VictorJuiz/thesis huggingface dataset:
Statistical mechanics of nucleic acids under mechanical stress

In this thesis, the response of DNA and RNA to linear and torsional mechanical stress is studied using coarse-grained models. Inspired by single-molecule assays developed over the last two decades, the end-to-end extension, buckling and torque response behaviour of the stressed molecules is probed under conditions similar to experimentally used setups. Direct comparison with experimental data yields excellent agreement for many conditions. Results from coarse-grained simulations are also compared to the predictions of continuum models of linear polymer elasticity.
A state diagram for supercoiled DNA as a function of twist and tension is determined. A novel confomational state of mechanically stressed DNA is proposed, consisting of a plectonemic structure with a denaturation bubble localized in its end-loop. The interconversion between this novel state and other, known structural motifs of supercoiled DNA is studied in detail. In particular, the influence of sequence properties on the novel state is investigated. Several possible implications for supercoiled DNA structures in vivo are discussed. Furthermore, the dynamical consequences of coupled denaturation and writhing are studied, and used to explain observations from recent single molecule experiments of DNA strand dynamics.
Finally, the denaturation behaviour, topology and dynamics of short DNA minicircles is studies using coarse-grained simulations. Long-range interactions in the denaturation behaviour of the system are observed. These are induced by the topology of the system, and are consistent with results from recent molecular imaging studies. The results from coarse-grained simulations are related to modelling of the same system in all-atom simulations and a local denaturation model of DNA, yielding insight into the applicability of these different modelling approaches to study different processes in nucleic acids.

Keywords: Single Molecules
Theoretical Physics
Biophysics
Biomaterials
supercoiling
Computer Simulations
Statistical Mechanics
DNA
Advisor: Louis, A
The structure, function and specificity of the Rhodobacter sphaeroides membrane-associated chemotaxis array

Bacterial chemotaxis is the movement of bacteria towards or away from chemical stimuli in the surrounding media. Bacteria respond to chemotactic signals through chemoreceptors which bind specific ligands and transduce signals through a modified two-component system. Typical chemoreceptors bind a ligand in the periplasm and signal across the inner membrane to the cytoplasmic chemosensory array through the inner membrane. Bacterial chemoreceptors must integrate multiple signals within an array of different receptor homologues to a single output. Chemoreceptors act cooperatively to allow a rapid signal spread across the array and large signal gain. Chemoreceptors adapt to a signal by chemical modification of their cytoplasmic domains in order respond across a wide range of effector concentrations. How bacterial chemoreceptors transduce signals through the inner membrane, integrate multiple effector responses, signal cooperatively and adapt to result in a single output signal is not currently fully known. In Rhodobacter sphaeroides, additional complexity arises from the presence of multiple homologues of various chemotactic components, notably the array scaffold protein CheW. Decoding this signalling mechanism and heterogeneity involved in this system is important in decoding the action of a biological system, with implications for biotechnology and synthetic biology.
This study used the two model systems Escherichia coli and R. sphaeroides to analyse the mechanism of signalling through bacterial chemoreceptors. Rational design of activity-shifting chemoreceptor mutations was undertaken and these variants were analysed in phenotypic and fluorescence localisation studies. Molecular-dynamics simulations showed an increase in flexibility of chemoreceptors corresponds to a decrease in kinase output activity, which was determined by the computational tracking of bacteria free-swimming in media. Fluorescence recovery after photobleaching was used to show that this increase in flexibility results in a decrease in binding of receptors to their array scaffold proteins. A two-hybrid screen also suggested that inter-receptor affinity is also likely to decrease. These results show that signalling through chemoreceptors is likely through a mechanism involving the selective flexibility of chemoreceptor cytoplasmic domains.
Analysis of R. sphaeroides chemoreceptors and CheW scaffold proteins in E. coli showed that it should be possible to design, from the bottom-up, a functional bacterial chemotaxis system in order to analyse individual protein specificity. Expression of R. sphaeroides MCPs in this E. coli system show the reconstitution of a chemotactic array, but not one capable of signalling specifically to proposed attractants. Results gained from this system suggest the R. sphaeroides CheW proteins are not homologous and their differential binding affinities may allow array activity 'fine-tuning'.

Keywords: Bacterial chemotaxis
Cell signalling
Rhodobacter sphaeroides
Advisor: Armitage, J
Assessment of local networking strategies to enhance clinical research capacity in Zambia

Well conducted clinical research leading to the generation of evidence based guidelines, in low- and middle-income countries has been viewed as the means of making significant improvements to global health. This is because these are the regions that bear the highest burden of disease and premature death. Several efforts over the past two decades have therefore focused on research capacity strengthening initiatives as a way of increasing the amount of clinical research conducted in these regions. The aim of this study was to evaluate if setting up a local online network and holding a skills sharing workshop would raise the knowledge and confidence of researchers in Zambia and enhance their capacity to conduct independent clinical research. This was a before and after study that involved open discussions about clinical research in Zambia through a local online platform (the Zambian Clinical Research Forum), on the Global Health Network. A total of 19 members took part in the study, 12 of whom were emerging researchers and 7 established researchers. In addition to the discussions, a one-day research skills sharing workshop was conducted after the period of the discussions that brought together those who were interested in the conduct of clinical research in Zambia. Structured questionnaires were used as the assessment tool and administered before and after the online discussions and at the workshop. The Zambian Clinical Research Forum stimulated discussions between emerging and established researchers on the conduct of clinical research in Zambia and resulted in an increase in the research self-confidence of the emerging researchers as opposed to that of the established researchers. The conduct of the one-day skills sharing workshop also enabled the sharing of information, skills and experiences based on the conduct of clinical research in Zambia. Participation in the online discussions however did not illicit a demonstrable change in the reported behaviour of the members in conducting clinical research related tasks. Furthermore, the discussions and interactions on the online platform were not continued beyond the study period. These findings indicate that the development of future network-based capacity building initiatives in Zambia should be underpinned by clear and achievable objectives that could drive the participation of those involved. There could also be a need to incorporate capacity building initiatives such as online platforms within the regular conduct of clinical research rather than as isolated ventures. This could be considered in Zambia by embedding such an online platform in institutions that can support this initiative and stimulate participation amongst their members.

Keywords: Networking
Online Platforms
Clinical Research
Capacity Building
Zambia
Advisor: Lang, T
Marsh, K
The Colonial Office and the plantation colonies, 1801-1834

This thesis is a study of the changing way in which part of the British Empire was being governed during a period of far reaching developments both in Britain and in the plantation colonies. The colonies referred to are the old British West Indian islands -- Jamaica, the Leewards group, Barbados, Dominica, St. Vincent, Grenada and Tobago -- and those colonies conquered by Britain during the Revolutionary and Napoleonic Wars in which sugar planting was carried on by means of slave labour. The dates chosen do not denote precise limits to the period. The Colonial Office had its unintended beginnings in 1801, in 1834 slaves were emancipated in the plantation colonies, and the central years for this study lie between these dates, certain themes are followed beyond them.
In this area and period an account is given of the changing of government. This concerns the institutions within the colonies and those in Britain which had a direct part in the conduct of colonial affairs; it involves the purpose of the institutions, their form and their interrelationships.
At the end or the 18th century the traditional way of governing the old plantation colonies was to leave internal government to those resident In the colony and to maintain virtually only sufficient authority in Britain to ensure the preservation of the system of trade and navigation. Under the old representative system the governor, in theory, possessed wide powers, in practice his authority was narrowly confined and the regular conduct of administration was beyond his control. Colonists had developed and adapted their institutions and powers so that they largely governed themselves. In Britain there was no desire to intervene in the internal affairs of the plantation colonies, nor was there the machinery to enable the executive to do so. The institutions which existed matched the contemporary concern to maintain the system of trade and navigation. Such colonial business that there was was executed by the department with the responsibility for the relevant service: there was no department with a general responsibility for the area of the colonies, nor was there any adequate method of coordinating the activities of the different ministers and boards involved with administration in the colonies. [Please see pdf. for full abstract.]
Lifescapes of a pipedream: a decolonial mixtape of structural violence & resistance along the Chad-Cameroon oil pipeline

People's narratives, interpretations and understandings of the Chad-Cameroon Oil Pipeline and pipeline actors emphasise the uneven exercise of power through which structural violence is effected and experienced. The complexity of the processes of structural violence along with local socio-political context and peoples' dynamic understandings thereof play major roles in shaping resistance practices, in complex ways in Kribi and Nanga-Eboko. Working from these narratives, I offer a theoretical re-articulation of structural violence as (i) tangible through the body, (ii) historically compounded, (iii) spatially compressed and (iv) enacted in a globalised geopolitical nexus by actors who are spatially nested within a racialised and gendered hierarchy of scale. Drawing from critical interdisciplinary work on violence, my theory of a triad of divergent, often interrelated and co-existing, distinguishable indexes of structural violence includes: infra/structural violence, industrial structural violence and institutionalized structural violence. The particular processes and mechanisms of uneven power within structural violence, local socio-political contexts and the epistemologies through which power is conceived (in this case I consider epistemologies of la sorcellerie, or witchcraft) inform resistance practices; I illuminate key operations (within geographies characterised by high levels of infra/structural violence) within the spatial practices of power that influence the tendency for resistance struggles to be quiet, spontaneous and/or labour-based. I conclude with a discussion of the political and intellectual value of academic work on life and being amid structural violence, emphasising the need to move beyond the invisible/visible dichotomy that has often informed intellectual work on structural violence.

Keywords: resource extraction
human geography
political geography
Advisor: Daley, P
Extending and combining single-molecule fluorescence methods to study site-specific recombination

Förster resonance energy transfer (FRET) has become an important tool for studying biochemical reactions at the single-molecule level, despite its increasing maturity there is an on-going effort to improve and expand the technique. This thesis presents methods for extending conventional two-colour single-molecule FRET measurements; by expanding the range and applicability of single-molecule fluorescence methods a greater variety of biological reactions can be studied, in greater detail than previously possible.
To circumvent the complexities of multi-colour FRET measurements and extend the range of observable distances I developed and characterised a new single-molecule fluorescence method termed tethered fluorophore motion (TFM). TFM is based on the existing technique of tethered particle motion (TPM) which relies on Brownian motion of a particle, attached to a surface by DNA, to probe the effective length of the DNA tether. TFM takes this concept and applies it at the single-fluorophore level, allowing simultaneous measurement of other fluorescence observables such as FRET and protein induced fluorescence enhancement (PIFE).
Having developed TFM I combined it with FRET to study site-specific recombinase proteins at the single-molecule level, in greater detail than possible by either technique alone. Studying the model tyrosine recombinase Cre, I extend and clarify previous ensemble observations regarding the order of DNA strand exchange, as well as uncovering a previously unobserved complex conformation and molecular heterogeneity. Finally, I used TFM-FRET to study the more complex XerCD recombination system and its interaction with the DNA translocase FtsK. I made observations, for the first time, of synaptic complex formation and of recombination at the single-molecule level, and these suggest intriguing and unexpected intermediates in the recombination reaction. I also combine TFM with PIFE to investigate the mechanism of DNA looping by FtsK.
The introduction of TFM, and its combination with other fluorescence techniques, allows observation of complex protein-DNA interactions from a variety of perspectives and will help expand the repertoire and applicability of single-molecule biophysical experiments.

Keywords: single molecule
TFM
FRET
recombinase
Advisor: Kapanidis, A
Modulation of immune cell niches for therapeutics in cancer and inflammatory diseases

Immune cell niches are microenvironments that support the survival of specific hematopoietic cells. The size of a given niche is dependent on survival and proliferation signals provided. Modulation of niche size can be a useful therapeutic tool, and a better understanding of the factors that control the size of immune cell niches can lead to more targeted therapies.
Here bone marrow and thymic niches were modulated with tyrosine kinase inhibition to achieve increased engraftment following stem cell transplantation (SCT). SCT resulting in mixed chimerism is curative for several benign blood diseases, but toxicities associated with myeloablative and cytotoxic conditioning regimens limit the application of SCT. Sunitinib inhibits multiple tyrosine kinases including KIT, an essential survival signal within the hematopoietic stem cell and thymic progenitor niches. Sunitinib therapy diminishes hematopoietic and thymic progenitor cells in mice and enhances accessibility of marrow and thymic niches to transplanted bone marrow. This provides a novel, non-cytotoxic approach to accomplish mixed hematopoietic chimerism.
The observation that T cells undergo increased proliferation and accumulate in IL-7R deficient mice compared to other lymphopenic hosts raised questions about the factors that control the size of the T cell niche. Understanding these factors is useful in designing therapeutics to increase T cell responses for treatment of many diseases including cancer. Dendritic cells (DCs) are well known for their ability to modulate T cell responses; however, very little is known about the role of IL-7R signaling on DCs. The data presented here show that bone marrow derived DCs treated with IL-7 were less able to induce T cell proliferation in coculture. In vivo systems using CD11cDTR mice showed a role for IL-7 signaling on CD11c+ cells in T cell homeostasis. Together these data suggest that IL-7R signaling on DCs is important for regulating the size of the T cell niche.

Keywords: Hematopoietic Stem cell transplant
tolerance
Interleukin 7
niche
Dendritic cell
IL-7
Sunitinib
KIT
Advisor: Powrie, F
Mackall, C
Droughts in future climate change in the UK

This thesis seeks to investigate the changes in the characteristics of 20th and 21st century meteorological droughts in the UK to address the following lines of inquiry: 1) How credible are rainfall-based indices in representing hydrological droughts, 2) How coherent are droughts?, 3) Can alternative method of analysis provide new (or additional) information on the uncertainties in climate models?, and 4) Will future drought characteristics change?. Key results, respectively, are summarized as follows:
• The drought severity index (DSI), can be considered a good proxy for assessing hydrological droughts as can be seen in its ability to capture the major hydrological events. The main caveat of the DSI is that there is often an underestimation of drought intensity and duration,
• Drought covariance is higher for the (i) wet season, (ii) moderate and (iii) shorter duration droughts,
• Evaluating climate models using drought statistics produces contrasting results compared with that using the model's precipitation fields. Drought statistics show biases which are largely negative, more intense, and have a greater spatial coverage.
• The projected ensemble-mean change is generally greater (and more widespread) for (i) moderate droughts and (ii) wet season compared with extreme droughts and the dry season, respectively with increases in drought intensity, drought covariance index, frequency of drought months and frequency of drought events for a given duration shown for England.

Keywords: climate change
model
droughts
UK
Advisor: New, M
Models of primate supraretinal visual representations

This thesis investigates a set of non-classical visual receptive field properties observed in the primate brain. Two main phenomena were explored. The first phenomenon was neurons with head-centered visual receptive fields, in which a neuron responds maximally to a visual stimulus in the same head-centered location across all eye positions. The second phenomenon was perisaccadic receptive field dynamics, which involves a range of experimentally observed response behaviours of an eye-centered neuron associated with the advent of a saccade that relocates the neuron's receptive field. For each of these two phenomena, a hypothesis was proposed for how a neural circuit with a suitable initial architecture and synaptic learning rules could, when subjected to visually-guided training, develop the receptive field properties in question. Corresponding neural network models were first trained as hypothesized, and subsequently tested in conditions similar to experimental tasks used to interrogate the physiology of the relevant primate neural circuits. The behaviour of the models was compared to neurophysiological observations as a metric for their explanatory power. In both cases the neural network models were in broad agreement with experimental observations, and the operation of these models was studied to shed light on the neural processing behind these neural phenomena in the brain.

Keywords: Neural Networks
Vision
Reference Frames
Computational Neuroscience
Advisor: Maitland, S
The effect of interpersonal power on cognitive processing: a behavioural and neural perspective

Interpersonal power, defined as the asymmetrical control over valued outcomes, has important effects on the way cognitive processing unfolds. This work explores the effect of power on basic cognitive processes, in addition to broader processes that appear at the level of social behaviour. I begin this thesis with an introductory chapter, followed by a chapter describing the theory and practice behind electro-encephalogram recordings. In Chapter 3, I explore the effect of power on attention selection using a task that requires the ability to focus or divide attention in space, while varying the amount of distractors. The results suggest that low-power participants (subordinates) are more susceptible to the presence of distractors, regardless of whether the task necessitates focused or divided attention. In this context, inhibition accounts for the results to a greater extent than spatial orienting. In Chapter 4, I explore the effect of power on early inhibition processes in the context of executive control, in a task which allows participants to allegedly observe each others’ performance and receive feedback. The results show that high power is associated with reduced behavioural accuracy on trials that require executive control. Event-related potential analyses show that power-holders devote reduced motivational resources to their targets compared to subordinates, but do not differ at the level of early conflict detection. Their feedback potential results show a greater expectation of rewards, but reduced subjective magnitude attributed to losses. Subordinates, on the other hand, are asymmetrically sensitive to power-holders’ targets. They expect fewer rewards, but attribute greater significance to losses. In Chapter 5, I show that subordinates are asymmetrically competent at remembering diagnostic choices made by power-holders. In a final general discussion chapter, I integrate the findings of the experiments, which point to multi-layered effects of power, conferring those who possess it and those who lack it with distinct cognitive processing styles that suit their adaptive needs. The results are consistent with a hypothesized link between subordination and up-regulation of vigilance and environmental sensitivity. Limitations and future directions are discussed.

Keywords: attention
social neuroscience
memory
power
EEG
Advisor: Nobre, A
Hewstone, M