DSpace Community:

New methods for the discovery and characterization of bacterial natural products

Wed, 01 Jan 2025 00:00:00 GMT

Title: New methods for the discovery and characterization of bacterial natural products Authors: Sumang, Felaine Anne Abstract: Actinomycetes are renowned for their ability to produce a wide array of natural products (NPs), with a broad range of applications. NPs are typically encoded by biosynthetic gene clusters (BGCs). Bioinformatic analysis of sequenced Actinomycetes genomes have shown that they possess many BGCs whose potential products are not detected under standard laboratory culture conditions. Advances in genome mining and molecular biology have led to the development of diverse strategies to activate these “cryptic” BGCs, but further improvements in these methods are warranted. This thesis explores multiple approaches for discovering novel bioactive compounds from Actinomycetes and investigating their BGCs. Chapters 3 and 4 focus on the development of a new bacterial artificial chromosome (BAC) vector, designated pJE2, and optimization of a protocol for genomic library construction enabling the isolation of large BGCs. This approach was applied to Actinomadura madurae T576, a producer of unusual sulphated metabolites, resulting in a BAC library from which a clone harbouring the complete 80 kbp BGC responsible for these metabolites was identified. Heterologous expression of this clone in Streptomyces albus successfully led to production of the sulphated metabolites. Screening of additional clones also revealed the successful capture of several previously uncharacterized BGCs. Chapter 5 focuses on a chemical elicitation method, using plant extracts to stimulate NP production in soil-derived Actinomycetes. Notably, hibiscus flower extract induced the production of the antibiotic thiolutin by Streptomyces strain MBN 2-2. Further analysis identified hibiscus acid and hydroxycitric acid as the elicitor compounds. The final chapter centres on associating putative BGCs with the synthesis of three novel antibiotics demurilactone A, persiathiacin, and quinovosamycin. In all three cases, insertional mutagenesis led to the abolition of antibiotic synthesis, thereby validating assignment of the BGCs to their respective antibiotics. Description: Ph. D. Thesis.

Structured cardiac assessment and treatment following exacerbations of Chronic Obstructive Pulmonary Disease

Wed, 01 Jan 2025 00:00:00 GMT

Title: Structured cardiac assessment and treatment following exacerbations of Chronic Obstructive Pulmonary Disease Authors: Kibbler, Joseph Abstract: Introduction: Heart disease is common in COPD, yet is inadequately managed due to systemic deficiencies in both diagnosis and treatment. Through a systematic review and meta-analysis of published studies, it is estimated that 10-20% of patients have undiagnosed left ventricular systolic dysfunction. During exacerbations of COPD (ECOPD), cardiac risk is temporally elevated. In view of these problems, a pilot randomised controlled trial, examining the feasibility and effect of inpatient structured cardiac assessment (SCA) to diagnose and prompt guideline recommended treatment of heart disease, was conducted. Methods: 115 inpatients with ECOPD were randomised 1:1 to receive usual care (UC, n=58) or SCA (n=57), comprising transthoracic echocardiography, CT coronary artery calcium scoring, 24-hour ECG, blood pressure and diabetes assessment. Follow-up was for 12 months. The prevalence of underdiagnosis and undertreatment of heart disease were captured, and potential outcome measures for future trials assessed. An economic analysis was also rehearsed. Results: Among patients undergoing SCA, 42/57 (73.7%) received a new cardiac diagnosis compared with 11/58 (19.0%; p<0.001) in UC. When heart disease was diagnosed, the proportion receiving optimal treatment at discharge was significantly higher in SCA (35/47 (74%) vs 4/11 (34%); p=0.029). There was no difference in days alive outside hospital between the arms. Survival curves for both adverse cardiovascular and cardiopulmonary events separated throughout follow-up, with ACE occurring in 17.2% in usual care vs. 10.5% in SCA in one year. The economic analysis suggested a low probability of cost-effectiveness, but estimates were very broad. Conclusions: A structured cardiac assessment during ECOPD significantly improved diagnosis and treatment of heart disease. Further research is needed in order to establish how to deliver SCA with the greatest clinical and economic effectiveness. Future interventional trials should use time to first adverse cardiovascular or cardiopulmonary event as the primary outcome. Description: PhD Thesis

Investigating the Role of Structural Variation in Male Infertility

Wed, 01 Jan 2025 00:00:00 GMT

Title: Investigating the Role of Structural Variation in Male Infertility Authors: Kalyon, Oguzhan Abstract: Infertility affects approximately one in six couples globally, with male factors contributing to roughly half of all cases. Although chromosomal abnormalities such as Klinefelter’s syndrome and Y chromosome microdeletions are well-established causes of male infertility (MI), nearly 40% of cases remain idiopathic. The role of structural variants (SVs) and dominant inheritance pattern has been understudied, primarily due to technical limitations in identifying SVs and the lack of patient-parent trio analyses required to investigate dominant de novo variants. In this thesis, we performed whole-genome sequencing (WGS) on 216 patients with idiopathic azoospermia and their parents to investigate SVs across different inheritance models, with a particular focus on the dominant model. Additionally, whole-exome sequencing (WES) was conducted on 234 additional patients with azoospermia. In these cohorts, we identified several SVs that clearly explained the patients' phenotypes, as well as numerous potentially causative SVs that revealed novel candidate male infertility genes and loci. This study demonstrates that WGS is an effective tool for studying SVs and significantly advances our understanding of the genetic basis of male infertility, particularly regarding the contribution of SVs. Description: PhD Thesis

How safe are electronic prescribing systems? Evaluating a simulation tool to assess the use of medication-related decision support in electronic prescribing systems in the UK

Wed, 01 Jan 2025 00:00:00 GMT

Title: How safe are electronic prescribing systems? Evaluating a simulation tool to assess the use of medication-related decision support in electronic prescribing systems in the UK Authors: Heed, Judith Abstract: Electronic prescribing (EP) is widely adopted in healthcare to enhance medication safety and efficiency. Evidence suggests that EP reduces medication errors and adverse drug events, though the extent of benefits can be influenced by several factors, including how the EP system was designed, implemented, customised, and adopted. The researcher considered these different challenges in Chapter 1 and highlighted the importance of optimising EP systems to maximise their benefits. A systematic review of the literature was conducted to explore tools that have been previously used to evaluate the safety of EP systems. Thirteen papers were identified that described tools that were implemented in USA, Canada, Austria, Denmark, France and Korea. (Chapter 2). No equivalent UK tool was found. To address this knowledge gap, the researcher described the development of the e-Prescribing Risk and Safety Evaluation (ePRaSE) tool in the UK and its different component parts (Chapter 3). The researcher then conducted an eDelphi study to obtain expert consensus on the level of risk associated with preventable EP events (Chapter 4). The usability and acceptability of the ePRaSE assessment was then explored using different qualitative methods (Chapter 5). Thirty-two healthcare professionals across 22 different NHS hospitals participated in semi-structured interviews (n=25) and thirteen think-aloud observations (n=20) involving 11 different EP systems. The tool was found to be useful and acceptable, with some areas for further improvement identified (Chapters 6-8). The researcher also presented quantitative results obtained from the national rollout of ePRaSE in 45 hospitals (Chapter 9). Variation in scores was observed, independent of EP system vendor and scope for improvement in EP system configuration was apparent. An overarching discussion and conclusion drawing on both qualitative and quantitative findings was presented in Chapter 10, and key recommendations made to further refine the ePRaSE assessment and help inform future research in this area. Description: PhD Thesis