VictorJuiz/thesis huggingface dataset:
Investigation and validation of the functional role of sMEK1 acetylation in DNA damage repair and HDACi-mediated radiosensitisation

Muscle-invasive bladder cancer (MIBC) most commonly affects the elderly with more than half of new diagnoses in the over 75-year age group. This means there is a need for less toxic treatments to improve treatment outcomes. Histone deacetylase inhibitors (HDACi) have emerged as effective, low toxicity radiosensitising agents, although the mechanism of radiosensitisation is not fully defined. This study investigates the radiosensitising effects of the HDAC inhibitor panobinostat (PAN) via a mechanism involving increased acetylation of non-histone proteins.
This project aimed to validate acetylation sites in non-histone proteins which were identified in a mass spectrometry screen following PAN treatment, and to investigate their functional roles in radiosensitisation. I hypothesised that specific acetylation sites in non-histone proteins could have vital roles in the DNA damage response (DDR). Of the identified acetylated non-histone proteins, suppressor of MEK1 (sMEK1), the regulatory subunit of serine/threonine-protein phosphatase 4 complex, was the primary focus, as it can act as a phosphatase for gamma H2A.X (γH2AX) upon completion of DNA repair. Cell lines were transfected with sMEK1 and subjected to PAN treatment and/or ionising radiation (IR) to detect time-course changes of DDR protein markers. A delayed DDR was observed in PAN-treated cells with persistently increased levels of phospho-ATM and γH2AX at 4 hours after recovery from IR, consistent with the radiosensitising activity of PAN. Endogenous sMEK1 protein was downregulated independent of PAN concentration between 8-24 hours, potentially through the regulation of mRNA expression. Reciprocal co-immunoprecipitations using anti-acetyl lysine and anti-HA antibodies confirmed the acetylation status of sMEK1 following PAN treatment. A transient interaction with the most abundant bromodomain protein, BRD4, was also detected in the chromatin compartment. Subcellular fractionation indicated significant nuclear localisation of sMEK1 immediately after IR in control DMSO cells, followed by migration to the chromatin fraction 4 hours later for γH2AX elimination. However, this was disrupted by PAN which resulted in less chromatin localisation at 4 hours after IR and higher levels of𝛾γH2AX than control. Downregulating endogenous sMEK1 in the cells via siRNA transfection not only resulted in an increase in radiosensitivity, but also a delay in the induction of the DDR, as indicated by a slower γH2AX signal intensity achieved at 2 hours. This supports the hypothesis of sMEK1 being a key protein in PAN radiosensitisation through its loss-offunction in the DDR pathway and changes in subcellular localisation.
In conclusion, I have shown that sMEK1 is regulated by PAN treatment and is acetylated. sMEK1 could therefore represent a clinically promising new radiosensitising drug target or biomarker to be further validated.

Advisor: Kiltie, A
Na, J
Nicholson, J
Understanding the effect of seasonal variability on the structure of ice shelves and meltwater plumes

Ice shelves are important to the climate system as they control the release of fresh water from ice sheets into the ocean, with consequences for sea level rise and ocean dynamics. Channels modifying basal melt rates and structural integrity have been observed inscribed in the undersides of some ice shelves. Observations indicate that some channels run in a direction transverse to ice flow and it has been suggested that these form due to seasonal variations in ocean properties.
This thesis analyses the effect of seasonal variability on ice shelves and meltwater plumes in the underlying ocean. A linear perturbation analysis on vertically integrated ice and plume models showed that seasonal forcing of subglacial discharge or ice flux can generate small ripples melted into the base of the ice shelf. These ripples did not develop into overdeepened channels, but the ripples caused by ice flux appear similar to basal terraces observed underneath some ice shelves. Code was developed to run 1-D nonlinear simulations with the vertically-integrated equations, producing similar results to the linear case. However, runs neglecting hydrostatic pressure gradients exhibited a feedback causing ice flux-generated ripples to grow into small proto-channels. A horizontally-integrated plume model was derived, incorporating the Coriolis force and transverse plume flow into a 1-D model which agreed well with a 3-D ocean simulation. Coupling this horizontally-integrated plume with a co-evolving ice shelf prevented proto-channels from forming. It appears unlikely that subglacial discharge or ice flux variations can give rise to observed transverse channels.
A new approach was developed to predict the evolution of internal radar reflectors observed within ice shelves, using vertically-integrated models of ice flow. It is hoped this approach might have applications for inverse modelling and data assimilation.

Keywords: Channelisation
Shallow Shelf Model
Ice Shelves
Pine Island Glacier
Plume Model
Advisor: Wells, A
Fine tuning gene expression levels in mammalian cells with engineered microRNA target sites

Precise, analogue regulation of gene expression is critical for development, homeostasis and regeneration in mammals. In contrast, widely employed experimental and therapeutic approaches such as knock-in/out strategies are more suitable for binary control of gene activity, while RNA interference (RNAi) can lead to pervasive off-target effects and unpredictable levels of repression. In this thesis, I report on a method for precise control of gene expression levels in mammalian cells based on engineered, synthetic microRNA response elements (MREs). To develop this system, we first tested a small panel of rationally designed MREs with various mismatches to miR-17 or miR-21. These MRE variants exerted predictable, stepwise control over reporter gene expression in a human cell line. Next, to improve the precision of MRE-based gene tuning, we established a high-throughput sequencing approach for measuring the efficacy of thousands of miR-17 MRE variants in parallel. This allowed us to create a library of microRNA silencing-mediated fine-tuners (miSFITs) of varying strength that can be employed to control the expression of user specified genes. A selection of miSFITs enabled precise, predictable tuning of PD-1, a co-inhibitory receptor expressed on T-cells and an important target for anti-tumour immunotherapy. In addition to tuning a PD-1 transgene in Jurkat T-cells, we successfully introduced miSFITs into the endogenous PD-1 3’UTR in embryonic stem cells using the CRISPR/Cas9 system. To further demonstrate the value of this technology, we also used a panel of miSFITs to tune the expression of a tumour-associated antigen in a mouse melanoma model. This analysis revealed that antigen expression level is a key determinant of the anti-tumour immune response in vitro and in vivo. miSFITs are a powerful tool for modulating gene expression levels with applications in research and cellular engineering.

Keywords: microRNA
Tumour immunology
Genome engineering
Synthetic biology
Advisor: Fulga, T
Milne, T
Investigation of magnetic field effects on protein photochemistry using cavity enhanced spectroscopy

Some animals, such as migratory birds, are known to have the ability to sense and use magnetic fields for orientation. At the heart of this remarkable ability is believed to be a photoinduced chemical reaction taking place within a blue-light receptor protein called cryptochrome (Cry). It is hypothesised that magnetic fields can play a decisive role in determining reaction rates (and, hence, yields) by acting on the spin states of spin correlated radical pairs (RPs) formed between a flavin chromophore and a tryptophan (Trp) electron-transfer (ET) chain within Crys.
In this work, cavity ring-down spectroscopy (CRDS) has been used for the detection of magnetic field effects (MFEs) via small changes in the differential absorbance (ΔΔA~10−6) of aqueous protein samples, with sub-microsecond time resolution. The photochemistry and effects of magnetic fields on European robin (Er) Cry, fruit fly Cry, and a plant Cry are characterised. In a key result for this field of research, an MFE in the photochemistry of ErCry is revealed for the first time, lending considerable support to its proposed involvement in bird magnetoreception. Using Cry mutants with modified Trp ET chains, the role of individual Trps in the manifestation of MFEs was explored. Replacing the terminal (i.e. fourth) Trp of the ET chain in ErCry with a redox inert amino acid is shown to significantly increase the optically-detected MFE, indicating that the RP formed between the flavin and the third Trp might be the primarily magnetically sensitive species.
To better understand the relevant biochemical processes in Cry, de novo designed artificial flavoproteins (maquettes) have been used to model the photochemistry of Cry (Chapter 4). The comparatively simple and adaptable design of these model proteins facilitates detailed MFE studies by reducing the complexity of natural Cry. In these maquettes, photoinduced ET leads to the formation of a RP which exhibits MFEs analogous to those in Crys. The profound effect of the donor-acceptor distance on the MFE is demonstrated using flavomaquettes with varying flavin-Trp distances.
The application of cavity enhanced spectroscopy to both natural cryptochromes and artificial flavoproteins, opens up new pathways for the detection and characterisation of MFEs in biologically relevant environments. The enhanced sensitivity of these approaches constitutes a significant step forward in understanding the underlying biochemical processes of animal magnetoreception.

Keywords: Maquette
Cryptochrome
Radical Pair Mechanism
Cavity Ring Down Spectroscopy
Magnetoreception
Advisor: Mackenzie, S
Timmel, C
Hore, P
The social and cultural history of the provincial fair in England, 1750-1850

This thesis seeks new ways to explain and explore the social and cultural history of fairs in provincial England between 1750 and 1850. It approaches the history of fairs from within and is primarily concerned with the experiences and priorities of those who organised and attended these events. It argues that fairs remained much more important to a much wider range of people and activities than has previously been supposed.
The first of four chapters of this thesis explores the role fairs played in the commercial networks and business practices of those trading goods, livestock, and entertainment there. The second considers links between fairs and the institutions of urban governance, uncovering the way in which fairs and their associated privileges and rituals both shaped and were used to communicate civic identities. The third examines the ways in which individuals understood the temporally and geographically liminal place of fairs in relation to the annual calendar, the lifecycle, and more permanent uses of urban space. Finally, the fourth chapter explores how the roles and meanings of fairs were presented and distorted in art, literature, and other cultural forms, and how the attitudes portrayed in these media in turn influenced the progression of these events.
By reassessing fairs in light of more established historiographies of commerce and civic identity as well as bringing new approaches to the discussion of these events, this thesis seeks to disrupt the existing narrative of the history of fairs and sketch the outline of a new narrative that is richer and more variegated. In doing so it invites a renewed challenge to the boundaries that have been asserted between business and pleasure, polite and popular, and rural and urban in this period.

Advisor: Harris, B
Towards the total synthesis of pectenotoxin-4: synthesis of the CDE and F rings

Chapter 1: Introduction
This chapter outlines the isolation and structural identification of the pectenotoxin (PTX) family of natural products, as well as their reported biological activity. Finally, the chapter will be concluded with the completed total syntheses of members of the pectentoxin family by Evans and Fujiwara.
Chapter 2: Development of a Conjugate Addition-Cyclisation Approach towards the D ring
This chapter outlines previous approaches to forming the bicyclic D ring, our proposed approach using a rhodium-catalysed 1,4-addition as the key C–C bond-forming reaction to synthesis PTX-4, and model studies to test the feasibility of this disconnection.
Chapter 3: Synthesis of the desired E ring fragment
This chapter outlines our current synthesis of the E ring of PTX-4 and the elaborations on the E ring side chain to utilise the rhodium-catalysed 1,4-addition and dihydroxylation/cyclisation sequence as developed in Chapter 2.
Chapter 4: Synthesis of the desired F ring fragment
This chapter outlines the reoptimisation and scale-up of the F ring synthesis previously published, with modifications to the protecting group strategy employed in preparation for the Julia coupling with the ABCDE fragment in our total synthesis of PTX-4.
Chapter 5: Experimental
This chapter outlines all the experimental procedures for the reactions described in this thesis, as well as the characterisation data for the compounds synthesised.
Chapter 6: Appendices
This chapter contains the Mosher’s ester analyses of compounds 282, 331, 463 and 539; as well as nOe analysis of compounds 351, 399, 400, 403, 447, 451 and 469 along with their 1H and 13C NMR spectra.
Chapter 7: References
This chapter contains the references cited within.

Keywords: 1,4-addition
asymmetric dihydroxylation
pectenotoxin
rhodium
Advisor: Donohoe, T
Science, scientism, and pseudoscience in die Reihe

This thesis examines the association of science and musical thought that surrounded the Anglophone reception of the West German publication die Reihe (German publication: 1955 – 1962; English edition: 1957 – 1968). While die Reihe presented the early writings of what would become some of the central figures in European compositional circles, the journal’s initial reception was damned through the association of writings of die Reihe with pseudoscience, therefore suggesting that the work was false and to be dismissed. In order to examine the various roles of scientific thought and processes in die Reihe three central areas are explored: to what extent can the epistemological stance of scientism account for the science-like content of the journal? Can a musical journal be considered as a work of pseudoscience? And how did the journal’s portrayal of the composer Anton Webern assist in codifying the musical practices of the authors with the processes and structures of scientific work? It can be seen that scientism can permeate thought and society in multiple and discreet ways, and that scientism can be seen to have influenced policy-makers in post-Second World War West Germany by encouraging a wider application of scientific ideas than had been seen previously. In the same way, the rhetoric of die Reihe’s chief editor, Herbert Eimert, indicates an epistemological stance that is consistent with scientistic values. The initial reception that accused die Reihe of being a work of pseudoscience is critically examined, and it is found that there is insufficient justification for the journal to be considered a work of pseudoscience, because that while it bears a superficial similarity with scientific writing, die Reihe is not itself engaged with scientific work. Finally, it is seen that the way in which Webern’s work and legacy is depicted in the journal is quite unlike how Webern’s work was actually conceived, and as such the framing of Webern as a proto-scientistic composer is another indication of scientism in the thought of die Reihe’s contributors.

Keywords: Epistemology
Eimert
Music
Darmstadt
die Reihe
Scientism
Complexity
Tuba
Stockhausen
Performance
Algorithmic
Piano
Composition
Oboe
Their allotted place: social conditions, survival strategies and comparative respectability among naval wives in mid-nineteenth century Portsea island

In exploring the social condition and survival strategies of wives and families of Royal Navy’s lower-deck seamen, this thesis brings to light a subset of the nineteenth-century population whose welfare and circumstances were capable of affecting naval manning. Located primarily in naval port towns, these women were dependent upon ill-paid men whose seagoing occupation necessitated long absences and placed them in situations of risk. In the eighteenth and nineteenth centuries a combination of low income, irregular pay, heightened chance of disability and breadwinner-absence had reduced many naval families to destitution, prompting family men to abandon naval service for better-paid work on shore. Anxious to stem the loss of experienced sailors, the Navy introduced a system by which families could be supported financially in their men’s absence. Surviving records of this allotment system - known to, but little explored by historians - are used here to reconstruct a previously neglected naval community. Mid-nineteenth century allotment declarations have identified more than 1500 naval dependants living in Portsea Island (modern-day Portsmouth). From cross-referencing of census and parish records, civil registration data and maps, study of this cohort reveals naval women’s geographical origins, family backgrounds, nuptiality, the timing and size of their families, their occupations, household structures and economic security, with context and proportion provided via local and national equivalents and selected comparator-groups. The emerging picture is of a near-tribal community of females whose roles as wife and mother, domestic stability and social standing were deeply affected by their connection to the Royal Navy.

Keywords: Nineteenth century
Royal Navy
Sailors' women
Naval wives
Portsmouth
Advisor: Rodger, N
Fate amenable to change: a technical and social history of Virtual Reality in the United States of America, from 1965 to 2005

Virtual Reality (VR) technology lacks a clear definition, unique application, or history, leading to difficulties in identifying primary source materials. This thesis establishes a workable definition of VR, incorporating it into cross-disciplinary methodologies to reveal and arrange newly-uncovered sources into a narrative, spanning 1965-2005. This narrative will hopefully encourage crystallisation around the proposed definition, providing value to developers and historians of technology.
Combining online database sampling, stacked surveys of diverse materials, and interviews, the author situates VR within a broader context of 20th and 21st century American social history. By integrating methodologies from Contemporary History, Economics, and Sociology, the newly-established definition is tested via the narrative, which is itself supported by new-found primary materials. That historical narrative assesses the impact of missing social and technical ‘standards’ in VR’s tumultuous past, with implications for both historians and designers of VR, as well as other modern technologies. The results suggest that, since the mid-1980s, exaggerated capabilities and science fiction applications, extolled by both developers and media writers, far outstripped technical reality (unbeknownst to consumers), forming reverse salients on the research and innovation crucial to any modern technological system’s viability. The period spanning the mid-1960s to mid-1980s witnessed much more limited research, centred around identifying valuable applications concurrently with system development, and long before the release of products. This earlier, more cautious period was demonstrably more successful because its VR applications, such as medical training and virtual design, persisted through the ‘VR Winter’ of the late 1990s when later ‘VRs’ did not. Thus, the definition provided is useful for reliably identifying new source materials through the database sampling and analytics methodology, developed therein, which is valuable to historians of VR.

Keywords: American Cultural Trends
Cyberpunk
Virtual Environments
American Popular Culture
Cyberspace
American Military Research
Virtual Space
Virtual Reality
Cold War
History
VR
Computers
American Social History
Advisor: Iliffe, R
Lordship and locality: multiple lordship in the north midlands during the long twelfth century (c.1066-c.1216)

This thesis addresses the phenomenon of multiple lordship in Leicestershire, Derbyshire, and Staffordshire, c.1066-1216, as a means of questioning the present historiographical dominance of the honour. It does so through a study of the multiple allegiances of the minor lords of this area. The first section addresses the origins of the practice of multiple allegiance in England, and traces its establishment in England in the first decades after the Conquest. Contemporary thought on the practice is then addressed. It is argued that the ideas of non-royal liege lordship are a guide to the aspects of the practice that concerned contemporaries, and shows how they sought to deal with these pragmatically. The second section draws on the thousands of private charters surviving for these three counties in order to provide a quantitative and qualitative framework for multiple allegiance. It is shown that families with multiple allegiance were roughly as common as those with a single lord by c.1216, and that many of these patterns were established by the early twelfth century. A series of case studies are then addressed which show that multiple allegiance often made families focus more on a particular locality, in which they sought to build up a base of power. The impact of lordship and locality, too, can be seen in the patterns of benefaction to religious houses. It is argued that in in studying twelfth century England, focus on the honour should be balanced with study of the locality.

Advisor: Garnett, G
Lambert, T