VictorJuiz/thesis huggingface dataset:
Role of mutual information for predicting contact residues in proteins
Keywords: protein complexes
mutual information
multiple sequence alignment
proteins
contact residues
correlated mutations

Mutual Information (MI) based methods are used to predict contact residues within proteins and between interacting proteins. There have been many high impact papers citing the successful use of MI for determining contact residues in a particular protein of interest, or in certain types of proteins, such as homotrimers. In this dissertation we have carried out a systematic study to assess if this popularly employed contact prediction tool is useful on a global scale.
After testing original MI and leading MI based methods on large, cross-species datasets we found that in general the performance of these methods for predicting contact residues both within (intra-protein) and between proteins (inter-protein) is weak. We observe that all MI variants have a bias towards surface residues, and therefore predict surface residues instead of contact residues. This finding is in contrast to the relatively good performance of i-Patch (Hamer et al. [2010]), a statistical scoring tool for inter-protein contact prediction. i-Patch uses as input surface residues only, groups amino acids by physiochemical properties, and assumes the existence of patches of contact residues on interacting proteins. We examine whether using these ideas would improve the performance of MI.
Since inter-protein contact residues are only on the surface of each protein, to disentangle surface from contact prediction we filtered out the confounding buried residues. We observed that considering surface residues only does indeed improve the interprotein contact prediction ability of all tested MI methods. We examined a specific "successful" case study in the literature and demonstrated that here, even when considering surface residues only, the most accurate MI based inter-protein contact predictor,MIc, performs no better than random. We have developed two novel MI variants; the first groups amino acids by their physiochemical properties, and the second considers patches of residues on the interacting proteins. In our analyses these new variants highlight the delicate trade-off between signal and noise that must be achieved when using MI for inter-protein contact prediction.
The input for all tested MI methods is a multiple sequence alignment of homologous proteins. In a further attempt to understand why the MI methods perform poorly, we have investigated the influence of gaps in the alignment on intra-protein contact prediction. Our results suggest that depending on the evaluation criteria and the alignment construction algorithm employed, a gap cutoff of around 10% would maximise the performance of MI methods, whereas the popularly employed 0% gap cutoff may lead to predictions that are no better than random guesses.
Based on the insight we have gained through our analyses, we end this dissertation by identifying a number of ways in which the contact residue prediction ability of MI variants may be improved, including direct coupling analysis.
Single photon sources in the infrared
Keywords: quantum dots
carbon nanotubes
single photon sources

This thesis reports the study of single photon sources that emit one infrared wavelength photon at a time, creating cavity quantum electrodynamical effects for applications such as quantum information processing. This work considers two major single photon sources: a) InAs single quantum dots and b) single carbon nanotubes, which both emit in the infrared range.
Photonic crystal slabs and photonic crystal waveguides are served as distinctive passive devices with manipulated photonic band-gaps to control the propagating light. A simulation of leaky modes of two-dimensional photonic crystal slabs is introduced to constrain model parameters in the device design. Fullerenes are used as fluorescent material to achieve resonance of a leaky mode with excitation 1492 nm and emission at 1519 nm and to see enhancement of the PL. We include novel characterization techniques and PL measurements to show sharp emission peaks from single quantum dots and successfully couple them to micro-cavities. The strong coupling effect is observed and is amongst the best examples of cavity-dot structures achieved to date.
Single-walled carbon nanotubes have shown anti-bunched light emission, thus we systematically study them as another possible candidate of single photon sources. PLE spectra show clear evidence of the existence of excited states, and time evolution measurements reveal the disorder induced diffusion, which separate the tubes into a series of quantum dots. These strongly confined states are concluded as the origin of the possibility that single-walled carbon nanotubes are single photon sources.
Syncrip regulates mRNA localisation and translation at the drosophila neuromuscular junction
Keywords: translation
mRNA localization
neuromuscular junction
syncrip
drosophila

Evidence in different systems suggests that local translation is involved in synaptic plasticity in both neuron and muscle, but the mechanism by which this occurs is still poorly understood. The mRNA-binding protein Syncrip is conserved from fly to mammals and is thought to be involved in localized translation in both oocytes and neurons. Previous work has shown that Syncrip associates with mRNAs encoding key synaptic proteins at the Drosophila larval neuromuscular junction. Here I show that Syncrip is necessary for the structure and function of the neuromuscular junction. First, the loss of Syncrip leads to overgrowth of the neuromuscular junction. Second, Syncrip is required for proper expression of the Ca2+-sensor Synaptotagmin1 at the presynapse, and loss of Syncrip causes a decrease in vesicle release probability. Third, while it was not possible to measure mRNA distribution in neurons, Syncrip mutants, like other perturbations in synaptic plasticity, correlate with changes in mRNA localization in muscle. Fourth, the overexpression and loss of Syncrip function suggest that the nuclear and nucleolar trafficking of the eukaryotic translation initiation factor eIF4E may be important to regulating synaptic morphology. These data suggest that Syncrip is involved in mRNA localization and translation in synaptic plasticity.
Novel di-branched monosaccharides and imino sugars
Keywords: sugars
glucose
diabetes
carbohydrate
glycogen phosphorylase
imino
branched

Branched chain sugars display a varied and valuable range of biological activities. This thesis concerns the synthesis of 3,5-di-C-methyl-D-glucose, a potential inhibitor of glycogen phosphorylase (GP), and therefore a proposed therapeutic agent for type 2 diabetes. Chapter 1 looks at the occurrence of branched sugars in the natural world and current therapies for type 2 diabetes. Inhibition of GP is explored, and the molecular modelling studies which led to the design of the project target. Chapter 1 also looks into the development of new foodstuffs, the chemistry and biochemistry of imino sugars and branched hydroxy proline analogues.
In Chapter 2, a range of different approaches to 3,5-di-C-methyl-D-glucose are investigated. Most of the initial investigations were carried out on the L-enantiomer, a readily available test system deriving from 2-C-methyl-D-ribono lactone. 2-C-Methyl-D-ribono lactone is synthesised rapidly from D-glucose in a one-pot reaction; as the key starting material for this work, the scalability of this process was investigated. One of the attempted syntheses of di-C-methyl glucose lead to the development of a route towards 3,5-di-C-methyl fructose, a novel dibranched ketose sugar. It was envisaged that through an enzymatic transformation, it might be possible to produce 3,5-di-C-methyl glucose stereoselectively. Synthesis of both enantiomers of 3,5-di-C-methyl glucose and mannose are reported, alongside results of GPb inhibition studies. Analysis of the preferred ring size of a range of di-C-methyl branched sugars and sugar lactones generated in this work is also presented.
Chapter 3 explores the chemistry of 2,4-di-C-methyl-L-arabinono lactone, a key intermediate in the synthesis of 3,5-di-C-methyl-L-glucose. From this lactone a novel deoxy sugar, 2-deoxy-2,4-di-C-methyl-L-arabinono lactone, was generated. Routes towards a selection of imino sugars were explored, resulting in the synthesis of a methyl branched isofagomine analogue. A substituted aziridine was synthesised, from which a route to a di-C-methyl branched piperidine was proposed, and a pyrrolidine. Also presented is a synthesis of a dihydroxy di-C-methyl branched proline analogue.
Detailed NMR analysis of several of the sugars generated in this work was carried out by Dr M. Wormald, of the University of Oxford Biochemistry department. The results of these investigations are presented in the Appendix.
Throughout this work, the presence of quaternary centres has posed a problem with the assignment of relative configuration. As a result, this work has been greatly supported by X-ray crystallography, and the structures shown herein were wholly generated by me. Several other crystals were run during the course of this work, not all pertaining to these projects, and are provided in the CD appendix.
Knowledge by way of prophecy
Keywords: Timothy Williamson
Moses Maimonides
Knowledge
Prophecy
Guide of the Perplexed

This thesis investigates whether beliefs acquired by way of prophecy are safe. By ‘prophecy’ I have in mind the presentation of the prophetic method as found in the Guide of the Perplexed, which was Moses Maimonides’ philosophical masterpiece. And by ‘safe’ I have in mind the work by Timothy Williamson on the safety condition for knowledge. Both authors have proven to be dominant forces on these respective topics. The significance of this investigation derives from the centrality of prophecy to the three monotheistic religions. My main goal in this thesis is to identify those safety risks associated with the prophetic method. In this manner I aim to undermine any presumption in favor of prophetic beliefs as a whole being safe. Importantly, this general conclusion does not entail of a specific prophetic belief p that p is unsafe. Additionally, the scope of these results is restricted to the model of prophecy found in the Guide.
The thesis begins with a critical elucidation of Williamson’s extensive work on the safety condition for knowledge. Particular attention is paid to those issues related to method individuation and Williamson’s cumulative conception of bases. Matters concerning these two topics inform the reading of Maimonides on prophecy found in the second chapter. In particular, I argue that Maimonides should be read as defending a cumulative conception of prophecy. As I emphasize several times during the chapter, the epistemology of prophecy cannot be reduced to the epistemology of testimony since prophecy for Maimonides does not involve the transfer of a proposition from God to the prophet. The third chapter is devoted to identifying those elements of the prophetic method that involve room for error. I argue that while all belief-forming methods in a fallibilist epistemology contain room for error, some are riskier than others. Prophecy should be considered one of the riskier sort. The fourth and final chapter shifts attention to non-standard semantics for ‘knows,’ David Lewis’s in particular. I argue that the interaction between such semantics and the laws governing prophecy in Jewish law is problematic. In particular, I demonstrate that such semantics destabilize the prophetic phenomenon. As such, we must either choose invariantism and gain stability, or choose non-standard semantics for ‘knows’ and live with this lack of stability.
The influence of selected flavonoids on the survival of retinal ganglion cells subjected to different types of oxidative stress
Keywords: retinal ganglion cells
Flavonoids
glaucoma
neuroprotection

The general aim of the thesis was to deduce whether selected naturally occurring flavonoids (genistein, epicatechin gallate (EC), epigallocatechin gallate (EGCG), baicalin) attenuate various secondary insults that may cause death of ganglion cells in primary open angle glaucoma (POAG).
An ischemic insult to the rat retina significantly causes the inner retina to degenerate indexed by changes of various antigens, proteins and mRNAs located to amacrine and ganglion cells. These changes are blunted in animals treated with genistein as has been shown for ECGC.
Studies conducted on cells (RGC-5 cells) in culture showed that hydrogen peroxide, L-buthionine sulfoximine (BSO)/glutamate and serum deprivation (mimicking oxidative stress), rotenone, sodium azide (affecting mitochondria function in specific ways) and light (where the mitochondria are generally affected) all generated reactive oxygen species and caused death of RGC-5 cells. EGCG was able to attenuate cell death caused by hydrogen peroxide, sodium azide and rotenone. Only EC was able to attenuate BSO/glutamate-induced cell death, in addition to cell death caused by hydrogen peroxide and rotenone. Genistein had no positive effect on cell death in experiments carried out on RGC-5 cells.
Exposure of RGC-5 cells to flavonoids showed that EC and EGCG increased the mRNA expression of endogenous antioxidants such as HO-1 (heme oxygenase 1) and Nrf-2 (nuclear erythroid factor-2-related factor 2). Light insult, rotenone and sodium azide activate the p38 (protein kinase 38) pathway, while only light and rotenone activate the JNK (c-Jun amino-terminal kinase) pathway. Serum deprivation affects mitochondrial apoptotic proteins causing an increase in the ratio of Bax/Bcl2 (Bax: Bcl-2-associated X protein; Bcl-2: B-cell lymphoma 2). An insult of light to RGC-5 cells, unlike that induced by sodium azide, is inhibited by necrostatin-1 and causes an activation of AIF (apoptosis-inducing factor) with alpha-fodrin being unaffected. These studies suggest that ganglion cell death caused by insults as may occur in POAG involves various cellular signaling pathways. The selected flavonoids have diverse actions in increasing cellular defense mechanisms, and in negating the effects of ischemia and specific types of oxidative stress. The results argue for the possible use of flavonoids in the treatment of POAG to slow down ganglion cell death.
Design and synthesis of myo-inositol (1,4,5)-trisphosphate receptor antagonists
Keywords: Calcium release
antagonist
inositol
inositol trisphosphates
IP3

<p>Well-regulated Ca2+ signalling is essential for every living organism, and disruption of this signalling can lead to diseases including heart failure, neurological disorders and diabetes. Intracellular Ca2+ levels are regulated by influx of extracellular Ca2+ through channels located in the cell membrane. In addition, release of Ca2+ from intracellular stores also plays an important role in controlling intracellular Ca2+ concentration. Of the three types of intracellular Ca2+ stores that have been characterised those with D-myo-Inositol 1,4,5 trisphosphate receptors (InsP3 Rs) showed a close relationship with cell proliferation. Hence, selective blockage of InsP3 Rs will allow better understanding of Ca2+ signalling and might also unveil novel treatment for cancers, in the long term. There were no selective InsP3 Rs antagonists known at the start of these studies. Based on the crystal structure of InsP3 Rs bound to InsP3 and SAR studies of InsP3, we designed and tested several InsP3 analogues. Compound 15, 16 and 23 acted as InsP3 R antagonists, though their selectivity for InsP3 Rs was not completely determined. Furthermore, we also attempted to improve the potency of 16 via substitution at the 1-postion phosphate. By considering the interaction formed between adenophosphostins and InsP3 Rs compounds (53-55) were designed and synthesised.</p> <p>In addition, analogues of compound 92, selected from an in silico screen, have led to the discovery of another novel scaffold that acts as an InsP3 R antagonist.</p>
Arginine methylation on E2F1
Keywords: E2F1
PTM
PRMT
arginine methylation

E2F1 is a transcription factor which paradoxically has major influence on both apoptosis and cell cycle progression. One of the most important questions in E2F1 biology therefore is the mechanism underlying regulation of these opposing physiological outcomes.
Post-translational modifications (PTM) provide proteins with an additional layer of complexity, potentially altering interactions with partner DNA and protein. The importance of arginine methylation has recently been implicated in modulating the activity of the tumour suppression pathway proteins, p53 and E2F1. Previous studies have established that the methyltransferase, PRMT5, is responsible for the symmetrical dimethylation of E2F1, which inhibits its pro-apoptotic activity.
In this thesis, E2F1 was found to be a substrate of PRMT1, which catalysed asymmetrical dimethylation of E2F1 at arginine 109. In addition, a positive correlation was found between the percentage of apoptotic cells and levels of PRMT1. Conversely, an increase in cancer cell colony formation was shown when the site of PRMT1 methylation on E2F1 was changed from arginine to lysine at position 109. These findings suggested a growth inhibition effect by PRMT1 methylation on E2F1.
At the transcriptional level, depletion of PRMT1 increased E2F1 binding to the promoter region of Cdc6, a cell cycle regulator, and decreased binding to the promoter region of Apaf1, which has a pro- apoptotic role. Genome-wide ChIP-sequencing technology was undertaken and results further clarified that the depletion of PRMT1 preferably enriched E2F1 binding to promoters of positive regulators of cell proliferation and promoters of the cell cycle.
Collectively, the findings of this thesis suggested that the opposing roles E2F1 demonstrated in promoting both cell proliferation and apoptosis was due to different types of arginine methylation which trigger E2F1 binding to different promoters.
Lastly, arginine methylation was shown to influence protein-protein interactions. PRMT5 induction resulted in the identification by mass spectrometry of β-catenin as an E2F1 interacting partner. As the Wnt/β-catenin signalling pathway is broadly recognised as having pro- cell proliferation activity, this finding is consistent with previous reports that suggest the oncogenic role PRMT5 methylation has on E2F1.
The branching fraction and CP asymmetry of B±→Ψπ± and B±→π±μ+μ− decays
Keywords: CP violation
flavour physics
LHCb
rare decays

Two analyses are performed using data collected by the LHCb experiment during 2011. Both consider decays of charged B mesons reconstructed in the π±μ+μ− final state. Decays involving dimuons provide an experimentally clean signature, even in the high-background environment of the √s = 7 TeV proton-proton collisions at the LHC. The first analysis measures the CP asymmetry of B±→Ψπ± decays using 0.37 fb-1 of data, where the dimuon decays of two resonances are considered, J/ψ→μ+μ− and ψ(2S)→μ+μ−. The branching fraction is measured relative to the Cabibbo favoured B±→ΨK± mode. The second analysis uses 1 fb-1 of data to make the first observation of the non-resonant B±→π±μ+μ− decay. The branching fraction is measured relative to that of B±→K±μ+μ−, and measurements of the CP asymmetry and the ratio of CKM matrix elements Vtd/Vts are obtained.
The branching fractions of the decays of interest are found to be
B(B±→J/ψ π±) = (3.88 ± 0.11 ± 0.15) x 10-5, B(B±→ψ(2S)π±) = (2.52 ± 0.26 ± 0.15) x 10-5 and B(B±→π±μ+μ−) = (2.48 + 0.57 −0.52 ± 0.17) x 10-8,
where the first uncertainty is related to the statistical size of the sample and the second quantifies systematic effects. The measured CP asymmetries in these modes are
A_CP^(J/ψπ) = 0.005 ± 0.027 ± 0.011, A_CP (ψ(2S)π) = 0.048 ± 0.090 ± 0.011 and A_CP (μμπ) = -0.045 ± 0.220 ± 0.066,
with no evidence of direct CP violation seen. The ratio of matrix elements is measured as
Vtd/Vts = 0.274 + 0.031 − 0.028 ± 0.008, which is in agreement with previous results.
How much substantive protection should investment treaties provide to foreign investment?
Keywords: indirect expropriation
law and economics
fair and equitable treatment
foreign investment
investment treaties

This thesis contributes to academic debate about the question: how much substantive protection should investment treaties (IITs) provide to foreign investment? Chapters 5 and 6 argue that arbitral tribunals have interpreted fair and equitable treatment and indirect expropriation provisions of existing IITs in several different ways. Each of these interpretations is sketched as a model level of protection that could be explicitly adopted by states in the future, either through inclusion in new IITs, or through amendment to existing IITs. In this way, the thesis defines a range of prospective options available to states concerning the level of protection to provide to foreign investment through IITs. The thesis evaluates the relative desirability of these different levels of protection.
The thesis argues that different levels of protection should be evaluated according to their likely consequences. The thesis develops a framework for inferring and understanding the likely consequences of adopting different levels of protection. The framework proposes that the consequences of a given level of protection can be understood in terms of its likely effect on: economic efficiency; the distribution of economic costs and benefits; flows of foreign direct investment into host states; the realisation of human rights and environmental conservation in host states; and respect for the rule of law in host states. Within this framework, the thesis provides an assessment and synthesis of existing empirical evidence and explanatory theory so far as they relate to the consequences of IIT protections. It also specifies the normative criteria by which these consequences should be evaluated. Through the application of this framework, the thesis concludes that lower levels of protection of foreign investment are, in general, likely to be more desirable than higher levels of protection.