VictorJuiz/thesis huggingface dataset:
Assessment of the functional impact of amino acid variants in DNA damage response proteins using orthologue complementation

The DNA in every cell of the human body is subject to a barrage of exogenous and endogenous mutagens, causing tens of thousands of DNA lesions per cell, per day. To counteract this assault, cells have evolved a network of proteins that work to detect and repair the DNA lesions, collectively known as the DNA damage response (DDR). Despite the actions of the DDR, DNA damage can persist and may lead to changes to the genetic code, in the form of missense, nonsense and silent mutations and chromosomal rearrangements. Mutagenesis in this manner contributes to diseases such as cancer and accelerated ageing. Therefore, preserving genomic integrity is of paramount importance for the health of the organism. In this thesis, I focus on the functional consequences of missense mutations, defined as base pair substitutions altering the amino acid coded for by the codon. The alternative amino acid incorporated into the protein, termed a ‘variant’, may cause disruption to protein activity depending on its location and characteristics. Disruption to protein activity can contribute to carcinogenesis, and is often used to stratify patients forming the basis for specific lines of treatment. Currently, a plethora of methods exist for interpreting the consequences of variants on protein function, but often lack a physiological readout or are limited in their throughput. Here, I describe a new method that provides an efficient, high-throughput means of assessing the impact of variants on protein function. It is based on complementation of a specific human gene knockout cell phenotype, by expression of a series of vertebrate orthologues with increasing evolutionary distance from human. Due to the natural variation of amino acid residues observed in orthologue sequences, full complementation with any given orthologue could reveal variants tolerated by the human protein at certain positions. Here, I test this methodology using proteins from the DDR, due to their extensive cross-species conservation, mutation in diseases such as cancer and relevance to synthetic lethality-based treatments. I show that this method can identify functional variants in DDR genes, as well as determining the importance of previously identified post-translational modification (PTM) sites. Collectively, this method is able to provide insight into impact of amino acid variants on protein function, which offers clinical benefits as well as furthering our understanding of protein regulation.

Advisor: Blackford, A
Clynes, D
Design and analysis of genetic feedback architectures for synthetic biology

Synthetic Biology seeks to design and assemble novel biological systems with favourable properties. It allows us to comprehend and modify the fundamental mechanisms of life and holds significant promise in revolutionizing current technologies ranging from medicine and biomanufacturing to energy and environmental protection. Biological processes constitute remarkably complex dynamical systems operating impeccably well in messy and constantly changing environments. Their ability to do so is rooted in sophisticated molecular control architectures crafted by natural evolutionary innovation over billions of years. Such control architectures, often blended with human-engineering approaches, are the key to realizing efficient and reliable synthetic biological systems. Aiming to accelerate the development of the latter, the present thesis addresses some fundamental challenges in biomolecular systems and control design.
We begin by elucidating biological mechanisms of temporal gradient computation, enabling cells to adjust their behaviour in response to anticipated environmental changes. Specifically, we introduce biomolecular motifs capable of functioning as highly tunable and accurate signal differentiators to input molecular signals around their nominal operation. We investigate strategies to deal with high-frequency input signal components which can be detrimental to the performance of most differentiators. We ascertain the occurrence of such motifs in natural regulatory networks and demonstrate the potential of synthetic experimental realizations. Our motifs can serve as reliable speed biosensors and can form the basis for derivative feedback control.
Motivated by the pervasiveness of Proportional-Integral-Derivative (PID) controllers in modern technological applications, we present the realization of a PID controller via biomolecular reactions employing, among others, our differentiator motifs. This biomolecular architecture represents a PID control law with set point weighting and filtered derivative action, offering robust regulation of a single-output biological process with enhanced dynamic performance and low levels of stochastic noise. It is characterized by significant ease of tuning and can be of particular experimental interest in molecular programming applications.
Finally, we investigate efficient regulation strategies for multi-output biological processes with internal coupling interactions, expanding previously established single-output control approaches. More specifically, we propose control schemes allowing for robust manipulation of the outputs in various ways, namely manipulation of their product/ratio, linear combinations of them as well as manipulation of each of the outputs independently. Our analysis is centered around two-output biological processes, yet the scalability of the proposed regulation strategies to processes with a higher number of outputs is highlighted. In parallel, their experimental implementability is explored in both in vivo and in vitro settings.

Advisor: Papachristodoulou, A
Cardelli, L
Degrowth and progress: a critical genealogy and contemporary analysis of growthism


This thesis interrogates the relationship between growth—using an expanded definition of the economic concept to mean an ecologically exclusionary mode of sociotechnical metabolism predicated on extraction and expansion—and progress, a metanarrative that facilitates political rhetorics co-reproducing growth. This thesis suggests that Anthropocenic challenges like inequalities in the distribution of human well-being indicators and global ecological harms can be understood as emerging from the historical trajectory of growth, the metaideology (“growthism”) that has arisen to systematize and operationalize it, and the metanarrative of progress that has co-reproduced it. As such, the study begins with a (non-Foucauldian) genealogy tracing the lineage of the idea of progress and its relationship to forms of growth(ism) that arose in the Early Dynastic Period in Mesopotamia. Using this lineage, based on Western sources and history, as context, the study then interrogates contemporary attitudes, values, and motivations among practitioners of political, social, and technological change as they relate to growth, degrowth—the discipline and tendency recently risen to critique growth—and narratives of progress. This analysis focuses on materials gathered from in-depth interviews with practitioners. The study finds patterns emerging through time in the relationship between modes of growth and narratives of progress that offer productive insights for degrowth—or “post-growth”—literature and Anthropocene dating. Further, the study finds patterns in practitioners’ receptiveness to growth, degrowth, and progress that yield productive insights for degrowth scholarship and activism.

Keywords: anthropocene
progress
growth
critical geography
degrowth
interview
historical
human ecology
ecology
qualitative
integrated geography
genealogy
Advisor: Eyre, N
Brophy, A
Making menstruation manageable: women in medicine, shifting menstrual capacity and new bodies of menstrual research

This thesis examines women doctors in the first half of the twentieth century, who were qualifying into a world which conceptualised women as rendered less capable by their menstruating bodies. They used their relative power within the profession to dismantle late nineteenth-century ideas about women’s bodies and menstruation, focusing their research on adolescent girls who were not yet set in their menstrual habits. Individual doctors such as Alice Sanderson Clow, the focus of Chapter One, blamed menstrual incapacity on the ‘sick role’ which middle- and upper-class women and girls were encouraged to take, and on menstrual myths which prevented bathing and exercise during the period. The Medical Women’s Federation conceptualised menstrual ‘disability’ as caused by a lack of puberty education and access to facilities and set out on a decades long campaign to provide education and improve what I have termed ‘menstrual infrastructure’. While these women doctors had varying ideas about the causes of menstrual ‘disability’ they were in agreement that it was not fundamental to the experience of womanhood, and that it could be relieved with social and pastoral intervention. In the second half of the twentieth century, women’s place within the medical profession, and in society, was becoming more secure. This meant that women doctors were able to articulate narratives about women’s bodies which did not necessarily conceive of them as fundamentally active and capable, without delegitimising their own authority as doctors. The medical women who came before them had succeeded in destabilising the idea that women’s bodies were universally rendered less capable by their reproductive capacity. This allowed space for new narratives of a pre-menstrual incapacity to evolve, championed by one woman doctor, Katharina Dalton, who aimed to help women to manage what she perceived to be the pathology of pre-menstrual experience, or PMS.

Keywords: Alice Sanderson Clow
feminist
periods
PMS
feminism
MWF
pre-menstrual syndrome
menstruation
medical women's federation
women in medicine
women doctors
Katharina Dalton
Advisor: De Bellaigue, C
Foley, D
Tractable probabilistic models for causal learning and reasoning

This thesis examines the application of tractable probabilistic modelling principles to causal learning and reasoning. Tractable probabilistic modelling is a promising paradigm that has emerged in recent years, which focuses on probabilistic models that enable exact and efficient probabilistic reasoning. In particular, the framework of probabilistic circuits provides a systematic language of the tractability of models for various inference queries based on their structural properties, with recent proposals pushing the boundaries of expressiveness and tractability. However, not all information about a system can be captured through a probability distribution over observed variables; for example, the causal direction between two variables can be indistinguishable from data alone. Formalizing this, Pearl’s Causal Hierarchy (also known as the information hierarchy) delineates three levels of causal queries, namely, associational, interventional, and counterfactual, that require increasingly greater knowledge of the underlying causal system, represented by a structural causal model and associated causal diagram. Motivated by this, we investigate the possibility of tractable causal modelling; that is, exact and efficient reasoning with respect to classes of causal queries. In particular, we identify three scenarios, separated by the amount of knowledge available to the modeler: namely, when the full causal diagram/model is available, when only the observational distribution and identifiable causal estimand are available, and when there is additionally uncertainty over the causal diagram. In each of the scenarios, we propose probabilistic circuit representations, structural properties, and algorithms that enable efficient and exact causal reasoning. These models are distinguished from tractable probabilistic models in that they can not only answer different probabilistic inference queries, but also causal queries involving different interventions and even different causal diagrams. However, we also identify key limitations that cast doubt on the existence of a fully general tractable causal model. Our contributions also extend the theory of probabilistic circuits by proposing new properties and circuit architectures, which enable the analysis of advanced inference queries including, but not limited to, causal inference estimands.

Keywords: tractable probabilistic models
causal inference
probabilistic circuits
causal discovery
Advisor: Kwiatkowska, M
The reception of troubadour poetry in sixteenth-century Italy, from the Questione della Lingua to Giovanni Maria Barbieri’s Arte del Rimare

This thesis discusses the rediscovery of troubadour poetry among Italian intellectuals of the sixteenth century focusing on how such activity connects with the debate on the vernacular known as the questione della lingua. It does so by examining the activity of six authors, to each of whom a chapter is dedicated: Angelo Colocci, Pietro Bembo, Mario Equicola, Lodovico Castelvetro, Benedetto Varchi, and Giammaria Barbieri. Their relationship with Occitan poetry is examined chiefly through the study of the manuscript sources they knew and the ways in which they situated the Occitan literary tradition in their own literary and ideological systems. The thesis demonstrates how the interest for troubadour poetry chiefly stemmed from the study of Petrarch and Dante and was interpreted by applying interpretative schemes developed within the questione della lingua. In turn, the thesis shows how the evolving knowledge of Occitan had a role in shaping these linguistic theories and the perceptions of the six authors studied with regard to the Romance literatures of the Middle Ages, as well as providing the authors with cultural and literary authority.
This thesis brings together in a single monographic form the many discoveries made by scholarship after the last major contribution on the matter (published in 1911), and at the same time offers a variety of new findings, including a reconsideration of the use of Occitan by Angelo Colocci, a re-evaluation of Varchi’s knowledge and interest for matters of Occitan poetry, and new findings regarding Castelvetro, Varchi, and Barbieri’s Occitan sources.
The thesis contains, in the appendix, a critical edition of a fundamental treatise representing one of the major contributions to Occitan studies in the sixteenth century, that is, Barbieri’s Arte del rimare. The edition draws upon the autograph manuscripts and the 1790 printed edition and follows the principles of authorial philology.

Keywords: Italian philology
Questione della lingua
Critical edition
Reception studies
Romance philology
History of philology
Occitan
Troubadour poetry
Advisor: Gilson, S
Atmospheric controls on mineral dust emission from Southern African source areas and their representation in numerical models

Mineral aerosol (dust) is a critical component of the earth system, affecting climate processes and biogeochemical cycles; accurate simulation of dust in coupled models is therefore essential, so as to avoid uncertainties in the representation of current and future climate. Evaluation of dust in climate models shows biases in simulated emissions and concentrations, with models failing to capture the observed wind speed distribution in dust source areas. A number of atmospheric processes have been identified as critical to the uplift of dust from Saharan source areas, with their misrepresentation in models a likely source of the bias in the simulated surface wind speed distribution. Very little work has been conducted in southern Africa; this is despite the identification of major source areas using remotely sensed data. The research conducted as part of this thesis therefore aims to identify the atmospheric processes driving dust emissions from southern Africa source areas, and evaluate their representation in numerical models.
High-resolution, in situ meteorological observations have been collected at the Etosha Pan, the most prominent dust source area in southern Africa. This data, used in conjunction with atmospheric reanalyses, has been used to characterise the meteorology of the source area across the two main dust seasons. Utilising a suite of satellite products, emissions from the pan (and southern Africa more generally) have been tracked across a range of temporal scales, which in turn has permitted an assessment of the atmospheric processes driving uplift. The in situ, reanalysis and satellite data also provide a constraint on model fields, and have been used to evaluate the representation of dust processes across southern Africa in the latest phase of coupled models.
Two mesoscale atmospheric processes have been shown to be especially important to dust emissions across southern Africa; namely, a nocturnal low level jet (NLLJ) during austral winter, and an integrated anabatic-sea breeze during austral summer. NLLJ’s are important emission mechanisms in North African source areas, however this is the first time the jet at Etosha has been linked to dust uplift. Thermally and topographically induced regional airflows have been observed along the west coast of southern Africa during austral summer, however this is the first time the sea breeze system has been shown to affect Etosha’s meteorology and hence dust emissions. The representation of these mechanisms in coupled models is mixed, and together with the treatment of land surface properties, helps to explain the inability of the models to capture the spatial distribution in uplift across southern Africa.

Keywords: sea breezes
dust emission
climate models
Southern African climate
remote sensing
reanalysis data
low level jets
Advisor: Washington, R
Engelstaedter, S
Interrupting two-pore channels 2 (TPC2) and sperm function enhancement

The proper functioning of sperm is essential for successful fertilization. Various physiological regulators control sperm motility, energy balance, capacitation, and the acrosomal reaction. Intracellular calcium ion (Ca2+) concentration and pH levels play a crucial role in regulating sperm physiology. Two pore channels 2 (TPC2), located on lysosomes, are involved in ion fluxes, and play a vital role in reproductive and embryonic development. This thesis aims to investigate the role of TPC2 as a mediator of sperm function. TPC2 knockout (KO) mice and wild type (WT) mice were used to study the role of TPC2 in sperm physiology. TPC2 KO sperm exhibited significantly increased motility and hyperactivation-related parameters associated with capacitation compared to WT sperm. Additionally, TPC2 KO sperm showed higher ATP content than WT controls. GPD2 protein, involved in tyrosine phosphorylation during sperm capacitation, was found to have significantly higher mRNA transcript levels in TPC2 KO sperm using RT-qPCR analysis. We utilized our model to understand specific molecular changes in TPC2 KO mouse sperm by measuring PPARα, which controls GPD2 activity. TPC2 KO sperm showed a shift towards oxidative phosphorylation, increased mitochondrial activity, and biogenesis. The antioxidant effect of TPC2 was more pronounced than in WT sperm, as indicated by the expression of antioxidant enzymes such as superoxide dismutase 1 and 2 (SOD1, SOD2). PGC1α, involved in mitochondrial biogenesis, was significantly increased in TPC2 KO sperm, suggesting a potential mechanism underlying the enhancement of sperm function in the absence of TPC2 activity. TPC2 KO sperm undergo capacitation at a faster rate than WT sperm, as evidenced by increased phosphorylation of protein kinase A substrates (PKAs) in TPC2 KO sperm compared to WT. Similar effects were observed in tyrosine phosphorylation and the acrosome reaction. As sperm capacitation is crucial for fertilization, non-capacitated TPC2 KO sperm demonstrated a higher fertility rate than WT sperm in in vitro fertilization (IVF) studies, supporting the notion that interfering with TPC2 activity enhances sperm physiological function. Moreover, TPC2 deficiency led to a more alkaline intracellular pH (pHi), which activated the CatSper channel and allowed increased influx of Ca2+. Additionally, the alkaline cytosol enhanced the activity of soluble adenylyl cyclase (sAC), leading to sperm capacitation through the activation of the cAMP/PKA signalling pathway, which may contribute to this characteristic. Together this work demonstrates that disturbing the activity of TPC2 improves sperm function and enhances fertilization capability.

Keywords: capacitation
Loss of TPC2 function enhanced sperm motility
and fertilization
Advisor: Parrington, J
The estates of the Norman dukes and the Norman kings of England 911-1135

This thesis examines the Norman ducal estates between 911 and 1106 and the English royal estates between 1066 and 1135. The stability and cohesion of these polities, during a period in which socio-political changes led to political decentralization in western Europe, is often explained by the strength of Norman and English institutions. This thesis argues that such institutions were built upon the tangible foundations of wealth and authority provided by the ducal and royal estates. The Introduction sets out the research questions, sketches the source material, and situates the thesis within the existing literature. Chapter 1 discusses the Norman evidence, and the methodological challenges it poses, for reconstructing ducal land. Chapter 2 analyses the early ducal estates between 911 and 1035, demonstrating their geographical distribution within Normandy and the fundamental role they played in the duchy’s formation. Chapter 3 continues the analysis of the ducal estates down to 1106 and discusses how they fit into the duchy’s wider tenurial framework by comparing them with the estates of the Norman aristocracy. Chapter 4 turns to England and explains how Domesday Book is used to identify, reconstruct, and estimate the value of the royal estates under the Confessor and the Conqueror. Chapter 5 demonstrates that royal land doubled in size between 1066 and 1086 but was also conceptually transformed by the conquest. By examining the Conqueror’s antecessores and the narrative accounts, Chapter 5 reconstructs the chronology and process by which this transformation occurred. Chapter 6 looks at the royal demesne under the Conqueror’s sons, who, out of political necessity, granted out considerable portions of Domesday’s terra regis, reducing it to its pre-conquest value. The Conclusion summarizes the principal findings of the thesis, emphasizing the importance of land in underpinning ducal and royal power to shape political structures in Normandy and England. Three appendices, in a separate volume, tabulate the data behind the analysis.

Keywords: ducal estates
Norman conquest
politics of land
royal estates
Domesday Book
England
Normandy
Advisor: Baxter, S