VictorJuiz/thesis huggingface dataset:
Characterisation of the mechanism of B-cell receptor triggering

B cells are key mediators of humoral immunity and rely on signals initiated by the B cell receptor (BCR). The structure of the BCR and mechanism of ligand binding are well characterised, but what remains to be understood is how ligand binding triggers intracellular signalling. A number of opposing models have been proposed. In this thesis, these models have been tested experimentally using a toolkit of reagents based on the HyHEL10 BCR and its natural ligand Hen-Egg Lysozyme (HEL). Whilst a receptor crosslinking-based model accounts for multivalent ligand presented in solution, the inability of monovalent ligands to trigger robust B cell signalling, except when they are surface-associated, implicates a second triggering mechanism. To narrow down potential theories of BCR triggering, the stoichiometry of the BCR in the resting state was established using multicolour fluorescence microscopy and shown to be predominantly monomeric. Using fluorescence imaging, it was found that BCR triggering by surface associated monovalent ligands correlated with the exclusion of the large phosphatases, CD45 and CD148, from regions of BCR/ligand engagement. In addition, BCR triggering was shown to be dependent on both the size of the BCR/ligand complex and the size of the extracellular domain of CD148. These findings suggest that the size-dependent exclusion of CD45/CD148 functions as a second mechanism of BCR triggering for surface bound ligand, and complements the ability of BCR to be directly triggered by cross- linking multivalent ligands. These observations have important implications in terms of differential signalling, and the positive and negative selection of B cells. The mature B cell immune response to foreign antigen is thought to be predominantly focused on membrane bound antigen, displayed via complement or immunogloblin Fc receptors, whilst soluble antigens may be tolerogenic or lead to T-independent activation, at high avidity. It is also to be expected that differential expression of CD45/CD148 on B cell subsets will tune their response to membrane bound antigens.

Advisor: Davis, S
Cornall, R
Colicin translocation through the E. coli cell envelope

Gram-negative bacteria have evolved mechanisms to kill other microbial species to compete for space and resources. One mechanism exploited by Escherichia coli is the production of bacteriocins called colicins, which target closely-related sensitive E. coli strains. Colicins bind with high affinity to outer membrane proteins on the surface of E. coli, and following contact with proteins in the periplasm and inner membrane, translocate a cytotoxic domain to kill the cell. Killing displays first-order kinetics which has been suggested to mean a single molecule is sufficient to kill a cell, although this has yet to be demonstrated.
The mechanism by which a folded colicin can cross two membranes to kill cells is still unknown, due to the lack of tools available. The aim of this research was to develop fluorescence-based microscopy tools to visualise colicin entry into E. coli and probe the mechanism of translocation in vivo.
ColE9 was labelled with organic fluorophores within its cytotoxic domain and retained its catalytic activity in vitro, however its in vivo activity was reduced. Microscopy was optimised using a ColE9 active site mutant and the AlexaFluor-647 dye, to generate a fluorescent probe capable of translocating into but not killing cells.
Translocation of ColE9*AF647 across the outer membrane (OM) was dependent on the PMF, in particular the electrical potential. Translocation of single-molecules of ColE9*AF647 to the cytoplasm was visualised for the first time in vivo; ~4-5 molecules were observed per cell, in 30 minutes at 37 °C. Two populations of ColE9*AF647 molecules were present; a mobile fraction with a diffusion coefficient similar to cytoplasmic GFP (~4-10 µm2/s) and an immobile fraction, the origins of which are unknown. Finally, the rate-limiting step for ColE9 translocation across the OM was shown to be passage through OmpF or OmpC, which could be modulated by the fluorophore used. The present work demonstrates that Tol-dependent colicins translocate across the OM in an energy-dependent manner and must be completely unfolded in order to translocate through OmpF or OmpC.

Advisor: Kleanthous, C
Rassam, P
Critical theories of biography in England 1800 - 1831

An examination, taken from published biographies and periodic reviews, such as the Quarterly, of the emerging consensus of what should be contained in a biography, and how it should be presented.
The years 1800 - 1851 mark the period when ideas about biography were first widely discussed. The critical principles are described as they evolved against the background of the huge proliferation of biography which accompanied the "Age of Personality." The past and present were generously documented with biographies long and short, although reviewers grew increasingly hostile to redundant and extended works. The emergence and acceptance of autobiography and literary biography were the most important innovations.
The complex task of framing an aesthetic for biography is then described. The major findings are the importance and place given to detail, the rejection of life—and-times and the welcoming of life-and-letters forms of biography. The argument that biographers should incorporate abundant original materials is then detailed, as it affected the use of letters, diaries, autobiography, anecdotes, and conversation. The discrediting of these original materials by over-use is traced. Lastly, two moralistic issues are considered; how a biographer might be truthful and yet conform to powerful demands not to speak unduly ill of the dead or to touch on taboo subjects, and the writing of biography for utilitarian purposes.
During the period biography was reviewed extensively for the first time, and reviews and independent assessments provide a large amount of material. Although the findings interestingly reflect the age at many points, nothing like a Romantic theory of biography emerges. Rather, the period established the major areas of biographical discussion, which are little altered 150 years later. The thesis deals also with unfamiliar areas of the work of many of the best known writers of the generation.

Keywords: Letters
Anecdotes
Diaries
Advisor: Butler, M
Colonisation and infection with antibiotic-resistant organisms in patients in the adult intensive care unit, hospital for tropical diseases, Ho Chi Minh City, Vietnam

In Vietnam, data about colonisation and subsequent infections with antibiotic-resistant organisms (AROs) are limited, particularly from intensive care units (ICUs). A prospective longitudinal study was conducted in Adult ICU, Hospital for Tropical Diseases, Vietnam from 10th November 2014 to 14th January 2016 to characterize colonisation, identify risk factors for colonisation and understand its relationship with infections by Staphylococcus aureus, Escherichia coli, Klebsiella spp., Pseudomonas aeruginosa, and Acinetobacter spp..
63.1% (529/838) of patients admitted to ICU were colonised with AROs. 61.3% (223/364) of patients with an ICU stay >48 hours acquired AROs colonisation in ICU. Increased Charlson Comorbidity Index score and receipt of antimicrobial therapy on ICU admission were significant risk factors for AROs acquisition. The proportion of patients with hospital-acquired infections (HAIs) was 23.4% (85/364), and AROs accounted for 41.5% (44/106) of pathogens causing HAIs. Vascular catheterization was identified as a risk factor for ICU-acquired bloodstream infection.
Of 67 Staphylococcus aureus isolates identified by conventional microbiology, 6 isolates (9%) were sequenced as Staphylococcus argenteus. Multilocus sequence typing (MLST) analysis indicated matching sequence types of infecting and previously colonizing isolates in 90% (9/10) and 94.4% (17/18) patients with HAIs by Staphylococcus aureus and Klebsiella pneumoniae, respectively. Phylogenetic analysis confirmed that ICU patients became infected with their previously colonizing Staphylococcus aureus ST188 (4 patients) or Klebsiella pneumoniae ST17, ST23 and ST86 (6 patients). Whole-genome sequencing helped to disprove 3 patient-to-patient transmission events (1 Staphylococcus aureus and 2 Klebsiella pneumoniae) that were suggested by MLST, and identified one additional Staphylococcus aureus transmission which was missed by other methods.
This thesis provides evidence of the high burden of antimicrobial resistance in Vietnam along with high rate of colonisation and infections with AROs. Therefore, the implementation of infection control measures and antimicrobial stewardship programs is urgently needed in Vietnam.

Keywords: Antibiotic-Resistant Organisms
Colonisation
Infection
Advisor: Thwaites, G
Payments, ecosystems and development: Payments for Environmental Services (PES) in the Mexican Lacandona rainforest

Payments for Environmental Services (PES) emerged as a popular forest conservation policy across the Global South since the 1990s, first in Latin America and then elsewhere. PES aim to reduce deforestation and degradation by providing payments to participants conditional on forest protection. PES attracted much attention among policy-makers as a potentially cost-effective and efficient conservation alternative, and for their poverty-alleviation prospects when operating among ‘poor’ forest-dwellers. This rising agenda has been accompanied by significant scholarly efforts to understand PES and their socioenvironmental effects. However, such understandings have overlooked local stakeholder perspectives, and evaluations have mostly examined short-term effects. Thus, less is known about PES’ long-term effects, their determinants, and how local stakeholders perceive them.
Using a multidisciplinary, multi-level, and dynamic livelihood approach combining geospatial and socioeconomic data collected from 2013-2017, this thesis helps to fill this gap by examining PES’ role in the broader livelihood strategies of six communities in the Mexican Lacandona Rainforest. The thesis makes three main contributions to PES literature. Methodologically, it presents a novel lens to understand PES effects, one that brings to the fore the voice of local stakeholders, while paying attention to evolving context and design aspects. Empirically, it shows that participants think about their livelihoods at broader temporal and spatial scales than short-term policies, which allows them to exert some control on the various policies they encounter. This longer-term thinking is reflected in the three analytical chapters in this thesis that examine how people engage with PES among other land uses, how communities devise payment distribution mechanisms, and how people combine multiple policies to pursue various goals. Conceptually, it shows that unless aspects of ‘context’, ‘design’, and ‘decision-making’ are examined simultaneously, PES’ manifold, multi-level, and evolving effects will not be sufficiently understood. Overall, the thesis shows that there are real implications for conceptualising rural development policy as an integrated ‘policy matrix’, instead of individual and self-contained policies.

Keywords: market-based conservation
Lacandon forest
deforestation
forest conservation policy
Mexico
Payments for Ecosystem Services (PES)
Advisor: Rival, L
Sánchez-Ancochea, D
New methods for identifying dune system reactivation drivers and responses, Nebraska Sandhills

Two billion people living in drylands are affected by land degradation and the destabilisation of surface sediments. However, a detailed understanding of the combined effects of natural and anthropogenic factors in contributing to sediment remobilisation is absent from the literature. A quantified awareness of vegetation cover sensitivities and resultant land degradation to forcing factors is needed if the vegetation and landscape response to future climatic changes and human pressure are to be better predicted.
Measuring past environmental response in a location with a known disturbance history allows us to identify thresholds and explore the relationship between disturbance forces and sedimentary response within a dryland environment. The Nebraska Sandhills, located in the Central Great Plains, is a semi-arid dune field with a reactivation history spanning the last 10,000 years and a well-documented history of forcing factors over recent decades. Whilst regional reactivations in the Central Great Plains have largely been attributed to palaeoclimatic change, the role of humans (e.g. The Dust Bowl of the 1930s), in particular over grazing, has also been cited as a potential cause of land degradation and sediment reactivation.
Using quartz luminescence dating, secondary datasets of forcing factors and statistical inference methods, this thesis identifies the record of sediment deposition in near-surface aeolian stratigraphies in the northern remits of the Nebraska Sandhills and explores the relationship between environmental sensitivity and external disturbance factors. High-resolution luminescence techniques allow us to construct a detailed chronological history of sedimentary deposition events over the last 900 years, producing a record of the environmental response across a range of aeolian features within the semi-arid setting. Combined with a detailed history of climatic, grazing and wildfire pressures, supervised machine learning techniques explore the relationship between forcing factor and environmental response, highlighting the importance of both regional and localised conditions in contributing to the heterogeneous sedimentary response found in the record.

Keywords: Landscape sensitivity
Drylands
Optically Stimulated Luminescence
Changepoint analysis
Artificial Neural Networks
Advisor: Bailey, R
Thomas, D
Investigation of the molecular effects of cooling human burns

Cooling of burns is key to acute burn management, and is a widely accepted practice in modern medicine. Cooled burns are less painful, heal more quickly, require fewer skin grafts, and leave less scarring. The vast majority of research in this area has used animal models, and focussed on optimising cooling, rather than investigating its mechanism. Cooling is not without risks and limitations, and understanding the mechanism might lead to pharmacological alternatives.
We aimed to develop a standardised human model for burning and cooling, and used this to investigate the transcriptional and proteomic effects of burning and cooling. This model used redundant skin discarded during surgery, and purpose-built apparatus for burn creation and cooling. Microvascular and other histological changes were demonstrated in response to burning, and modified by cooling. RNA and protein extracts from cooled and uncooled samples of burned and unburned skin were analysed with RNAseq and LC/MS3 techniques, respectively. Findings were validated with immunohistochemistry and qPCR.
We demonstrated that there was a significant change in 22% of the transcriptome of the skin, with gene ontologies related to wounding, angiogenesis, inflammation, haemostasis, innate immune response, degranulation and chemotaxis among those significantly upregulated. Downregulated ontologies included keratinisation, epidermal differentiation, hair follicle development and cornified envelope. Cooling of burns significantly increased the transcription of genes related to hair follicle differentiation while reducing the transcription of heat-shock proteins.
Burning caused significant activation of the complement and coagulation cascades, while cooling reduced the scale of these changes. Immunohistochemistry confirmed complement proteins, including the membrane-attack complex (MAC) localised to the immediate area of the blistered epidermis, as were fibrinogen and platelets, with evidence of early neutrophil migration.
We have demonstrated the role of complement and coagulation activation as a damage-amplifying agent following thermal injury, and the role of cooling in attenuating this effect. The preservation of transcription of follicle-related genes indicates preservation of epidermal appendages as sites of re-epithelialisation.
Complement blockade is already utilised in the management of autoimmune conditions, and transplant rejection, and could modify the complement activation in burns, reducing injury-progression, and the associated systemic effects, and improving patient outcomes.

Keywords: Complement
Thermal injury
Coagulation
Transcriptomics
Human
Proteomics
Cooling
Advisor: Harris, A
Furniss, D
Investigating the molecular, metabolic, and psychological effects of minocycline

An immune component has been suggested to underlie the pathophysiology of psychiatric diseases, and is thought to involve pro-inflammatory cytokines. Thus, there is the potential for drugs with anti-inflammatory properties to act as therapeutic agents for psychiatric illnesses. Minocycline has shown promise in pre-clinical animal models and early phase clinical trials for a variety of psychiatric disorders. Previous studies on minocycline have also shown its ability to suppress microglia activity and reduce inflammatory cytokine levels, and its behavioural effects on depressive-like behaviour in animals and humans. However, the underlying mechanisms that lead to minocycline’s psychotropic effects are not clear.
This dissertation investigated the proposal that the anti-inflammatory mechanisms of minocycline underlie its psychotropic effects, as well as explored the pathways that mediate inflammation-induced behavioural changes. To that end, four studies were conducted. The first study looked at inflammation-induced modulation of GluN2 subunit expression and downstream signalling, effects which were rescued by prior treatment with minocycline (Chapter Two). The second study explored the effects of inflammation and minocycline administration on plasma and brain metabolites in mice (Chapter Three). The third study and fourth study investigated the psychological effects (Chapter Four) and biochemical effects (Chapter 5) of an acute dose of minocycline in healthy volunteers. It was revealed that minocycline administration decreased fear misclassification, increased contextual learning, decreased levels of the inflammatory marker CRP, and increased serum lipoprotein.
Overall, minocycline was able to ameliorate inflammation-induced changes, suggesting that anti-inflammatory mechanisms are linked to glutamatergic signalling and synaptic transmission which lead to downstream psychotropic effects. However, metabolomic analysis also revealed changes in lipid metabolism and energy-related metabolites that could potentially underlie a separate mechanism for minocycline’s actions. Nevertheless, given the association between metabolites, and inflammation, it is possible that these pathways interact.

Keywords: NMDA Receptors
Minocycline
Emotional Processing
Metabolomics
Advisor: Burnet, P
Marriage and fertility in China and Japan

Declining family formation among women and closely related trends such as postponed marriages, rising age at first childbirth, and low fertility rates have been observed in modern China and Japan. In this light, understanding the determinants of women’s marriage and fertility decisions carries important sociological and policy implications. However, most of the extant research is impeded by lack of theory and a poor understanding of local cultural and institutional contexts. Existing research largely involves generating statistical relationships between socioeconomic status related variables and family formation outcomes. This methodology is insufficient for explaining the phenomenon in China and Japan where family formation is also influenced by context-specific factors such as gendered norms in the family and workplace. There is also a knowledge gap on how the relationships between these variables varies across China and Japan, which have had undergone similar but non-identical economic and demographic transformations.
I use data from the Chinese General Social Survey, the Japanese Social Stratification and Mobility Survey, the East Asia Social Survey, and the Panel Study of Family Dynamics to address the following questions: 1) How do son preference, co-residence with parents and education affect women’s second births in China? 2) How are the labour market conditions of women and their husbands at the point of marriage associated with women’s transition to motherhood in Japan? 3) How do parental roles in the matching process change women’s family formation decisions in China and Japan? The key findings are that firstly, context-specific factors, such as son preference in China, have a large and significant effect on family formation. Secondly, other parties, such as parents, play an important role in women’s family formation in these societies. Thirdly, there is a substantial degree of heterogeneity in the way that these factors contribute to family formation in China and Japan.

Advisor: Kan, M
The mythological epics of Dracontius in their socio-political context

The poet Blossius Aemilius Dracontius was active at Carthage during the late 5th century AD, a period when that part of the Roman Empire had long since fallen to the Vandals. Given his position of being a Roman and Catholic vir clarissimus under Germanic and Arian overlords, as well as his imprisonment by the Vandal king Gunthamund (r. 484-496) for reasons related to his poetry, he was likely to have been involved, willingly or unwillingly, in the political world of Vandal Carthage.
Within his oeuvre are Latin poems of both secular and Christian inspiration. This thesis concentrates on four short epic poems on mythological subjects from the former category: Hylas, De Raptu Helenae, Medea, Orestis tragoedia. Each displays idiosyncratic treatment of their respective material, including significant changes to commonly-transmitted versions of the myths, interaction with figures of the Latin literary tradition, and thematic manipulation. This thesis takes the position that, as a learned and well-read writer, trained in the rhetorical skills needed for the lawcourts, Dracontius was well aware of the propensity for Latin epic to mix contemporary socio-political comment into its narrative.
The thesis examines these four texts in the context of the poet’s artistic technique, his relationship to the society in which he finds himself, his attitudes towards the nature of kingship and powerful, threatening female figures. It is then concluded that these texts exhibit features which can be interpreted as having socio-political and historical significance, relating both to the poet’s immediate Vandal milieu, as well as more generally with questions of Roman continuity. In so doing, it reveals the poet’s shifting loyalties and views on his and his fellow-Romans’ situation under Vandal rule.

Advisor: Harrison, S
Kaufmann, H