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Rose viruses: Understanding the current status and protecting the future of the UK rose sector
Get PDFPh. D. Thesis.The rose (Rosa spp.) is the national flower of England and one of the most valued ornamental
flowering shrubs grown around the globe. Despite the spread of rose viruses and their
importance in rose cultivation, they have not been studied in detail in the United Kingdom (UK)
since the 1980s. Molecular methods have evolved since then, and as a result they have rarely
been deployed to study these viruses. In the UK many viruses have been reported previously
infecting roses such as arabis mosaic virus (genus Nepovirus) and strawberry latent ringspot
virus (family Secoviridae). However, numerous viruses have been identified infecting roses in
recent years, especially with the application of high-throughput sequencing (HTS). Diagnosis
is fundamental to facilitate the management of plant diseases, and early detection is essential
for successful biosecurity campaigns, for example against rose rosette virus (RRV; genus
Emaravirus), which is devastating roses in the USA and Canada, and was recently discovered
in India (2017). In this project, different molecular (PCR, qPCR and HTS) and serological
methods (ELISA) have been used to understand the baseline of viruses present in roses in the
UK. Detailed experiments were performed to compare various targeted and non-targeted
methods, including two different pipelines for HTS data analysis, Angua and EDNA. RT-qPCR
showed the highest sensitivity for the detection of known viruses, whereas ELISA was
identified as the technique with the lowest sensitivity. The Angua and the EDNA pipelines
showed non-significant differences in sensitivity from RT-qPCR except in the detection of viral
agents with lower titre. The advantages of HTS as a potential future front-line diagnostic tool
are described. The performance of this study has allowed the estimation of the prevalence of
some previously reported viruses in the UK but also the identification of Rosa spp. as a new
host for viruses that are widespread in the country. This work resulted in three first virus records
in the UK (rose cryptic virus-1, rose spring dwarf virus, and sweetbriar rose curly top virus),
and the discovery of a new virus species (rosa ilarvirus-1; genus Ilarvirus). Furthermore, this
research has proven a connection between the movement of plant pathogens and the trade in
roses as cut flowers.DEFRA, Royal Horticultural Societ
Towards the Total Synthesis of the Polyketide Natural Product DEM30355/A and Associated Crystallisation Studies
Get PDFPhD ThesisDue to the continuing rise in drug resistant pathogenic bacteria, there is an urgent need for
new Mode of Action antibiotics. We have identified the polyketide natural product
DEM30355/A as a potential new Mode of Action antibiotic versus Methicillin-resistant
Staphylococcus aureus. This project aims to develop a synthetic route to DEM30355/A and its
synthetic analogues to support new antibiotic development.
We have shown that the ABC anthracene-like core of DEM30355/A can be constructed by
employing a key tandem, Michael-Dieckmann reaction. The functionalised C-ring was
synthesised via a stereoselective Michael-Wittig reaction introducing the desired C-4a/C-10a
C=C double bond, C-2 methyl and C-3 ethyl ester, followed by a stereoselective Rubottom
oxidation to introduce the required hydroxyl group at C-3. A Michael-Dieckmann reaction
between the A-ring and C-ring precursors allowed access to the ABC fused ring carbon
skeleton of our target DEM30355/A, with a significant number of the required functional
groups in place. Future work will focus on lactone ring formation, oxidation of the C-ring and
installation of the B-ring C=C double bond between C-10/C-10a (Scheme 1.00).
Scheme 1.00: Synthesis of the ABC fused ring core of DEM30355/A via a key Michael-Dieckmann cyclisation.
Our synthetic work was supported by crystallographic studies including an investigation into
the propensity of shikimate esters to form high Z’ structures and the crystallisation of
biologically active small molecules. Our results serve to further confirm the tandem Michael-Dieckmann reaction as a robust method of coupling functionalised aromatic rings for the
construction of natural product scaffolds
The importance of adaptor proteins and cell signalling in the control of peptidoglycan synthesis
Get PDFPh. D. Thesis.Bacterial cell division is a complex process that requires tight co-ordination and regulation of
chromosome replication and segregation, and the synthesis and remodelling of the bacterial
cell wall. The peptidoglycan sacculus is synthesised by peptidoglycan synthases and it is a vital
component of the bacterial cell structure, to withstand the turgor of the cell to prevent its
lysis FtsZ is one of the first proteins to localise at midcell during cell division where it forms a
ring-like structure, the Z-ring, at the inner face of the cytoplasmic membrane. After Z-ring
formation, the divisome is recruited to the division site to form the septum and the
elongasome is positioned at the side wall for elongation. Both the elongasome and the
divisome are dynamic macromolecular complexes composed of numerous proteins at
unknown stoichiometries and it is thought there are proteins in both complexes that are yet
to be discovered. Understanding bacterial cell division at the molecular and cellular level is an
important area of research to enable the development of novel antibiotics as well as
comprehending one of biology’s fundamental questions.
GpsB is a conserved Gram-positive cytosolic protein that plays an important role in the
elongation-division cycle by acting as a scaffold to control the relative spatial arrangements of
peptidoglycan synthases (PBPs). In this thesis the molecular interactions of GpsB with
cytoplasmic mini-domains of PBPs from two human pathogens (Listeria monocytogenes and
Streptococcus pneumoniae) are described using structural and biochemical techniques. The
importance of the critical interacting residues for the GpsB:PBP interaction for cell wall growth
and viability of L. monocytogenes and S. pneumoniae were analysed in collaboration with the
Halbedel, and Massidda and Winkler groups, respectively. A novel function of PBP binding was
introduced into DivIVA, a cell division regulator and GpsB homolog, by protein engineering in
an attempt to understand the functional divergence between GpsB and DivIVA. Potential
building blocks for the development of GpsB:PBP inhibitors were identified in the form of
small fragments by an X-ray crystallography-based fragment screening experiment at
Diamond Light Source.
Eukaryote-like serine/threonine protein kinases (eSTPKs) and partner phosphatases (eSTPs)
are conserved in Gram-positive bacteria. They consist of an intracellular N-terminal kinase
domain and an extracellular sensing region linked by a short transmembrane helix. The
external regulatory region is comprised of three or four PASTA domains that bind to
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peptidoglycans and compounds containing beta-lactams. eSTPKs are involved in the
regulation of many cellular processes including development of regulation, control of cell
growth, stress response, virulence and sporulation. The eSTPK/eSTP pair from L.
monocytogenes are PrkA and PrpC.
This thesis concerns the importance of autophosphorylation for the function of the kinase
domain of PrkA (PrkA-KD) and that phosphorylation of serine 173 is crucial for activation,
agreeing with the mechanism of activation of Stk1 in Staphylococcus aureus. The previously
uncharacterised phosphoprotein Lmo1503 (renamed ReoM) is a homologue of IreB from
Enterococcus faecalis, a negative regulator of cephalosporin resistance. It is confirmed that
ReoM is a substrate of the PrkA/PrpC pair and the crystal structure of the full length ReoM
protein is presented. Isothermal titration calorimetry determined the interaction of ReoM and
PrkA-KD is within the nanomolar range and there is a ten-fold reduction in affinity with a PrkAKDS173A mutation. The Halbedel group have linked ReoM phosphorylation to the activation of
ClpCP-dependent degradation of the primary UDP-GlcNAc 1-carboxyvinyltransferase in L.
monocytogenes, MurA. We therefore propose that cell wall integrity sensing by PrkA is
coupled to the first committed step of peptidoglycan synthesis through the intermediate
proteins ReoM and ClpCP
Ethnic disparaties in the prevalence of overweight and obesity among women and children in high income countries : the case for Aftican migrant women and children
Get PDFPhD ThesisExcess body weight in women of child-bearing age can have severe consequences for
maternal and child health, including reduced fertility, pregnancy complications, an increased
risk of child obesity and increased susceptibility to non-communicable diseases. Black women
and children in high-income countries (HICs) have a disproportionately higher prevalence of
overweight and obesity compared to other ethnic groups. However, there is a lack of evidence
on the weight status of African migrant women and children living in HICs, and on these
women’s weight perceptions and perceived risks of overweight and obesity.
In the first phase of this thesis, I used systematic review, meta-analysis and framework
synthesis methods to explore the weight status of African migrant women and children living
in HICs, and the dietary and physical activity (PA) behaviours of African migrant women. Metaanalyses
results showed that African migrant women had higher body mass index (BMI)
(weighted mean difference (WMD)=1.95 Kg/m2, 95%CI 1.16–2.75) and higher odds of
overweight (OR=2.45, 95%CI 1.65–3.63), obesity (OR=2.09, 95%CI 1.41–3.12) and
combined overweight/obesity (OR=2.09, 95%CI 1.41–3.12) compared to non-African women
from HICs. Children of African migrant women also had higher mean birthweights
(WMD=48.71g, 95%CI 4.19g–93.24g), higher odds of overweight (OR=1.50, 95%CI 1.00–
2.24), obesity (OR=2.28, 95%CI 1.37–3.78), combined overweight/obesity (OR=2.08, 95%CI
1.40–3.11) and macrosomia (OR=1.83, 95%CI 1.77–1.89), and lower odds of low birthweight
(OR=1.06, 95%CI 0.56–2.02) compared to children of non-African women. Risks of
overweight and obesity were higher for women and children from North Africa, while data were
lacking for sub-Saharan Africa. African migrant women had bicultural dietary patterns,
inadequate intakes of iron, folate, and calcium, excessive sodium intakes, and reduced PA
levels. There were data gaps on potential confounders that may influence maternal and child
weight status, associations between maternal characteristics and child weight outcomes, and
weight-related behaviours of pregnant African migrant women.
In the second phase, I explored the weight perceptions of African migrant women living in the
UK, their perceived risks of overweight and obesity to themselves and their children, and the
sociocultural and migration-related influences of these. Interviews conducted with 23 African
migrant women from Nigeria, Ghana and Cameroon were analysed through thematic analysis.
Key themes identified were: ‘we are not at risk’, ‘bigger is better’, acculturation, ‘a child cannot
be too fat’ and infant feeding as a balancing act. The women’s perceptions were influenced by
their understandings and lay interpretations of body weight terms, which differed from
mainstream knowledge. Perceived risk factors for obesity included: diet, genetics, childbearing
and living the ‘easy life’ in the UK. PA was mostly interpreted as sport or exercise and was not
an intrinsic part of their culture. Post-migration changes in weight perceptions included
increased knowledge of healthy weight-related behaviours, awareness of unhealthy cultural
practices and preference for smaller body sizes (for themselves but not their children).
Pregnancy was associated with heightened weight-awareness, while preconception weight
was believed to have no influence on women’s health or pregnancy. Midwives and relatives
were useful information sources for pregnancy weight, and challenges with weight
management in pregnancy included families encouraging weight gain; food cravings;
unhealthy food in the UK and unfamiliar dietary advice from midwives. Women tended to
disregard weight-related advice from health care providers, while valuing advice from friends
and family.
This thesis identifies African migrant women and children as high-risk groups for overweight
and obesity, and highlights the role of migration and socio-cultural influences on their weight
status, behaviours and perceptions. There is a need for culturally-tailored interventions to
support weight management in this population, especially taking into account their
multicultural identities. Further research and interventions addressing the risk factors and
areas of need identified could help prevent further increases in obesity, and contribute towards
narrowing the inequality gaps in health outcomes among migrant populations in HICs
Identifying new genes and molecular mechanisms in mitochondrial disease
Get PDFPh. D. ThesisAn estimated 1158 nuclear encoded proteins function within mammalian mitochondria.
Over the past ten years the increased implementation of next generation sequencingdriven diagnostics, particularly whole exome sequencing (WES), has resulted in the
identification of over 150 nuclear genes not previously implicated in mitochondrial
disease, necessitating extensive functional studies to determine and confirm
pathogenicity. Over one third of reported mitochondrial disease-causing nuclear
genetic variants reside in genes encoding proteins with a role in mtDNA gene
expression. The overarching aim of my research project was to functionally validate
novel candidate mitochondrial disease variants, focusing on those identified in genes
encoding proteins with roles in mitochondrial translation, in order to achieve genetic
diagnoses for affected patients.
WES of two unrelated patients with early-onset neurological disease presentations
identified different and previously unreported variants in the GFM2 gene encoding
ribosome recycling factor mtEFG2. Differential and tissue-specific patterns of
combined OXPHOS defects were identified in each patient. Novel compound
heterozygous variants in the TSFM gene, encoding the elongation factor mtEF-Ts,
were identified in a single patient presenting with adult-onset hypertrophic
cardiomyopathy. The abundance of mtEF-Ts was significantly decreased in patient
fibroblasts and cardiac tissue. The resulting OXPHOS deficiency was most severe in
cardiac tissue, accompanied by decreased levels of elongation factor mtEF-Tu.
A homozygous nonsense mutation in the MRPL47 gene, encoding a mitoribosomal
large subunit (LSU) protein, was identified in three unrelated paediatric patients
presenting with metabolic acidosis, epilepsy and liver involvement. Patient fibroblasts
exhibited disorders of translation and combined OXPHOS defects. Some truncated
MRPL47 protein was visualised within the destabilised LSU. Variants in MRPL65, a
second LSU gene, were identified in five paediatric patients presenting with
overlapping clinical features including developmental delay, ataxia and nystagmus.
Attempts to generate a CRISPR/Cas9 MRPL65 knock-out cell line were unsuccessful
due to polyploidy of the target genomic region, highlighting the importance of
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karyotyping in gene editing studies. MRPL65 cDNA analysis in a single patient
identified retention of intronic sequence due to a +5 splice variant. Patient fibroblasts
displayed normal levels of MRPL65 and OXPHOS proteins, but appeared to exhibit a
defect in mitochondrial translation alongside some abnormal assembly of the LSU.
This work expands upon our current knowledge of Mendelian mitochondrial disorders,
adding to a growing list of nuclear genes implicated in disorders of translation and
achieving genetic diagnosis in the presented families. Tissue-specific defects illustrate
the complexity of the pathomechanisms underlying these disorders and highlight the
gaps in our understanding of adaptive compensatory mechanisms employed in
different tissues. This research also emphasises the importance of identifying and
characterising multiple families when assigning pathogenicity to novel disease-causing
variants.Lily Foundatio
NPM, e-government and the modernization of public services in the Sultanate of Oman
Get PDFPhD ThesisThis thesis critically examines the development and implementation of e-government projects in the Sultanate of Oman after 2003 when the government published its intention, in the spirit of new public management (NPM), to raise the quality and performance of key public services. At the core of the research is a comparative analysis of five in-depth case studies of representative service modernization projects driven by the introduction of new information systems. The goal of the research is to evaluate the performance of NPM inspired projects in Oman to learn lessons that might lead to beneficial changes in future policy and practice. The study considers inter alia the goals and strategy of the Omani government, the selections and design of modernization projects, problems of execution and obstacles to change, and the reasons for differing degrees of success achieved in meeting project objectives.
The five case studies of Omani e-government modernization projects were developed mainly from interviews conducted with officials in government departments at different levels of management and managers directly responsible for project design and implementation. Further interviews with experts and policymakers focused on government strategy, policymaking and project monitoring. These interviews were especially important in locating the five case studies in a wider strategic, cultural and historical context. Documentary evidence was gathered whenever possible on individual projects and on government’s strategic plans and policies. Taken together, the researcher accumulated a large and rich collection of data sources, which were analyzed taking a bottom up, inductive, grounded theoretical approach, enabling the researcher to develop fresh theoretical perspectives, interpretations and practical recommendations.
The study is the first to document, analyse and evaluate the modernization of public services in Oman, and one of few to examine in-depth the adoption of NPM methods in developing countries. Lack of financial resources, failure to define appropriate measures of individual and organizational performance and lack of interest in training were found to be the main reasons limiting the success of projects. From a comparative perspective, however, degrees of success varied considerably, highlighting that proper planning, project management and training invariably paid dividends, explaining differences in outcomes. Finally, the research extends our theoretical understanding of NPM projects in developing countries, highlighting the importance of feasibility studies and stakeholder participation in formulating public sector improvement policies
The ‘authoritarian turn’ in environmental planning? examining the conflict over shale gas ‘fracking’ in England
Get PDFPhD ThesisThe aim of this thesis is to critically examine the changes in the dominant regime
within environmental planning in England. Scholars have argued that although a
‘post-political regime’ had come to dominate English planning at the beginning of the
last decade, the ongoing economic crisis and ‘perpetual austerity’ have led to a rise in
right wing populism and a turn towards authoritarian rhetoric and governance. The
planning literature has yet to contribute to the conceptualisation of the ‘authoritarian
turn’, and the literature on authoritarianism has yet to examine its implication for
environmental planning decisions at an institutional level. The aim of this thesis is to
contribute to filling these gaps.
The thesis’ starting point is a tentative hypothesis that there is a turn towards more
authoritarian (yet still neoliberal) planning regime following a crisis in the ‘postpolitical’. Using a Political Discourse Analysis approach, the thesis examines the
highly contested case of shale gas fracking to show how the political challenge from
an anti-fracking movement has undermined the legitimacy of a ‘post-political
regime’. Through the analysis of: planning and policy documents and other related
texts, 23 unstructured interviews with the different sides of the conflict, and nonparticipant observation of protest sites the thesis traces the emergence of an
increasingly authoritarian planning regime in two key shale gas planning decisions
(in Lancashire and North Yorkshire) and subsequent government interventions in
the planning process.
The move towards the new regime is conceptualised as increasingly executive led,
punitive and antagonistic, drawing on a ‘state of exception’ to justify central
government’s interventions and the bypassing of existing democratic processes. The
authoritarian turn, however, is limited by legal and political provisions that govern
shale gas fracking in England. The thesis shows, and provides a novel framework for
analysing, the crisis of post-political planning and an ongoing authoritarian tur
Visibility and acceptance of discrete-sampling artifacts in visual displays
No full textPh. D. Thesis.Digital visual displays are aimed to provide an illusion of a continuous reality through a
discrete presentation of visual information. This thesis explored three topics on (i) angular, (ii)
spatial, and (iii) temporal sampling characteristics, related to distortion visibility, acceptance,
and discomfort. In the first topic, we addressed the issue of optimizing the view density
in continuous parallax visualization by replicating the changing views of a 3-D object for
a moving observer. We measured the visibility of the related artifacts and evaluated the
performance of full-reference visual quality metrics. We found that the state-of-the-art metrics
can indirectly characterize artifact visibility and established a quantitative relationship for
threshold estimation on varying conditions. The second topic addressed the relation of the
contrast sensitivity function (CSF) to adaptation luminance and specifically its asymptotic
behavior at high light levels essential to modern high-luminance displays. Using a custombuilt system, we measured the CSF at relatively high luminance levels and spatial frequency
range, integrating our dataset to the existing research. We found a gradual transition among
the linear to DeVries-Rose to Weber regions with steeper slopes for higher frequencies and
lower luminance. A further decreasing region was located at low to intermediate frequencies.
Following this construct, we adopted a model consisting of central elements in the visual
signal processing and proposed an eight-parameter form for the CSF in the luminance domain.
The final topic addressed the effects of frame rate on distortion acceptance and its impact on
visual discomfort during regular display use. We assessed the perceived symptoms, preference,
and task performance under varying conditions. The measurements indicated that for nondemanding everyday tasks, the frame rate could be reasonably reduced without severe effects
on the observer; however, this tolerance diminished under more dynamic content. A potential
association of discomfort with the blinking activity was also discussed.European Union’s Horizon 2020 research
and innovation program under the Marie Skłodowska-Curie grant agreement No 676401,
European Training Network on Full Parallax Imaging and Huawei Technologies Co., Lt
Calm Displays and Their Applications : Making Emissive Displays Mimic Reflective Surfaces Using Visual Psychophysics, Light Sensing and Colour Science
Get PDFPh. D. Thesis.Our environment is increasingly full of obtrusive display panels, which become illuminating surfaces when on, and void black rectangles when off. Some researchers argue that emissive displays are incompatible with Weiser and Seely Brown's vision of "calm technology", due to their inability to seamlessly blend into the background. Indeed, Mankoff has shown that for any ambient technology, the ability to move into the periphery is the most relevant factor in their usability. In this thesis, a background mode for displays is proposed based on the idea that displays can look like an ordinary piece of reflective paper showing the same content.
The thesis consists of three main parts. In the first part (Chapter 4), human colour matching performance between an emissive display and reflective paper under chromatic lighting conditions is measured in a psychophysical experiment. We find that threshold discrimination ellipses vary with condition (16.0×6.0 ΔEab on average), with lower sensitivity to chroma than hue changes. Match distributions are bimodal for some conditions. In the second part (Chapter 5), an algorithm enabling emissive displays to look like reflective paper is described and evaluated, giving an average error of ΔEab = 10.2 between display and paper. A field study showed that paper-like displays are more acceptable in bedrooms and that people are more likely to keep them always on than normal displays. Finally, the third part (Chapter 6) concerns the development and four-week trial of a paper-like display application. Using the autobiographical design method, a system for sharing bedtime with a remote partner was developed. We see that once unobtrusive, display systems are desired for use even in spaces like bedrooms.
Paper-like displays enable both emerging and existing devices to move into the periphery and become “invisible”, and therefore provide a new building block of calm technology that is not achievable using simple emissive displays
Bilingual Code Switching Patterns in Libyan Arabic-English School-Aged Children: A Study of Linguistic and Communicative Competence
Get PDFPh. D. Thesis.The aim of this study was to investigate language use in school-aged Arabic-English bilingual children growing up in the UK. Specifically, the main focus was to examine how bilingual children’s linguistic and communicative competence is reflected through their use of code switching in their interactions with other bilingual speakers. 30 children of Libyan families living aged between 8 and 11 were recruited for this study and were audio recorded while interacting with their friends in a Libyan Arabic school context, and with members of their families at home. Standardized language tests in both languages and sociolinguistic questionnaires were used to measure language competence, language use and the social context underpinning the children’s language development. All the children had been living in the UK since their early childhood and were fluent in both languages but were English-dominant. All of the parents had good command of English and positive attitudes towards their children’s bilingualism but preferred their children to use Arabic at home. Analyses of the children’s code switches revealed advanced levels of linguistic and communicative competence. This was exhibited through the children’s ability to alternate between the two codes without violating their syntactic or morphological constraints; it also showed in the way the children capitalized on their combined repertoire to index particular social and/or pragmatic motivations during their interactions with their interlocutors, enhancing their communicative strategies. The study makes an original contribution to the grammatical study of code switching, presenting results from two languages rarely looked at in combination; it also adds to existing research demonstrating the positive contribution of CS to bilingual discourse strategies.Libyan Ministry of Higher Educatio