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Synthesis and Functionalisation of Bridged Bicyclic amines
No full textBridged bicyclic amines are attractive building blocks for medicinal chemists as they are sp3 rich and present two nitrogen atoms for functionalisation. Despite this, they are often difficult to synthesise, requiring multistep synthesis routes, some of which require the use of hazardous reagents. Here we demonstrate that a variety of novel functionalised [4.2.1] bridged bicyclic diamines can be synthesised efficiently from simple ketones using a Beckmann rearrangement strategy. Furthermore, we show that each nitrogen can be selectively functionalised post rearrangement through a protection and deprotection sequence
Deep generative neural networks for nonlinear analysis and in-situ assessment of masonry
No full textFrom design to dialogue: a design-informed study on the experiences of Black undergraduates in Higher Education
Get PDFThis exploratory study employs design-based research methods to examine the experiences of Black undergraduate students in UK higher education institutions (HEIs). Through creative journals, participatory workshops, and expert consultation, the research investigates how design methodologies can amplify student voices and generate actionable insights for institutional change.
Seven Black undergraduate students participated in the initial phase through creative journals and interactive workshops. Their experiences informed the development of emotive design scenarios, which were then evaluated by ten EDI experts from UK universities. The study utilised remote participation methods, adapting traditional design approaches for digital engagement during the COVID-19 pandemic.
Key findings reveal persistent challenges in three areas: institutional barriers to accessing support, the disconnect between EDI rhetoric and implementation, and the impact of cultural isolation on student wellbeing. The research demonstrates how design-based approaches can generate rich insights into Black student experiences while providing novel tools for institutional dialogue and change.
This study contributes to the field through its innovative application of design methodologies to EDI research in higher education. The findings offer practical recommendations for enhancing Black student support services and developing more inclusive institutional practices. Future research directions include longitudinal applications of design-based methods and exploration of hybrid approaches to participatory engagement in EDI work
Potential of green engineering solutions toward sustainable residential buildings: a case study of Saudi Arabia
Get PDFIsolation, characterisation and assessment of therapeutic potential of bacteriophages which infect P. multocida
Get PDFPasteurella multocida (P. multocida) is a significant veterinary pathogen causing infections in avian and mammalian species, leading to substantial economic losses globally, particularly where multidrug-resistant (MDR) strains complicate treatment. Bacteriophage therapy presents a potential alternative to combat these infections, especially where conventional antibiotics are failing. This study aimed to isolate and characterise novel P. multocida phages from environmental sources and evaluate their therapeutic potential.
Fifteen distinct bacteriophages specifically targeting P. multocida were successfully isolated from raw sewage samples. All isolates were identified as tailed phages smillar to the Siphoviridae like morphology, possessing icosahedral capsids and linear double-stranded deoxyribonucleic acid (dsDNA) genomes. Physiological characterisation revealed stability across a pH range of 4-10 and temperatures up to 50°C, with three phages demonstrating notable tolerance up to 60°C. The phages exhibited narrow host ranges and moderate replication kinetics, with an average latent period of 40 minutes and burst sizes ranging from 30.2 to 52.5 PFU/cell. Genomic analysis confirmed high sequence similarity among the isolates and classified them as temperate Mu-like phages (Vieuvirus genus), closely related to prophages found in P. multocida genomes but distinct from previously characterised lytic phages. In vivo assessment using a Galleria mellonella infection model with selected phages (P1 and N1) demonstrated that prophylactic administration provided significantly greater protection against lethal P. multocida challenge compared to therapeutic treatment
ZEB1 signalling in endothelial cell heterogeneity
Get PDFEndothelial cells (ECs) are at the core of vascular homeostasis, enabling angiogenesis, immune cell trafficking and barrier function. Zinc-finger E-box binding protein 1 (ZEB1) has recently emerged as a central regulator of EC plasticity, particularly through its roles in endothelial-to-mesenchymal transition (EndoMT) and vessel remodelling. Here, we test the hypothesis that ZEB1 expression dynamically modulates EC heterogeneity and specialisation during both developmental and pathological angiogenesis. Using siRNA knockdown (KD) and chromatin immunoprecipitation (ChIP)-seq in human umbilical vein endothelial cells (HUVECs), we show that ZEB1 broadly influences genes controlling cell adhesion, immune responses and tip-cell identity and cooperates with ETS and AP-1 transcription factors. Analyses of publicly available scRNA-seq datasets revealed ZEB1 enrichment in specialised EC subpopulations across multiple tissues, including venous-capillary ECs in the spleen, tip cells in the retina, tumour-associated ECs and floor ECs of the subcapsular sinus of the lymph node. Further analysis of myocardial infarction scRNA-seq data demonstrated that ZEB1 contributes to a partial EndoMT phenotype, wherein ECs retain some endothelial traits while acquiring mesenchymal characteristics. A text-mining approach further uncovered a proposed ZEB1 regulatory network in EndoMT. Finally, we demonstrate that adult induced ZEB1 knockout in adult retina ECs does not alter vascular area or number of ECs. Collectively, these findings position ZEB1 as a context-dependent modulator of ECs
Glutamate receptor-mediated m6A-RNA regulation of synaptic plasticity and neuronal function
No full textCoordinated neuronal activity is fundamental for brain function and relies on tightly regulated molecular processes. Epitranscriptomic mechanisms, particularly N6-methyladenosine (m6A) RNA modification, have emerged as important regulators of RNA stability and translation. This modification is implicated in synaptic plasticity, the activity-dependent changes in synaptic strength that underly learning, memory, and cognition. Dysregulation of such processes contributes to neurological disorders. Increasing evidence links altered m6A dynamics to neurodegenerative diseases, including Parkinson’s disease and Dementia with Lewy bodies, both of which are characterised by α-synuclein pathology. However, the precise molecular mechanisms linking m6A to synaptic dysfunction and disease remain poorly understood.
In this thesis, I tested the hypothesis that transcripts central to synaptic plasticity, including those relevant to synucleinopathies, are differentially m6A-modified across the brain, and that activation of glutamate receptors alters the interactions between m6A-RNAs, their effector proteins, and α-synuclein. The thesis further explored whether m6A regulation of plasticity occurs within a broader framework of cross-talk with other RNA modifications and mitochondrial processes.
Analysis of high-throughput m6A-RNA sequence data of multiple human brain regions revealed region-specific modification patterns. The cerebellum displayed the highest enrichment of m6A-modified transcripts, while ionotropic glutamate receptor subunits GRIN2A and GRIA2 were among the most highly and multi-modified. These findings suggest that m6A modification may display regional diversity in brain function regulation.
In vitro studies using differentiated SH-SY5Y (dSH-SY5Y) neuronal cells demonstrated that m6A modifications are highly dynamic in response to receptor stimulation. Activation of NMDA, AMPA, and kainate receptors (NMDAR, AMPAR and KAR) revealed distinct temporal patterns of m6A-RNA colocalisation with m6A effector proteins. Notably, KAR activation for 5 minutes increased YTHDF2 colocalisation with m6A in both cytoplasmic and postsynaptic compartments, whereas NMDAR and AMPAR activation produced significant reductions. The m6A demethylase, ALKBH5 showed increased postsynaptic region colocalisation with m6A after activation of all receptor subtypes, and NMDAR stimulation enhanced demethylase activity in both cytoplasmic and synaptic fractions. These results suggest that m6A-RNA is dynamically regulated during early phases of synaptic plasticity.
Transcriptome-wide profiling of NMDA-stimulated dSH-SY5Y cells further identified differential m6A modification of synapse-relevant transcripts, including those encoding glutamate receptors, SNARE proteins, cytoskeletal elements, and mitochondrial respiratory chain components. This highlights the role of m6A in regulating transcripts critical for both synaptic signalling and cellular energetics.
The relationship between m6A and α-synuclein was also investigated. While the SNCA transcript was not extensively modified, SNCG, which encodes γ-synuclein, was highly multi-modified. Colocalisation studies revealed that phosphorylated α-synuclein associates with m6A-RNAs at presynaptic sites, and that this association increases following oxidative stress. These findings suggest a functional link between m6A and α-synuclein biology, with potential implications for synaptic vulnerability in neurodegenerative disease.
Finally, evidence was obtained for cross-system regulation between m6A and other RNA modifications. Reciprocal modification of transcripts encoding m6A and m5C effector proteins was observed, and proteomic analyses revealed shared functional pathways involving phosphorylation, SUMOylation, ubiquitination, and mitochondrial processes. Colocalisation of m6A with m5C and m3C after NMDAR activation further supported the view that multiple RNA modifications act cooperatively to regulate neuronal plasticity.
In conclusion, this thesis demonstrates that m6A-RNA modification is a rapid, dynamic regulator of glutamate receptor-mediated synaptic plasticity. It acts on key synaptic and mitochondrial transcripts, interacts with α-synuclein at presynaptic sites under stress conditions, and engages in crosstalk with other RNA modification systems. Together, these findings establish m6A-RNA regulatory dynamics as a central epitranscriptomic mechanism that integrates neurotransmission, mitochondrial function, and RNA modification networks, providing novel insight into synaptic regulation and disease mechanisms
The relationship between hyperacusis and tinnitus; an exploration of measures, characteristics, and lived experiences
No full textTinnitus and hyperacusis are known to co-occur, but very little is known about the relationship between them, or the lived experiences of people who have both. The co-occurrence of tinnitus and hyperacusis introduces significant difficulties for the assessment and management of the conditions, hyperacusis measures are limited, and tinnitus measures do not capture co-occurrence in a way that reflects the true experience of people with both conditions. This research aimed to investigate the relationship between hyperacusis and tinnitus by characterising people who have co-occurring hyperacusis and tinnitus and exploring their lived experiences. A scoping review of research in people with tinnitus and hyperacusis was conducted and identified gaps in knowledge regarding basic demographic level information of people with tinnitus and hyperacusis, and the chronology of the two conditions. The most frequent measure of hyperacusis in research was found to be the Hyperacusis Questionnaire (HQ), for which significant issues with the underlying structural and content validity have been noted. This was used to inform the conceptualisation of a series of studies that aimed to address (1) whether hyperacusis questionnaires are fit for purpose in adults who have co-occurring hyperacusis and tinnitus, and (2) what is the real lived experience of having both conditions. Firstly, a readability assessment of five hyperacusis questionnaires, incusing the HQ was conducted, and found that all questionnaires exceeded recommended reading levels (5th to 6th grade), and all had considerable inter-item variability. High readability can compromise the reliability of data gathered using questionnaires, which are crucial for assessment and management of hyperacusis. A cross-sectional mixed-method study comprising of an online demographic survey (Phase 1) and semi-structured interviews (Phase 2) was conducted to gather characteristics of people with co-occurring hyperacusis and tinnitus, and their lived experiences. Finally, the first evaluation of the HQ in a population with co-occurring hyperacusis and tinnitus was carried out, inspecting structural and content validity, reliability, and responsiveness of the scale. The underlying structure was not confirmed in this population, and results indicate that the HQ may not be a valid measure of hyperacusis in people with co-occurring tinnitus and hyperacusis
Computation pathology for a better understanding of breast cancer behaviour
No full textBackground
Oestrogen receptor (ER)-positive tumours constitute more than 70% of all breast cancer (BC) and are typically treated with endocrine therapy (ET). While ER positivity is currently defined by ≥1% nuclear staining on immunohistochemistry (IHC), this threshold does not fully capture the biological and clinical heterogeneity of ER-positive tumours. Quantitative ER expression levels and ER-regulated gene profiles are significantly correlated with tumour characteristics, patient outcomes and response to therapy. Furthermore, ER-low positive BC and invasive lobular carcinoma (ILC) represent diagnostic and therapeutic challenges within ER-positive BC subgroup. This study aims, first, to comprehensively assess the clinical, molecular, and morphological characteristics of ER-positive BC, and second, to identify biomarkers predictive of ET response and to investigate the role of tumour microenvironment (TME) and histological subtype in prognostication and treatment stratification. The addition of a computational pathology approach plays a key role in extracting quantitative insights from digital pathology data, enabling a deeper understanding of tumour heterogeneity and aiding in the development of predictive models for personalised treatment in ER-positive BC. The use of artificial intelligence (AI) has revolutionised cancer research, providing significant value in assessing subtle and complex histological and molecular features. This project also utilised AI to decipher specific features associated with ER-positive BC.
Methods
This study utilised multiple large, well-characterised cohorts, including more than 7,000 Nottingham BC patients, as well as transcriptomic data from The Cancer Genome Atlas (TCGA) and the METABRIC datasets. ER expression was evaluated semi-quantitatively using IHC percentage, staining intensity, and the histochemical score (H-score), and further analysed using RT-qPCR and in situ hybridisation (ISH) to quantify ESR1 mRNA. Differential gene expression analysis was carried out to explore key ER-regulated genes. Prognostic and predictive genes were validated at the mRNA and protein levels. Stromal morphology and tumour-infiltrating lymphocytes (TILs) were assessed using whole slide images and AI algorithms. ILC subtypes were histologically evaluated, and their nuclear morphology was further characterised using digital image analysis. The survival outcomes and prognostic biomarkers of ILC were also investigated.
Results
Quantitatively higher ER expression was associated with favourable prognostic features and a better response to ET therapy, with maximal benefit observed at 100% expression. Tumours with ≥10% ER staining behaved more like ER-positive cancers, while those with 1–9% expression demonstrated clinicopathological similarity to ER-negative BC. Repeat IHC and molecular validation confirmed that a substantial proportion of ER-low positive tumours were, in fact, ER-negative. ESR1 mRNA analysis further improved diagnostic accuracy and identified additional ER-positive cases that were diagnosed as ER-negative BC on IHC. The ER H-score proved to be an independent prognosticator, with outcome stratification at thresholds of 30, 100, and 200. Following analysis of a large number of ER-regulated genes, progesterone receptor (PR) and GREB1 emerged as robust and strong predictors of ET response. SUSD3 was also highly expressed in ER-positive BC and was associated with favourable outcomes and ET responsiveness. High stromal TILs and fibroblast content were associated with a more aggressive tumour characteristics and poor prognosis in luminal BC. Conversely, a high stroma-to-tumour ratio was associated with better outcomes. AI-based quantification of TILs offered greater objectivity and prognostic value compared with visual assessment alone. ILC, accounting for 11% of BC, exhibited marked heterogeneity. Classic ILC (cILC) was associated with more favourable survival compared with invasive ductal carcinoma of no special type. Contrasting this, pleomorphic (pILC) and high-grade solid ILC (sILC) variants comprised a distinct, aggressive subgroup characterised by poor chemotherapy response and higher rates of recurrence and BC-specific mortality. The morphology of pILC was heterogeneous and showed apocrine and non-apocrine subtypes with distinct features. Furthermore, high expression of INO80C and RECQL4 was associated with poor outcomes in ILC.
Conclusions
This study demonstrated that ER-positive BC is not a biologically uniform entity. Quantitative ER assessment, molecular profiling, and identification of novel biomarkers can significantly enhance the prediction of ET response. An ER expression threshold of ≥10% more accurately defines true ER positivity. RNA-based methods, RT-qPCR and ISH can complement IHC to enhance diagnostic accuracy and treatment decisions. The prognosis of ILC could be further refined by identifying aggressive subtypes and prognostic biomarkers, thereby guiding personalised treatment strategies. Digital image analysis and AI algorithms have proven significant value in assessing specific features that can be challenging for pathologists and can improve the objectivity of specific prognostic and predictive variables in BC. Including these assessments in routine practice can help improve risk stratification for patients with ER-positive BC
EnACTing change: an exploration of older adults experiences of change with Acceptance and Commitment Therapy
Get PDFBackground
Older adults (OAs) are an increasing demographic, with a range of physical health and mental health challenges that are unprioritized. Psychotherapy has utility with OAs, despite assumptions about their difficulties engaging due to the comorbidities of their physical and mental health and social stressors. The promising evidence base and the transdiagnostic and practical nature of Acceptance and Commitment Therapy (ACT) makes it appear uniquely suited for this client group (Petkus & Wetherell., 2013; Robert et al., 2016). However, there is a lack of exploration of the processes of change for ACT, for OAs, and generally – despite that understanding processes of change is thought allow for the optimisation of psychotherapy (Kazdin, 2007).
Methods
This thesis project completed secondary qualitative analysis using Change Interview data from three Hermeneutic Single Case Efficacy Design series studies that used ACT interventions with OAs with dementia, or depression and anxiety, or who were hearing voices. An inductive-deductive reflexive thematic analysis was used, and the inductive analysis allowed for exploration of OAs experiences of change. The deductive analysis allowed for exploration of the theoretically proposed ACT-specific and common factors processes that might have underpinned experiences of change. Analysis was completed on the semantic and latent levels of meaning, and saliency analysis and consultation with an expert by experience were used to enhance analysis.
Results
Three themes were generated from the data and highlighted that participants experiences of change were moderated by whether it was the right time for them to engage considering their circumstances and access to internal and external resources, that therapy led to behavioural changes and realisations, and that they experienced they experienced positive therapeutic relationships and their therapists as skilled, but that therapy was exposing. ACT-specific processes of psychological flexibility were evidenced throughout, but so were the processes of psychological inflexibility. This might explain some of the variance in change captured in the original studies.
Discussion
This thesis has provided a unique contribution to the literature by highlighting how OAs experienced change, the contexts that impact their experiences of change, and the therapy-specific and common factors processes that mapped onto their experiences of change. The findings have provided evidence towards the transdiagnostic nature of ACT. The findings are theoretically aligned the findings with the understanding of change-processes, the behavioural origins of ACT. However, the results give greater detail about the contexts and types of factors that impact OAs experiences of change, and provide experiential evidence to supplement the current evidence base for ACT. Future research would do well to address the limitations of this study in terms of the limited diversity of OAs, and to consider using current ideas like social capital or stabilisation to help OAs to engage at the right time and with the right resources to benefit from therapy.
This study has also provided evidence towards the utility of secondary qualitative analysis for the field of contextual behavioural science, and how Change Interview data can be used to provide new insights with populations where research can be burdensome
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