanced but have been attributed to Abydos. At this site, memorial chapels have been identified archaeologically, and some stelae have been found in association with them. Thus, the site offers a materialisation of constellations of relationships. Possible reconstructions of such chapels – one from Saqqara and two from Abydos – are presented in chapter 4, and the impact they may have had on the social memory of visitors is assessed. Display, presence, and performance were some of the ways in which the social role of those groups was communicated. Chapter 5 is concerned with how change and time may be represented in apparently static objects. On the basis of the model of the developmental cycle of domestic groups first introduced by Meyer Fortes, the dynamism of the social fabric is explored through three case studies of groups at different stages of their developmental cycle. The strategies of survival can be seen pervasively in the monumental record, allowing for a glimpse into time and change in kin groups. The conclusion (chapter 6) offers a holistic approach to the material presented in the thesis, emphasising the ways in which the different theoretical approaches proposed intertwine with the material.

Keywords: agency
Egyptology
kinship
households
stelae
archaeology
social structure
developmental cycle
Abydos
memory
material studies
kin groups
anthropology of kinship
families
Advisor: Baines, J
Frood, E
Perfect and imperfect rights, duties and obligations: from Hugo Grotius to Immanuel Kant

In this doctoral thesis, Kant's distinction between perfect and imperfect duties is examined. The thesis begins with an exploration of how the distinction originates and evolves in the writings of three of Kant's most prominent natural law predecessors: Hugo Grotius, Samuel von Pufendorf, and Christian Wolff. The thesis then moves on to Kant's own writings. It is argued that Kant draws the perfect-imperfect distinction in as many as twelve different ways, that these ways are not entirely consistent with one another, and that many of them, even taken by themselves, do not hold up to scrutiny. Furthermore, it is argued that Kant's claim that perfect duties always trump imperfect duties - which can be referred to as "the priority claim" - is not actually supported by any one of the ways in which Kant draws the perfect-imperfect distinction. After this critical reading of Kant's writings, the thesis then switches gears and a more "positive" project is attempted. It is argued that the perfect-imperfect distinction, even though it does not support the priority claim, is not altogether normatively neutral or uninteresting. In particular, for some of the ways in which the distinction is drawn, it is shown that the distinction yields the following normative implication: Sometimes perfect duties override imperfect duties and all other times there is no priority one way or the other. Finally, it is explained that this normative implication - which can be referred to as the "privilege claim" - translates into the following practical directive: When there is a conflict between a perfect duty and an imperfect duty, sometimes one must act in conformity with the former duty and all other times one is free to choose which of the two duties to act in conformity with. This practical directive represents the ultimate finding of this thesis.

Keywords: Immanuel Kant
Ethics
Philosophy of Law
Hugo Grotius
Modern Philosophy
Samuel Pufendorf
Advisor: Hills, A
Gardner, J
The logic of political conflict in the late Middle Ages: a comparative study of urban political conflicts in Italy and the southern Low Countries, c. 1370-1440 

This thesis examines urban political conflict in the late Middle Ages (c. 1370-1440) in Europe’s most heavily urbanised regions, Italy and the Southern Low Countries. Conflicts have frequently been viewed in the context of an emerging state-controlled political order, and have been interpreted either as forms of disruptive disorder, or as affirmations of political processes shaped by states. This thesis suggests that urban conflict should be studied not in the context of a state-controlled political order, but within the political framework provided by the numerous semi-autonomous jurisdictional institutions inside and outside cities (such as guilds, parishes or contending outside powers). This pluralistic order of politics gave rise to a form of political order sui generis which expressed itself in two ways. According to a general logic of conflict (Part One), particular rationales for justifying conflict (Chapter One) and specific political practices ranging from concealed protest to urban warfare (Chapter Two) were embedded in this multi-faceted and shifting political framework. Action groups could be negotiated and renegotiated around the resources provided by the city’s multiple legitimating institutions (Chapter Three). At the same time, such political institutions were configured differently in different cities, and this also generated a particular logic which lay at the basis of different systems of conflict (Part Two). Levels of conflict could, in fact, vary greatly between Bologna and Liège (Chapter Four), Florence and Tournai (Chapter Five), and Lille and Verona (Chapter Six), where, on the basis of different underlying political institutions, diverse practices of conflict and forms of association prevailed. The pluralistic order of politics itself was, therefore, a form of political organisation which crystallised around conflict. It gave rise to a logic which put conflict at the centre of the political order of late medieval cities.

Keywords: politics and government
France
cities and towns
conflict
Belgium
Italy
Advisor: Vale, M
Rosser, G