VictorJuiz/thesis huggingface dataset:
Study of the interaction between the influenza A virus polymerase and GTPase Rab11a

The influenza A virus (IAV) genome that consists of eight viral RNA (vRNA) segments is transcribed and replicated by the viral heterotrimeric RNA-dependent RNA polymerase (RdRP) complex, composed of polymerase acidic (PA), polymerase basic 1 (PB1), and PB2, subunits, in the cell nucleus. Replicated vRNA segments are assembled with RdRP and oligomeric nucleoprotein into viral ribonucleoprotein (vRNP) complexes which are exported from the nucleus and transported across the cytoplasm to be packed into progeny virions. The GTPase Rab11a associated with recycling endosomes is believed to contribute to this process by mediating the cytoplasmic transport of vRNPs. However, how vRNPs interact with Rab11a remains poorly understood. In this D.Phil. project, I have utilised a combination of biochemical and structural approaches to characterise the interaction between the IAV RdRP and Rab11a. Initially, using a GST pull-down assay, I showed that the interaction between the IAV RdRP and Rab11a is direct, and that the 627- domain of PB2 is required for this interaction. Furthermore, my study demonstrated for the first time that Rab11a has a differential specificity for vRNP but not cRNP. Analysis of the Rab11a interactome further revealed that IAV infection reduces Rab11a binding to Rab11-family interacting partners (Rab11-FIPs), thereby altering the stoichiometry of cytoplasmic motor proteins bound by Rab11a. Using mutant Rab11a in a GST pull-down assay, this study provides the first evidence that IAV RdRP binds to the same site on Rab11a as Rab11-FIPs. It was also investigated here whether Rab11a has a role in determining the host specificity of influenza viruses. However, this study could not identify any adaptive mutations in PB2 that may affect the interaction between RdRP and Rab11a. Moreover, the study also did not identify the exact site of Rab11a binding on the viral RdRP using cryo- electron microscopy. However, performing a small-angle X-ray scattering analysis I showed that C-terminal two thirds of PB2 (PB2-C) and Rab11a form a well-folded protein complex in solution, and confirmed in a controlled pull-down assay that the interaction between PB2-C and Rab11a is direct. Finally, I have also established a workflow to study the interaction between IAV vRNPs and Rab11a in the context of live infected cells using full field cryo-X-ray microscopy. The findings of my D.Phil. work expand our understanding of the cytoplasmic transport of the influenza virus vRNPs. Identifying the exact site of Rab11a binding on the viral RdRP could uncover a novel target site for the development of an influenza antiviral drug.

Keywords: Rab11a
cytoplasmic trafficking
RNA polymerase
PB2 polymerase subunit
influenza virus
Field theoretical studies of nonequilibrium systems with long-range interactions

Characterising the effects of correlated fluctuations in nonequilibrium systems is an essential step in modelling many natural and synthetic processes. This thesis uses stochastic and field-theoretical approaches to investigate the rich macroscopic behaviour arising from nonequilibrium fluctuations in two systems: strong electrolytes driven by an external electric field and chemotactic particles with generalised gradient-sensing mechanisms. The common feature shared by these systems is the presence of nonlocal Coulombic interactions among their constituent particles. In electrolytes, these are electrostatic interactions governed by the Poisson equation; in chemotactic systems, on the other hand, diffusing chemical signals secreted by each particle mediate nonlocal interactions, which, in the limit of fast-diffusing signals, are governed by a similar Poisson relation.
In the first case, we study the stochastic dynamics of a driven electrolyte using the Dean-Kawasaki formalism and show that it exhibits scale invariance notwithstanding the Debye screening effects. Accordingly, the correlation functions of the driven electrolyte take power-law forms, in sharp contrast to the exponentially screened correlations in equilibrium electrolytes. These correlations give rise to fluctuation-induced forces between neutral boundaries that confine the electrolyte. In the Casimir geometry, we show that these nontrivial forces are generally long ranged and have transient parts that decay algebraically over time. We also find that the steady-state fluctuation force can be tuned in magnitude and direction by adjusting the external electric field.
In the second case, our focus is on self-chemotactic systems, namely collections of living or synthetic particles that release fast-diffusing chemical signals in their environment while responding to signal gradients by adjusting their motion. Based on scaling analysis and microscopic considerations, we devise a natural generalisation of the conventional Keller-Segel model by incorporating the effect of particle polarity into the stochastic density equations. We examine the associated large-scale properties of the system, first by studying its symmetry properties where we identify an emergent Galilean symmetry, and then through dynamical renormalisation group analysis of its critical state. We find exact scaling exponents, which show that density fluctuations are super-diffusive and the number fluctuations are non-Poissonian.

Keywords: Electrolytes
Stochastic Field theory
Long-range interactions
Langevin dynamics
Fluctuation-induced forces
Chemotaxis
Renormalisation group theory
Scaling laws
Advisor: Golestanian, R
After the Ballets Russes: movement and modernism in British theatre, 1914-1935

This thesis illuminates the significant yet frequently overlooked contribution that Serge Diaghilev’s Ballets Russes made to the development of British theatrical modernism. The extraordinary historical importance of leading dramatists and theatre practitioners such as Harley Granville Barker, J. M. Barrie, Terence Gray, and W. H. Auden has long been recognised, yet the debts they owed to Diaghilev’s company have remained neglected. This thesis recovers a striking selection of these debts, tracing the complex ways in which Barker, Barrie, Gray, and Auden gestured to various formal and aesthetic aspects of Diaghilev ballets in their endeavours to create total theatre art. Galvanised by the philosophical conditions of Britain’s early twentieth-century theatre scene, which saw growing interest in Nietzschean responses to classical drama and Wagnerian notions of the Gesamtkunstwerk, these theatre figures found inspiration in the formal and choreographic innovations of the Ballets Russes—particularly those pioneered by the revolutionary choreographer Michel Fokine. It was chiefly by taking these innovations as a point of departure that this diverse group of dramatists and theatre practitioners began to experiment with using the moving body to express aspects of dramatic texts, harnessing the company’s avant-garde repertoire to the service of advancing theatrical modernism. The first full-length study of the wider theatrical significance of Diaghilev’s company in the context of British drama and dramaturgy, this thesis offers new insight into the genesis, evolution, and performance of distinctive new theatrical forms, including a whimsical balletic burlesque and a deeply political poetic dramatic satire, as well as prominent modernist stagings of Shakespearean comedy and classical Greek tragedy.
Grounded in extensive archival study, historical research, and textual, choreographic, and photographic analysis, this thesis provides a fresh account of underexplored areas of modernism in performance. It unfolds the nuanced ways in which the theatrical legacy of the Ballets Russes enhanced, inflected, and intertwined with a plurality of the period’s broader dramatic and dramaturgical developments, elucidating its relationship to everything from the Wagnerian theatre theories of Adolphe Appia and Edward Gordon Craig to the iconoclastic aesthetics of central European expressionism, from the Mallarméan concerns of symbolist playwrights such as W. B. Yeats and Maurice Maeterlinck to the new forms of embodied stage poetics pioneered by figures such as Jacques Copeau, Rolf de Maré, and Jean Cocteau. In recovering the Ballets Russes’ role in British theatre history, this thesis thus illuminates a series of new artistic networks, expands understandings of some of the most eminent dramatists and theatre practitioners of early twentieth-century Britain, and uncovers a selection of literary and dramaturgical innovations that have previously been neglected in studies of British modernism.

Advisor: Jones, S
Investigation into structural and functional relationships of short-chain dehydrogenases and reductases (SDRs) using a compound library

The short-chain dehydrogenases/reductases (SDR) protein family is one of the largest and most evolutionarily conserved protein superfamilies known to date. SDRs show a remarkable ability to accommodate hundreds of reactions/substrates by using the versatile nucleotide binding domain as their central scaffold. SDRs are implicated in many different disease pathways, and represent a ‘druggable’ enzyme class, which has generated extensive biotechnological and pharmaceutical interest. For 28 human SDR members, the three- dimensional structures have been determined. Despite this, almost 25 % of human SDR members still have unknown functions, and many members lack any chemical descriptors. To address the dearth of ligand knowledge, 28 SDRs were cloned, expressed and purified to further characterise members by the application of differential scanning fluorimetry (DSF). A family annotation through cofactor preference, substrate accommodation and subcellular localisation has shown a few distinctive traits within the SDR family. This in silico approach has led to the creation of a systematic flow chart, which provides a starting point to identify substrate classes for orphan SDRs. Cofactor and inhibitor screening of SDRs by DSF has shown Tm shifts that are in-line with previous experimental data. DSF screening showed the decryption of 6 cofactor preferences for orphan SDRs, five of which have been confirmed in crystal structures. In contrast, screening of substrates in DSF produce little thermal stability (15 % detection rate), rendering it difficult to distinguish specific substrates for orphan SDRs. However, over 70 % of SDRs screened in DSF with known enzyme activity produce thermal shifts with compounds that resemble their substrate structures. This can therefore infer substrate classes for orphan SDRs that compare well with those from computational predictions. DSF screening against a ligand library has led to the discovery of the first small molecule binders for Nmr-like family domain-conatining protein 1 (NMRAL1) and selective inhibitors for Hydroxyprostaglandin dehydrogenase (HPGD). The use of small molecule ligands identified from DSF has also contributed to the success of crystal formation in the case of Hydroxysteroid dehydrogenase-like protein 2 (HSDL2) and Dehydrogenase/reductase SDR family member 2 (DHRS2). Overall this study has provided a platform for ligand screening to further structurally characterise the SDR family.

Keywords: short-chain dehydrogenases/reductases
SDR
differential scanning fluorimetry
TM shift
structural genomics
cofactor
DSF
SGC
Advisor: Oppermann, U
Modelling the spectra of exoplanets

Extrasolar planets (exoplanets) are planetary-mass objects that orbit different stars in our galaxy. To date, there have been over 4000 of these objects discovered, with a bias towards objects that transit their host star. This thesis focuses on interpreting the emission spectra of hot to ultra-hot Jupiter exoplanets. These are Jupiter-sized objects which orbit close to their host star, resulting in high effective temperatures and a tidally-locked orbital configuration.
The study of the emission spectra of exoplanets lets us probe the vertical chemical and thermal structure of the planet's atmosphere. The majority of the current observations are of hot to ultra-hot Jupiter planets, as the day-side flux is readily measurable with current telescopes. Therefore the first part of the thesis focuses on upgrading the NEMESIS model to calculate H− opacities and implementing a temperature-pressure parameterisation that can handle temperature profiles that can span the parameter space that contain non-inverted and inverted profiles.
These objects exhibit large day-night contrasts due to their tidally-locked nature, and it has been shown that this is detectable with current observations. We explore in this thesis the biases that can arise when studying an exoplanet with a non homogeneous thermal structure. We find that if we assume the thermal structure to be uniform on the disc, this can lead to spurious detection of molecules. We show that by retrieving the nightside and the dayside of the planet simultaneous we can perform an unbiased retrieval. We find that if the nightside contribution is small enough, a simple dilution factor can be used to account for the spatial inhomogeneity of the atmosphere.
Finally, we explore how scattering clouds can affect the way we interpret the emission spectra of cloudy exoplanets. We show that using a model that does not contain scattering to study the emission spectra of a cloudy exoplanet can lead to incorrectly inferred chemical abundances and also an erroneous detection of a thermal inversion. To provide a more agnostic approach to the modelling of clouds, in this thesis we have developed a novel technique to retrieve the cloud scattering properties, namely the single scattering albedo, which approximately encapsulates the real and imaginary refractive index spectra and the particle size of the cloud condensing species.
This thesis has broader impacts on the exoplanet community. The tools developed for hot and large planets will ensure that when moving to study smaller and cooler objects in the future, we can trust that our techniques are well verified.

Keywords: spectral retrieval
astronomy
exoplanets
Advisor: Irwin, P
Aigrain, S
Parmentier, V
Comparative biology of γδ T cells and the gut microbiota: studies with avian and murine systems

Interactions between the mucosal immune system, the microbiota and pathogens in the gut have far reaching implications for the host in terms of disease. The enteric mucosal immune system is known to develop in tandem with the microbiota during maturation and they drive changes in each other over time. γδ T cells are an enigmatic T cell subset which are greatly enriched at the intestinal mucosa and despite being in close contact with the microbiota, interactions between the two are not well described. This thesis aims to elucidate these interactions using Next Generation Sequencing methods to probe the TCR gamma repertoire and microbiota of both chicken and mouse, which fundamentally differ in terms of number of circulating γδ T cells.
This thesis first establishes a TCR gamma repertoire sequencing strategy in chicken. This strategy required an updated annotation of the gamma locus, indicating its evolution by tandem duplication. This enabled the first TCR gamma repertoire analysis in chicken, revealing that a single V gene segment, TRGV3.3, with a highly diverse, private CDR3 repertoire, was dominant in all tissues.
This annotated chicken gamma locus is then used to investigate the gut TCR gamma repertoire of Germ Free (GF) chickens, which lack an enteric microbiota. Surprisingly, the differences observed in the TCR gamma repertoire of these animals were relatively minor, suggesting that avian γδ T cells do not depend on the microbiota for development. To examine the reverse relationship, the gut microbial community of a recently constructed TCRγ ‐/‐ chicken strain, which lacked functional γδ T cells, was examined. The microbiota of these animals was again mostly unaffected, though reductions in potentially beneficial genera, such as Bifidobacterium, were observed in caecal contents.
Mixed Campylobacter strain infections are then utilised as an initiator of inflammation and dysbiosis in the chicken, resulting in a loss of homeostasis, which allows the examination of the γδ T cell-microbiota relationship in that context. Large differences in microbiota composition and changes IV to the TCR gamma repertoire were observed. Interestingly these changes were dependant on the composition of the mixed strain Campylobacter infection.
Finally, a mouse model is used to examine whether the finding that the microbiota is largely unaffected in the absence of γδ T cells is specific to chicken or whether it has a general applicability. Studies in mouse also allowed the investigation of a lack of gut tropic TRGV7 γδ T cells and thymic development on both the gut TCR gamma repertoire and the microbiota. In contrast to what was observed in chicken, all of these γδ T cell perturbations in mice lead to large scale microbiota changes when compared with Wild Type.
The findings presented in this thesis provide the first detailed insight into the interactions between γδ T cells and the enteric microbiota of chickens and further explore the generality of these findings through similar experiments in mice.

Advisor: Smith , A
Precision in the understanding and treatment of paranoia

Improvements are needed in the effectiveness and accessibility of cognitive behavioural therapy (CBT) for psychosis. One route to improving efficacy is to take a translational approach, focussing on one proposed causal mechanism at a time, and testing specific therapeutic techniques that may help to modify this mechanism. This thesis aims for precision at multiple stages. First, through focussing on a single psychotic experience, paranoia, and a single putative causal mechanism, negative cognition. Second, through testing interventions that target specific aspects of negative cognition in order to reduce paranoia. Third, through conducting studies using a manipulation method to gain precise causal evidence. Finally, using immersive virtual reality (VR) to accurately measure paranoia, train therapeutic techniques in a controlled setting, and, when automated, increase access to evidence-based therapy. Chapter 1 introduces these conceptual and methodological approaches to precision. A systematic review (Chapter 2) found that the manipulation method has to date been infrequently used in psychosis research. Chapters 3, 4, and 5 each report a study that combines the three approaches – specificity, manipulation, and VR. Chapter 3 found that training in compassionate coach imagery, practised in VR social environments, caused significant reductions in paranoia mediated by increases in self-compassion. Chapter 4 found that training in loving kindness meditation, practised in VR, caused significant reductions in paranoia that were mediated by increases in compassion for others. Chapter 5, in contrast, found that altering body posture prior to entering VR had a negligible effect on increasing feelings of power, and no subsequent effect on paranoia. Following this experimental work on modifying negative beliefs, Chapter 6 considered how such beliefs might form in the first place. Using a large epidemiologically representative adolescent sample and a smaller adult sample it was found that parental verbal and physical abuse, over-control, and lack of care were significantly associated with paranoia and negative self and other beliefs. Network analysis did not find that the relationship between parenting and paranoia was mediated by negative self and other beliefs. Finally, given the limited access to CBT for psychosis, Chapter 7 explored the feasibility of implementing automated VR therapy onto psychiatric inpatient wards. A thematic analysis of qualitative data found that both patients and staff believed VR would be beneficial in this setting, but that certain practical barriers needed to be overcome. Overall, this thesis provides initial evidence of the benefits in taking an early-stage translational approach to treatment development for paranoia, showing that even single therapeutic interventions can bring about large effects, and these techniques can now be tested in clinical populations.

Keywords: implementation
parenting
virtual reality
delusions
paranoia
compassion
psychosis
Advisor: Freeman, D
Waite, F
Beauty work: consumption, gender and hope in Yaounde, Cameroon

Against the backdrop of trade and media liberalisation following the end of the Cold War, this dissertation examines visual self-fashioning among young Bamileke women struggling to attain social adulthood in Yaoundé, Cameroon. It asks why young women living in precarious conditions invest in beauty, dress and photographs of themselves to the extent they do. In order to answer this question, the thesis, moves beyond semiotic understandings of consumption and analyses self-fashioning in embodied and material terms. From this perspective, investments in beauty, dress and photographs not only index dreams and imaginations, but emerge as a set of skills and embodied knowledge that I propose to call “beauty work”. Each chapter examines different skills and collectively illustrate how, through their investments, young women can alter their social positions and create upward paths of social mobility. Thus, for young women beauty, dress and photographs became means by which to fashion and refashion social adulthood in a social, economic and political context where other paths—as employment and education—are compromised.
In developing the notion of beauty work, this thesis contributes to the anthropological and Africanist literature on consumption, gender and hope. First, it challenges understanding of consumption as imitation in semiotic terms and argues for an understanding of imitation as valued skills and embodied knowledge in relation to notions of personhood. Second, insofar as beauty work encompasses skills, it reveals women as industrious. Thus, this thesis challenges understandings of beauty work in terms of empowerment versus resistance and instead discusses how female aesthetic subjectivities through beauty work are being made. The discussion foregrounds notion of femininity as a skill for crafting surface and in doing so illustrates how beauty work defies patriarchal and colonial regimes of recognition. Third, insofar as beauty work relies on newness, it redirects the temporality of embodied knowledge to the not-yet. Thus, this thesis argues, visual self-fashioning is performative of embodied hope when young women dress and photograph themselves to fashion social adulthood. Together the three arguments by drawing out the key role of the body, skills and the senses offer a new approach to understanding of investments in consumer capitalism for young women from Western Africa in particular, and in doing so illuminate workings of aesthetic capitalism in general.

Keywords: West Africa
beauty and fashion
young women
photography
Advisor: Zeitlyn, D