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Now showing 1 - 5 of 11

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The MeerKAT Faint Radio Source Population
(University of the Western Cape, 2025) Mdwadube, Mfundo
This research presents a comprehensive multi-wavelength characterisation of the faint radio source population in the ADFS, covering approximately 10 deg2 near the South Ecliptic Pole and comprising a catalogue of 19 406 radio sources detected at 1.28 GHz. Using a dedicated cross-matching graphical user interface adapted from the MIGHTEE (2018) project, approximately 66% of the radio sources were successfully associated with optical and infrared counterparts from the HELP–ADFS master catalogue, with redshift information obtained for 8 944 sources (_ 46% of the full sample). During the cross-matching process, two giant radio galaxies (GRGs) were identified: GRG1 at RA _ 71.39_, Dec _ 􀀀52.9_ with a projected size of _ 1.41 Mpc at I = 0.667, and GRG2 at RA _ 70.33_, Dec _ 􀀀53.54_ with a projected size of _ 1.3 Mpc at I _ 0.24. Spectral energy distribution (SED) fitting using CIGALE was successfully performed for 7 874 sources, corresponding to _ 41% of the full radio catalogue and _ 88% of the redshift-identified sample. Based on the Bayesian AGN fraction and WISE colour–colour diagnostics, 2 116 sources were classified as active galactic nuclei (AGN) and 5 759 as star-forming galaxies (SFGs), with 984 sources remaining unclassified due to unconverged or missing SED fits. Approximately 558 AGN (_ 26% of the AGN population) satisfy the WISE AGN wedge selection criteria. The infrared–radio correlationwas investigated using the @IR parameter. The SFG population exhibits a well-defined correlation with a median @IR = 2.635_0.013, while AGN show systematically lower values (@IR _ 1.95 _ 0.016), consistent with excess radio emission arising from non-thermal AGNrelated processes.
Utilizing reclaimed water to enhance the sustainability of the water environment in valley urbanization in Chongqing
(University of the Western Cape, 2025) Ma, Nian
The process of urbanization would result in a series of environmental issues, posing significant challenges to the urban water environment and consequently impact the overall sustainability of urban development. The evaluation of the sustainability of urban water environment has attracted more and more attention from scholars and urban planners in both governments and civil societies. Climate change will exacerbate water scarcity and, along with population growth, land use and energy choices, make the sustainability of water environment a moving target. The cities in valley areas face greater uncertainty in environmental integrity due to their unique spatial patterns and hydrological and water resources conditions. This thesis evaluates the sustainability of the water environment sustainability and the role of reclaimed water use on sustainability in valley cities in Chongqing, Southwestern China, which, like most Chinese cities, are still in the process of urbanization. The study classified valley cities and identified their water environment characteristics by building models of “conceptual valley city” and “conceptual water system”. An evaluation indicator system and methodology for assessing water environment sustainability in valley cities are developed through a comprehensive challenging analysis. The indicator framework encompasses four elements: water resource diversity, water environment quality, water ecological health, and low carbon emissions.
Identification of Operons in clostridium difficile
(University of the Western Cape, 2025) Gountin, Hwenude Judicaëlle Chance
Clostridium difficile (C. difficile), an anaerobic, spore-forming, Gram-positive bacterium, is a major nosocomial pathogen that causes severe, toxin-mediated diarrhea and pseudomembranous colitis. Previous studies of pathogenic bacteria, including C. difficile, have investigated the operon structures and their roles in drug resistance and pathogenicity. Despite significant progress in understanding the genome and pathogenesis of C. difficile, predicting operon structures that contribute to its adaptability and virulence remains a challenge. Existing computational tools provide only partial insights, often limited by incomplete genome annotations, environmental variability, and the overwhelming complexity of bacterial regulatory networks. Consequently, there is a need for improved computational frameworks that integrate genomic, transcriptomic, and functional data to accurately predict and analyze operons in C. difficile. Recently, COSMO, an operon predictor developed using ML techniques, was employed to investigate the operon structures and their roles in drug resistance and pathogenicity in Mycobacterium tuberculosis. In this study, the COSMO algorithm was applied to a published Clostridium genomic dataset. Using COSMO and published RNA-seq datasets for Clostridium difficile, we identified and annotated operons in wild-type (WT) and vanS-mutant strains in the presence or absence of vancomycin or ramoplanin. This study (1) assessed the performance of the COSMO model operon predictions using a set of 28 experimentally validated operons (EVOs), and (3) evaluated the functional implications of the genomic organization of operons in response to vancomycin and ramoplanin antibiotic exposure. COSMO correctly identified 23 of the 28 EVOs, yielding high precision (88.46%) but relatively low sensitivity (45%), with an overall F1 score of 59.74%. The COSMO operon predictions were validated using 28 EVOs across WT and vanS mutant strains in the presence and absence of the two antibiotics. The COSMO algorithm proved reliable across the six experimental conditions, correctly identified 27 out of 28 EVOs each time, but failed to predict one EVO (cprABCK operon CD630_RS07455-CD630_RS07465). Fewer operons retain their original size in the presence of vancomycin in WT strain, and both expansions and contractions in operon boundaries were observed. Similarly, exposure to ramoplanin showed that 19 of the 28 EVOs retained their gene organization and gene content. The data suggest that, in a WT strain, both vancomycin and ramoplanin disrupt the underlying operon organization during the stress response.
The in vitro effect of SARS coronavirus 2 co-infection on lytic reactivation of an oncogenic herpesvirus
(University of the Western Cape, 2025) Roman, Kayleigh
The gamma-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV) has oncogenic potential, particularly in immunosuppressed patients, and Kaposi’s sarcoma (KS) is the most common AIDS-related malignancy. KS is of particular significance in Sub-Saharan Africa, where both HIV and KSHV prevalence are high. KSHV displays a biphasic life cycle consisting of latent and lytic stages, and the lytic phase is associated with active virus replication and disease pathology. The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, presents an additional undetermined risk of cancer development, affecting already vulnerable populations. Recent clinical studies suggest that there may be potential interplay between SARS-CoV-2 infection and reactivation of opportunistic herpesvirus infections. The present study aimed to design an in vitro model for investigating the effects of SARS-CoV-2 co-infection on KSHV lytic reactivation. Vero E6 cells were stably infected with rKSHV allowing for the establishment of latency in the cells (Vero E6 rKSHV), with the potential for reactivation upon exposure to specific conditions. Vero E6 rKSHV cells were used to determine if infection with SARS-CoV-2 live virus, or infection with a pseudovirus bearing SARS-CoV-2 spike(S), or just SARS-CoV-2 S protein treatment alone could initiate KSHV lytic reactivation. Both live virus and pseudovirus infection of the latently infected cells was sufficient to induce KSHV lytic reactivation. Importantly, no reactivation was observed in response to a pseudovirus bearing an unrelated envelope protein. Direct treatment with S protein also did not produce the same effect. We speculate that the KSHV reactivation seen in this cell model was induced by an indirect S protein-mediated mechanism. The data gathered in this study contributes to the current understanding of KSHV lytic reactivation in the context of respiratory virus infection. While the underlying mechanisms require further investigation, this study provides evidence supporting the clinical observations of KSHV lytic reactivation in COVID-19 patients.
Developing a high throughput screening assay for the discovery of SARS-CoV-2 entry inhibitors
(University of the Western Cape, 2025) Adams, Ethan
Despite the development and global distribution of vaccines, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continues to pose a public health challenge. Infections continue to persist today due to rapid mutation in the spike (S) protein, the target for vaccine-induced neutralizing antibodies. These mutations result in reduced vaccine efficacy and subsequent immune evasion by the virus, underscoring the urgent need for antiviral drugs to expand upon disease therapies. Identification of novel antiviral compounds can be achieved through the development of a robust assay suitable for high throughput screening (HTS). This assay must demonstrate high reproducibility and low variability to ensure reliable screening. To evaluate assay robustness, the statistical parameter Z-factor (Z’) was employed. This study aimed to develop a HTS assay to measure SARS-CoV-2 entry, and to validate the assay for HTS applications. To assess SARS-CoV-2 entry, a vesicular stomatitis virus (VSV)-based pseudovirus system was utilized, enabling work under biosafety level 2 (BSL-2) conditions.