VictorJuiz/thesis huggingface dataset:
Structural, functional and computational studies on the SLC7 family of amino acid transporters

Amino acids are central components of the cell as protein building blocks, nitrogen sources and metabolic and cell signalling regulators. As such amino acid concentration in the cytosol and cellular compartments must be regulated. The SLC7 family of amino acid transporters provides a central gateway of amino acids to the cell. There is increasing understanding of mammalian SLC7 members, primarily, through structural and functional studies on prokaryotic and, recently, some human homologues. However, a member of the cationic amino acid transporter (CAT) subfamily remains of unknown function, prompting us to uncover its structure-function relationship. This thesis reports the first cryoEM structure of a eukaryotic SLC7A4 homologue, from Arabidopsis thaliana (AtCAT4), closely related to the mammalian SLC7A4 by conserving a key acidic residue, and other CATs responsible for the transport of L-arginine, L-lysine, and L-ornithine into the cell. AtCAT4 structural elucidation required the selection and generation of a nanomolar affinity sybody binder. The structure was solved in the apo outward-open state and showed AtCAT4 has an APC fold with two additional TM helices previously unobserved, likely involved in homodimerisation. Structural comparisons revealed an intricate electrostatic gating mechanism, which rearranges upon substrate binding, uncovering early steps of the transport cycle. AtCAT4 binding assays and MD simulation showed recognition of L-arginine, L-lysine, and L-ornithine with differential preferences for each. Human SLC7A4 however did not transport cationic amino acids, but preliminary data support a role for L-leucine transport. Structural analyses and mutagenesis suggested the root of the homologue discrepancy to be two bulky, hydrophobic residues absent from AtCAT4 and other CATs. The current structure serves as a template to further understand mammalian cationic amino acid transport via the SLC7 family. AtCAT4 was solved with a steroid lipid bound, similar to other SLC7s. With multiscale-MD and in vitro transport assays we suggest two cholesterol binding sites for HATs which stabilise transporter SLC7-SLC3 heterodimerisation and conformational state.

Keywords: protein-lipid interactions
SLC7 transporters
structural biology
membrane proteins
electron cryomicroscopy
CAT4
SLC7A4
amino acid transporters
synthetic nanobodies
cholesterol interactions
Advisor: Biggin, P
Newstead, S
The maintenance and spread of cooperation in social networks in natural populations

Social interaction is crucial for social animals to thrive, but it comes with both benefits and costs. The social network approach helps to identify how social processes like cooperation are influenced by individual and population-level characteristics. Factors like individual recognition, familiarity, and social stability play a role in promoting tolerance and cooperation; and understanding these factors can provide insights into how social networks, cooperation, and other social behaviors evolve in different species. In this thesis, I examine how social processes interact with spatial and temporal factors to influence fitness and other outcomes in wild birds (Paridae).
I begin by establishing a theoretical foundation for my work by reviewing the concepts of cooperation and individual recognition and how they can be better understood through a social network approach (Chapters 2 & 3). Using experimental data, I explore the processes that may impact cooperative behavior by examining leading behavior during mixed-species foraging (Chapter 4) and demonstrate that motivation and dominance, as well as spatio- temporal effects, are determinants of this behavior. Drawing on these insights, I then use long-term breeding data to show that familiarity among neighbors as well as familiarity within breeding pairs influences fitness (Chapter 5). I also demonstrate that different kinds of social relationships have different effects on reproductive outcomes (Chapter 6).
All in all, I demonstrate that social connections have implications for fitness, and highlight the importance of accounting for spatial, temporal, and cognitive components when studying the ecology and evolution of sociality.

Keywords: social network
cooperation
individual recognition
fitness
sociality
Advisor: Sheldon, B
Firth, J
Cole, E
Development of a microfluidic-based platform for delayed vaccine delivery

Incomplete vaccination poses a significant challenge to disease eradication efforts, resulting in approximately 1.5 million preventable deaths each year. A single-injection method for administering a full course of immunisation would help to improve global coverage, reduce preventable deaths, and alleviate logistical and cost burdens during outbreaks. Biodegradable polymer microparticles have been studied previously for controlled vaccine release, but traditional manufacturing methods lead to particles with inconsistent size, vaccine loading, and release rates, preventing the development of encapsulated delayed release or single-dose vaccines.
The goal of this thesis was to develop and assess a delayed vaccine delivery system using microfluidics. Firstly, a microfluidic emulsification system within a chip was designed for the production of double emulsion formulations by introducing a step in the height in the microfluidic channel. This enabled reliable production of double emulsions required for creating uniform liquid core – solid shell particles (LCSS particles). The system produced fully loaded particles of varying size and thickness, suitable for the application by injection delivery, with throughput rates of 300Hz and higher. Compared to previously reported systems, this microfluidic system offers significant advantages, including better emulsification reliability and uniformity, postproduction quality control of particles, and scale-up potential.
The ability of particles to achieve delayed release was studied in vitro demonstrating pulsatile release after a lag phase. Duration of the lag phase was determined by the molecular weight and L:G ratio of the PLGA polymer used as the shell and could be extended from a couple of weeks to months. Finally, in vivo proof-of-concept of the utility of the particles was demonstrated in the context of a leading malaria candidate vaccine R21 in a mouse challenge model. Changing the particle formulation enabled to achieve different immune response delays. Moreover, a single injection of a priming vaccine with the booster dose encapsulated within particles resulted in higher immunogenicity and efficacy than a dose-matched priming vaccine alone. These findings provide key evidence for the potential of this system to achieve high vaccine efficacy with a single injection.

Keywords: Microparticles
Microfluidics
Vaccine
Microcapsules
Delayed Drug Delivery
Single-Shot Vaccine
Vaccine Delivery
Advisor: Milicic, A
Hill, A
Stride, E
In praise of vanity : the Augustinian analysis of the benefits of vice from Port-Royal to Mandeville

This is a study in the moral and political thought of the French Catholic Augustinian moralistes of the third quarter of the Seventeenth Century, and their Protestant successors, Pierre Bayle and Bernard Mandeville.
Although La Rochefoucauld, Pascal, and Nicole are best known for their closely observed and pessimistic analyses of human nature, this thesis focuses on a second feature of their thought: their arguments for the constructive potential of human corruption. The moralistes' starting point is provided by Augustinian and 'reason of state' accounts of the necessity that the human condition imposes upon us of making good use of bad means. Eager to challenge what they deemed to be a facile and conceited commitment to a natural virtue amongst their humanistic contemporaries, the French Augustinians elaborated upon this account in an original direction; they offered an exceptionally optimistic analysis of the possibilities of human cupidity, presenting it as the stuff from which a remarkably happy social life might be generated. Indeed they went so far as to offer satirical vindications not merely of the exploitation of human corruption, but of human corruption itself.
Of course the moralistes' arguments did not simply replicate one another, and the main body of the thesis attempts to distinguish between the different elaborations they gave to their defences of vanity. After a chapter on political and cultural context, Chapter 2 explores some of the sources of the moralistes' arguments in the writings of St. Augustine, and the sceptical humanists, especially Montaigne. The third chapter is devoted to La Rochefoucauld; having offered an account of the Augustinian intentions of the Maximes, the last part of this chapter seeks to draw attention to the presence in that work of a satirical vindication of vice and vanity. Pascal is the central figure in this study, and both Chapters 4 and 5 highlight the existence in the early parts of the Pensées of an audacious defence of the vanity of the people against their philosophical critics. The penultimate chapter is devoted to Nicole's more cautious and derivative account of the obligation of respecting conventions of civility and political obedience which channel vice in a beneficial direction.
Chapter 7 argues that Bayle's and Mandeville's well-known paradoxes concerning the potential of corruption run along lines already laid down by the Port-Royalists. In other words (and as the Conclusion suggests) Bayle's and Mandeville's analyses should be seen, like those of the Catholic moralistes, as contributions to a tradition which reaches through sixteenth-century Tacitists and sceptics like Montaigne, to the Enlightenment - a tradition which played an important but relatively neglected role in shaping eighteenth-century debates about commerce and virtue.

Keywords: ethics
intellectual life
political science
Mandeville
Augustinians
Bernard Mandeville
Catholics
abbeys
Protestantism
vice
Bayle
France
Augustinian
abbey
Protestants
vanity
Port-Royal des Champs
Pierre Bayle
Advisor: Robertson, J
Brockliss, L
The palace and the parish: the Church of England's approach to interreligious relations with Muslims nationally and locally, 2005-2021

This dissertation examines the character of the established Church of England’s engagement with Islam from 2005 to 2021. It contends that there is a dual method which can be understood on the levels of the national and the local. With a view to the national, the year 2005 marked the Church of England’s founding of Presence and Engagement, a programme whose remit is “to think about the reality of religious diversity and how it might shape mission and ministry.” There are five core Presence and Engagement reports spanning 2005 to 2017 which are analysed alongside their concomitant General Synod debates. The Church of England’s approach to interreligious engagement with Islam on a national level is a process of inward-facing dialogue, wherein the Church of England’s chief concern is how its own identity qua national church is affected by the growth of Islam in England. As such, the Presence and Engagement reports are analysed as documentary evidence of the Church of England’s emerging subjecthood as it encounters an increasingly multireligious England. The discussion of the national level forms Part 1 of this dissertation. Part 2 of this dissertation considers the local level through a case study of the Church of England’s Diocese of Birmingham. The case study is based on ethnographic interviews with parish priests and other central Anglican figures, conducted in 2020 through 2021. It finds that the local church participates in outward-facing interreligious dialogue with Muslim individuals and communities through diverse activities in everyday life, challenging the notion of dialogue as formal. While the national and the local levels have differing priorities, they share a common vocabulary, e.g., hospitality, witness, and love, and the central motif of the parochial system. This vocabulary is used by actors across the Church to understand how they should engage with Muslims.

Keywords: religion in the United Kingdom
anthropology of religion
Church of England
Christian-Muslim relations
Anglicanism
interreligious dialogue
Islam
Advisor: Hausner, S
Chapman, M
Visually guided motion through complex environments

The ability of animals to swiftly move through cluttered environments has inspired biologists interested in understanding its underlying mechanisms and engineers interested in applying its underpinning principles. To avoid colliding with obstacles, animals first need to detect that an object may be in their way. A decision then needs to be made about avoiding contact with the object so that locomotor strategies can be adjusted accordingly. In this thesis, I break down the problem of how animals negotiate clutter into three distinct, but related questions: 1) What information is needed to avoid collisions, and how do animals perceive it?; 2) how do animals choose between alternative paths to take?; 3) how are such choices implemented? I study these questions in two model species that inhabit open spaces but regularly encounter clutter: the homing pigeon (Columba livia) and the Picasso triggerfish (Rhinecanthus aculeatus). I frame their clutter negotiation behaviour as a process of sequential gap selection, allowing me to decompose it into components that can be independently evaluated. In Chapter 2, I use a combined experimental and modelling approach to model pigeons' steering behaviour algorithmically in a two-alternative forced-choice task. The birds are tracked flying inside a large hall whose open exit was separated from the release point by a curtain creating two vertical gaps. I find that their flights are best modelled by delayed proportional navigation, the same steering controller that has been used to implement all basic geometries observed in pursuit behaviour. In Chapter 3, I use a high-speed motion capture system to track pigeons flying through an artificial forest of vertical poles. I find bird gap choices are best captured by an autoregressive model, including information about the exit location, the cartesian distance between the closest obstacles, and the apparent visual gaps between all the obstacles ahead. In Chapter 4, I use a similar experimental paradigm to investigate how fish negotiate clutter, a behaviour which has never been studied in fish before. I find evidence of fish choosing clearances most directly aligned with their target based on egocentric visual cues. Finally, I show how these components can be combined to simulate realistic animal trajectories through clutter. Overall, the results of my thesis provide a valuable new framework for looking at how animals move through complex environments.

Keywords: obstacle avoidance
visual guidance
fish
bird flight
gap negotiation
animal behaviour
motion capture
vision
Advisor: Taylor, G
Newport, C
Exploring endometrial cellular heterogeneity and its role in endometriosis using single-cell transcriptomics

The human endometrium, the inner mucosal lining of the uterus, undergoes cycles of shedding, regeneration, growth, and differentiation on a monthly basis in response to steroid hormones. In endometriosis, endometrial-like cells grow outside of the uterus, and are associated with debilitating chronic pain and subfertility that can have a substantial negative impact on quality of life. Yet, it is not fully understood how the endometrium achieves its immense regenerative capacity and whether the cellular make-up of the endometrium in health and endometriosis differs. Studies profiling the endometrium at the single-cell level have so far analysed only a limited number of cells and samples, making it difficult to disentangle the inherent heterogeneity of this dynamic tissue. In this thesis I aimed to generate a comprehensive cellular map of the endometrium in a large set of donors with/without endometriosis both during natural menstrual cycles and when taking exogenous hormonal therapy. I hypothesised that by analysing a large set of endometrial biopsies we can uncover novel cell populations and disease-specific transcriptomic signatures.
The single-cell map presented in this thesis consists of ~600,000 whole cells and nuclei from 90 individuals, and was compiled by integrating data newly generated during my studies with two previously published datasets. Focusing on the epithelial and mesenchymal cell lineages, I defined novel cell populations that appear around the time of ovulation and window of implantation. Moreover, I observed cell populations specific to taking various forms of exogenous hormonal therapy. Additionally, I utilised the in vivo endometrial cellular map to dissect the cellular heterogeneity of in vitro endometrial organoids and organoid-stromal cell cocultures. Analysing ~100,000 cells, I described a population of cells expressing MUC5B, PAEP, and TFF3 as a feature present in organoids from donors with endometriosis. Altogether, the cellular maps of the endometrium in vivo and in vitro presented in this thesis have the potential to serve as a great resource to further study endometrial function and associated pathologies, as well as guide the development of novel clinical in vitro models of the endometrium.

Keywords: endometrium
organoids
single-cell genomics
endometriosis
Advisor: Zondervan, K
Becker, C
Vento-Tormo, R
Dragovic, R
Southcombe, J
Generalised young measures and lower semi-continuity of integral functionals

The purpose of this thesis is to study representations of integral functionals of the form u → ∫Ω f(u(x))dµ(x) =: F(u) (0.0.1), when
• u ∈ Lᵖ(Ω, µ, Rᵈ) varies in different topologies,
• µ is a non-negative finite Borel measure,
• f: Rᵈ → R is continuous and has p-growth |f(z)| ≤ C(1 + |z|ᵖ).
If a sequence (uⱼ)ⱼ converges strongly in Lᵖ to some u ∈ Lᵖ(Ω, µ, Rᵐ), one can always pass to the limit under the integral sign in (0.0.1) and obtain that F(uⱼ) → F(u). However, a sequence (uⱼ)ⱼ bounded in Lᵖ(Ω, µ, Rᵐ) is not always relatively compact in the strong topology, and this happens exactly when (uⱼ)ⱼ oscillates or when (|uⱼ|ᵖ)ⱼ concentrates. In this case, F(uⱼ), in general, does not converge to F(u). After constructing a formula representing accumulation points of F(uⱼ) for sequences (uⱼ)ⱼ that are only bounded in Lᵖ(Ω, µ, Rᵐ), and so allowed to oscillate and concentrate, we use it to solve classical problems in the calculus of variations that involve gradients.
We mainly focus on classes of functions whose derivatives are integrable, for example, when u = ∇v or u = (v, ∇v), with v ∈ W¹ʼᵖ(Ω, Rᵐ). This problem has been largely studied for 1
When a sequence (uⱼ)ⱼ is bounded in Lᵖ(Ω, µ, Rᵐ), it can happen that (|uⱼ|ᵖ)ⱼ , which is a sequence bounded in L¹(Ω, µ), converges to a measure singular with respect to µ. There is extensive literature on representations of (0.0.1) when f(z) has a homogeneous-like behaviour for large values of z, but the general case has not been studied in depth.
Here we prove a new representation of limits of bounded sequence (uⱼ)ⱼ in Lᵖ(Ω, µ, Rᵐ) of (0.0.1), which are called Young Measures. Such a representation is an improvement of the well-known construction by DiPerna and Majda in [36] and enables us to manipulate such limits similarly to Alibert and Bouchitté [6], but for any continuous f that has p-growth. This is necessary as quasi-convexity does not entail a homogeneous-like behaviour of f(z) for large values of z ∈ Rᵐⁿ, when m, n > 1, so the classical theory of Young Measures cannot always be used.
Via our representation, we are able to prove a characterisation of Gradient Young Measures, which are generalised limits of sequence (∇uⱼ)ⱼ with (uⱼ)ⱼ bounded in W¹ʼ¹ (Ω, Rᵐ), in greater generality than previously achieved. We are also able to improve the lower semi-continuity result for measure derivatives in [65], to the case v = (u, Du/µ) in (0.0.1), and we also show that minimising sequences of the Dirichlet problem of (0.0.1) in W¹ʼᵖ, under a sharp p-coercivity condition, are equi-integrable when p > 1.
The importance and originality of our framework are that we can show that many properties of different classes of generalised Young Measures are essentially the same as in the classical case developed in [6], where only a small class of integrands was considered. Our framework also enables us to perform arithmetic-like operations on objects that were previously too abstract to be manipulated.

Keywords: quasi-convexity
separable compactifications
lower semi-continuity
functions of bounded variations
vector measures
Advisor: Kristensen, J
Understanding the roles of cellular RNA-binding proteins in HIV-1 infection

The Human Immunodeficiency virus type 1 (HIV-1) is the causative agent of Acquired Immune Deficiency Syndrome (AIDS) which is currently estimated to affect 37.9 million people globally, representing a serious threat to global health. Developing a fundamental understanding of the HIV-1 life cycle is paramount in the search for a cure. RNA is a central molecule in HIV-1 biology due to its dual function as messenger and genome. However, the small number of proteins encoded by HIV-1 is insufficient to enable virus infection. Hence, HIV-1 hijacks cellular RNA-binding proteins (RBPs) to fulfil its life cycle. Using in virion RNA-interactome capture we identified 104 cellular RBPs interacting with HIV-1 RNA within the viral capsid. My DPhil aimed to identify which of these RBPs regulate HIV-1 infection. By screening RBP-knockout cell lines I uncovered the effects of MKRN1, FAM120A, LSM14A, MSN, LCK, CIRBP and YBX3 on HIV-1 infection. Further analysis into the role of MKRN1 revealed a novel function for MKRN1 in the positive regulation of HIV-1 viral particle release from the plasma membrane. Additionally, I have developed a tool, HIV-1INscarlet, to enable the visualisation of the early stages of HIV-1 infection from viral particle entry to integration using super-resolution microscopy. This tool will allow for future experiments into the role of MKRN1 inside the HIV-1 capsid during the early stages of infection. Together, this work highlights novel cellular regulators of HIV-1 infection and further validates the crucial role conducted by cellular RBPs in HIV-1 infection.

Keywords: HIV-1
MKRN1
RNA-binding protein
host-pathogen interaction
virus
Advisor: Castello, A
Sattentau, Q