VictorJuiz/thesis huggingface dataset:
Exon skipping peptide-pmos for correction of dystrophin in mouse models of duchenne muscular dystrophy
Keywords: magnetic resonance imaging
Duchenne muscular dystrophy
antisense-olignucleotide

Duchenne muscular dystrophy (DMD) is a fatal, muscle-wasting disorder due to mutations/deletions in the dystrophin gene. Whilst improvements in palliative care have increased the life expectancy of patients, cardiomyopathy and respiratory complications are still the leading causes of death. A potential therapy for the treatment of DMD is antisense oligonucleotides (AOs), which modulate dystrophin pre-mRNA splicing to restore the dystrophin reading frame and generate a truncated functional protein. Conjugation of AOs to cell penetrating peptides (CPP), such as Pip5e-, significantly improves delivery to skeletal muscles and to the heart, which is imperative given the impact of cardiomyopathy to mortality. However, it should be noted that the contribution of skeletal muscles, such as the core respiratory muscle, the diaphragm, in dystrophic cardiopulmonary function is poorly understood.
The specific aims of the work in this thesis were to (i) understand the effect of the diaphragm on cardiac function using magnetic resonance imaging (MRI), (ii) screen a number of derivatives of Pip5e (Pip6) in an effort to discover further promising peptides and define the properties integral to heart penetrating capacity, and (iii) assess whether Pip6-PMOs restore cardiac function (MRI) following a repeat, low dose regimen. In short, the specific restoration of dystrophin in the diaphragm of the dystrophic mouse model, the mdx mouse, did not improve cardiac function, highlighting the importance of a body-wide therapy. The screening of multiple Pip5e-PMO derivatives revealed 3 promising peptides with improved cardiac splicing capacity; however, serial deletions of amino acids from the central core resulted in the diminution of dystrophin restoration, possibly due to a reduction in hydrophobicity. Finally, the Pip6-PMO treatment regimen substantially restored dystrophin protein (28% in heart) and stabilised cardiac function, even with an increased work load. In conclusion, this study illustrates the importance of a body-wide treatment, such as the CPP strategy (Pip-PMO). These Pip-PMO conjugates demonstrate high dystrophin restoration in a number of muscles, including cardiac muscle, and have a beneficial effect on cardiac function.
MiR-215 regulates differentiation in colorectal cancer stem cells
Keywords: colorectal cancer
cancer stem cells
RNA biology
microRNAs
p53

Since the initial description of cancer stem cells (CSCs) as a self-renewing subpopulation of malignant cells with tumor-initiating capacity, a growing body of evidence has supported the existence of CSCs in virtually every tumor type. Our previous work in colorectal cancer has identified the transcription factor CDX1 as a key regulator of colorectal CSC differentiation. CDX1 expression is frequently lost in colorectal cancer, resulting in more aggressive, poorly differentiated tumors with higher proportions of CSCs. Many miRNAs have been implicated in tumor suppression and carcinogenesis, but the roles of miRNAs in differentiation, particularly in colorectal cancer, remain poorly understood. We began by identifying miRNAs downstream of CDX1 by using high-throughput small-RNA sequencing to profile miRNA expression in two pairs of colorectal cancer cell lines with stable CDX1 overexpression or knockdown. Validation of candidates identified by RNAseq in a larger cell line panel revealed miR-215 to be most significantly correlated with CDX1 expression. ChIP-qPCR and promoter reporter assays confirmed that CDX1 directly transactivates miR-215 transcription. MiR-215 is depleted in FACS-enriched CSCs compared to unsorted samples. Overexpression of miR-215 in poorly-differentiated, highly clonogenic cell lines causes growth arrest and a dramatic decrease in colony formation. miR-215 knockdown using a miRNA sponge causes an increase in clonogenicity and impairs differentiation in CDX1-high cell lines. Indeed, the effects of CDX1 expression on both gene expression and colony morphology can be attenuated by miR-215 inhibition, indicating that miR-215 is a functional mediator of CDX1. Microarray studies following miR-215 overexpression indicate that miR-215 induces terminal differentiation-associated growth arrest, due in part to direct silencing of BMI1 expression and de-repression of BMI1 target genes including CDKN1A. Our work situates miR-215 as a link between CDX1 expression and BMI1 repression that governs differentiation in colorectal cancer. We further characterize another miRNA-transcription factor axis in colorectal cancer, and we identify the novel miR-3189-3p as a potent effector of cell death with potential therapeutic implications.
Miscible flow through porous media
Keywords: viscous fingering
enhanced oil recovery
Saffman-Taylor
miscible

This thesis is concerned with the modelling of miscible fluid flow through porous media, with the intended application being the displacement of oil from a reservoir by a solvent with which the oil is miscible. The primary difficulty that we encounter with such modelling is the existence of a fingering instability that arises from the viscosity and the density differences between the oil and solvent. We take as our basic model the Peaceman model, which we derive from first principles as the combination of Darcy’s law with the mass transport of solvent by advection and hydrodynamic dispersion. In the oil industry, advection is usually dominant, so that the Péclet number, Pe, is large. We begin by neglecting the effect of density differences between the two fluids and concentrate only on the viscous fingering instability. A stability analysis and numerical simulations are used to show that the wavelength of the instability is proportional to Pe^−1/2, and hence that a large number of fingers will be formed. We next apply homogenisation theory to investigate the evolution of the average concentration of solvent when the mean flow is one-dimensional, and discuss the rationale behind the Koval model. We then attempt to explain why the mixing zone in which fingering is present grows at the observed rate, which is different from that predicted by a naive version of the Koval model. We associate the shocks that appear in our homogenised model with the tips and roots of the fingers, the tip-regions being modelled by Saffman-Taylor finger solutions. We then extend our model to consider flow through porous media that are heterogeneous at the macroscopic scale, and where the mean flow is not one dimensional. We compare our model with that of Todd & Longstaff and also models for immiscible flow through porous media. Finally, we extend our work to consider miscible displacements in which both density and viscosity differences between the two fluids are relevant.
Of friendship and hospitality: Victorian women’s travel writing on Meiji Japan
Keywords: Postcolonialism
Victorian Literature
Travel Writing
Victorian Female Travellers
Politics of Friendship
Japonisme in Victorian Britain
Representation of Japan

This thesis explores the possibility and challenges of international/interracial female friendship and anti-communitarian hospitality through writings of Victorian female travellers to Meiji Japan between 1854 and 1918. It features three travellers, viz. Isabella Bird, Mary Crawford Fraser, and Marie Stopes.
The introduction delineates the context of key events in the Anglo-Japanese relationship and explores the representation of Japan in Victorian travelogues and literary works.
Chapter I considers the philosophical dialogue between Jean-Luc Nancy, Maurice Blanchot, and Jacques Derrida on community, friendship, and hospitality. It demonstrates the potential of applying their thinking, notwithstanding its occasional complicity, to an analysis of the place of hitherto marginalised groups, women and foreigners, in Western philosophical models.
Chapter II examines relationships between Bird and Japanese natives, especially her interpreter, Ito in Unbeaten Tracks in Japan (1880) in terms of questions of stable identity and translation. It further undertakes a comparative study between the travelogue and Itō no koi (2005) by Nakajima Kyōko. I explore the afterlife of Bird in Japanese literature.
Chapter III investigates friendships in Fraser’s A Diplomatist’s Wife in Japan (1898). It uncovers her connection with Japanese female writers in oblivion, Yei Theodra Ozaki and Wakamatsu Shizuko. I discuss the influence her friendships had on Fraser’s fictional works such as The Stolen Emperor (1903), especially on the fair portrayals of Japanese women.
Chapter IV explores friendships between the sexes in Stopes’ A Journal from Japan (1910) and articulates its relationship with Love-Letters of a Japanese (1911) and Plays of Old Japan (1913). I examine Stopes’ romantic relationship with Fujī Kenjirō and its influence on her career in sexology. It also investigates Stopes’ collaboration with Sakurai Jōji on Nō translation and exposes complex gender, racial, and linguistic politics.
The conclusion explores three Japanese female travellers to Victorian Britain, focusing on their contact with local women. It considers Tsuda Umeko’s Journal in London, Yasui Tetsu’s Wakakihi no ato, and Yosano Akiko’s Pari yori (1914).
The Structural Basis of the Disabling of the Actin Polymerization Machinery by Yersinia
Keywords: actin cytoskeleton
plague
Yersinia
Structural biology
actin

Yersinia pestis is a human pathogen and the causative agent of bubonic plague, responsible for causing three massive pandemics, resulting in hundreds of millions of deaths in the 14th century alone. Yersinia’s virulence stems from its ability to overcome host immune defences by the injection of six Yersinia outer proteins (Yops) into the host cells via its Type III secretion system. One of these Yops, YopO specifically disables the actin polymerization machinery, leading to the crippling of phagocytosis. YopO consists of a GDI domain which sequesters Rac and Rho, and a kinase domain, the activity of which is dependent on host actin. Little is known about the targets of the kinase domain and the mechanism of function of YopO remains incomplete.
In this work, YopO was crystallized in complex with actin, revealing that YopO binds to actin on subdomain 4, away from the 'hotspot’ between subdomains 1 and 3 which is involved in binding most actin-binding proteins. The structure reveals how recruitment of YopO-bound actin monomers stalls actin polymerization by steric hindrance. The structure also demonstrates how YopO uses actin for self-activation and suggests that actin is being used by YopO as bait for recruitment into actin machineries. Using SILAC mass spectrometry, actin cytoskeletal machineries within macrophages that recruit YopO are identified and these include, amongst others: VASP family proteins, gelsolin family proteins, formins and WASP. Of these, VASP, EVL, diaphanous1, WASP and gelsolin have been identified to be phosphorylated by YopO and were validated by in vitro phosphorylation. This work demonstrates that YopO uses actin as a scaffold for selection of kinase substrates, enabling targeted phosphorylation of the actin machinery and provides insight into the regulation of the actin cytoskeleton by phosphorylation under non-pathogenic conditions.
Cytotoxic T-Cells in HIV-1: "The Good" and "The Bad"
Keywords: antigen sensitivity
HIV
cytotoxic T-cells

CD8+ T-cell antigen sensitivity is critical for optimal control of persistent viral infections, including HIV-1. The devastating HIV-1 pandemic may be countered by development of a cytotoxic T lymphocyte based vaccine if qualities associated with protection can be defined at the molecular level. However, the heterogeneity of the total viral-specific CTL response confounds identification of protective correlates and T-cell sensitivity is no exception and remains controversial. To address this issue we reduced the heterogeneity of the HIV-1 CTL response to single units, generating 19 CTL clones that recognise the same HIV-1 derived epitope restricted by HLA B*08. Correlation of functional assays directly with the ability of each clone to control HIV-1 replication in vitro, the “viral suppression assay,” identified antigen sensitivity as a key quality for anti-viral efficacy. Remarkably, four clones from this panel, isolated from one individual, a long-term non-progressor, all used an identical TCR yet had distinct antigen sensitivity and suppressive activity. Two of these clones were characterised in detail, and had distinct cytokine profiles, regulated by epigenetic mechanisms, and differential expression of a group of cell surface receptors with the potential to modulate the signalling threshold to antigen. Expression of the TNFα locus of the high sensitivity clone with “Good” suppression was repressed by DNA methylation. Understanding how CTL qualities required for optimal control of HIV-1 replication differentiate and are then enriched in the total CTL response, and if repression of TNFα contributes to this process, will contribute to rational vaccine design. This is the first evidence that avidity maturation in CD8+ T cells with the same TCR affinity occurs in viral infections in humans as reported in the mouse. This suggests the induction of high sensitivity CTL will be critical for an effective HIV-1 vaccine, but offers hope that this can be achieved even in individuals without protective HLA alleles, by further exploration of peripheral avidity maturation and epigenetic regulation of the HIV-1 specific CD8+ T-cell response.
Bubbles: sensors for the micro world
Keywords: low-index optical trapping
microbubble
ultrasound

It has been proposed that coated gas microbubbles, currently used as ultrasound contrast agents could also be used as microscale sensors due to the sensitivity of their acoustic response to changes in their environment. However, their behaviour is not fully understood and there remains considerable scope for improving their characterisation. The aim of this thesis is to improve the theoretical description of microbubble dynamics under ultrasound excitation with the ultimate aim of assessing the regimes in which they could be exploited most effectively as sensors.
Previous theoretical and experimental work relating to the confinement and acoustic excitation of microbubbles is reviewed. Specifically, optical trapping as a method for the isolation and manipulation of individual bubbles is studied for use in developing a sensor. An assessment of the existing models’ validity is undertaken. This is followed by the development of models for optical trapping of single microbubbles, and the coupled radial and translational motion of a microbubble under ultrasound excitation, which includes time dependent phenomena. The latter model is used to perform a sensitivity analysis to determine the uncertainty associated with using microbubbles as sensors. The potential for uniquely characterising the shell of the microbubble from experimental data is also assessed.
Subsequent chapters present the results from a combination of computer simulations and experimental data, used to develop and assess the validity of the new models for describing microbubble behaviour. Particularly, the model is used to simulate the response of a dilute suspension of microbubbles undergoing large amplitude oscillations and single microbubbles undergoing lipid shedding. The optimal regimes in which microbubbles may be utilised as sensors for liquid physical properties and local pressure variations are then assessed. Finally, a summary of the conclusions and areas for further work is presented.
Trees and graphs: congestion, polynomials and reconstruction
Keywords: partition function
spanning tree congestion
reconstruction
regularity lemma
random graphs
inverse problems

Spanning tree congestion was defined by Ostrovskii (2004) as a measure of how well a network can perform if only minimal connection can be maintained. We compute the parameter for several families of graphs. In particular, by partitioning a hypercube into pieces with almost optimal edge-boundaries, we give tight estimates of the parameter thereby disproving a conjecture of Hruska (2008). For a typical random graph, the parameter exhibits a zigzag behaviour reflecting the feature that it is not monotone in the number of edges. This motivates the study of the most congested graphs where we show that any graph is close to a graph with small congestion.
Next, we enumerate independent sets. Using the independent set polynomial, we compute the extrema of averages in trees and graphs. Furthermore, we consider inverse problems among trees and resolve a conjecture of Wagner (2009). A result in a more general setting is also proved which answers a question of Alon, Haber and Krivelevich (2011).
After briefly considering polynomial invariants of general graphs, we specialize into trees. Three levels of tree distinguishing power are exhibited. We show that polynomials which do not distinguish rooted trees define typically exponentially large equivalence classes. On the other hand, we prove that the rooted Ising polynomial distinguishes rooted trees and that the Negami polynomial determines the subtree polynomial, strengthening results of Bollobás and Riordan (2000) and Martin, Morin and Wagner (2008). The top level consists of the chromatic symmetric function and it is proved to be a complete invariant for caterpillars.
Genetic analyses of MAP kinase signalling in mouse gonad development
Keywords: testis determination
mouse
sexual development
mammalian sex determination
p38 MAPK
MAPK signalling

Sexual development begins with the process by which the bipotential gonads of the embryonic urogenital ridge develop into either testes or ovaries. In the mouse, sex determination occurs at around 11.5 dpc and depends on the presence or absence of the Y chromosome and the associated activity of the testis-determining gene, Sry, in supporting cell precursors. The mutually antagonistic male and female developmental pathways are regulated by many cellular and molecular processes, disruption of which can lead to disorders of sex development (DSDs). However, many of the molecular mechanisms regulating the differentiation of the two gonads are still unknown.
The boygirl (byg) mutant was identified in an ENU-based forward genetic screen for embryos with gonadal abnormalities. On the C57BL/6J background, XY byg/byg homozygotes exhibited complete embryonic gonadal sex reversal. The defective gene in byg, Map3k4, is a component of the mitogen-activated protein (MAP) kinase signalling pathway and provides the first evidence for a function of this pathway in sex determination.
This thesis describes experiments aimed at investigating the cellular and molecular basis of the sex reversal phenotype associated with the XY Map3k4byg/byg mutant. Cellular characterisations revealed a defect in male-specific proliferation at 11.5 dpc, which was attributed to a defect in Sry up-regulation. Elucidation of the downstream kinases activated by MAP3K4 during sex determination was attempted, with particular focus on identifying a role for p38α MAP kinase (MAPK). Using a conditional knockout approach, the function of p38α in Steroidogenic factor-1 (Sf1)-positive somatic cells was assessed. However, specific inactivation in these cells did not affect gonad development. Conditional inactivation of Map3k4 itself in these Sf1¬-positive cells also did not disrupt gonad development, suggesting that this pathway is either initiated in a different cell lineage or at an earlier stage than deletion driven by Sf1-Cre can disrupt. Conditional inactivation of p38α in the Müllerian duct mesenchyme and ovarian granulosa cells using Amhr2-Cre did reveal a function for p38α in female fertility, but did not disrupt embryonic sexual development. Gene knockdown in organ culture was attempted to determine a role for multiple p38 MAPKs in all cell types of the gonad. Therefore, this thesis details further characterisations of a novel signalling pathway important for the expression of Sry, focussing on the role of the p38 MAPKs.
Topological phases of matter, symmetries, and K-theory
Keywords: K-theory
Topological matter

This thesis contains a study of topological phases of matter, with a strong emphasis on symmetry as a unifying theme. We take the point of view that the "topology" in many examples of what is loosely termed "topological matter", has its origin in the symmetry data of the system in question. From the fundamental work of Wigner, we know that topology resides not only in the group of symmetries, but also in the cohomological data of projective unitary-antiunitary representations. Furthermore, recent ideas from condensed matter physics highlight the fundamental role of charge-conjugation symmetry. With these as physical motivation, we propose to study the topological features of gapped phases of free fermions through a Ζ2-graded C*-algebra encoding the symmetry data of their dynamics.
In particular, each combination of time reversal and charge conjugation symmetries can be associated with a Clifford algebra. K-theory is intimately related to topology, representation theory, Clifford algebras, and Ζ2-gradings, so it presents itself as a powerful tool for studying gapped topological phases. Our basic strategy is to use various K-theoretic invariants of the symmetry algebra to classify symmetry-compatible gapped phases. The super-representation group of the algebra classifies such gapped phases, while its K-theoretic difference-group classifies the obstructions in passing between two such phases. Our approach is a noncommutative version of the twisted K-theory approach of Freed--Moore, and generalises the K-theoretic classification first suggested by Kitaev. It has the advantage of conceptual simplicity in its uniform treatment of all symmetries. Physically, it encompasses phenomena which require noncommutative algebras in their description; mathematically, it clarifies and provides rigour to the meaning of "homotopic phases", and easily explains the salient features of Kitaev's Periodic Table.