VictorJuiz/thesis huggingface dataset:
Molecular assembly and interactions of membrane proteins and viral glycoproteins using mass photometry
Keywords: label-free
membrane protein
in solution
single-molecule imaging
HIV-1
SARS-CoV-2
mass photometry
viral glycoprotein
interferometric scattering

Integral membrane proteins (IMPs) and their interactions form the basis underlying many processes essential for life of all living organisms. Despite their pivotal importance, they are challenging to study due to the presence of a bilayer-embedded transmembrane domain requiring astute strategies to achieve solubilisation in aqueous environments. Here we present mass photometry as a novel technique to investigate IMPs and their interactions in a variety of membrane mimetic systems, uncovering the interactions underlying the bacterial outer membrane architecture. We then apply mass photometry to viral membrane glycoproteins, the HIV-1 envelope spike and SARS-CoV-2 spike, and their interactions with a soluble inhibiting protein and host cell receptor, respectively. In both cases, we describe how the oligomeric nature of the involved proteins facilitates intermolecular crosslinking, facilitating enhanced inhibition.
We begin by establishing the applicability of mass photometry to measure a variety of membrane mimetic systems, including detergents, by determining the molecular weight of different IMPs in detergents, amphipols, lipid nanodiscs, and native nanodiscs. We further show the heterogeneity stemming from native membrane protein extraction with native nanodiscs, as well as the utility of mass photometry in predicting IMP functionality in different lipid nanodisc assemblies. We apply these findings to characterise the architecture and interactions between the IMP of the Gram-negative bacterial outer membrane, providing important insights into the outer membrane island formation and contributions to antibiotic resistance.
Next, we focus on the interactions of the HIV-1 envelope spike glycoprotein with its natural inhibitor, banana lectin BanLec. Through careful mass photometry measurements, we determine the dynamics of this multivalent interaction, resulting in the formation of highly heterogeneous species through intermolecular crosslinking. This approach is then applied to investigate the mechanism behind SARS-CoV-2 infection. We measure the interactions between the viral spike and its human host cell receptor, ACE2, showing the importance of its dimeric nature for achieving its full neutralisation potential through spike crosslinking.
This work introduced mass photometry as an important tool for membrane protein research with broad applications in protein-protein interactions as well as in characterisation of complex heterogeneous reactions important in viral infections.
Functional analysis of the African swine fever virus MGF360 and MGF505 proteins, and its application to vaccine development
Keywords: African swine fever virus

African swine fever virus (ASFV) is a deadly haemorrhagic pathogen of swine. In recent years, ASFV has spread beyond Africa and continues to ravage European and Asian pig herds, posing a severe socio-economic threat. No vaccines are currently available leaving preventive and extermination measures as the only course of action. The virus’ dsDNA genome is up to 190kb in length, and contains 5 clusters of paralogous genes known as Multigene family (MGF) genes close to both termini. Genes of MGF360 and MGF505 clusters have been implicated in the subversion of the innate immune system, and their absence is known to attenuate virulent isolates, however their specific mechanism of action is unknown. Here I have characterised the functions of MGF360-10L, 11L, 12L, 13L, 14L, MGF505-1R, 2R and 3R, by performing in silico and in vitro analysis. I revealed that these MGF genes inhibit the interferon signalling pathways at the level of the transcription factors or below. MGF360-12L and MGF505-1R were demonstrated to both contain a functional novel Cullin-RING-E3 ubiquitin ligase (CRL) recruitment motif, which was indispensable for the inhibitory action of MGF505- 1R on the interferon pathway. Moreover MGF505-1R reduced levels of endogenous p300, a cofactor essential in the transcription of type-I Interferon and other genes. Mutagenesis of the CRL motif restored p300 levels, indicating that MGF505-1R targets the p300 cofactor for CRL driven ubiquitination and subsequent proteasomal degradation. I applied the knowledge gained here to the rational development of vaccine candidates. Two profiles of MGF genes were deleted from the virulent Georgia07/1, and the impact on ex vivo ISG expression, and in vivo attenuation in pigs was assessed. This revealed the specific genes potentially key for attenuation. Overall, I have advanced knowledge on understanding the molecular mechanisms of the ASFV MGF360 and MGF505 proteins and identified two of those with critical roles during virus infection.
The Septuagint and legal traditions
Keywords: Egypt
Septuagint
Law
Greek
Old Testament
Hebrew
Bible

There are many minor differences between the Masoretic Text of the biblical laws and the Septuagint’s translation. What led the Septuagint’s translators to deviate from the Vorlage? Was it a matter of textual exegesis, development of halakhah, custom among the local Jewish community, or influence of contemporary Egyptian law? This thesis evaluates past scholarship, establishes the meaning of the Septuagint through contemporary texts, and compares the Septuagint to early rabbinic halakhah. This thesis argues that “intermediaries”—i.e., traditions of interpretation that arose between the time of composition and the time of translation—often shaped the translator’s understanding of the biblical laws. This thesis introduces new evidence to support the proposal of influence of Egyptian law on the Septuagint.
Security technologies and the global criminalization of migration: MIDAS, the IOM, and outsourcing border control
Keywords: Nigeria
border criminology
IOM
crimmigration
pragmatism
biometrics

This thesis contributes to border criminology scholarship by focusing on practices and technologies that contribute to the merging of border control and criminal justice in the Global South. Specifically, I examine the role of the International Organization for Migration (IOM) and its Migration Information and Data Analysis System (MIDAS) in shaping border controls in Nigeria. Empirically, the thesis draws on elite interviews with IOM officials, document analysis of technical and policy documents authored by the organization and by Nigerian federal authorities, and non-participant field observations in Abuja, Nigeria. Theoretically, I propose a synthesis of performativity and pragmatism as a useful analytical framework for understanding the political effects of MIDAS. Applying this theoretical framework to my primary empirical material, I make three substantive arguments. First, by highlighting the active role of Nigerian federal officials in shaping the roll-out of MIDAS, I argue for the importance of foregrounding Southern agency in analyses of crimmigration control as a global phenomenon. Nigerian officials actively utilize the border control system to engage in performances of ‘biometric statehood,’ to affirm their political authority domestically vis-à-vis competing political actors and to constitute the Nigerian state as a legitimate actor within the international system of sovereign states. Second, I characterize the IOM’s MIDAS-related capacity-building practices as pedagogical performances, intended to affirm its technical expertise and supposed political neutrality. The organization’s officials and public communications exhibit a solutionist understanding of migration, through which the latter is conceptualized as a technical, rather than political, problem that the IOM is well-placed to ‘solve.’ In Nigeria, key to this ‘solution’ has been the merging of the legal and practical frameworks of migration control and criminal justice. Finally, I argue that the technical components of MIDAS itself serve to constitute migration as a governable ‘problem’ amenable to techno-solutionist crimmigration control interventions.
Reactor neutrinos in a gadolinium-loaded Super-Kamiokande
Keywords: neutrino
particle physics
super-kamiokande
nuclear reactor
physics

In July of 2020, Super-Kamiokande (SK), a 50 kt water Cherenkov detector, entered its new phase: SK-Gd [1]. In this phase, the detector’s once-ultrapure water was doped with 0.02% gadolinium sulphate octahydrate by mass, increased to 0.06% in July 2022. This provides far greater sensitivity to neutron captures, thereby increasing the detection efficiency of electron antineutrinos interacting via inverse beta decay. One such source of these neutrinos is the numerous fission products in nuclear reactor cores. To date, only one reactor neutrino interaction has been identified in a large scale water Cherenkov detector [2], in part due to their energy spectrum extending less than 10 MeV above the Cherenkov threshold of positrons in water. A search has been performed for reactor neutrinos in data obtained by SK’s Wideband Intelligent Trigger (WIT) system from December 2020 to October 2021, using a boosted decision tree-based selection method. The search intended to identify an increase in event rate consistent with that expected due to the restart of 9 Japanese reactor cores between December of 2020 and October of 2021. Apparent issues with the WIT data between March and August of 2021 motivated the comparison of the rates measured in the data before and after this period. Though the measured rate up to March 2021 of (1.6 ± 0.2) d−1 was consistent with predictions, the rate measured between August and October 2021 was found to be (8.8 ± 0.4) d−1, far in excess of the predicted rate of 3.7 d−1. While not inconsistent with the expected total interaction rate of 9.75 d−1, an unreasonably large signal efficiency would be required for this increase to be solely explained by reactor restarts. One suspected cause of this increase is the persistence of issues with the WIT data from March 2021, continuing after August, when the data was previously thought to be once again stable. As such, this work cannot conclusively say that reactor neutrinos have been identified in SK; however, the Monte Carlo studies presented in this thesis indicate that the experiment has this capability.
Parameterizing the impact of fjord circulation on the ocean forcing of melting ice sheets
Keywords: parameterization
greenland
cryosphere
GFD
ice-ocean interaction
fjords

Freshwater flux from the melting of the Greenland Ice Sheet (GrIS) accounts for 15% of the observed rise in global-mean sea level since 1993, with the rate of mass loss expected to increase as ocean temperatures rise. Exchanges of heat and freshwater between the GrIS and the ocean are mediated by circulation in proglacial fjords, ubiquitous around the coast of Greenland. Fjord circulation occurs on length scales which are too small to be resolved in contemporary Earth system models, representing a fundamental limitation in the ability of these models to form accurate long-term predictions of global climate. To include ice-ocean interaction mediated by fjord circulation, a sub-grid scale parameterization scheme is required. Here we take the first steps towards developing such a scheme, exploring and characterising several first-order controls on circulation within fjords.
This thesis develops theoretical understanding of fjord circulation in a regime dominated by the injection of subglacial discharge at the grounding line. We employ computational modelling of idealised fjords and develop scaling laws for the vertical structure of the flow when averaged across the width of the fjord. We produce a dynamically motivated prediction of cross-fjord velocities at the ice face, which is used to predict submarine melt rates across the entire glacial terminus. These theoretical developments are used as the basis for a simple multi-layered box-model parameterization of fjord circulation in an estuarine regime, which is tested under a range of forcing conditions. Finally, we investigate the impact of bathymetric sills on plume-driven circulation. Within fjords with shallow sills, the stratification differs significantly from that of the neighbouring ocean outside of the sill, and submarine melt rates are reduced relative to sill-less fjords given a realistic ocean stratification. The work in this thesis could be used as the basis for a sub-grid scale parameterization scheme, with the potential to be extended to include additional geophysical processes in the future.
Biochemical isolation and mass spectrometric analysis of the CpG island proteome
Keywords: gene regulation
CpG islands
mass spectrometry
chromatin proteomics

Cytosine methylation is a pervasive DNA modification in vertebrate genomes that occurs predominantly in the context of sparsely distributed CpG dinucleotides. In contrast to the bulk genome, short genomic elements referred to as CpG islands (CGIs) feature a high GC content and clusters of non-methylated CpGs. CGIs co-localise with the majority of gene promoters where their distinct DNA sequence features enables the recruitment and assembly of transcription regulating complexes. Thus, as sites of transcription initiation, CGIs exert an important function in controlling promoter activity and gene expression. Despite their importance, it remains unclear how this is mechanistically achieved and how CGI dysfunction contributes to diseases such as cancer. This is largely due to the fact that the majority of our mechanistic insights into CGI function come from candidate-based approaches such as chromatin immunoprecipitation coupled to sequencing, which are inherently biased and limit us to investigating one protein at a time. The capacity to attribute detailed mechanistic understanding to CGI function has been hampered by our lack of a comprehensive inventory of proteins that contribute to their maintenance and function.
To overcome this fundamental lack of understanding, I have developed a new biochemical approach to isolate CGI chromatin from the bulk genome in order to investigate the CGI proteome in an unbiased manner using mass spectrometry. Applying next generation sequencing, I validated on the genome level that this method is suitable for specific enrichment of CGIs from mouse embryonic stem cells. Mass spectrometry data revealed many known CGI interactors, and it provided new leads for further investigation of potentially novel CGI-associated proteins. By deleting selected components of the CGI proteome, I uncovered CGI protein composition changes that pointed to new interrelations between the components of the gene regulation network at CGI promoters. Finally, using calibrated ChIP-sequencing as an orthogonal approach, I verified for selected proteins that the CGI proteome alterations were caused by changes in genomic occupancy. In conclusion, this work presents the first method to investigate the CGI proteome and its alterations comprehensively and unbiasedly in different conditions. Ultimately, this method can advance our knowledge of how CGIs contribute to gene regulation in developmental processes and pathogenesis.
Religious institutions in 19th-century Tehran: shariʿa law in a city in transition
Keywords: religious institution
social change
Shariʿa law
Qajar
Iran
Persia

The Nāṣirī period (5 September 1848 CE to 1 May 1896 CE) was a period of massive social transition embedded in the pretext of the Iranian modernization process. The rapid multidimensional developments of Iranian society turned it into a unique time frame for applying an institutional approach to socio-historical research. By concentrating on the continuity and change of the Shiʿi religious institutions (RIs) in Iranian society, this research investigates how social groups and institutions facilitated changes in RIs. The research chooses a set of RIs which have had a unique status in the Iranian society: waqf, mosque, takyih, madrasa, and imāmzādih.
The main question of this thesis is: How and under what influences did the RIs change in the Nāṣirī period? This question rises several secondary questions: How did Shiʿi shariʿa law regulate continuity and change of RIs? What sort of changes occurred in RIs in Tehran during this period? Which factors facilitated the changes?
Changes in RIs are subject to considerable restrictions and limitations rooted in Shiʿi shariʿa law and popular religious culture. However, cadastral surveys, censuses, maps, and historical accounts produced in the Qajar period reveal clear evidence of considerable changes in RIs, in terms of both quality and quantity. This thesis documents those changes and proposes explanations for some of the indigenous and exogenous factors that facilitated them at the individual, institutional, and environmental levels.
Synthesis and properties of 2d layered semiconductors and heterostructures
Keywords: epitaxy
chemical vapour deposition
photodetectors
defects
gallium sulfide
two-dimensional (2D) materials
transition metal dichalcogenides

More than a decade after the successful isolation of the first monolayer two-dimensional (2D) layered materials in 2004, a major focus in contemporary material science research is to expand the 2D family with novel layered materials or vertical layered heterostructures (VLHs) presenting extraordinary properties. Especially, 2D layered semiconductors with various bandgaps are considered as promising candidates for versatile applications in nanoelectronics, optoelectronics, sensors, etc. This DPhil project aims to contribute to the field by developing fundamental knowledge in the synthesis of 2D layered semiconductors and their VLHs via vapour phase deposition, and also in subsequent characterisation of their material properties for optoelectronic applications.
Simple direct sulfurization process was first developed for 2D semiconductor MoS2 which employs glass as a precursor-soluble substrate. This approach enables low cost and large-area uniformity as well as self-limiting crystal thickness and small nucleation density. Understanding of the diffusion-controlled dissolution and interface-limited precipitation processes facilitated morphological tuning of the MoS2 single crystals. Then, thickness- and stoichiometric-controlled growth of 2D GaS, a wide bandgap semiconductor, was achieved by chemical vapour deposition (CVD). A detailed investigation was performed into the stoichiometry- and thickness-dependent stability, optical and optoelectronic properties of GaS.
Both layer-by-layer growth and stacking assembly are commonly used for fabrication of 2D VLHs. Based on the Frenkel-Kontorova model, a general framework was proposed for understanding the origin of small twist angles in high-mismatch epitaxially-grown VLHs. Experimentally, the framework was tested on CVD-grown epitaxial GaS/MoS2 and GaS/graphene by scanning transmission electron microscopy. Finally, the non-stoichiometric GaS0.87 was stacked with WS2 to investigate optoelectronic behaviour of the bilayer VLH. The band alignment and charge transfer behaviour of the isotype type-II heterojunction were probed by various spectroscopic characterisation techniques. In addition, both large linear dynamic range and large photoresponsivity across the visible light spectrum were observed for GaS0.87/WS2 photodetectors.
Studies on immunoreceptor activation and SARS-CoV-2 RBD/ACE2 interactions
Keywords: non-catalytic tyrosine phosphorylated receptors
SARS-CoV-2
CD5 and CD6

The immune system must maintain a very fine balance recognising threats without damaging healthy cells and it uses cell surface non-catalytic tyrosine phosphorylated receptors (NTRs) to achieve this. In order to study this complex behaviour this work has taken a reductionist approach, using artificial systems in order to control as many variables as possible. The use of a generic cell surface ligand system to activate NTRs has suggested that they share a common mechanism for activation and shed light on specific characteristics of this mechanism. While NTRs are significantly different in terms of sequence homology they share similar structural characteristics which make them sensitive to receptor ligand dimensions. I was also able to show that altering the valency of the ligand could improve activation, but this was not due to clustering of the receptor. The mobility of the ligand was shown not to influence activation. Finally, changing the affinity of the ligand suggests the presence of a kinetic proofreading step during receptor activation.
This system was then applied to the accessory immune receptors CD5 and CD6. Until now, they have been very difficult to understand as they have been reported to both increase and decrease TCR activation. Using a combination of the generic ligand system and mutagenesis I was able to identify and characterise activatory and inhibitory effects of CD5 and CD6. The activatory effect was dependent on ligand engagement and expression of the TCR and comprised of contributions from both the extracellular domain through adhesion and signalling through the cytoplasmic tail. The inhibitory effects were independent of ligand engagement and, in the case of CD6, required the cytoplasmic tyrosine residue 489. CD5 was also suggested to exhibit a dual role with the extracellular domain inducing activation and the cytoplasmic tail responsible for inhibition.
Lastly, due to the emergence of the SARS-CoV-2 virus, the focus of my study shifted from receptor-ligand interactions in the immune response to characterise the effect of common mutations on the interaction of the SARS-CoV-2 Spike protein and its cell surface receptor on human cells ACE2. I purified and obtained detailed affinity data for nine ACE2 missense variants which are present in the human population plus one found through in silico saturation mutagenesis. I then purified and obtained detailed affinity and kinetic data for nineteen RBD constructs which contain mutations found in the common SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, Delta, and Omicron).
Prudential implications of intrafirm structure: the segmentation of global systemically important banks
Keywords: banking
corporate law
systemic risk
financial regulation

Modern finance is increasingly dominated by large financial firms made up of many legal entities. This trend is particularly pronounced for global systemically important banks (G-SIBs), which often have over a thousand subsidiaries that are connected through a complex and opaque web of wide- ranging explicit and tacit relationships. There is widespread acceptance that such complex intrafirm structures affect a G-SIB’s risk profile, but the nature of these risks are only superficially understood. This thesis articulates a framework for characterising intrafirm structures and applies that framework to G-SIBs to explore the relationship between intrafirm structure and prudential risk.
The thesis yields three important contributions to scholarly and public policy debates surrounding the regulation of G-SIBs. First, the thesis develops an analytical framework rooted in network theory that facilitates the qualitative and quantitative characterisation and study of intrafirm structures. Second, the thesis elucidates the sources of intrafirm segmentation along entity lines and, building on the network-based framework proposed to study intrafirm structures, develops a tractable approach to study the consequences of intrafirm segmentation for a G-SIB’s risk profile. Third, drawing on a case study of the UK ring-fencing regime, the thesis explores the central role of intrafirm governance to the success of regulatory intrafirm segmentation policies and highlights how intrafirm governance may create unique vulnerabilities to their credibility.