VictorJuiz/thesis huggingface dataset:
How the protein antibiotic pyocin S5 kills Pseudomonas aeruginosa
Keywords: membrane
transport
pyocin

Antimicrobial resistance is a deadly threat that is on the rise globally. Failure of small molecule antibiotic drug discovery programs and an increasing understanding of the dangers of antibiotic-induced dysbiosis of the microbiome have led to interest in bacteriocins as narrow-spectrum antibiotics. Pyocin S5 (PyoS5), a protein antibiotic against Pseudomonas aeruginosa, is the most potent colicin-like bacteriocin known but its structure and molecular mechanism remain poorly understood. This thesis presents the crystal structure of PyoS5, an elongated molecule with three structured domains and an unresolved N-terminal region, which enabled the functional, biochemical and biophysical characterization of this molecule. With its central domain, PyoS5 binds to common polysaccharide antigen (CPA), a lipopolysaccharide (LPS) antigen which acts as a receptor and accumulates the antibiotic on the cell surface. This is followed by binding to the outer membrane protein FptA, a TonB-dependent transporter (TBDT), by the N-terminal domain. A chimeric protein of Escherichia coli TonB and P. aeruginosa TonB1 allowed us to reconstruct the PyoS5 import process in E. coli, an approach that revealed that FptA acts as the translocator and that TonB1 energizes the import process by directly interacting with the N-terminal region of PyoS5. This import process and the structure of PyoS5 show strong similarity with those of PyoS2, which suggests that they are common to several pyocins targeting different TBDTs and delivering different cytotoxic domains into P. aeruginosa.
The doctor-patient relationship and encounter in the nineteenth-century French novel
Keywords: doctor-patient encounter
doctor-patient relationship
medicine
nineteenth-century French novel
science

This thesis investigates the representation of the doctor-patient relationship and encounter in the nineteenth-century French novel. It incorporates and compares a number of authors, most notably Honoré de Balzac, Jean-Jacques Rousseau, George Sand, Stendhal, and Émile Zola, as well as contemporary medical treatises and theses. Using a historicist approach to inform literary close readings, this thesis recreates the medical and scientific discourse which surrounded the nineteenth-century novel. It argues that the doctor-patient relationship and encounter can be understood as a way that the nineteenth-century French novel gains traction on contemporary medicine, since both foreground the extent to which medicine was understood as an art and practice as well as a science. The thesis argues that the difference between doctor-patient relationship and encounter was particularly useful for authors of the period. The doctor-patient relationship represents an ideal form of medicine; whereas the bedside medical encounter, as depicted in literature, offers readers a more dissonant conception of medicine. I argue that the doctor-patient relationship and encounter narrativize medicine in the nineteenth-century novel, allowing authors to present and interpret medicine as embedded within narrative. The doctor-patient relationship and encounter are particularly useful for the development of plot and characterization, despite or indeed because of the medical plot’s peripherality to the novel. This thesis is not restricted to any singular field of medicine; it encompasses themes such as the figure of the country doctor, the history of gynaecology, tuberculosis, cholera, hysteria, and the medical authorisation of miracles. The thesis concludes with a discussion of monetized medical relationships. Overall, this thesis demonstrates that the doctor-patient relationship and encounter, and in particular the cleavage between them, is key to understanding the representation of contemporary medicine and science by the nineteenth-century French novel.
Pastor Tillich: the justification of the doubter
Keywords: theology of Paul Tillich
doctrine of justification
modern German theology

This dissertation is a study of Paul Tillich’s early theological development from his student days until the end of the First World War, set against the backdrop of church politics in Wilhelmine Germany and with particular reference to his early sermons. The central questions are: Where did Tillich ‘land’ theologically after the war? And how did he get there?
The project offers a different focus from the majority of Tillich scholarship which understands Tillich primarily as a philosophical theologian. For before and during the First World War, Tillich was Pastor Tillich. Notwithstanding his philosophical study and academic ambitions, in the period 1904–18 he was studying theology to become a pastor, leading a Christian student group, working periodically as a pastor in Berlin churches, and preaching to soldiers. Through exposition of Tillich's early sermons, the pastoral context of his early thought becomes clear.
Alongside the chronological boundary of 1919, the account is limited to one central theme, Tillich’s notion of the justification of the doubter. In 1919 Tillich wrote an essay, Rechtfertigung und Zweifel [Justification and Doubt], for the faculty in Berlin, claiming the main problem of his systematic thought was the religious dialectic of doubt. This 1919 essay is compared with Tillich’s writing across genres before and during the First World War.
The influence of Schelling on Tillich’s theology is well established. This dissertation also explores the role of Søren Kierkegaard, Ernst Troeltsch, Martin Kähler, Wilhelm Herrmann, Wilhelm Lütgert, Fritz Medicus and Tillich’s father Johannes Tillich, distinguishing between Tillich’s later autobiographical statements and the witness of archival sources.
Drawing on material largely unknown to English-language scholarship, this chronologically and thematically focused dissertation on the issue of doubt in Tillich’s early theology offers a significantly original, contextualised account of Tillich’s early life in Germany. It should therefore be of interest not only to Tillich scholars, but to any interested in the history of modern theology, as an example of how biography and theology are intertwined.
‘We are the nobodies': youth violence, marginality and social cleansing in Colombia
Keywords: Colombia
Violence
Crime
Latin America
Youth
Social Cleansing
Marginality

Colombia’s ‘transition to peace’ faces various challenges. One is the activity of drug- related criminal organisations, which use adolescents to carry out low-level tasks. Based on 18 months of ethnographic fieldwork, this thesis explores the lives and perspectives of a group of adolescents who are starting to engage in criminal activities and the violence associated with them in the town of San Carlos and in the close-by city Medellín. Informal conversations with these youths and regular observation of their activities, as well as engagement with their families and communities, reveal aspects of their lives that mainstream discourses and statistics about violence cannot account for. The central question I ask is why and how some youths engage in organised crime and violence, despite the enthusiasm for peace currently permeating their country. I propose that these youths’ involvement in crime and violence is shaped by the precarity and ontological insecurity that characterise their lives. First, this thesis describes the process whereby these youths are progressively marginalised and come to be conceived as worthless and killable, through a number of practices ranging from stigmatisation and corporal punishment to police harassment and social cleansing. It then explores how they react to marginalisation by both embracing an oppositional identity and striving to overcome it. Having been made to feel like ‘nobodies’, they see joining a criminal group as the only way of ‘becoming somebody’, in social, economic and moral terms. However, I also show that the process of deciding to engage in crime and violence is experienced with a great deal of ambivalence and hesitation, as evidenced by these youths’ contradictory moral discourses about violence. By contextualising these findings within Colombia’s political juncture, this thesis questions clear-cut distinctions between conflict and its aftermath, and points towards further transformations that need to take place for peace to last.
Improving outcomes for resistant rectal cancer
Keywords: radiation
rectal cancer

The management of locally advanced rectal cancer involves the use of neoadjuvant chemoradiotherapy but up to 20% of patients have no discernible response. Understanding the factors that mediate resistance to treatment is therefore an important clinical research question. The work in this thesis aimed to further understand potential biological contributors to therapeutic resistance by exploring the contribution of the KEAP1-NRF2 pathway in-vitro and evaluating it as a potential biomarker in-vivo.
Using RNAi and clonogenic assays, NRF2 knockdown produced a radiosensitive phenotype in intrinsically resistant cell line models but had no effect in the most radiosensitive cell line. An attempt at CRIPSR isogenic validation of the RNAi was also made. Using a CRISPR isogenic activating mutation, radioresistance was induced in this previously sensitive cell line. Overexpression of NRF2 also induced chemoresistance to the commonly used radiosensitizers in clinical practice.
RNA sequencing was carried out on both NRF2 downregulated (radiosensitive) and NRF2 upregulated (radioresistant) cell line models to better understand the mechanism of radioresistance. NRF2 downregulation produces a marked reduction in amino acid metabolism, particularly glutamine/asparagine, relative to control conditions. Overexpression of NRF2 produced the opposite effect. The data suggest an NRF2 regulated ‘switch’ of metabolism in favour of an anabolic, proliferative phenotype which produces radioresistance.
To understand the clinical relevance of NRF2 signalling a bioinformatic approach was used. A metagene signature of 36 NRF2 regulated genes to aggregate pathway expression was derived and trained using publically available datasets. The resulting transcriptomic biomarker demonstrated that high NRF2 expression was associated with worse survival outcomes in 1,360 validation patients from public resources and the S:CORT collaboration. Interestingly NRF2 expression was significantly enriched in Consensus Molecular Subtype 4, suggesting a further refinement of the molecular transcriptomic classification of colorectal cancer.
Lastly higher NRF2 expression was shown to be associated with a worse response to neoadjuvant chemotherapy, as measured by the neoadjuvant rectal score, in a curated cohort of 127 rectal cancers who received standard of care treatment. This validates the in-vitro cell line findings and supports an important role for NRF2 signalling in prognosis and therapeutic resistance in colorectal cancer.
Pan-genomic analysis of clonal bacterial samples using nanopore reads and genome graphs
Keywords: Reference graphs
Nanopore
Pangenome

Bacterial genetic variation originates through multiple mechanisms, including mutations during replication, movement of mobile elements, and various forms of recombination. As a result, genomes can be highly divergent with only a small fraction of genes core to all and a large pangenome of genes which have been identified in one or more sequenced samples.
In this context, the ability to accurately detect genetic variation throughout the pangenome and compare many genomes remains a difficult problem. Here we present a novel pangenome reference graph structure, which represents the known genetic variation within a species as a collection of `floating' graphs. Each of these represents some homologous region such as a cluster of genes. By approximating a sequenced genome as a mosaic of genomes from the reference panel, this design forms the basis for a systematic framework in which to analyse diverse sets of samples where a single reference would be inappropriate.
Applying this method to E. coli, we demonstrate how it enables us to describe genetic variation at both a coarse (gene presence) and a fine (SNP/indel) level. We demonstrate how this enables us to successfully compare divergent genomes within a species, gaining dramatically higher sensitivity to SNP variation than single reference-genome approaches. We go on to demonstrate how this method enables us to investigate global genetic variation in K. pneumoniae, and to describe the spectrum of allele frequencies in accessory genes.
The method works for either long Nanopore or short Illumina reads, and we hope will provide the basis for addressing many questions in diverse datasets.
Computational insights into organic and organometallic catalysis
Keywords: catalysis
mechanisms
Density functional theory (DFT)
theoretical investigations

This thesis presents computational studies of some catalytic systems in both organic and organometallic chemistry using density functional theory (DFT). With these studies, we show how electronic structure theory such as DFT can complement experimental studies in elucidating and unravelling complex mechanisms. In Chapter 1, we give an overview of the theoretical background governing computational quantum chemistry and electronic structure theories. We then look at how theory is translated to the quantitative study of chemical reactivity and selectivity through simple transition state theory. Chapters 2 and 3 look at organocatalysis. In Chapter 2, we discuss computational work on the oxidant-promoted, hole-catalysed cyclobutanation between two unsymmetrical olefins (Scheme 0 (a)). Chemoselectivity (of reacting olefins), regioselectivity and stereoselectivity (of product formations) were explored. Chapter 3 discusses the mechanistic investigation of a novel bifunctional hydroxyphosphine catalyst, coupling with terminal phenylsilane reductant, in catalytic Staudinger reduction of azide to amine (Scheme 0 (b)). Chapters 4 to 7 look at the catalytic C–H bond functionalisations using transition-metal catalysts. In Chapter 4, we discuss Pd-catalysed δ-selective C(sp3)–H arylation of α-amino acids (Scheme 0 (c)). In Chapter 5 and Chapter 6, we look at the mechanisms underlying Pd-catalysed meta-selective C(sp2)–H allylation using unbiased internal olefin as an allyl surrogate and alkynylation via inverse Sonogashira coupling using trialkylsilylated bromoalkyne, respectively (Scheme 0 (d)). In Chapter 7, we look at using different transition metal catalysts to effect the regiodivergent C(sp2)–H arylation of isoquinolone (Scheme 0 (e)). Chapter 8 gives some concluding remarks regarding the field of computational chemistry in organic and organometallic catalyses and some outlook to the future of chemistry using other computational tools apart from those used in this thesis.
PARP1 resolves DNA replication defects in PCNA-associated DNA repair disorder
Keywords: Okazaki fragments
PARP1
DNA repair
PCNA
DNA replication

Proliferating cell nuclear antigen (PCNA) is an essential cofactor for DNA replication and repair. The toroidal structure of a PCNA trimer makes it a sliding clamp protein, which utilizes its interdomain connecting loop (IDCL) interacting with PIP-box containing proteins to recruit these clients to sites of DNA replication to enable their functions. In 2014, the Crosby and Green laboratories reported a novel DNA repair disorder with clinical features including short stature, hearing loss, premature aging, telangiectasia, neurodegeneration, and photosensitivity, which results from a homozygous missense (p.Ser228Ile) alteration of PCNA so it is named PCNA-associated DNA repair disorder (PARD).
Previous structural studies have shown that the S228I alteration of PCNA results in a dramatic conformational change of the IDCL, and biochemical studies indicated a profound perturbation of PCNA's interaction with many of its interaction partners, including FEN1, LIG1, Cdt1, DNMT1 and XPG. Patient-derived cells exhibited marked abnormalities in response to UV irradiation, displaying substantial reductions in both UV survival and RNA synthesis recovery. However, no evidence for DNA replication defects has been found in these patient-derived cells. The aim of this thesis was to determine cellular pathways that are affected by the S228I alteration and to uncover mechanisms by which PCNAS228I cells tolerate the perturbed PCNA interactions in specific pathways.
An isogenic PCNAS228I knock-in hTERT RPE-1 cell line was generated using CRISPR-Cas9 technique. Phenotypes observed in patient-derived cells were recapitulated in the knock-in cell line. By applying survival assays with treatment of different chemical agents, we showed most DNA repair pathways unaffected, except that PCNAS228I cells were more sensitive to treatment with the PARP inhibitor olaparib than WT controls.
By comet assay as well as immunostaining of γH2AX, I showed that olaparib induced more DNA damage in cells with the PCNAS228I alteration, and FACS analysis showed perturbed cell cycle progression after PARP inhibition. By using an inhibitor of PARG, I detected high levels of PAR chains being formed at replication forks in PCNAS228I cells. Thus I proposed that the PCNAS228I mutation results in abnormal interactions between PCNA and key enzymes needed for normal Okazaki fragment maturation at replication forks. The resultant persistent single-strand breaks are processed via a back-up, PARP-dependent mechanism to ensure completion of lagging strand synthesis.
Overall, these data have implications both for the etiology of PCNA-associated repair disorder as well as suggesting novel circumstances in which PARP-inhibition might be of use in the cancer clinic.
Towards practical applications of quantum optics
Keywords: Quantum Random Number Generator
Quantum Teleportation

This DPhil thesis presents two key works towards practical applications of quantum optics. Both works are novel and achieve competitive state-of-the-art results.
Today's most widely used method of encoding quantum information in optical qubits is the dual-rail basis, often carried out through the polarisation of a single photon. On the other hand, many stationary carriers of quantum information | such as atoms | couple to light via the single-rail encoding in which the qubit is encoded in the number of photons. As such, interconversion between the two encodings is paramount in order to achieve cohesive quantum networks. In the first part of this thesis, we demonstrate this by generating a hybrid entangled resource between the two encodings and using it to teleport a dual-rail qubit onto its singlerail counterpart. Our key results yield an average fidelity of F = (92:8±2:2)% for the teleportation and F = (89:7 ± 2:1)% for entanglement swapping, thus confirming the applicability of this scheme towards a real-world implementation. This work completes the set of tools necessary for the interconversion between the three primary encodings of a qubit in the optical field: single-rail, dual-rail and continuous-variable.
A remarkable aspect of quantum theory is that certain measurement outcomes are entirely unpredictable to all possible observers. Such quantum events can be harnessed to generate numbers whose randomness is asserted based upon the underlying physical processes. In the second part of this thesis, we formally introduce and experimentally demonstrate an ultrafast optical quantum randomness generator that uses a totally untrusted photonic source and whose idea we have patented. While considering completely general quantum attacks, we certify randomness at a rate of 1:1 Gbps with a rigorous security parameter of 10-20. Our security proof is entirely composable, thereby allowing the generated randomness to be utilised for arbitrary applications in cryptography and beyond.
Neural network models of hierarchical map-based planning in the brain
Keywords: MDP
Cognitive Maps
Navigation
Hierarchical Planning

Many researchers have tried to model how model-based behaviour is produced in the brain, and specifically how environmental knowledge is learned and used in the form of cognitive maps. Previous work has proposed various cellular substrates that might encode a cognitive map, as well as several possible mechanisms for self-organising these maps. Current models also agree to some extent on the planning mechanism that produces goal-directed actions using a cognitive map, although they propose subtly different implementations of this planning mechanism, and a variety of mechanisms for extending it. We felt that this previous work was limited in several important ways: there was little consensus on how these cognitive maps were represented and how they were formed, the planning mechanism that was used seemed to be inherently limited to performing relatively simple tasks, and there had been little consideration of how these mechanisms would scale up beyond laboratory tasks.
This thesis makes several important advances. Firstly, the planning mechanism that is used by the majority of current neural models on this subject propagates a decaying signal through the environment to create a gradient that points towards the goal. However, this decaying signal will eventually decay to nothing, limiting the scale and complexity of tasks that can be solved in this manner. Based on the idea, originally proposed by Ponulak et al. 2013, that a wavefront propagating from a goal state can carry information about the direction of that goal state, we propose a novel planning mechanism that does not require decaying activity.
Unlike the model proposed by Ponulak et al., the mechanism that we propose is: able to work in a state-action map, able to output explicit actions to move towards the goal, able to perform planning without altering synaptic weights, able to plan in nondeterministic environments, and able to interface with a hierarchical mechanism. We also propose several ways in which a network which implements this planning mechanism can self-organise during unsupervised exploration. We demonstrate that the neural substrate for the cognitive map, the mechanisms required to plan using this map and the cognitive map itself can all be learned using local Hebbian learning, in an unsupervised manner.We compare and contrast these mechanisms in terms of both their effectiveness and their biological plausibility.
Finally, we extend the model with a hierarchical planning mechanism: a layer of cells that can identify frequently-used sequences of actions and reuse them to significantly increase the efficiency of planning. This increase in efficiency is largest for tasks with longer, more complex solutions. We speculate that this may explain the apparent ability of humans and animals to perform model-based planning on both small scales (laboratory experiments) and on large scales (outdoor travel) without a noticeable loss of efficiency.