Implications of Lantana camara invasion on rural livelihoods and native woody species in the Kavango Zambezi Transfrontier Conservation Area, Zimbabwe
- Authors: Francis, Buhle
- Date: 2024-04-05
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/435896 , vital:73210 , DOI 10.21504/10962/435896
- Description: Lantana (Lantana camara Linn, Verbenaceae) is an invasive alien species found in many disturbed and conservation habitats worldwide. Much work has been conducted on the impacts that L. camara has on ecosystems and communities living in affected areas. In some localities, interventions to eradicate L. camara have been made to reduce the impacts, with follow-up assessments on the benefits of these restoration efforts at some locations. However, L. camara continues to spread globally, and the Zambezi Transfrontier Conservation Area (KAZA TFCA) in Zimbabwe has not been spared. The KAZA TFCA is an important area for biodiversity conservation, ecotourism, and enabling and encouraging regional peace, cooperation and socio-economic advancement. This study was carried out in the KAZA TFCA, covering the Hwange District in Zimbabwe, with the primary aim to ascertain the effects of L. camara on rural livelihoods, native woody species and the soil properties of KAZA TFCA, and whether the policy environment and passive restoration efforts have been effective in controlling it in the area. The study employed a mixed-methods approach using both qualitative and quantitative methodologies to resolve the research problem. Firstly, 102 plots were randomly established in the study areas where native woody species were recorded. In the first section of the Communal area, there were 60 plots in total comprising of 34 invaded and 8 uninvaded. In the other section of the Communal area, 21 plots were sampled, with 7 invaded, 7 control and the other 7 cleared. In the Victoria Falls National Park, 18 plots were established which comprised of 12 invaded and 6 uninvaded. In the Victoria Falls Rainforest area, 21 plots were established which comprised of 7 invaded, 7 cleared and 7 control. The criteria of selecting 102 plots was based on a number of factors which included; Research objectives, Randomisation, Historical data (From locals and Environmental Management Agency), Environmental variables, Spatial distribution if invasion, Accessibility, Budget and Time constraints. A total of 72 soil samples were collected for laboratory analysis of nitrogen, pH, organic carbon, phosphorous and potassium. The 72 soil samples were considered based on available funding for analysis. This soil samples collected samples were representative of the entire study site. In the Communal areas, 300 household questionnaires (representing approximately 12.35% of the total number of 2 430 households) were administered, two focus groups with elderly residents were conducted, and 11 key informant interviews were held. One-way ANOVAs and several multivariate tests were conducted to assess the impact of L. camara invasion on native woody species composition and soil properties. Descriptive statistics were used to conduct a cost-benefit analysis of the presence of L. camara in the study sites. This was coupled with a principal component analysis to assess vulnerability of respondents to invasion, based on variables such as age, gender and level of education. One-way ANOVAs and multivariate analysis were also used to assess if passive restoration contributed to the recovery of native woody vegetation and the improvement of soil properties. In invaded plots, restoration natural recovery occurred after removing the L. camara invasion with no further intervention done after the removal. Document and thematic analyses were conducted to evaluate perceptions and knowledge of policy and legislation pertaining to L. camara management. Lantana camara negatively affected the native woody species, as evidenced by a reduction in species richness, abundance, density, height and canopy cover. Lantana camara also altered soil properties such as texture, chemical composition, colour and porosity, as found by comparing invaded and non-invaded plots in both the Park and Communal areas. Once L. camara invades an area it tends to become dominant at the expense of native species, many of which are a source of livelihood for the local people. Thus, displacement of native species by L. camara potentially increases the vulnerability of local people, some of whom are already experiencing challenges, such as drought and human-wildlife conflict. The invasion of L. camara was found to date back over eight decades ago. Based on focus group discussions with elderly participants, the initial invasion of L. camara in the Ndlovu Communal area was approximated to 1942. This invasion was noted to have begun in ward 2 of Ndlovu Communal area and spread to the other four wards in the study area over 16 years. Despite the challenges of losses and costs induced by the invasion of L. camara, benefits and gains were reported in some areas. For example, in the protected areas, the fruits of L. camara are eaten by birds, while bees use the flowers for honey production. It is noted that L. camara seeds spread through bird droppings become a cost to the environment through further proliferation of the invasion. In some communal areas, households use L. camara for hedges, herbal medicine, cane for furniture, and as an ornament. The relative losses and gains associated with L. camara are context-specific and are dependent on several factors. In this study, the presence of L. camara resulted in negative impacts that included the reduced area of productive land for crops and grazing. Combined, the mean costs borne were US$ 483 household-1 year-1. Furthermore, the combined mean benefits of L. camara, such as use as live fencing around homesteads and fields, mosquito repellent, fruit, fire kindling and ornaments, protection of fowls from raptors, and the prevention of gully erosion along watercourses, were valued at US$ 716 household-1 year-1, thereby exceeding the costs by 48%. However, most (62%) households experienced a net negative cost-benefit ratio. The overall mean value across the sample indicates benefits outweigh costs because a minority of households experience large net benefits. Although L. camara is invasive in the area, communities have taken advantage of its presence to find uses that contribute to their day-to-day lives. Despite the use of L. camara by communities, efforts to remove it have been made in some parts of the Ndlovu Communal area as well as in the Parks (Victoria Falls and Rainforest). The study investigated the impact of passive restoration on native woody species and soil properties. The findings showed a significant improvement in species richness and diversity in cleared plots compared with invaded plots. The species composition differed in the cleared, invaded and uninvaded plots with specific species favouring the different types of “treatments”. This showed the relationship between invasion and associated species. Soil properties had visible differences due to passive restoration, with figures of cleared sites consistently being intermediates of invaded and uninvaded plots. Despite the passive restoration projects, an analysis of knowledge and management showed that most local respondents whose age ranged between 25- 93 years, did not consider L. camara to be invasive but viewed it as part of the vegetation in the area. They also took little responsibility for its management. A further analysis of documents and policies related to the management of invasive alien species found that there were legal instruments in place for the management of invasive alien plants in Zimbabwe, including L. camara. The key informant interviews and the questionnaire surveys showed conflicting views on perceptions and opinions about whose responsibility it was to manage L. camara, with communities saying it is the authority’s responsibility, while some of the authorities suggested that it was everyone’s responsibility. However, some of the key informants highlighted the need to review the policies, guided by empirical studies on of the impacts of L. camara. Currently, it appears the policies are adopted from international bodies as a means of alignment to global policies, but they are not contextualised to suit the dynamics in the country. Overall, the study showed that the presence of L. camara in the KAZA TFCA has notable negative impacts on the native woody vegetation, as well as on local livelihoods, but some households have adapted to using L. camara to benefit them. This, however, has implications for efforts to stop the spread of L. camara if its presence is considered a benefit by some and a cost by others. The efforts to remove L. camara show that the native woody vegetation recovered. The study showed the need to raise awareness of the invasive nature of L. camara because some respondents did not consider it invasive. Findings from this study have implications for the management of L. camara in KAZA TFCA and similar areas, and inferences can be made to assist in the management of other invasive alien plants. , Thesis (PhD) -- Faculty of Science, Environmental Science, 2024
- Full Text:
- Date Issued: 2024-04-05
- Authors: Francis, Buhle
- Date: 2024-04-05
- Subjects: Uncatalogued
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/435896 , vital:73210 , DOI 10.21504/10962/435896
- Description: Lantana (Lantana camara Linn, Verbenaceae) is an invasive alien species found in many disturbed and conservation habitats worldwide. Much work has been conducted on the impacts that L. camara has on ecosystems and communities living in affected areas. In some localities, interventions to eradicate L. camara have been made to reduce the impacts, with follow-up assessments on the benefits of these restoration efforts at some locations. However, L. camara continues to spread globally, and the Zambezi Transfrontier Conservation Area (KAZA TFCA) in Zimbabwe has not been spared. The KAZA TFCA is an important area for biodiversity conservation, ecotourism, and enabling and encouraging regional peace, cooperation and socio-economic advancement. This study was carried out in the KAZA TFCA, covering the Hwange District in Zimbabwe, with the primary aim to ascertain the effects of L. camara on rural livelihoods, native woody species and the soil properties of KAZA TFCA, and whether the policy environment and passive restoration efforts have been effective in controlling it in the area. The study employed a mixed-methods approach using both qualitative and quantitative methodologies to resolve the research problem. Firstly, 102 plots were randomly established in the study areas where native woody species were recorded. In the first section of the Communal area, there were 60 plots in total comprising of 34 invaded and 8 uninvaded. In the other section of the Communal area, 21 plots were sampled, with 7 invaded, 7 control and the other 7 cleared. In the Victoria Falls National Park, 18 plots were established which comprised of 12 invaded and 6 uninvaded. In the Victoria Falls Rainforest area, 21 plots were established which comprised of 7 invaded, 7 cleared and 7 control. The criteria of selecting 102 plots was based on a number of factors which included; Research objectives, Randomisation, Historical data (From locals and Environmental Management Agency), Environmental variables, Spatial distribution if invasion, Accessibility, Budget and Time constraints. A total of 72 soil samples were collected for laboratory analysis of nitrogen, pH, organic carbon, phosphorous and potassium. The 72 soil samples were considered based on available funding for analysis. This soil samples collected samples were representative of the entire study site. In the Communal areas, 300 household questionnaires (representing approximately 12.35% of the total number of 2 430 households) were administered, two focus groups with elderly residents were conducted, and 11 key informant interviews were held. One-way ANOVAs and several multivariate tests were conducted to assess the impact of L. camara invasion on native woody species composition and soil properties. Descriptive statistics were used to conduct a cost-benefit analysis of the presence of L. camara in the study sites. This was coupled with a principal component analysis to assess vulnerability of respondents to invasion, based on variables such as age, gender and level of education. One-way ANOVAs and multivariate analysis were also used to assess if passive restoration contributed to the recovery of native woody vegetation and the improvement of soil properties. In invaded plots, restoration natural recovery occurred after removing the L. camara invasion with no further intervention done after the removal. Document and thematic analyses were conducted to evaluate perceptions and knowledge of policy and legislation pertaining to L. camara management. Lantana camara negatively affected the native woody species, as evidenced by a reduction in species richness, abundance, density, height and canopy cover. Lantana camara also altered soil properties such as texture, chemical composition, colour and porosity, as found by comparing invaded and non-invaded plots in both the Park and Communal areas. Once L. camara invades an area it tends to become dominant at the expense of native species, many of which are a source of livelihood for the local people. Thus, displacement of native species by L. camara potentially increases the vulnerability of local people, some of whom are already experiencing challenges, such as drought and human-wildlife conflict. The invasion of L. camara was found to date back over eight decades ago. Based on focus group discussions with elderly participants, the initial invasion of L. camara in the Ndlovu Communal area was approximated to 1942. This invasion was noted to have begun in ward 2 of Ndlovu Communal area and spread to the other four wards in the study area over 16 years. Despite the challenges of losses and costs induced by the invasion of L. camara, benefits and gains were reported in some areas. For example, in the protected areas, the fruits of L. camara are eaten by birds, while bees use the flowers for honey production. It is noted that L. camara seeds spread through bird droppings become a cost to the environment through further proliferation of the invasion. In some communal areas, households use L. camara for hedges, herbal medicine, cane for furniture, and as an ornament. The relative losses and gains associated with L. camara are context-specific and are dependent on several factors. In this study, the presence of L. camara resulted in negative impacts that included the reduced area of productive land for crops and grazing. Combined, the mean costs borne were US$ 483 household-1 year-1. Furthermore, the combined mean benefits of L. camara, such as use as live fencing around homesteads and fields, mosquito repellent, fruit, fire kindling and ornaments, protection of fowls from raptors, and the prevention of gully erosion along watercourses, were valued at US$ 716 household-1 year-1, thereby exceeding the costs by 48%. However, most (62%) households experienced a net negative cost-benefit ratio. The overall mean value across the sample indicates benefits outweigh costs because a minority of households experience large net benefits. Although L. camara is invasive in the area, communities have taken advantage of its presence to find uses that contribute to their day-to-day lives. Despite the use of L. camara by communities, efforts to remove it have been made in some parts of the Ndlovu Communal area as well as in the Parks (Victoria Falls and Rainforest). The study investigated the impact of passive restoration on native woody species and soil properties. The findings showed a significant improvement in species richness and diversity in cleared plots compared with invaded plots. The species composition differed in the cleared, invaded and uninvaded plots with specific species favouring the different types of “treatments”. This showed the relationship between invasion and associated species. Soil properties had visible differences due to passive restoration, with figures of cleared sites consistently being intermediates of invaded and uninvaded plots. Despite the passive restoration projects, an analysis of knowledge and management showed that most local respondents whose age ranged between 25- 93 years, did not consider L. camara to be invasive but viewed it as part of the vegetation in the area. They also took little responsibility for its management. A further analysis of documents and policies related to the management of invasive alien species found that there were legal instruments in place for the management of invasive alien plants in Zimbabwe, including L. camara. The key informant interviews and the questionnaire surveys showed conflicting views on perceptions and opinions about whose responsibility it was to manage L. camara, with communities saying it is the authority’s responsibility, while some of the authorities suggested that it was everyone’s responsibility. However, some of the key informants highlighted the need to review the policies, guided by empirical studies on of the impacts of L. camara. Currently, it appears the policies are adopted from international bodies as a means of alignment to global policies, but they are not contextualised to suit the dynamics in the country. Overall, the study showed that the presence of L. camara in the KAZA TFCA has notable negative impacts on the native woody vegetation, as well as on local livelihoods, but some households have adapted to using L. camara to benefit them. This, however, has implications for efforts to stop the spread of L. camara if its presence is considered a benefit by some and a cost by others. The efforts to remove L. camara show that the native woody vegetation recovered. The study showed the need to raise awareness of the invasive nature of L. camara because some respondents did not consider it invasive. Findings from this study have implications for the management of L. camara in KAZA TFCA and similar areas, and inferences can be made to assist in the management of other invasive alien plants. , Thesis (PhD) -- Faculty of Science, Environmental Science, 2024
- Full Text:
- Date Issued: 2024-04-05
A social history of midwifery practices in colonial Ibadan, Nigeria, 1893 - 1960
- Olorunnibe, Folaranmi Flourish
- Authors: Olorunnibe, Folaranmi Flourish
- Date: 2022-10-14
- Subjects: Midwifery Nigeria Ibadan , Nigeria History 1900-1960 , Nigeria Politics and government To 1960 , Nigeria Social conditions To 1960 , Maternal health services Nigeria Ibadan , Ibadan (Nigeria) Colonial influence
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/408716 , vital:70519 , DOI 10.21504/10962/408716
- Description: This thesis examines the introduction and development of western medical practices in colonial spaces with particular reference to midwifery practices in colonial Ibadan, Nigeria, from 1893 to 1960. This has become necessary because of the importance placed on childbirth and maternal healthcare in the twentieth century. The trends and changes in midwifery and midwifery practices in colonial Ibadan are seen as reflections of other transformations in British African colonies at large. The study begins with a detailed historical analysis of the major metropolitan and local factors that informed the introduction and development of Western obstetrics in colonial Ibadan, Nigeria. It proceeds to examine the development of Western midwifery practices in colonial Ibadan; highlighting the contributions of the Ibadan people to the development of Western midwifery practices and emphasizing policies affecting development, and implementation of Western obstetrics. The thesis goes further to reveal the prejudiced nature of colonial medical policies, and the ways it shaped various responses especially from rural folks who were particularly marginalized since the 1920s when maternal healthcare policies was implemented in the urban areas till the 1950s when a reformed policy for rural medical service scheme was introduced to the rural folks. Thus, influencing the ways they imagined and appropriated ideas of western obstetrics alongside African traditional midwifery practices. The idea is to demonstrate in this thesis the extent to which the precincts in colonial medical policies, most especially the establishment of maternity hospitals, clinics and dispensaries, and the institutionalization of western obstetrics, inspired critical and ingenious responses from colonial doctors, colonial officials, the missionaries, patients, African trained midwives, traditional medical practitioners and the African population in general. Placing all of these historical events within a wider context, this thesis borrows insights from the social history of medicine in an attempt to reconstruct the colonial medical practices in Ibadan, Nigeria, through the sites of midwifery practices and maternal welfare services from 1893 to 1960. This is in addition to its dependence on a comparatively rich, but skewed historical evidence, including a plethora of annual medical reports, official reports of the department of medical and sanitary services, official correspondences within the colonial government in Ibadan and Nigeria, and between the colonial government and the colonial office in the United Kingdom. Details of African responses to medical policies were garnered from oral testimonies, newspaper publications and correspondences between the African public and the colonial government in Ibadan. In exploring this historical evidence, the thesis reveals very interesting details of colonial perceptions about African health and their underlining motives for introducing western medical ideas, the various medical schemes and policies used in driving colonial interest and the ways Africans imagined, re-imagined, and appropriated Western medical practices. , Thesis (PhD) -- Faculty of Humanities, History, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Olorunnibe, Folaranmi Flourish
- Date: 2022-10-14
- Subjects: Midwifery Nigeria Ibadan , Nigeria History 1900-1960 , Nigeria Politics and government To 1960 , Nigeria Social conditions To 1960 , Maternal health services Nigeria Ibadan , Ibadan (Nigeria) Colonial influence
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/408716 , vital:70519 , DOI 10.21504/10962/408716
- Description: This thesis examines the introduction and development of western medical practices in colonial spaces with particular reference to midwifery practices in colonial Ibadan, Nigeria, from 1893 to 1960. This has become necessary because of the importance placed on childbirth and maternal healthcare in the twentieth century. The trends and changes in midwifery and midwifery practices in colonial Ibadan are seen as reflections of other transformations in British African colonies at large. The study begins with a detailed historical analysis of the major metropolitan and local factors that informed the introduction and development of Western obstetrics in colonial Ibadan, Nigeria. It proceeds to examine the development of Western midwifery practices in colonial Ibadan; highlighting the contributions of the Ibadan people to the development of Western midwifery practices and emphasizing policies affecting development, and implementation of Western obstetrics. The thesis goes further to reveal the prejudiced nature of colonial medical policies, and the ways it shaped various responses especially from rural folks who were particularly marginalized since the 1920s when maternal healthcare policies was implemented in the urban areas till the 1950s when a reformed policy for rural medical service scheme was introduced to the rural folks. Thus, influencing the ways they imagined and appropriated ideas of western obstetrics alongside African traditional midwifery practices. The idea is to demonstrate in this thesis the extent to which the precincts in colonial medical policies, most especially the establishment of maternity hospitals, clinics and dispensaries, and the institutionalization of western obstetrics, inspired critical and ingenious responses from colonial doctors, colonial officials, the missionaries, patients, African trained midwives, traditional medical practitioners and the African population in general. Placing all of these historical events within a wider context, this thesis borrows insights from the social history of medicine in an attempt to reconstruct the colonial medical practices in Ibadan, Nigeria, through the sites of midwifery practices and maternal welfare services from 1893 to 1960. This is in addition to its dependence on a comparatively rich, but skewed historical evidence, including a plethora of annual medical reports, official reports of the department of medical and sanitary services, official correspondences within the colonial government in Ibadan and Nigeria, and between the colonial government and the colonial office in the United Kingdom. Details of African responses to medical policies were garnered from oral testimonies, newspaper publications and correspondences between the African public and the colonial government in Ibadan. In exploring this historical evidence, the thesis reveals very interesting details of colonial perceptions about African health and their underlining motives for introducing western medical ideas, the various medical schemes and policies used in driving colonial interest and the ways Africans imagined, re-imagined, and appropriated Western medical practices. , Thesis (PhD) -- Faculty of Humanities, History, 2022
- Full Text:
- Date Issued: 2022-10-14
In silico substrate binding profiling for SARS-COV-2 main protease (mpro) using hexapeptide substrates
- Authors: Zabo, Sophakama
- Date: 2022-10-14
- Subjects: COVID-19 (Disease) , Peptides , Chymotrypsin like , Chymotrypsin , Proteases , Proteolytic enzymes
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365566 , vital:65760
- Description: COVID-19, as a disease resulting from SARS-CoV-2 infection, and a pandemic has had a devastating effect on the world. There are limited effective measures that control the spread and treatment of COVID-19 illness. The homodimeric cysteine main protease (Mpro) is crucial to the life cycle of the virus, as it cleaves the large polyproteins 1a and 1ab into matured, functional non-structural proteins. The Mpro exhibits high degrees of conservation in sequence, structure and specificity across coronavirus species, making it an ideal drug target. The Mpro substrate-binding profiles remain, despite the resolution of its recognition sequence and cleavage points (Leu-Gln↓(Ser/Ala/Gly)). In this study, a series of hexapeptide sequences containing the appropriate recognition sequence and cleavage points were generated and screened against the Mpro to study these binding profiles, and to further be the basis for efficiency-driven drug design. A multi-conformer hexapeptide substrate library comprising optimised 81000 models of 810 unique sequences was generated using RDKit within the context of python. Terminal capping with ACE and NMe was effected using SMILES and SMARTS matching. Multiple hexapeptides were complexed with chain B of crystallographic Mpro (PDS ID: 6XHM), following the validation of chain B for this purpose using AutoDock Vina at high levels of exhaustiveness (480). The resulting Vina scores ranged between -8.7 and -7.0 kcal.mol-1, and the reproducibility of best poses was validated through redocking. Ligand efficiency indices were calculated to identify substrate residues with high binding efficiency at their respective positions, revealing Val (P3), Ala (P1′); and Gly and Ala (P2′ and P3′) as leading efficient binders. Binding efficiencies were lowered by molecular weight. Substrate recognition was assessed by mapping of binding subsites, and Mpro specificity was evaluated through the resolution of intermolecular interaction at the binding interface. Molecular dynamics simulations for 20 ns were performed to assess the stability and behaviour of 132 Mpro systems complexed with KLQ*** substrates. Principal component analysis (PCA), was performed to assess II protein motions and conformational changes during the simulations. A strategy was formulated to classify and evaluate relations in the Mpro PCA motions, revealing four main clades of similarity. Similarity within a clade (Group 2) and dissimilarity between clades were confirmed. Trajectory visualisation revealed complex stability, substrate unbinding and dimer dissociation for various Mpro systems. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
- Authors: Zabo, Sophakama
- Date: 2022-10-14
- Subjects: COVID-19 (Disease) , Peptides , Chymotrypsin like , Chymotrypsin , Proteases , Proteolytic enzymes
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/365566 , vital:65760
- Description: COVID-19, as a disease resulting from SARS-CoV-2 infection, and a pandemic has had a devastating effect on the world. There are limited effective measures that control the spread and treatment of COVID-19 illness. The homodimeric cysteine main protease (Mpro) is crucial to the life cycle of the virus, as it cleaves the large polyproteins 1a and 1ab into matured, functional non-structural proteins. The Mpro exhibits high degrees of conservation in sequence, structure and specificity across coronavirus species, making it an ideal drug target. The Mpro substrate-binding profiles remain, despite the resolution of its recognition sequence and cleavage points (Leu-Gln↓(Ser/Ala/Gly)). In this study, a series of hexapeptide sequences containing the appropriate recognition sequence and cleavage points were generated and screened against the Mpro to study these binding profiles, and to further be the basis for efficiency-driven drug design. A multi-conformer hexapeptide substrate library comprising optimised 81000 models of 810 unique sequences was generated using RDKit within the context of python. Terminal capping with ACE and NMe was effected using SMILES and SMARTS matching. Multiple hexapeptides were complexed with chain B of crystallographic Mpro (PDS ID: 6XHM), following the validation of chain B for this purpose using AutoDock Vina at high levels of exhaustiveness (480). The resulting Vina scores ranged between -8.7 and -7.0 kcal.mol-1, and the reproducibility of best poses was validated through redocking. Ligand efficiency indices were calculated to identify substrate residues with high binding efficiency at their respective positions, revealing Val (P3), Ala (P1′); and Gly and Ala (P2′ and P3′) as leading efficient binders. Binding efficiencies were lowered by molecular weight. Substrate recognition was assessed by mapping of binding subsites, and Mpro specificity was evaluated through the resolution of intermolecular interaction at the binding interface. Molecular dynamics simulations for 20 ns were performed to assess the stability and behaviour of 132 Mpro systems complexed with KLQ*** substrates. Principal component analysis (PCA), was performed to assess II protein motions and conformational changes during the simulations. A strategy was formulated to classify and evaluate relations in the Mpro PCA motions, revealing four main clades of similarity. Similarity within a clade (Group 2) and dissimilarity between clades were confirmed. Trajectory visualisation revealed complex stability, substrate unbinding and dimer dissociation for various Mpro systems. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-10-14
Molecular characterization of microbial communities in the Sundays and Swartkops estuaries impacted by anthropogenic activities
- Kgomokhumo, Tlhoafalang Evah
- Authors: Kgomokhumo, Tlhoafalang Evah
- Date: 2022-04-06
- Subjects: Microbial ecology South Africa Sundays Estuary (Eastern Cape) , Microbial ecology South Africa Swartkops River Estuary , Estuarine health Effect of human beings on South Africa Sundays Estuary (Eastern Cape) , Estuarine health Effect of human beings on South Africa Swartkops River Estuary , Microorganisms South Africa Sundays Estuary (Eastern Cape) Molecular aspects , Microorganisms South Africa Swartkops River Estuary Molecular aspects , Eutrophication South Africa Sundays Estuary (Eastern Cape) , Eutrophication South Africa Swartkops River Estuary , Algal blooms South Africa Sundays Estuary (Eastern Cape) , Algal blooms South Africa Swartkops River Estuary
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/290994 , vital:56806
- Description: Anthropogenic activities are of concern in estuarine systems as they are the main source of water degradation. Water pollution in estuaries is indicated by eutrophication and the presence of pathogens and bacterial indicators which affect biodiversity and energy flow. This study focused on two geographically linked estuaries, namely the Sundays and Swartkops Estuaries. The Sundays Estuary is primarily impacted by agricultural activities in the river catchment with increased nutrients levels, particularly of total oxidised nitrogen (TOxN), likely derived from these farming activities. In contrast, the Swartkops Estuary, which is heavily influenced by urban/industrial activities, reflected increased levels of phosphates likely from wastewater and sewage water contamination from residential areas, leaking pipes, and poorly managed sewage treatment plants. The central objective of this study was to assess microbial population profiles and diversity impacted by agricultural activities in Sundays Estuary and industrial/urban-influenced Swartkops Estuary using 16S and 18S rRNA gene metabarcoding. A distinct difference in eukaryotic composition and diversity was evident between the two sampling exercises in 2018 and 2019 in Sundays Estuary. The eutrophication of both the Sundays and Swartkops estuaries was evident in the repeated occurrences of bloom events. In the Sundays Estuary, a bloom of Heterosigma akashiwo was observed in 2018 whilst Cyclotella dominated the estuary in 2019. The Swartkops Estuary exhibited seasonal variation in phytoplankton composition with Bacillariophyceae blooms in the upper reaches of the estuary in summer and increased prevalence of Dinophyceae in spring. Bacterial taxonomic variation was also noted between the two contrasting estuaries. Although members of the Proteobacteria dominated both estuaries, Gammaproteobacteria were in increased abundance in Sundays Estuary while members of Alphaproteobacteria were in high relative abundance in the marine dominated Swartkops Estuary. Members of the Bacteroidetes were the second most abundant bacterial phylum in both estuaries. Bacterial indicators of agricultural anthropogenic impacts identified in Sundays Estuary included members of Sporichthyaceae, Erysipelotrichaceae, Nostocaceae, and NS11-12_marine_group while some taxa such as the Flavobacteriaceae, Cryomorphaceae, and Halieaceae reflected their capability in degrading the phytoplankton bloom biomass present in the estuary. The urban impacts on the Swartkops Estuary was reflected by the contamination of the estuary with potential pathogens including Aeromonas caviae, Vibrio fluvialis, Mycobacterium intracellulare, Vibrio cholerae, and Bacillus cereus. Bacterial community profiles of the major water inflow points into the Swartkops Estuary included members of the Burkholderiaceae, Rhodocyclaceae, Aeromonadaceae, and Arcobacteriaceae which are typically indicative of raw sewage contamination. The Motherwell canal, which runs through informal settlements, was the most polluted input source with high levels of anthropogenic nutrients and pathogenic bacteria. The Chatty river, which also runs through townships, recorded increased nutrient concentrations and low bacterial richness and diversity which was likely due to an Arthrospira bloom at the time of sampling. The overall results of this study identified sources of pollution in Sundays and Swartkops Estuaries and highlighted the impacts of anthropogenic inputs on microbial population profiles and diversity. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
- Full Text:
- Date Issued: 2022-04-06
- Authors: Kgomokhumo, Tlhoafalang Evah
- Date: 2022-04-06
- Subjects: Microbial ecology South Africa Sundays Estuary (Eastern Cape) , Microbial ecology South Africa Swartkops River Estuary , Estuarine health Effect of human beings on South Africa Sundays Estuary (Eastern Cape) , Estuarine health Effect of human beings on South Africa Swartkops River Estuary , Microorganisms South Africa Sundays Estuary (Eastern Cape) Molecular aspects , Microorganisms South Africa Swartkops River Estuary Molecular aspects , Eutrophication South Africa Sundays Estuary (Eastern Cape) , Eutrophication South Africa Swartkops River Estuary , Algal blooms South Africa Sundays Estuary (Eastern Cape) , Algal blooms South Africa Swartkops River Estuary
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/290994 , vital:56806
- Description: Anthropogenic activities are of concern in estuarine systems as they are the main source of water degradation. Water pollution in estuaries is indicated by eutrophication and the presence of pathogens and bacterial indicators which affect biodiversity and energy flow. This study focused on two geographically linked estuaries, namely the Sundays and Swartkops Estuaries. The Sundays Estuary is primarily impacted by agricultural activities in the river catchment with increased nutrients levels, particularly of total oxidised nitrogen (TOxN), likely derived from these farming activities. In contrast, the Swartkops Estuary, which is heavily influenced by urban/industrial activities, reflected increased levels of phosphates likely from wastewater and sewage water contamination from residential areas, leaking pipes, and poorly managed sewage treatment plants. The central objective of this study was to assess microbial population profiles and diversity impacted by agricultural activities in Sundays Estuary and industrial/urban-influenced Swartkops Estuary using 16S and 18S rRNA gene metabarcoding. A distinct difference in eukaryotic composition and diversity was evident between the two sampling exercises in 2018 and 2019 in Sundays Estuary. The eutrophication of both the Sundays and Swartkops estuaries was evident in the repeated occurrences of bloom events. In the Sundays Estuary, a bloom of Heterosigma akashiwo was observed in 2018 whilst Cyclotella dominated the estuary in 2019. The Swartkops Estuary exhibited seasonal variation in phytoplankton composition with Bacillariophyceae blooms in the upper reaches of the estuary in summer and increased prevalence of Dinophyceae in spring. Bacterial taxonomic variation was also noted between the two contrasting estuaries. Although members of the Proteobacteria dominated both estuaries, Gammaproteobacteria were in increased abundance in Sundays Estuary while members of Alphaproteobacteria were in high relative abundance in the marine dominated Swartkops Estuary. Members of the Bacteroidetes were the second most abundant bacterial phylum in both estuaries. Bacterial indicators of agricultural anthropogenic impacts identified in Sundays Estuary included members of Sporichthyaceae, Erysipelotrichaceae, Nostocaceae, and NS11-12_marine_group while some taxa such as the Flavobacteriaceae, Cryomorphaceae, and Halieaceae reflected their capability in degrading the phytoplankton bloom biomass present in the estuary. The urban impacts on the Swartkops Estuary was reflected by the contamination of the estuary with potential pathogens including Aeromonas caviae, Vibrio fluvialis, Mycobacterium intracellulare, Vibrio cholerae, and Bacillus cereus. Bacterial community profiles of the major water inflow points into the Swartkops Estuary included members of the Burkholderiaceae, Rhodocyclaceae, Aeromonadaceae, and Arcobacteriaceae which are typically indicative of raw sewage contamination. The Motherwell canal, which runs through informal settlements, was the most polluted input source with high levels of anthropogenic nutrients and pathogenic bacteria. The Chatty river, which also runs through townships, recorded increased nutrient concentrations and low bacterial richness and diversity which was likely due to an Arthrospira bloom at the time of sampling. The overall results of this study identified sources of pollution in Sundays and Swartkops Estuaries and highlighted the impacts of anthropogenic inputs on microbial population profiles and diversity. , Thesis (MSc) -- Faculty of Science, Biochemistry and Microbiology, 2022
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- Date Issued: 2022-04-06
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