VictorJuiz/thesis huggingface dataset:
Biophysical Studies of Oligonucleotides Containing Duplex Stabilising Modifications

Chemically modified DNA and RNA probes have been used in numerous diagnostic (e.g. fluorogenic PCR and in situ hybridisation) and therapeutic (e.g. exon-skipping and antisense) applications to increase duplex stability and facilitate mismatch discrimination. There is a constant need for well-studied modifications, and to this end X-pyrene was evaluated as a new cytosine analogue that combines enhanced π-stacking, hydrogen bonding and electrostatic interactions to greatly increase the stability of bulged DNA duplexes and DNA/RNA hybrid duplexes. X-pyrene is highly selective for guanine, and even more importantly duplex stability is reduced dramatically when X-pyrene or a neighbouring base is mismatched. NMR and fluorescence studies indicate that the pyrene moiety stacks within the DNA double helix. To enable easier access to this modification, a reductive amination labelling strategy was developed to produce pyrene-functionalised nucleobase analogues which allowed an easier synthesis of X-pyrene. Amino C6 dT was successfully functionalised with this methodology as well, obtaining the duplex stabilising mono- and di-labelled products. Additionally, a much simpler pyrene-modified thymidine monomer (U-pyrene) was selected for further studies. Single and multiple additions of U-pyrene were found to significantly increase the melting temperature of dsDNA without perturbing the B-DNA duplex, as shown by UV and CD spectroscopy. Interestingly, thermodynamic studies showed that four additions of U-pyrene increased the binding constant of a 14-mer oligonucleotide to its complementary strand 10000-fold when compared to the unmodified control. Two oligonucleotides containing a single addition of U-pyrene were also crystallised and their structures were studied by X-ray diffraction. To the author's knowledge these represent the first examples of X-ray crystal structures of a chemically modified pyrene oligonucleotide. They also proved to be of great interest as they highlight the capacity of U-pyrene to facilitate the production of interesting nanostructures.

Keywords: DNA
Nucleic Acids
RNA
Crystallography
Labelling of Oligonucleotides
Pyrene
Advisor: Brown, T
Surface modified polymers for controlled macroscopic functions

This thesis is concerned with the chemical modification of polymer surfaces to confer various functionalities for controlled macroscopic functions, and in particular, photochromic activity and drug delivery. In this collaboration project, the first two years spent in Oxford placed emphasis on the development of a versatile synthetic route for surface modification of polymers with proof of concept. The next two years were spent at the Singapore Institute of Manufacturing Technology (SIMTech) for translational research, which involved the application of the processes developed in Oxford for large area surface engineering, and testing of the surface modified polymers.
Different approaches to modify surface of polymer by chemical methods were investigated, and compared to analogous chemistry in solution. The best surface modification approach was then optimised to determine the most suitable system for translation. A library of polymers with variation in end group, and with expansion of substrate scope, was characterised in detail for chemical and macroscopic properties. In particular, drug delivery properties were investigated using hole-plate bioassays and HPLC-MS methods, and it was found that the antibiotic, Penicillin V, was still active after being loaded onto the polymer scaffolds, with surface modified polymers binding and releasing more drug than the corresponding controls. Incorporation of the spiropyran units on to the polymer surfaces also demonstrated good photochromic activities.
With the transfer of the technology to SIMTech, surface modification processes were re-designed and tested on a variety of 2D engineering polymers. Macroscopic function of photochromic activity, change in surface wettability and drug delivery were investigated.
Lastly, a surprising finding on adhesion function generated from the diaryldiazo compound is disclosed, with preliminary results of lap-shear and t-peel tests showing high levels of adhesion. Moreover, when tested with sol-gel coatings, enhanced adhesion of the coating was found.

Advisor: Moloney, M
Cyclic alkenylsiloxanes: synthesis and application towards incednam

This thesis explores the use of cyclic alkenylsiloxanes in Hiyama cross-coupling reactions for the stereospecific construction of the Z-pentaenyl system of incednam, the aglycon of incednine. The early chapters continue the investigation of the previously developed C6-C13 lynchpin cyclic diethyl alkenylsiloxane, accessed by controlled semi-hydrogenation of alkynylsiloxane. Later chapters discuss the development of a novel strategy to access the more reactive cyclic dimethyl alkenylsiloxanes and their application towards the synthesis of incednam.

Advisor: Anderson, E
Conceptualizing religion and spirituality in secular schools: a qualitative study of Alberta schooling

Over most of the 20th Century, many educational systems around the world became increasingly secular, notably with lessening involvement of religious institutions. However, what it means to offer secular education to an increasingly diverse student population is emerging as a contemporary international educational issue. The face of immigration, the rights of Aboriginals, and increasingly diverse and individual forms of religiosity and spirituality have implications for secular education today. This qualitative study of Alberta schooling provides an example of a setting that underwent a high degree of secularization in the 1960's-1980's. A litigious but interpretive boundary exists for the extent educationists were to engage students in thinking about religion and spirituality. Yet, teachers operated with a high degree of autonomy. With these contextual factors as a backdrop, this study explored how a hierarchical sample of Alberta policy-makers, administrators, and teachers conceptualized religion and spirituality for secular secondary schools. Results show that Alberta Education conceptualized space for the conservative religious and Aboriginal communities, but not mainstream students. The students operated in a 'leave your faith at the door' secular model, curriculum was rationalized, and the function of schooling was perceived as preparing students for work. Findings show that principals and teachers challenged the lack of space for mainstream students to engage in the concepts of religion and spirituality. They argued the secular model disadvantaged mainstream students in exercising their right to religious freedom and developing religious literacy and sensitivity skills and it also prevented non-religious students from gaining access to religious/spiritual concepts and tools to facilitate wellbeing and resiliency.

Keywords: de-colonization
spirituality
education
Structural and biochemical characterisation of bacterial metallo-β-lactamases

One of the most prominent ways by which bacteria develop resistance to the widely used β-lactam antibiotics is by production of β-lactamases. Metallo-β-lactamases (MBLs) in particular pose an increasing public health risk due to the wide dissemination and broad substrate profile. The successful development of novel MBL inhibitors for clinical use is also dependent on sufficient understanding of the structural and functional properties of the target MBLs. From a medicinal chemistry point of view, the combination of biological diversity and structural similarity of MBLs presents a rather challenging task for the development of selective small molecules for inhibitors for bacterial MBLs. The progress made in this quest thus far is discussed at length in the introduction (Chapter 1).
Robust and affordable high throughput screening platforms are indispensable in drug development. Chapter 2 of the thesis describes the identification of a novel cephalosporinbased substrates, CLS405, for MBL activity and inhibition assays. The CLS405-based assay is used in an exemplary screening of potential MBL inhibitors, resulting in the identification of N-hydroxythiazoles as novel MBL inhibitor scaffolds. An umbelliferone-derived cephalosporin substrate (FC-5) is also investigated for application in screening of MBL activity in vivo.
Clinically useful MBL inhibitors must have a sufficient breadth of selectivity against multiple variants MBLs; this is particularly challenging due to the rapid MBL evolution. In Chapters 3 and 4, comparative studies of the activity, stability and structural properties of some of the clinically reported variants of the New Delhi metallo-β-lactamases (NDMs) are described. Nominal differences are noted in the kinetic parameters of the recombinant proteins, except for the apparent substrate inhibition observed with nitrocefin for variants containing the M154L substitution. Further investigations reveal significant differences in thermal stability of the NDM variants with the double mutants (NDM-5, NDM-7, NDM-8 and NDM-12) being the most stable variants, suggesting that protein stability may be a driver of MBL evolution.
The Verona imipenemase metallo-β-lactamases (VIM) enzymes are among the most widely distributed MBLs with &GT;40 variants reported (Chapter 5). Comparative studies on the biochemical and biophysical properties were carried out for five VIM variants: VIM-1, VIM- 2, VIM-4, VIM-5 and VIM-38. Clear differences in the thermal stabilities of the variants are observed, despite their similar β-lactamase activities, as previously shown for NDM variants. Interestingly, the variants show marked differences in the inhibition profile, with isoquionolone-based inhibitors selectively inhibiting VIM-5 and VIM-38 compared to VIM-1 and VIM-2.
Overall, the work supports the proposal that protein stability may be an important factor in MBL evolution. Crucially, the study highlights the importance of screening MBL variants during inhibitor development programs.

Advisor: Schofield, C
A 2'-alkynylnucleotide strategy for site-directed spin labelling of DNA

This thesis describes the synthesis of derivatives of 2'-ethynyl-2'-deoxynucleosides, and their conversion into phosphoramidite building blocks for DNA synthesis. Herein is also outlined the preparation of azide-bearing nitroxyl radicals. After site-selective incorporation of 2'-alkynylnucleosides into DNA using a standard solid-supported phosphoramidite protocol, the modified oligonucleotides were spin labelled with the azide-bearing nitroxyl spin labels via the Cu(I)-catalysed azide-alkyne [3+2] Huisgen cycloaddition (CuAAC or 'click' reaction). The destabilising effect of the spin labelling was determined by UV denaturation studies and circular dichroism, and the spin labelled DNA was investigated by EPR spectroscopy. It was found that this novel site-directed spin labelling strategy afforded conformationally restricted systems, and that the structure of the spin label exerts a significant influence on the results.

Keywords: chemistry
nucleic acids
nitroxyl
EPR
nitroxide
spin labelling
DNA
organic chemistry
Advisor: Anderson, E
Differentiation and magmatism on the HED parent body

The Howardite-Eucrite-Diogenite (HED) meteorites are a suite of basalts, cumulates and breccias which originate from one di↵erentiated parent body, and are linked to the asteroid Vesta. The HEDs are petrologically diverse with a range of major, minor and trace element compositions. Early crystallisation ages are recorded and so the HEDs provide us with a unique snapshot into the early solar system. The aim of this thesis is to investigate the petrogenesis of the eucrites and diogenites by addressing two questions. What is the Bulk Silicate Vesta (BSV) composition? What differentiation and magmatic processes have occurred? Putative BSV compositions were derived from the geochemistry of the meteorites and geophysical observations of Vesta. Series of one-atmosphere experiments and thermodynamic models investigated the BSV phase relations. Olivine crystallised at &Tilde;1625 °C, followed by orthopyroxene at &Tilde;1350 °C and feldspar at &Tilde;1125 °C. Low-Ca pyroxene-melt partition coefficients for the minor and trace elements were measured. The compatibility of the REEs and HFSEs in low- Ca pyroxene increased by a factor of three, as temperature decreased from 1300-1125 °C and calcium content increased from Wo0.5-Wo8. These partition coefficients were combined with the observed phase relations to perform geochemical trace element calculations of differentiation and magmatic processes. My results suggest that BSV had an Mg#(100&ast;(Mg/(Mg+Fe2+)) between 75-80, &GT;43 wt. % SiO2, 2.5× CI refractory lithophile elements, 0.5 wt. % MnO and 0.75 wt. % Cr2O3. A three stage model for Vesta's evolution is suggested. Firstly, extensive if not global partial melting of BSV. Then, equilibrium crystallisation of the mantle and fractional crystallisation of mantle-derived melts produced diogenitic cumulates and eucrite liquids, accounting for the range in major and trace element abundances. The re-equilibration of trapped melt in cumulates is also thought to have occurred. Finally, crustal anatexis produced the range in trace element fractionations seen.

Keywords: Experimental Petrology
HED
Asteroid
Petrology
Advisor: Wood, B
The wellbeing of adolescents during the primary-secondary school transition

The transition to secondary school can represent a significant life event for many adolescents and can adversely affect their psychological adjustment and wellbeing. Little is known about how adjustment to this transition can be facilitated for young people. The review paper critically evaluated the evidence-base for school transition programmes that target pupil's mental wellbeing. A keyword search of abstract databases was conducted and 20 studies were evaluated. The majority of studies could not conclude that their intervention improved mental wellbeing to a statistically significant level, and numerous methodological limitations weaken the existing evidence-base. However, the most promising areas of research pertain to intervening with the parents and teachers of adolescents experiencing school transition. Further research should investigate this further.
The empirical paper employed a qualitative methodology to examine how adolescents make sense of and create meaning from their experience of going to boarding school, and to explore what can be done to facilitate this adjustment. Ten female and male adolescents were interviewed in their second year of attending boarding school. The interviews, analysed using lnterpretative Phenomenological Analysis, yielded three superordinate themes: 1) 'Home is where the heart is', which captures adolescents experiences of homesickness, the stronger relationships formed with their family, and the development of new attachment figures with their house matron and peers, 2) 'Living in a bubble', which reflects a feeling of being constrained at boarding school and an awareness of it being a hierarchical environment, and 3) 'Gaining familiarity with the place and just being me' as adolescents appeared to positively adjust over time. Results are discussed in terms of attachment, coping and adjustment theories and models of psychosocial development. Clinical and organisational implications for professionals working in boarding schools, as well as suggestions for future research arc discussed.

Keywords: wellbeing
adolescents
primary-secondary
school
transition
Advisor: Canham, L
Investigating continental deformation using PS InSAR

I use Persistant Scatterer Interferometric Synthetic Aperture Radar (PS InSAR) to measure interseismic strain accumulation across the Kunlun Fault, observe and model the postseismic signal associated with the Mw 7.8 2001 Kokoxili earthquake, and map strain in Western Turkey. PS InSAR selects pixels whose echo is dominated by a single scatterer in a series of interferograms (Hooper et al., 2004). To date most tectonic signals measured with InSAR have used Differential InSAR (DifSAR) rather than PS InSAR. I compare PS InSAR and DifSAR across the Kunlun Fault to obtain equivalent slip rates of 9.5 mm/yr and 10.5 mm/yr, respectively. I show that regions which are incoherent in DifSAR, are coherent using PS InSAR.
Knowledge of slip rates along faults has important implication in terms of seismic hazard and is key to our understanding of the mechanical behaviour of the crust and mantle; for example they can be used to test the prediction of various models (Van Der Woerd et al., 2002). I show slip rate variability on the eastern Kunlun Fault in Tibet with rates reducing eastwards by upwards of 9 mm/yr over a region of upwards of 80 km to a slip rate of 2.4 mm/yr towards the fault tip.
To date both afterslip and viscoelastic relaxation have been proposed as plausible mechanisms (Wen et al., 2012) for the Kokoxili earthquake. I model afterslip across the Kunlun Pass Fault using rate and state friction to create a series of models with various preseismic slip rates and frictional parameters. I then perform a parameter space search to find the best fitting models to ENVISAT data from 2003-2010. I compare the best fit afterslip model with viscoelastic relaxation to show that viscoelastic relaxation gives a better fit to the data.
A number of studies have looked at interseismic strain accumulation across the North Anatolian and East Anatolian faults, e.g. Walters et al. (2014); Yamasaki et al. (2013), but relatively little work has been done on a fault scale across the grabens in Western Turkey. GPS data for the region shows fairly uniform strain (Aktug et al., 2009). I compare PS InSAR with GPS data to see whether the spatial resolution of the GPS is too low to resolve strain localisation. I then combine the two data sets to generate velocity and strain rate maps, which can be used for seismic hazard assessment, and to distinguish between different dynamic models of continental deformation.

Advisor: Parsons, B
Wright, T
Holley, R
Structural and functional characterization of reconstituted alpha − amino − 3 − hydroxy − 5 − methyl − 4 − isoxazole propionic acid receptors

This thesis describes a novel reconstitution of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs) for the purposes of structural characterization by atomic force microscopy (AFM) and functional characterization by electrical recordings of lipid bilayers.
AMPARs are glutamate gated ion channels, ubiquitous in the vertebrate central nervous system where they mediate fast excitatory neurotransmission. In a healthy brain, AMPARs are involved in memory formation and learning and their dysfunction has been related to numerous neurological disorders such as Alzheimer's disease, epilepsy, schizophrenia and many others.
AMPARs were reconstituted at high and low densities. Densely reconstituted samples contained &GT;100 receptors per μm2, a value comparable to the AMPAR density at synapses. This allowed, for the first time, the imaging of full length tetrameric AMPARs in native-like conditions and with clearly assigned domains: the extracellular domains extended 14 nm above the membrane in agreement with electron microscopy (EM) and X-ray crystallography data. Lipid-protein interactions were studied in samples with low protein density with the receptors showing preference for lipids in the liquid crystalline phase. The activity of the reconstituted receptors was confirmed through single-channel recordings.
This is the first case in which an AMPAR has been reconstituted and given (a) single-channel recordings with (b) physiologically plausible conductance levels and (c) pharmacological and no-protein controls and (d) structure. As a result, previously reported biochemistry and EM are now for the first time available in concert with AFM and single-channel recordings for a purified AMPAR of known composition.

Keywords: Glutamate receptors
reconstitution
atomic force microscopy
bilayer recordings
Advisor: Ryan, JF
Authentication protocols in pervasive computing

The popularity of personal computing devices (e.g. smart cards) exposes users to risks, notably identity theft, and creates new requirements for secure communication. A recently proposed approach to creating secure communication is to use human trust and human interactions. These approaches potentially eliminate the need for passwords as in Bluetooth, shared secrets or trusted parties, which are often too complex and expensive to use in portable devices.
In this new technology, handheld devices exchange data (e.g. payment, heart rates or public keys) over some medium (e.g. WiFi) and then display a short and non-secret digest of the protocol's run that the devices' human owners manually compare to ensure they agree on the same data, i.e. human interactions are used to prevent fraud.
In this thesis, we present several new protocols of this type which are designed to optimise the work required of humans to achieve a given level of security. We discover that the design of these protocols is influenced by several principles, including the ideas of commitment without knowledge and separation of security concerns, where random and cryptographic attacks should be tackled separately.
Underpinning the technology is a new cryptographic function, termed a keyed digest function, which produces a short number for humans to compare. This is similar to the notion of a universal hash function, but its output length is shorter (e.g. 16 bits). Hence, it should be faster to compute. We propose several digest constructions using Toeplitz matrices, integer multiplication and pseudorandom numbers. The application of digest functions leads us to develop more efficient alternatives to standard digital signatures.
Our protocol security analysis leads to a new bound on the key length for an almost universal hash function, which can be derived by the pigeon-hole principle. The new bound turns out to be tighter than another similar bound derived from the combination of the Singleton bound in coding theory and an equivalence between error-correcting codes and almost universal hash functions.

Advisor: Roscoe, A