VictorJuiz/thesis huggingface dataset:
Mutational analysis of membrane traffic in Arabidopsis thaliana
Keywords: forward genetics
Arabidopsis thaliana
membrane trafficking

To identify novel and essential components of the plant membrane trafficking mechanisms, Arabidopsis membrane trafficking mutants from fluorescent protein-based forward genetic screens were characterized. First, four novel glutathione synthase (GSH2) mutant alleles featured swollen endoplasmic reticulum (ER)-derived bodies that accumulated a soluble secretory marker. Consistent with the role of GSH2 in glutathione biosynthesis, the loss-of-function mutant alleles exhibited gamma-glutamylcysteine (γ-EC) hyperaccumulation and glutathione deficiency. The aberrant ER morphology was ascribed to the γ-EC accumulation. Redox-sensitive fluorescent protein revealed that gsh2 seedlings maintained a reduced cytoplasm at steady state but were more sensitive to oxidative challenge. Second, Mut 21 was a conditional mutant that accumulated a secretory marker in the alkalized apoplast at restrictive temperature (31˚C). The mutant was identified as carrying a mutant allele of tuftelin-interacting protein 11 (TFIP11), which has been implicated in regulating redifferentiation and cell proliferation through a cytokinin signalling pathway. Hence, it was postulated that the changes in response to cytokinin affect auxin-mediated acidification of the apoplast. Third, Mut 43 was a conditional mutant that accumulated a soluble secretory marker in the ER and unidentified punctate structures at restrictive temperature, and exhibited perturbations in ER export of a soluble protein marker. Moreover, the mutant showed severe growth defects and abnormal radial root swelling in the apical elongation zone. A mutation identification method through deep-sequencing of the wild-type siblings in outcrossed heterozygous mutant families was developed and tested in Mut 43. At the time when this thesis was prepared, bioinformatic analysis has assigned Mut 43 to the bottom arm of chromosome two and predicted a 300kb mapping interval based on the observed bias in single nucleotide polymorphism ratios. This work demonstrates the feasibility of using forward genetics to study plant-specific aspects of membrane trafficking mechanisms and incorporates new technology to streamline the process of gene identification.
Characterisation of cytoplasmic uridyl transferases in yeast and human cells
Keywords: uridylation
cell cylce
ZCCHC11
Cid1

Regulation of gene expression by terminal addition of uridyl residues to RNA substrates has recently emerged as a widespread phenomenon in eukaryotes. Studies in organisms ranging from fission yeast to human cells have shown that uridylation of RNA 3' ends stimulates rapid RNA degradation. However, many questions regarding the specificity of the uridyl transferases, the broad range of their substrates and the consequences of their loss are still unanswered. In light of this, the uridyl transferases Cid1 in Schizosaccharomyces pombe and ZCCHC11 in human cells and their roles in the regulation of gene expression were further characterised in this study. To begin with, the biochemistry of the Cid1 protein complex responsible for uridylation in Schizosaccharomyces pombe was analysed in more detail by mass spectrometry and in vitro assays. These experiments provided insights into the modulation of Cid1 activity by accessory factors. Next, the role of the human uridyl transferase ZCCHC11 in the regulation of replication- dependent histone mRNAs was examined. Results showed that ZCCHC11 is required for efficient destabilisation of histone mRNAs following inhibition or completion of DNA replication. In agreement with this finding, cDNA sequencing experiments showed that ZCCHC11-mediated uridylation is particularly prevalent at the end of S phase. Finally, this thesis also explored the phenotype resulting from ZCCHC11 knock-down with respect to the human cell cycle. Depletion of ZCCHC11 led to the occurrence of DNA damage and activation of the DNA integrity checkpoint, which in turn resulted in cell cycle delay. Taken together, the data presented in this thesis extend current knowledge of the uridyl transferases and their actions in fission yeast and human cells and provide a link between RNA regulation and cell cycle control.
The influence of the quasi-biennial oscillation on the stratospheric polar vortices
Keywords: dynamics
polar vortex
annular mode
stratosphere
quasi-biennial oscillation
Holton-Tan relationship

The mean strengths of the wintertime stratospheric polar vortices are known to be related to the phase of the quasi-biennial oscillation (QBO) in the tropical stratosphere from circulation statistics - the "Holton-Tan relationship". The principal topic of this thesis is improving understanding of the mechanism behind the QBO's influence.
Following the example of previous studies, the QBO influence on the Northern Hemisphere (NH) extratropics on monthly time scales in an observational reanalysis is examined, and is shown to closely resemble the stratospheric Northern annular mode (NAM). It is argued that this may not be informative about the mechanism, as the response could be NAM-like for many different mechanisms. It is suggested that examining the transient response of the NH extratropics to forcing by the QBO would be much more informative, particularly on time scales of a few days.
In a primitive equation model of the middle atmosphere, the long-term stratospheric NH response to imposed zonal torques is often found to be NAM-like under perpetual January conditions, with wave feedbacks making a very important contribution. However, the response in runs with a seasonal cycle is not NAM-like. Investigation of the transient responses indicates the wave feedbacks are qualitatively similar in each case but only strong enough under perpetual January conditions to make the long-term response NAM-like. This supports the hypothesis that feedbacks from large-scale dynamics tend to make the stratospheric response to arbitrary forcings NAM-like, and therefore indicates that the long-term response is not generally useful for understanding forcing mechanisms. Examining the short-term transient response to known torques is found to be more successful at inferring information about the torques than several other previously proposed methods.
Finally, the short-term transient response of the NH extratropics to forcing by the easterly QBO phase in a general circulation model is found to be consistent with the proposed mechanism of Holton and Tan (1980), indicating that this mechanism plays a role in the Holton-Tan relationship.
Embeddings of infinite groups into Banach spaces
Keywords: group theory
mapping class group
hyperbolic
relatively hyperbolic
metric geometry

In this thesis we build on the theory concerning the metric geometry of relatively hyperbolic and mapping class groups, especially with respect to the difficulty of embedding such groups into Banach spaces.
In Chapter 3 (joint with Alessandro Sisto) we construct simple embeddings of closed graph manifold groups into a product of three metric trees, answering positively a conjecture of Smirnov concerning the Assouad-Nagata dimension of such spaces. Consequently, we obtain optimal embeddings of such spaces into certain Banach spaces. The ideas here have been extended to other closed three-manifolds and to higher dimensional analogues of graph manifolds.
In Chapter 4 we give an explicit method of embedding relatively hyperbolic groups into certain Banach spaces, which yields optimal bounds on the compression exponent of such groups relative to their peripheral subgroups. From this we deduce that the fundamental group of every closed three-manifold has Hilbert compression exponent one.
In Chapter 5 we prove that relatively hyperbolic spaces with a tree-graded quasi-isometry representative can be characterised by a relative version of Manning's bottleneck property. This applies to the Bestvina-Bromberg-Fujiwara quasi-trees of spaces, yielding an embedding of each mapping class group of a closed surface into a finite product of simplicial trees. From this we obtain explicit embeddings of mapping class groups into certain Banach spaces and deduce that these groups have finite Assouad-Nagata dimension. It also applies to relatively hyperbolic groups, proving that such groups have finite Assouad-Nagata dimension if and only if each peripheral subgroup does.
The stress-strain behaviour of soils containing gas bubbles
Keywords: glass
soil reinforcement

The stress-strain behaviour of unsaturated soils containing discrete bubbles of gas has been studied in a programme of experimental and theoretical research. The research is of particular relevance to the offshore environment, where bubbles of methane, nitrogen and carbon dioxide are formed within the seabed by the decomposition of organic matter. The presence of these gas bubbles can have a major influence on the engineering properties of the soil. As gas bubbles in marine sediments are typically much larger than the normal void spaces, the bubbles cannot be considered as simply changing the compressibility of the pore fluid. Chapters 2 to 4 describe a series of undrained triaxial tests on reconstituted samples of clayey silt from an estuarine site. Bubbles of methane were formed within the soil by using a chemical technique. The test results provide evidence of the effect of gas bubbles on the undrained shear strength, together with useful information on the stress-strain behaviour prior to failure, the generation of pore pressures during shearing, the elastic moduli and the isotropic consolidation behaviour. A theoretical model for soils containing large gas bubbles is developed in Chapter 5. The model consists of spherical bubble cavities surrounded by a matrix of saturated soil. In the following three chapters various aspects of the soil behaviour are examined by analysing the theoretical model. Chapter 6 covers the elastic moduli, Chapter 7 the consolidation behaviour and Chapter 8 the undrained shear strength. In Chapter 9 the predictions of the theoretical model are compared with the experimental results. The agreement between theory and experiment is excellent, suggesting that the theoretical approach developed and analysed in Chapters 5 to 8 is a reasonable model for the behaviour of soils containing large gas bubbles.
Optimization of endwall film-cooling in axial turbines
Keywords: turbine endwall cooling
film cooling
heat transfer
aerodynamics

Considerable reductions in gas turbine weight and fuel consumption can be achieved by operating at a higher turbine entry temperature. The move to lean combustors with flatter outlet temperature profiles will increase temperatures on the turbine endwalls. This work will study methods to improve endwall film cooling, to allow these advances.
Turbine secondary flows are caused by a deficit in near-wall momentum. These flow features redistribute near-wall flows and make it difficult to film-cool endwalls. In this work, endwall film cooling was studied by CFD and validated by experimental measurements in a linear cascade. This study will add to the growing body of evidence that injection of high momentum coolant into the upstream boundary layer can suppress secondary flows by increasing near-wall momentum. The reduction of secondary flows allows for effective cooling of the endwall. It is also noted that excess near-wall momentum is undesirable. This leads to upwash on the vane, driving coolant away from the endwall.
A passive-scalar tracking method has been devised to isolate the contribution of individual film cooling holes to cooling effectiveness. This method was used to systematically optimize endwall cooling systems. Designs are presented which use half the coolant mass flow compared to a baseline design, while maintaining similar cooling effectiveness levels on the critical trailing endwall. By studying the effect of coolant injection on vane inlet total pressure profile, secondary flows were suppressed and upwash on the vane was reduced.
The methods and insight obtained from this study were applied to a high pressure nozzle guide vane endwall from a current engine. The optimized cooling system developed offers significant improvement over the baseline.
Imaging the assembly of the Staphylococcal pore-forming toxin alpha-Hemolysin
Keywords: Staphylococcus aureus
single-molecule fluorescence
droplet-on-hydrogel bilayers
electrophysiology
lipid bilayers
pore-forming toxin
single-channel electrical recording
droplet bilayers
assembly
alpha-Hemolysin

Alpha-hemolysin is a pore-forming toxin secreted by pathogenic Staphylococcus aureus. Its spontaneous oligomerization and assembly into a trans-bilayer beta-barrel pore is a model for the assembly of many other pore-forming toxins. It is studied here in vitro as a means to probe general membrane protein oligomerization and lipid bilayer insertion. This thesis details the results of experiments to develop and implement a novel in vitro lipid bilayer system, Droplet-on-Hydrogel Bilayers (DHBs) for the single-molecule imaging of alpha-hemolysin assembly. Chapter 2 describes the development of DHBs and their electrical characterization. Experiments show the detection of membrane channels in SDS-PAGE gels post-electrophoresis and DHBs use as a platform for nanopore stochastic sensing. Chapter 3 describes the engineering and characterization of fluorescently-labelled monomeric alpha-hemolysin for use in protein assembly imaging experiments described in Chapter 6. Chapter 4 describes the characterization of DHB lipid fluidity and suitability for single-molecule studies of membrane protein diffusion. In addition, a novel single-particle tracking algorithm is described. Chapter 5 describes experiments demonstrating simultaneous electrical and fluorescence measurements of alpha-hemolysin pores embedded within DHBs. The first multiple-pore stochastic sensing in a single-lipid bilayer is also described. Chapter 6 describes experiments studying the assembly of alpha-hemolysin monomers in DHBs. Results show that alpha-hemolysin assembles rapidly into its oligomeric state, with no detection of long-lived intermediate states.
A study of Y Seint Greal in relation to La Queste del Saint Graal and Perlesvaus
Keywords: French prose literature
Welsh prose literature
Perlesvaus
Queste del Saint Graal
Y Seint Greal
Arthurian romances

[Short abstract]. The Middle Welsh prose romance, Y Seint Greal has long been recognised as a translation of two early thirteenth century French Grail romances, La Queste del Saint Graal and Perlesvaus, but so far no comprehensive study has been made of the relationship between them, nor of the Welsh text as a work of literature in its own right. This study first puts Y Seint Greal into its proper context, as a product of the close links between France and Wales in the later Middle Ages, and as part of a surge of translation of foreign material into Welsh that began in the mid thirteenth century. Manuscript and other evidence indicates that Y Seint Greal was commissioned by the uchelwr (nobleman) Hopcyn ap Thomas of Glamorgan, at the end of the fourteenth century, both translator and scribe probably working in Neath or Margam Cistercian Abbey. The translator presents the Queste and Perlesvaus as two parts of a whole, creating a number of problems of consistency within Y Seint Greal. Moreover, comparison of the Welsh text with its French sources shows that the translator was insensitive to some of their qualities, and that his tendency to abridge has sometimes undermined the structure and coherence of the romances. However, many of the translation's apparent weaknesses can be ascribed to the redactor's concern to adapt his French material for the new audience. Overtly foreign elements are removed and efforts made to harmonise events and characters of the French romances with those of native Welsh tradition. The translator was familiar with earlier Welsh prose narrative, which has influenced his style, and he has drawn on the earlier romance of Peredur. Y Seint Greal was not intended to be a faithful translation but a bridge between Welsh and continental Arthurian traditions.
‘It was the worst of times; it was the worst of times’ Popular Prophecy, Rapture Fiction, and the Imminent Apocalypse in Contemporary American Evangelism
Keywords: Premillennial Dispensationalism
Christian Apocalypticism
Horror
Tim LaHaye
Paranoia
The Left Behind series
Rapture fiction
Modern American Evangelicalism
Anxiety
The Rapture
Prophecy

This thesis explores how the Rapture fiction and popular prophecy of modern American premillennial dispensationalism shapes the eschatological beliefs of its readership. This will be accomplished through a text-based critical analysis of the anxiety narratives of the Bible study and exegetical guides of the Tim LaHaye Prophecy Library, and its counterpart, the Left Behind fiction series. This thesis represents the first scholarly analysis of the Tim LaHaye Prophecy Library, and the first situation of Left Behind fiction within its theological context. It will be proposed that these two sets of texts shape the eschatological beliefs of their readers through a discursive ‘streamlining’ that is performed in several ways. Firstly, the historical development of the movement will be examined, exploring the evolution of a specific premillennial dispensationalist hermeneutic and its ‘channelling’ through particular cultural institutions. Secondly, an analysis of the Tim LaHaye Prophecy Library and Left Behind fiction will demonstrate that this premillennial dispensationalist hermeneutic is almost exclusively communicated through anxiety narratives which focus on expressions of horror, isolation, powerlessness and paranoia. It will be argued that these narratives serve to explore ‘abjective’ elements of premillennial dispensationalist belief, re-integrating them into the fabric of the faith. Particular attention will be paid to these abjective elements, which include the role of the eschatological body, the nature of individual salvation, and the perpetual deferment of the Rapture. As such, the popular media of premillennial dispensationalism serves as a further channel for the discursive streamlining of the movement’s prophetic scheme. Finally, this thesis proposes that the ‘deprivation’ theory of millennial appeal does not adequately explain the appeal and success of premillennial dispensationalism. As such, the following analysis will suggest that an alternate critical analysis of the movement, concentrating on its tropes of anxiety, serves to better explain the continued appeal of this ideology.
Three-dimensional device structures for photovoltaic applications
Keywords: dye sensitized
periodic microstructures
photovoltaics
solar cells

Harnessing solar energy has become a promising clean and renewable energy source alternative to fossil fuels since the development of low-cost dye sensitized solar cells (DSSC) and organic photovoltaic solar cell devices. Their power-conversion efficiencies, below 13% and 9% respectively, still limit the economic viability of these technologies. The geometry and optical properties of photonic crystals can be used to improve the absorption and charge collection efficiencies of these devices. This thesis describes the fabrication of TiO2 DSSC and ZnO-polymer solar cell devices based on a three-dimensional photonic crystal structure. Photonic crystal polymer structures were produced by holographic lithography and thermally stabilized in order to be used as templates for atomic layer deposition (ALD) of various metal oxides. For this purpose, an ALD apparatus was built and ALD processes for the growth of TiO2, ZnO, Al2O3, ZnO:Al, and Zr3N4 were established and deposited on photonic crystal templates. After ALD, the template was removed by calcination at 500°C, at which ZnO:Al films lost their conductivity of 250 S/cm preventing their use as transparent conducting oxide (TCO) electrodes. The produced 90 nm TiO2 photonic crystal shell DSSC and TiO2 inverse replica devices based on the dye N-719 and iodine/iodide redox electrolyte provided power-conversion efficiencies of 0.9% and 0.49% respectively and their diffusion lengths were 2× and 3× longer than that of a nanocrystalline reference device respectively. ZnO-polymer devices, comprising a P3HT layer as absorber and PEDOT:PSS film as hole-transporter, were also investigated.
An analytical study of the cone penetration test
Keywords: cone penetrometer
clay

The quasi-static penetration of a cone penetrometer into clay can be formulated as a steady state problem by considering a steady flow of soil past a stationary cone. The soil velocities are estimated from the flow field of an inviscid fluid, and the incompressibility condition is achieved by adopting a stream function formulation. Emphasis is placed on obtaining an accurate velocity estimate and this is accomplished by a solution of the Navier-Stokes equations. The strain rates are evaluated from the flow field using a finite difference scheme. The clay is modelled as a homogeneous incompressible elastic-perfectly plastic material and the soil stresses are computed by integrating along streamlines from some initial stress state in the upstream region. These stresses do not in general obey the equilibrium equations, although one of the two equations can be satisfied by an appropriate choice of the mean stress. Several attempts have been made to use the remaining equilibrium equation to obtain an improved velocity estimate and three plausible iterative methods are detailed in this thesis. In a second study, a series of finite element calculations on the cone penetration problem is performed. In modelling the penetration process, the cone is introduced in a pre-formed hole and some initial stresses assumed in the soil, incremental displacements are then applied to the cone until a failure condition is reached. Although the equilibrium condition is satisfied very closely in the finite element calculations, it is extremely difficult to achieve a steady state solution. In a third series of computations, the stresses evaluated by the strain path method are used as the starting condition for the finite element analysis. This is believed to give the most realistic solution of the cone penetration problem because both the steady state and equilibrium conditions are approximately satisfied. Numerically derived cone factors are presented and these are found to depend on the rigidity index of the soil and the in situ stresses. The pore pressure distribution in the soil around the penetrometer is estimated using Henkel's empirical equation. The dissipation analysis is based on Terzaghi's uncoupled consolidation theory. The governing equation is formulated in the Alternating-Direction-Implicit finite difference scheme. This formulation is unconditionally stable and variable time steps are used to optimise the solution procedure. The dissipation curves are found to be significantly affected by the rigidity index of the soil and a dimensionless time factor is proposed to account for this effect.