A classification of large wetlands in Africa’s elevated drylands based on their formation, structure, and hydrological functioning using Earth Observation (EO) data and Geographic Information System (GIS)
- Authors: Lidzhegu, Zwidofhelangani
- Date: 2020
- Subjects: Wetlands -- Africa -- Classification , Wetlands -- Africa -- Research , Wetlands -- Africa -- Monitoring , Topographical surveying -- Africa , Hydrological surveys == Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142668 , vital:38100
- Description: Due to wetland inaccessibility and limited wetland geomorphological studies, there is limited information on the geomorphological origin and hydrological functioning of different types of wetlands in Africa’s elevated drylands. As a result, there is limited information for the development of a comprehensive wetland classification system that classifies wetlands based on long-term geomorphic processes that determine their formation and shape, their structure and hydrological functioning. Therefore, the current study was designed to classify large wetlands in Africa’s elevated drylands based on processes that determine their formation, and shape their structure and hydrological functioning using remote sensing and Geographic Information System (GIS) techniques. Although wetlands perform a number of hydrological functions including groundwater recharge and water purification, the current study focuses mainly on their flood attenuation function. Detailed analysis of topographic information was undertaken using Shuttle Radar Topographic Mission (SRTM) elevations measured at the scale of 30 m x 30 m. LandsatLook and Google Earth images, tectonic as well as geological data were used as supplementary data for developing an understanding of the origin, structure and hydrological characteristics of wetlands. The Principal Component Analysis (PCA) of wetland environmental variables was used to identify and explain wetland heterogeneity. The results of the study showed that fluvial processes, tectonic history and the evolution of Africa’s landscape played a fundamental role in the formation and evolution of wetlands. This study demonstrates a wide range of processes that contribute to wetland formation, structure and functioning. At one extreme it is clear that tectonic processes may be primarily responsible for the creation of basins that host wetlands. At another extreme, wetlands may be structured primarily by fluvial processes. At a third extreme are wetlands that superficially appear to be structured by fluvial processes, but which have their structures modified by gradual rising of the base level at their distal ends, either through marginal uplift adjacent to rift valleys, or through aggradation of a floodplain that blocks a tributary valley. Overall, the classification of wetlands considered in this study can be summarised into four distinct groupings, with two of these divided further into two groupings each: (1) Tectonic basins with little or no indication of fluvial development (Bahi and Wembere wetlands), (2) Tectonic basins evolving towards a wetland with a structure increasingly shaped by fluvial characteristics (Usangu wetland), (3) Fluvially modified valleys with a local base level at the toe of the wetland such as a resistant lithology or a tectonic control that limits the rate of incision of easily weathered and eroded lithologies, leading to valley widening and longitudinal slope reduction, which are of two distinct types: (a) With a catchment on Kalahari Group sediment that is transported fluvially as bedload, and therefore with no prominent alluvial ridge or backwater depressions (Upper Zambezi and Barotse wetlands), (b) With a catchment that produces abundant fine sediment that is deposited as overbank sediments, leading to channel migration via meandering and to the construction of an elevated alluvial ridge (Lufira wetland), (4) Fluvially modified basins with evidence of gradual elevation of the base level at the toe of the wetland, which are of two types: (a) Tectonic marginal rift valley uplift such that they behave more as depression wetlands rather than as wetlands shaped by fluvial processes (Kafue and Luapula wetlands), (b) Tributary valley wetlands blocked by aggradation of the trunk valley (Lukanga wetland). In conclusion, although few geomorphological studies have been conducted on southern African wetlands because of their inaccessibility, Africa’s surface topography and its historical evolution, as well as aridity, provide an opportunity for illustrating the important role that the long-term tectonic, geological and geomorphological processes play in determining wetland origin, structure and dynamics. GIS methodology and Earth Observation (EO) data on the other hand, provide a practical means for acquiring information on inaccessible and hard to traverse wetland systems. A novel cut-and-fill approach for delineating wetlands from a Digital Elevation Model (DEM) was presented as another way in which GIS methodology and Earth Observation (EO) data can provide practical means for assessing inaccessible and hard to traverse wetland systems.
- Full Text:
- Date Issued: 2020
- Authors: Lidzhegu, Zwidofhelangani
- Date: 2020
- Subjects: Wetlands -- Africa -- Classification , Wetlands -- Africa -- Research , Wetlands -- Africa -- Monitoring , Topographical surveying -- Africa , Hydrological surveys == Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/142668 , vital:38100
- Description: Due to wetland inaccessibility and limited wetland geomorphological studies, there is limited information on the geomorphological origin and hydrological functioning of different types of wetlands in Africa’s elevated drylands. As a result, there is limited information for the development of a comprehensive wetland classification system that classifies wetlands based on long-term geomorphic processes that determine their formation and shape, their structure and hydrological functioning. Therefore, the current study was designed to classify large wetlands in Africa’s elevated drylands based on processes that determine their formation, and shape their structure and hydrological functioning using remote sensing and Geographic Information System (GIS) techniques. Although wetlands perform a number of hydrological functions including groundwater recharge and water purification, the current study focuses mainly on their flood attenuation function. Detailed analysis of topographic information was undertaken using Shuttle Radar Topographic Mission (SRTM) elevations measured at the scale of 30 m x 30 m. LandsatLook and Google Earth images, tectonic as well as geological data were used as supplementary data for developing an understanding of the origin, structure and hydrological characteristics of wetlands. The Principal Component Analysis (PCA) of wetland environmental variables was used to identify and explain wetland heterogeneity. The results of the study showed that fluvial processes, tectonic history and the evolution of Africa’s landscape played a fundamental role in the formation and evolution of wetlands. This study demonstrates a wide range of processes that contribute to wetland formation, structure and functioning. At one extreme it is clear that tectonic processes may be primarily responsible for the creation of basins that host wetlands. At another extreme, wetlands may be structured primarily by fluvial processes. At a third extreme are wetlands that superficially appear to be structured by fluvial processes, but which have their structures modified by gradual rising of the base level at their distal ends, either through marginal uplift adjacent to rift valleys, or through aggradation of a floodplain that blocks a tributary valley. Overall, the classification of wetlands considered in this study can be summarised into four distinct groupings, with two of these divided further into two groupings each: (1) Tectonic basins with little or no indication of fluvial development (Bahi and Wembere wetlands), (2) Tectonic basins evolving towards a wetland with a structure increasingly shaped by fluvial characteristics (Usangu wetland), (3) Fluvially modified valleys with a local base level at the toe of the wetland such as a resistant lithology or a tectonic control that limits the rate of incision of easily weathered and eroded lithologies, leading to valley widening and longitudinal slope reduction, which are of two distinct types: (a) With a catchment on Kalahari Group sediment that is transported fluvially as bedload, and therefore with no prominent alluvial ridge or backwater depressions (Upper Zambezi and Barotse wetlands), (b) With a catchment that produces abundant fine sediment that is deposited as overbank sediments, leading to channel migration via meandering and to the construction of an elevated alluvial ridge (Lufira wetland), (4) Fluvially modified basins with evidence of gradual elevation of the base level at the toe of the wetland, which are of two types: (a) Tectonic marginal rift valley uplift such that they behave more as depression wetlands rather than as wetlands shaped by fluvial processes (Kafue and Luapula wetlands), (b) Tributary valley wetlands blocked by aggradation of the trunk valley (Lukanga wetland). In conclusion, although few geomorphological studies have been conducted on southern African wetlands because of their inaccessibility, Africa’s surface topography and its historical evolution, as well as aridity, provide an opportunity for illustrating the important role that the long-term tectonic, geological and geomorphological processes play in determining wetland origin, structure and dynamics. GIS methodology and Earth Observation (EO) data on the other hand, provide a practical means for acquiring information on inaccessible and hard to traverse wetland systems. A novel cut-and-fill approach for delineating wetlands from a Digital Elevation Model (DEM) was presented as another way in which GIS methodology and Earth Observation (EO) data can provide practical means for assessing inaccessible and hard to traverse wetland systems.
- Full Text:
- Date Issued: 2020
Dynamics of stimulated luminescence in natural quartz: Thermoluminescence and phototransferred thermoluminescence
- Authors: Folley, Damilola Esther
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146255 , vital:38509
- Description: Natural quartz has remained an important mineral that is of topical interest in luminescence and dosimetry-related research. We investigate the dynamics of stimulated luminescence on this material through thermoluminescence (TL) and phototransferred thermoluminescence (PTTL). Measurements were made on unannealed natural quartz as well as quartz annealed at 800 and 1000̊C. The samples were annealed for 10 minutes and for 1 hour. The material, in its un- and annealed state has its main peak between 68 and 72̊C when measured at 1Cs ̃1 after a dose of 50 Gy. A study of dosimetric features and kinetic analysis was carried out on two prominent peaks, peak I and III for all the samples. The peaks show a sublinear dose response for irradiation doses between 10 and 300 Gy. Kinetic analysis shows that peak I is a first-order peak and peak III a general-order peak. Interestingly, we observe for peak I for the sample annealed at 800̊C for 1 hour an inverse thermal quenching behaviour. We demonstrate that a peak affected with an inverse thermal quenching-like behaviour can still show effect of thermal quenching when the dose the sample is irradiated to is significantly reduced. We ascribe the apparent dependence of thermal quenching on dose to competition between radiative and non-radiative transitions at the recombination centre. Peaks I, II, and III for all the samples were reproduced under phototransfer when the peaks, initially removed by preheating to a certain temperature are exposed to 470 and 525 nm light. The infuence of duration of illumination on the PTTL intensity of these peaks corresponding to various preheating temperatures is modelled using coupled first-order dfferential equations. The model is based on systems of acceptors and donors whose number and role depends on preheating temperature
- Full Text:
- Date Issued: 2020
- Authors: Folley, Damilola Esther
- Date: 2020
- Subjects: Thermoluminescence , Quartz
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146255 , vital:38509
- Description: Natural quartz has remained an important mineral that is of topical interest in luminescence and dosimetry-related research. We investigate the dynamics of stimulated luminescence on this material through thermoluminescence (TL) and phototransferred thermoluminescence (PTTL). Measurements were made on unannealed natural quartz as well as quartz annealed at 800 and 1000̊C. The samples were annealed for 10 minutes and for 1 hour. The material, in its un- and annealed state has its main peak between 68 and 72̊C when measured at 1Cs ̃1 after a dose of 50 Gy. A study of dosimetric features and kinetic analysis was carried out on two prominent peaks, peak I and III for all the samples. The peaks show a sublinear dose response for irradiation doses between 10 and 300 Gy. Kinetic analysis shows that peak I is a first-order peak and peak III a general-order peak. Interestingly, we observe for peak I for the sample annealed at 800̊C for 1 hour an inverse thermal quenching behaviour. We demonstrate that a peak affected with an inverse thermal quenching-like behaviour can still show effect of thermal quenching when the dose the sample is irradiated to is significantly reduced. We ascribe the apparent dependence of thermal quenching on dose to competition between radiative and non-radiative transitions at the recombination centre. Peaks I, II, and III for all the samples were reproduced under phototransfer when the peaks, initially removed by preheating to a certain temperature are exposed to 470 and 525 nm light. The infuence of duration of illumination on the PTTL intensity of these peaks corresponding to various preheating temperatures is modelled using coupled first-order dfferential equations. The model is based on systems of acceptors and donors whose number and role depends on preheating temperature
- Full Text:
- Date Issued: 2020
Exploring and modelling the effects of agricultural land management and climate change on agroecosystem services in the Eastern Cape, South Africa
- Authors: Choruma, Dennis Junior
- Date: 2020
- Subjects: Agricultural ecology -- South Africa -- Eastern Cape , Agriculture -- Environmental aspects -- South Africa -- Eastern Cape , Crops and climate -- South Africa -- Eastern Cape , Corn -- Climatic factors -- South Africa -- Eastern Cape , Land use -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146756 , vital:38554
- Description: The aims of this study were to evaluate the impacts of agricultural land management strategies and climate change on irrigated maize production in the Eastern Cape, South Africa. To achieve these aims, the study was guided by two overarching research questions, subsequently broken down into more specific questions. The first research question examined the reasons behind farmers’ current agricultural land management practices, the values they assigned to different agroecosystem services, their perceptions of climate change and the adaptation strategies they used to address challenges associated with agricultural crop production and climate change. To answer these questions, a survey of conventional farmers in the Eastern Cape was carried out. The survey targeted farmers who used fertilisers and irrigation water in their day to day farming. Results showed that farmers recognised the different benefits that agroecosystems provided even though they were not familiar with the term ‘ecosystem services.’ Farmers assigned a high value to food provisioning compared to other agroecosystem services and managed their farms for maximum crop yields or maximum crop quality. Fertiliser and irrigation water management decisions were based on multiple factors such as cost, availability of farming equipment and crop yield or crop quality considerations. Survey results showed that while most farmers were able to state the amount of fertiliser used per growing season, the majority of farmers did not know the amount of water they used per growing season. From the farmers’ survey it was recommended that extension services and agricultural education programmes be strengthened in the region to increase farmers’ knowledge on effective agricultural land management strategies that support sustainable intensification. The second research question investigated the effects of agricultural land management strategies and climate change on crop yields in the Eastern Cape. This investigation was done in three steps. First, a crop model, the Environmental Policy Integrated Climate (EPIC) model was calibrated and validated using limited field data from maize variety trials carried out at the Cradock Research Farm in the Eastern Cape. Calibration and validation results proved satisfactory with model efficiencies (Nash Sutcliffe, NSE) greater than 0.5 for both calibration and validation. It was concluded that limited data from field trials on maize that only included grain yield and agricultural land management dates can be used for the calibration of the EPIC model to simulate maize production under South African conditions. In the second step, the calibrated model was applied to simulate different irrigation and fertiliser management strategies for maize production in the Eastern Cape. Different irrigation and Nitrogen (N) fertiliser levels were compared to find optimal irrigation and N fertiliser management strategies that would increase maize yields while minimising environmental pollution (nitrate leaching). Model outputs were also compared to the average yields obtained in the field trials (baseline) and to maize yields reported by farmers in the farmers’ survey. Results showed that improved management of irrigation water and N fertiliser could improve farmers’ maize yields from approximately 7.2 t ha-1 to approximately 12.2 t ha-1, an increase of approximately 69%. Results also revealed a trade-off between food provision and nitrate leaching. Simulations showed that increasing N fertiliser application under sufficient irrigation water levels would increase maize yields, however, this would be accompanied by an increase in N leaching. Lastly, the EPIC model was then applied to simulate the effects of future climate change on irrigated maize production in the Eastern Cape. For these simulations, the model was driven by statistically downscaled climate data derived from three General Circulation Models (GCMs) for two future climate periods, (2040-2069) and (2070-2099), under two Representative Concentration Pathways (RCPs): RCP 4.5 and RCP 8.5. Future maize yields were compared to the baseline (1980-2010) maize yield average. All three climate models predicted a decline in maize yields, with yields declining by as much as 23.8% in RCP 8.5, 2070-2099. Simulations also predicted increases in average daily maximum and minimum temperatures for both the two future climate periods under both RCPs. Results also indicated a decrease in seasonal irrigation water requirements. Nitrate leaching was projected to significantly increase towards the end of the century, increasing by as much as 373.8% in RCP 8.5 2070-2099. Concerning farmers’ perceptions of climate change, results showed that farmers were aware of climate change and identified temperature and rainfall changes as the most important changes in climate that they had observed. To adapt to climate change, farmers used a variety of adaptation strategies such as crop rotations and intercropping. Apart from challenges posed by climate change, farmers also faced other challenges such as access to markets and access to financial credit lines, challenges that prevented them from effectively adapting to climate change. The study therefore recommended that appropriate and adequate strategies be designed to help farmers in the region offset the projected decrease in maize production and increase crop yields while minimising negative environmental impacts.
- Full Text:
- Date Issued: 2020
- Authors: Choruma, Dennis Junior
- Date: 2020
- Subjects: Agricultural ecology -- South Africa -- Eastern Cape , Agriculture -- Environmental aspects -- South Africa -- Eastern Cape , Crops and climate -- South Africa -- Eastern Cape , Corn -- Climatic factors -- South Africa -- Eastern Cape , Land use -- South Africa -- Eastern Cape
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/146756 , vital:38554
- Description: The aims of this study were to evaluate the impacts of agricultural land management strategies and climate change on irrigated maize production in the Eastern Cape, South Africa. To achieve these aims, the study was guided by two overarching research questions, subsequently broken down into more specific questions. The first research question examined the reasons behind farmers’ current agricultural land management practices, the values they assigned to different agroecosystem services, their perceptions of climate change and the adaptation strategies they used to address challenges associated with agricultural crop production and climate change. To answer these questions, a survey of conventional farmers in the Eastern Cape was carried out. The survey targeted farmers who used fertilisers and irrigation water in their day to day farming. Results showed that farmers recognised the different benefits that agroecosystems provided even though they were not familiar with the term ‘ecosystem services.’ Farmers assigned a high value to food provisioning compared to other agroecosystem services and managed their farms for maximum crop yields or maximum crop quality. Fertiliser and irrigation water management decisions were based on multiple factors such as cost, availability of farming equipment and crop yield or crop quality considerations. Survey results showed that while most farmers were able to state the amount of fertiliser used per growing season, the majority of farmers did not know the amount of water they used per growing season. From the farmers’ survey it was recommended that extension services and agricultural education programmes be strengthened in the region to increase farmers’ knowledge on effective agricultural land management strategies that support sustainable intensification. The second research question investigated the effects of agricultural land management strategies and climate change on crop yields in the Eastern Cape. This investigation was done in three steps. First, a crop model, the Environmental Policy Integrated Climate (EPIC) model was calibrated and validated using limited field data from maize variety trials carried out at the Cradock Research Farm in the Eastern Cape. Calibration and validation results proved satisfactory with model efficiencies (Nash Sutcliffe, NSE) greater than 0.5 for both calibration and validation. It was concluded that limited data from field trials on maize that only included grain yield and agricultural land management dates can be used for the calibration of the EPIC model to simulate maize production under South African conditions. In the second step, the calibrated model was applied to simulate different irrigation and fertiliser management strategies for maize production in the Eastern Cape. Different irrigation and Nitrogen (N) fertiliser levels were compared to find optimal irrigation and N fertiliser management strategies that would increase maize yields while minimising environmental pollution (nitrate leaching). Model outputs were also compared to the average yields obtained in the field trials (baseline) and to maize yields reported by farmers in the farmers’ survey. Results showed that improved management of irrigation water and N fertiliser could improve farmers’ maize yields from approximately 7.2 t ha-1 to approximately 12.2 t ha-1, an increase of approximately 69%. Results also revealed a trade-off between food provision and nitrate leaching. Simulations showed that increasing N fertiliser application under sufficient irrigation water levels would increase maize yields, however, this would be accompanied by an increase in N leaching. Lastly, the EPIC model was then applied to simulate the effects of future climate change on irrigated maize production in the Eastern Cape. For these simulations, the model was driven by statistically downscaled climate data derived from three General Circulation Models (GCMs) for two future climate periods, (2040-2069) and (2070-2099), under two Representative Concentration Pathways (RCPs): RCP 4.5 and RCP 8.5. Future maize yields were compared to the baseline (1980-2010) maize yield average. All three climate models predicted a decline in maize yields, with yields declining by as much as 23.8% in RCP 8.5, 2070-2099. Simulations also predicted increases in average daily maximum and minimum temperatures for both the two future climate periods under both RCPs. Results also indicated a decrease in seasonal irrigation water requirements. Nitrate leaching was projected to significantly increase towards the end of the century, increasing by as much as 373.8% in RCP 8.5 2070-2099. Concerning farmers’ perceptions of climate change, results showed that farmers were aware of climate change and identified temperature and rainfall changes as the most important changes in climate that they had observed. To adapt to climate change, farmers used a variety of adaptation strategies such as crop rotations and intercropping. Apart from challenges posed by climate change, farmers also faced other challenges such as access to markets and access to financial credit lines, challenges that prevented them from effectively adapting to climate change. The study therefore recommended that appropriate and adequate strategies be designed to help farmers in the region offset the projected decrease in maize production and increase crop yields while minimising negative environmental impacts.
- Full Text:
- Date Issued: 2020
Investigating visual literacy development through advertisements: a case of Grade 7 English Language Teaching in Mount Frere District, Eastern Cape
- Authors: Mbuqe, Zolile Patrick
- Date: 2020
- Subjects: Visual literacy , English language -- Study and teaching -- Audio-visual aids , Second language acquisition -- South Africa , English language -- Study and teaching -- Activity programs , Advertising -- Study and teaching , Visual learning , English language -- Study and teaching -- South Africa
- Language: English
- Type: text , Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/143458 , vital:38248
- Description: Although the Curriculum and Assessment Policy Statement lists visual literacy as one of the aspects of English First Additional Language in Grades 4-12, many teachers face challenges in teaching it. This study aimed to investigate visual literacy development through advertisements. Drawing on Cultural Historical Activity Theory, this qualitative intervention designed two research phases in which data was collected and analysed. The first phase, a pre-intervention, included lesson observation, analysis of documents and post-lesson semi-structured interviews. Based on Phase One findings and using advertisements as an entry point in developing visual literacy, Phase Two occurred at a change laboratory workshop and engaged eight teachers with the dynamics of meaning making and teaching. This data was analysed using elements of social semiotics and Serafini’s resource practices. The key findings are that despite low visual literacy understanding and practices, rigorous formative intervention indicated advancement in teachers’ understanding of visual literacy. In addition, through this intervention, teachers developed agency in dealing with schooling adversities such as lack of resources and knowledge hence further formative intervention research in visual literacy is recommended for both EFAL subject advisors and teachers.
- Full Text:
- Date Issued: 2020
- Authors: Mbuqe, Zolile Patrick
- Date: 2020
- Subjects: Visual literacy , English language -- Study and teaching -- Audio-visual aids , Second language acquisition -- South Africa , English language -- Study and teaching -- Activity programs , Advertising -- Study and teaching , Visual learning , English language -- Study and teaching -- South Africa
- Language: English
- Type: text , Thesis , Masters , MEd
- Identifier: http://hdl.handle.net/10962/143458 , vital:38248
- Description: Although the Curriculum and Assessment Policy Statement lists visual literacy as one of the aspects of English First Additional Language in Grades 4-12, many teachers face challenges in teaching it. This study aimed to investigate visual literacy development through advertisements. Drawing on Cultural Historical Activity Theory, this qualitative intervention designed two research phases in which data was collected and analysed. The first phase, a pre-intervention, included lesson observation, analysis of documents and post-lesson semi-structured interviews. Based on Phase One findings and using advertisements as an entry point in developing visual literacy, Phase Two occurred at a change laboratory workshop and engaged eight teachers with the dynamics of meaning making and teaching. This data was analysed using elements of social semiotics and Serafini’s resource practices. The key findings are that despite low visual literacy understanding and practices, rigorous formative intervention indicated advancement in teachers’ understanding of visual literacy. In addition, through this intervention, teachers developed agency in dealing with schooling adversities such as lack of resources and knowledge hence further formative intervention research in visual literacy is recommended for both EFAL subject advisors and teachers.
- Full Text:
- Date Issued: 2020
Mechanism of action of non-synonymous single nucleotide variations associated with α-carbonic anhydrases II, IV and VIII
- Authors: Sanyanga, T. Allan
- Date: 2020
- Subjects: Carbonic anhydrase , Carbonic anhydrase -- Therapeutic use , Nucleotides
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167346 , vital:41470
- Description: The carbonic anhydrase (CA) group of enzymes are Zinc (Zn2+) metalloproteins responsible for the reversible hydration of CO2 to bicarbonate (BCT or HCO− 3 ) and protons (H+) for the facilitation of acid-base balance and homeostasis within the body. Across all organisms, a minimum of six CA families exist, including, α (alpha), β (beta), γ (gamma), δ (delta), η (eta) and ζ (zeta). Some organisms can have more than one family, with exception to humans that contain the α family solely. The α-CA family comprises of 16 isoforms (CA-I to CA-XV) including the CA-VIII, CA-X and CA-XI acatalytic isoforms. Of the catalytic isoforms, CA-II and CA-IV possess one of the fastest rates of reaction, and any disturbances to the function of these enzymes results in CA deficiencies and undesirable phenotypes. CA-II deficiencies result in osteopetrosis with renal tubular acidosis and cerebral calcification, whereas CA-IV deficiencies result in retinitis pigmentosa 17 (RP17). Phenotypic effects generally manifest as a result of poor protein folding and function due to the presence of non-synonymous single nucleotide variations (nsSNVs). Even within the acatalytic isoforms such as CA-VIII that llosterically regulates the affinity of inositol triphosphate (IP3) for the IP3 receptor type 1 (ITPR1) and regulates calcium (Ca2+) signalling, the presence of SNVs also causes phenotypes cerebellar ataxia, mental retardation, and dysequilibrium syndrome 3 (CAMRQ3). Currently the majority of research into the CAs is focused on the inhibition of these proteins to achieve therapeutic effects in patients via the control of HCO− production or reabsorption as observed in glaucoma and diuretic medications. Little research has therefore been devoted into the identification of stabilising or activating compound that could rescue protein function in the case of deficiencies. The main aim of this research was to identify and characterise the effects of nsSNVs on the structure and function of CA-II, CA-IV and CA-VIII to set a foundation for rare disease studies into the CA group of proteins. Combined bioinformatics approaches divided into four main objectives were implemented. These included variant identification, sequence analysis and protein characterisation, force field (FF) parameter generation, molecular dynamics (MD) simulation and dynamic residue network analysis (DRN). Six variants for each of the CA-II, CA-IV and CA-VIII proteins with pathogenic annotations were identified from the HUMA and Ensembl databases. These included the pathogenic variants K18E, K18Q, H107Y, P236H, P236R and N252D for CA-II. CA-IV included the pathogenic R69H, R219C and R219S, and benign N86K, N177K and V234I variants. CA-VIII included pathogenic S100A, S100P, G162R and R237Q, and benign S100L and E109D variants. CA-II has been more extensively studied than CA-IV and CA-VIII, therefore residues essential to its function and stability are known. To discover important residues and regions within the CA-IV and CA-VIII proteins sequence and motif analysis was performed across the α-CA family, using CA-II as a reference. Sequence analysis identified multiple conserved residues between the two acatalytic CA-II and CA-IV, and the acatalytic CA-VIII isoforms that were proposed to be essential for protein stability. With exception to the benign N86K CA-IV variant, none of the other pathogenic or benign CA-II, CA-IV and CA-VIII SNVs were located at functionally or structurally important residues. Motif analysis identified 11 conserved and important motifs within the α-CA family. Several of the identified variants were located on these motifs including K18E, K18Q, H107Y and N252D (CA-II); N86K, R219C, R219S and V234I (CA-IV); and E109D, G162R and R237Q (CA-VIII). As there were no x-ray crystal structures of the variant proteins, homology modelling was performed to calculate the protein structures for characterisation. In CA-VIII, the substitution of Ser for Pro at position 100 (variant S100P) resulted in destruction of the β-sheet that the SNV was located on. Little is known about the mechanism of interaction between CA-VIII and ITPR1, and residues involved. SiteMap and CPORT were used to identify binding site amino for CA-VIII and results identified 38 potential residues. Traditional FFs are incapable of performing MD simulations of metalloproteins. The AMBER ff14SB FF was extended and Zn2+ FF parameters calculated to add support for metalloprotein MD simulations. In the protein, Zn2+ was noted to have a charge less than +1. Variant effects on protein structure were then investigated using MD simulations. Root mean square deviation (RMSD) and radius of gyration (Rg) results indicated subtle SNV effects to the variant global structure in CA-II and CA-IV. However, with regards to CA-VIII RMSD analysis highlighted that variant presence was associated with increases to the structural rigidity of the protein. Principal component analysis (PCA) in conjunction with free energy analysis was performed to observe variant effects on protein conformational sampling in 3D space. The binding of BCT to CA-II induced greater protein conformational sampling and was associated with higher free energy. In CA-IV and CA-VIII PCA analysis revealed key differences in the mechanism of action of pathogenic and benign SNVs. In CA-IV, wild-type (WT) and benign variant protein structures clustered into single low energy well hinting at the presence of more stable structures. Pathogenic variants were associated with higher free energy and proteins sampled more conformations without settling into a low energy well. PCA analysis of CA-VIII indicated the opposite to CA-IV. Pathogenic variants were clustered into low energy wells, while the WT and benign variants showed greater conformational sampling. Dynamic cross correlation (DCC) analysis was performed using the MD-TASK suite to determine variant effects on residue movement. CA-II WT protein revealed that BCT and CO2 were associated with anti-correlated and correlated residue movement, highlighting at opposite mechanisms. In CA-IV and CA-VIII variant presence resulted in a change to residue correlation compared to the WT proteins. DRN analysis was performed to investigate SNV effects of residue accessibility and communication. Results demonstrated that SNVs are associated with allosteric effects on the CA protein structures, and effects are located on the stability assisting residues of the aromatic clusters and the active site of the proteins. CA-II studies discovered that Glu117 is the most important residue for communication, and variant presence results in a decrease to the usage of the residue. This effect was greatest in the CA-II H107Y SNV, and suggests that variants could have an effect on Zn2+ dissociation from the active site. Decreases to the usage of Zn2+ coordinating residues were also noted. Where this occurred, compensatory increases to the usage of other primary and secondary coordination residues were observed, that could possibly assist with the maintenance of Zn2+ within the active site. The CA-IV variants R69H and R219C highlighted potentially similar pathogenic mechanisms, whereas N86K and N177K hinted at potentially similar benign mechanisms. Within CA-VIII, variant presence was associated with changes to the accessibility of the N-terminal binding site residues. The benign CA-VIII variants highlighted possible compensatory mechanisms, whereby as one group of N-terminal residues loses accessibility, there was an increase to the accessibility of other binding site residues to possibly balance the effect. Catalytically, the proton shuttle residue His64 in CA-II was found to occupy a novel conformation named the “faux in” that brought the imidazole group even closer to the Zn2+ compared to the “in” conformation. Overall, compared to traditional MD simulations the incorporation of DRN allowed more detailed investigations into the variant mechanisms of action. This highlights the importance of network analysis in the study of the effects of missense mutations on the structure and function of proteins. Investigations of diseases at the molecular level is essential in the identification of disease pathogenesis and assists with the development of specifically tailored and better treatment options especially in the cases of genetically associated rare diseases.
- Full Text:
- Date Issued: 2020
- Authors: Sanyanga, T. Allan
- Date: 2020
- Subjects: Carbonic anhydrase , Carbonic anhydrase -- Therapeutic use , Nucleotides
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/167346 , vital:41470
- Description: The carbonic anhydrase (CA) group of enzymes are Zinc (Zn2+) metalloproteins responsible for the reversible hydration of CO2 to bicarbonate (BCT or HCO− 3 ) and protons (H+) for the facilitation of acid-base balance and homeostasis within the body. Across all organisms, a minimum of six CA families exist, including, α (alpha), β (beta), γ (gamma), δ (delta), η (eta) and ζ (zeta). Some organisms can have more than one family, with exception to humans that contain the α family solely. The α-CA family comprises of 16 isoforms (CA-I to CA-XV) including the CA-VIII, CA-X and CA-XI acatalytic isoforms. Of the catalytic isoforms, CA-II and CA-IV possess one of the fastest rates of reaction, and any disturbances to the function of these enzymes results in CA deficiencies and undesirable phenotypes. CA-II deficiencies result in osteopetrosis with renal tubular acidosis and cerebral calcification, whereas CA-IV deficiencies result in retinitis pigmentosa 17 (RP17). Phenotypic effects generally manifest as a result of poor protein folding and function due to the presence of non-synonymous single nucleotide variations (nsSNVs). Even within the acatalytic isoforms such as CA-VIII that llosterically regulates the affinity of inositol triphosphate (IP3) for the IP3 receptor type 1 (ITPR1) and regulates calcium (Ca2+) signalling, the presence of SNVs also causes phenotypes cerebellar ataxia, mental retardation, and dysequilibrium syndrome 3 (CAMRQ3). Currently the majority of research into the CAs is focused on the inhibition of these proteins to achieve therapeutic effects in patients via the control of HCO− production or reabsorption as observed in glaucoma and diuretic medications. Little research has therefore been devoted into the identification of stabilising or activating compound that could rescue protein function in the case of deficiencies. The main aim of this research was to identify and characterise the effects of nsSNVs on the structure and function of CA-II, CA-IV and CA-VIII to set a foundation for rare disease studies into the CA group of proteins. Combined bioinformatics approaches divided into four main objectives were implemented. These included variant identification, sequence analysis and protein characterisation, force field (FF) parameter generation, molecular dynamics (MD) simulation and dynamic residue network analysis (DRN). Six variants for each of the CA-II, CA-IV and CA-VIII proteins with pathogenic annotations were identified from the HUMA and Ensembl databases. These included the pathogenic variants K18E, K18Q, H107Y, P236H, P236R and N252D for CA-II. CA-IV included the pathogenic R69H, R219C and R219S, and benign N86K, N177K and V234I variants. CA-VIII included pathogenic S100A, S100P, G162R and R237Q, and benign S100L and E109D variants. CA-II has been more extensively studied than CA-IV and CA-VIII, therefore residues essential to its function and stability are known. To discover important residues and regions within the CA-IV and CA-VIII proteins sequence and motif analysis was performed across the α-CA family, using CA-II as a reference. Sequence analysis identified multiple conserved residues between the two acatalytic CA-II and CA-IV, and the acatalytic CA-VIII isoforms that were proposed to be essential for protein stability. With exception to the benign N86K CA-IV variant, none of the other pathogenic or benign CA-II, CA-IV and CA-VIII SNVs were located at functionally or structurally important residues. Motif analysis identified 11 conserved and important motifs within the α-CA family. Several of the identified variants were located on these motifs including K18E, K18Q, H107Y and N252D (CA-II); N86K, R219C, R219S and V234I (CA-IV); and E109D, G162R and R237Q (CA-VIII). As there were no x-ray crystal structures of the variant proteins, homology modelling was performed to calculate the protein structures for characterisation. In CA-VIII, the substitution of Ser for Pro at position 100 (variant S100P) resulted in destruction of the β-sheet that the SNV was located on. Little is known about the mechanism of interaction between CA-VIII and ITPR1, and residues involved. SiteMap and CPORT were used to identify binding site amino for CA-VIII and results identified 38 potential residues. Traditional FFs are incapable of performing MD simulations of metalloproteins. The AMBER ff14SB FF was extended and Zn2+ FF parameters calculated to add support for metalloprotein MD simulations. In the protein, Zn2+ was noted to have a charge less than +1. Variant effects on protein structure were then investigated using MD simulations. Root mean square deviation (RMSD) and radius of gyration (Rg) results indicated subtle SNV effects to the variant global structure in CA-II and CA-IV. However, with regards to CA-VIII RMSD analysis highlighted that variant presence was associated with increases to the structural rigidity of the protein. Principal component analysis (PCA) in conjunction with free energy analysis was performed to observe variant effects on protein conformational sampling in 3D space. The binding of BCT to CA-II induced greater protein conformational sampling and was associated with higher free energy. In CA-IV and CA-VIII PCA analysis revealed key differences in the mechanism of action of pathogenic and benign SNVs. In CA-IV, wild-type (WT) and benign variant protein structures clustered into single low energy well hinting at the presence of more stable structures. Pathogenic variants were associated with higher free energy and proteins sampled more conformations without settling into a low energy well. PCA analysis of CA-VIII indicated the opposite to CA-IV. Pathogenic variants were clustered into low energy wells, while the WT and benign variants showed greater conformational sampling. Dynamic cross correlation (DCC) analysis was performed using the MD-TASK suite to determine variant effects on residue movement. CA-II WT protein revealed that BCT and CO2 were associated with anti-correlated and correlated residue movement, highlighting at opposite mechanisms. In CA-IV and CA-VIII variant presence resulted in a change to residue correlation compared to the WT proteins. DRN analysis was performed to investigate SNV effects of residue accessibility and communication. Results demonstrated that SNVs are associated with allosteric effects on the CA protein structures, and effects are located on the stability assisting residues of the aromatic clusters and the active site of the proteins. CA-II studies discovered that Glu117 is the most important residue for communication, and variant presence results in a decrease to the usage of the residue. This effect was greatest in the CA-II H107Y SNV, and suggests that variants could have an effect on Zn2+ dissociation from the active site. Decreases to the usage of Zn2+ coordinating residues were also noted. Where this occurred, compensatory increases to the usage of other primary and secondary coordination residues were observed, that could possibly assist with the maintenance of Zn2+ within the active site. The CA-IV variants R69H and R219C highlighted potentially similar pathogenic mechanisms, whereas N86K and N177K hinted at potentially similar benign mechanisms. Within CA-VIII, variant presence was associated with changes to the accessibility of the N-terminal binding site residues. The benign CA-VIII variants highlighted possible compensatory mechanisms, whereby as one group of N-terminal residues loses accessibility, there was an increase to the accessibility of other binding site residues to possibly balance the effect. Catalytically, the proton shuttle residue His64 in CA-II was found to occupy a novel conformation named the “faux in” that brought the imidazole group even closer to the Zn2+ compared to the “in” conformation. Overall, compared to traditional MD simulations the incorporation of DRN allowed more detailed investigations into the variant mechanisms of action. This highlights the importance of network analysis in the study of the effects of missense mutations on the structure and function of proteins. Investigations of diseases at the molecular level is essential in the identification of disease pathogenesis and assists with the development of specifically tailored and better treatment options especially in the cases of genetically associated rare diseases.
- Full Text:
- Date Issued: 2020
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