VictorJuiz/thesis huggingface dataset:
Characterising the small heat shock proteins: structure and regulation

The small heat shock protein HSP27 is expressed throughout the body and involved in a variety of cellular processes. Its multiple roles may all be mediated by its ability to chaperone partially folded protein substrates, and its malfunction is implicated in a range of diseases such as motor neuropathy and neurodegeneration. Here I describe structural, dynamical and functional investigations into this protein, particularly regarding its regulation by oxidation and phosphorylation. The foundations of this work were a protein crystal structure obtained on the oxidised core domain of the wild-type protein, which forms a disulphide-locked dimer, and additional structures that contain neuropathy-associated mutations. Observations of a structurally variable region, namely the β2-strand at the beginning of the core domain, led us to probe the nature of this region in solution and examine whether phosphorylation at the nearby phosphoserine site led the β2 to bind more strongly to the core domain, as phosphorylation elicits HSP27 oligomer disruption and activity modulation. I am able to postulate on the structural effect of mutation using the mutant crystal structures, and report the first structure showing the interface formed by the HSP27 core domain dimer in the ‘antiparallel III’ register. This finding, in tandem with the unusual nature of the intact intra-subunit disulphide bond reported here, motivated studies into the role of this disulphide in the redox response of the HSP27 chaperone. These include dynamical studies on the subunit exchange of the protein and functional investigations showing that the disulphide is formed in the cell and that chaperone behaviour depends on the oxidation state. Moreover, I show that the redox potential of the disulphide is affected by mutation, as is the change in chaperone response on oxidation. Taken together, I suggest that HSP27 is regulated by oxidation through the intra-dimer disulphide, which allows it to respond to oxidative stress within the cell.

Keywords: Motor neuropathy
Phosphorylation
Domain swapping
Molecular dynamics
Oxidation
Alpha crystallin
T151I
Beta2 strand
NMR
Native mass spectrometry
Cyclic voltammetry
Square wave voltammetry
HSPB1
Molecular chaperone
Oligomerisation
Chaperone assays
Alpha-crystallin domain
Disulphide bond
Core domain
Disulfide bond
Ion mobility
Mass spectrometry
Protein crystallography
R136W
T164A
Regulation
Proteostasis
Small Heat Shock Protein
HSP27
SDS-PAGE
Advisor: Benesch, J
Robinson, C
Chordal sparsity in control and optimization of large-scale systems

Many large-scale systems have inherent structures that can be exploited to facilitate their analysis and design. This thesis investigates how chordal graph properties can be used to develop scalable methods for solving three classes of problems: sparse semidefinite programs (SDPs), distributed control of networked systems, and sum-of-squares (SOS) programs. By exploiting the properties of chordal graphs and sparse positive semidefinite matrices, we present decomposition methods that are able to scale these problems to much larger instances.
The first part of this thesis proposes a new conversion framework for large-scale SDPs characterized by chordal sparsity. This framework is analogous to standard conversion techniques for interior-point methods, but is more suitable for the application of first-order methods. We develop efficient algorithms based on the alternating direction method of multipliers (ADMM) for sparse SDPs in either primal or dual standard form, and for their homogeneous self-dual embedding. The algorithms are made available in the open-source conic solver CDCS. CDCS is the first open-source first-order solver that exploits chordal decomposition and can detect infeasible problems. We demonstrate the performance of CDCS in standard analysis problems of large-scale networked systems.
The second part of this thesis is concerned with solution scalability and model privacy in distributed control of networked systems. Specifically, we apply chordal decomposition in sparse Lyapunov-type linear matrix inequalities arising from structured stabilization and optimal decentralized control of networked systems. We introduce a sequential method based on the clique-intersection property of a clique tree for structured stabilization. This strategy greatly improves the computational efficiency for large-scale sparse systems. In addition, we propose an ADMM algorithm that can maintain model privacy when solving the optimal decentralized control problem.
Finally, we consider large-scale SOS programs. We identify an inherent partial orthogonality in the formulation when recasting general SOS programs using the standard monomial basis. In addition, we extend the well-established chordal decomposition/completion results for sparse positive semidefinite matrices to a subset of SOS matrices. Using a new graph-theoretic viewpoint, we build an explicit relationship between chordal decomposition in SOS optimization and two other recent techniques — DSOS and SDSOS optimization. We demonstrate that chordal decomposition can bring significant speed-ups for large-scale sparse SOS programs.

Keywords: Large-scale systems
Distributed control
Decomposition methods
First-order methods
Chordal sparsity
Advisor: Papachristodoulou, A
A cognitive approach to assessment for learning: assessing the impact of changing formative assessment practices in a secondary school science faculty.

This research and development project took place across a science faculty in a UK state secondary school. Following trials, an assessment intervention was introduced to all science classes across key stages three and four in one academic year. The intervention sought to improve on an aspect of formative assessment, regular short tests, by combining literature on formative and summative assessment design and implementation with evidence from cognitive science relating to the nature of learning over time and how to improve it. The design of the intervention came from applying ideas from research to the specific context of the school, science faculty, staff and students at School X.
Quantitative analysis suggests an improvement in examination performance for students of all abilities in years 9 and 10 but a slight decrease in examination performance for students in years 7 and 8. Student and teacher opinion about the intervention is that it benefits learning. The primary reasons for this benefit are identified as improved diagnostic feedback as a result of increasing the inferential capacity of the assessment and improvements in the self-regulatory behaviour of students.

Keywords: MLT
MLT2018
To what extent can girls' levels of academic risk-taking be raised in Year 6 maths lessons.

When starting my first teaching job at an all girls’ school, I was struck by the disparity that I saw in the classroom between the number of times that pupils were willing to put their hands up in maths lessons compared to English lessons. It was clear that something was preventing the girls from fully participating in maths and that they generally seemed less confident. One year later, after carrying out a scoping study, it was clear that there was a difference in opinion between many parents and teachers over mistakes, success and what should motivate children. For me, this was of greater significance as my class were aged between 10 and 11, about to go through puberty and its associated self-image changes and were soon to leave Junior School for Senior School. Thus, this research and development project emerged with an aim to merge the home and school views on risk-taking, success and failure, and ultimately to help the girls to take more academic risks.
The study centered around a school-based intervention which was administered to all pupils in my class. The risk-taking lessons were designed to educate the girls about what risk-taking was and allowed the girls to analyse their motivation, their responses to failure and success, and the changes that they could make to help improve these. All of this lesson material was then sent to participating parents, who were able also to become educated over the school attitudes towards risk-taking. Pupils were encouraged to explain these lessons to their parents to strengthen this home-school link.
Parent and pupil questionnaires and lesson observations were used to collect data, which started to show some positive changes. Some pupils started to put their hands up more often, they responded more positively in lessons to failures or disagreements, and they became more aware of what risk-taking was. In addition, parents felt more able to support risk-taking at home, reflected some similar language surrounding risk-taking to pupils, and some felt that their daughters were less upset by failures. However, the study was limited by that fact that interviews were not included and follow up interviews would be necessary to validate some of the findings. It would also be of benefit to extend the study period, so that subtle changes over a greater time could be studied.

Keywords: MLT
MLT2018
Modulators of MHC class I-related protein 1-mediated antigen presentation

The monomorphic MHC class I-related protein 1 (MR1) presents bacterial metabolites to mucosal-associated invariant T (MAIT) cells, an innate-like subset of T lymphocytes. The known MAIT-activating MR1 ligands are intermediates of riboflavin synthesis, a pathway specific to certain fungi and bacteria and, thus, intrinsically non-self for humans. Here, a combination of hypothesis-generating and hypothesis-testing approaches was used to identify novel modulators of this non-classical antigen presentation pathway. In particular, a functional genetic screening technique based on insertional mutagenesis of the near-haploid human cell line HAP1 was employed to discover novel players in MR1 antigen presentation and trafficking. The most significant positive regulator of MR1 surface expression identified in this screen was β2-microglobulin, confirming its indispensable role in the surface translocation of MR1. A number of other putative regulators of MR1 trafficking were taken forward into a CRISPR/Cas9-based validation approach and the ER-localised transporter ATP13A1 was found to affect MR1-mediated antigen presentation by modulating the size of the intracellular pool of MR1. In addition, the role of the soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE) Sec22b in MR1-mediated antigen presentation was investigated as knock-down of Sec22b has previously been reported to control MHC class I-mediated cross-presentation. MR1 surface expression was reduced upon Sec22b knock-down and while the SNARE itself did not appear to play a role, RNA sequencing of a Sec22b deficient cell line revealed a number of potential regulators of MR1. Lastly, the capacity of cellular riboflavin transporters to mediate MR1 ligand import was investigated. Treatment with the riboflavin analogue lumiflavin resulted in decreased MR1 surface expression in various human cell lines by a mechanism that appeared to be independent of the inhibition of riboflavin import. Together, these data contribute to an increasing understanding of MR1-mediated antigen presentation, which is essential for harnessing the therapeutic potential of MAIT cells.

Keywords: Antigen Presentation
MAIT cells
MR1
Advisor: Cerundolo, V
Salio, M
Klenerman, P
An action research study of learning centred leadership in an American High School

This study examines the leadership practices of a number of leaders in an American High School. The school is currently engaged in a major change process with the introduction of three action plans which will have significant implications for its teaching and learning process.
An essential aim of the study was to provide an informed view of how leaders were responding to the challenges of these changes, and in particular, how their practices were impacting on staff learning. In doing so, it was hoped that findings would inform and support the future directions of leadership in the school.
Knowledge of the school, strongly suggested that leadership practices at the school are consistent with a developing model of leadership that may be defined as 'learning centred'. A learning centred leadership model, after Southworth (2003) was used as the analytical framework for the research. The principles and practices of this model were explored in relation to how the leaders at the school were 'leading learning' and developing as 'leaders of learning'.
This is an interpretative action research project. Through this process I sought to answer questions with regard to the school's developing leadership practices and how these were impacting on the teaching and learning process in the school. The action research required a collaborative working in a cyclic process. A range of data was collected and triangulation was used in its analysis.
My findings are indicative of broad based practice in the school, where leaders are engaged in leading learning in a purposeful collaborative culture, with developing and supporting one another's practice as the norm.
Evidence demonstrates also, that leaders are continuing to develop their practices as leaders of learning, and as such, my conclusions are, that learning centred leadership is continuing to develop at the school, in ways consistent with its principles and practices.

Keywords: MLT
MLT2016
The mechanism of action and physiological role of PLCζ at fertilisation

Activation of the egg by the sperm is a key developmental event that in mammals triggered by the sperm-induced calcium oscillations. This has been proposed to be caused by the sperm-factor phospholipase C isoform zeta (PLCζ), although this remained a matter of debate for nearly 15 years.
The first part of this thesis demonstrates the successful use of the novel CRISPR/Cas9 gene editing technology in targeting the coding sequence of PLCζ gene in mouse embryos that subsequently has led to the creation of the first mouse model lacking the functional expression of PLCζ.
The main part of the thesis investigates the phenotype of the produced homozygous knockout male mutants. Functional analysis showed no adverse effects from the mutation on spermatogenesis, and normal sperm functional parameters. Although PLCζ-null sperm failed to trigger Ca2+ oscillations following ICSI procedures, experiments involving in vitro fertilisation, or fertilisation in vivo by natural mating, revealed that live offspring can still be conceived, albeit at greatly reduced efficiency and after a significant time delay. These findings suggest a yet-to-be identified PLCζ-independent route in mammalian egg activation that is completely dependent on sperm-egg membranes interactions.
Lastly, oocytes fertilised in vivo and in vitro by PLCζ-null sperm were found to be polyspermic. The significant finding supports the role of PLCζ protein in generating the standard Ca2+ oscillations that which govern the cortical and zonal reactions and membrane establishment following fertilisation. Oolemmal membrane localisation of Juno proteins post fertilisation showed complete dependency on sperm-oocyte interaction. However, Juno shedding mechanism failed to block the polyspermic fertilisation caused by lacking the expression of PLCζ. Thus, contradicting the proposed roles of Juno in establishing oocyte membrane block to supernumerary fertilisation in mammals.

Keywords: Fertilisation
Polyspermy
Embryology
Gene editing
Calcium signalling
CRISPR/Cas9
Phospholipase C Zeta.
Alternative pathway in egg activation
Advisor: Parrington, J
Pelagiaria (Teleostei: Acanthomorpha) as a non-analogue adaptive radiation

Pelagiaria is an anatomically disparate clade of open-ocean fishes identified through molecular studies, comprising 16 families not previously united on the basis of morphology. It has been postulated that ecologically distinct lineages of Pelagiaria diverged rapidly early in the Paleogene. This differs from ‘model’ adaptive radiations like cichlid fishes and Anolis lizards in age and geographic scale, but corresponds closely to patterns in Cenozoic mammals, the group where the concept was first defined. Well-preserved material from the UK, Angola and other sites provides an opportunity to investigate the evolutionary history of Pelagiaria and test these hypotheses of adaptive radiation. I use micro computed tomography (μCT) to investigate key three-dimensionally preserved fossils belonging to groups now assigned to Pelagiaria, focussing on scombrids (tunas, mackerels) and trichiuroids (snake mackerels). I develop character sets for trichiuroids and scombrids, allowing placement of key fossils associated with these groups. I also use μCT to collect three-dimensional cranial landmark data from 68 extant species of Pelagiaria, representing 15/16 extant families and a quarter of living species. These phenotypic data are studied in combination with a time-calibrated molecular phylogeny, which I apply using multiple comparative approaches. Results indicate that Pelagiaria showed an initial, diffusive phase of phenotypic evolution in the early Paleogene, followed by constrained patterns of cranial change from the Eocene onward. This adds quantitative support to previous hypotheses of adaptive radiation in the group, and suggest Pelagiaria might represent a useful a new study system for investigating this key macroevolutionary concept.

Keywords: landanichthys
fossil fishes
morphology
pelagiaria
evolution
phylogenetics
eocoelopoma
trichiuridae
scombridae
gempylidae
Advisor: Friedman, M
Giles, S
Johanson, Z
New anion receptors for molecular recognition and organocatalysis

This thesis describes the investigation of anion binding molecules in application to molecular recognition and organocatalysis. A focus is made on exploring the properties of σ-hole interactions: halogen and chalcogen bonding which are scarcely studied in the context of anion sensing, especially in an aqueous environment.
Chapter 2 describes the preliminary design of a tetradentate XB anion receptor. This system is shown to be effective for anion complexation in organic solvent media, more so than the isostructural HB analogues. Fluorescent sensing and chiral discrimination capabilities are also demonstrated.
Chapter 3 discusses the water-soluble, preorganised XB and ChB anion receptors. This provides the first examples of charge-neutral, all-XB and all-ChB host molecules to be used for anion binding in water. In addition to the fundamental studies of anion coordination, applications in fluorescent and electrochemical anion sensing are shown.
Chapter 4 details the development of biomimetic transesterification catalysts that include an oxyanion hole function. The series of compounds is iterated towards high reactivity, arriving at highly effective catalysts with a modular, easily customised structure.

Keywords: chalcogen bonding
transesterification
anion sensing
molecular recognition
anion binding
anion recognition
halogen bonding
Advisor: Smith, M
Beer, P
Asymmetric syntheses of the pseudodistomin alkaloids

This thesis centres on asymmetric syntheses of the pseudodistomin alkaloids, initially targeting a member of the family that had yet to be subjected to laboratory synthesis, followed by the development and execution of a unified strategy for the synthesis of all of the known pseudodistomin alkaloids as well as non-natural analogues.
Chapter 1 presents a comprehensive and critical review of all literature reports relating to the isolation, structural elucidation and syntheses of the pseudodistomin alkaloids to date, culminating in the realisation of aims for this thesis.
Chapter 2 describes the first total asymmetric synthesis of pseudodistomin E, culminating in confirmation of the assigned absolute configuration and correlation with the 1H and 13C NMR spectroscopic data originally reported for the natural product in the isolation study.
Chapter 3 reviews the first-generation synthesis and details the evaluation of a range of model systems to facilitate the development of a unified strategy for the synthesis of the pseudodistomin alkaloids and non-natural analogues, culminating in an optimised proposed synthetic strategy.
Chapter 4 discusses the development and execution of a general strategy for the asymmetric syntheses of the pseudodistomin alkaloids, culminating in the total asymmetric syntheses of all of the known pseudodistomin alkaloids and a representative non-natural analogue.
Chapter 5 offers independent assignments of the relative and absolute configurations of the pseudodistomin alkaloids, followed by a comparison of spectroscopic data with literature reports, culminating in correlation with the data provided for the natural materials.
Chapter 6 contains full experimental procedures and characterisation data for all compounds synthesised in Chapters 2–4.

Advisor: Davies, S
Singly and co-doping of ZnO thin films by spray pyrolysis

Indium-based transparent conducting oxides (TCOs) are widely used in optoelectronic devices. An important goal of this project is to search for TCOs that have reduced In content or indeed no In. The cheap zinc-based TCOs are good candidates to replace expensive indium-based TCOs in applications. A co-doping protocol has been established using both Si and In to obtain films with both good optical and electrical properties. This co-doping strategy can dramatically reduce the cost of the expensive element In while maintaining better optoelectronic performances compared to singly doped ZnO thin films.
The spray pyrolysis technique is used to deposit TCO thin films, which is famous for its lower cost compared with physical deposition methods such as sputtering. I have studied the detailed properties of singly doped (Si or In) ZnO together with co-doped (Si and In together) ZnO thin films. I have also related their optoelectronic performances with structures, elemental compositions, and chemical environment to understand their properties in depth.
It is the first time co-doped ZnO thin films based on Si and In have been successfully synthesised with high optoelectronic performances. Therefore, it is a basis for further development in co-doping and material design. The total chemical composition of elements in the bulk of a TCO material has not been measured previously. Nevertheless, I have studied these to see the limitations or restrictions in doping, thus understanding how doping affects optoelectronic properties including metal-insulator transition. Our ultimate goal is to develop an applicable deposition method and find suitable TCO materials to meet application requirements on both the optoelectronic performance and cost.

Keywords: ZnO
Semiconductor
Thin Film
Materials
Grain Boundary
Spray Pyrolysis
Chemistry
Zinc Oxide
Transparent Conductive Oxide
Doping
TCO
Advisor: Edwards, P