List of Titles

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Molecular Detection of Antibiotic-Resistant Genes in Pseudomonas aeruginosa from Nonclinical Environment: Public Health Implications in Mthatha, Eastern Cape Province, South Africa

- Mojisola Clara Hosu, Sandeep Vasaikar, Grace Emily Okuthe, Teke Apalata

Authors: Mojisola Clara Hosu , Sandeep Vasaikar , Grace Emily Okuthe , Teke Apalata
Date: 5 January 2021
Subjects: Microbiology
Language: English
Type: Journal Article
Identifier: http://hdl.handle.net/11260/2417 , vital:41877
Description: Evaluation of resistant profiles and detection of antimicrobial-resistant genes of bacterial pathogens in the nonclinical milieu is imperative to assess the probable risk of dissemination of resistant genes in the environment. .is paper sought to identify antibiotic-resistant genes in Pseudomonas aeruginosa from nonclinical sources in Mthatha, Eastern Cape, and evaluate its public health implications. Samples collected from abattoir wastewater and aquatic environment were processed by membrane filtration and cultured on CHROMagarTM Pseudomonas medium. Species identification was performed by autoSCAN-4 (Dade Behring Inc., IL). Molecular characterization of the isolates was confirmed using real-time polymerase chain reaction (rPCR) and selected isolates were further screened for the possibility of harboring antimicrobial resistance genes. Fifty-one Pseudomonas species were recovered from abattoir wastewater and surface water samples, out of which thirty-six strains were Pseudomonas aeruginosa (70.6%). .e P. aeruginosa isolates demonstrated resistance to aztreonam (86.1%), ceftazidime (63.9%), piperacillin (58.3%), cefepime (55.6%), imipenem (50%), piperacillin/tazobactam (47.2%), meropenem (41.7%), and levofloxacin (30.6%). Twenty out of thirty-six P. aeruginosa displayed multidrug resistance profiles and were classified as multidrug-resistant (MDR) (55.6%). Most of the bacterial isolates exhibited a high Multiple Antibiotic Resistance (MAR) Index ranging from 0.08 to 0.69 with a mean MAR index of 0.38. In the rPCR analysis of fifteen P. aeruginosa isolates, 14 isolates (93.3%) were detected harboring blaSHV, six isolates (40%) harbored blaTEM, and three isolates (20%) harbored blaCTX-M, being the least occurring ESBL. Results of the current study revealed that P. aeruginosa isolates recovered from nonclinical milieu are resistant to frontline clinically relevant antipseudomonal drugs. .is is concerning as it poses a risk to the environment and constitutes a public health threat. Given the public health relevance, the paper recommends monitoring of multidrug-resistant pathogens in effluent environments.
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VIVA Comrade Moss

- NUMSA

Authors: NUMSA
Date: 25 April
Subjects: NUMSA
Language: English
Type: text
Identifier: http://hdl.handle.net/10962/109640 , vital:33163 , SALHA 14b : NUMSA
Description: The last 'Trial Update" reported on Comrade Moss’s case until mid-March. This report covers the period from that time up until 25th April.STADLER - "ANC EXPERT" Brigadier Stadler testified that the ANC had made certain calls to organisations within the country which, according to his "research", had been followed by organisations in the country. As examples he gave the ANC’s call for ungovernability, the formation of organs of people’s power and the destruction of town councils. During cross-examination Stadler conceded that he was not able to give examples of any direct link between the ANC and organisations inside the coutry but he said an inference could be drawn by looking at the ANC’s call and the behaviour of organisations inside the country.
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Date Issued: 25 April

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Morphology, histology and histochemistry of the digestive tract of the Banded tilapia, Tilapia sparrmanii (Perciformes: Cichlidae)

- Grace E. Okuthe, Bongile Bhomela

Authors: Grace E. Okuthe , Bongile Bhomela
Date: December 23, 2020
Subjects: Fish, gastrointestinal tract, histo-architecture
Language: English
Type: Journal Article
Identifier: http://hdl.handle.net/11260/2425 , vital:41881
Description: ABSTRACT. This study described anatomical, histological and histochemical features of the mucosal layer of the digestive tract of Tilapia sparrmanii Smith, 1840, an omnivorous freshwater fish endemic to Southern Africa. This species exhibited a short thick oesophagus with long deep longitudinal folds (466.68 ± 16.91 µm), and a thick (173.50 ± 10.92 µm) muscular layer that allow the passage of large food items. The mucosa was lined with stratified secretory epithelium rich in goblet cells that secreted neutral and acid mucins. The stomach was a sac-like structure with simple tubular glands surrounded by connective tissue. The mucosa was lined with simple columnar epithelium and the lamina propria exhibited a well-developed layer of gastric glands that occupied the entire length of the cardio-fundic region. The stomach mucosa consisted of epithelial cells with intense neutral mucin secretion which protects against gastric juice. Neck cells of gastric glands synthesized neutral and acid mucins. The intestine was highly coiled and presented a complex pattern of transversal folds internally (villi). Villi length decreased progressively from the anterior to the posterior intestine (p < 0.0001). Tunica muscularis of the mid-intestine had the thinnest thickness among all parts of the intestine (p < 0.0001). Goblet cells whose numbers increased towards the rectum secreted both acid and neutral mucins. The results indicate structural similarities of T. sparrmanii GIT with other tilapia species and will be useful for understanding the physiology of the digestive systems as well as functional components of the GIT.
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The prevalence of insufficient iodine intake in pregnancy in Africa: Protocol for a systematic review and meta-analysis

- Charles Bitamazire Businge, Benjamin Longo-Mbenza, Andre Pascal Kengne

Authors: Charles Bitamazire Businge , Benjamin Longo-Mbenza , Andre Pascal Kengne
Date: 22-8-2019
Language: English
Type: text , article
Identifier: http://hdl.handle.net/11260/3387 , vital:43338 , https://systematicreviewsjournal.biomedcentral.com/articles/10.1186/s13643-019-1092-7#citeas
Description: Background: Insufficient iodine intake in pregnancy is associated with many adverse pregnancy outcomes. About 90% of African countries are at risk of iodine deficiency due to poor soils and dietary goitrogens. Pregnancy predisposes to insufficient iodine nutrition secondary to increased physiological demand and increased renal loss. Iodine deficiency is re-emerging in countries thought to be replete with pregnant women being the most affected. This review seeks to identify the degree of iodine nutrition in pregnancy on the entire African continent before and after the implementation of national iodization programmes. Methods: A systematic search of published literature will be conducted for observational studies that directly determined the prevalence of insufficient iodine intake among pregnant women in Africa. Electronic databases and grey literature will be searched for baseline data before the implementation of population-based iodine supplementation and for follow-up data up to December 2018. Screening of identified articles and data extraction will be conducted independently by two investigators. Risk of bias and methodological quality of the included studies will be assessed using a risk of bias tool. Appropriate meta-analytic techniques will be used to pool prevalence estimates from studies with similar features, overall and by major characteristics including the region of the study, time period (before and after implementation of iodization programmes), sample size and age. Heterogeneity of the estimates across studies will be quantified and publication bias investigated. This protocol is reported according to Preferred Reporting Items for Systematic reviews and Meta-Analysis protocols (PRISMA-P) 2015 guidelines. Discussion This review will help ascertain the impact of national iodization programmes on the iodine nutrition status in pregnancy in Africa and advise policy on the necessity for monitoring and mitigating iodine deficiency in pregnancy in Africa. This review is part of a thesis that will be submitted to the Faculty of Health Sciences, University of Cape Town, for the award of a PhD in Medicine whose protocol has been granted ethics approval (UCT HREC 135/2018). In addition, the results will be published in a peer-reviewed journal.
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Date Issued: 22-8-2019

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Ethnobotany and conservation biology of Warburgia salutaris (G.Bertol.) Chiov., a threatened medicinal plant in southern Mozambique

- Senkoro, Annae Maria

Authors: Senkoro, Annae Maria
Date: 2022-04-08
Subjects: Uncatalogued
Language: English
Type: Doctoral thesis , text
Identifier: http://hdl.handle.net/10962/232967 , vital:50042 , DOI 10.21504/10962/232967
Description: Warburgia salutaris, locally known as “chibaha” (Ronga, Tsonga), “isiBhaha” (Zulu) and “siBhaha” (Siswati), is one of the most highly-valued medicinal plant species in southern Africa. Its bark has long been employed to treat bacterial and fungal infections, and it is often a front line herbal treatment for malaria. The species is popular in rural and urban areas due to its lower price compared to commercial pharmaceuticals and because of its long-standing spiritual and symbolic significance. Consequently, W. salutaris is threatened in Malawi, South Africa and Swaziland and is believed to be extincted in the wild in Zimbabwe. In Mozambique, where the tree is confined to the southern part of the country, it is considered vulnerable due to high local demand and cross-border export. Although there is limited research, further work is urgently needed to provide the basis for options and strategies to achieve desired outcomes. This study aimed to explore different approaches for the conservation of W. salutaris in the Lebombo Mountains (LM), the Tembe River (TR) and the Futi Corridor (FC) areas, in southern Mozambique. For this, potential distribution, socio cultural factors that influenced sustainable management of the species, demography, harvest impact, genetic diversity and population differentiation were considered. The kuenm package in R, 2 846 occurrence and 11 environmental data were used to model the potential current and future distribution in 2050 and 2070 using four general circulation models (CESM1(BGC), ACCESS1.3, FIO-ESM and IPSL-CM5A-MR) under representative concentration pathways (RCPs) 4.5 and 8.5. The extent of occurrence (EOO) and habitat suitability (HS) were also determined. Stratified random semi-structured interviews with 182 heads of households were carried out to explore cultural and socio incentives of use, compared knowledge distribution, determine local management practices and explore local ecological knowledge related to the species in the three study areas. In addition, 17 focus group discussion were conducted to clarify issues raised during household interviews. One hundred and twenty four quadrants were used to determine the abundance and population structure. The Simpson index of dominance, permutation index and quotient between consecutive classes were used to assess population stability, and an eight point scale was used to evaluate the extent of bark damages. Genomic deoxyribonucleic acid (gDNA) (n=48) was used to assessed genetic diversity and population structure through the newly developed single sequence repeats (SSR) molecular markers. Model selected was statistical significant for prediction of potential distribution of W. salutaris in southern Mozambique (partial ROC =0.00, omission rate = 0.04 and delta AICc = 0.00). The current environmental conditions mostly explained by climatic predictor, indicated in general, the potential distribution on areas of occurrence observed during the field work in southern Mozambique. Future project suggested an increase of climatic suitable areas in all the general circulation models in both conservative and pessimistic climatic scenarios (RCPs 4.5 and 8.5, respectively) in 2050 and 2070, and consequently the increase of HS and the EOO. Results of this work suggests W. salutaris would not extinct at least in the coming 50 years due to climate change but other threats such as overexploitation of the species need to be addressed. With increase of climatic suitable areas, conservation and management of this species could focus on reintroduction and cultivation for recovery of the species, with the help of time. W. salutaris was used for medicinal purposes to treat 12 health problems, with the bark being the most commonly used part (92% of informants). Knowledge of the species uses differed significantly between the three study areas but not with respondent gender or age. Informants also mentioned a considerable number of alternative species of W. salutaris (37 species in LM, 33 species in TR and 17 species in FC). Local ecological knowledge on the ecological niche of the species also varied substantial in the three areas with both types of knowledge generally higher in the Tembe River area. Local management practises were revealed mostly on harvesting through vertical bark stripping cited by 100% of informants in TR, 61.6% FC and 51.7 LM (71% of all informants). Yet most (64.3% of all informants, corresponding to 98.4% in TR, 51.7% in Fc and 41.7% LM) used non-traditional harvesting tools (machete) bark removal. For sustainable use of the species, consideration should be given to combined conservation strategies such as the use of alternative species with the same application, substitution of bark by leaves, and increases in alternative sources of plant material through cultivation. The densities of alive stems were not statistically different in the three areas but was higher in LM (mean of 4500.3±9209.8 stems/ha). Equally the mean densities of recruits (diameter ≤2 cm) were not considerable different but was higher in the FC (3296.8±9116.7 stems/ha). The regression analyses for the three study area revealed negative slopes, indicating more recruits and fewer individuals in larger classes. The Simpson indexes of dominance, permutation indexes and quotients between the consecutive size classes suggested some levels of population instability in the three areas. Harvesting took place in the eight point scale, all size classes were harvested but preference was higher on intermediate (15.1-20 cm) or larger (>20 cm) size classes in all the study areas but gatherers avoided harvesting bark from recruits. Although the mean densities of harvested stem was not significant this work indicated higher levels of stem destruction in FC. Harvested dead stems ware significant in the three areas and FC had the higher of (39.5±85.9 stems/ha) compared to 7.6±19.1 and 2.1±4.3 in TR and LM, respectively. Equally, the density of physiologically stressed stems differed substantially in the three areas with higher in FC 20.5± 75.5 stems/ha compared to 18.7±82.9 stems/ha in TR and 3.8±11.8 stems/ha in LM. This results suggests implementation of protection measures such as the inclusion of the species in the national CITES list to regulated cross-border trade and strengthening of the law enforcement. Genetic diversity, structure and gene flow in the exiting populations of southern Mozambique revealed that despite fragmentation and overexploitation, this species maintains a relatively high level of genetic diversity supporting the existence of random mating. Two genetic groups were found corresponding to the northern (LM and TR) and southern (FC) areas. The study suggests that, if local extinctions occurred in Mozambique, the pepper-bark tree persisted in sufficient numbers to retain a large proportion of genetic diversity. Management plans should concentrate on maintaining this high level of genetic variability through both in and ex-situ conservation actions. , Thesis (PhD) -- Faculty of Science, Environmental Science, 2022
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Date Issued: 2022-04-08

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The characterization of GTP Cyclohydrolase I and 6-Pyruvoyl Tetrahydropterin Synthase enzymes as potential anti-malarial drug targets

- Khairallah, Afrah Yousif Huseein

Authors: Khairallah, Afrah Yousif Huseein
Date: 2022-04-08
Subjects: Uncatalogued
Language: English
Type: Doctoral thesis , text
Identifier: http://hdl.handle.net/10962/233784 , vital:50127 , DOI 10.21504/10962/233784
Description: Malaria remains a public health problem and a high burden of disease, especially in developing countries. The unicellular protozoan malaria parasite of the genus Plasmodium infects about a quarter of a billion people annually, with an estimated 409 000 death cases. The majority of malaria cases occurred in Africa; hence, the region is regarded as endemic for malaria. Global efforts to eradicate the disease led to a decrease in morbidity and mortality rates. However, an enormous burden of malaria infection remains, and it cannot go unnoticed. Countries with limited resources are more affected by the disease, mainly on its public health and socio-economic development, due to many factors besides malaria itself, such as lack of access to adequate, affordable treatments and preventative regimes. Furthermore, the current antimalarial drugs are losing their efficacy because of parasite drug resistance. The emerged drug resistance has reduced the drug efficacy in clearing the parasite from the host system, causing prolonged illness and a higher risk of death. Therefore, the emerged antimalarial drug resistance has hindered the global efforts for malaria control and elimination and established an urgent need for new treatment strategies. When the resistance against classical antimalarial drugs emerged, the class of antifolate antimalarial medicines became the most common alternative. The antifolate antimalarial drugs target the malaria parasite de novo folate biosynthesis pathway by limiting folate derivates, which are essential for the parasite cell growth and survival. Yet again, the malaria parasite developed resistance against the available antifolate drugs, rendering the drugs ineffective in many cases. Given the previous success in targeting the malaria parasite de novo folate biosynthesis pathway, alternative enzymes within this pathway stand as good targets and can be explored to develop new antifolate drugs with novel mechanisms of action. The primary focus of this thesis is to contribute to the existing and growing knowledge of antimalarial drug discovery. The study aims to characterise the malaria parasite de novo folate synthesis pathway enzymes guanosine-5'-triphosphate (GTP) cyclohydrolase I (GCH1) and 6-pyruvoyl tetrahydropterin synthase (PTPS) as alternative drug targets for malaria treatment by using computational approaches. Further, discover new allosteric drug targeting sites within the two enzymes' 3D structures for future drug design and discovery. Sequence and structural analysis were carried out to characterise and pinpoint the two enzymes' unique sequence and structure-based features. From the analyses, key sequence and structure differences were identified between the malaria parasite enzymes relative to their human homolog; the identified sites can aid significantly in designing and developing new antimalarial antifolate drugs with good selectivity toward the parasites’ enzymes. GCH1 and PTPS contain a catalytically essential metal ion in their active site; therefore, force field parameters were needed to study their active sites accurately during all-atom molecular dynamic simulations (MD). The force field parameters were derived through quantum mechanics potential energy surface scans of the metals bonded terms and evaluated via all-atom MD simulations. Proteins structural dynamics is imperative for many biological processes; thus, it is essential to consider the structural dynamics of proteins whilst understanding their function. In this regard, the normal mode analysis (NMA) approach based on the elastic network model (ENM) was employed to study the intrinsic dynamics and conformations changes of GCH1 and PTPS enzymes. The NMA disclosed essential structural information about the protein’s intrinsic dynamics and mechanism of allosteric modulation of their binding properties, further highlighting regions that govern their conformational changes. The analysis also disclosed hotspot residues that are crucial for the proteins' fold stability and function. The NMA was further combined with sequence motif results and showed that conserved residues of GCH1 and PTPS were located within the identified key structural sites modulating the proteins' conformational rearrangement. The characterized structural features and hotspot residues were regarded as potential allosteric sites of important value for the design and development of allosteric drugs. Both GCH1 and PTPS enzymes have never been targeted before and can provide an excellent opportunity to overcome the antimalarial antifolate drug resistance problem. The data presented in this thesis contribute to the understanding of the sequence, structure, and global dynamics of both GCH1 and PTPS, further disclose potential allosteric drug targeting sites and unique structural features of both enzymes that can establish a solid starting point for drug design and development of new antimalarial drugs of a novel mechanism of actions. Lastly, the reported force field parameters will be of value for MD simulations for future in-silico drug discovery studies involving the two enzymes and other enzymes with the same Zn2+ binding motifs and coordination environments. The impact of this research can facilitate the discovery of new effective antimalarial medicines with novel mechanisms of action. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
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Date Issued: 2022-04-08

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Visualisation processes in teaching patterns and their generalisation: perceptions and experiences from senior phase mathematics teachers

- Chatima, Simon

Authors: Chatima, Simon
Date: 2022-04-08
Subjects: Uncatalogued
Language: English
Type: Master's thesis , text
Identifier: http://hdl.handle.net/10962/232936 , vital:50039
Description: This study investigated how senior phase mathematics teachers used visualisation approaches to teach patterns and their generalisation as a result of an intervention programme. This project is an integral component of the VIPRO MATHS Project and one of a number of post-graduate research projects which has a particular focus on visualisation processes in mathematics education in the Southern African region. This case study of Senior Phase mathematics teachers in the Chris Hani West District (CHW) in the Eastern Cape Province of South Africa used a social constructivist theory. The study is grounded within an interpretive paradigm explanatory qualitative method design. It surveyed thirty-seven Senior Phase mathematics teachers from schools in the CHW district to get an idea of how teachers teach patterns and their generalisation, prior to an intervention process. After the survey, nine teachers were purposively selected to take part in an intervention programme. They were then observed (teaching) and interviewed to get their perceptions about what factors enable and/or constrain the teaching of patterns and their generalisation when visualisation approaches were used. The data from the survey questionnaire responses, the lesson observations and the interviews were analysed qualitatively. The findings from the survey questionnaire responses revealed that teachers in CHW district value the use of visualisation approaches, although they used visuals to teach patterns in a way that lacked depth, skill and rigor prior to the intervention. Challenges such as difficulty in keeping abreast with the prescribed syllabus, the lack of resources, time constraints, and the limited knowledge of algebra learners have for successfully transferring pictorial representations to symbolic presentations, emerged from the survey data. This necessitated the need for an intervention which focused on the use of a variety of visual strategies and tools to teach patterns and their generalisation effectively. Data from lesson observations showed that all observed participant teachers used visuals to generate image- related questions and created platforms for lively classroom discussions. The teachers used the generated questions to build on learners’ prior knowledge and to promote learner understanding of pattern dynamics that stem from pictorial representations. The data from the interviews revealed that teachers’ perceptions had drastically changed after the intervention. This was because they were now equipped and empowered to effectively make use of visual strategies that enabled them to: build on learners’ prior knowledge, to manipulate visuals for the purpose of prompting learning, develop cognitive perception in learners, cultivate learner innovation and originality and enhance problem solving techniques. This study concludes that the use of visuals enhanced conceptual teaching of patterns and their generalisation in the observed participants. This has the potential to provide mathematics education researchers and curriculum developers with a strong basis to include visualisation processes and strategies into the design of policy documents and to initiate further research efforts. The implications for the teachers are that learners need to be taught ways to create and interpret visual representations in order to understand the dynamics of transferring a pictorial pattern to its resultant symbolic representation expressing pattern regularity. It is also hoped that the results of this study will be utilised by mathematics subject advisers and teacher training institutions to improve the teaching of patterns and their generalisation. , Thesis (MEd) -- Faculty of Education, Education, 2022
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Date Issued: 2022-04-08

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Alcohol use among women attending antenatal care in Buffalo City, Eastern Cape

- Bredenkamp, Petrus Johannes

Authors: Bredenkamp, Petrus Johannes
Date: 2022-04-07
Subjects: Uncatalogued
Language: English
Type: Master's thesis , text
Identifier: http://hdl.handle.net/10962/234358 , vital:50188
Description: Alcohol use during pregnancy is known to cause neurodevelopmental disorders in offspring, known as Fetal Alcohol Spectrum Disorders (FASD). High prevalence of FASD has been observed in certain parts South Africa, but many areas of the country remain unstudied, and factors contributing to drinking among pregnant women are poorly understood. This study surveyed 1099 women attending antenatal care at public primary healthcare facilities in the Buffalo City Metropolitan Area in the Eastern Cape. Data was collected using the Alcohol Use Identification Test, a 10-item self-report measure of drinking behaviour in isiXhosa, English, and Afrikaans. Factors associated with alcohol use, risky drinking, binge drinking, and hazardous/harmful drinking were identified using logistic regression. A minority of the sample reported alcohol use (64%). Among those reporting alcohol use, most reported occasional binge drinking (63%) and met criteria for risky drinking (59%) and hazardous/harmful drinking (52%). Living with a regular drinker was significantly associated with alcohol use (OR 1.98, 95% CI 1.51 – 2.58), risky drinking (OR 2.03, 95% CI 1.49 – 2.76), binge drinking (OR 2.21, 95% CI 1.64 – 2.97), and hazardous/harmful drinking (OR 2.0, 95% CI 1.41 – 2.99). However, women who were married/cohabiting were less likely to report alcohol use (OR .71, 95% CI .53 - .95). Experiencing intimate partner violence during the current pregnancy was associated with alcohol use (OR 2.42, 95% CI 1.38 – 4.27) and hazardous/harmful drinking (OR 2.62, 95% CI 1.32 – 5.22). In this study, women who identified as Coloured were more likely to report alcohol use than Women who identified as African (OR 2.74, 95% CI 1.4 – 5.36). These findings simultaneously provide evidence of problematic drinking among pregnant women in a previously understudied area and show that external factors affect women’s drinking behaviour during pregnancy. Interventions aimed at reducing the incidence of FASD should consider alcohol use by pregnant women in the context of their lived experiences. , Thesis (MA) -- Faculty of Humanities, Psychology, 2022
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Date Issued: 2022-04-07

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Magnitude

- Seddon, Deborah Ann

Authors: Seddon, Deborah Ann
Date: 2022-04-07
Subjects: Uncatalogued
Language: English
Type: Master's thesis , text
Identifier: http://hdl.handle.net/10962/234400 , vital:50192
Description: My thesis is a collection of lyric, narrative, and prose poetry directed towards two forms of death – physical death and the disavowal of the self. Many poems focus on the death of my mother, and the work required after loss to sort through a family’s life in my Harare childhood home. This associative exploration draws together childhood memories, encounters with physical objects, letters, and songs, as well as with the city and its people. Tadeusz Rózewicz’s Mother Departs has influenced my approach to writing of my mother’s death, particularly how to grant her a voice in the telling. I also draw on the poetry of Harmony Holiday and Pascal Petite, in their attention to the complexities and emotional dangers of the mother-daughter bond. Other poems draw on the work of Adrienne Rich, Audre Lorde, Judy Grahn, Ocean Vuong, and Saeed Jones, in terms of imagining queer life into poetry, the use of the erotic as a means of empowerment, and developing a queer political identity, to examine various aspects of queer love, including the heartaches associated with self-denial. , Thesis (MA) -- Faculty of Humanities, School of Languages and Literatures, 2022
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Date Issued: 2022-04-07

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Needs assessment for gender-sensitive training in substance use disorder treatment for gender-nonconforming people

- Tao, Lane

Authors: Tao, Lane
Date: 2022-04-07
Subjects: Uncatalogued
Language: English
Type: Master's thesis , text
Identifier: http://hdl.handle.net/10962/234339 , vital:50187
Description: Research suggests that queer people face both general discrimination and inadequate support in substance use disorder (SUD) treatment. One recommendation made by scholarship to address this is to improve the treatment capabilities of practitioners, thus improving practitioner readiness and reducing access barriers for a potentially at-risk population. The purpose of this study is to explore SUD treatment practitioners’ experiences of treating queer clients and identify their training needs. Semi-structured interviews were conducted with seven registered mental healthcare practitioners operating in Cape Town, South Africa. Data was analysed via thematic analysis, using a social constructionist approach to gender and practitioner knowledge. The findings reflect a strong interest in gender-sensitive training to better prepare practitioners for treating queer clients. Participants provided feedback on areas in need of improvement and made recommendations on how training should be conducted. Findings indicate that queer clients may enter treatment with a high burden of trauma due to discrimination, and that healthcare structures abiding by a binary approach to gender may not be able to address queer people’s diverse needs. Recommendations for future research are made, with particular emphasis on including queer people in surveillance data. Target areas for training programmes are described, with emphasis on terminological understanding and accessibility of training. , Thesis (MA) -- Faculty of Humanities, Psychology, 2022
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Date Issued: 2022-04-07

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Skipping stones

- Le Roux, Jade-Eden

Authors: Le Roux, Jade-Eden
Date: 2022-04-07
Subjects: Uncatalogued
Language: English
Type: Master's thesis , text
Identifier: http://hdl.handle.net/10962/234389 , vital:50191
Description: My thesis takes the form of a novella exploring suicide and the unanswered questions it leaves. The main protagonist is a young girl who struggles to come to terms with her best friend’s suicide. The work is situated in contemporary South Africa, where inequality and depression is rife, especially among young people, and social media too often provides a smokescreen to conceal emotions. My writing is motivated by my desire to explore the human condition and the world around me, through my own subjective lens of experience. By working between fact and fiction I seek to trouble conventional narratives attached to suicide and highlight the subjectivity of truth. I am influenced by Lydia Davis's ability to write obliquely about loss, and her light-handed approach to emotionally charged topics; Susan Steinberg's dark motifs, vivid imagery, and her fragmented narrative that captures the characters’ responses to trauma and interrogates the notion of truth; Lidia Yuknavitch's cinematic imagery and immediacy of tone and compact storytelling; and Kate Zambreno's poetic prose that lends itself to clear societal commentary. , Thesis (MA) -- Faculty of Humanities, School of Languages and Literatures, 2022
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Date Issued: 2022-04-07

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Influence of argon ion implantation on the thermoluminescence properties of aluminium oxide

- Khabo, Bokang

Authors: Khabo, Bokang
Date: 2022-04-06
Subjects: Uncatalogued
Language: English
Type: Master's thesis , text
Identifier: http://hdl.handle.net/10962/234220 , vital:50173
Description: The influence of argon ion implantation on the thermoluminescence properties (TL) of aluminium oxide (alumina) was investigated. Aluminium oxide (Al2O3) samples were implanted with 80 keV Ar ions. An unimplanted sample and samples implanted at fluences of 1×1014, 5×1014, 1×1015, 5×1015, 1×1016 Ar+/cm2 were irradiated at a dose of 40 Gy and heated at a rate of 1°C/s using a Risø reader model TL/OSL-DA-20 equipped with a Hoya U-340 filter. The thermoluminescence glow curves showed five distinct peaks with main peaks at 178°C, 188°C, 176°C, 208°C, 216°C and 204°C for the unimplanted sample as well as implanted samples. The peak positions of the samples were independent of the irradiation dose suggesting that the samples were characterised by first order kinetics. This was also confirmed by the TM-TSTOP analysis. It was observed that the TL intensity decreases with fluence of implantation. This observation suggests that the concentration of electron traps responsible for thermoluminescence decreases with ion implantation. The decrease in electron concentration might be due to the formation of non-radiative transition bands or the creation of defect clusters and extended defects following the ion implantation and ion fluence increases. The stopping and range of atoms in matter (SRIM) program was used to correlate the TL response of Al2O3 with defects under ion implantation. Subsequent to ion implantation, it was found that the number of oxygen vacancies which are related to electron traps are higher than the number of aluminium vacancies. Kinetic analysis was carried out using the initial rise, Chens peak shape, various heating rate, the whole glow curve, glow curve fitting and the isothermal decay methods. The activation energy was found to be around 0.8 eV and the frequency factor to be of the order 108 𝑠−1 regardless of the implantation fluence. This means that argon ion implantation did not affect the nature of electron traps. The dosimetric features of samples were also investigated at doses in the range of 40 – 200 Gy. Samples generally showed a superlinear response at doses less than 140 Gy and sublinear response at doses higher than 160 Gy. , Thesis (MSc) -- Faculty of Science, Physics and Electronics, 2022
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Date Issued: 2022-04-06

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Sequence, structure, dynamics, and substrate specificity analyses of bacterial Glycoside Hydrolase 1 enzymes from several activities

- Veldman, Wayde Michael

Authors: Veldman, Wayde Michael
Date: 2022-04-06
Subjects: Uncatalogued
Language: English
Type: Doctoral thesis , text
Identifier: http://hdl.handle.net/10962/233805 , vital:50129 , DOI 10.21504/10962/233810
Description: Glycoside hydrolase 1 (GH1) enzymes are a ubiquitous family of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. Despite their conserved catalytic domain, these enzymes have many different enzyme activities and/or substrate specificities as a change of only a few residues in the active site can alter their function. Most GH1 active site residues are situated in loop regions, and it is known that enzymes are more likely to develop new functions (broad specificity) if they possess an active site with a high proportion of loops. Furthermore, the GH1 active site consists of several subsites and cooperative binding makes the binding affinity of sites difficult to measure because the properties of one subsite are influenced by the binding of the other subsites. Extensive knowledge of protein-ligand interactions is critical to the comprehension of biology at the molecular level. However, the structural determinants and molecular details of GH1 ligand specificity and affinity are very broad, highly complex, not well understood, and therefore still need to be clarified. The aim of this study was to computationally characterise the activity of three newly solved GH1 crystallographic structures sent to us by our collaborators, and to provide evidence for their ligand-binding specificities. In addition, the differences in structural and biochemical contributions to enzyme specificity and/or function between different GH1 activities/enzymes was assessed, and the sequence/structure/function relationship of several activities of GH1 enzymes was analysed and compared. To accomplish the research aims, sequence analyses involving sequence identity, phylogenetics, and motif discovery were performed. As protein structure is more conserved than sequence, the discovered motifs were mapped to 3D structures for structural analysis and comparisons. To obtain information on enzyme mechanism or mode of action, as well as structure-function relationship, computational methods such as docking, molecular dynamics, binding free energy calculations, and essential dynamics were implemented. These computational approaches can provide information on the active site, binding residues, protein-ligand interactions, binding affinity, conformational change, and most structural or dynamic elements that play a role in enzyme function. The three new structures received from our collaborators are the first GH1 crystallographic structures from Bacillus licheniformis ever determined. As phospho-glycoside compounds were unavailable for purchase for use in activity assays, and as the active sites of the structures were absent of ligand, in silico docking and MD simulations were performed to provide evidence for their GH1 activities and substrate specificities. First though, the amino acid sequences of all known characterised bacterial GH1 enzymes were retrieved from the CAZy database and compared to the sequences of the three new B. licheniformis crystallographic structures which provided evidence of the putative 6Pβ-glucosidase activity of enzyme BlBglH, and dual 6Pβ-glucosidase/6Pβ-galactosidase (dual-phospho) activity of enzymes BlBglB and BlBglC. As all three enzymes were determined to be putative 6Pβ-glycosidase activity enzymes, much of the thesis focused on the overall analysis and comparison of the 6Pβ-glucosidase, 6Pβ-galactosidase, and dual-phospho activities that make up the 6Pβ-glycosidases. The 6Pβ-glycosidase active site residues were identified through consensus of binding interactions using all known 6Pβ-glycosidase PDB structures complexed complete ligand substrates. With regards to the 6Pβ-glucosidase activity, it was found that the L8b loop is longer and forms extra interactions with the L8a loop likely leading to increased L8 loop rigidity which would prevent the displacement of residue Ala423 ensuring a steric clash with galactoconfigured ligands and may engender substrate specificity for gluco-configured ligands only. Also, during molecular dynamics simulations using enzyme BlBglH (6Pβ-glucosidase activity), it was revealed that the favourable binding of substrate stabilises the loops that surround and make up the enzyme active site. Using the BlBglC (dual-phospho activity) enzyme structure with either galacto- (PNP6Pgal) or gluco-configured (PNP6Pglc) ligands, MD simulations in triplicate revealed important details of the broad specificity of dual-phospho activity enzymes. The ligand O4 hydroxyl position is the only difference between PNP6Pgal and PNP6Pgal, and it was found that residues Gln23 and Trp433 bind strongly to the ligand O3 hydroxyl group in the PNP6Pgal-enzyme complex, but to the ligand O4 hydroxyl group in the PNP6Pglc-enzyme complex. Also, His124 formed many hydrogen bonds with the PNP6Pgal O3 hydroxyl group but had none with PNP6Pglc. Alternatively, residues Tyr173, Tyr301, Gln302 and Thr321 formed hydrogen bonds with PNP6Pglc but not PNP6Pgal. Lastly, using multiple 3D structures from various GH1 activities, a large network of conserved interactions between active site residues (and other important residues) was uncovered, which most likely stabilise the loop regions that contain these residues, helping to retain their positions needed for binding molecules. Alternatively, there exists several differing residue-residue interactions when comparing each of the activities which could contribute towards individual activity substrate specificity by causing slightly different overall structure and malleability of the active site. Altogether, the findings in this thesis shed light on the function, mechanisms, dynamics, and ligand-binding of GH1 enzymes – particularly of the 6Pβ-glycosidase activities. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2022
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Date Issued: 2022-04-06

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Statistical and Mathematical Learning: an application to fraud detection and prevention

- Hamolomo, Sisipho

Authors: Hamolomo, Sisipho
Date: 2022-04-06
Subjects: Uncatalogued
Language: English
Type: Master's thesis , text
Identifier: http://hdl.handle.net/10962/233795 , vital:50128
Description: Credit card fraud is an ever-growing problem. There has been a rapid increase in the rate of fraudulent activities in recent years resulting in a considerable loss to several organizations, companies, and government agencies. Many researchers have focused on detecting fraudulent behaviours early using advanced machine learning techniques. However, credit card fraud detection is not a straightforward task since fraudulent behaviours usually differ for each attempt and the dataset is highly imbalanced, that is, the frequency of non-fraudulent cases outnumbers the frequency of fraudulent cases. In the case of the European credit card dataset, we have a ratio of approximately one fraudulent case to five hundred and seventy-eight non-fraudulent cases. Different methods were implemented to overcome this problem, namely random undersampling, one-sided sampling, SMOTE combined with Tomek links and parameter tuning. Predictive classifiers, namely logistic regression, decision trees, k-nearest neighbour, support vector machine and multilayer perceptrons, are applied to predict if a transaction is fraudulent or non-fraudulent. The model's performance is evaluated based on recall, precision, F1-score, the area under receiver operating characteristics curve, geometric mean and Matthew correlation coefficient. The results showed that the logistic regression classifier performed better than other classifiers except when the dataset was oversampled. , Thesis (MSc) -- Faculty of Science, Statistics, 2022
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Date Issued: 2022-04-06

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The use of the cochineal insect, Dactylopius tomentosus Lamarck, as a biological control agent for the invasive alien thistle cholla, Cylindropuntia pallida (Rose) F.M. Knuth in South Africa

- Zozo, Ekhona

Authors: Zozo, Ekhona
Date: 2022-04-06
Subjects: Uncatalogued
Language: English
Type: Master's thesis , text
Identifier: http://hdl.handle.net/10962/233823 , vital:50131
Description: Cylindropuntia pallida (Rose) F.M. Knuth (Cactaceae) is an invasive alien plant in South Africa indigenous in the southern U.S.A. and Mexico. Large infestations of this species can be found in the Kalahari and arid Karoo regions of South Africa, which is also present in Namibia. Because it is a very spiny cactus, dense infestations have a negative impact on agriculture and natural ecosystems. This cactus has become naturalised to the extent that eradication is impossible and the negative impacts are steadily increasing due to its increasing distribution and density. The cochineal insect, Dactylopius tomentosus Lamarck (Dactylopiidae), is native in Mexico and parts of North America, such as Texas, Arizona, and New Mexico in the U.S.A. This cochineal species is highly specialized and associated only with Cylindropuntia species, a group of cacti that are primarily restricted to the same areas. It has been introduced into Australia and South Africa as a biological control agent to control various invasive alien Cylindropuntia species. This cochineal species has several biotypes specific to certain Cylindropuntia species hosts. A biotype is a clade that cannot be differentiated morphologically from others but has different host ranges and impacts depending on the host plant species. Included amongst biotypes that have been released in South Africa are D. tomentosus ‘imbricata’ and D. tomentosus ‘cholla’ for the biological control of Cylindropuntia imbricata (Haw.) F.M. Knuth (Cactaceae) and Cylindropuntia fulgida (Engelmann) F.M. Knuth var. mamillata (Schott ex Engelmann) Backeb. (Cactaceae), respectively. These biotypes have resulted in both host plants being under substantial control in South Africa. The first part of this thesis evaluated which of the two D. tomentosus biotypes already in use in South Africa could be an effective biological control agent for C. pallida. This was done by assessing the fitness of the cochineals on the three cactus species and assessing the impact that each of the cochineals has on each of the target weed species. Should these biotypes prove ineffective, there is a third biotype, namely D. tomentosus ‘californica var. parkerii’, which researchers in Australia have worked on and have found to be suitably host-specific for release in Australia and suitably damaging to C. pallida in that country. Therefore, this new biotype could be released in South Africa if it is required. Sexually compatible biological control agents, especially those closely related and occurring in close spatial proximity to one another, may interbreed and the impacts of this hybridisation are difficult to predict. It is important to understand the outcomes of the hybridisation of cochineal because it can affect the impact of the biological control agents and thus the control of the target weed. The second part of this thesis investigated the impacts of the hybridisation of the two cochineal biotypes by assessing the damage the agents would have on the target weed, and on C. imbricata and C. fulgida var. mamillata, in the presence of one or both cochineal biotypes. The ‘cholla’ biotype performed better on C. pallida than the ‘imbricata’ biotype, but neither biotype could control C. pallida to an extent similar to the control they provide for their respective target weeds, C. imbricata and C. fulgida var. mamillata. Both the ‘cholla’ biotype and hybrids of the two biotypes of cochineal were effective at killing C. pallida when both C. imbricata and C. fulgida var. mamillata were also present. This suggests that the ‘cholla’ or hybrids may be effective at controlling C. pallida when either C. imbricata or C. fulgida var. mamillata are also present in the field due to the high population density of cochineal that results under these circumstances. There are, however, many C. pallida infestations in South Africa where the plant is problematic and is isolated from other Cylindropuntia species, and these populations are unlikely to be controlled by the ‘cholla’ biotype or the hybrids. Neither of the cochineal biotypes that are used for biological control in South Africa are suitably damaging to C. pallida to warrant their use as biological control agents for this species. Dactylopius tomentosus ‘californica var. parkerii’ is therefore recommended for release based on its host-specificity and impact to C. pallida in Australia. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2022
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Date Issued: 2022-04-06

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