Most Haunted and the Convergence of Traditional Belief and Popular Television

Koven, M. (2007). Most Haunted and the Convergence of Traditional Belief and Popular Television. Folklore. 118(2), pp.183-202. RAE2008

Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals

Kingston-Smith, A. H., Merry, R. J., Leemans, D. K., Thomas, Howard, Theodorou, M. K. (2005). Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals. British Journal of Nutrition, 93(1), 73-79. Sponsorship: DEFRA / BBSRC RAE2008

RinA controls phage-mediated packaging and transfer of virulence genes in gram-positive bacteria

Phage-mediated transfer of microbial genetic elements plays a crucial role in bacterial life style and evolution. In this study, we identify the RinA family of phage-encoded proteins as activators required for transcription of the late operon in a large group of temperate staphylococcal phages. RinA binds to a tightly regulated promoter region, situated upstream of the terS gene, that controls expression of the morphogenetic and lysis modules of the phage, activating their transcription. As expected, rinA deletion eliminated formation of functional phage particles and significantly decreased the transfer of phage and pathogenicity island encoded virulence factors. A genetic analysis of the late promoter region showed that a fragment of 272 bp contains both the promoter and the region necessary for activation by RinA. In addition, we demonstrated that RinA is the only phage-encoded protein required for the activation of this promoter region. This region was shown to be divergent among different phages. Consequently, phages with divergent promoter regions carried allelic variants of the RinA protein, which specifically recognize its own promoter sequence. Finally, most Gram-postive bacteria carry bacteriophages encoding RinA homologue proteins. Characterization of several of these proteins demonstrated that control by RinA of the phage-mediated packaging and transfer of virulence factor is a conserved mechanism regulating horizontal gene transfer.

Computer-Mediated Communication and Ecclesiological Challenges To and From the Reformed Tradition

Communities of faith have appeared online since the inception of computer -­ mediated communication (CMC)and are now ubiquitous. Yet the character and legitimacy of Internet communities as ecclesial bodies is often disputed by traditional churches; and the Internet's ability to host the church as church for online Christians remains a question. This dissertation carries out a practical theological conversation between three main sources: the phenomenon of the church online; ecclesiology (especially that characteristic of Reformed communities); and communication theory. After establishing the need for this study in Chapter 1, Chapter 2 investigates the online presence of Christians and trends in their Internet use, including its history and current expressions. Chapter 3 sets out an historical overview of the Reformed Tradition, focusing on the work of John Calvin and Karl Barth, as well as more contemporary theologians. With a theological context in which to consider online churches in place, Chapter 4 introduces four theological themes prominent in both ecclesiology and CMC studies: authority; community; mediation; and embodiment. These themes constitute the primary lens through which the dissertation conducts a critical-­confessional interface between communication theory and ecclesiology in the examination of CMC. Chapter 5 continues the contextualization of online churches with consideration of communication theories that impact CMC, focusing on three major communication theories: Narrative Theory; Interpretive Theory; and Speech Act Theory. Chapter 6 contains the critical conversation between ecclesiology and communication theory by correlating the aforementioned communication theories with Narrative Theology, Communities of Practice, and Theo-­Drama, and applying these to the four theological themes noted above. In addition, new or anticipated developments in CMC investigated in relationship to traditional ecclesiologies and the prospect of cyber-­ecclesiology. Chapter 7 offers an evaluative tool consisting of a three-­step hermeneutical process that examines: 1) the history, tradition, and ecclesiology of the particular community being evaluated; 2) communication theories and the process of religious-­social shaping of technology; and 3) CMC criteria for establishing the presence of a stable, interactive, and relational community. As this hermeneutical process unfolds, it holds the church at the center of the process, seeking a contextual yet faithful understanding of the church.

Face Identification by a Cascade of Rejection Classifiers

Nearest neighbor search is commonly employed in face recognition but it does not scale well to large dataset sizes. A strategy to combine rejection classifiers into a cascade for face identification is proposed in this paper. A rejection classifier for a pair of classes is defined to reject at least one of the classes with high confidence. These rejection classifiers are able to share discriminants in feature space and at the same time have high confidence in the rejection decision. In the face identification problem, it is possible that a pair of known individual faces are very dissimilar. It is very unlikely that both of them are close to an unknown face in the feature space. Hence, only one of them needs to be considered. Using a cascade structure of rejection classifiers, the scope of nearest neighbor search can be reduced significantly. Experiments on Face Recognition Grand Challenge (FRGC) version 1 data demonstrate that the proposed method achieves significant speed up and an accuracy comparable with the brute force Nearest Neighbor method. In addition, a graph cut based clustering technique is employed to demonstrate that the pairwise separability of these rejection classifiers is capable of semantic grouping.

Investigation of catalyst effects in enantioselective copper- and rhodium-mediated transformations of α-diazocarbonyl compounds

This thesis describes the synthesis and reactivity of a series of α-diazocarbonyl compounds with particular emphasis on the use of copper-bis(oxazoline)-mediated enantioselective C–H insertion reactions leading to enantioenriched cyclopentanone derivatives. Through the use of additives, the enantioselectivity achieved with the copper catalysts for the first time reaches synthetically useful levels (up to 91% ee). Chapter one provides a comprehensive overview of enantioselective C–H insertions with α-diazocarbonyl compounds from the literature. The majority of reports in this section involve rhodium-catalysed systems with limited reports to date of asymmetric C–H insertion reactions in the presence of copper catalysts. Chapter two focuses on the synthesis and C–H insertion reactions of α-diazo-β-keto sulfones leading to α-sulfonyl cyclopentanones as the major product. Detailed investigation of the impact of substrate structure (both the sulfonyl substitutent and the substituent at the site of insertion), the copper source, ligand, counterion, additive and solvent was undertaken to provide an insight into the mechanistic basis for enantiocontrol in the synthetically powerful C–H insertion process and to enable optimisation of enantiocontrol and ligand design. Perhaps the most significant outcome of this work is the enhanced enantioselection achieved through use of additives, substantially improving the synthetic utility of the asymmetric C–H insertion process. In addition to the C–H insertion reaction, mechanistically interesting competing reaction pathways involving hydride transfer are observed. Chapter three reports the extension of the catalyst-additive systems, developed for C–H insertions with α-diazo-β-keto sulfones in chapter two, to C–H insertion in analogous α-diazo-β-keto phosphonate and α-diazo-β-keto ester systems. While similar patterns were seen in terms of ligand effects, the enantiopurities achieved for these reactions were lower than those in the cyclisations with analogous α-diazo-β-keto sulfones. Extension of this methodology to cyclopropanation and oxium ylide formation/[2,3]-sigmatropic rearrangement was also explored. Chapter four contains the full experimental details and spectral characterisation of all novel compounds synthesised in this project, while details of chiral stationary phase HPLC analysis and X-ray crystallography are included in the appendix.

Characterization of TRAF6 mediated ubiquitination of presenilins and γ-secretase substrates

Post-translational modification of the γ-secretase protease complexes and their substrates has an important role in controlling receptor-initiated signalling events, which are critically important in the pathogenesis of cancer, inflammatory and Alzheimer’s disease. Our lab has previously characterised an interaction between TRAF6 and presenilin-1, which lead to the identification of interleukin-1 (IL-1) receptor type 1 (IL-1R1) and Toll-like receptor-4 (TLR4) as novel γ-secretase substrates. Subsequently our group showed that TRAF6 promoted ubiquitination and γ-secretase cleavage of IL-1R1. The aim of this project is to study the association between TRAF6 and the presenilins, the critical γ-secretase complex components, and to determine the functional importance of TRAF6-mediated ubiquitination of γ-secretase substrates. Firstly, we show that the full-length presenilins are novel substrates of TRAF6-mediated Lysine-63-linked polyubiquitination. Secondly, we show that co-expression of TRAF6 and the presenilins increases the stability and alters the turnover of the presenilins. Thirdly, we reveal that TRAF6-mediated ubiquitination of presenilin does not affect γ-secretase enzyme activity, but may regulate the full-length presenilin functions such as ER Ca2+ signalling. Previously, we have reported IL-1R1 as a novel substrate of TRAF6-mediated ubiquitination. In this study, we identified five lysine residues in the IL-1R1 intracellular domain targeted by TRAF6-mediated polyubiquitination. Furthermore, mutagenesis of these five lysine residues led to decreased IL-1R1 cell surface expression, precluded the ectodomain shedding and attenuated the responsiveness to IL-1β stimulation, demonstrating the critical role of TRAF6 in IL-1R1 trafficking.

The role of presenilin 1 and presenilin 2 in IL-1β-, LPS- and TNFα- mediated signalling events

The importance of γ-secretase protease activities in development, neurogenesis and the immune system are highlighted by the diversity of its substrates and phenotypic characterization of Presenilin (PS)-deficient transgenic animals. Since the discovery of Amyloid precursor protein (APP) and it’s cleavage by γ-secretase complexes, over 90 other type I membrane proteins have been identified as γ-secretase substrates. We have identified interleukin-1 (IL-1) receptor type I (IL-1R1), toll-like receptor 4 (TLR4) and tumour necrosis factor-α (TNFα) receptor-1 (TNFR1) as novel substrates for - secretase cleavage, which play an important role in innate immunity. In this study, using PS-deficient cells and PS-knockout animal models we examined the role of PS proteins, PS1 and PS2, in IL-1R1-, TLR4- and TNFR1- mediated inflammatory responses. Data presented show that in response to IL- 1β, lipopolysaccharide (LPS) or TNFα, immortalised fibroblasts from PS2- deficient animals have diminished production of specific cytokines and chemokine, with differential reduction in nuclear factor-κB (NF-κB) and (mitogen activated protein kinase) MAPK activities. In contrast, no defect in the response to IL-1β, LPS or TNFα was observed in PS1-deficient immortalised fibroblasts. These observations were confirmed using bone marrow-derived macrophages from PS2-null mice, which also display impaired responsiveness to IL-1β- and LPS, with decreased production of inflammatory cytokines. Furthermore, in whole animal in vivo responses, we show that PS2-deficient animals display ligand (IL-1β, LPS and TNFα)-dependent alterations in the production of specific pro-inflammatory cytokines or chemokines. Importantly, this reduced responsiveness to IL-1β, LPS or TNFα is independent of γ- secretase protease activity and γ-secretase cleavage of TNFR1, IL-1R1 or TLR4. These observations suggest a novel γ-secretase-independent role of PS2 in the regulation of innate immune responsiveness and challenge current concepts regarding the regulation of IL-1β-, LPS- and TNFα-mediated immune signalling.

Investigation of lactic acid bacteria mediated bioprotection with applications in cereal industry. Case-study: malting process

Antifungal compounds produced by Lactic acid bacteria (LAB) metabolites can be natural and reliable alternative for reducing fungal infections pre- and post-harvest with a multitude of additional advantages for cereal-base products. Toxigenic and spoilage fungi are responsible for numerous diseases and economic losses. This thesis includes an overview of the impact fungi have on aspects of the cereal food chain. The applicability of LAB in plant protection and cereal industry is discussed in detail. Specific case studies include Fusarium head blight, and the impact of fungi in the malting and baking industry. The impact of Fusarium culmorum infected raw barley on the final malt quality was part of the investigation. In vitro infected barley grains were fully characterized. The study showed that the germinative energy of infected barley grains decreased by 45% and grains accumulated 199 μg.kg-1 of deoxynivalenol (DON). Barley grains were subsequently malted and fully characterized. Fungal biomass increased during all stages of malting. Infected malt accumulated 8-times its DON concentration during malting. Infected malt grains revealed extreme structural changes due to proteolytic, (hemi)-cellulolytic and starch degrading activity of the fungi, this led to increased friability and fragmentation. Infected grains also had higher protease and β-glucanase activities, lower amylase activity, a greater proportion of free amino and soluble nitrogen, and a lower β-glucan content. Malt loss was over 27% higher in infected malt when compared to the control. The protein compositional changes and respective enzymatic activity of infected barley and respective malt were characterized using a wide range of methods. F. culmorum infected barley grains showed an increase in proteolytic activity and protein extractability. Several metabolic proteins decreased and increased at different rates during infection and malting, showing a complex F. culmorum infection interdependence. In vitro F. culmorum infected malt was used to produce lager beer to investigate changes caused by the fungi during the brewing processes and their effect on beer quality attributes. It was found, that the wort containing infected malt had a lower pH, a higher FAN, higher β-glucan and a 45% increase in the purging rate, and led to premature yeast flocculation. The beer produced with infected malt (IB) had also a significantly different amino acid profile. IB flavour characterization revealed a higher concentration of esters, fusel alcohols, fatty acids, ketones, and dimethylsulfide, and in particular, acetaldehyde, when compared to the control. IB had a greater proportion of Strecker aldehydes and Maillard products contributing to an increased beer staling character. IB resulted in a 67% darker colour with a trend to better foam stability. It was also found that 78% of the accumulated mycotoxin deoxynivalenol in the malt was transferred into beer. A LAB cell-freesupernatant (cfs), produced in wort-base substrate, was investigated for its ability to inhibit Fusarium growth during malting. Wort was a suitable substrate for LAB exhibiting antifungal activity. Lactobacillus amylovorus DSM19280 inhibited 104 spores.mL-1 for 7 days, after 120 h of fermentation, while Lactobacillus reuteri R29 inhibited 105 spores.mL-1 for 7 days, after 48 h of fermentation. Both LAB cfs had significant different organic acid profiles. Acid-base antifungal compounds were identified and, phenyllactic, hydroxy-phenyllactic, and benzoic acids were present in higher concentrations when compared to the control. A 3 °P wort substrate inoculated With L. reuteri R29 (cfs) was applied in malting and successfully inhibited Fusarium growth by 23%, and mycotoxin DON by 80%. Malt attributes resulted in highly modified grains, lower pH, higher colouration, and higher extract yield. The implementation of selected LAB producing antifungal compounds can be used successfully in the malting process to reduce mould growth and mycotoxin production.