BODIPY dyes for application in the photo-oxidation of pollutants, photodynamic antimicrobial chemotherapy, and nonlinear optics
- Authors: Kelechi, Lebechi Augustus
- Date: 2020
- Subjects: Dyes and dyeing -- Chemistry , Fluorescent probes , Fluorescence spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140298 , vital:37859
- Description: The synthesis and structural characterization of a series of BODIPY dyes to analyze both the effects of halogenations at the 2,6-positions and the introduction of styryl groups at the 3,5-positions. The photophysical properties of these dyes were investigated to determine their suitability as singlet oxygen-generating photosensitiser dyes for application in photocatalytic degradation of azo dyes and in photodynamic antimicrobial chemotherapy (PACT). Upon halogenation, the dyes showed high to moderate singlet oxygen quantum yields. The potential utility of electrospun polystyrene (PS) nanofibres embedded with halogenated BODIPY dyes for the photocatalytic degradation of Orange G and Methyl Orange from textile industry effluents were investigated. A comparison of the singlet oxygen quantum yield of the BODIPY dyes in solution and when embedded in the PS nanofibres support demonstrates that its photosensitiser properties are maintained in the nanofibre mats. The photocatalytic degradation properties of the PS nanofibres for Orange G and Methyl Orange were determined by using a 530 nm and 660 nm light-emitting diodes. The rate of photodegradation increases with both the Orange G and Methyl Orange concentrations and follows pseudo-first-order kinetics. The PACT activities of brominated BODIPYs on Escherichia coli and Staphylococcus aureus were investigated. Log reduction values of over 9 were obtained during the photoinactivation of Staphylococcus aureus. To be able to red-shift the main spectral band of the BODIPY dyes into the therapeutic window, styryl groups were introduced at the 3,5-positions through a modified Knoevenagel condensation reaction. Because the red-shifted spectral band lies above 532 nm, the second harmonic of the Nd:YAG laser, there is very minute absorption at this wavelength. One of the novel brominated BODIPY dyes was investigated for its potential utility as optical limiting materials in nonlinear optics (NLO), and the dyes demonstrated typical nonlinear absorption behaviour characterised by reverse saturable absorption (RSA) in Z-scan measurements. Excellent optical limiting parameters were obtained for third-order susceptibility and hyperpolarisability.
- Full Text:
- Date Issued: 2020
- Authors: Kelechi, Lebechi Augustus
- Date: 2020
- Subjects: Dyes and dyeing -- Chemistry , Fluorescent probes , Fluorescence spectroscopy
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/140298 , vital:37859
- Description: The synthesis and structural characterization of a series of BODIPY dyes to analyze both the effects of halogenations at the 2,6-positions and the introduction of styryl groups at the 3,5-positions. The photophysical properties of these dyes were investigated to determine their suitability as singlet oxygen-generating photosensitiser dyes for application in photocatalytic degradation of azo dyes and in photodynamic antimicrobial chemotherapy (PACT). Upon halogenation, the dyes showed high to moderate singlet oxygen quantum yields. The potential utility of electrospun polystyrene (PS) nanofibres embedded with halogenated BODIPY dyes for the photocatalytic degradation of Orange G and Methyl Orange from textile industry effluents were investigated. A comparison of the singlet oxygen quantum yield of the BODIPY dyes in solution and when embedded in the PS nanofibres support demonstrates that its photosensitiser properties are maintained in the nanofibre mats. The photocatalytic degradation properties of the PS nanofibres for Orange G and Methyl Orange were determined by using a 530 nm and 660 nm light-emitting diodes. The rate of photodegradation increases with both the Orange G and Methyl Orange concentrations and follows pseudo-first-order kinetics. The PACT activities of brominated BODIPYs on Escherichia coli and Staphylococcus aureus were investigated. Log reduction values of over 9 were obtained during the photoinactivation of Staphylococcus aureus. To be able to red-shift the main spectral band of the BODIPY dyes into the therapeutic window, styryl groups were introduced at the 3,5-positions through a modified Knoevenagel condensation reaction. Because the red-shifted spectral band lies above 532 nm, the second harmonic of the Nd:YAG laser, there is very minute absorption at this wavelength. One of the novel brominated BODIPY dyes was investigated for its potential utility as optical limiting materials in nonlinear optics (NLO), and the dyes demonstrated typical nonlinear absorption behaviour characterised by reverse saturable absorption (RSA) in Z-scan measurements. Excellent optical limiting parameters were obtained for third-order susceptibility and hyperpolarisability.
- Full Text:
- Date Issued: 2020
Developing social indicators for the evaluation of natural resource management programmes using a capability approach in the Eastern Cape, South Africa
- Authors: Human, Johanna Susanna
- Date: 2020
- Subjects: Environmental education -- South Africa -- Eastern Cape , Natural resources -- Management -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Sustainable development -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Environmental economics -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Subsistence farming -- South Africa -- Eastern Cape , Watersheds -- South Africa -- Eastern Cape , Capabilities approach (Social sciences) , Tsitsa River Catchment (Eastern Cape, South Africa)
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/147348 , vital:38628
- Description: The dissertation investigates how the capability approach can be used to develop social indicators for a natural resource management (NRM) programme. The study aimed to develop an understanding of what the beneficiaries of the programme value being and doing to guide the development of social indicators that will take into consideration their personal development aspirations. These valued beings and doings were then overlaid with the programme goals and objectives to identify and select the final indicators. The study was situated in the Tsitsa catchment in the Eastern Cape, South Africa and was part of a natural resource management programme, focused on land restoration and avoided degradation. Methods used to collect data for this study and develop an understanding of what the residents’ valued beings and doings were, included semi-structured interviews, workshops and document analysis. The research population was non-homogenous. I tried to include voices representing different prominent groups of land users in the study. This included established commercial farmers, emerging commercial farmers, commercial forestry, residents residing in communal areas and engaged with subsistence farming and residents from these communal areas who are now residing elsewhere but continue to have connections to the catchment. Understanding the voices of these different groups who reside in the catchment was important to develop an inclusive understanding of what residents of the catchment valued beings and doings were. The research process was supported by participatory approaches. This process, and the lessons learnt during the research process, were valuable for the further development and implementation of the planned participatory monitoring evaluation reflection and learning (PMERL) framework. The research process involved learning from the research participants about their valued beings and doings and what was important for the programme implementers. Some of the research participants from the Rhodes University implementation team (RUIT) were also involved in selecting the indicators they thought the programme should monitor. Overall, using the capability approach helped me to gain insight and understanding with regard to what the valued beings and doings are for the residents of the catchment and what they would like development programmes, such as the Tsitsa Project, to address. It was surprising to find many areas of overlap between the valued beings and doings of the different residents in the catchment, as well as the similarities between these and the goals and objectives of the Tsitsa Project. In conclusion, using the capability approach was useful to learn what was important for the residents of the catchment to help develop the social indicators but also to learn how to guide and steer participatory monitoring and evaluation processes in the future.
- Full Text:
- Date Issued: 2020
- Authors: Human, Johanna Susanna
- Date: 2020
- Subjects: Environmental education -- South Africa -- Eastern Cape , Natural resources -- Management -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Sustainable development -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Environmental economics -- Study and teaching (Continuing education) -- South Africa -- Eastern Cape , Subsistence farming -- South Africa -- Eastern Cape , Watersheds -- South Africa -- Eastern Cape , Capabilities approach (Social sciences) , Tsitsa River Catchment (Eastern Cape, South Africa)
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/147348 , vital:38628
- Description: The dissertation investigates how the capability approach can be used to develop social indicators for a natural resource management (NRM) programme. The study aimed to develop an understanding of what the beneficiaries of the programme value being and doing to guide the development of social indicators that will take into consideration their personal development aspirations. These valued beings and doings were then overlaid with the programme goals and objectives to identify and select the final indicators. The study was situated in the Tsitsa catchment in the Eastern Cape, South Africa and was part of a natural resource management programme, focused on land restoration and avoided degradation. Methods used to collect data for this study and develop an understanding of what the residents’ valued beings and doings were, included semi-structured interviews, workshops and document analysis. The research population was non-homogenous. I tried to include voices representing different prominent groups of land users in the study. This included established commercial farmers, emerging commercial farmers, commercial forestry, residents residing in communal areas and engaged with subsistence farming and residents from these communal areas who are now residing elsewhere but continue to have connections to the catchment. Understanding the voices of these different groups who reside in the catchment was important to develop an inclusive understanding of what residents of the catchment valued beings and doings were. The research process was supported by participatory approaches. This process, and the lessons learnt during the research process, were valuable for the further development and implementation of the planned participatory monitoring evaluation reflection and learning (PMERL) framework. The research process involved learning from the research participants about their valued beings and doings and what was important for the programme implementers. Some of the research participants from the Rhodes University implementation team (RUIT) were also involved in selecting the indicators they thought the programme should monitor. Overall, using the capability approach helped me to gain insight and understanding with regard to what the valued beings and doings are for the residents of the catchment and what they would like development programmes, such as the Tsitsa Project, to address. It was surprising to find many areas of overlap between the valued beings and doings of the different residents in the catchment, as well as the similarities between these and the goals and objectives of the Tsitsa Project. In conclusion, using the capability approach was useful to learn what was important for the residents of the catchment to help develop the social indicators but also to learn how to guide and steer participatory monitoring and evaluation processes in the future.
- Full Text:
- Date Issued: 2020
Technology in conservation: towards a system for in-field drone detection of invasive vegetation
- James, Katherine Margaret Frances
- Authors: James, Katherine Margaret Frances
- Date: 2020
- Subjects: Drone aircraft in remote sensing , Neural networks (Computer science) , Drone aircraft in remote sensing -- Case studies , Machine learning , Computer vision , Environmental monitoring -- Remote sensing , Invasive plants -- Monitoring
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143408 , vital:38244
- Description: Remote sensing can assist in monitoring the spread of invasive vegetation. The adoption of camera-carrying unmanned aerial vehicles, commonly referred to as drones, as remote sensing tools has yielded images of higher spatial resolution than traditional techniques. Drones also have the potential to interact with the environment through the delivery of bio-control or herbicide, as seen with their adoption in precision agriculture. Unlike in agricultural applications, however, invasive plants do not have a predictable position relative to each other within the environment. To facilitate the adoption of drones as an environmental monitoring and management tool, drones need to be able to intelligently distinguish between invasive and non-invasive vegetation on the fly. In this thesis, we present the augmentation of a commercially available drone with a deep machine learning model to investigate the viability of differentiating between an invasive shrub and other vegetation. As a case study, this was applied to the shrub genus Hakea, originating in Australia and invasive in several countries including South Africa. However, for this research, the methodology is important, rather than the chosen target plant. A dataset was collected using the available drone and manually annotated to facilitate the supervised training of the model. Two approaches were explored, namely, classification and semantic segmentation. For each of these, several models were trained and evaluated to find the optimal one. The chosen model was then interfaced with the drone via an Android application on a mobile device and its performance was preliminarily evaluated in the field. Based on these findings, refinements were made and thereafter a thorough field evaluation was performed to determine the best conditions for model operation. Results from the classification task show that deep learning models are capable of distinguishing between target and other shrubs in ideal candidate windows. However, classification in this manner is restricted by the proposal of such candidate windows. End-to-end image segmentation using deep learning overcomes this problem, classifying the image in a pixel-wise manner. Furthermore, the use of appropriate loss functions was found to improve model performance. Field tests show that illumination and shadow pose challenges to the model, but that good recall can be achieved when the conditions are ideal. False positive detection remains an issue that could be improved. This approach shows the potential for drones as an environmental monitoring and management tool when coupled with deep machine learning techniques and outlines potential problems that may be encountered.
- Full Text:
- Date Issued: 2020
- Authors: James, Katherine Margaret Frances
- Date: 2020
- Subjects: Drone aircraft in remote sensing , Neural networks (Computer science) , Drone aircraft in remote sensing -- Case studies , Machine learning , Computer vision , Environmental monitoring -- Remote sensing , Invasive plants -- Monitoring
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143408 , vital:38244
- Description: Remote sensing can assist in monitoring the spread of invasive vegetation. The adoption of camera-carrying unmanned aerial vehicles, commonly referred to as drones, as remote sensing tools has yielded images of higher spatial resolution than traditional techniques. Drones also have the potential to interact with the environment through the delivery of bio-control or herbicide, as seen with their adoption in precision agriculture. Unlike in agricultural applications, however, invasive plants do not have a predictable position relative to each other within the environment. To facilitate the adoption of drones as an environmental monitoring and management tool, drones need to be able to intelligently distinguish between invasive and non-invasive vegetation on the fly. In this thesis, we present the augmentation of a commercially available drone with a deep machine learning model to investigate the viability of differentiating between an invasive shrub and other vegetation. As a case study, this was applied to the shrub genus Hakea, originating in Australia and invasive in several countries including South Africa. However, for this research, the methodology is important, rather than the chosen target plant. A dataset was collected using the available drone and manually annotated to facilitate the supervised training of the model. Two approaches were explored, namely, classification and semantic segmentation. For each of these, several models were trained and evaluated to find the optimal one. The chosen model was then interfaced with the drone via an Android application on a mobile device and its performance was preliminarily evaluated in the field. Based on these findings, refinements were made and thereafter a thorough field evaluation was performed to determine the best conditions for model operation. Results from the classification task show that deep learning models are capable of distinguishing between target and other shrubs in ideal candidate windows. However, classification in this manner is restricted by the proposal of such candidate windows. End-to-end image segmentation using deep learning overcomes this problem, classifying the image in a pixel-wise manner. Furthermore, the use of appropriate loss functions was found to improve model performance. Field tests show that illumination and shadow pose challenges to the model, but that good recall can be achieved when the conditions are ideal. False positive detection remains an issue that could be improved. This approach shows the potential for drones as an environmental monitoring and management tool when coupled with deep machine learning techniques and outlines potential problems that may be encountered.
- Full Text:
- Date Issued: 2020
Thermoluminescence and phototransferred phermoluminescence of synthetic quartz
- Authors: Dawam, Robert Rangmou
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145849 , vital:38472
- Description: The main aim of this investigation is on thermoluminescence and phototransferred thermoluminescence of synthetic quartz. Thermoluminescence was one of the tools used in characterising the electron traps parameters. The samples of quartz annealed at various temperatures up to 900̊C and the unannealed were used. The thermoluminescence glow curve was measured at 1̊C s~ 1 following beta irradiation to 40 Gy from the samples annealed at 500̊C and the unannealed consist of main peak at 70̊C and secondary peaks at 110, 180 and 310̊C. In comparison, the thermoluminescence glow curve for the sample annealed at 900̊C have main peak at 86̊C and the secondary ones at 170 and 310̊C. The kinetic analysis was carried out only on the main peak in each case. The activation energy was found to be decreasing with increase in annealing temperatures. The samples annealed at 500̊C and the unannealed were found to be affected by thermal quenching while sample annealed at 900̊C shows an inverse quenching for irradiation dose of 40 Gy. However, when the dose was reduce to 3 Gy the effects of thermal quenching was manifested. The activation energy of thermal quenching was also found to decrease with increase in annealing temperature. Thermally assisted optically stimulated luminescence measurement was carried out using continuous wave optical stimulated luminescence (CW-OSL). The samples studied were those annealed at 500̊C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The CW-OSL is stimulated using 470 nm blue LEDs at sample temperatures between 30 and 200̊C. It is measured after preheating to either 300 and 500̊C. When the integrated OSL intensity is plotted as a function of measurement temperature, the intensity goes through a peak. The increase in OSL intensity as a function of temperature is associated to thermal assistance and the decrease to thermal quenching. The kinetic parameters were evaluated by fitting the experimental data. The values of activation energies of thermal quenching are the same within experimental uncertainties for all the experimental conditions. This shows that annealing temperature, duration of annealing and irradiation dose have a negligible influence on the recombination site of luminescence using OSL. Phototransferred thermoluminescence (PTTL) induced from annealed samples using 470 nm blue light was also investigated. The quartz were annealed at 500 _C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The glow curves of conventional TL measured at 1 _C s1 following irradiation to 200 Gy shows six peaks in each case labelled I-VI for ease of reference whereas peaks observed under PTTL are referred to as A1 onwards. Only the first three peaks were reproduced under phototransfer for the sample annealed at 900̊C for 60 minutes and 1000̊C C for 10 minutes. Interestingly, for the intermediate duration of annealing of 30 minutes, the only peak that appears under phototransfer is the A1. For quartz annealed at 900̊C for 10 minutes, the PTTL appears as long as the preheating temperature does not exceed 560̊C. All other annealing temperatures, PTTL only appears for preheating to 450 and below. This shows that the occupancy of deep electron traps at temperatures beyond 450̊C or 560̊C is low. The activation energy for peaks A1, A2 and A3 were calculated. The PTTL peaks were studied for thermal quenching and peaks A1 and A3 were found to be affected. The activation energies for thermal quenching were determined as 0.62 ± 0.04 eV and 0.65 ± 0.02 eV for peaks A1 and A3 respectively. The experimental dependence of PTTL intensity on illumination time is modelled using sets of coupled linear differential equations based on systems of donors and acceptors whose number is determined by preheating temperature.
- Full Text:
- Date Issued: 2020
- Authors: Dawam, Robert Rangmou
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/145849 , vital:38472
- Description: The main aim of this investigation is on thermoluminescence and phototransferred thermoluminescence of synthetic quartz. Thermoluminescence was one of the tools used in characterising the electron traps parameters. The samples of quartz annealed at various temperatures up to 900̊C and the unannealed were used. The thermoluminescence glow curve was measured at 1̊C s~ 1 following beta irradiation to 40 Gy from the samples annealed at 500̊C and the unannealed consist of main peak at 70̊C and secondary peaks at 110, 180 and 310̊C. In comparison, the thermoluminescence glow curve for the sample annealed at 900̊C have main peak at 86̊C and the secondary ones at 170 and 310̊C. The kinetic analysis was carried out only on the main peak in each case. The activation energy was found to be decreasing with increase in annealing temperatures. The samples annealed at 500̊C and the unannealed were found to be affected by thermal quenching while sample annealed at 900̊C shows an inverse quenching for irradiation dose of 40 Gy. However, when the dose was reduce to 3 Gy the effects of thermal quenching was manifested. The activation energy of thermal quenching was also found to decrease with increase in annealing temperature. Thermally assisted optically stimulated luminescence measurement was carried out using continuous wave optical stimulated luminescence (CW-OSL). The samples studied were those annealed at 500̊C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The CW-OSL is stimulated using 470 nm blue LEDs at sample temperatures between 30 and 200̊C. It is measured after preheating to either 300 and 500̊C. When the integrated OSL intensity is plotted as a function of measurement temperature, the intensity goes through a peak. The increase in OSL intensity as a function of temperature is associated to thermal assistance and the decrease to thermal quenching. The kinetic parameters were evaluated by fitting the experimental data. The values of activation energies of thermal quenching are the same within experimental uncertainties for all the experimental conditions. This shows that annealing temperature, duration of annealing and irradiation dose have a negligible influence on the recombination site of luminescence using OSL. Phototransferred thermoluminescence (PTTL) induced from annealed samples using 470 nm blue light was also investigated. The quartz were annealed at 500 _C for 10 minutes, 900̊C for 10, 30, 60 minutes and 1000̊C for 10 minutes prior to use. The glow curves of conventional TL measured at 1 _C s1 following irradiation to 200 Gy shows six peaks in each case labelled I-VI for ease of reference whereas peaks observed under PTTL are referred to as A1 onwards. Only the first three peaks were reproduced under phototransfer for the sample annealed at 900̊C for 60 minutes and 1000̊C C for 10 minutes. Interestingly, for the intermediate duration of annealing of 30 minutes, the only peak that appears under phototransfer is the A1. For quartz annealed at 900̊C for 10 minutes, the PTTL appears as long as the preheating temperature does not exceed 560̊C. All other annealing temperatures, PTTL only appears for preheating to 450 and below. This shows that the occupancy of deep electron traps at temperatures beyond 450̊C or 560̊C is low. The activation energy for peaks A1, A2 and A3 were calculated. The PTTL peaks were studied for thermal quenching and peaks A1 and A3 were found to be affected. The activation energies for thermal quenching were determined as 0.62 ± 0.04 eV and 0.65 ± 0.02 eV for peaks A1 and A3 respectively. The experimental dependence of PTTL intensity on illumination time is modelled using sets of coupled linear differential equations based on systems of donors and acceptors whose number is determined by preheating temperature.
- Full Text:
- Date Issued: 2020
Understanding of the underlying resistance mechanism of the Kat-G protein against isoniazid in Mycobacterium tuberculosis using bioinformatics approaches
- Authors: Barozi, Victor
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Isoniazid , Drug resistance in microorganisms , Proteins -- Microbiology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146592 , vital:38540
- Description: Tuberculosis (TB) is a multi-organ infection caused by rod-shaped acid-fast Mycobacterium tuberculosis. The World Health Organization (WHO) ranks TB among the top 10 fatal infections and the leading the cause of death from a single infection. In 2017, TB was responsible for an estimated 1.3 million deaths among both the HIV negative and positive populations worldwide (WHO, 2018). Approximately 23% (roughly 1.7 billion) of the world’s population is estimated to have latent TB with a high risk of reverting to active TB infection. In 2017, an estimated 558,000 people developed drug resistant TB worldwide with 82% of the cases being multi-drug resistant TB (WHO, 2018). South Africa is ranked among the 30 high TB burdened countries with a TB incidence of 322,000 cases in 2017 accounting for 3% of the world’s TB cases. TB is curable and is clinically managed through a combination of intensive and continuation phases of first-line drugs (isoniazid, rifampicin, ethambutol, and pyrazinamide). Second-line drugs which include fluoroquinolones, injectable aminoglycoside and injectable polypeptides are used in cases of first line drug resistance. The third-line drugs include amoxicillin, clofazimine, linezolid and imipenem. These have variable but unproven efficacy to TB and are the last resort in cases of total drug resistance (Jilani et al., 2019). TB drug resistance to first-line drugs especially isoniazid in M. tuberculosis has been attributed to single nucleotide polymorphisms (SNPs) in the catalase peroxidase enzyme (katG), a protein important in the activation of the pro-drug isoniazid. The SNPs especially at position 315 of the katG enzyme are believed to reduce the sensitivity of the M. tuberculosis to isoniazid while still maintaining the enzyme’s catalytic activity - a mechanism not completely understood. KatG protein is important for protecting the bacteria from hydro peroxides and hydroxyl radicals present in an aerobic environment. This study focused on understanding the mechanism of isoniazid drug resistance in M. tuberculosis as a result of high confidence mutations in the katG through modelling the enzyme with its respective variants, performing MD simulations to explore the protein behaviour, calculating the dynamic residue network analysis (DRN) of the variants in respect to the wild type katG and finally performing alanine scanning. From the MD simulations, it was observed that the high confidence mutations i.e. S140R, S140N, G279D, G285D, S315T, S315I, S315R, S315N, G316D, S457I and G593D were not only reducing the backbone flexibility of the protein but also reducing the protein’s conformational variation and space. All the variant protein structures were observed to be more compact compared to the wild type. Residue fluctuation results indicated reduced residue flexibility across all variants in the loop region (position 26-110) responsible for katG dimerization. In addition, mutation S315T is believed to reduce the size of the active site access channel in the protein. From the DRN data, residues in the interface region between the N and C-terminal domains were observed to gain importance in the variants irrespective of the mutation location indicating an allosteric effect of the mutations on the interface region. Alanine scanning results established that residue Leucine at position 48 was not only important in the protein communication but also a destabilizing residue across all the variants. The study not only demonstrated change in the protein behaviour but also showed allosteric effect of the mutations in the katG protein.
- Full Text:
- Date Issued: 2020
- Authors: Barozi, Victor
- Date: 2020
- Subjects: Mycobacterium tuberculosis , Isoniazid , Drug resistance in microorganisms , Proteins -- Microbiology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/146592 , vital:38540
- Description: Tuberculosis (TB) is a multi-organ infection caused by rod-shaped acid-fast Mycobacterium tuberculosis. The World Health Organization (WHO) ranks TB among the top 10 fatal infections and the leading the cause of death from a single infection. In 2017, TB was responsible for an estimated 1.3 million deaths among both the HIV negative and positive populations worldwide (WHO, 2018). Approximately 23% (roughly 1.7 billion) of the world’s population is estimated to have latent TB with a high risk of reverting to active TB infection. In 2017, an estimated 558,000 people developed drug resistant TB worldwide with 82% of the cases being multi-drug resistant TB (WHO, 2018). South Africa is ranked among the 30 high TB burdened countries with a TB incidence of 322,000 cases in 2017 accounting for 3% of the world’s TB cases. TB is curable and is clinically managed through a combination of intensive and continuation phases of first-line drugs (isoniazid, rifampicin, ethambutol, and pyrazinamide). Second-line drugs which include fluoroquinolones, injectable aminoglycoside and injectable polypeptides are used in cases of first line drug resistance. The third-line drugs include amoxicillin, clofazimine, linezolid and imipenem. These have variable but unproven efficacy to TB and are the last resort in cases of total drug resistance (Jilani et al., 2019). TB drug resistance to first-line drugs especially isoniazid in M. tuberculosis has been attributed to single nucleotide polymorphisms (SNPs) in the catalase peroxidase enzyme (katG), a protein important in the activation of the pro-drug isoniazid. The SNPs especially at position 315 of the katG enzyme are believed to reduce the sensitivity of the M. tuberculosis to isoniazid while still maintaining the enzyme’s catalytic activity - a mechanism not completely understood. KatG protein is important for protecting the bacteria from hydro peroxides and hydroxyl radicals present in an aerobic environment. This study focused on understanding the mechanism of isoniazid drug resistance in M. tuberculosis as a result of high confidence mutations in the katG through modelling the enzyme with its respective variants, performing MD simulations to explore the protein behaviour, calculating the dynamic residue network analysis (DRN) of the variants in respect to the wild type katG and finally performing alanine scanning. From the MD simulations, it was observed that the high confidence mutations i.e. S140R, S140N, G279D, G285D, S315T, S315I, S315R, S315N, G316D, S457I and G593D were not only reducing the backbone flexibility of the protein but also reducing the protein’s conformational variation and space. All the variant protein structures were observed to be more compact compared to the wild type. Residue fluctuation results indicated reduced residue flexibility across all variants in the loop region (position 26-110) responsible for katG dimerization. In addition, mutation S315T is believed to reduce the size of the active site access channel in the protein. From the DRN data, residues in the interface region between the N and C-terminal domains were observed to gain importance in the variants irrespective of the mutation location indicating an allosteric effect of the mutations on the interface region. Alanine scanning results established that residue Leucine at position 48 was not only important in the protein communication but also a destabilizing residue across all the variants. The study not only demonstrated change in the protein behaviour but also showed allosteric effect of the mutations in the katG protein.
- Full Text:
- Date Issued: 2020
A physiological study on a commercial reef fish to quantify the relationship between exploitation and climate change resilience
- Authors: Duncan, Murray Ian
- Date: 2019
- Subjects: Chrysoblephus laticeps -- Climatic factors , Chrysoblephus laticeps -- Physiology , Sparidae -- South Africa -- Climatic factors , Reef fishes -- South Africa -- Climatic factors , Fish populations -- South Africa -- Climatic factors , Fish populations -- Measurement , Fish populations -- Monitoring , Fisheries -- South Africa -- Environmental aspects , Ocean temperature -- Physiological effect -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/76541 , vital:30599
- Description: The persistence of harvested fish populations in the Anthropocene will be determined, above all, by how they respond to the interacting effects of climate change and fisheries exploitation. Predicting how populations will respond to both these threats is essential for any adaptive and sustainable management strategy. The response of fish populations to climate change is underpinned by physiological rates and tolerances, and emerging evidence suggests there may be physiological-based selection in capture fisheries. By quantifying important physiological rates of a model species, the endemic seabream, Chrysoblephus laticeps, across ecologically relevant thermal gradients and from populations subjected to varying intensities of commercial exploitation, this thesis aimed to 1) provide the first physiologically grounded climate resilience assessment for a South African linefish species, and 2) elucidate whether exploitation can drive populations to less physiologically resilient states in response to climate change. To identify physiologically limiting sea temperatures and to determine if exploitation alters physiological trait distributions, an intermittent flow respirometry experiment was used to test the metabolic response of spatially protected and exploited populations of C. laticeps to acute thermal variability. Exploited populations showed reduced metabolic phenotype diversity, fewer high-performance aerobic scope phenotypes, and a significantly lower aerobic scope curve across all test temperatures. Although both populations maintained a relatively high aerobic scope across a wide thermal range, their metabolic rates were compromised when extreme cold events were simulated (8 °C), suggesting that predicted future increases in upwelling frequency and intensity may be the primary limiting factor in a more thermally variable future ocean. The increment widths of annuli in the otoliths of C. laticeps from contemporary and historic collections were measured, as a proxy for the annual growth rate of exploited and protected populations. Hierarchical mixed models were used to partition growth variation within and among individuals and ascribe growth to intrinsic and extrinsic effects. The best model for the protected population indicated that the growth response of C. laticeps was poorer during years characterised by a high cumulative upwelling intensity, and better during years characterised by higher mean autumn sea surface temperatures. The exploited population growth chronology was too short to identify an extrinsic growth driver. The growth results again highlight the role of thermal variability in modulating the response of C. laticeps to its ambient environment and indicate that the predicted increases in upwelling frequency and intensity may constrain future growth rates of this species. A metabolic index (ϕ), representing the ratio of O2 supply to demand at various temperatures and oxygen concentrations, was estimated for exploited and protected populations of C. laticeps and used to predict future distribution responses. There was no difference in the laboratory calibrations of ϕ between populations, and all data was subsequently combined into a single piecewise (12 °C) calibrated ϕ model. To predict the distribution of C. laticeps, ϕ was projected across a high-resolution ocean model of the South African coastal zone, and a species distribution model implemented using the random forest algorithm and C. laticeps occurrence points. The future distribution of C. laticeps was estimated by predicting trained models across ocean model projections up to 2100. The best predictor of C. laticeps’ current distribution was minimum monthly ϕ and future predictions indicated only a slight range contraction on either edge of C. laticeps’ distribution by 2100. In order to provide policy makers, currently developing climate change management frameworks for South Africa’s ocean, with a usable output, the results of all research chapters were combined into a marine spatial model. The spatial model identified areas where C. laticeps is predicted to be resilient to climate change in terms of physiology, growth and distribution responses, which can then be prioritised for adaptation measures, such as spatial protection from exploitation. While these results are specific to C. laticeps, the methodology developed to identify areas of climate resilience has broad applications across taxa. From a global perspective, perhaps the most salient points to consider from this case study are the evidence of selective exploitation on physiological traits and the importance of environmental variability, rather than long-term mean climate changes, in affecting organism performance. These ideas are congruent with the current paradigm shift in how we think of the ocean, selective fisheries, and how they relate to organism climate resilience.
- Full Text:
- Date Issued: 2019
- Authors: Duncan, Murray Ian
- Date: 2019
- Subjects: Chrysoblephus laticeps -- Climatic factors , Chrysoblephus laticeps -- Physiology , Sparidae -- South Africa -- Climatic factors , Reef fishes -- South Africa -- Climatic factors , Fish populations -- South Africa -- Climatic factors , Fish populations -- Measurement , Fish populations -- Monitoring , Fisheries -- South Africa -- Environmental aspects , Ocean temperature -- Physiological effect -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/76541 , vital:30599
- Description: The persistence of harvested fish populations in the Anthropocene will be determined, above all, by how they respond to the interacting effects of climate change and fisheries exploitation. Predicting how populations will respond to both these threats is essential for any adaptive and sustainable management strategy. The response of fish populations to climate change is underpinned by physiological rates and tolerances, and emerging evidence suggests there may be physiological-based selection in capture fisheries. By quantifying important physiological rates of a model species, the endemic seabream, Chrysoblephus laticeps, across ecologically relevant thermal gradients and from populations subjected to varying intensities of commercial exploitation, this thesis aimed to 1) provide the first physiologically grounded climate resilience assessment for a South African linefish species, and 2) elucidate whether exploitation can drive populations to less physiologically resilient states in response to climate change. To identify physiologically limiting sea temperatures and to determine if exploitation alters physiological trait distributions, an intermittent flow respirometry experiment was used to test the metabolic response of spatially protected and exploited populations of C. laticeps to acute thermal variability. Exploited populations showed reduced metabolic phenotype diversity, fewer high-performance aerobic scope phenotypes, and a significantly lower aerobic scope curve across all test temperatures. Although both populations maintained a relatively high aerobic scope across a wide thermal range, their metabolic rates were compromised when extreme cold events were simulated (8 °C), suggesting that predicted future increases in upwelling frequency and intensity may be the primary limiting factor in a more thermally variable future ocean. The increment widths of annuli in the otoliths of C. laticeps from contemporary and historic collections were measured, as a proxy for the annual growth rate of exploited and protected populations. Hierarchical mixed models were used to partition growth variation within and among individuals and ascribe growth to intrinsic and extrinsic effects. The best model for the protected population indicated that the growth response of C. laticeps was poorer during years characterised by a high cumulative upwelling intensity, and better during years characterised by higher mean autumn sea surface temperatures. The exploited population growth chronology was too short to identify an extrinsic growth driver. The growth results again highlight the role of thermal variability in modulating the response of C. laticeps to its ambient environment and indicate that the predicted increases in upwelling frequency and intensity may constrain future growth rates of this species. A metabolic index (ϕ), representing the ratio of O2 supply to demand at various temperatures and oxygen concentrations, was estimated for exploited and protected populations of C. laticeps and used to predict future distribution responses. There was no difference in the laboratory calibrations of ϕ between populations, and all data was subsequently combined into a single piecewise (12 °C) calibrated ϕ model. To predict the distribution of C. laticeps, ϕ was projected across a high-resolution ocean model of the South African coastal zone, and a species distribution model implemented using the random forest algorithm and C. laticeps occurrence points. The future distribution of C. laticeps was estimated by predicting trained models across ocean model projections up to 2100. The best predictor of C. laticeps’ current distribution was minimum monthly ϕ and future predictions indicated only a slight range contraction on either edge of C. laticeps’ distribution by 2100. In order to provide policy makers, currently developing climate change management frameworks for South Africa’s ocean, with a usable output, the results of all research chapters were combined into a marine spatial model. The spatial model identified areas where C. laticeps is predicted to be resilient to climate change in terms of physiology, growth and distribution responses, which can then be prioritised for adaptation measures, such as spatial protection from exploitation. While these results are specific to C. laticeps, the methodology developed to identify areas of climate resilience has broad applications across taxa. From a global perspective, perhaps the most salient points to consider from this case study are the evidence of selective exploitation on physiological traits and the importance of environmental variability, rather than long-term mean climate changes, in affecting organism performance. These ideas are congruent with the current paradigm shift in how we think of the ocean, selective fisheries, and how they relate to organism climate resilience.
- Full Text:
- Date Issued: 2019
Large scale spatio-temporal forcing of pelagic-coastal coupling: disentangling the effects of environmental change on intertidal invertebrate recruitment
- Authors: Muñiz, Carlota Fernández
- Date: 2019
- Subjects: Dinoflagellates -- South Africa , Coastal ecology -- South Africa , Climatic changes -- South Africa , Benthic ecology -- South Africa , Agulhas Current , Ocean temperature -- Agulhas Current , Ocean temperature -- Physiological effect
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/151541 , vital:39140
- Description: Marine systems are driven by the relationships among organisms and environmental conditions. Anthropogenic-induced changes during the past decades have started to alter climatic drivers which have the potential to alter the physical, chemical and biological environment. In coastal systems, biogeography is influenced by the temporal variability in the conditions of the water mass. In addition, many marine benthic organisms develop in the water mass and rely on the conditions that link the pelagic and benthic systems for population maintenance. Such pelagic-coastal coupling indicates that changes in the trophic system during development can be transferred to the adult populations through changes in propagule supply. Thus, changes in environmental conditions can influence benthic populations directly (e.g. through larval advection) or indirectly, through their influence on the phytoplankton community (e.g. through the development of HABs). The South African coastline shows clear alongshore patterns of faunal biomass and species richness. On the south coast, strong longitudinal patterns of recruitment of intertidal organisms exist, with areas of particularly high recruitment. HABs of unprecedented spatio-temporal magnitude have recently developed along the south coast, including the areas where benthic recruitment is most intense. The present thesis used these blooms to study changes in intertidal recruitment directly or indirectly associated with their occurrence. Using a combination of remote sensing data to study the environmental conditions of the water mass in the innermost part of the Agulhas Bank, and estimates of mussel and barnacle recruitment rates to integrate the effects of conditions in the water mass during larval development, this thesis aimed to: (1) understand the conditions that triggered the development of an HAB of the dinoflagellate Lingulodinium polyedrum during summer of 2014, (2) determine the direct or indirect effects of that bloom on recruitment of intertidal organisms, and understand the factors that affect recruitment along the coast, (3) determine if the environmental factors during bloom development produced any carryover effects on recruit growth and mortality, and (4) determine the factors that drive changes in community biomass and composition along the south coast, the long-term trends in those factors, and possible changes experienced in recent years. Water column stability during spring, before the development of the red tide, followed by alternating periods of upwelling and relaxation during summer and autumn, seemed to promote the development and persistence of L. polyedrum. Recruitment of mussels and barnacles was estimated during the reproductive season of mussels in 2014, coinciding with the red tide, and during the following year. Alongshore patterns in recruitment were found, with higher mussel recruitment in the absence of the red tide and the opposite pattern in barnacles. Alongshore patterns in SST and chlorophyll matching those of recruitment were also found, with higher SSTs and lower chlorophyll during the red tide than the following year. Growth and mortality rates in barnacles did not differ between years during the first five months after settlement. This suggests that the factors which produced differences in recruitment between years did not produce carryover effects detectable at the temporal scales studied. Further analysis of 15 years of satellite-derived environmental data showed significant cooling trends potentially driven by a long-term seasonal acceleration of the Agulhas Current in autumn around two upwelling centres on the south coast, coinciding temporally with the reproductive period of mussels and barnacles, and spatially with the areas of highest recruitment. In addition, the comparison of SST and chl-a conditions during the first and the second half of the period of study showed that seasonality of both variables has changed in large areas over the shelf, with increasing importance of shorter-term variability, which would in turn decrease environmental predictability. Thus, the conditions observed during the present study, particularly during 2015, when upwelling seemed to be more intense, may presage the potential effects of identified long-term cooling trends at the upwelling centres. Although the general trend shows cooling around those areas, conditions can vary greatly among years, favouring different taxa. Changes in the Agulhas Current System are affected by changes in distant areas in the Indian Ocean basin. Such tele-connection is unlikely to be unique to this system and indicates the importance of understanding trends in major large scale climatic drivers and their regional effects in order to make predictions about coastal systems.
- Full Text:
- Date Issued: 2019
- Authors: Muñiz, Carlota Fernández
- Date: 2019
- Subjects: Dinoflagellates -- South Africa , Coastal ecology -- South Africa , Climatic changes -- South Africa , Benthic ecology -- South Africa , Agulhas Current , Ocean temperature -- Agulhas Current , Ocean temperature -- Physiological effect
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/151541 , vital:39140
- Description: Marine systems are driven by the relationships among organisms and environmental conditions. Anthropogenic-induced changes during the past decades have started to alter climatic drivers which have the potential to alter the physical, chemical and biological environment. In coastal systems, biogeography is influenced by the temporal variability in the conditions of the water mass. In addition, many marine benthic organisms develop in the water mass and rely on the conditions that link the pelagic and benthic systems for population maintenance. Such pelagic-coastal coupling indicates that changes in the trophic system during development can be transferred to the adult populations through changes in propagule supply. Thus, changes in environmental conditions can influence benthic populations directly (e.g. through larval advection) or indirectly, through their influence on the phytoplankton community (e.g. through the development of HABs). The South African coastline shows clear alongshore patterns of faunal biomass and species richness. On the south coast, strong longitudinal patterns of recruitment of intertidal organisms exist, with areas of particularly high recruitment. HABs of unprecedented spatio-temporal magnitude have recently developed along the south coast, including the areas where benthic recruitment is most intense. The present thesis used these blooms to study changes in intertidal recruitment directly or indirectly associated with their occurrence. Using a combination of remote sensing data to study the environmental conditions of the water mass in the innermost part of the Agulhas Bank, and estimates of mussel and barnacle recruitment rates to integrate the effects of conditions in the water mass during larval development, this thesis aimed to: (1) understand the conditions that triggered the development of an HAB of the dinoflagellate Lingulodinium polyedrum during summer of 2014, (2) determine the direct or indirect effects of that bloom on recruitment of intertidal organisms, and understand the factors that affect recruitment along the coast, (3) determine if the environmental factors during bloom development produced any carryover effects on recruit growth and mortality, and (4) determine the factors that drive changes in community biomass and composition along the south coast, the long-term trends in those factors, and possible changes experienced in recent years. Water column stability during spring, before the development of the red tide, followed by alternating periods of upwelling and relaxation during summer and autumn, seemed to promote the development and persistence of L. polyedrum. Recruitment of mussels and barnacles was estimated during the reproductive season of mussels in 2014, coinciding with the red tide, and during the following year. Alongshore patterns in recruitment were found, with higher mussel recruitment in the absence of the red tide and the opposite pattern in barnacles. Alongshore patterns in SST and chlorophyll matching those of recruitment were also found, with higher SSTs and lower chlorophyll during the red tide than the following year. Growth and mortality rates in barnacles did not differ between years during the first five months after settlement. This suggests that the factors which produced differences in recruitment between years did not produce carryover effects detectable at the temporal scales studied. Further analysis of 15 years of satellite-derived environmental data showed significant cooling trends potentially driven by a long-term seasonal acceleration of the Agulhas Current in autumn around two upwelling centres on the south coast, coinciding temporally with the reproductive period of mussels and barnacles, and spatially with the areas of highest recruitment. In addition, the comparison of SST and chl-a conditions during the first and the second half of the period of study showed that seasonality of both variables has changed in large areas over the shelf, with increasing importance of shorter-term variability, which would in turn decrease environmental predictability. Thus, the conditions observed during the present study, particularly during 2015, when upwelling seemed to be more intense, may presage the potential effects of identified long-term cooling trends at the upwelling centres. Although the general trend shows cooling around those areas, conditions can vary greatly among years, favouring different taxa. Changes in the Agulhas Current System are affected by changes in distant areas in the Indian Ocean basin. Such tele-connection is unlikely to be unique to this system and indicates the importance of understanding trends in major large scale climatic drivers and their regional effects in order to make predictions about coastal systems.
- Full Text:
- Date Issued: 2019
The relative roles of ecosystem services and disservices in rural livelihoods in the Eastern Cape, South Africa
- Authors: Herd-Hoare, Shannon
- Date: 2019
- Subjects: Ecosystem services -- Health aspects -- South Africa , South Africa -- Rural conditions , Biodiversity -- South Africa -- Health aspects , Rural development -- South Africa -- Health aspects
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94080 , vital:30998
- Description: Since the publication of the Millennium Ecosystem Assessment report there has been a marked increase in research into various aspects of ecosystem services (ES). While ES are essential to human wellbeing, the literature has overlooked that some ecosystem goods and services also undermine human wellbeing. These are known as Ecosystem Disservices (EDS). This study aims to counter this imbalance in research, specifically in the context of rural livelihoods which are frequently dependent on local ES but often ill-equipped to manage EDS. The objectives of this study, conducted in three rural villages along a gradient of habitat diversity, were to identify a range of ES and EDS, determine their perceived contributions to or effects on the wellbeing of respondents, and identify modifications in livelihood strategies in response to EDS. The research made use of household surveys in conjunction with participatory learning and action techniques, such as focus group discussions in which ranking and trendline exercises, timelines, and participatory mapping were conducted. Findings indicated that although numerous participants were involved in the harvest of multiple ES, such as Non-Timber Forest Products (NTFPs), livestock outputs, crops and marine wildlife, they simultaneously experienced losses from EDS, such as ticks, unpalatable grass species, monkeys, and Lantana camara invasion which undermined livelihoods to varying degrees. The role of ES and EDS in livelihoods was expressed in economic terms, representing a common framework with which to illustrate the magnitude of their contribution or loss. For example, the average value of livestock goods and services, amongst those who owned and used outputs, was highest in the least biodiverse village at R9 753 per annum, while the corresponding value of potential livestock goods and services lost due to EDS, despite active implementation of prevention measures, totalled R22 426. Further, the average value of cultivated plots in the most biodiverse village could have totalled approximately R20 958, but because of EDS, represented less than 20% of this value. Further, the findings highlighted that the most biodiverse village also had the highest number of EDS, supporting Dunn (2010) who hypothesised that the number of EDS increases with the number of ES. Based on these findings, I propose that a comprehensive framework which systematically contextualises both the positive and negative contributions of ES is needed to grasp the full picture of how local people conceive and engage with nature to facilitate an understanding of the resulting practices and processes.
- Full Text:
- Date Issued: 2019
- Authors: Herd-Hoare, Shannon
- Date: 2019
- Subjects: Ecosystem services -- Health aspects -- South Africa , South Africa -- Rural conditions , Biodiversity -- South Africa -- Health aspects , Rural development -- South Africa -- Health aspects
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/94080 , vital:30998
- Description: Since the publication of the Millennium Ecosystem Assessment report there has been a marked increase in research into various aspects of ecosystem services (ES). While ES are essential to human wellbeing, the literature has overlooked that some ecosystem goods and services also undermine human wellbeing. These are known as Ecosystem Disservices (EDS). This study aims to counter this imbalance in research, specifically in the context of rural livelihoods which are frequently dependent on local ES but often ill-equipped to manage EDS. The objectives of this study, conducted in three rural villages along a gradient of habitat diversity, were to identify a range of ES and EDS, determine their perceived contributions to or effects on the wellbeing of respondents, and identify modifications in livelihood strategies in response to EDS. The research made use of household surveys in conjunction with participatory learning and action techniques, such as focus group discussions in which ranking and trendline exercises, timelines, and participatory mapping were conducted. Findings indicated that although numerous participants were involved in the harvest of multiple ES, such as Non-Timber Forest Products (NTFPs), livestock outputs, crops and marine wildlife, they simultaneously experienced losses from EDS, such as ticks, unpalatable grass species, monkeys, and Lantana camara invasion which undermined livelihoods to varying degrees. The role of ES and EDS in livelihoods was expressed in economic terms, representing a common framework with which to illustrate the magnitude of their contribution or loss. For example, the average value of livestock goods and services, amongst those who owned and used outputs, was highest in the least biodiverse village at R9 753 per annum, while the corresponding value of potential livestock goods and services lost due to EDS, despite active implementation of prevention measures, totalled R22 426. Further, the average value of cultivated plots in the most biodiverse village could have totalled approximately R20 958, but because of EDS, represented less than 20% of this value. Further, the findings highlighted that the most biodiverse village also had the highest number of EDS, supporting Dunn (2010) who hypothesised that the number of EDS increases with the number of ES. Based on these findings, I propose that a comprehensive framework which systematically contextualises both the positive and negative contributions of ES is needed to grasp the full picture of how local people conceive and engage with nature to facilitate an understanding of the resulting practices and processes.
- Full Text:
- Date Issued: 2019
Policy responses to the sexual and reproductive health of queer youth in the global south: a systematic review
- Authors: Moore, Sarah-Ann
- Date: 2018
- Subjects: Sexual minorities -- Africa , Sexual minorities -- Asia , Sexual minorities -- Caribbean Area , Sexual health -- Developing countries , Reproductive health -- Developing countries , Reproductive health services -- Developing countries , Communication in reproductive health -- Developing countries , Sexual minorities -- Youth -- Developing countries , Medical policy -- Developing countries , Homophobia -- Developing countries
- Language: English
- Type: text , Thesis , Masters , MSocSc
- Identifier: http://hdl.handle.net/10962/63021 , vital:28355
- Description: Concerns surrounding youth sexual and reproduction health (SRH) are deeply embedded within systems of heteronormativity and ciscentrism. Resultantly, youth SRH is filtered through a lens of heterosexual and cisgender experience, rendering invisible the SRH needs of queer youth. Importantly, a failure to recognise queer experiences of SRH has implications for normative subject positions, which enjoy stronger institutional support and constitute legitimate ways of being. As such, the failure to recognise queer youth as health care subjects within policy has far reaching consequences for their sexual and reproductive health. Within this research, a sexual and reproductive justice (SRJ) framework is adopted as a backdrop for exploring policy documents related to youth SRH within selected global South countries in Africa, Asia, and the Caribbean. The final data set comprises of 1035 policy excerpts extracted from 152 policies across these three regions. Research takes the form of a systematic review utilising a deductive framing and positioning thematic analysis. Analysis identifies framings of youth SRH and explores the subject positions assigned to queer youth in relation to these identified framings, with the understanding that the manner in which youth SRH concerns are framed and queer youth are positioned within policies provides an important foundation for the implementation of SRH-related policy. Findings demonstrate that policy responses to youth SRH are most often framed in terms of a public health approach. As a result, dominant understandings of youth SRH serve to reduce youth sexuality to notions of infections and impact, which may speak to an overreliance on biomedical and population-level health models. Themes emerging within human rights framings demonstrate a presumption that rights are equally afforded to, and freely exercised by, all individuals once legally secured, failing to engage with the creation of enabling conditions to realise these rights. Although context and culture framings were by no means exhaustive examples of SRJ, they provide an interesting insight into how such SRJ concerns might be integrated into policy. Importantly, policy responses demonstrate a general pattern hypervisibility of men who have sex with men (MSM) standing in marked contrast to the invisibility of queer youth and other adult queer populations. Within policy extracts, both youth and „MSM‟ are positioned as particularly prone to poor SRH outcomes. By virtue of their inclusion within both populations, queer youth may be considered as especially at risk for, or vulnerable to, such outcomes. Relatedly, these populations (and by extension queer youth) are positioned as in need of correction, containment, and/or protection by those occupying „gatekeeping‟ positions (e.g. health care providers). The positioning of „MSM‟ solely within the context of HIV/AIDS serves to link same-sex sexualities (and at times gender non-conformity) with harmful consequences, suggesting that the positioning of queer youth could similarly serve to conflate their SRH needs with concerns around HIV/AIDS. Many of the subject positions deployed in policies serve to deny the potential for youth and „MSM‟ agency, strength, and resilience. Thus, queer youth subjects are unlikely to be positioned as empowered, autonomous, and agentic. Across both framing and positioning themes, a number of key shortcomings were observed. For the most part, policy responses fail to acknowledge the influence of social, economic, political, and cultural forces that may serve to hinder SRH outcomes according to particular contexts and the intersection of multiple and varied social identities. By obscuring these broader contextual factors and power relations, policy responses may serve to hold individual youth responsible for poor SRH outcomes. In failing to engage with the potential for diversity within youth populations, these populations are largely homogenised. Finally, the need for the creation of an enabling environment in order to secure sexual and reproductive health is largely unacknowledged within policy responses.
- Full Text:
- Date Issued: 2018
- Authors: Moore, Sarah-Ann
- Date: 2018
- Subjects: Sexual minorities -- Africa , Sexual minorities -- Asia , Sexual minorities -- Caribbean Area , Sexual health -- Developing countries , Reproductive health -- Developing countries , Reproductive health services -- Developing countries , Communication in reproductive health -- Developing countries , Sexual minorities -- Youth -- Developing countries , Medical policy -- Developing countries , Homophobia -- Developing countries
- Language: English
- Type: text , Thesis , Masters , MSocSc
- Identifier: http://hdl.handle.net/10962/63021 , vital:28355
- Description: Concerns surrounding youth sexual and reproduction health (SRH) are deeply embedded within systems of heteronormativity and ciscentrism. Resultantly, youth SRH is filtered through a lens of heterosexual and cisgender experience, rendering invisible the SRH needs of queer youth. Importantly, a failure to recognise queer experiences of SRH has implications for normative subject positions, which enjoy stronger institutional support and constitute legitimate ways of being. As such, the failure to recognise queer youth as health care subjects within policy has far reaching consequences for their sexual and reproductive health. Within this research, a sexual and reproductive justice (SRJ) framework is adopted as a backdrop for exploring policy documents related to youth SRH within selected global South countries in Africa, Asia, and the Caribbean. The final data set comprises of 1035 policy excerpts extracted from 152 policies across these three regions. Research takes the form of a systematic review utilising a deductive framing and positioning thematic analysis. Analysis identifies framings of youth SRH and explores the subject positions assigned to queer youth in relation to these identified framings, with the understanding that the manner in which youth SRH concerns are framed and queer youth are positioned within policies provides an important foundation for the implementation of SRH-related policy. Findings demonstrate that policy responses to youth SRH are most often framed in terms of a public health approach. As a result, dominant understandings of youth SRH serve to reduce youth sexuality to notions of infections and impact, which may speak to an overreliance on biomedical and population-level health models. Themes emerging within human rights framings demonstrate a presumption that rights are equally afforded to, and freely exercised by, all individuals once legally secured, failing to engage with the creation of enabling conditions to realise these rights. Although context and culture framings were by no means exhaustive examples of SRJ, they provide an interesting insight into how such SRJ concerns might be integrated into policy. Importantly, policy responses demonstrate a general pattern hypervisibility of men who have sex with men (MSM) standing in marked contrast to the invisibility of queer youth and other adult queer populations. Within policy extracts, both youth and „MSM‟ are positioned as particularly prone to poor SRH outcomes. By virtue of their inclusion within both populations, queer youth may be considered as especially at risk for, or vulnerable to, such outcomes. Relatedly, these populations (and by extension queer youth) are positioned as in need of correction, containment, and/or protection by those occupying „gatekeeping‟ positions (e.g. health care providers). The positioning of „MSM‟ solely within the context of HIV/AIDS serves to link same-sex sexualities (and at times gender non-conformity) with harmful consequences, suggesting that the positioning of queer youth could similarly serve to conflate their SRH needs with concerns around HIV/AIDS. Many of the subject positions deployed in policies serve to deny the potential for youth and „MSM‟ agency, strength, and resilience. Thus, queer youth subjects are unlikely to be positioned as empowered, autonomous, and agentic. Across both framing and positioning themes, a number of key shortcomings were observed. For the most part, policy responses fail to acknowledge the influence of social, economic, political, and cultural forces that may serve to hinder SRH outcomes according to particular contexts and the intersection of multiple and varied social identities. By obscuring these broader contextual factors and power relations, policy responses may serve to hold individual youth responsible for poor SRH outcomes. In failing to engage with the potential for diversity within youth populations, these populations are largely homogenised. Finally, the need for the creation of an enabling environment in order to secure sexual and reproductive health is largely unacknowledged within policy responses.
- Full Text:
- Date Issued: 2018
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