VictorJuiz/thesis huggingface dataset:
Enzymatic synthesis of chemically modified DNA for analytical and diagnostic applications

Functionalised nucleotides have found widespread adoption in applications ranging from genome labelling to disease diagnostics. A popular means of introducing these modifications into nucleic acids is via the copper-catalysed azide-alkyne cycloaddition reaction. However, the toxicity of copper limits its use in vivo. Therefore, the copper-free strain-promoted azide-alkyne cycloaddition (SPAAC) and inverse electron demand Diels-Alder (IEDDA) reactions were evaluated as a means of directly and indirectly labelling DNA and RNA. A variety of cyclooctyne, trans-cyclooctene and azide functionalised deoxyuridine triphosphates were synthesised and shown to be incorporated by primer extension, polymerase chain reaction (PCR) and reverse transcription. Bulky cyclooctyne and trans-cyclooctene triphosphates demonstrated moderate incorporation efficiency, while azide nucleotides with smaller functional groups were better substrates. PCR products of ca. 500 base pairs with 100% sequence fidelity can be formed, where all thymidine sites are replaced with azidohexanamidopropargyl deoxyuridine. These modified duplex products were efficiently labelled with fluorophores using the SPAAC and IEDDA reactions, and can be converted to fluorescent single-stranded probes through exonuclease digestion and streptavidin magnetic bead separation of the duplex followed by fluorophore-labelling. To expand the utility of this methodology, a new and simple single-tube dual labelling strategy was demonstrated to give a range of mixed dual coloured probes. Nucleosides bearing azide, trans-cylcooctene modifications and a fluorescent base analogue were evaluated for direct cellular DNA labelling and detection. When cultured adenocarcinoma A549 cells were treated with these nucleosides, then chemically fixed and fluorescently labelled by the SPAAC or IEDDA reaction, cytoplasmic staining without nuclear DNA labelling was observed. To improve the efficiency of fluorescent labelling of genomic DNA in cultured cells, phenyl isopropyl alanine-protected nucleoside monophosphates were prepared in an attempt to directly deliver 5' phosphorylated nucleosides into the cells. Preliminary fluorescence studies indicate bright foci in addition to cytoplasmic staining, the origins of which require further study.

Keywords: fluorescent labelling
IEDDA
SPAAC
DNA modification
Advisor: Brown, T
Single-molecule FRET studies in live bacteria

Single-molecule fluorescence and single-molecule Förster resonance energy transfer (FRET) have proven enormously successful in understanding molecular and cellular processes over the last two decades. However, in vivo single-molecule FRET studies are still very difficult, mainly because they require site-specifically labelled biomolecules with photostable organic dyes.
In this work, I established single-molecule FRET studies in live bacteria and applied the developed method to study mechanisms of gene expression and gene regulation. To begin with, I optimised a recently developed internalisation method based on electroporation for the efficient loading of bacterial cells with organic dye-labelled nucleic acids and proteins while maintaining cell viability.
Following these studies, I internalised labelled tRNA molecules, measured their diffusion coefficient, and showed that most tRNA molecules diffuse freely in live bacteria. I also showed that bound tRNA molecules are predominantly at the cell periphery and compete with the endogenous tRNA pool during translation using antibiotic controls and simulations.
Finally, I studied transcription initiation in vivo by internalising promoter DNAs with different FRET labelling schemes reporting on individual steps in transcription initiation. Thus, I observed single-molecule FRET signatures attributed to open complex formation, DNA scrunching during initial transcription, and promoter escape, which were not present in null-promoter DNA and antibiotic controls.
By carefully designing single-molecule FRET assays, I imagine single-molecule FRET studies to become a major tool in understanding protein dynamics, and elucidating mechanistic details of gene regulation processes in living cells.

Keywords: Single-molecule fluorescence
Single-molecule FRET
Gene expression
Advisor: Kapanidis, A
Records of and controls on temporal variations in activity at arc volcanoes

Many attributes of volcanic activity, whether physical, geochemical/petrological, or geophysical, change over timescales from minutes to millions of years. Understanding the nature of these variations and their controls is essential both for hazard assessment and to understand volcanic and magmatic processes. Arc volcanism entails a relatively broad range of eruption styles and magma compositions, and thus wide-ranging hazards and a variety of eruption records. Despite their significance, records of activity for many arc volcanoes are inadequately characterised, so any temporal variability is poorly constrained. In this thesis, I investigate temporal variations in different styles of activity (dome-forming, Plinian-style, and effusive/glaciovolcanic) on a range of timescales (days–years, millennia, and hundreds of ky, respectively), from diverse records (seismicity, tephra deposits, and effusive eruption products), at four arc volcanoes. I analyse seismic time-series from Soufrière Hills Volcano (Montserrat) and Volcán de Colima (Mexico) using two statistical techniques, identifying temporal variation in the extent of long-range correlations and randomness in these data, which has potential to inform real-time monitoring and constrain eruptive processes. I also present new composition data for and review previous studies of tephra deposits from Volcán Hudson (Chile), revising its explosive eruption history and finding previously unrecognised shifts in the magma composition erupted through the Holocene. I also describe and analyse sequences of lithofacies from effusive eruptions of a range of magma compositions from Volcán Sollipulli (Chile), inferring varying extents of interaction with ice during their emplacement, and so changes in eruption style through time. These case studies highlight the importance of detailed characterisation of temporally varying records of volcanic activity, and some of the limitations of and uncertainties in these records and their interpretation.

Keywords: Sollipulli
glaciovolcanism
lava dome
igneous geochemistry
palaeoclimate
entropy
volcano-ice interaction
tephra
detrended fluctuation analysis
palaeoenvironment
hyaloclastite
time-series analysis
eruption
Montserrat
Soufrière Hills
Chile
lithofacies
volcano seismology
Mexico
Andes
Patagonia
Hudson
stratovolcano
volcano monitoring
caldera
Colima
Advisor: Pyle, D
Mather, T
Mee, K
Caesar’s Castor: the cult of the Dioscuri in Rome from the mid-Republic to the early Principate

This thesis examines the development of the cult of the Dioscuri in Rome from the mid-Republic to the end of the Julio-Claudian dynasty. This was a period of great political and social upheaval and of religious change. Through a detailed examination of the cult of the Dioscuri, I trace how the cult developed and adapted in conjunction with religious, political and cultural changes within Roman society. I furthermore examine how the cult changed and explore the reasons why those changes occurred at that time and in that place.
Chapter One surveys the two temples of Castor and Pollux in Rome, focusing in particular on their temple in the Roman Forum. Using archaeological and literary evidence, I argue that this temple was a central stage for many of the pivotal events and speeches of the late Republic. Chapter Two examines the epiphanies of the Dioscuri, most commonly associated with battles and their aftermath, although later appearing to commemorate the deaths of prominent individuals such as Julius Caesar and Drusus the Elder. I examine how the epiphanic tradition of the Dioscuri changed over time and ask why it was these gods in particular who rode to aid Rome. Chapter Three turns to exploring the relationships Castor and Pollux were said to possess with groups in Roman society, in particular horsemen, boxers and sailors. I examine how these relationships were formed and publicised and how they benefitted both the mortals and the gods. Chapter Four explores how a different aspect of the Dioscuri became prominent in the imperial period: their fraternal harmony. Castor and Pollux were linked to and compared with pairs of potential imperial successors. I explore the purposes of this comparison and how apt it was for the different pairings.
Throughout this thesis, I examine some of the most prominent aspects of the cult of the Dioscuri in Rome within the wider context of history, culture and politics, arguing that the cult was a fully integrated part of Roman society as a whole.

Keywords: Castor, Pollux, Dioscuri, Religion, Politics
Advisor: Bispham, E
The purpose of the Book of Numbers in relation to the rest of the Pentateuch and post-exilic Judaism

A mosquito once landed in a nudist colony. "How very excellent," he was heard to remark, "But just where do I begin?" This is the dilemma faced by any critic dealing with tne Pentateuch. If he examines the whole, then he is open to the charge that he has carried his conclusions about one book over into his consideration of the others. On the other hand, when he treats one book by itself, he is always in danger of a certain off-balance. This thesis falls into the letter class of investigation; it is therefore admitted that there are a certain number of loose ends, although every attempt will be made to see Numbers in the context of the Pentateuch as a whole. Nonetheless it is apparent that it is legitimate to consider a book of the Pentateuch by itself. For example, Genesis, although written as part of a series in its present form, can be dealt with as a book having meaning in itself. The theory that the present division of the Pentateuch into five books is a result of a mechanical process after the work was completed is not axiomatic. To the contrary it will be argued that the Book of Numbers is a book in the same sense that Genesis is a book, namely a part of a series, but with a specific theme and purpose of its own.

Keywords: Pentateuch
Regulatory T cells in skin homeostasis and inflammation

Regulatory T cells (Tregs) are crucial controllers of inflammation. Patients with a genetic defect in the lineage defining transcription factor Foxp3 suffer from a broad spectrum of autoimmune diseases, including early manifestation of various types of skin inflammation. However, our knowledge about the properties of skin resident regulatory T cells under homeostatic and pathologic conditions and in particular in inflammatory diseases of the skin such as psoriasis is limited.
In order to address this open question, phenotypic characterization and transcriptomic analyses of murine skin Tregs were performed. The majority of CD4+ T cells in homeostatic skin express the transcription factor Foxp3. These Tregs show a unique profile, are mainly thymic derived nTregs and are enriched in markers associated with a highly suppressive phenotype such as CD25, CD103, IL-10, ST2, and GATA-3. To delineate the role of Tregs in psoriasis-like inflammation, the imiquimod model of psoriasiform inflammation was used. Tregs are significantly increased during skin inflammation and retain their suppressive phenotype and trancriptome. Treg depletion before and during imiquimod treatment led to exacerbated inflammation and dense leukocytic infiltrate in the dermis and epidermis. Furthermore, the exacerbated inflammation was characterized by a significant increase in IL-12 and infiltration of IFN- γ and TNF-α producing, T-bet+ CD8+ and CD4+ T cells. IL-23 and IL-17 secreting dermal γδ T cells are pathogenic in the imiquimod model, but their cell numbers decreased in the absence of Tregs. Functional experiments demonstrated that myeloid-derived type I Interferon drove the exacerbated inflammation, which was dependent on CD4+ and CD8+ T cells. In conclusion, skin Tregs have a protective role in psoriasis-like inflammation and depletion of Tregs causes disease exacerbation and triggers an altered cytokine profile and cellular infiltrate. These findings assist in our understanding of tissue resident Tregs and how they maintain homeostasis and prevent inflammation in the skin.

Advisor: Powrie, F
Ogg, G
The reign of Emperor John II Komnenos, 1087-1143

Despite ruling over arguably the most powerful Christian nation in the period, in a time when European and middle-eastern history entered a new phase of interaction due to the Crusades, John’s reign has received little scholarly attention. The only major monograph is Chalandon's Les Comnènes from 1912, since which a number of new sources have come to light, together with numerous studies on his contemporaries. Despite the impression that sources are lacking for his reign, in fact there are over 50,000 words of court letters and poetry that allow us to take the political pulse of the Komnenian court. When incorporated with the extra information found in Syriac, Arabic, Russian, Hungarian and many other texts, archaeological remains, sigillographic and numismatic evidence, John’s reign is in fact very well covered, and ripe for analysis. Between fieldwork in Turkey, Serbia and Kosovo and translations of these previously unused texts, this thesis contains new material on top of over a century of updated methodologies and research since Chalandon.
As such, this thesis will reevaluate assumptions concerning John and his reign, including rewriting the narrative itself, which has previously been distorted due to the agendas of the few sources used. Through the reconstruction of this narrative John's empire can be reexamined, and how it operated in the changed world of the twelfth century determined. The empire found itself in a more multi-polar power dynamic, and tackled this by operating more as an empire than it had as a larger polity as in the previous century: incorporating other peoples as clients and emphasing the rhetoric of imperial piety and legitimacy of the Roman empire. Equally, all of John’s actions on the frontiers were fuel for the political theatre that was Constantinople, and this dynamic shaped his actions and resulted in the empire that Manuel inherited.

Keywords: John II Komnenos
Anatolian Castles
Komnenoi
12th Century
Byzantine
Komnenian
Crusader States
Balkan Castles
Advisor: Whittow, M
Religion and ethnic identity: Gurung experiences of belonging in the UK

This thesis seeks to identify the place and significance of religion in constructions of ethnic identity and experiences of belonging among Gurungs in the UK. It assesses both the vision of Gurung ethnic identity put forward by ethnic organizations, which is itself much disputed, and the extent to which this vision either reflects or shapes religion 'on the ground'. It argues that debates and controversies surrounding Gurung religious identity are influenced by ethnic politics in Nepal, by social changes and modernist ideas about the superiority of world religions over local traditions, by the pervasive discourse regarding exclusivity in religion, as well as by historical, but highly contested, status differences within Gurung society. It also suggests that those debates are complicated by divergent conceptions of 'religion', and of how 'religion' relates to 'culture'.
When considering religion 'on the ground', the thesis assesses the extent to which Buddhism and Bon are practised as an expression of Gurung culture, thus reinforcing a sense of belonging within the Gurung community, and the extent to which particular religious traditions strengthen a broader Nepali identity or universal orientation, whereby religious belonging outweighs ethnic loyalties. It concludes that both orientations are in evidence and, in general, are considered mutually reinforcing. However, from the perspective of Christian Gurungs and followers of Sai Baba - paths often considered foreign to Gurung culture - a tension is more evident. For many Nepalis, however, religious identity is complex and multiple. Many include elements of different religious traditions in their regular practice and there is a whole range of customs, values, attitudes and understandings of religion which are shared by Nepalis but which are understood to belong to no particular religion, or to all. I suggest that it is as much through these aspects of religion, as through commitment to the vision of Gurung religious identity officially promoted, that a sense of commonality and belonging is created within the diaspora.

Keywords: diaspora
migration
Gurungs
Nepal
Nepali diaspora
Belonging
Advisor: Gellner, D
Hausner, S
Jansenism, holy living and the Church of England: historical and comparative perspectives, c. 1640 - c. 1700

This thesis examines the impact in mid- to later-seventeenth century England of the major contemporary religious controversy in France. The debates associated with this controversy, which revolved around the formal condemnation of a heresy popularly called Jansenism, involved fundamental questions about the doctrine of grace and moral theology, about the life of the Church and the conduct of individual Christians. In providing an analysis of the main themes of the controversy, and an account of instances of English interest, the thesis argues that English Protestant theologians in the process of working out their own views on basic theological questions recognised the relevance of the continental debates. It is further suggested that the theological arguments evolved by the French writers possess some value as a point of comparison for the developing views of English theologians. Where the Jansenists reasserted an Augustinian emphasis on the gratuity of salvation against Catholic theologians who over-valued the powers of human nature, the Anglican writers examined here, arguing against Protestant theologians who denied nature any moral potency, emphasised man’s contribution to his own salvation. Both arguments have been seen to contain a corrosive individualism, the former through its preoccupation with the luminous experience of grace, the latter through its tendency to elide grace and moral virtue, and reduce Christianity to the voluntary ethical choices of individuals. These assessments, it is argued here, misrepresent the theologians in question. Nevertheless, their thought did encourage greater individualism and moral autonomy. For both groups, their opponents' theological premises were deficient to the extent that they vitiated morality; and in both cases their responses, centring on the transformation of the inner man by love, privileged the moral responsibility of the individual. Their moral 'rigorism', it is suggested, focusing on the affective experience of conversion, represented in both cases an attempt to provide a sound empirical basis for Christian faith and practice in the fragmented intellectual context of post-reformation Europe.

Advisor: Maltby, J
Parish, R
Complex assemblages,  complex social structures:  rural settlements in the upper and middle Thames Valley 100bc to ad100

Late Iron Age and Early Roman Britain has often been homogenised by models that focus on the resistance/assimilation dichotomy during the period of transition. The main objective of this thesis is to examine the rural settlements of this period through the lens of Cultural Theory in order to tease out the more nuanced and diverse human landscape that the material suggests. This approach begins to develop new ways of thinking about the variability observed in rural settlement from the end of the Middle Iron Age (MIA) to the beginning of the 2nd century AD. The selected study area is the Upper and Middle Thames Valley. The thesis uses the grid/group designations of Mary Douglas' Cultural Theory as a tool to produce a more multifaceted picture of the period, exploring the assemblages of these rural settlements to understand the nature of the socio-political structures of the region, beyond the anonymity of tribal affiliation and the faceless economical dichotomy of high and low status.
The structure of the thesis is as follows: Chapter 2 summarises the state of play in the study of Late Iron Age and Early Roman Britain within the study area. The strengths and weakness of Cultural Theory, how it has been used in the past, and what role it has played in this research will be introduced in Chapter 3. Chapter 4 presents the dataset and the patterns observed, as well as why and how the types of artefacts examined are integral to the formation of the worldview of people. Chapter 5 offers interpretation of the data through the lens of the Cultural Theory model whilst Chapters 6, 7, and 8 place six case studies from the Upper and Middle Thames Valley under inspection and show in greater detail the potential of Cultural Theory as a tool for thinking about rural settlement variation.
This study re-characterises the rural Upper and Middle Thames Valley as a place where there was a wide variety of worldviews during the period of great cultural and socio-political transition of the centuries straddling the turn of the first millennium. It suggests that the varying success and longevities of these rural settlements may have depended upon the ability of their inhabitants to either change their worldviews or to find similarities in the new organisation of their world.

Advisor: Gosden, C
Debt in late antique Egypt, 400-700 ce – approaches to a time in transition

Modern scholars are deeply divided over the extent to which early Byzantine provinces such as Egypt adopted imperial Roman law. This thesis undertook a diachronic study of the published debt acknowledgements from Egypt and Nessana for the fifth through seventh centuries CE to examine the degree of adoption of imperial legal changes. The debt acknowledgements are one of the largest sets of papyri documents for this period, consisting of 283 Greek and fifty-seven Coptic documents. Having created a database of these documents, in their original Greek or Coptic plus an English translation and information from the major commentaries, I had an unparalleled opportunity to analyse change, both legal and socio-economic.
The research shows that while many legal changes, including the requirement for regnal dating and changes in the liability of co-debtors, were generally adopted, there was resistance to other changes. For example, the interest rate reduction ordered by Justinian I in 528 was clearly disseminated because some documents reflect the reduction. Most people, however, continued to charge the earlier higher rates. Furthermore, some sectors of the population appear to have struggled with the imperial changes. Model formats for a simplified Greek debt acknowledgement and a very similar Coptic debt acknowledgement were developed and disseminated in the sixth century. These simplified formats did not use regnal dating or many of the other customary clauses of the formal Greek debt acknowledgment. The early development of these simplified formats, together with evidence of the privatisation and localisation of many imperial functions, including dispute resolution, support the view that the later sixth century experienced an unravelling of ties with the Roman Empire. The catastrophic seventh century, with its civil wars and Persian and Arab invasions, resulted in a shift in language from Greek to Coptic for personal legal documents. The disruption of the seventh century, however, only accelerated and finalised a process of change that was already well established in the sixth century.

Advisor: Whittow, M
Sirks, B