VictorJuiz/thesis huggingface dataset:
Characterisation of syncoilin
Keywords: ventral root
amyotrophic lateral sclerosis
syncoilin
neurons
axon caliber
peripherin
intermediate filaments

Syncoilin is a 64kDa intermediate filament protein (IF) first studied because it binds to the dystrophin associated protein complex (DAPC) through α-dystrobrevin. Syncoilin is highly expressed in skeletal and cardiac muscle, but the function of syncoilin in muscle remains largely unknown. A recently generated syncoilin null (sync-/-) mouse has almost no muscle phenotype. This thesis makes significant progress in characterising the function of syncoilin in muscle and nerve and discovering a phenotype in the sync-/- mouse. The first half of this thesis attempts to further elucidate the function of syncoilin in muscle. Two new syncoilin isoforms were discovered in muscle, and syncoilin was shown to be upregulated in muscle during atrophy and regeneration. Sync+/+ and sync-/- primary muscle cell lines were generated in an attempt to elucidate a signalling role for syncoilin in muscle, but no difference was discovered between the two cell lines in cell growth, drug resistance or protein synthesis. Recent discoveries from this laboratory reveal that syncoilin is also expressed in neurons. The second half of this thesis is an attempt to characterise the function of syncoilin in neurons. Two potential syncoilin neuronal binding partners were examined. Syncoilin and α-tubulin bind via co-immunoprecipitation, but there is no co-localisation between the two proteins in sciatic nerve. Peripherin was shown to co-localise with syncoilin in sciatic nerve, and co-transfections suggest that syncoilin acts to regulate peripherin filament formation. Finally, a neuronal analysis of the sync-/- mouse shows decreased motor function in a range of behavioural tests. This observation is confirmed with the discovery that motor neurons in the sync-/- mouse have decreased axon calibre when compared to the sync+/+ mouse. The possibility that syncoilin plays a vital role in neuronal function is a significant discovery and opens an exciting new avenue of research.
A study of irradiation damage in iron and Fe-Cr alloys
Keywords: iron
radiation damage
transmission electron microscopy

Irradiation damage structures induced in pure Fe and Fe-Cr (up to 14%Cr) alloys by 2 MeV Fe+ ion irradiations in the temperature range 300-460°C were investigated by transmission electron microscopy. Specimens were irradiated in bulk to doses of 1.5 x 1019 Fe+/m2 (about 2.5 displacements per atom: dpa) and 4.5 x 1019 Fe+/m2 (about 7 dpa).
In most cases, damage took the form of dislocation loops with diameters from 2-100nm; the loops were distributed uniformly within all the samples. At higher irradiation temperatures (400°C, 460°C), complex microstructures such as finger loops (50nm in width and 1 micron in length) and perpendicular <100> loop clusters, were observed in both pure Fe and Fe-Cr samples.
Loop sizes and densities were seen to change as a function of irradiation temperature and dose. Loop sizes were seen to increase as the increase of irradiation temperatures and doses, while loop densities only increased with increasing doses and decreased as increasing temperatures. Loops with both types of Burgers vectors (<100> and ½<111>) were observed in all the samples. The proportion of <100> loops was higher in Fe than that in Fe-Cr alloys at the same irradiation condition, which has can be attributed to the high mobility of ½<111> loops in Fe, so that a large proportion of them will escape to the (001) foil surface.
A transition in loop Burgers vectors as a consequence of increasing temperature was observed. In Fe, the proportion of <100> loops increased with increasing irradiation temperature from 40% at 300°C to 60% at 460°C. A similar trend was found in the Fe-Cr alloys, but due to the higher proportion of ½<111> loops in these alloys, the increase of <100> loops was not that obvious, being from 30% at 300°C to 45% at 460°C(Fe-11Cr).
The effects of irradiation dose rate on the formation of dislocation loops by 2 MeV Fe+ ions were also investigated. These irradiations were carried out at 300°C with two different implantation dose rates: 6 x 10-4 dpa/s and 3 x 10-5 dpa/s. The implantation dose for both implantations was 0.38 x 1019 Fe+/m2 (0.5 dpa). Both the average loop size and loop densities for the Fe-Cr specimens subjected to the high dose rate irradiation were higher than that in the low dose rate irradiations. Take Fe-14Cr as an example, that the loop densities in high dose rate irradiation increased about 90% compared to that in low dose rate, and the average loop size in high dose rate irradiation was 30% larger than that in low dose rate irradiation.
The ‘inside-outside contrast’ method was applied to determine the loop nature in all the samples. It was found that all the large loops (>5nm) are of interstitial type. Any vacancies are believed to exist in the form of small dislocation loops (<5nm) or sub-microscopic voids.
Meaning in life: tales from aging Japan
Keywords: ageing
meaning in life
Japan
ikigai
narrative
old age

Amidst widespread concerns about aging on several levels ranging from the personal to the societal, this dissertation examines the construction of meaning in life and older age in contemporary Japan. Based on an ethnographic account of a community salon in Southern Osaka, it explores the experiences of older people and their ideas of the good and meaningful life, while arguing that than an anthropology of the elderly can reveal a far wider scope of issues than aging alone. Drawing on a socio-narratological approach, I show how stories connect people, form a shared body of knowledge, inform our understanding of the everyday, and provide frameworks for our choices. I argue that the capacity of narratives to create coherence and make sense of seemingly random and unconnected events can help to reveal existential issues, and that narrative analysis may therefore be a powerful tool for creating an existential anthropology capable of elucidating and understanding deeply personal dilemmas in their social and cultural context.
The ethnography and life stories of elderly salon goers, volunteers and others involved in a local Non-Profit Organisation raise important issues of autonomy and dependence, sociality and isolation, care and concern. People express concern for others through practices ranging from gift-giving, visiting, balanced forms of polite yet friendly discourse, the provision of information, and volunteering in the salon and beyond. I argue that older Japanese are as much providers of care as recipients of it, thereby challenging the constructed image of the elderly as frail and dependent, even though maintaining independence relies paradoxically on cultivating multiple dependencies on others. Navigating the tensions between the benefits of rich social ties and a desired level of separation in which the burden imposed is minimised, or between dependence and freedom, emerges as central to the balancing acts required for living well.
Aristotle's Poetics in Renaissance England
Keywords: classical education
classical reception
literary theory
Philip Sidney

This thesis brings to light evidence for the circulation and first-hand reception of Aristotle's Poetics in sixteenth-century England. Though the Poetics upended literary thinking on the Continent in the period, it has long been considered either unavailable in England, linguistically inaccessible to the Greekless English, or thoroughly mediated for English readers by Italian criticism. This thesis revisits the evidentiary basis for each of these claims in turn. A survey of surviving English booklists and library catalogues, set against the work's comprehensive sixteenth-century print-history, demonstrates that the Poetics was owned by and readily accessible to interested readers; two appendices list verifiable and probable owners of the Poetics respectively. Detailed philological analysis of passages from Sir Philip Sidney’s Defence of Poesie proves that he translated directly from the Greek; his and his contemporaries' reading methods indicate the text circulated bilingually as standard. Nor was Sidney’s polyglot access unusual in literary circles: re-examination of the history of Greek education in sixteenth-century England indicates that Greek literacy was higher and more widespread than traditional histories of scholarship have allowed. On the question of mediation, a critical historiography makes clear that the inherited assumption of English reliance on Italian intermediaries for classical criticism has drifted far from the primary evidence. Under these reconstituted historical conditions, some of the outstanding episodes in the sixteenth-century English reception of the Poetics from John Cheke and Roger Ascham in the 1540s to Sidney and John Harington in the 1580s and 1590s are reconsidered as articulate evidence of reading, thinking about, and responding to Aristotle's defining contribution to Renaissance literary thought.
Evolution of nickel hyperaccumulation in Alyssum L.
Keywords: phylogenetics
taxonomy
nickel hyperaccumulation

Phylogenetic studies are providing powerful new insights into the evolution of complex traits. Metal hyperaccumulation is an unusual and complex physiological trait found in about 500 plant species and is associated with an exceptionally high degree of tolerance of metalliferous soils. Alyssum L. (Brassicaceae) is the largest known hyperaccumulator genus, comprising approximately 188 species distributed throughout the Mediterranean region and south-west Asia. Approximately one-quarter of these are largely restricted to areas of serpentine soils and have the ability to accumulate nickel to high concentrations in shoot tissue. This genus provides a good example in which to study the origins of a complex physiological trait, but its phylogeny is currently poorly understood.
To produce a well-resolved phylogenetic tree to investigate the number and timing of origins of nickel hyperaccumulation within Alyssum, DNA sequences were generated for four chloroplast regions (matK, rps16–trnK, trnD–T and trnL–F) from 170 of 255 species in the tribe Alysseae. Additional sequencing was carried out for the chloroplast genes ndhF and rbcL and the nuclear gene PHYA. A Bayesian analysis employing a relaxed uncorrelated lognormal molecular clock and multiple fossil-age calibration points was carried out to reconstruct a time-calibrated phylogeny of this tribe using appropriate outgroups.
Optimization of the nickel hyperaccumulation trait onto the resulting phylogenetic tree suggests that nickel hyperaccumulation arose twice in the Alysseae in the late Miocene/early Pliocene: 3.3–8.3 Mya in Alyssum and 6.3–8.8 Mya in Bornmuellera. The single origin in Alyssum is strongly associated with a significant acceleration in net species diversification rate, suggesting the ability to hyperaccumulate nickel could have provided a key evolutionary innovation facilitating rapid range expansion and subsequent species diversification. The scattered distribution of nickel hyperaccumulators across small island-like patches of serpentine soil suggests that allopatric speciation may have driven rapid diversification in this clade.
Respiratory disturbances in congenital heart disease
Keywords: respiratory system
chest deformities
congenital heart disease
respiratory disturbances
haemodynamism

The work described in this thesis has been carried out over the period 1958-1965, having been begun during the tenure of a residency at the University of Colorado, Denver, U.S.A. At this time, surgery for the closure of septal defects was being actively carried out, and interest was aroused, in two clinical features which were apparent from close contact with this programme. The first was the nature of the chest deformities associated with septal defects; the second, the striking alleviation of symptoms which followed successful closure of these defects. The reasons for these phenomena were by no means clear and the subsequent work has been concerned with an attempt to understand them. (Cont.)
Bayesian learning methods for modelling functional MRI
Keywords: Independent Component Analysis
Neuroscience
Bayesian inference
FMRI

Bayesian learning methods are the basis of many powerful analysis techniques in neuroimaging, permitting probabilistic inference on hierarchical, generative models of data. This thesis primarily develops Bayesian analysis techniques for magnetic resonance imaging (MRI), which is a noninvasive neuroimaging tool for probing function, perfusion, and structure in the human brain.
The first part of this work fits nonlinear biophysical models to multimodal functional MRI data within a variational Bayes framework. Simultaneously-acquired multimodal data contains mixtures of different signals and therefore may have common noise sources, and a method for automatically modelling this correlation is developed. A Gaussian process prior is also used to allow spatial regularization while simultaneously applying informative priors on model parameters, restricting biophysically-interpretable parameters to reasonable values.
The second part introduces a novel data fusion framework for multivariate data analysis which finds a joint decomposition of data across several modalities using a shared loading matrix. Each modality has its own generative model, including separate spatial maps, noise models and sparsity priors. This flexible approach can perform supervised learning by using target variables as a modality. By inferring the data decomposition and multivariate decoding simultaneously, the decoding targets indirectly influence the component shapes and help to preserve useful components.
The same framework is used for unsupervised learning by placing independent component analysis (ICA) priors on the spatial maps. Linked ICA is a novel approach developed to jointly decompose multimodal data, and is applied to combined structural and diffusion images across groups of subjects. This allows some of the benefits of tensor ICA and spatially-concatenated ICA to be combined, and allows model comparison between different configurations. This joint decomposition framework is particularly flexible because of its separate generative models for each modality and could potentially improve modelling of functional MRI, magnetoencephalography, and other functional neuroimaging modalities.
Patient-specific models of cerebral aneurysm evolution
Keywords: cerebral aneurysm
CFD
patient-specific model

A cerebral aneurysm (CA) is an abnormal distension of the wall of an artery in the brain, which results from arterial wall weakening. CAs are poorly understood, but are believed to be the result of a combination of biological and life-style factors. The low incidence of rupture coupled with risks of interventional treatments provide motivation for identifying and treating only those aneurysms at risk of rupture. Computational models of aneurysm evolution may provide great insight into CA disease mechanisms, and guide clinical decision-making.
It is well known that vascular cells sense mechanical forces exerted by bloodflow (i.e. haemodynamic forces), which are translated into a myriad of intra- and inter-cellular responses. In this thesis, hypotheses on the role of the patient-specific haemodynamic environment on the evolution of CAs is examined. Arterial geometries are obtained from images of patient-specific vasculature, and the physiological aneurysm is virtually removed and replaced by a novel, fluid-solid-growth (FSG) model. The model incorporates a constitutive model for the artery, growth and remodelling (G&R;) hypotheses for arterial wall constituents, and links between G&R; and the haemodynamic environment, which is simulated utilising computational fluid dynamics.
It is observed that coupling G&R; to the patient-specific haemodynamic environment profoundly impacts the shape and size of the evolving aneurysm geometry; in some cases, the model aneurysm is qualitatively similar to the corresponding physiological aneurysm. This provides tentative support for the hypotheses on haemodynamics-induced G&R; investigated here, and motivates the need for improved understanding of arterial adaptation to physiological conditions. This will facilitate the improvement and validation of the model, and may ultimately lead to predictive models with clinical application on a patient-specific basis.
Understanding the Ediacaran assemblages of Avalonia: a palaeoenvironmental, taphonomic and ontogenetic study
Keywords: Ediacaran
Avalonia
Newfoundland
taphonomy
ichnology

The Ediacaran Period, stretching from 635–542 million years ago, is one of the most dynamic intervals in the history of life. It witnessed the rapid transition from a microbially-dominated world, which had existed undisturbed for almost three billion years, to a Phanerozoic biosphere that is greatly modified by the interactions between macro-organisms and Earth surface systems. Ediacaran successions worldwide contain enigmatic assemblages of fossilised soft-bodied organisms. Determining the biological affinities of these fossils represents one of the major challenges in modern palaeontology.
This thesis addresses some of the fundamental questions surrounding the Ediacara biota of the Avalon region from taphonomic, ontogenetic and palaeoenvironmental perspectives. Up-to-date stratigraphic ranges are produced for Avalonian macro-organisms, documenting spatial and temporal trends in their occurrence. New fossil assemblages are described, which include populations of juvenile rangeomorphs, and one of the earliest examples of community succession in the fossil record. The previously unexplained fossil Ivesheadia Boynton and Ford 1996 is re-described as a taphomorph, preserving the remains of Ediacaran macro-organisms that had died and undergone microbial decay on the seafloor prior to burial. This hypothesis implies considerable time-averaging of Avalonian palaeocommunities, and consequently suggests that the preserved fossil assemblages do not represent census populations of living organisms at the time of burial. Microbial decay is experimentally demonstrated to replicate aspects of Ivesheadia-type morphology, supporting the arguments presented herein for the preservation of microbially-induced taphomorphs during the Ediacaran.
Finally, the discovery of the oldest evidence for metazoan locomotion, from 565Ma horizons at Mistaken Point in Newfoundland, suggests that motile macro-organisms were present amongst the Ediacara biota, ~20Myrs before the Cambrian boundary. This portrayal of Ediacaran palaeobiology views the deep-marine Avalonian ecosystems as diverse assemblages of both macro- and micro-organisms. Such palaeoenvironments preserve rare evidence of organisms capable of locomotion, and are likely to have included metazoans.
Targeting the mevalonate pathway for pharmacological intervention
Keywords: nitrogen containing bisphosphonates
osteoporosis
inhibition
farnesyl pyrophosphate synthase
drug binding
Rab geranyl geranyl transferase

Farnesyl pyrophosphate synthase (FPPS) is a key branch point enzyme in the mevalonate pathway and the main molecular target of nitrogen-containing bisphosphonates (N-BPs), potent inhibitors of osteoclastic activity and the leading drug of choice for conditions characterized by excessive bone resorption. The main aim of this thesis is to investigate the interaction of N-BPs with FPPS in order to gain further insights into the mechanism of drug inhibition. Kinetic and crystallographic studies following site-directed mutagenesis of FPPS reveal key residues involved in stabilization of carbocation intermediate, substrate binding and formation of a tight enzyme-inhibitor complex. The aromatic ring of Tyr204 is involved in N-BP binding but not in the catalytic mechanism, where the hydroxyl moiety plays an important role. Lys200 is implicated in regulation of substrate binding, product specificity and enzyme isomerization which leads to a tight binding inhibition. Phe239 is considered important for the FPPS C-terminal switch which stabilizes substrate binding and promotes the inhibitor induced isomerized state. The highly conserved Arg112, Asp103 and Asp107 are pivotal for catalysis. Successful purification of the full length of Rab geranylgeranyl transferase (RGGT) complex downstream of the FPPS in the mevalonate pathway was achieved and may lead to co-crystallization with BP analogues and identification of the putative site of drug binding. Investigation of the in vitro effect of N-BPs on osteoclastogenesis suggest a correlation with FPPS inhibition kinetics for the most potent N-BPs but indicate an alternative mechanism of the disruption of bone resorption by alendronate. Together these results highlight the importance of the multiple interactions of N-BPs with side-chain residues of FPPS which dictate their strength of binding and advance the understanding of their pharmacophore effect.
Real-time single-molecule observations of conformational changes in DNA polymerase
Keywords: DNA POLYMERASE
BIOPHYSICS
SINGLE-MOLECULE
KINETICS
CONFORMATIONAL DYNAMICS

Genetic information is encoded in the long sequence of bases which form DNA, which is replicated during cell division by enzymes known as DNA Polymerases. Polymerases replicate DNA extremely accurately to avoid errors which can cause cell death and diseases such as cancer, although the mechanisms behind these extraordinary fidelities are not well understood.
A large conformational change in the protein, in which the “fingers" subdomain closes around an incoming nucleotide, is thought to be implicated in these fidelity mechanisms. Here we present an assay to monitor this conformational change in single polymerase molecules, in real-time. We achieve this using total-internal-reflection-fluorescence (TIRF) microscopy to monitor the fluorescence resonance energy transfer (FRET) of an intra-protein dye labelled DNA Polymerase I (KF) as it binds to surface-immobilised DNA.
Initially, we investigated the polymerase fingers-conformations during the pre-chemistry polymerisation reaction, resolving forward and backward rates which would be challenging to observe using ensemble techniques. These observations confirmed that KF closes rapidly around complementary nucleotide, but we discovered that the reverse step, fingers-opening, is particularly slow relative to chemistry. These finger kinetics act to remove the influence of the reaction rate-limiting step on fidelity, surprising given decades of investigations have focused on the rate-limiting step as the key determinant of fidelity. We also use our kinetic measurements to quantify contributions of different reaction steps to the macroscopic error rate of the polymerase.
Subsequently, we developed our assay to investigate the fingers-conformations across the entire DNA polymerisation reaction. We observed single-nucleotide incorporations, and processive DNA polymerisation at high and low nucleotide concentrations, which suggested heterogeneous nucleotide incorporation rates. The observations demonstrated that the post-chemistry slow step that limits processive polymerisation occurs before post-chemistry fingers-opening, or is accounted for by post-chemistry fingers-opening. We observe a correlation in turn-over kinetics and binary complex kinetics, suggesting that turn-over rates could be limited by the intrinsic dynamics of the binary complex, as seen in other protein systems, although more work is needed on this.