Geological and geophysical assessment of groundwater vulnerability to contamination in selected general landfill sites in the Eastern Cape Province, South Africa
- Authors: Mepaiyeda, Seyi
- Date: 2019
- Subjects: Groundwater -- Pollution Sanitary landfills
- Language: English
- Type: Thesis , Doctoral , PhD (Geology)
- Identifier: http://hdl.handle.net/10353/12227 , vital:39217
- Description: Increasing expansion, population and urbanization have resulted in high volume of waste generated daily in South Africa. Most municipalities in the Eastern Cape are experiencing challenges in effective waste disposal, thus resulting in pollution of the air, soil and groundwater by the percolation of harmful contaminants into the environment from landfill leachate. Groundwater resources are limited in South Africa due to itssemi-arid nature. Also, there islimited information available, not only about where it occurs but how to manage it so that its quality does not depreciate to unacceptable levels. A combination of these factors coupled with a gap between waste policy and its subsequent implementation may be disastrous to South Africa. This research examines the impact of landfill sites on groundwater resources at three selected sites in the Eastern Cape Province using an integrated geological and geophysical approach. The methodology adopted include: an exhaustive literature review on waste management policies and practices in South Africa and Eastern Cape specifically. It also involved remote sensing for the study of geomorphology and structural interpretations of lineaments. Field excursions, analysis of physico-chemical and geochemical properties of groundwater obtained from monitoring boreholes and leachate pond in the vicinity of the landfill sites was also carried out. Combined induced polarization (IP) and electrical resistivity measurements for geophysical assessment of groundwater vulnerability and petrographical analysis was alos adopted. Data analysis and interpretation of the obtained results showed that the selected landfill sites are generally characterized by a 4-layer Earth structure with an average depth to top of the bedrock between 15 m - 30 m. Plant-rock association observed from the aerial photo-interpretation showed groundwater potential around the locality of the landfill sites with a dendritic to poorly drained x patterns and moderate to high topography. Structural controls such as the presence of lineaments and a fractured bedrock beneath, which are excellent pathways for the migration of leachate, particularly at the Berlin and King Williams Town landfill sites were observed. Analysis of physico-chemical and geochemical properties of water samples showed contamination of the groundwater by heavy metals and some of the physico-chemical properties were above the generally acceptable limits (WHO). These include high electrical conductivity (EC) and total dissolved solid (TDS) values observed in the groundwater samples from the King Williams Town landfill which indicated a downward transfer of leachate into the groundwater. The difference in EC and TDS values for boreholes BH2 and BH1 (9892 µS/cm, 4939 mg/L and 6988 µS/cm, 3497 mg/L respectively), showed that concentration of contaminants increased towards the centre of the landfill. Interpretation of the obtained results from the Berlin landfill showed the presence of heavy metals in groundwater samples in high concentrations. This indicated the dumping of toxic and hazardous waste substances on the landfill, contrary to the landfill design and classification. This could have harmful effect on plants and animals. Integrated geophysical assessment showed the presence of leachate plumes on pseudosections across the landfill sites. This was further corroborated on the chargeability pseudosections. Resistivity and IP pseudosections from the Berlin landfill showed a 4-layered Earth structure and anomalous zones of resistivity (≤ 112 Ώ-m) and low chargeability (≤1.25 ms) in the top layers. This is indicative of percolating leachate plume in the unsaturated zone. Contaminants ranging from unsaturated waste with high ion content to dense aqueous phase liquid contaminants, characterized by low resistivity (34 Ώm to 80 Ώ-m) and low chargeability values (0.05 ms to 5.75 ms) were identified across the Alice landfill. Results from the King Williams Town Landfill revealed plume contamination to a depth of about 75 m, well within the aquiferous zone. xi It is suggested that waste disposal practices should be improved by proper waste inspection and classification at landfills prior to disposal, use of lining and cap material to prevent leaching of contaminants into the groundwater below and the construction of waste cells and containment structures. This will go a long way in mitigating groundwater contamination due to landfilling at the study areas
- Full Text:
- Date Issued: 2019
- Authors: Mepaiyeda, Seyi
- Date: 2019
- Subjects: Groundwater -- Pollution Sanitary landfills
- Language: English
- Type: Thesis , Doctoral , PhD (Geology)
- Identifier: http://hdl.handle.net/10353/12227 , vital:39217
- Description: Increasing expansion, population and urbanization have resulted in high volume of waste generated daily in South Africa. Most municipalities in the Eastern Cape are experiencing challenges in effective waste disposal, thus resulting in pollution of the air, soil and groundwater by the percolation of harmful contaminants into the environment from landfill leachate. Groundwater resources are limited in South Africa due to itssemi-arid nature. Also, there islimited information available, not only about where it occurs but how to manage it so that its quality does not depreciate to unacceptable levels. A combination of these factors coupled with a gap between waste policy and its subsequent implementation may be disastrous to South Africa. This research examines the impact of landfill sites on groundwater resources at three selected sites in the Eastern Cape Province using an integrated geological and geophysical approach. The methodology adopted include: an exhaustive literature review on waste management policies and practices in South Africa and Eastern Cape specifically. It also involved remote sensing for the study of geomorphology and structural interpretations of lineaments. Field excursions, analysis of physico-chemical and geochemical properties of groundwater obtained from monitoring boreholes and leachate pond in the vicinity of the landfill sites was also carried out. Combined induced polarization (IP) and electrical resistivity measurements for geophysical assessment of groundwater vulnerability and petrographical analysis was alos adopted. Data analysis and interpretation of the obtained results showed that the selected landfill sites are generally characterized by a 4-layer Earth structure with an average depth to top of the bedrock between 15 m - 30 m. Plant-rock association observed from the aerial photo-interpretation showed groundwater potential around the locality of the landfill sites with a dendritic to poorly drained x patterns and moderate to high topography. Structural controls such as the presence of lineaments and a fractured bedrock beneath, which are excellent pathways for the migration of leachate, particularly at the Berlin and King Williams Town landfill sites were observed. Analysis of physico-chemical and geochemical properties of water samples showed contamination of the groundwater by heavy metals and some of the physico-chemical properties were above the generally acceptable limits (WHO). These include high electrical conductivity (EC) and total dissolved solid (TDS) values observed in the groundwater samples from the King Williams Town landfill which indicated a downward transfer of leachate into the groundwater. The difference in EC and TDS values for boreholes BH2 and BH1 (9892 µS/cm, 4939 mg/L and 6988 µS/cm, 3497 mg/L respectively), showed that concentration of contaminants increased towards the centre of the landfill. Interpretation of the obtained results from the Berlin landfill showed the presence of heavy metals in groundwater samples in high concentrations. This indicated the dumping of toxic and hazardous waste substances on the landfill, contrary to the landfill design and classification. This could have harmful effect on plants and animals. Integrated geophysical assessment showed the presence of leachate plumes on pseudosections across the landfill sites. This was further corroborated on the chargeability pseudosections. Resistivity and IP pseudosections from the Berlin landfill showed a 4-layered Earth structure and anomalous zones of resistivity (≤ 112 Ώ-m) and low chargeability (≤1.25 ms) in the top layers. This is indicative of percolating leachate plume in the unsaturated zone. Contaminants ranging from unsaturated waste with high ion content to dense aqueous phase liquid contaminants, characterized by low resistivity (34 Ώm to 80 Ώ-m) and low chargeability values (0.05 ms to 5.75 ms) were identified across the Alice landfill. Results from the King Williams Town Landfill revealed plume contamination to a depth of about 75 m, well within the aquiferous zone. xi It is suggested that waste disposal practices should be improved by proper waste inspection and classification at landfills prior to disposal, use of lining and cap material to prevent leaching of contaminants into the groundwater below and the construction of waste cells and containment structures. This will go a long way in mitigating groundwater contamination due to landfilling at the study areas
- Full Text:
- Date Issued: 2019
Grabcuts for image segmentation: a comparative study of clustering techniques
- Authors: Manzi, Nozuko Zuleika
- Date: 2019
- Subjects: Algorithms , Computer graphics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14494 , vital:39995
- Description: Image segmentation is the partitioning of a digital image into small segments such as pixels or sets of pixels. It is significant as it allows for the visualization of structures of interest, removing unnecessary information. In addition, image segmentation is used in many fields like, for instance healthcare for image surgery, construction, etc. as it enables structure analysis. Segmentation of images can be computationally expensive especially when a large dataset is used, thus the importance of fast and effective segmentation algorithms is realised. This method is used to locate objects and boundaries (i.e. foreground and background) in images. The aim of this study is to provide a comparison of clustering techniques that would allow the Grabcuts for image segmentation algorithm to be effective and inexpensive. The Grabcuts based method, which is an extension of the graph cut based method, has been instrumental in solving many problems in computer vision i.e. image restoration, image segmentation, object recognition, tracking and analysis. According to Ramirez,et.al [47], the Grabcuts approach is an iterative and minimal user interaction algorithm as it chooses a segmentation by iteratively revising the foreground and background pixels assignments. The method uses min-cut/ max-flow algorithm to segment digital images proposed by Boykov and Jolly [9]. The input of this approach is a digital image with a selected v region of interest (ROI). The ROI is selected using a rectangular bounding box. The pixels inside the bounding box are assigned to the foreground, while the others are assigned to the background. In this study, the Grabcuts for image segmentation algorithm designed by [48] with a Gaussian Mixture Model (GMM) based on the Kmeans and Kmedoids clustering techniques are developed and compared. In addition, the algorithms developed are allowed to run on the Central Processing Unit (CPU) under two scenarios. Scenario 1 involves allowing the Kmeans and Kmedoids clustering techniques to the Squared Euclidean distance measures to calculate the similarities and dissimilarities in pixels in an image. In scenario 2, the Kmeans and Kmedoids clustering techniques will use the City Block distance measure to calculate similarities as well as dissimilarities between pixels in a given image. The same images from the Berkeley Segmentation Dataset and Benchmark 500 were used as input to the algorithms and the number of clusters, K, was varied from 2 to 5. It was observed that the Kmeans clustering technique outperformed the Kmedoids clustering technique under the two scenarios for all the test images with K varied from 2 to 5, in terms of runtime required. In addition, the Kmeans clustering technique obtained more compact and separate clusters under scenario 1, than its counterpart. On the other hand, the Kmedoids obtained more compact and separate clusters than the Kmeans clustering technique under scenario 2. The silhouette validity index favoured the smallest number of clusters for both clustering techniques as it suggested the optimal number of clusters for the Kmeans and Kmedoids clustering techniques under the two scenarios was 2. Although the Kmeans required less computation time than vi its counterpart, the generation of foreground and background took longer for the GMM based on Kmeans than it did for the GMM based on Kmedoids clustering technique. Furthermore, the Grabcuts for image segmentation algorithm with a GMM based on the Kmedoids clustering technique was computationally less expensive than the Grabcuts for image segmentation algorithm with a GMM based on the Kmeans clustering technique. This was observed to be true under both scenario 1 and 2. The Grabcuts for image with the GMM based on the Kmeans clustering techniques obtained slightly better segmentation results when the visual quality is concerned, than its counterpart under the two scenarios considered. On the other hand, the BFscores showed that the Grabcuts for image segmentation algorithm with the GMM based on Kmedoids produces images with higher BF-scores than its counterpart when K was varied from 2 to 5 for most of the test images. In addition, most of the images obtained the majority of their best segmentation results when K=2. This was observed to be true under scenario 1 as well as scenario 2. Therefore, the Kmedoids clustering technique under scenario 2 with K=2 would be the best option for the segmentation of difficult images in BSDS500. This is due to its ability to generate GMMs and segment difficult images more efficiently (i.e. time complexity, higher BF-scores, more under segmented rather than over segmented images, inter alia.) while producing comparable visual segmentation results to those obtained by the Grabcuts for image segmentation: GMM-Kmeans.
- Full Text:
- Date Issued: 2019
- Authors: Manzi, Nozuko Zuleika
- Date: 2019
- Subjects: Algorithms , Computer graphics
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14494 , vital:39995
- Description: Image segmentation is the partitioning of a digital image into small segments such as pixels or sets of pixels. It is significant as it allows for the visualization of structures of interest, removing unnecessary information. In addition, image segmentation is used in many fields like, for instance healthcare for image surgery, construction, etc. as it enables structure analysis. Segmentation of images can be computationally expensive especially when a large dataset is used, thus the importance of fast and effective segmentation algorithms is realised. This method is used to locate objects and boundaries (i.e. foreground and background) in images. The aim of this study is to provide a comparison of clustering techniques that would allow the Grabcuts for image segmentation algorithm to be effective and inexpensive. The Grabcuts based method, which is an extension of the graph cut based method, has been instrumental in solving many problems in computer vision i.e. image restoration, image segmentation, object recognition, tracking and analysis. According to Ramirez,et.al [47], the Grabcuts approach is an iterative and minimal user interaction algorithm as it chooses a segmentation by iteratively revising the foreground and background pixels assignments. The method uses min-cut/ max-flow algorithm to segment digital images proposed by Boykov and Jolly [9]. The input of this approach is a digital image with a selected v region of interest (ROI). The ROI is selected using a rectangular bounding box. The pixels inside the bounding box are assigned to the foreground, while the others are assigned to the background. In this study, the Grabcuts for image segmentation algorithm designed by [48] with a Gaussian Mixture Model (GMM) based on the Kmeans and Kmedoids clustering techniques are developed and compared. In addition, the algorithms developed are allowed to run on the Central Processing Unit (CPU) under two scenarios. Scenario 1 involves allowing the Kmeans and Kmedoids clustering techniques to the Squared Euclidean distance measures to calculate the similarities and dissimilarities in pixels in an image. In scenario 2, the Kmeans and Kmedoids clustering techniques will use the City Block distance measure to calculate similarities as well as dissimilarities between pixels in a given image. The same images from the Berkeley Segmentation Dataset and Benchmark 500 were used as input to the algorithms and the number of clusters, K, was varied from 2 to 5. It was observed that the Kmeans clustering technique outperformed the Kmedoids clustering technique under the two scenarios for all the test images with K varied from 2 to 5, in terms of runtime required. In addition, the Kmeans clustering technique obtained more compact and separate clusters under scenario 1, than its counterpart. On the other hand, the Kmedoids obtained more compact and separate clusters than the Kmeans clustering technique under scenario 2. The silhouette validity index favoured the smallest number of clusters for both clustering techniques as it suggested the optimal number of clusters for the Kmeans and Kmedoids clustering techniques under the two scenarios was 2. Although the Kmeans required less computation time than vi its counterpart, the generation of foreground and background took longer for the GMM based on Kmeans than it did for the GMM based on Kmedoids clustering technique. Furthermore, the Grabcuts for image segmentation algorithm with a GMM based on the Kmedoids clustering technique was computationally less expensive than the Grabcuts for image segmentation algorithm with a GMM based on the Kmeans clustering technique. This was observed to be true under both scenario 1 and 2. The Grabcuts for image with the GMM based on the Kmeans clustering techniques obtained slightly better segmentation results when the visual quality is concerned, than its counterpart under the two scenarios considered. On the other hand, the BFscores showed that the Grabcuts for image segmentation algorithm with the GMM based on Kmedoids produces images with higher BF-scores than its counterpart when K was varied from 2 to 5 for most of the test images. In addition, most of the images obtained the majority of their best segmentation results when K=2. This was observed to be true under scenario 1 as well as scenario 2. Therefore, the Kmedoids clustering technique under scenario 2 with K=2 would be the best option for the segmentation of difficult images in BSDS500. This is due to its ability to generate GMMs and segment difficult images more efficiently (i.e. time complexity, higher BF-scores, more under segmented rather than over segmented images, inter alia.) while producing comparable visual segmentation results to those obtained by the Grabcuts for image segmentation: GMM-Kmeans.
- Full Text:
- Date Issued: 2019
Impact of adoption of drought tolerant maize varieties on yield in the face of climate change: A case of Salima, Chikwawa and Karonga districts, Malawi
- Rukasha, Conscience Tanyaradzwa
- Authors: Rukasha, Conscience Tanyaradzwa
- Date: 2019
- Subjects: Climatic changes Food security Dry farming
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15628 , vital:40491
- Description: Drought is a huge limiting factor in maize production, mainly in the rain-fed agriculture of subSaharan Africa. In response to this threat, drought-tolerant (DT) maize varieties have been developed with an aim to ensure maize productivity under drought conditions. This study assessed the impact of smallholder farmers’ adoption of DT maize varieties on maize productivity. The first step into understanding the impact of adoption of these varieties on smallholder farmers’ productivity was to first identify the varieties that they were growing. To achieve this, data was collected through the means of a household survey of 600 farmers from Karonga, Chikwawa and Salima districts in Malawi. The major findings drawn were that though most of the farmers have adopted the use of hybrids, as they are fairly common among the varieties that are being grown, most of these hybrids were not drought tolerant varieties. Previous studies had concluded that most of the farmers in Malawi were still growing local varieties. Results from this study showed a major increase in the use of hybrids with SC403 being the most grown variety. The second step in the analysis of the impact of DT maize adoption was to analyse the level and intensity of adoption of these varieties among the smallholder farmers. This was done using a Double Hurdle Model. The results from the double hurdle showed that only 23% of the sampled farmers were growing one or more DT varieties on their plots. Generally, farmers’ decision to use improved agricultural technologies and the intensity of the use in a given period of time are hypothesized to be influenced by a combined effect of various factors such as household characteristics, socioeconomic and physical environments in which farmers operate. The results in this study have shown that the geographical location of farmers plays a significant role in the decision to adopt as well as off-farm income and input subsidies. In terms of intensity, the results revealed that the farmers allocated an average of 0.46 ha of their land under maize cultivation to DT varieties. The results also showed that the intensity of adoption was influenced by gender, household size, whether or not the farmer is recycling the seed and soil fertility. The next step in the study was analysing the impact that intra-seasonal weather variability had on maize productivity. This was done by using daily weather variables for the whole growing season so as to take into account evaporation, rain gaps and other intra seasonal weather limitations. The Just and Pope Production Function was used to analyse the impact of intra-seasonal weather vi variability on productivity. The results suggest that the amount and distribution of rainfall have a strong impact on the development of the maize crop and consequently the quantity harvested. From the results, there was evidence of high variability in rainfall characteristics in terms of the intraseasonal distribution which in turn translated into high variability in maize quantity harvested by the smallholder farmers in Malawi. Lastly, the Endogenous Switching Regression Model was used to analyse the impact of adoption of DT varieties on yield. The results showed that the adoption of DT varieties increases productivity. The use of counterfactual data from the Endogenous Switching Regression (ESR) allowed for an in-depth analysis of the productive implications. The results from the ESR model showed that the farm households that did not adopt, had they adopted, they would have increased their productivity. Furthermore, the results indicated that the use of DT maize varieties successfully delivered relatively less reliance on the total and net rainfall, that is, adopters managed to support their productivity in the face of changing climate while the non-adopters were adversely affected by an increase in temperature and decrease in total rainfall. Adoption of DT varieties increased output among smallholder farmers by 441.33 kg which translates to a 41% increase. Conclusively, the results from this study showed that smallholder farmers are adopting new and improved hybrids and improved OPVs and moving away from the use of local varieties. However the new varieties they are currently using are mostly not DT varieties. This is an interesting finding because the farmers when asked about their preferred traits in maize seed mentioned drought tolerance, therefore the low level of adoption points to numerous factors. These factors include lack of awareness of these varieties among smallholder farmers and unavailability of seed. The results also showed that the level of adoption was low among the farmers. With respect to productivity, this study has shown that adoption of DT varieties by smallholder farmers will increase their yield in the face of climate change
- Full Text:
- Date Issued: 2019
- Authors: Rukasha, Conscience Tanyaradzwa
- Date: 2019
- Subjects: Climatic changes Food security Dry farming
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15628 , vital:40491
- Description: Drought is a huge limiting factor in maize production, mainly in the rain-fed agriculture of subSaharan Africa. In response to this threat, drought-tolerant (DT) maize varieties have been developed with an aim to ensure maize productivity under drought conditions. This study assessed the impact of smallholder farmers’ adoption of DT maize varieties on maize productivity. The first step into understanding the impact of adoption of these varieties on smallholder farmers’ productivity was to first identify the varieties that they were growing. To achieve this, data was collected through the means of a household survey of 600 farmers from Karonga, Chikwawa and Salima districts in Malawi. The major findings drawn were that though most of the farmers have adopted the use of hybrids, as they are fairly common among the varieties that are being grown, most of these hybrids were not drought tolerant varieties. Previous studies had concluded that most of the farmers in Malawi were still growing local varieties. Results from this study showed a major increase in the use of hybrids with SC403 being the most grown variety. The second step in the analysis of the impact of DT maize adoption was to analyse the level and intensity of adoption of these varieties among the smallholder farmers. This was done using a Double Hurdle Model. The results from the double hurdle showed that only 23% of the sampled farmers were growing one or more DT varieties on their plots. Generally, farmers’ decision to use improved agricultural technologies and the intensity of the use in a given period of time are hypothesized to be influenced by a combined effect of various factors such as household characteristics, socioeconomic and physical environments in which farmers operate. The results in this study have shown that the geographical location of farmers plays a significant role in the decision to adopt as well as off-farm income and input subsidies. In terms of intensity, the results revealed that the farmers allocated an average of 0.46 ha of their land under maize cultivation to DT varieties. The results also showed that the intensity of adoption was influenced by gender, household size, whether or not the farmer is recycling the seed and soil fertility. The next step in the study was analysing the impact that intra-seasonal weather variability had on maize productivity. This was done by using daily weather variables for the whole growing season so as to take into account evaporation, rain gaps and other intra seasonal weather limitations. The Just and Pope Production Function was used to analyse the impact of intra-seasonal weather vi variability on productivity. The results suggest that the amount and distribution of rainfall have a strong impact on the development of the maize crop and consequently the quantity harvested. From the results, there was evidence of high variability in rainfall characteristics in terms of the intraseasonal distribution which in turn translated into high variability in maize quantity harvested by the smallholder farmers in Malawi. Lastly, the Endogenous Switching Regression Model was used to analyse the impact of adoption of DT varieties on yield. The results showed that the adoption of DT varieties increases productivity. The use of counterfactual data from the Endogenous Switching Regression (ESR) allowed for an in-depth analysis of the productive implications. The results from the ESR model showed that the farm households that did not adopt, had they adopted, they would have increased their productivity. Furthermore, the results indicated that the use of DT maize varieties successfully delivered relatively less reliance on the total and net rainfall, that is, adopters managed to support their productivity in the face of changing climate while the non-adopters were adversely affected by an increase in temperature and decrease in total rainfall. Adoption of DT varieties increased output among smallholder farmers by 441.33 kg which translates to a 41% increase. Conclusively, the results from this study showed that smallholder farmers are adopting new and improved hybrids and improved OPVs and moving away from the use of local varieties. However the new varieties they are currently using are mostly not DT varieties. This is an interesting finding because the farmers when asked about their preferred traits in maize seed mentioned drought tolerance, therefore the low level of adoption points to numerous factors. These factors include lack of awareness of these varieties among smallholder farmers and unavailability of seed. The results also showed that the level of adoption was low among the farmers. With respect to productivity, this study has shown that adoption of DT varieties by smallholder farmers will increase their yield in the face of climate change
- Full Text:
- Date Issued: 2019
Incidence of cholera-causing and non cholera-causing pathogenic vibrio species in the river-k and two of its feeder wastewater treatment plants in the Raymond Mhlaba municipality, Eastern Cape province of South Africa
- Authors: Gcilitshana, Onele
- Date: 2019
- Subjects: Water -- Purification -- South Africa -- Eastern Cape Effluent quality -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15145 , vital:40190
- Description: Despite technological advances in water treatment and improved sanitation in many developing countries, acute microbial diseases still thrive and continue to distress millions of people. This is due to the high number of rural dwellers that still source water for drinking and other domestic uses from contaminated rivers. In South Africa, there have been reports on waterborne disease outbreaks, and specifically in the area understudy, two records of diarrhoeal outbreaks associated with consumption of river water were reported within the last decade. All those outbreaks and previous reports on isolation of other pathogenic bacteria within the area necessitated the conduction of this study in order to identify the potential causes of the cholera-associate diarrheal outbreaks previously reported in the area and nationally. This study was designed to assess the incidence of cholera-causing and non-cholera causing pathogens in final effluents and surface waters of the Raymond Mhlaba Local Municipality, Eastern Cape Province, South Africa. RiverK which serves as a major resource for domestic activities, agricultural practices as well as an abstraction point for a potable water treatment plant was used for this study. River-K freshwater and final effluents of its two feeder wastewater treatment plants were sampled monthly, over a twelve-month period (December 2016–November 2017). For purposes of confidentiality, the names of the wastewater treatment plants and river involved are coded in this report. A total of 108 water samples were assessed for the physicochemical parameters that influence the presence of Vibrio pathogens. For bacteriology, the membrane filtration method followed by polymerase chain reaction (PCR) was adopted to assess the incidence of cholera-causing and non-choleracausing Vibrio pathogens, as well as their virulence-associated genes from the two wastewater treatment plants and their receiving waterbody (River-K). Antibiotic susceptibility profiles of identified Vibrio species were determined using the disc diffusion method against a panel of xvi sixteen antibiotics commonly used as antimicrobial drugs of Vibrio infections. Multiple antibiotics resistance index (MARI) and phenotypes (MARP) were measured, and the existence of antibiotic resistance genes was evaluated by PCR using specific primer sets. Most of the physicochemical parameters measured (pH, TDS, temperature, salinity and DO) complied with the recommended standards for drinking water, while some fell short of the recommended limits (EC, turbidity, TSS, free chlorine). From the presumptive Vibrio isolates, 64.3% (476/740) were confirmed by PCR, with their Vibrio densities across all sampling points ranging between 0 and 2.7 × 104 CFU/100 mL, with high counts recorded in summer, hence their positive significant correlation (P< 0.01) with temperature. From the confirmed Vibrio isolates, only V. cholerae (53/476), V. mimicus (21/476) and V. parahaemolyticus (5/476) were detected. For virulence-associated genes, virulence genes homologous to V. cholerae virulence determinants, namely ompU (35%), TCP (14%), ACE (11%), ctx (7%) and HylA (4.5%) were widespread (independently) amongst the V. cholerae and V. mimicus species, while V. parahemolyticus isolates (100%) produced only the ToxR gene. Antibiogram profiling found resistance against some antibiotics such as Nalidixic acid (65%), Polymyxin B (43.8%) etc. The MAR indices ranged between 0 and 0.67 with 41.3% of the isolates recording MAR index values above 0.2. The results presented high degrees of MARPs ranging from four to eleven antimicrobials. For resistance gene detection, the SXT element was detected in 66% of the isolates, while cat1 (93%) was the most predominant, followed by aac (68%), ant (61%), with bla-V (7.1%) as the least detected gene. Findings from this study suggest that the wastewater effluents from the two wastewater treatment plants are potential sources of pathogenic Vibrio species and River-K contains a high quantity of pathogenic Vibrio species with fluctuating seasonal variations that reaffirm temperature as a strong reason for their abundance. The antibiotic-resistant Vibrio species isolated here carry a pool of virulence-associated genes and xvii antibiotic resistance genes, presenting a health threat to the communities that use it directly for domestic and irrigation purposes. In conclusion, some surface waters in the Eastern Cape Province, South Africa are widely contaminated with cholera-causing and non-cholera causing Vibrio pathogens; furthermore, some wastewater treatment plants are ineffective in adequately removing microbial contaminants and have become sources of pathogenic bacteria to their receiving waterbodie
- Full Text:
- Date Issued: 2019
- Authors: Gcilitshana, Onele
- Date: 2019
- Subjects: Water -- Purification -- South Africa -- Eastern Cape Effluent quality -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15145 , vital:40190
- Description: Despite technological advances in water treatment and improved sanitation in many developing countries, acute microbial diseases still thrive and continue to distress millions of people. This is due to the high number of rural dwellers that still source water for drinking and other domestic uses from contaminated rivers. In South Africa, there have been reports on waterborne disease outbreaks, and specifically in the area understudy, two records of diarrhoeal outbreaks associated with consumption of river water were reported within the last decade. All those outbreaks and previous reports on isolation of other pathogenic bacteria within the area necessitated the conduction of this study in order to identify the potential causes of the cholera-associate diarrheal outbreaks previously reported in the area and nationally. This study was designed to assess the incidence of cholera-causing and non-cholera causing pathogens in final effluents and surface waters of the Raymond Mhlaba Local Municipality, Eastern Cape Province, South Africa. RiverK which serves as a major resource for domestic activities, agricultural practices as well as an abstraction point for a potable water treatment plant was used for this study. River-K freshwater and final effluents of its two feeder wastewater treatment plants were sampled monthly, over a twelve-month period (December 2016–November 2017). For purposes of confidentiality, the names of the wastewater treatment plants and river involved are coded in this report. A total of 108 water samples were assessed for the physicochemical parameters that influence the presence of Vibrio pathogens. For bacteriology, the membrane filtration method followed by polymerase chain reaction (PCR) was adopted to assess the incidence of cholera-causing and non-choleracausing Vibrio pathogens, as well as their virulence-associated genes from the two wastewater treatment plants and their receiving waterbody (River-K). Antibiotic susceptibility profiles of identified Vibrio species were determined using the disc diffusion method against a panel of xvi sixteen antibiotics commonly used as antimicrobial drugs of Vibrio infections. Multiple antibiotics resistance index (MARI) and phenotypes (MARP) were measured, and the existence of antibiotic resistance genes was evaluated by PCR using specific primer sets. Most of the physicochemical parameters measured (pH, TDS, temperature, salinity and DO) complied with the recommended standards for drinking water, while some fell short of the recommended limits (EC, turbidity, TSS, free chlorine). From the presumptive Vibrio isolates, 64.3% (476/740) were confirmed by PCR, with their Vibrio densities across all sampling points ranging between 0 and 2.7 × 104 CFU/100 mL, with high counts recorded in summer, hence their positive significant correlation (P< 0.01) with temperature. From the confirmed Vibrio isolates, only V. cholerae (53/476), V. mimicus (21/476) and V. parahaemolyticus (5/476) were detected. For virulence-associated genes, virulence genes homologous to V. cholerae virulence determinants, namely ompU (35%), TCP (14%), ACE (11%), ctx (7%) and HylA (4.5%) were widespread (independently) amongst the V. cholerae and V. mimicus species, while V. parahemolyticus isolates (100%) produced only the ToxR gene. Antibiogram profiling found resistance against some antibiotics such as Nalidixic acid (65%), Polymyxin B (43.8%) etc. The MAR indices ranged between 0 and 0.67 with 41.3% of the isolates recording MAR index values above 0.2. The results presented high degrees of MARPs ranging from four to eleven antimicrobials. For resistance gene detection, the SXT element was detected in 66% of the isolates, while cat1 (93%) was the most predominant, followed by aac (68%), ant (61%), with bla-V (7.1%) as the least detected gene. Findings from this study suggest that the wastewater effluents from the two wastewater treatment plants are potential sources of pathogenic Vibrio species and River-K contains a high quantity of pathogenic Vibrio species with fluctuating seasonal variations that reaffirm temperature as a strong reason for their abundance. The antibiotic-resistant Vibrio species isolated here carry a pool of virulence-associated genes and xvii antibiotic resistance genes, presenting a health threat to the communities that use it directly for domestic and irrigation purposes. In conclusion, some surface waters in the Eastern Cape Province, South Africa are widely contaminated with cholera-causing and non-cholera causing Vibrio pathogens; furthermore, some wastewater treatment plants are ineffective in adequately removing microbial contaminants and have become sources of pathogenic bacteria to their receiving waterbodie
- Full Text:
- Date Issued: 2019
Isolation and characterization of extracts of Rosmarinus officinalis l. And comparative evaluation of its antimicrobial activity and selected types of antibiotics against some bacteria species
- Authors: Gbede,Remi
- Date: 2019
- Subjects: Rosmarinus Essences and essential oils Lamiaceae Medicinal plants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19142 , vital:39875
- Description: Rosmarinus officinalis L. is known extensively for its multifunctional purposes. The essential oil has been widely used in cosmeceuticals and several ethnopharmacological values. In vitro studies have demonstrated the antibacterial activity of essential oils (EOs) of Rosmarinus officinalis L. against Staphylococcus aureus ATCC 25923, Vibrio cholerae DSM 19283, Escherichia coli ATCC 8739, Pseudomonas aeruginosa ATCC 27853 and Bacillus cereus. These different bacteria were screened against antibiotics such as Tetracycline, Ampicillin Sodium salt, Erythromycin and Amoxicillin, and some standards namely rosmarinic acid, carnosic acid and carnosol, and also against the methanol, acetone, chloroform and dichloromethane extracts of rosemary. The essential oils of Rosmarinus officinalis L. showed significant inhibitory properties compared to antibiotics with various degrees of growth inhibition. The standards exhibited some activities against the organisms. The GC/MS analysis of the essential oil revealed 34 compounds present with most components acting in synergy to bring about antibacterial activities. The antiplasmodial and cytotoxic activities of two leaf extracts of Rosmarinus officinalis (with hexane and dichloromethane as solvents) using standard procedure were studied. The findings justify the claims on the efficacy of plants for therapeutic uses for antifungal, antibacterial and anti-inflammatory properties. Antiplasmodial activity of Rosmarinus officinalis recorded IC50 values of 9.99 µg/ml and 9.76 µg/ml in hexane and dichloromethane respectively.
- Full Text:
- Date Issued: 2019
- Authors: Gbede,Remi
- Date: 2019
- Subjects: Rosmarinus Essences and essential oils Lamiaceae Medicinal plants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19142 , vital:39875
- Description: Rosmarinus officinalis L. is known extensively for its multifunctional purposes. The essential oil has been widely used in cosmeceuticals and several ethnopharmacological values. In vitro studies have demonstrated the antibacterial activity of essential oils (EOs) of Rosmarinus officinalis L. against Staphylococcus aureus ATCC 25923, Vibrio cholerae DSM 19283, Escherichia coli ATCC 8739, Pseudomonas aeruginosa ATCC 27853 and Bacillus cereus. These different bacteria were screened against antibiotics such as Tetracycline, Ampicillin Sodium salt, Erythromycin and Amoxicillin, and some standards namely rosmarinic acid, carnosic acid and carnosol, and also against the methanol, acetone, chloroform and dichloromethane extracts of rosemary. The essential oils of Rosmarinus officinalis L. showed significant inhibitory properties compared to antibiotics with various degrees of growth inhibition. The standards exhibited some activities against the organisms. The GC/MS analysis of the essential oil revealed 34 compounds present with most components acting in synergy to bring about antibacterial activities. The antiplasmodial and cytotoxic activities of two leaf extracts of Rosmarinus officinalis (with hexane and dichloromethane as solvents) using standard procedure were studied. The findings justify the claims on the efficacy of plants for therapeutic uses for antifungal, antibacterial and anti-inflammatory properties. Antiplasmodial activity of Rosmarinus officinalis recorded IC50 values of 9.99 µg/ml and 9.76 µg/ml in hexane and dichloromethane respectively.
- Full Text:
- Date Issued: 2019
Land rental policy and land market in Mashonaland East Province, Zimbabwe: implications on farmer decisions, efficiency and equity under A1 and A2 models
- Authors: Tatsvarei , Simbarashe
- Date: 2019
- Subjects: Farms, Small Agricultural extension work
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15666 , vital:40501
- Description: Government promulgated the land rental policy starting in the year 2007. The policy required that A1 (market residual) and A2 (indigenous commercial) farmers pay rentals to the state. Since then, there has also been an emerging trend in which farmers have been renting in and out land, resulting in an informal market for land rentals. The study therefore assessed farmers’ perceptions of land rental policy and evaluated the possible association of this policy to farmers’ decision making on land rental markets as well as its implications on farmers’ efficiency and equity. The study was carried out in Mashonaland East Province of Zimbabwe, covering two districts, Goromonzi and Marondera. The focus was specifically on A1 and A2 farmers, as the rental policy was directed at these resettlement models only and much of the informal land rental markets were prevalent among these categories of farmers. Data collection utilised the survey approach. This was supported by key informant interviews and focus group discussions, with a final sample of 339 households selected using multi-stage sampling method. Survey data were transcribed on CsPro 6, and analysed using Stata, SPSS and Frontier 4.1. Results showed that about a third of household respondents was from Marondera and twothirds was from Goromonzi, while 79% and 21% was A1 and A2 farmers respectively. About 80% was male headed households and the remainder was female headed households. About half of the households were not participating in land rental markets while the other half was split almost equally between those renting-in and renting-out land. In general, A2 farmers were better in agricultural productivity than A1 farmers. It was concluded that farmers had a fairly good knowledge of the agricultural land rental policy enunciated in the Finance Bills. A1 farmers were more knowledgeable than A2 farmers, but no vii significant differences were observed between male and female headed households and farmers involved and not involved in land rental markets. Farmers’ attitudes in relation to policy were categorised as fair, with significant differences based on gender and land market participation. Practice scores showed a poor adherence to policy for all categories of farmers. Overall perceptions of farmers on rental policy was inferred as fair with significant differences existing between land rental market participants and non-participants (autarky). The results of a bivariate Tobit model results showed that the decision to rent-in land was significantly influenced by gender, household income, permanent labour, cultivated area, tenure certainty, irrigable land size and crop diversification. On the other hand, age, permanent labour, irrigable land size and crop diversification significantly influenced farmers’ decisions to rent-out land. The conclusion was that household characteristics, land endowments and transaction costs significantly influenced the decision to rent-in land while the former two were strong in influencing renting-out decisions. Results from the linearized Cobb Douglas model showed that economic efficiency for most farmers was above 50%. Farmers renting-out land under A1 were found to be the most economically efficient, followed by those who were renting-in and least efficient were farmers not participating in land rental markets, though the differences were marginal. For the A2 model, renting-in farmers were the most efficient, followed by those in autarky position, while renting-out farmers were the least. Overall, the most efficient farmers were those renting-in, followed by those renting-out while farmers in autarky were the least efficient. Overall efficiency was higher for A2 farmers than for A1 farmers. For farmers not participating in rental markets, the sources of inefficiency were crop type, crop area and labour. For farmers renting-in, it was proportion of irrigable land, size of irrigable land, crop type, crop area and viii labour, while inefficiency drivers for renting-out farmers were crop type and associated area. Equity analysis showed that participation in land rental markets reduced inequality for farmers in the two districts and male and female headed households. Inequality was increased among A1 farmers and remained unchanged among A2 farmers. Overall, the emerging position was that participation in land rental markets resulted in higher efficiency and reduced inequality in land holding among the sampled farmers. It is recommended that government should be consistent on land rental policy and bring into place effective administration of land rental policy. Government may also consider formal acceptance of land rental markets in light of the marginal efficiency and equity benefits shown in the study. However, formalizing land rental markets alone may not be a panacea to improved efficiency and needs to be supported by other productivity measures given the average efficiency values for farmers. Crop and livestock production based on compatibility with the natural regions and defined minimum size of land should be encouraged to improve efficiency
- Full Text:
- Date Issued: 2019
- Authors: Tatsvarei , Simbarashe
- Date: 2019
- Subjects: Farms, Small Agricultural extension work
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15666 , vital:40501
- Description: Government promulgated the land rental policy starting in the year 2007. The policy required that A1 (market residual) and A2 (indigenous commercial) farmers pay rentals to the state. Since then, there has also been an emerging trend in which farmers have been renting in and out land, resulting in an informal market for land rentals. The study therefore assessed farmers’ perceptions of land rental policy and evaluated the possible association of this policy to farmers’ decision making on land rental markets as well as its implications on farmers’ efficiency and equity. The study was carried out in Mashonaland East Province of Zimbabwe, covering two districts, Goromonzi and Marondera. The focus was specifically on A1 and A2 farmers, as the rental policy was directed at these resettlement models only and much of the informal land rental markets were prevalent among these categories of farmers. Data collection utilised the survey approach. This was supported by key informant interviews and focus group discussions, with a final sample of 339 households selected using multi-stage sampling method. Survey data were transcribed on CsPro 6, and analysed using Stata, SPSS and Frontier 4.1. Results showed that about a third of household respondents was from Marondera and twothirds was from Goromonzi, while 79% and 21% was A1 and A2 farmers respectively. About 80% was male headed households and the remainder was female headed households. About half of the households were not participating in land rental markets while the other half was split almost equally between those renting-in and renting-out land. In general, A2 farmers were better in agricultural productivity than A1 farmers. It was concluded that farmers had a fairly good knowledge of the agricultural land rental policy enunciated in the Finance Bills. A1 farmers were more knowledgeable than A2 farmers, but no vii significant differences were observed between male and female headed households and farmers involved and not involved in land rental markets. Farmers’ attitudes in relation to policy were categorised as fair, with significant differences based on gender and land market participation. Practice scores showed a poor adherence to policy for all categories of farmers. Overall perceptions of farmers on rental policy was inferred as fair with significant differences existing between land rental market participants and non-participants (autarky). The results of a bivariate Tobit model results showed that the decision to rent-in land was significantly influenced by gender, household income, permanent labour, cultivated area, tenure certainty, irrigable land size and crop diversification. On the other hand, age, permanent labour, irrigable land size and crop diversification significantly influenced farmers’ decisions to rent-out land. The conclusion was that household characteristics, land endowments and transaction costs significantly influenced the decision to rent-in land while the former two were strong in influencing renting-out decisions. Results from the linearized Cobb Douglas model showed that economic efficiency for most farmers was above 50%. Farmers renting-out land under A1 were found to be the most economically efficient, followed by those who were renting-in and least efficient were farmers not participating in land rental markets, though the differences were marginal. For the A2 model, renting-in farmers were the most efficient, followed by those in autarky position, while renting-out farmers were the least. Overall, the most efficient farmers were those renting-in, followed by those renting-out while farmers in autarky were the least efficient. Overall efficiency was higher for A2 farmers than for A1 farmers. For farmers not participating in rental markets, the sources of inefficiency were crop type, crop area and labour. For farmers renting-in, it was proportion of irrigable land, size of irrigable land, crop type, crop area and viii labour, while inefficiency drivers for renting-out farmers were crop type and associated area. Equity analysis showed that participation in land rental markets reduced inequality for farmers in the two districts and male and female headed households. Inequality was increased among A1 farmers and remained unchanged among A2 farmers. Overall, the emerging position was that participation in land rental markets resulted in higher efficiency and reduced inequality in land holding among the sampled farmers. It is recommended that government should be consistent on land rental policy and bring into place effective administration of land rental policy. Government may also consider formal acceptance of land rental markets in light of the marginal efficiency and equity benefits shown in the study. However, formalizing land rental markets alone may not be a panacea to improved efficiency and needs to be supported by other productivity measures given the average efficiency values for farmers. Crop and livestock production based on compatibility with the natural regions and defined minimum size of land should be encouraged to improve efficiency
- Full Text:
- Date Issued: 2019
Mapping soil factors influencing erosion using machine leaerning algorithms in the t35 d-e catchment in the Eastern Cape Province
- Du Plessis, Casparus Jacobus
- Authors: Du Plessis, Casparus Jacobus
- Date: 2019
- Subjects: Soils -- Analysis Soil erosion
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17106 , vital:40850
- Description: The need for detailed spatial soil information is increasing in the fields of environmental studies, agriculture as well as engineering practices. Regarding soil erosion in South Africa, border lines between sensitive soil forms in the Duplex soil group and resistant soil forms in the Oxidic soil group need to be mapped to a high accuracy to prevent/manage erosion and major soil losses. In third world countries like South Africa, digital soil mapping (DSM) with the use of machine learning can provide the solutions to fill numerous gaps in these related fields. Local DSM research has been ongoing at the University of the Free State and related institutions for the past eleven years. It has also been used commercially and can therefore be regarded as fruitful. The National Resource Management unit of the Department of Environmental Affairs required a soil map regarding the susceptibility of the soil to erosion for catchment T35 D-E (87 000 hectares) in the Mzimvubu management area of the Eastern Cape, South Africa. Through a DSM approach, machine learning was used to predict the occurrence of soil forms and soil families in accordance with the South African Soil Classification System. A total of 591 soil observations were made at specific points, pre-determined with the conditioned Latin Hypercube sampling (cLHS) method. These pre-determined points were classified into nineteen soil forms and forty eight soil families. The soils were then further divided into nine soil groups, based on their inherent sensitivity to erosion. Outlier observations were omitted from the dataset to create a reliable framework to predict the soil groups as influenced by the SCORPAN factors. These soil groups were mapped and evaluated with an accuracy of 68% and a Kappa statistic value of 0.42 that compare well with other soil maps, both locally and internationally. Mapping soil with an acceptable accuracy with such a high level of detail on catchment scale would be a tremendous advantage to soil scientists and environmental workforces in southern Africa. Future work should focus on DSM training, to broaden the base of DSM skills available in southern Africa. This will ensure that soil information would be included in addressing an increasing amount of real world problems at catchment scales.
- Full Text:
- Date Issued: 2019
- Authors: Du Plessis, Casparus Jacobus
- Date: 2019
- Subjects: Soils -- Analysis Soil erosion
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17106 , vital:40850
- Description: The need for detailed spatial soil information is increasing in the fields of environmental studies, agriculture as well as engineering practices. Regarding soil erosion in South Africa, border lines between sensitive soil forms in the Duplex soil group and resistant soil forms in the Oxidic soil group need to be mapped to a high accuracy to prevent/manage erosion and major soil losses. In third world countries like South Africa, digital soil mapping (DSM) with the use of machine learning can provide the solutions to fill numerous gaps in these related fields. Local DSM research has been ongoing at the University of the Free State and related institutions for the past eleven years. It has also been used commercially and can therefore be regarded as fruitful. The National Resource Management unit of the Department of Environmental Affairs required a soil map regarding the susceptibility of the soil to erosion for catchment T35 D-E (87 000 hectares) in the Mzimvubu management area of the Eastern Cape, South Africa. Through a DSM approach, machine learning was used to predict the occurrence of soil forms and soil families in accordance with the South African Soil Classification System. A total of 591 soil observations were made at specific points, pre-determined with the conditioned Latin Hypercube sampling (cLHS) method. These pre-determined points were classified into nineteen soil forms and forty eight soil families. The soils were then further divided into nine soil groups, based on their inherent sensitivity to erosion. Outlier observations were omitted from the dataset to create a reliable framework to predict the soil groups as influenced by the SCORPAN factors. These soil groups were mapped and evaluated with an accuracy of 68% and a Kappa statistic value of 0.42 that compare well with other soil maps, both locally and internationally. Mapping soil with an acceptable accuracy with such a high level of detail on catchment scale would be a tremendous advantage to soil scientists and environmental workforces in southern Africa. Future work should focus on DSM training, to broaden the base of DSM skills available in southern Africa. This will ensure that soil information would be included in addressing an increasing amount of real world problems at catchment scales.
- Full Text:
- Date Issued: 2019
Medicinal Plants Used to Treat and Manage Respiratory Infections in the Limpopo Province, South Africa: Phytotherapeutic Study of Bapedi Traditional Healers’ Practices
- Authors: Semenya, Sebua Silas
- Date: 2019
- Subjects: Medicinal plants Respiratory infections -- Alternative treatment
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15716 , vital:40512
- Description: There is paucity of data on South African traditional healers’ (THs) phytotherapeutic practices regarding respiratory infections (RIs). Several people in South Africa are contracting RIs due to prevalence of risk factors. This situation is exacerbated by limited modern health care facilities and associated personnel in some provinces in the country. The primary objectives of this study were twofold. First purpose was to execute a comprehensive social and ethnobotanical surveys aimed at (a) establishing the types of RIs treated by THs and diagnosis techniques used, (b) plants used as therapies for RIs and associated indigenous knowledge practices, (c) source/s of plants used as medicines, (d) harvesting practices, current local availability status, conservation status and threats of indigenous plants as well as the level of conservation knowledge possessed by THs. The second objective was to assess the therapeutic value of the four most frequently used plant species by THs by (a) analysing the phytochemical profile of the plant extracts, (b) their antioxidant activities, and (c) their antibacterial activities. Information linked to the social and ethnobotanical surveys was gathered via a semi-structured questionnaires, supplemented by field observations during face-to-face interview with 240 conveniently selected THs practicing in the municipalities of Capricorn, Sekhukhune and Waterberg districts of the Limpopo Province, South Africa. Data were generally analysed using Microsoft Excel and Statistical Package for the Social Sciences (SPSS). In addition to these softwares, ethnobotanical data were analysed via quantitative ethnobotanical indexes namely use mention (UM), fidelity level (FL), use value (UV) and preference ranking (PR). For laboratory experiments, qualitative phytochemical constitutes of the crude extracts were determined using the standard screening methods. The antioxidant activities of acetone, dichlomethane, hexane, methanol and water crude extracts were evaluated using qualitative and quantitative 2, 2-diphenyl-1-picrylhydrazyl (DPPH) assays. Antibacterial activities of these extracts was assessed using microdilution and bioautography assays. Six types of RIs; tuberculosis (84.1%), sore throat (65%), asthma (58.3%), sinusitis (55%), pneumonia (53.3%) and rhinitis (43.7%) were treated by THs practicing as herbalists (58.7%), herbalists and diviners (40.5%), and diviners (0.4%). The identification of these RIs was based on the patients’ presentation of certain clinical symptoms, with THs practicing both herbalism and divination additionally using bone casting. There was a broad overlap between the clinical signs used to diagnose most of the RIs, and the specificity of symptoms followed when ascertaining an individual infection was low. A total of 224 plant species (83% indigenous and 16.9% exotics) belonging to 177 genera and 85 botanical families, mainly the Fabaceae (25 spp.) and Asteraceae (16 spp.) were used by THs as herbal medicines for the aforesaid RIs and perceived related symptoms (RSs). Most of the documented plant species were used for tuberculosis (82.1%) and asthma (46.4%). Roots (64%) and leaves (13%) formed an important mainstay for medicinal recipes preparations. Different routes of administering these recipes were noted, with oral (75.6%) and nasal (18.8%) being the most preferred. The most widely used species by THs to treat and manage all the six RIs with high UM, FL, UV and PR values included Clerodendrum ternatum, Cryptocarya transvaalensis, Enicostema axillare, Lasiosiphon caffer and Stylochaeton natalensis. Overall larger numbers of species used by Bapedi THs including the mentioned ones are recorded for the first time in scientific literature as remedies for RIs and RSs, thus reflecting a need for more similar studies amongst other ethnic groups of South Africa and elsewhere. The phytochemical screening of four most used plants C. ternatum, C. transvaalensis, E. axillare and L. caffer crude extracts revealed the presence of alkaloids, anthraquinones, cardiac glycosides, flavonoids, phlobatannin, saponins, steroids, tannins and terpenes. All plants including those that did not display any antioxidant activities using qualitative DPPH assay displayed a certain level of scavenging activity when quantified, with the mentioned extracts from E. axillare (water and hexane), L. caffer (water and acetone) and C. ternatum (acetone) showing excellent activity almost comparable to a standard antioxidant drug (ascorbic acid). Plant extracts from all used solvents were active against Mycobacterium smegmatis, Klebsiella pneumoniae, Staphylococcus aureus and Pseudomonas aeruginosa with miniumum bactericidal concentration values ranging between 0.019 and 2.5 mg/ml depending on the plant species. Some of plant extracts exhibited minimum inhibitory concentration values ranging between 0.63 to 2.5 mg/ml. This study showed that most of the diagnosis methods used by Bapedi THs and their herbal medicines have the potential to contribute towards the management and treatment of RIs and RSs. iii | Page Future endeavour should be focused on the following: (a) possibility of collaboration between questioned THs and local western health care practitioners in the treatment of these diseases, and (b) isolation, purification and characterization of the biologically active compounds from extract of the above-stated plants, amongst other inquiries.
- Full Text:
- Date Issued: 2019
- Authors: Semenya, Sebua Silas
- Date: 2019
- Subjects: Medicinal plants Respiratory infections -- Alternative treatment
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15716 , vital:40512
- Description: There is paucity of data on South African traditional healers’ (THs) phytotherapeutic practices regarding respiratory infections (RIs). Several people in South Africa are contracting RIs due to prevalence of risk factors. This situation is exacerbated by limited modern health care facilities and associated personnel in some provinces in the country. The primary objectives of this study were twofold. First purpose was to execute a comprehensive social and ethnobotanical surveys aimed at (a) establishing the types of RIs treated by THs and diagnosis techniques used, (b) plants used as therapies for RIs and associated indigenous knowledge practices, (c) source/s of plants used as medicines, (d) harvesting practices, current local availability status, conservation status and threats of indigenous plants as well as the level of conservation knowledge possessed by THs. The second objective was to assess the therapeutic value of the four most frequently used plant species by THs by (a) analysing the phytochemical profile of the plant extracts, (b) their antioxidant activities, and (c) their antibacterial activities. Information linked to the social and ethnobotanical surveys was gathered via a semi-structured questionnaires, supplemented by field observations during face-to-face interview with 240 conveniently selected THs practicing in the municipalities of Capricorn, Sekhukhune and Waterberg districts of the Limpopo Province, South Africa. Data were generally analysed using Microsoft Excel and Statistical Package for the Social Sciences (SPSS). In addition to these softwares, ethnobotanical data were analysed via quantitative ethnobotanical indexes namely use mention (UM), fidelity level (FL), use value (UV) and preference ranking (PR). For laboratory experiments, qualitative phytochemical constitutes of the crude extracts were determined using the standard screening methods. The antioxidant activities of acetone, dichlomethane, hexane, methanol and water crude extracts were evaluated using qualitative and quantitative 2, 2-diphenyl-1-picrylhydrazyl (DPPH) assays. Antibacterial activities of these extracts was assessed using microdilution and bioautography assays. Six types of RIs; tuberculosis (84.1%), sore throat (65%), asthma (58.3%), sinusitis (55%), pneumonia (53.3%) and rhinitis (43.7%) were treated by THs practicing as herbalists (58.7%), herbalists and diviners (40.5%), and diviners (0.4%). The identification of these RIs was based on the patients’ presentation of certain clinical symptoms, with THs practicing both herbalism and divination additionally using bone casting. There was a broad overlap between the clinical signs used to diagnose most of the RIs, and the specificity of symptoms followed when ascertaining an individual infection was low. A total of 224 plant species (83% indigenous and 16.9% exotics) belonging to 177 genera and 85 botanical families, mainly the Fabaceae (25 spp.) and Asteraceae (16 spp.) were used by THs as herbal medicines for the aforesaid RIs and perceived related symptoms (RSs). Most of the documented plant species were used for tuberculosis (82.1%) and asthma (46.4%). Roots (64%) and leaves (13%) formed an important mainstay for medicinal recipes preparations. Different routes of administering these recipes were noted, with oral (75.6%) and nasal (18.8%) being the most preferred. The most widely used species by THs to treat and manage all the six RIs with high UM, FL, UV and PR values included Clerodendrum ternatum, Cryptocarya transvaalensis, Enicostema axillare, Lasiosiphon caffer and Stylochaeton natalensis. Overall larger numbers of species used by Bapedi THs including the mentioned ones are recorded for the first time in scientific literature as remedies for RIs and RSs, thus reflecting a need for more similar studies amongst other ethnic groups of South Africa and elsewhere. The phytochemical screening of four most used plants C. ternatum, C. transvaalensis, E. axillare and L. caffer crude extracts revealed the presence of alkaloids, anthraquinones, cardiac glycosides, flavonoids, phlobatannin, saponins, steroids, tannins and terpenes. All plants including those that did not display any antioxidant activities using qualitative DPPH assay displayed a certain level of scavenging activity when quantified, with the mentioned extracts from E. axillare (water and hexane), L. caffer (water and acetone) and C. ternatum (acetone) showing excellent activity almost comparable to a standard antioxidant drug (ascorbic acid). Plant extracts from all used solvents were active against Mycobacterium smegmatis, Klebsiella pneumoniae, Staphylococcus aureus and Pseudomonas aeruginosa with miniumum bactericidal concentration values ranging between 0.019 and 2.5 mg/ml depending on the plant species. Some of plant extracts exhibited minimum inhibitory concentration values ranging between 0.63 to 2.5 mg/ml. This study showed that most of the diagnosis methods used by Bapedi THs and their herbal medicines have the potential to contribute towards the management and treatment of RIs and RSs. iii | Page Future endeavour should be focused on the following: (a) possibility of collaboration between questioned THs and local western health care practitioners in the treatment of these diseases, and (b) isolation, purification and characterization of the biologically active compounds from extract of the above-stated plants, amongst other inquiries.
- Full Text:
- Date Issued: 2019
Multi-temporal assessment of chlorophyll-a concentration in estuarine waters: a case study of sundays and swartkops estuaries, Eastern Cape Province
- Authors: Gwazani, Nothando
- Date: 2019
- Subjects: Chlorophyll -- South Africa Estuaries -- South Africa
- Language: English
- Type: Thesis , Masters , MSc (Applied Remote Sensing & GIS)
- Identifier: http://hdl.handle.net/10353/11972 , vital:39123
- Description: Estuaries are productive and delicate marine systems, which are of commercial, recreational and aesthetic value as they reflect the land use of a catchment by creating “nutrient traps”, these nutrients are absorbed by water and later released into the coastal oceans. Disturbances in an estuary influence a wide variety of habitats and organisms in a marine ecosystem, for example, high chlorophyll-a affects marine species that utilize calm waters, food and turbid water found in estuaries. The degradation of South African estuaries is an on-going accelerating process; therefore, there is a need for preservation measures for estuarine ecosystems by means of monitoring nutrient flow. This research was aimed at assessing the use of OLCI ocean color products in monitoring chl-a concentration and impacts of the estuaries in Algoa Bay. OLCI on the Sentinel platforms, coupled with OCNN and OC4ME algorithms were employed to assess the distribution of chlorophyll-a in Swartkops and Sunday’s estuaries. OC4Me and OCNN are the default models designed for OLCI data. However, the OLCI resolution was not able to measure the chl-a concentration within these estuaries. Therefore, satellite product assessment was primarily focused on the Algoa bay scale due to the resolution of the available data. SNAP and Matlab were applied for the production of the final products. Accuracy assessment was used to check the agreement between the in situ datasets of chl-a and the final processed satellite products. Results of this investigation point that OCNN did not perform well in the study as compared to OC4Me and it did not produce accurate results in areas with very high biomass concentration. The research concludes by recommending the use of higher resolution data such as Sentinel 2 MSI (10m, 20m, and 60m resolution) for resolving chlorophyll-a within these estuaries.
- Full Text:
- Date Issued: 2019
- Authors: Gwazani, Nothando
- Date: 2019
- Subjects: Chlorophyll -- South Africa Estuaries -- South Africa
- Language: English
- Type: Thesis , Masters , MSc (Applied Remote Sensing & GIS)
- Identifier: http://hdl.handle.net/10353/11972 , vital:39123
- Description: Estuaries are productive and delicate marine systems, which are of commercial, recreational and aesthetic value as they reflect the land use of a catchment by creating “nutrient traps”, these nutrients are absorbed by water and later released into the coastal oceans. Disturbances in an estuary influence a wide variety of habitats and organisms in a marine ecosystem, for example, high chlorophyll-a affects marine species that utilize calm waters, food and turbid water found in estuaries. The degradation of South African estuaries is an on-going accelerating process; therefore, there is a need for preservation measures for estuarine ecosystems by means of monitoring nutrient flow. This research was aimed at assessing the use of OLCI ocean color products in monitoring chl-a concentration and impacts of the estuaries in Algoa Bay. OLCI on the Sentinel platforms, coupled with OCNN and OC4ME algorithms were employed to assess the distribution of chlorophyll-a in Swartkops and Sunday’s estuaries. OC4Me and OCNN are the default models designed for OLCI data. However, the OLCI resolution was not able to measure the chl-a concentration within these estuaries. Therefore, satellite product assessment was primarily focused on the Algoa bay scale due to the resolution of the available data. SNAP and Matlab were applied for the production of the final products. Accuracy assessment was used to check the agreement between the in situ datasets of chl-a and the final processed satellite products. Results of this investigation point that OCNN did not perform well in the study as compared to OC4Me and it did not produce accurate results in areas with very high biomass concentration. The research concludes by recommending the use of higher resolution data such as Sentinel 2 MSI (10m, 20m, and 60m resolution) for resolving chlorophyll-a within these estuaries.
- Full Text:
- Date Issued: 2019
Muscle nanostructure and physicochemical characteristics of South African A and AB mutton classes
- Authors: Mdikili, Zizipho
- Date: 2019
- Subjects: Meat -- Quality -- South Africa
- Language: English
- Type: Thesis , Masters , (MSc) (Animal Science)
- Identifier: http://hdl.handle.net/10353/12005 , vital:39126
- Description: Significant variations exist in quality of red meat due to the effect of various intrinsic and extrinsic factors. Research has been conducted in early 1990s to prove that carcasses from A and AB classes differ in meat quality due to age variation. This led to a conclusion that the two should be separated in the South African Red meat Classification System (SARCS). However, an interesting debate arose from a carcass classification workshop that A and AB meat classes have the same quality and thus must be integrated into one class in the carcass classification system. In addition, as much as it can be debated that these classes have the same quality, it is also possible that slight differences exist between the two since they are from different age groups. The current study was therefore developed and two trials were conducted to evaluate the impact of age differences on physicochemical attributes and muscle nanostructure of A and AB classes in sheep. In the first trial a total of ninety (n=90) Dorper sheep of the same sex but different age groups slaughtered at a high throughput abattoir in the Eastern Cape province were used to evaluate meat ultimate pH (pH24), colour (L* , a* , b* , H* , C* ), thawing loss (TL%), cooking loss (CL%) and tenderness (Warner Bratzler Shear Force - WBSF) of A and AB classes, whereas, on the second trial forty (n=40) Dorper sheep were used to evaluate muscle nanostructure and its relationship with tenderness. Meat samples were harvested from the Muscularis longissimuss thoracis et lumborum (LTL) for v meat quality and nanostructure measurements. The results showed significant variations (P<0.05) between the two classes for lean a* , H* and CL%. Significant differences (P<0.01) were observed in pH24, TL% and WBSF between A and AB classes. However, there were no significant differences (P>0.05) observed in meat L*, b* and C * . Ultimate pH was negatively correlated with thawing loss and some colorimetric attributes of lamb such as lightness, yellowness and hue angle. Moreover, tenderness was positively correlated with cooking and thawing losses. Significant differences were not (P>0.05) observed in sarcomere length, myofibrilar diameter and shear force between A and AB classes. Both sarcomere length and myofibrilar diameter were not correlated (P>0.05) with meat tenderness. These results suggest that A and AB classes are the same in nanostructure and that muscle nanostructure of these two classes is not related to meat tenderness. It was concluded that meat from sheep carcasses falling under the A and AB classes in the South African classification system vary greatly in physicochemical quality. Moreover, sheep carcasses from A and AB classes have the same sarcomere lengths and hence, they do not differ in meat tenderness (WBSF). However, when these classes were observed under a microscope, slight differences were noted in sarcomere lengths and myofibrilar diameters, which led to a conclusion that the two should remain as separated classes because their combination would result in the expansion of the non-uniformity of red meat tenderness. Therefore, A and AB classes should not be combined in the South African classification system. Further research is, however, recommended to evaluate the influence of other factors that were not examined in the current study.
- Full Text:
- Date Issued: 2019
- Authors: Mdikili, Zizipho
- Date: 2019
- Subjects: Meat -- Quality -- South Africa
- Language: English
- Type: Thesis , Masters , (MSc) (Animal Science)
- Identifier: http://hdl.handle.net/10353/12005 , vital:39126
- Description: Significant variations exist in quality of red meat due to the effect of various intrinsic and extrinsic factors. Research has been conducted in early 1990s to prove that carcasses from A and AB classes differ in meat quality due to age variation. This led to a conclusion that the two should be separated in the South African Red meat Classification System (SARCS). However, an interesting debate arose from a carcass classification workshop that A and AB meat classes have the same quality and thus must be integrated into one class in the carcass classification system. In addition, as much as it can be debated that these classes have the same quality, it is also possible that slight differences exist between the two since they are from different age groups. The current study was therefore developed and two trials were conducted to evaluate the impact of age differences on physicochemical attributes and muscle nanostructure of A and AB classes in sheep. In the first trial a total of ninety (n=90) Dorper sheep of the same sex but different age groups slaughtered at a high throughput abattoir in the Eastern Cape province were used to evaluate meat ultimate pH (pH24), colour (L* , a* , b* , H* , C* ), thawing loss (TL%), cooking loss (CL%) and tenderness (Warner Bratzler Shear Force - WBSF) of A and AB classes, whereas, on the second trial forty (n=40) Dorper sheep were used to evaluate muscle nanostructure and its relationship with tenderness. Meat samples were harvested from the Muscularis longissimuss thoracis et lumborum (LTL) for v meat quality and nanostructure measurements. The results showed significant variations (P<0.05) between the two classes for lean a* , H* and CL%. Significant differences (P<0.01) were observed in pH24, TL% and WBSF between A and AB classes. However, there were no significant differences (P>0.05) observed in meat L*, b* and C * . Ultimate pH was negatively correlated with thawing loss and some colorimetric attributes of lamb such as lightness, yellowness and hue angle. Moreover, tenderness was positively correlated with cooking and thawing losses. Significant differences were not (P>0.05) observed in sarcomere length, myofibrilar diameter and shear force between A and AB classes. Both sarcomere length and myofibrilar diameter were not correlated (P>0.05) with meat tenderness. These results suggest that A and AB classes are the same in nanostructure and that muscle nanostructure of these two classes is not related to meat tenderness. It was concluded that meat from sheep carcasses falling under the A and AB classes in the South African classification system vary greatly in physicochemical quality. Moreover, sheep carcasses from A and AB classes have the same sarcomere lengths and hence, they do not differ in meat tenderness (WBSF). However, when these classes were observed under a microscope, slight differences were noted in sarcomere lengths and myofibrilar diameters, which led to a conclusion that the two should remain as separated classes because their combination would result in the expansion of the non-uniformity of red meat tenderness. Therefore, A and AB classes should not be combined in the South African classification system. Further research is, however, recommended to evaluate the influence of other factors that were not examined in the current study.
- Full Text:
- Date Issued: 2019
Muscle nanostructure, fat colour related fatty acids and Check-All-That-Apply visual profiling of South African A2 beef longissimus
- Authors: Soji, Zimkhitha
- Date: 2019
- Subjects: Meat -- Quality
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15264 , vital:40332
- Description: The main objective of this study was to determine the effect of muscle nanostructure on tenderness, fat colour related fatty acids and Check-All-That-Apply visual profiling of South African A2 beef longissimus. Fifty two A-class steers (n=52) of five breeds (Bonsmara (n=19), Beef master (n=7), Hereford (n=9) and Simbra (n=17)) typically processed in different South African feedlots were studied. The animals were humanely slaughtered at an abattoir following the commercial standard procedures. Fat colour measurements (CIE b*) were taken at the P8 site on hot carcasses at the abattoir. Carcass mass (warm and cold) was recorded at the slaughter line before chilling (warm) and after chilling (cold) while pH0 and temperature were measured at 45 minutes post-mortem on the Longissimus thoracis et lumborum (LTL) muscle. Thereafter, a 20 g subsection of the LTL muscle on the left side of each carcass was sampled for muscle nanostructure analysis. At 24 hours post-slaughter, ultimate pH (pH24) was measured, further subsections of the LTL muscle (20 g) were harvested for further muscle nanostructure analysis and 2.5 kg of the LTL muscle was also harvested for analysis of tenderness, fatty acids and sensory evaluation. The muscle nanostructure (myofibril diameter (MYD), myofibril spacing (MYS), muscle fibre diameter (MFD), muscle fibre spacing (MFS) and sarcomere length (SL)) was analysed using the scanning electron microscope (SEM) while tenderness was measured using Warner Bratzler Shear Force after 45mins, 24hrs, 3 and 7 days aging period at -20 ºC refrigerator temperature. Some proximate fractions (total extractable intramuscular fat (Fat %), Fat Free Dry matter (FFDM %) and Moisture content) and fatty acid profile were measured using extracted fat and fatty acid indices (desaturase index, atherogenicity index) were calculated. Lastly a Check-All-That-Apply visual profiling method rated by an 80-member consumer panel was done to assess consumer meat preferences and perceptions of Bonsmara, Hereford and Simbra A2 fresh steaks. At 45mins post-slaughter breed affected (P<0.05) MYD and MYS, while at 24hrs breed affected MFD and MFS only. Early post-mortem pH (pH0) had no effect on the muscle nanostructure and tenderness while ultimate pH (pH24) affected MYD and MYS only. Muscle temperature at 45mins affected (P<0.05) the MYD, MFD and MFS, while 24hrs muscle temperature affected (P<0.05) MYD only. Tenderness was not related to the muscle nanostructure early post-mortem and there was no uniformity on the changes in muscle nanostructure and tenderness from early post-mortem to 24hrs against the multifaceted carcass mass, muscle pH and temperature effects. During ageing, breed affected the MYD and MYS at 45mins, while at 24hrs in addition to the myofibril structure breed also had an effect on muscle fibre bundle characteristics (MFD and MFS). The changes in MYD, MYS and MFS became constant on day 3 while variations in the MFD still progressed. There was no uniformity on the SL pattern during ageing and a very weak linear relationship between tenderness, SL, MFD and MFS was observed. Notably there was also no uniformity on how the muscle texture features; including the surface structure, fibre separation, and the mechanism of muscle contraction and relaxation; changed throughout the ageing period across and within the breeds. Moreover, breed had a significant effect on pentadecyclic acid, total saturated fatty acids (SFA) and docosahexanoic acid. Differences (P<0.05) in SFA, monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), n-6, n-3, fatty acid ratios, and desaturase index were observed among the white, creamy-white and creamy fat colour. The distribution of fatty acid classes was SFA>MUFA>PUFA in descending order of concentrations of mean values (44.19:40.06:15.75, respectively), while the n-6: n-3 ratio was 12:1. In sensory evaluation, consumers indicated how they would prefer to pay premium for meat with guaranteed muscle and fat colour, low fat content, high marbling and tenderness. Consumers observed breed differences (P<0.05) in muscle fibre separation and muscle colour. The overall liking of each attribute was more on moderate bright cherry red lean colour, moderate yellow fat, very abundant marbling and slight separation of muscle fibres. Differences on discrete liking of each attribute among consumers had an effect on the overall liking of each steak with Hereford steaks being more preferred by consumers. It was concluded that meat from beef animals within the same feeding regime has a different fatty acid composition owing to different breed synthetic pathways and feed ingredients and that meat tenderness is not affected by the muscle nanostructure early post-mortem. However, during ageing, meat tenderness is directly linked to breed related myofibril structure changes in particular the myofibril diameter, spacing between myofibrils and their interaction; while the muscle texture features, fibre diameter, spacing between muscle fibres and sarcomere length explain the non-uniformity of beef tenderness. Also the organoleptic and health related quality of meat assumed more importance among consumers in sensory evaluation. Thus meat classification systems should include more credence aspects or indicators that support credence quality of meat
- Full Text:
- Date Issued: 2019
- Authors: Soji, Zimkhitha
- Date: 2019
- Subjects: Meat -- Quality
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15264 , vital:40332
- Description: The main objective of this study was to determine the effect of muscle nanostructure on tenderness, fat colour related fatty acids and Check-All-That-Apply visual profiling of South African A2 beef longissimus. Fifty two A-class steers (n=52) of five breeds (Bonsmara (n=19), Beef master (n=7), Hereford (n=9) and Simbra (n=17)) typically processed in different South African feedlots were studied. The animals were humanely slaughtered at an abattoir following the commercial standard procedures. Fat colour measurements (CIE b*) were taken at the P8 site on hot carcasses at the abattoir. Carcass mass (warm and cold) was recorded at the slaughter line before chilling (warm) and after chilling (cold) while pH0 and temperature were measured at 45 minutes post-mortem on the Longissimus thoracis et lumborum (LTL) muscle. Thereafter, a 20 g subsection of the LTL muscle on the left side of each carcass was sampled for muscle nanostructure analysis. At 24 hours post-slaughter, ultimate pH (pH24) was measured, further subsections of the LTL muscle (20 g) were harvested for further muscle nanostructure analysis and 2.5 kg of the LTL muscle was also harvested for analysis of tenderness, fatty acids and sensory evaluation. The muscle nanostructure (myofibril diameter (MYD), myofibril spacing (MYS), muscle fibre diameter (MFD), muscle fibre spacing (MFS) and sarcomere length (SL)) was analysed using the scanning electron microscope (SEM) while tenderness was measured using Warner Bratzler Shear Force after 45mins, 24hrs, 3 and 7 days aging period at -20 ºC refrigerator temperature. Some proximate fractions (total extractable intramuscular fat (Fat %), Fat Free Dry matter (FFDM %) and Moisture content) and fatty acid profile were measured using extracted fat and fatty acid indices (desaturase index, atherogenicity index) were calculated. Lastly a Check-All-That-Apply visual profiling method rated by an 80-member consumer panel was done to assess consumer meat preferences and perceptions of Bonsmara, Hereford and Simbra A2 fresh steaks. At 45mins post-slaughter breed affected (P<0.05) MYD and MYS, while at 24hrs breed affected MFD and MFS only. Early post-mortem pH (pH0) had no effect on the muscle nanostructure and tenderness while ultimate pH (pH24) affected MYD and MYS only. Muscle temperature at 45mins affected (P<0.05) the MYD, MFD and MFS, while 24hrs muscle temperature affected (P<0.05) MYD only. Tenderness was not related to the muscle nanostructure early post-mortem and there was no uniformity on the changes in muscle nanostructure and tenderness from early post-mortem to 24hrs against the multifaceted carcass mass, muscle pH and temperature effects. During ageing, breed affected the MYD and MYS at 45mins, while at 24hrs in addition to the myofibril structure breed also had an effect on muscle fibre bundle characteristics (MFD and MFS). The changes in MYD, MYS and MFS became constant on day 3 while variations in the MFD still progressed. There was no uniformity on the SL pattern during ageing and a very weak linear relationship between tenderness, SL, MFD and MFS was observed. Notably there was also no uniformity on how the muscle texture features; including the surface structure, fibre separation, and the mechanism of muscle contraction and relaxation; changed throughout the ageing period across and within the breeds. Moreover, breed had a significant effect on pentadecyclic acid, total saturated fatty acids (SFA) and docosahexanoic acid. Differences (P<0.05) in SFA, monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), n-6, n-3, fatty acid ratios, and desaturase index were observed among the white, creamy-white and creamy fat colour. The distribution of fatty acid classes was SFA>MUFA>PUFA in descending order of concentrations of mean values (44.19:40.06:15.75, respectively), while the n-6: n-3 ratio was 12:1. In sensory evaluation, consumers indicated how they would prefer to pay premium for meat with guaranteed muscle and fat colour, low fat content, high marbling and tenderness. Consumers observed breed differences (P<0.05) in muscle fibre separation and muscle colour. The overall liking of each attribute was more on moderate bright cherry red lean colour, moderate yellow fat, very abundant marbling and slight separation of muscle fibres. Differences on discrete liking of each attribute among consumers had an effect on the overall liking of each steak with Hereford steaks being more preferred by consumers. It was concluded that meat from beef animals within the same feeding regime has a different fatty acid composition owing to different breed synthetic pathways and feed ingredients and that meat tenderness is not affected by the muscle nanostructure early post-mortem. However, during ageing, meat tenderness is directly linked to breed related myofibril structure changes in particular the myofibril diameter, spacing between myofibrils and their interaction; while the muscle texture features, fibre diameter, spacing between muscle fibres and sarcomere length explain the non-uniformity of beef tenderness. Also the organoleptic and health related quality of meat assumed more importance among consumers in sensory evaluation. Thus meat classification systems should include more credence aspects or indicators that support credence quality of meat
- Full Text:
- Date Issued: 2019
Nutritional and pharmacological profile of moringa oleifera lam. Leaves cultivated in the South African ecotype
- Authors: Yako, Zomsa
- Date: 2019
- Subjects: Moringa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14605 , vital:40021
- Description: Moringa oleifera Lam. is native to the Indian ecotype, which has become naturalized in many tropic and subtropic regions worldwide, thus a great variation in the bioactive compounds of the plant is recorded. The introduction of Moringa oleifera to South Africa occurred in the turn of the twentieth century with the aim of combating malnourishment, aiding health and fostering economic development. Therefore, this study was conducted with the aim of evaluating and authenticating the nutritional parameters, essential oil and bioactive components found in the various solvent extracts of Moringa oleifera leaves cultivated in the South African ecotype. It also elucidated some of the plants medicinal properties by investigating the antioxidant and antibacterial properties of the plant. The essential oil of the leaves was extracted using two methods (solvent free microwave extraction and hydrodistillation) and analysed using Gas Chromotography/Mass Spectrometer. The safety profile of the leaves was investigated using brine shrimp model. The results from the study revealed that Moringa oleifera leaves cultivated in South Africa were rich in crude protein levels (28.72%) and carbohydrate (28.84%). Among the minerals tested for, the leaves contained high content of calcium (1603.33 mg/100 g), potassium (1690 mg/100 g), zinc (13.03 mg/100 g) and iron (21.13 mg/100 g). The vitamin E content had the highest concentration (89.43 mg/100 g) among the vitamins evaluated. The leaves of Moringa oleifera had low quantities of antinutrients in relation to minerals, thus ensuring nutrients availability. This study identified 15 fatty acids in the dried leaves of Moringa. The highest fatty acid detected were polyunsaturated fatty acids, linoleic acid (56.36) and alpha-linolenic acid (687.58), 7 of the fatty acids were saturated fatty acids, though relatively low besides stearic acid. 15 amino acids were present, 7 of which were essential amino acids, namely; threonine, tyrosine, methionine, valine, phenylalanine, isoleucine and leucine. vi Among the phytochemicals evaluated, the aqueous extract gave the highest total phenolic content (21.01 ± 2.315 mg GAE/g), the acetone extract gave the highest proanthocyanidin (15.33 3.5 mg CE/g) and flavonoid contents (25.04±3.28 mg QE/g), while saponin and alkaloid contents were 27.73 ± 9.97% and 7.32 ± 2.73 % respectively. All the extracts exhibited high radical scavenging power against the 2,2- diphenyl-1-picrylhydrazyl radical with an IC50 less than 0.025 mg/mL. Aqueous extract gave the highest capacity based on ABTS and TAC assays with IC50 of 0.074 mg/ mL and 0.055 mg/mL respectively. Ethanol extract exhibited the least antioxidant capacity among the extracts, as well as the least antimicrobial activity on both Gram −ve and Gram +ve bacteria with all its minimum inhibitory concentration values greater than 5 mg/mL. The acetone extract exhibited the strongest antimicrobial activity among the extracts. A total of 8 and 24 chemical compounds were found from the solvent-free microwave extracted and hydrodistilled oils, respectively. The major components found from hydrodistillation were 2-Hexanal (16.37%), Nonanal (6.09%), 5 9-undecadien-2-one 6, 10 dimethyl- (e) - (8.01%), trans-beta-Ionone (8.02%) and octadecane (9.67%). For the solvent free microwave extracted oil, Benzene acetaldehyde (5.68%), Octadecane, Pentacosane and Eicosane which were 11.03%, were the major components. Toxicity evaluation revealed that mortality was time dependent. As the exposure period increased, mortality kept increasing. The hatching success of the cysts in acetone, aqueous and ethanol extracts were 35.7, 33.6 and 35.2% respectively. Acetone extract showed the most prominent hatching success. Hatchability and lethality were in a concentration dependent fashion. Among the extracts, acetone extract exhibited the highest lethality (12.3%) to the nauplii, followed by ethanol (10.9%), then aqueous (5.6%) extracts. All the results obtained from this study suggest that Moringa has the potential of eradicating malnutrition and aid health. It contains the necessary nutritional and bioactive compounds and the leaves proved not to be toxic at the levels (0.0625 – 1 mg/mL) tested.
- Full Text:
- Date Issued: 2019
- Authors: Yako, Zomsa
- Date: 2019
- Subjects: Moringa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14605 , vital:40021
- Description: Moringa oleifera Lam. is native to the Indian ecotype, which has become naturalized in many tropic and subtropic regions worldwide, thus a great variation in the bioactive compounds of the plant is recorded. The introduction of Moringa oleifera to South Africa occurred in the turn of the twentieth century with the aim of combating malnourishment, aiding health and fostering economic development. Therefore, this study was conducted with the aim of evaluating and authenticating the nutritional parameters, essential oil and bioactive components found in the various solvent extracts of Moringa oleifera leaves cultivated in the South African ecotype. It also elucidated some of the plants medicinal properties by investigating the antioxidant and antibacterial properties of the plant. The essential oil of the leaves was extracted using two methods (solvent free microwave extraction and hydrodistillation) and analysed using Gas Chromotography/Mass Spectrometer. The safety profile of the leaves was investigated using brine shrimp model. The results from the study revealed that Moringa oleifera leaves cultivated in South Africa were rich in crude protein levels (28.72%) and carbohydrate (28.84%). Among the minerals tested for, the leaves contained high content of calcium (1603.33 mg/100 g), potassium (1690 mg/100 g), zinc (13.03 mg/100 g) and iron (21.13 mg/100 g). The vitamin E content had the highest concentration (89.43 mg/100 g) among the vitamins evaluated. The leaves of Moringa oleifera had low quantities of antinutrients in relation to minerals, thus ensuring nutrients availability. This study identified 15 fatty acids in the dried leaves of Moringa. The highest fatty acid detected were polyunsaturated fatty acids, linoleic acid (56.36) and alpha-linolenic acid (687.58), 7 of the fatty acids were saturated fatty acids, though relatively low besides stearic acid. 15 amino acids were present, 7 of which were essential amino acids, namely; threonine, tyrosine, methionine, valine, phenylalanine, isoleucine and leucine. vi Among the phytochemicals evaluated, the aqueous extract gave the highest total phenolic content (21.01 ± 2.315 mg GAE/g), the acetone extract gave the highest proanthocyanidin (15.33 3.5 mg CE/g) and flavonoid contents (25.04±3.28 mg QE/g), while saponin and alkaloid contents were 27.73 ± 9.97% and 7.32 ± 2.73 % respectively. All the extracts exhibited high radical scavenging power against the 2,2- diphenyl-1-picrylhydrazyl radical with an IC50 less than 0.025 mg/mL. Aqueous extract gave the highest capacity based on ABTS and TAC assays with IC50 of 0.074 mg/ mL and 0.055 mg/mL respectively. Ethanol extract exhibited the least antioxidant capacity among the extracts, as well as the least antimicrobial activity on both Gram −ve and Gram +ve bacteria with all its minimum inhibitory concentration values greater than 5 mg/mL. The acetone extract exhibited the strongest antimicrobial activity among the extracts. A total of 8 and 24 chemical compounds were found from the solvent-free microwave extracted and hydrodistilled oils, respectively. The major components found from hydrodistillation were 2-Hexanal (16.37%), Nonanal (6.09%), 5 9-undecadien-2-one 6, 10 dimethyl- (e) - (8.01%), trans-beta-Ionone (8.02%) and octadecane (9.67%). For the solvent free microwave extracted oil, Benzene acetaldehyde (5.68%), Octadecane, Pentacosane and Eicosane which were 11.03%, were the major components. Toxicity evaluation revealed that mortality was time dependent. As the exposure period increased, mortality kept increasing. The hatching success of the cysts in acetone, aqueous and ethanol extracts were 35.7, 33.6 and 35.2% respectively. Acetone extract showed the most prominent hatching success. Hatchability and lethality were in a concentration dependent fashion. Among the extracts, acetone extract exhibited the highest lethality (12.3%) to the nauplii, followed by ethanol (10.9%), then aqueous (5.6%) extracts. All the results obtained from this study suggest that Moringa has the potential of eradicating malnutrition and aid health. It contains the necessary nutritional and bioactive compounds and the leaves proved not to be toxic at the levels (0.0625 – 1 mg/mL) tested.
- Full Text:
- Date Issued: 2019
Nutritional quality of sausage made with edible meat waste and the perception of consumers on offal product in Eastern Cape Province, South Africa
- Authors: Oluwasegun, Babatunde Alao
- Date: 2019
- Subjects: Meat -- Quality
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/19021 , vital:40094
- Description: Meat processing at the abattoir provides meat by product and waste while, the major part of the muscle which constitutes a third is edible. The edible by products (EBP) of meat have a notable position in our day-to-day life and are used in diverse forms. However, the quality of offal meat may differ according to intrinsic and extrinsic attributes that may occasionally be shaped by the attitude of consumers towards the products. Therefore, the first objective of this thesis focused on features that might influence consumer preferences and their perception of offal meat. A total of 202 consumers from three Municipalities in Amathole District were randomly sampled using exponential nondiscriminative snowball sampling. Data were gathered through a structured questionnaire containing open ended and closed ended questions. The study showed that consumers were more influenced by the freshness, price and availability of the product and these factors are used to determine the purchase outlet. Differences were observed in the offal meat consumption between the age groups. Age groups 25-34 (29.7%) and 35-44 (27.4%) showed the highest offal meat consumption, while the decline was observed in age groups of 55-64 (11.9%), 65- 74 (5.9%) and 75-85 (0.01%) respectively. The most preferred purchase point for offal meat in this study was in butcheries. However, it was observed that the factors influencing offal consumption in Amathole District were similar to meat consumption except that, offals were mainly purchased at butcher shops. The second objective in this study was to determine the sensory characteristics and consumer acceptance of sausages with 10% fat, 30% edible meat waste and 50% edible meat waste. Sensory descriptive attributes such as appearance, texture, colour, taste, flavour and overall acceptance of the sausage were evaluated by sensory panel (n = 60). The sensory panel comprised of students from undergraduates, post-graduates, post-doctoral fellows and lecturers at the University of Fort Hare. The findings of the study indicated that 50% replacement of xiii edible meat waste was similar to the commercial 10% fat with regard to several sensory attributes and pooled liking. Therefore, the utilization of the edible meat waste in production of sausages has the potential to increase profitability in meat industry and minimise meat waste in the industry. However, the cooking method that was more acceptable to consumers in this study was using the microwave as compared to oven-grilling. Furthermore, the effects of different cooking methods (microwave and oven-grilling) on proximate and mineral composition of the formulated sausages were determined. However, the cooking process appeared to have a significant effect on most of the minerals in the sausage. The cooking methods had a significant effect at P <0.01 on the nutrients composition of the formulated sausage. It was observed that the nutritional values of the sausage was better preserved after the cooking process due to higher mean values obtained after cooking. The mean values for calcium (173.1, 221.76, 231.29), potassium (444.57, 158.58, 156.67), magnesium (84.43, 257.97, 127.27), zinc (52.94, 35.27, 27.13), copper (8.8, 7.07, 4.44), manganese (8.74, 0.65, 0.08), sodium (589.42, 604.45, 529.79) and iron (63.3, 85.38, 74.81) in cooked. And the mean values for calcium (286.18, 132.18, 114.79), potassium (206.64, 113.83, 207.81), magnesium (189.89, 33.97, 48.11), zinc (61.05, 28.09, 26.44), copper (2.92, 2.73, 3.89), manganese (1.42, 0.11, 0.35), sodium (566.47, 530.79, 527.35) and iron (77.56, 58.68, 45.42) in uncooked sausage varied greatly among the treatments. Although, the disparities in the mineral content may be attributed to the different edible meat waste from different parts of the cattle which are either from feedlot or pastured based. In regard to the results obtained from proximate and mineral composition, microwave cooking method was found to be the best cooking technique for healthy eating. Finally, the effect of frying with two different oils (sunflower oil and olive oil) on the fatty acid composition of sausage made with edible meat waste was examined. The results revealed that beef sausage containing 70% edible meat wastes and 30% beef (T1) had a higher fat content xiv (25.7%±0.83%) than other treatments. On the other hand, beef sausage fortified with 10% fat and 90% beef (T3) had the lowest fat content but highest FFDM (55.85±0.57%) and moisture content (69.15±0.62) than other treatments. Despite the increase in omega-3: omega-6 fatty acid ratio in the sausage treatments after cooking, the mean value of omega-3: omega-6 fatty acid ratio was greater than 1:5 (0.2) which is within the FAO/WHO recommended range. The omega-3: omega-6 association is well-known for its importance in the diet because it is a key factor for balanced eicosanoid production in the living organism. The significant reduction in saturated fatty acids after cooking showed that there could also be a positive influence on the human health if consumed. Therefore, it may be concluded from the findings of the study that sausage made with edible meat waste as fat replacer is safe for human consumption.
- Full Text:
- Date Issued: 2019
- Authors: Oluwasegun, Babatunde Alao
- Date: 2019
- Subjects: Meat -- Quality
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/19021 , vital:40094
- Description: Meat processing at the abattoir provides meat by product and waste while, the major part of the muscle which constitutes a third is edible. The edible by products (EBP) of meat have a notable position in our day-to-day life and are used in diverse forms. However, the quality of offal meat may differ according to intrinsic and extrinsic attributes that may occasionally be shaped by the attitude of consumers towards the products. Therefore, the first objective of this thesis focused on features that might influence consumer preferences and their perception of offal meat. A total of 202 consumers from three Municipalities in Amathole District were randomly sampled using exponential nondiscriminative snowball sampling. Data were gathered through a structured questionnaire containing open ended and closed ended questions. The study showed that consumers were more influenced by the freshness, price and availability of the product and these factors are used to determine the purchase outlet. Differences were observed in the offal meat consumption between the age groups. Age groups 25-34 (29.7%) and 35-44 (27.4%) showed the highest offal meat consumption, while the decline was observed in age groups of 55-64 (11.9%), 65- 74 (5.9%) and 75-85 (0.01%) respectively. The most preferred purchase point for offal meat in this study was in butcheries. However, it was observed that the factors influencing offal consumption in Amathole District were similar to meat consumption except that, offals were mainly purchased at butcher shops. The second objective in this study was to determine the sensory characteristics and consumer acceptance of sausages with 10% fat, 30% edible meat waste and 50% edible meat waste. Sensory descriptive attributes such as appearance, texture, colour, taste, flavour and overall acceptance of the sausage were evaluated by sensory panel (n = 60). The sensory panel comprised of students from undergraduates, post-graduates, post-doctoral fellows and lecturers at the University of Fort Hare. The findings of the study indicated that 50% replacement of xiii edible meat waste was similar to the commercial 10% fat with regard to several sensory attributes and pooled liking. Therefore, the utilization of the edible meat waste in production of sausages has the potential to increase profitability in meat industry and minimise meat waste in the industry. However, the cooking method that was more acceptable to consumers in this study was using the microwave as compared to oven-grilling. Furthermore, the effects of different cooking methods (microwave and oven-grilling) on proximate and mineral composition of the formulated sausages were determined. However, the cooking process appeared to have a significant effect on most of the minerals in the sausage. The cooking methods had a significant effect at P <0.01 on the nutrients composition of the formulated sausage. It was observed that the nutritional values of the sausage was better preserved after the cooking process due to higher mean values obtained after cooking. The mean values for calcium (173.1, 221.76, 231.29), potassium (444.57, 158.58, 156.67), magnesium (84.43, 257.97, 127.27), zinc (52.94, 35.27, 27.13), copper (8.8, 7.07, 4.44), manganese (8.74, 0.65, 0.08), sodium (589.42, 604.45, 529.79) and iron (63.3, 85.38, 74.81) in cooked. And the mean values for calcium (286.18, 132.18, 114.79), potassium (206.64, 113.83, 207.81), magnesium (189.89, 33.97, 48.11), zinc (61.05, 28.09, 26.44), copper (2.92, 2.73, 3.89), manganese (1.42, 0.11, 0.35), sodium (566.47, 530.79, 527.35) and iron (77.56, 58.68, 45.42) in uncooked sausage varied greatly among the treatments. Although, the disparities in the mineral content may be attributed to the different edible meat waste from different parts of the cattle which are either from feedlot or pastured based. In regard to the results obtained from proximate and mineral composition, microwave cooking method was found to be the best cooking technique for healthy eating. Finally, the effect of frying with two different oils (sunflower oil and olive oil) on the fatty acid composition of sausage made with edible meat waste was examined. The results revealed that beef sausage containing 70% edible meat wastes and 30% beef (T1) had a higher fat content xiv (25.7%±0.83%) than other treatments. On the other hand, beef sausage fortified with 10% fat and 90% beef (T3) had the lowest fat content but highest FFDM (55.85±0.57%) and moisture content (69.15±0.62) than other treatments. Despite the increase in omega-3: omega-6 fatty acid ratio in the sausage treatments after cooking, the mean value of omega-3: omega-6 fatty acid ratio was greater than 1:5 (0.2) which is within the FAO/WHO recommended range. The omega-3: omega-6 association is well-known for its importance in the diet because it is a key factor for balanced eicosanoid production in the living organism. The significant reduction in saturated fatty acids after cooking showed that there could also be a positive influence on the human health if consumed. Therefore, it may be concluded from the findings of the study that sausage made with edible meat waste as fat replacer is safe for human consumption.
- Full Text:
- Date Issued: 2019
Ontological Model for Xhosa Beadwork in Marginalised Rural Communities: A Case of the Eastern Cape
- Authors: Tinarwo, Loyd
- Date: 2019
- Subjects: Ontology Beadwork
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15749 , vital:40516
- Description: In South Africa, computational ontologies have gained traction and are increasingly viewed as one of the viable solutions to address the problem of fragmented and unstructured nature of indigenous knowledge (IK) particularly in the marginalized rural communities. The continual existence of IK in tacit form has impeded the use of IK as a potential resource that can catalyze socio-economic and cultural development in South Africa. This study was, therefore, designed to address part of this challenge by developing a Xhosa Beadwork Ontology (XBO) with the goal of structuring the domain knowledge into a reusable body of knowledge. Such a reusable body of knowledge promotes efficient sharing of a common understanding of Xhosa Beadwork in a computational form. The XBO is in OWL 2 DL. The development of the XBO was informed by the NeOn methodology and the iterativeincremental ontology development life cycle within the ambit of Action Research (AR). The XBO was developed around personal ornamentation Xhosa Beadwork consisting of Necklace, Headband, Armlet, Waistband, Bracelet, and Anklet. In this study, the XBO was evaluated focused on ascertaining that the created ontology is a comprehensive representation of the Xhosa Beadwork and is of the required standard. In addition, the XBO was documented into a human understandable and readable resource and was published. The outcome of the study has indicated that the XBO is an adequate, shareable and reusable semantic artifact that can indeed support the formalization and preservation of IK in the domain of Xhosa Beadwork
- Full Text:
- Date Issued: 2019
- Authors: Tinarwo, Loyd
- Date: 2019
- Subjects: Ontology Beadwork
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15749 , vital:40516
- Description: In South Africa, computational ontologies have gained traction and are increasingly viewed as one of the viable solutions to address the problem of fragmented and unstructured nature of indigenous knowledge (IK) particularly in the marginalized rural communities. The continual existence of IK in tacit form has impeded the use of IK as a potential resource that can catalyze socio-economic and cultural development in South Africa. This study was, therefore, designed to address part of this challenge by developing a Xhosa Beadwork Ontology (XBO) with the goal of structuring the domain knowledge into a reusable body of knowledge. Such a reusable body of knowledge promotes efficient sharing of a common understanding of Xhosa Beadwork in a computational form. The XBO is in OWL 2 DL. The development of the XBO was informed by the NeOn methodology and the iterativeincremental ontology development life cycle within the ambit of Action Research (AR). The XBO was developed around personal ornamentation Xhosa Beadwork consisting of Necklace, Headband, Armlet, Waistband, Bracelet, and Anklet. In this study, the XBO was evaluated focused on ascertaining that the created ontology is a comprehensive representation of the Xhosa Beadwork and is of the required standard. In addition, the XBO was documented into a human understandable and readable resource and was published. The outcome of the study has indicated that the XBO is an adequate, shareable and reusable semantic artifact that can indeed support the formalization and preservation of IK in the domain of Xhosa Beadwork
- Full Text:
- Date Issued: 2019
Perceptions of climate change and adaptation strategies: the case of smallholder farmers of Raymond Mhlaba, Port Saint Johns’ and Ingquza Hill local municipality in the Eastern Cape.
- Authors: Maya, Okuhle
- Date: 2019
- Subjects: Climatic changes Farms, Small
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17271 , vital:40871
- Description: Climate change has become indisputable judging from the observed global variations in precipitation, increases in average temperatures, rising average sea levels and melting of ice. The climate phenomenon has since evolved globally and it has been largely documented by scholars. Because of the increases in global temperatures, weather patterns have also changed. This change has resulted in debates on climate change as well as how to respond to it. Various scholars across the world have expressed their opinions about climate change; its causes, impacts and adaptation. In addition, there has been a growing body of literature and studies focusing on smallholder farmers’ perceptions of climate change. Without a doubt, climate change will and has left a group of people, communities and countries vulnerable. In particular, developing countries and poor communities in sub-Saharan Africa are expected to be affected the most by the impacts of climate change. This is mainly because of the region’s dependence on natural resources and their limited capacity to adapt. Literature further adds that vulnerability is on condition of the community’s socioeconomic characteristics and physical surroundings. Climate change variations pose a threat to the agricultural sector and food security of households relying on subsistence farming for survival. Climate variations such as decrease in rainfall and increased hot seasons have been reported to have led to a decline in food production, death of livestock and outbreaks human and animal diseases. The study’s main aim was to determine the smallholder farmers’ perceptions of climate change and adaptation strategies in Raymond Mhlaba, Port Saint Johns’ and Ingquza Hill local municipalities. Particularly, the study looked at the factors influencing these perceptions and the factors affecting the smallholder farmers’ choice of adaptation strategies used in response to climate change. Investigating perception provides insights into the fundamental drivers of behavioural changes in the face of climate change. On their part, adaptation options are greatly shaped by the nature of an individual’s behaviour. The study was carried out in 3 local municipalities (Raymond Mhlaba, Port St Johns’ and Ingquza Hill) in the Eastern Cape, South Africa. The research design applied in this study was cross sectional design where data are collected at a single point in time. Multistage sampling technique was used in selecting respondents from the local municipalities. Stratification was then done to group farmers according to their vi wards and locations. Lastly, purposive sampling was used to select households and smallholder farmers practising crop and livestock production. A total of 211 smallholder farmers constituted the sample size for the study. A close-ended questionnaire was used to conduct structured interviews of household heads. The study utilized both qualitative and quantitative approach. Data collected were coded and entered in Microsoft Excel and transferred to Statistical Package for Social Scientists (SPSS, version 25) for analyses. Descriptive statistics was used to determine the climate change perceptions of smallholder farmers and also to explore the adaptation strategies used by farmers to cope with the impacts of climate change. The findings were explained using frequencies, means and variances. Multinomial Logistic Regression (MNL) was used to determine the factors affecting the choice of adaptation strategies used by smallholder farmers and the probability that a farmer would choose a particular strategy. The results from the study revealed most of the respondents as being able to identify the perceived changes in climate with the environmental changes that they observed. The respondents perceived climate change as an increase in drought period, increase in average temperatures, decrease and variations in rainfall, shortened growing season, crop failure, pests and diseases. However, most of the smallholder farmers disagreed with the frequency of flood incidences as they have not experienced these in their areas. In terms of responses to these changes in climate, the smallholder farmers have used a number of adaptation strategies to cope. Most of the farmers used crop diversification, organic manure, soil and water conservation practices, while others simply did not adapt and some used all the available adaptation strategies identified in this study. The results from the MNL revealed that occupation, household size and years spent in school (education) generally had a positive influence on the choice of adaptation strategy used by smallholder farmers. On the other hand, age; farming systems and membership of a farmers’ association were negatively affecting the smallholder farmers’ choice of adaptation strategy to use in response to climate change. Much support is needed in terms of disseminating information and knowledge among smallholder farmers about climate change and its adaptation strategies. This can be possible through improving extension services, and providing credit to smallholder farmers
- Full Text:
- Date Issued: 2019
- Authors: Maya, Okuhle
- Date: 2019
- Subjects: Climatic changes Farms, Small
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17271 , vital:40871
- Description: Climate change has become indisputable judging from the observed global variations in precipitation, increases in average temperatures, rising average sea levels and melting of ice. The climate phenomenon has since evolved globally and it has been largely documented by scholars. Because of the increases in global temperatures, weather patterns have also changed. This change has resulted in debates on climate change as well as how to respond to it. Various scholars across the world have expressed their opinions about climate change; its causes, impacts and adaptation. In addition, there has been a growing body of literature and studies focusing on smallholder farmers’ perceptions of climate change. Without a doubt, climate change will and has left a group of people, communities and countries vulnerable. In particular, developing countries and poor communities in sub-Saharan Africa are expected to be affected the most by the impacts of climate change. This is mainly because of the region’s dependence on natural resources and their limited capacity to adapt. Literature further adds that vulnerability is on condition of the community’s socioeconomic characteristics and physical surroundings. Climate change variations pose a threat to the agricultural sector and food security of households relying on subsistence farming for survival. Climate variations such as decrease in rainfall and increased hot seasons have been reported to have led to a decline in food production, death of livestock and outbreaks human and animal diseases. The study’s main aim was to determine the smallholder farmers’ perceptions of climate change and adaptation strategies in Raymond Mhlaba, Port Saint Johns’ and Ingquza Hill local municipalities. Particularly, the study looked at the factors influencing these perceptions and the factors affecting the smallholder farmers’ choice of adaptation strategies used in response to climate change. Investigating perception provides insights into the fundamental drivers of behavioural changes in the face of climate change. On their part, adaptation options are greatly shaped by the nature of an individual’s behaviour. The study was carried out in 3 local municipalities (Raymond Mhlaba, Port St Johns’ and Ingquza Hill) in the Eastern Cape, South Africa. The research design applied in this study was cross sectional design where data are collected at a single point in time. Multistage sampling technique was used in selecting respondents from the local municipalities. Stratification was then done to group farmers according to their vi wards and locations. Lastly, purposive sampling was used to select households and smallholder farmers practising crop and livestock production. A total of 211 smallholder farmers constituted the sample size for the study. A close-ended questionnaire was used to conduct structured interviews of household heads. The study utilized both qualitative and quantitative approach. Data collected were coded and entered in Microsoft Excel and transferred to Statistical Package for Social Scientists (SPSS, version 25) for analyses. Descriptive statistics was used to determine the climate change perceptions of smallholder farmers and also to explore the adaptation strategies used by farmers to cope with the impacts of climate change. The findings were explained using frequencies, means and variances. Multinomial Logistic Regression (MNL) was used to determine the factors affecting the choice of adaptation strategies used by smallholder farmers and the probability that a farmer would choose a particular strategy. The results from the study revealed most of the respondents as being able to identify the perceived changes in climate with the environmental changes that they observed. The respondents perceived climate change as an increase in drought period, increase in average temperatures, decrease and variations in rainfall, shortened growing season, crop failure, pests and diseases. However, most of the smallholder farmers disagreed with the frequency of flood incidences as they have not experienced these in their areas. In terms of responses to these changes in climate, the smallholder farmers have used a number of adaptation strategies to cope. Most of the farmers used crop diversification, organic manure, soil and water conservation practices, while others simply did not adapt and some used all the available adaptation strategies identified in this study. The results from the MNL revealed that occupation, household size and years spent in school (education) generally had a positive influence on the choice of adaptation strategy used by smallholder farmers. On the other hand, age; farming systems and membership of a farmers’ association were negatively affecting the smallholder farmers’ choice of adaptation strategy to use in response to climate change. Much support is needed in terms of disseminating information and knowledge among smallholder farmers about climate change and its adaptation strategies. This can be possible through improving extension services, and providing credit to smallholder farmers
- Full Text:
- Date Issued: 2019
Pharmacological Evaluation and Medicinal Potential of Vachellia Karroo (Hayne) Banfi & Galasso Pods traditionally used to treat Sexually Transmitted Diseases in the Eastern Cape, South Africa.
- Authors: Maposa, Sandisiwe
- Date: 2019
- Subjects: Medicinal plants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14583 , vital:40017
- Description: Vachellia karroo is widely used in folk medicine in the Eastern Cape Province South Africa, however, the pods are usually discarded as waste. The current study was conducted to evaluate the phytochemical content and the antioxidant activity of V. karroo pods. The pods were extracted using acetone, distilled water, hexane and methanol. The total phenol, flavonoid, proanthocyanidin, alkaloid and saponin contents of the various extracts were determined spectrometrically and antioxidant activity was evaluated using inhibition of 2,2-diphenyl-1- picrylhydrazyl (DPPH), 2,2´-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid (ABTS), nitric oxide (NO) radicals, while total antioxidant capacity (TAC) was estimated by the phosphomolybdenum assay. V. karro pods had significant amounts of total phenols, flavonoids and proanthocynadin, although, proanthocynadin was not detected in the aqueous and hexane extracts. Methanol and acetone extracts showed higher phenolic, proanthocynadin and flavonoids contents (52.47 ± 6.82 and 29.31 ± 1.49), (334.8±85.1 and 231.22 ±1.80),(288±4.26 & 208.2±17.7) compared to the aqueous and hexane extracts. The alkaloid and saponin contents were 26.67 and 12.85 % respectively. The IC50 values of the methanol extract for DPPH, ABTS and total antioxidant capacity (TAC) were 0.345, 0.017 and 0.116 mg/mL, respectively. Methanol extract of V. karroo pod showed higher polyphenolic content of all the extracts analysed with corresponding strong free radical scavenging potential. These underutilized pods could serve as a new source of antioxidant compounds which could help in combating various ailments. The great antioxidant activity displayed by V. karroo pods extract supports the therapeutic use of this plant in traditional medicine and are attributed to the phytochemical content.The current information suggests that extracts from Vachellia karroo pods might be a ix cheap potential source of natural antioxidants that could be of great importance for the treatment of free radical related diseases. Furthermore, it makes a case for the utilization of the pods instead of discarding them as waste materials. The evaluation of antimicrobial potential of Vachellia karroo extracts was carried out using agar dilution assay against 8 bacterial strains-4 gram-positive [ Enterococcus faecalis (ATCC 29212), Staphylococcus aureus (OK), Bacillus subtilis KZN, Bacillus cereus, and Streptococcus pyogenes] and 4 gram-negative strains[ Vibrio cholera, Klebsiella pneumonia (ATCC 4352), Pseudomonas aeruginosa (ATCC 19582), Salmonella typhi (OK) ]. Six fungal isolates[ Trichophyton mucoides ATCC 201382, Candida albicans (ATCC 10231), Candida glabatra, Penicillium chrysogenum, Aspergillus fumigatus, Penicillum aurantiogriseum] were usedor antifungal assessment. The methanol extract exhibited broad-spectrum activity, with Gram-positive strains being more sensitive than Gram-negative strains. The extracts also showed great inhibition against Candida albicans the fungal isolate responsible for causing candidiasis in women. Since the pods showed promising antimicrobial activity, they could serve as a cheap source for the treatment and management of these sexually transmitted infections. The brine shrimp toxicity test revealed successful hatching of the cysts was in the order: Aqueous extract> methanol extract> hexane extract> acetone extract. The hatching of nauplii was in a concentration dependent fashion, with hatching success decreasing with increase in concentration of extracts. Lethality of extracts determined based on Meyerʼs index of toxicity, showed that the acetone and hexane extracts of V. karroo were moderately toxic. The results of this study indicated that aqueous and methanolic extracts of Vachellia karroo pods were not toxic, therefore supporting its traditional therapeutic usage. This implies that rather than discard x the pods as is waste as it being currently done, Vachellia karroo pods could be salvaged and processed along with the leaves, thus reducing environmental pollution. Proximate parameters (moisture, ash, crude fibre, crude fat, proteins, and carbohydrate) were evaluated using ALASA methods, and elemental analysis by ICP-OES technique. Nutritional analysis showed that V. karroo pods had low content of crude fat and high content of crude fibre, ash, crude protein, and carbohydrate sufficient to meet the recommended dietary allowances. The pods were rich in major minerals Ca, K, P and Mg, with sufficient amount of trace elements Na, Fe, Zn, and Cu. The outcome of this study suggests that Vachellia karroo pods have good nutritional potentials to support or complement the recommended dietary allowance and could be a cheap source of essential nutrients that could help in ameliorating most nutritional challenges as well as contribute remarkably to the amount of nutrient intake in human and animal diets.
- Full Text:
- Date Issued: 2019
- Authors: Maposa, Sandisiwe
- Date: 2019
- Subjects: Medicinal plants
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14583 , vital:40017
- Description: Vachellia karroo is widely used in folk medicine in the Eastern Cape Province South Africa, however, the pods are usually discarded as waste. The current study was conducted to evaluate the phytochemical content and the antioxidant activity of V. karroo pods. The pods were extracted using acetone, distilled water, hexane and methanol. The total phenol, flavonoid, proanthocyanidin, alkaloid and saponin contents of the various extracts were determined spectrometrically and antioxidant activity was evaluated using inhibition of 2,2-diphenyl-1- picrylhydrazyl (DPPH), 2,2´-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid (ABTS), nitric oxide (NO) radicals, while total antioxidant capacity (TAC) was estimated by the phosphomolybdenum assay. V. karro pods had significant amounts of total phenols, flavonoids and proanthocynadin, although, proanthocynadin was not detected in the aqueous and hexane extracts. Methanol and acetone extracts showed higher phenolic, proanthocynadin and flavonoids contents (52.47 ± 6.82 and 29.31 ± 1.49), (334.8±85.1 and 231.22 ±1.80),(288±4.26 & 208.2±17.7) compared to the aqueous and hexane extracts. The alkaloid and saponin contents were 26.67 and 12.85 % respectively. The IC50 values of the methanol extract for DPPH, ABTS and total antioxidant capacity (TAC) were 0.345, 0.017 and 0.116 mg/mL, respectively. Methanol extract of V. karroo pod showed higher polyphenolic content of all the extracts analysed with corresponding strong free radical scavenging potential. These underutilized pods could serve as a new source of antioxidant compounds which could help in combating various ailments. The great antioxidant activity displayed by V. karroo pods extract supports the therapeutic use of this plant in traditional medicine and are attributed to the phytochemical content.The current information suggests that extracts from Vachellia karroo pods might be a ix cheap potential source of natural antioxidants that could be of great importance for the treatment of free radical related diseases. Furthermore, it makes a case for the utilization of the pods instead of discarding them as waste materials. The evaluation of antimicrobial potential of Vachellia karroo extracts was carried out using agar dilution assay against 8 bacterial strains-4 gram-positive [ Enterococcus faecalis (ATCC 29212), Staphylococcus aureus (OK), Bacillus subtilis KZN, Bacillus cereus, and Streptococcus pyogenes] and 4 gram-negative strains[ Vibrio cholera, Klebsiella pneumonia (ATCC 4352), Pseudomonas aeruginosa (ATCC 19582), Salmonella typhi (OK) ]. Six fungal isolates[ Trichophyton mucoides ATCC 201382, Candida albicans (ATCC 10231), Candida glabatra, Penicillium chrysogenum, Aspergillus fumigatus, Penicillum aurantiogriseum] were usedor antifungal assessment. The methanol extract exhibited broad-spectrum activity, with Gram-positive strains being more sensitive than Gram-negative strains. The extracts also showed great inhibition against Candida albicans the fungal isolate responsible for causing candidiasis in women. Since the pods showed promising antimicrobial activity, they could serve as a cheap source for the treatment and management of these sexually transmitted infections. The brine shrimp toxicity test revealed successful hatching of the cysts was in the order: Aqueous extract> methanol extract> hexane extract> acetone extract. The hatching of nauplii was in a concentration dependent fashion, with hatching success decreasing with increase in concentration of extracts. Lethality of extracts determined based on Meyerʼs index of toxicity, showed that the acetone and hexane extracts of V. karroo were moderately toxic. The results of this study indicated that aqueous and methanolic extracts of Vachellia karroo pods were not toxic, therefore supporting its traditional therapeutic usage. This implies that rather than discard x the pods as is waste as it being currently done, Vachellia karroo pods could be salvaged and processed along with the leaves, thus reducing environmental pollution. Proximate parameters (moisture, ash, crude fibre, crude fat, proteins, and carbohydrate) were evaluated using ALASA methods, and elemental analysis by ICP-OES technique. Nutritional analysis showed that V. karroo pods had low content of crude fat and high content of crude fibre, ash, crude protein, and carbohydrate sufficient to meet the recommended dietary allowances. The pods were rich in major minerals Ca, K, P and Mg, with sufficient amount of trace elements Na, Fe, Zn, and Cu. The outcome of this study suggests that Vachellia karroo pods have good nutritional potentials to support or complement the recommended dietary allowance and could be a cheap source of essential nutrients that could help in ameliorating most nutritional challenges as well as contribute remarkably to the amount of nutrient intake in human and animal diets.
- Full Text:
- Date Issued: 2019
Phase Plane Analysis of Linear Systems in Dynamic Mathematical Models
- Authors: Marange, Simukai Daniel
- Date: 2019
- Subjects: Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14715 , vital:40064
- Description: A plethora of dynamic mathematical models exist and to understand and master all of them would be a gargantuan task. The author had, nonetheless, attempted to outline some of the methods used to analyse linear systems in modeling. Systems techniques are fundamental to current research in molecular cell-biology. The systems-approach stands in stark contrast to the historically, reductionist paradigm of molecular biology. Field work can be very dangerous. The main purpose of this study was to come up with the best analysis that would be used without going to the real field and thus saving time, money and risks associated with remote field localities. This research showed that the best analysis depends on the nature of the objectives intended to be solved by the model. Phase plane analysis on linear systems assisted in gaining deeper knowledge on the characteristics of such systems. This work analysed some dynamic models looking at phase planes, bifurcation, sensitivity and stability. The research provided a qualitative analysis of the processes not a numerical analysis.
- Full Text:
- Date Issued: 2019
- Authors: Marange, Simukai Daniel
- Date: 2019
- Subjects: Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14715 , vital:40064
- Description: A plethora of dynamic mathematical models exist and to understand and master all of them would be a gargantuan task. The author had, nonetheless, attempted to outline some of the methods used to analyse linear systems in modeling. Systems techniques are fundamental to current research in molecular cell-biology. The systems-approach stands in stark contrast to the historically, reductionist paradigm of molecular biology. Field work can be very dangerous. The main purpose of this study was to come up with the best analysis that would be used without going to the real field and thus saving time, money and risks associated with remote field localities. This research showed that the best analysis depends on the nature of the objectives intended to be solved by the model. Phase plane analysis on linear systems assisted in gaining deeper knowledge on the characteristics of such systems. This work analysed some dynamic models looking at phase planes, bifurcation, sensitivity and stability. The research provided a qualitative analysis of the processes not a numerical analysis.
- Full Text:
- Date Issued: 2019
Rural household dietary diversity and food security in Raymond Mhlaba local municipality
- Authors: Mnukwa, Minentle Lwando
- Date: 2019
- Subjects: Food security
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17282 , vital:40872
- Description: In order to formulate or implement relevant food security programmes in rural areas, it is important to have a deep understanding of the food security status of rural households. Accordingly, this study was conducted to assess the food security status of rural households in Raymond Mhlaba Local Municipality. The study also sought to identify the socio-economic characteristics that influence household food security status. The research relied on primary data. Primary data were collected by using a structured questionnaire, which covered both demographic features of respondent households, and their recent food consumption patterns. The household survey was conducted among 272 participants of Raymond Mhlaba Local Municipality. Statistical tools employed in this study included both descriptive and inferential statistics. The main descriptive statistics used were frequency tables, means and percentages in relation to a number of demographic characteristics and food security indicators. The main indicator of food security/insecurity used in the study was the Household Dietary Diversity Score (HDDS). After calculating the HDDS for each household, households were defined as either food secure or insecure depending on whether their HDDS was above or below the average HDDS. A logistic regression model (binary or dichotomous) was then used to identify socio-economic factors that influence some households to have above-average rather than below-average food security levels. The Binary logistic regression model revealed that four out of eight variables included in the model were significant in explaining the variation in the food security situation of households in the study areas, namely age of household head, education level of household head, household income and household size. Of these, the first three were positively associated with aboveaverage food security status, while household size had a negative association. A Tobit model was further used to identify the determinants of the household dietary diversity score. The exact same variables were significant from the Tobit analysis, and in the same manner.
- Full Text:
- Date Issued: 2019
- Authors: Mnukwa, Minentle Lwando
- Date: 2019
- Subjects: Food security
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/17282 , vital:40872
- Description: In order to formulate or implement relevant food security programmes in rural areas, it is important to have a deep understanding of the food security status of rural households. Accordingly, this study was conducted to assess the food security status of rural households in Raymond Mhlaba Local Municipality. The study also sought to identify the socio-economic characteristics that influence household food security status. The research relied on primary data. Primary data were collected by using a structured questionnaire, which covered both demographic features of respondent households, and their recent food consumption patterns. The household survey was conducted among 272 participants of Raymond Mhlaba Local Municipality. Statistical tools employed in this study included both descriptive and inferential statistics. The main descriptive statistics used were frequency tables, means and percentages in relation to a number of demographic characteristics and food security indicators. The main indicator of food security/insecurity used in the study was the Household Dietary Diversity Score (HDDS). After calculating the HDDS for each household, households were defined as either food secure or insecure depending on whether their HDDS was above or below the average HDDS. A logistic regression model (binary or dichotomous) was then used to identify socio-economic factors that influence some households to have above-average rather than below-average food security levels. The Binary logistic regression model revealed that four out of eight variables included in the model were significant in explaining the variation in the food security situation of households in the study areas, namely age of household head, education level of household head, household income and household size. Of these, the first three were positively associated with aboveaverage food security status, while household size had a negative association. A Tobit model was further used to identify the determinants of the household dietary diversity score. The exact same variables were significant from the Tobit analysis, and in the same manner.
- Full Text:
- Date Issued: 2019
Sedimentology and shale gas potential of the Ecca Group, Karoo Supergroup in the Eastern Cape, South Africa
- Authors: Nemanashi , Tshisikhaiwe
- Date: 2019
- Subjects: Sedimentology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14616 , vital:40023
- Description: The aim of the study was to establish a deeper understanding on the stratigraphy, sedimentology, petrology, organic geochemistry and diagenesis of the Ecca Group, and to provide new insight on the shale gas occurrence and potential of the Ecca Group, Karoo Supergroup in the southern Karoo Basin. The Ecca Group stratigraphy is divided into five formations from the bottom upwards, namely the Prince Albert, Whitehill, Collingham, Ripon and the Fort Brown Formations. The stratigraphy of the five studied stratigraphy’s formations is now sub-divided into two new different members each. These subdivision was based on field investigation of lithological features, sedimentary structures, facies characteristics and stratigraphic correlation points. Each member has been assigned a lithological name. Sixteen sedimentary facies have been identified in the study area and were subdivided into six distinctive facies associations (FA 1, FA 2, FA 3, FA 4, FA 5 and FA 6). Sedimentological characteristics of facies associations identified indicate that the Ecca Group sediments initially accumulated in a deep marine environment, progressed through turbidite, shallow marine and ended in lacustrine and deltaic environments. The stratigraphic succession of the Ecca Group constitutes a perfect regression sequence, indicating that the marine water gradually retreated and the sea-level gradually dropped. Grain size analysis was performed on twenty four Ecca Group sandstone samples. Statistical parameters of grain-size statistical parameters, linear discriminate functions, passega diagrams and bivariate analysis were used to reveal the hydrodynamic conditions and depositional environments. The results indicated that the Ecca Group sandstones are mostly fine to very fine grained, near-symmetrical, mesokurtic and indicative of dominance of low energy environments. The linear discriminate function analysis for the Prince Albert, Whitehill, Collingham and Ripon Formations samples indicates that the majority of the deposits were by turbidity currents all in a deep marine environment; whilst of the Fort Brown Formation samples are lacustrine/deltaic deposits. The depositional mechanism C-M plot indicates that majority of the Ecca Group sediments clustered in the PQ and QR field suggesting deposition mainly by suspension, rolling or saltation as well as graded suspension. Modal mineral composition analysis indicates that the main framework grains of the Ecca Group sandstones are quartz, feldspar as well as lithic fragments derived from metamorphic, igneous and sedimentary rocks with a few from volcanic origin. The Ecca Group sandstones iii are immature compositionally and can be classified as feldspathic wackes and lithic wackes. The QFL ternary diagram revealed a dissected and recycled orogen arc provenance; whereas QmFLt ternary diagram point to dissected arc and transitional arc sources to an active continental margin as well as recycled provenance. These provenance characteristics suggest a metamorphic and plutonic terrains influence as the main source rock with minor debris derived from recycled sedimentary rocks. The weathering diagram and semi-quantitative weathering index suggests that the sandstones from the Ecca are mostly from a plutonic source area under arid to humid climatic conditions. The detrital modal compositions of these Ecca Group sandstones are related to a strike-slip setting, back arc to continental margin setting. Diagenetic features of the Ecca sandstones and shales are subdivided into early, late (burial) and uplift-related diagenetic stages. Mechanical compaction, recrystallization, cementation, replacement and the dissolution of framework grains or cements are some of the main diagenetic processes that largely affected the Ecca sediments. Early diagenetic processes include cementation, point/planar contact, formation of pyrite, hematite cements and mineral inversions. Recrystallization, replacement, compaction, overgrowth, albitization, seritisation, illitization, concave-convex and suture contacts as well as dissolution took place mostly in the later diagenetic stage due to increase of temperature and pressure as burial depth increased. The uplift-related diagenetic stage was mostly affected by deformation and fracturing, calcitization, dissolution, erosion and weathering. Diagenetic processes largely affected the porosity and permeability of the reservoir rock properties of the Ecca Group. Organic geochemistry results indicate that the sediments were highly weathered and the TOC values ranging from 0.10 to 7.35 wt% with mostly less than 0.5%, which indicate the source rocks have poor oil potential. The majority of the Ecca Shales have HI values less than 50 mg HC/g, TOC indicating Type-IV kerogen mostly derived from reworked organic matter with very little hydrocarbon generation potential. The relatively high Tmax (oC) and vitrinite reflective values indicate that most shales are thermally over-matured thus they have low hydrocarbon pontential.
- Full Text:
- Date Issued: 2019
- Authors: Nemanashi , Tshisikhaiwe
- Date: 2019
- Subjects: Sedimentology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/14616 , vital:40023
- Description: The aim of the study was to establish a deeper understanding on the stratigraphy, sedimentology, petrology, organic geochemistry and diagenesis of the Ecca Group, and to provide new insight on the shale gas occurrence and potential of the Ecca Group, Karoo Supergroup in the southern Karoo Basin. The Ecca Group stratigraphy is divided into five formations from the bottom upwards, namely the Prince Albert, Whitehill, Collingham, Ripon and the Fort Brown Formations. The stratigraphy of the five studied stratigraphy’s formations is now sub-divided into two new different members each. These subdivision was based on field investigation of lithological features, sedimentary structures, facies characteristics and stratigraphic correlation points. Each member has been assigned a lithological name. Sixteen sedimentary facies have been identified in the study area and were subdivided into six distinctive facies associations (FA 1, FA 2, FA 3, FA 4, FA 5 and FA 6). Sedimentological characteristics of facies associations identified indicate that the Ecca Group sediments initially accumulated in a deep marine environment, progressed through turbidite, shallow marine and ended in lacustrine and deltaic environments. The stratigraphic succession of the Ecca Group constitutes a perfect regression sequence, indicating that the marine water gradually retreated and the sea-level gradually dropped. Grain size analysis was performed on twenty four Ecca Group sandstone samples. Statistical parameters of grain-size statistical parameters, linear discriminate functions, passega diagrams and bivariate analysis were used to reveal the hydrodynamic conditions and depositional environments. The results indicated that the Ecca Group sandstones are mostly fine to very fine grained, near-symmetrical, mesokurtic and indicative of dominance of low energy environments. The linear discriminate function analysis for the Prince Albert, Whitehill, Collingham and Ripon Formations samples indicates that the majority of the deposits were by turbidity currents all in a deep marine environment; whilst of the Fort Brown Formation samples are lacustrine/deltaic deposits. The depositional mechanism C-M plot indicates that majority of the Ecca Group sediments clustered in the PQ and QR field suggesting deposition mainly by suspension, rolling or saltation as well as graded suspension. Modal mineral composition analysis indicates that the main framework grains of the Ecca Group sandstones are quartz, feldspar as well as lithic fragments derived from metamorphic, igneous and sedimentary rocks with a few from volcanic origin. The Ecca Group sandstones iii are immature compositionally and can be classified as feldspathic wackes and lithic wackes. The QFL ternary diagram revealed a dissected and recycled orogen arc provenance; whereas QmFLt ternary diagram point to dissected arc and transitional arc sources to an active continental margin as well as recycled provenance. These provenance characteristics suggest a metamorphic and plutonic terrains influence as the main source rock with minor debris derived from recycled sedimentary rocks. The weathering diagram and semi-quantitative weathering index suggests that the sandstones from the Ecca are mostly from a plutonic source area under arid to humid climatic conditions. The detrital modal compositions of these Ecca Group sandstones are related to a strike-slip setting, back arc to continental margin setting. Diagenetic features of the Ecca sandstones and shales are subdivided into early, late (burial) and uplift-related diagenetic stages. Mechanical compaction, recrystallization, cementation, replacement and the dissolution of framework grains or cements are some of the main diagenetic processes that largely affected the Ecca sediments. Early diagenetic processes include cementation, point/planar contact, formation of pyrite, hematite cements and mineral inversions. Recrystallization, replacement, compaction, overgrowth, albitization, seritisation, illitization, concave-convex and suture contacts as well as dissolution took place mostly in the later diagenetic stage due to increase of temperature and pressure as burial depth increased. The uplift-related diagenetic stage was mostly affected by deformation and fracturing, calcitization, dissolution, erosion and weathering. Diagenetic processes largely affected the porosity and permeability of the reservoir rock properties of the Ecca Group. Organic geochemistry results indicate that the sediments were highly weathered and the TOC values ranging from 0.10 to 7.35 wt% with mostly less than 0.5%, which indicate the source rocks have poor oil potential. The majority of the Ecca Shales have HI values less than 50 mg HC/g, TOC indicating Type-IV kerogen mostly derived from reworked organic matter with very little hydrocarbon generation potential. The relatively high Tmax (oC) and vitrinite reflective values indicate that most shales are thermally over-matured thus they have low hydrocarbon pontential.
- Full Text:
- Date Issued: 2019
Sequencing, assembly and annotation of the mitochondrial and plastid genomes of Gelidium pristoides (Turner) Kützing from Kenton-on-Sea, South Africa
- Authors: Mangali, Sandisiwe
- Date: 2019
- Subjects: Gelidium -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19109 , vital:39883
- Description: The genome is the complete set of an organism's hereditary information that contains all the information necessary for the functioning of that organism. Complete nuclear, mitochondrial and plastid DNA constitute the three main types of genomes which play interconnected roles in an organism. Genome sequencing enables researchers to understand the regulation and expression of the various genes and the proteins they encode. It allows researchers to extract and analyse genes of interests for a variety of studies including molecular, biotechnological, bioinformatics and conservation and evolutionary studies. Genome sequencing of Rhodophyta has received little attention. To date, no published studies are focusing on both whole genome sequencing and sequencing of the organellar genomes of Rhodophyta species found in along the South African coastline. This study focused on genome sequencing, assembly and annotation mitochondrial and plastid genomes of Gelidium pristoides. Gelidium pristoides was collected from Kenton-on-Sea and was morphologically identified at Rhodes University. Its genomic DNA was extracted using the Nucleospin® Plant II kit and quantified using Qubit 2.0, Nanodrop and 1% agarose gel electrophoresis. The Ion Plus Fragment Library kit was used for the preparation of a 600 bp library, which was sequenced in two separate runs through the Ion S5 platform. The produced reads were quality-controlled through the Ion Torrent server version 5.6. and assessed using the FASTQC program. The SPAdes version 3.11.1 assembler was used to assemble the quality-controlled reads, and the resultant genome assembly was quality-assessed using the QUAST 4.1 software. The mitochondrial genome was selected from the produced Gelidium pristoides draft genome using mitochondrial genomes of other Gelidiales as search queries on the local BLAST algorithm of the BioEdit software. Contigs matching the organellar genomes were ordered according to the mitochondrial genomes of other Gelidiales using the trial version of Geneious R11.12 software. The plastid genome was also selected following the same approach but using plastid genomes of Gelidium elegans and Gelidium vagum as search queries. Gaps observed in the organellar genomes were closed by amplification of the relevant gap using polymerase chain reaction with newly designed primers and Sanger sequencing. Open reading frames for both organellar genomes were annotated using the NCBI ORF-Finder and alignments obtained from BlastN and BlastX searches from the NCBI database, while the tRNAs and rRNAs were identified using the tRNAscan-SE1.21 vi and the RNAmmer 1.2 servers. The circular physical map of the mitochondrial genome was constructed using the CGView server. Lastly, in silico analysis of cytochrome c oxidase 3 and Heat Shock Protein 70 was performed using the PRIMO and the SWISS-MODEL pipelines respectively. Their phylogenies were analysed through Clustal omega and the trees viewed on TreeView 1.6.6 software. Qubit and Nanodrop genomic DNA qualification revealed A260/A280 and A230/A260 ratios of 1.81 and 1.52 respectively. The 1% agarose gel electrophoresis further confirmed the good quality of the genomic DNA used for library preparation and sequencing. Pre-assembly quality control of reads resulted in a total of 30 792 074 high-quality reads which were assembled into a total of 94140 contigs, making up an estimated genome length of 217.06 Mb. The largest contig covered up to 13.17 kb of the draft genome, and an N50 statistic value of 3.17 kb was obtained. The G.pristoides mitochondrial genome mapped into a circular molecule of 25012 bp, with an overall GC content of 31.04% and a total of 45 genes distributed into 20 tRNA-coding, 2 rRNAcoding genes and 23 protein-coding genes, mostly adopting the modified genetic code of Rhodophyta. The SecY and rps12 genes overlapped by 41 bp. This study presents a partial plastid genome composed of 89 (38%) fully annotated genes, of which 71 are protein-coding, and 18 are distributed among 15 tRNA-coding, 2 rRNA-coding and 1 RNaseP RNA-coding genes. Sixty-one (26%) partial protein-coding genes were predicted, while approximately 84 (36%) genes are not yet predicted. In silico analysis of the cytochrome c oxidase and heat shock protein 70 showed that the gene sequences obtained in this study and the resultant transcribed protein have sequences and structures that are similar to those from several other different species, thus validating the integrity of the genome sequences. This study provides genomic data necessary for understanding the genomic constituent of G.pristoides and serve as a foundation for studies of individual genes and for resolving evolutionary relationships.
- Full Text:
- Date Issued: 2019
- Authors: Mangali, Sandisiwe
- Date: 2019
- Subjects: Gelidium -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/19109 , vital:39883
- Description: The genome is the complete set of an organism's hereditary information that contains all the information necessary for the functioning of that organism. Complete nuclear, mitochondrial and plastid DNA constitute the three main types of genomes which play interconnected roles in an organism. Genome sequencing enables researchers to understand the regulation and expression of the various genes and the proteins they encode. It allows researchers to extract and analyse genes of interests for a variety of studies including molecular, biotechnological, bioinformatics and conservation and evolutionary studies. Genome sequencing of Rhodophyta has received little attention. To date, no published studies are focusing on both whole genome sequencing and sequencing of the organellar genomes of Rhodophyta species found in along the South African coastline. This study focused on genome sequencing, assembly and annotation mitochondrial and plastid genomes of Gelidium pristoides. Gelidium pristoides was collected from Kenton-on-Sea and was morphologically identified at Rhodes University. Its genomic DNA was extracted using the Nucleospin® Plant II kit and quantified using Qubit 2.0, Nanodrop and 1% agarose gel electrophoresis. The Ion Plus Fragment Library kit was used for the preparation of a 600 bp library, which was sequenced in two separate runs through the Ion S5 platform. The produced reads were quality-controlled through the Ion Torrent server version 5.6. and assessed using the FASTQC program. The SPAdes version 3.11.1 assembler was used to assemble the quality-controlled reads, and the resultant genome assembly was quality-assessed using the QUAST 4.1 software. The mitochondrial genome was selected from the produced Gelidium pristoides draft genome using mitochondrial genomes of other Gelidiales as search queries on the local BLAST algorithm of the BioEdit software. Contigs matching the organellar genomes were ordered according to the mitochondrial genomes of other Gelidiales using the trial version of Geneious R11.12 software. The plastid genome was also selected following the same approach but using plastid genomes of Gelidium elegans and Gelidium vagum as search queries. Gaps observed in the organellar genomes were closed by amplification of the relevant gap using polymerase chain reaction with newly designed primers and Sanger sequencing. Open reading frames for both organellar genomes were annotated using the NCBI ORF-Finder and alignments obtained from BlastN and BlastX searches from the NCBI database, while the tRNAs and rRNAs were identified using the tRNAscan-SE1.21 vi and the RNAmmer 1.2 servers. The circular physical map of the mitochondrial genome was constructed using the CGView server. Lastly, in silico analysis of cytochrome c oxidase 3 and Heat Shock Protein 70 was performed using the PRIMO and the SWISS-MODEL pipelines respectively. Their phylogenies were analysed through Clustal omega and the trees viewed on TreeView 1.6.6 software. Qubit and Nanodrop genomic DNA qualification revealed A260/A280 and A230/A260 ratios of 1.81 and 1.52 respectively. The 1% agarose gel electrophoresis further confirmed the good quality of the genomic DNA used for library preparation and sequencing. Pre-assembly quality control of reads resulted in a total of 30 792 074 high-quality reads which were assembled into a total of 94140 contigs, making up an estimated genome length of 217.06 Mb. The largest contig covered up to 13.17 kb of the draft genome, and an N50 statistic value of 3.17 kb was obtained. The G.pristoides mitochondrial genome mapped into a circular molecule of 25012 bp, with an overall GC content of 31.04% and a total of 45 genes distributed into 20 tRNA-coding, 2 rRNAcoding genes and 23 protein-coding genes, mostly adopting the modified genetic code of Rhodophyta. The SecY and rps12 genes overlapped by 41 bp. This study presents a partial plastid genome composed of 89 (38%) fully annotated genes, of which 71 are protein-coding, and 18 are distributed among 15 tRNA-coding, 2 rRNA-coding and 1 RNaseP RNA-coding genes. Sixty-one (26%) partial protein-coding genes were predicted, while approximately 84 (36%) genes are not yet predicted. In silico analysis of the cytochrome c oxidase and heat shock protein 70 showed that the gene sequences obtained in this study and the resultant transcribed protein have sequences and structures that are similar to those from several other different species, thus validating the integrity of the genome sequences. This study provides genomic data necessary for understanding the genomic constituent of G.pristoides and serve as a foundation for studies of individual genes and for resolving evolutionary relationships.
- Full Text:
- Date Issued: 2019