VictorJuiz/thesis huggingface dataset:
Modification and application of glycosidases to create homogeneous glycoconjugates

In the post-genomic era, recognition of the importance of sugars is increasing in biological research. For the precise analysis of their functions, homogeneous materials are required. Chemical synthesis is a powerful tool for preparation of homogeneous oligosaccharides and glycoconjugates. Glycosidases are potent catalysts for this purpose because they realize high stereo- and regio- selectivities under conditions benign to biomolecules without repetitive protection/deprotection procedures.
A glycosynthase is an aritificial enzyme which is derived from a glycosidase and is devised for glycosylation reaction. To suppress the mechanistically inherent oligomerization side reaction of this class of biocatalysts, a glycosidase with plastic substrate recognition was engineered to afford the first α-mannosynthase. This novel biocatalyst showed low occurrence of oligomerized products as designed and was applied to prepare a wide range of oligosaccharides.
Glycosidases are also valuable tools for glycan engineering of glycoconjugates, which is a pivotal issue in the development of pharmaceutical agents, including immunoglobulin G (IgG)-based drugs. EndoS, an endo-β-N-acetylglucosaminidase from Streptococcus pyogenes, natively cleaves N-glycans on IgG specifically. When the latent glycosylation activity of this enzyme was applied, the N-glycan remodelling of full-length IgG was successfully achieved for the first time and a highly pure glycoform was obtained using the chemically synthesized oxazoline tetrasaccharide as glycosyl donor. This biocatalytic reaction allows development of a novel type of antibody-drug conjugates (ADCs) in which drug molecules are linked to N-glycans site-specifically. For this purpose, glycans with bioorthogonal reaction handles were synthesized and conjugated to IgG. A model reaction using a dye compound as reaction partner worked successfully and the synthetic method for this newly designed ADC was validated.
Glycan trimming of glycoproteins expressed from Pichia pastoris was performed using exoglycosidases to derive homogeneous glycoform. Jack Bean α-mannosidase (JBM) trimmed native N-glycans down to the core trisaccharide structure but some of the glycoforms were discovered to be resistant to the JBM activity. Enzymatic analyses using exoglycosidases suggested that the JBM-resistant factor was likely to be β-mannoside. In summary, this work advanced application of modified glycosidases for preparation of oligosaccharides and also demonstrated biocatalytic utility of glycosidases to produce biologically relevant glycoconjugates with homogeneous glycoforms.

Keywords: antibody-drug conjugate
oligosaccharide
glycosidase
glycoprotein
endo-beta-N-acetylglucosaminidase
glycosynthase
glycan trimming
Advisor: Davis, BG
Advances in electrochemical simulation and its application to electroanalysis

This thesis is concerned with the simulation of various electrochemical experiments and its application to electroanalysis.
Chapter 1 outlines the fundamental principles of electrochemistry which are of importance for the reading of this thesis. Chapter 2 then outlines the methods used in the numerical simulation of electrochemical experiments.
Chapters 3 and 4 are concerned with the electrochemistry of nanoparticles, and how this is affected by the presence of near wall hindered diffusion. In Chapter 3, a computational model to simulate anodic particle coulometry of nanoparticles in the presence of hindered diffusion is developed, and the effect of this hindered diffusion investigated. The model is then applied to simulate experimental data. Chapter 4 looks at the effect of hindered diffusion on the adsorption of nanoparticles on electrode surfaces, and investigates the effects of this adsorption on electrochemical experiments with nanoparticles generally.
Chapters 5, 6 and 7 are concerned with band electrodes in isolation, in a pair and in an array respectively. In Chapter 5, a model to simulate double potential step chronoamperometry at an individual band electrode is developed, and used to successfully simulate experimental data. Chapter 6 looks at dual band electrodes used in generator-collector mode, and how this can be used to simultaneously measure the concentration of two species in solution. Chapter 7 looks at interdigitated arrays of band and ring electrodes in generator-collector mode, and develops a model to simulate cyclic voltammetry in both cases, as well as investigating under what conditions interdigitated ring arrays may be modelled as interdigitated band arrays.
Chapter 8 develops a model to simulate chronoamperometry and cyclic voltammetry at porous electrodes, and investigates the consequences for electroanalysis of having a porous layer.
Finally, Chapter 9 investigates the Marcus-Hush theory of electron transfer kinetics, and looks at the effect of the kinetically limited currents resulting from this theory to the equivalence relation between microdisc electrodes and sphere-on-a-surface electrodes.

Keywords: Electrochemistry
Electroanalysis
Computational electrochemictry
Advisor: Compton, R
Quivers and the modular representation theory of finite groups

The purpose of this thesis is to discuss the rôle of certain types of quiver which appear in the modular representation theory of finite groups. It is our concern to study two different types of quiver. First of all we construct the ordinary quiver of certain blocks of defect 2 of the symmetric group, and then apply our results to the alternating group and to the theory of partitions. Secondly, we consider connected components of the stable Auslander-Reiten quiver of certain groups G with normal subgroup N. The main interest lies in comparing the tree class of components of N-modules, with the tree class of components of these modules induced up to G.

Advisor: Erdmann, K
Mechanistic studies on semiconductor electrodes

A study has been undertaken of the detailed photoelectrochemistry of a number of III-V and oxide semiconductors. In particular, the work has been aimed at obtaining a material which can act as a stable and efficient photoelectrode for the solar photoelectrolysis of water. However to achieve this aim, it was considered essential to obtain a far deeper understanding of the mechanisms of the electrochemical reactions taking place at the semiconductor/electrolyte interface.
The mechanism for Hydrogen evolution from the surfaces of the p-type III-V materials has represented a particular problem. P-type GaP was chosen as the representative member of the III-V materials and a mechanistic study has been made of the material using a.c. and d.c. experiments in addition to a detailed interfacial impedance analysis. A model for the Hydrogen evolution reaction has been proposed invoking surface bound Hydrogen atoms as both intermediates in the desired reaction and also as photogenerated surface states in parasitic recombination reactions. With the experience of the work on p-GaP, the analagous mechanisms to those found on p-GaP have been found to be consistent with results obtained on p-GaAs, p-InP and p-GaSb. However for these latter materials, additional complexities have arisen from their greater instability with respect to cathodic corrosion.
A method has been sought for modifying the surface of the III-V materials in order to obtain improved Hydrogen evolution efficiencies. Such a modification has been discovered for p-GaP by the adsorption of a Ruthenium species from solutions of crude RuC13.xH20. Its mode of operation is discussed at length.
For the oxide materials, a semiconducting oxide has been sought that possesses the ideal band energies and bandgap to obtain optimum photoefficiencies for the photoelectrclysis of water. The design constraints for such a material are presented and some results on a number of novel oxide semiconductors are discussed in relation to their use in such photoelectrolysis cells.

Advisor: Goodenough, J
Hamnett, A
Characterisation of global regulators that control expression of a flagella system in Rhodobacter sphaeroides

The α-proteobacterium Rhodobacter sphaeroides expresses one ﬂagellar system (Fla1) and two chemotaxis operons (cheOp2 and cheOp3) under laboratory conditions. It has another ﬂagellar system (Fla2) with a proposed cognate chemotaxis operon (cheOp1) which until recently had not been seen to be expressed. Here we characterised Fla2 motility and show that cheOp1 can be expressed under Fla2-inducing conditions. Putative Fla2&plus; strains AM1 and N29 were incubated on Sistrom's media and expression of the Fla2 system was conﬁrmed with western blotting and mass spectrometry. The Fla2 motility pattern was signiﬁcantly different to Fla1 when measured on soft nutrient agar and by analysing free swimming cells. Fla2&plus; strains swam in a corkscrew-like pattern which may favour movement through bioﬁlms. Fla2&plus; AM1 and N29 were signiﬁcantly deﬁcient in their capacity to form bioﬁlms compared to Fla1&plus; WS8N. AM1 and N29 were found to contain mutations in cckA and plasmids expressing these mutations were able to switch expression of Fla1 in WS8N to Fla2. Expression of mutant cckA also affected cheOp2 and cheOp3 expression and induced expression of cheOp1. Some members of the α-proteobacteria are known to engage in lifestyle switches from motile to sessile growth. It is suggested that a similar switch occurs in R. sphaeroides which uses the Fla1 system for motility in liquid environments and for the initial attachments to surfaces and the Fla2 system for movement through the highly-viscous bioﬁlm. For the ﬁrst time we have also shown expression of cheOp1 which may engage in cross-talk with the cheOp2 and cheOp3-expressed chemotaxis system. These results have implications for the regulation of dual ﬂagellar systems in the α-proteobacteria.

Keywords: Fla1
Rhodobacter sphaeroides
Rhodobacter
flagella
chemotaxis
Fla2
Advisor: Armitage, J
Football and immigrant communities: transnational diaspora politics, Identities, and integration in Turkish-speaking ethnic football in London

This thesis is on the Turkish-speaking community, comprising Turkish-Cypriots, Turks from Turkey, and Kurds from Turkey, and ethnic community football in London, which has been conceptualised as a transnational social field. It is intended as a contribution in the debates on the growing importance of issues of diasporic communities, their identity politics, and cultural integration in a context of ‘super-diversity’.
There are three major analytical themes. The first is transnational diaspora politics, which is redefined to comprise any relationship of power or interest by mobilising diasporic connections. I argue that the Turkish-speaking community uses ethnic football as a means for communal mobilisation around and representation of their ethnic identity in the public space of London, a city of unique political-economic and symbolic significance for the Cyprus Conflict which helped create the Turkish and Greek Cypriot football leagues in London. I show that the Turkish-speaking community has ever since used football to create and maintain a bridge between London and all the different locations of the community including Cyprus, Turkey, Germany, and beyond.
The second major theme is collective identities and how they are (re)produced, represented, and manifested in the diaspora. I argue that the nature of the field of ethnic football as a familiar, open, and welcoming space conveniently positioned between the Turkish-speaking private sphere and the British/Londoner public space has been a major factor accounting for the effectiveness of various identity projects to be pursued within this field. Lastly, after presenting the historical link between modern competitive sports and masculinity, I claim that the one defining aspect of all the ethnic identities reproduced within the field is their masculine character.
The last analytical theme is the cultural integration of immigrant communities. Without adopting a normative definition of cultural integration, I have considered the implications of involvement in ethnic community football in terms of belonging, social inclusion, marginalisation, and the psychological development and well-being of the individuals involved. The presented and analysed discussion rejects any automatic causal link between involvement in sports and integration or that involvement in mono-ethnic sporting organisations and segregation. Having reviewed a few exemplary organisations, which used football for integration purposes, and the nature of the ethnic community leagues, I have also argued in this thesis that the field of ethnic community football, again due to its specific nature, structure, and position between the private and public spaces, offers a great potential to be engaged by local and national governments in the service of integration policies.

Keywords: diaspora politics
Turkish-speaking community in London
ethnic football
gender and masculinity
integration through sport
Advisor: Keith, M
A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase

The segmented negative-sense vRNA genome of influenza A virus is replicated via a complementary RNA (cRNA) intermediate by the viral RNA-dependent RNA polymerase (RdRP). The replicative intermediate has been thought to exist as a complementary ribonucleoprotein (cRNP) complex. Development of an RNA-based affinity-purification strategy for the isolation of viral ribonucleoprotein complexes enabled the structural and functional characterisation of the previously uncharacterised cRNP complex. The cRNP exhibits a filamentous double-helical organisation with defined termini, containing the viral RdRP at one end and a loop structure at the other end. In vitro characterisation of cRNP activity led to a proposal of a model of vRNA synthesis that relies on a trans-activating RdRP.
The viral RdRP is an important host range determinant indicating that its function is affected by interactions with cellular factors. However, the identities and the roles of most of these factors remain unknown. Affinity-purification followed by mass spectrometry was performed to identify cellular proteins that interact with the viral RdRP. 171 cellular proteins were found to co-purify with the viral RdRP, the most abundant of which were chaperones, cytoskeletal proteins, importins, proteins involved in ubiquitination, kinases and phosphatases, mitochondrial and ribosomal proteins. Among the phosphatases, three subunits of the cellular serine/threonine-protein phosphatase 6 (PP6) were identified. PP6 was found to interact directly with the PB1 and PB2 subunits of the viral RdRP, and siRNA-mediated knockdown of the catalytic subunit of PP6 in infected cells resulted in the reduction of viral RNA accumulation and the attenuation of virus growth. Taken together, these results suggest that PP6 interacts with and positively regulates the activity of the influenza virus RdRP.

Keywords: RNA polymerase
RNA synthesis
influenza
Advisor: Fodor, E
Progress towards ultra-rapid DNA sequencing with protein nanopores

The sequencing of individual DNA strands with nanopores is being developed as a rapid, low-cost platform in which bases are identified in order as a DNA strand is transported through a pore under an electrical potential. Several challenges remain and this thesis focuses on one major area, the base identification properties of the α-hemolysin (αHL) nanopore. Under the potentials required for threading, DNA translocates too fast for single bases to be identified. However, immobilization of the DNA within the pore increases the residence time and therefore improves the precision of the electrical current reading and allows for the small differences in current flow, associated with different sequences, to be observed. DNA molecules with a 3′-terminal biotin-tag were complexed with streptavidin. Streptavidin is too large to be transported through the αHL pore and therefore the DNA-btn•streptavidin complex is not fully translocated; thus, the DNA strand is immobilized within the pore. Using this approach the nucleobase recognition properties of the αHL pore were mapped. The data suggest that the transmembrane β barrel domain of the pore contains at least three nucleobase recognition sites, termed R1, R2 and R3.
Additional sequence information can be gained when multiple recognition sites are employed within a single αHL pore, as compared to the simple case of a single recognition site. Recognition site R1, which is located near the central constriction, can be modified by site-directed mutagenesis of Met-113. It was observed that amino acids with related side chains produce similar patterns of nucleobase recognition. Amino acids that provide an energy barrier to ion flow (e.g. bulky or hydrophobic residues) strengthen base identification, while amino acids that lower the barrier, weaken identification. Deletion and site-directed mutagenesis were used to remove one recognition site and generate an αHL pore with a truncated β barrel domain that contains only two recognition sites.

Advisor: Bayley, H
Magnetism in quasi-low-dimensional systems investigated with muon spin rotation and high magnetic fields

This thesis presents the investigation of magnetism in a selection of low-dimensional systems and its relation to other physical properties, such as superconductivity. The techniques employed are muon spin rotation and pulsed magnetic field magnetisation. The ability of muons to directly probe the local field is used to study SrFeAsF, which is a parent compound of the high-temperature superconducting pnictides. This revealed that the magnetic and structural transitions are separated in this system. I then demon- strate the coexistence of magnetism and superconductivity in NaFeAs for the first time. This discovery is of great interest since the interplay between magnetism and supercon- ductivity is thought to play an important role for high-temperature superconductivity. I further investigate the effect of partially replacing Fe with Co in NaFeAs. I study the ordering and spin reorientation in the Mott insulator Sr₂IrO₄, which has been suggested as a possible high-temperature superconductor. The complex magnetism observed in this system is contrasted to that in related iridates Ca₄IrO₆, Ca₅Ir₃O₁₂ and Sr₃Ir₂O₇. By combining pulsed-field magnetization and low magnetic field experiments with μSR on a series of coordination polymers. I am able to determine the size and direction of the magnetic exchange interaction. I demonstrate how it is possible to adjust the in- teractions by altering the molecular architecture of these Cu-based spin- 1 2 compounds. This is a significant contribution since it will lead to the targeted design of magnetic systems that can be utilized to experimentally test fundamental theories of magnetism.

Keywords: superconductivity
muon spin rotation
magnetism
quasi-low-dimensional systems
coordination polymers
high magnetic fields
transition metal oxides
Advisor: Blundell, S
The grammar and poetics of Mūrti-Sevā

This thesis offers a multi-faceted exploration of image worship theology and practice within a Vaishnava Hindu theistic devotional tradition founded in the sixteenth century, flourishing today largely in north and northeast India and, since recently, spreading worldwide. The thesis serves two aims. First, it augments existing scholarship on Hindu temple image worship and Caitanya (Gaudīya) Vaishņavism by focusing on two contemporary temple communities one in the north Indian pilgrimage centre Vrindavan, the second near Watford, outside London. These represent, respectively, an "embodied community" and a "missionizing tradition," following Barbara Holdrege's typology in her studies of Hindu and Jewish traditions. By considering the practice of worship (mūrti-sevā) in terms of two persistent themes, namely rule-governed practice (vaidhī-sādhana) and emotion-driven practice (rāgānuga-sādhana), I show how the elements of "embodiment" and "missionizing" blend to produce variations on the overarching theme of Krsna bhakti, devotion to Kŗşna as the supreme divinity. Second, by focusing on the divine image in these two temples and the practice of worship, I offer one study of how "religious truth" is understood within these communities in terms of three dimensions of truth proposed by the Comparative Religious Ideas Project at Boston University (1995-1999; Robert C. Neville, et al., Religious Truth, State University of New York Press, 2001). At the same time I offer an attempt to extend the scope of that project by adding the dimensions of physical image and ritual practice to its existing dimension, religious ideas. I show how the central notion of devotion to Kŗşna as God (bhagavān) entails a complex web of discursive, ritual, and narrative expression to sustain image worship as a truth of embodiment/practice (the opposite of failure) which is also expressive truth (the opposite of deceit) that follows from propositional/epistemological truth (the opposite of error).

Advisor: Professor Francis X. Clooney, S
American ways and their meaning: Edith Wharton’s post-war fiction and American history, ideology, and national identity

This thesis argues that Edith Wharton’s assessment of American ways and their meaning in her post-war fiction has been widely misread. Its title derives from French Ways and Their Meaning (1919), which she wrote to educate her countrymen about French culture and society. Making sense of America was as great a challenge to Wharton. Much of her later fiction was for a long time dismissed by critics on the grounds that she had failed to ‘make sense’ of America. Wharton was troubled by American materialism and optimism, yet she believed in a culturally significant future for her nation. She advocated – and wrote – an American fiction that looked critically at society and acknowledged the nation’s ties to Europe. Sometimes her assessment of American ways is reductive, and presented in a tone that her critics, then and since, found off- putting and snobbish. But her skepticism about American modernity was penetrating and prophetic, and has not been given its due.
In criticism over the last two decades, a case for the place of Wharton’s post-war fiction in canons of feminism and modernism has been persuasively made. The thesis responds to these positions, but makes its own argument that the post-war writing reflects broader shift in American identity and ideology. The thesis is broadly historicist in its strategy, opening with a discussionofthereputationofthesetextsandthatoftheauthormoregenerally. Afterthat entry-point, it is organized thematically, with four chapters covering topics that are seen as key components of American ideology in Wharton’s post-war writing. These include modernity, gender equality, the American Dream of social mobility, and American exceptionalism. The thesis concludes with an assessment of Wharton’s prognostications in the context of twenty-first century America.

Keywords: 1930s
globalization
Americanization
World War I
Scott Fitzgerald
Edith Wharton
flapper
1920s
'The Age of Innocence'
' modernism
Jazz Age
American Dream
'Twilight Sleep
'The Buccaneers'
Sinclair Lewis
Advisor: Lee, H
Adverbs in conceptual semantics

The thesis discusses and evaluates semantic representations of predicate-oriented modification (specifically by manner adverbs) and participant-oriented evaluative modification (by so-called “subject-oriented” adverbs). Analyses are proposed within the framework of Conceptual Semantics.

Keywords: formal semantics
participant-oriented evaluative modification
predicate-oriented modification (by manner adverbs)
conceptual semantics
adverbs
Advisor: Dalrymple, M