A comparison of muscle fatigue responses between static and quasi-static exertions
- Authors: Nel, Conrad
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3475 , vital:20502
- Description: Background: This study examined localized muscle fatigue responses from sub-maximal quasi-static work protocols and additionally how it compares to purely static work. The goal was to produce research that enhances the understanding of the demands on muscles during manual work to aid in preventing injuries stemming from localized muscle fatigue. Injury rates remain a problem in manual labour sectors, particularly for the lower back and shoulder regions for the manufacturing, service and construction sectors, and for knee and elbow flexors in the sports sector. Few studies have looked at quasi-static work and what the resulting fatigue characteristics are, especially when compared to purely static or purely dynamic work. This comparison is particularly important due to the fact that risk assessment tools that are currently utilized to assess risk in the working environment are based on fatigue studies that focus on purely static or purely dynamic work. This requires attention as many working situations are neither static nor dynamic, but rather quasi-static in nature, with aspects of both dynamic and static muscle components. The scope of this study only encompasses the comparison between purely static and quasi-static work. Objectives: This study had two objectives, firstly, to determine what the fatigue characteristics of quasi-static work are and how it compares to fully static work. Secondly, to determine whether an underlying static component within an otherwise dynamic muscle force affects localized muscle fatigue compared to quasi-static work that has equal amounts of effort but with no underlying static component. Methods: Four experimental conditions were tested, each on four muscles, namely the medial deltoid, bicep brachii, bicep femoris and erector spinae muscles. To test the two objectives of this study, 16 volunteers performed a five minute fatigue protocol, that either entailed a fully static condition which involved: 1) producing a steady force at 25 percent of maximum voluntary force, 2) a quasi-static condition with fully dynamic muscle force that alternates the required force level between zero and 50 percent of maximum force, 3) a quasi-static condition with an underlying static component of five percent of maximum force, or 4) a quasi-static condition with a large underlying static component of 15 percent of maximum force. All the experimental conditions in this study had the same average workload of 25 percent of maximum voluntary force over time and thus total workload. The dependant variables of interest were ratings of perceived exertion, changes in muscle fibre recruitment (% of maximum EMG activity), maximum force and center frequency from a spectral analysis of the surface electromyography. These were measured throughout the protocols at one minute intervals to determine how muscle fatigue progressed, and how the fatigue responses differed between conditions. Results: The data from comparing fully static and quasi-static work showed that of the variables measured, the rating of perceived exertion (RPE) and maximum force data indicated that for bicep brachii and bicep femoris muscles, fully static work is more fatiguing than work that alternates between zero and 50 percent of maximum force. The results for the medial deltoid and erector spinae muscles were inconclusive. The findings regarding the comparison between quasi-static conditions with and without an underlying static component revealed that an underlying static component results in greater fatigue when compared to a quasi-static condition with no static component. The results may also suggest that a larger static component coupled with a smaller peak force results in less fatigue than a condition with a small underlying static component coupled with a higher peak force in some scenarios, provided total work is kept constant. All conditions had to have the same workload in order to be validly compared and thus the condition with a larger underlying static component had a lower peak force compared to the condition with no underlying static component or the condition with a small underlying static component. Conclusions: This study presented evidence that quasi-static work does not induce fatigue when measured by RPE and drop in maximum force in the same way as static work. Additionally, the results indicate that a larger underlying static component does not necessarily fatigue a muscle faster if the overall workload is kept constant. However, the results do suggest that any underlying static component will increase the demand on a muscle when compared to a muscle exertion with no static component. When considering the available literature on how muscles fatigue during low level static contractions, the current understanding is that the larger the force during a static contraction, the faster the onset of fatigue and decrements in performance occur. The results of this study suggest that this same relationship cannot be applied to quasi-static work where an underlying static component is part of an otherwise dynamic muscle force. Thus total workload or peak force may play a larger role than the static muscle exertion in some scenarios.
- Full Text:
- Authors: Nel, Conrad
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3475 , vital:20502
- Description: Background: This study examined localized muscle fatigue responses from sub-maximal quasi-static work protocols and additionally how it compares to purely static work. The goal was to produce research that enhances the understanding of the demands on muscles during manual work to aid in preventing injuries stemming from localized muscle fatigue. Injury rates remain a problem in manual labour sectors, particularly for the lower back and shoulder regions for the manufacturing, service and construction sectors, and for knee and elbow flexors in the sports sector. Few studies have looked at quasi-static work and what the resulting fatigue characteristics are, especially when compared to purely static or purely dynamic work. This comparison is particularly important due to the fact that risk assessment tools that are currently utilized to assess risk in the working environment are based on fatigue studies that focus on purely static or purely dynamic work. This requires attention as many working situations are neither static nor dynamic, but rather quasi-static in nature, with aspects of both dynamic and static muscle components. The scope of this study only encompasses the comparison between purely static and quasi-static work. Objectives: This study had two objectives, firstly, to determine what the fatigue characteristics of quasi-static work are and how it compares to fully static work. Secondly, to determine whether an underlying static component within an otherwise dynamic muscle force affects localized muscle fatigue compared to quasi-static work that has equal amounts of effort but with no underlying static component. Methods: Four experimental conditions were tested, each on four muscles, namely the medial deltoid, bicep brachii, bicep femoris and erector spinae muscles. To test the two objectives of this study, 16 volunteers performed a five minute fatigue protocol, that either entailed a fully static condition which involved: 1) producing a steady force at 25 percent of maximum voluntary force, 2) a quasi-static condition with fully dynamic muscle force that alternates the required force level between zero and 50 percent of maximum force, 3) a quasi-static condition with an underlying static component of five percent of maximum force, or 4) a quasi-static condition with a large underlying static component of 15 percent of maximum force. All the experimental conditions in this study had the same average workload of 25 percent of maximum voluntary force over time and thus total workload. The dependant variables of interest were ratings of perceived exertion, changes in muscle fibre recruitment (% of maximum EMG activity), maximum force and center frequency from a spectral analysis of the surface electromyography. These were measured throughout the protocols at one minute intervals to determine how muscle fatigue progressed, and how the fatigue responses differed between conditions. Results: The data from comparing fully static and quasi-static work showed that of the variables measured, the rating of perceived exertion (RPE) and maximum force data indicated that for bicep brachii and bicep femoris muscles, fully static work is more fatiguing than work that alternates between zero and 50 percent of maximum force. The results for the medial deltoid and erector spinae muscles were inconclusive. The findings regarding the comparison between quasi-static conditions with and without an underlying static component revealed that an underlying static component results in greater fatigue when compared to a quasi-static condition with no static component. The results may also suggest that a larger static component coupled with a smaller peak force results in less fatigue than a condition with a small underlying static component coupled with a higher peak force in some scenarios, provided total work is kept constant. All conditions had to have the same workload in order to be validly compared and thus the condition with a larger underlying static component had a lower peak force compared to the condition with no underlying static component or the condition with a small underlying static component. Conclusions: This study presented evidence that quasi-static work does not induce fatigue when measured by RPE and drop in maximum force in the same way as static work. Additionally, the results indicate that a larger underlying static component does not necessarily fatigue a muscle faster if the overall workload is kept constant. However, the results do suggest that any underlying static component will increase the demand on a muscle when compared to a muscle exertion with no static component. When considering the available literature on how muscles fatigue during low level static contractions, the current understanding is that the larger the force during a static contraction, the faster the onset of fatigue and decrements in performance occur. The results of this study suggest that this same relationship cannot be applied to quasi-static work where an underlying static component is part of an otherwise dynamic muscle force. Thus total workload or peak force may play a larger role than the static muscle exertion in some scenarios.
- Full Text:
A longitudinal study of DNS traffic: understanding current DNS practice and abuse
- Authors: Van Zyl, Ignus
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3707 , vital:20537
- Description: This thesis examines a dataset spanning 21 months, containing 3,5 billion DNS packets. Traffic on TCP and UDP port 53, was captured on a production /24 IP block. The purpose of this thesis is twofold. The first is to create an understanding of current practice and behavior within the DNS infrastructure, the second to explore current threats faced by the DNS and the various systems that implement it. This is achieved by drawing on analysis and observations from the captured data. Aspects of the operation of DNS on the greater Internet are considered in this research with reference to the observed trends in the dataset, A thorough analysis of current DNS TTL implementation is made with respect to all response traffic, as well as sections looking at observed DNS TTL values for ,za domain replies and NX DOMAIN flagged replies. This thesis found that TTL values implemented are much lower than has been recommended in previous years, and that the TTL decrease is prevalent in most, but not all EE TTL implementation. With respect to the nature of DNS operations, this thesis also concerns itself with an analysis of the geoloeation of authoritative servers for local (,za) domains, and offers further observations towards the latency generated by the choice of authoritative server location for a given ,za domain. It was found that the majority of ,za domain authoritative servers are international, which results in latency generation that is multiple times greater than observed latencies for local authoritative servers. Further analysis is done with respect to NX DOM AIN behavior captured across the dataset. These findings outlined the cost of DNS miseonfiguration as well as highlighting instances of NXDOMAIN generation through malicious practice. With respect to DNS abuses, original research with respect to long-term scanning generated as a result of amplification attack activity on the greater Internet is presented. Many instances of amplification domain scans were captured during the packet capture, and an attempt is made to correlate that activity temporally with known amplification attack reports. The final area that this thesis deals with is the relatively new field of Bitflipping and Bitsquatting, delivering results on bitflip detection and evaluation over the course of the entire dataset. The detection methodology is outlined, and the final results are compared to findings given in recent bitflip literature.
- Full Text:
- Authors: Van Zyl, Ignus
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3707 , vital:20537
- Description: This thesis examines a dataset spanning 21 months, containing 3,5 billion DNS packets. Traffic on TCP and UDP port 53, was captured on a production /24 IP block. The purpose of this thesis is twofold. The first is to create an understanding of current practice and behavior within the DNS infrastructure, the second to explore current threats faced by the DNS and the various systems that implement it. This is achieved by drawing on analysis and observations from the captured data. Aspects of the operation of DNS on the greater Internet are considered in this research with reference to the observed trends in the dataset, A thorough analysis of current DNS TTL implementation is made with respect to all response traffic, as well as sections looking at observed DNS TTL values for ,za domain replies and NX DOMAIN flagged replies. This thesis found that TTL values implemented are much lower than has been recommended in previous years, and that the TTL decrease is prevalent in most, but not all EE TTL implementation. With respect to the nature of DNS operations, this thesis also concerns itself with an analysis of the geoloeation of authoritative servers for local (,za) domains, and offers further observations towards the latency generated by the choice of authoritative server location for a given ,za domain. It was found that the majority of ,za domain authoritative servers are international, which results in latency generation that is multiple times greater than observed latencies for local authoritative servers. Further analysis is done with respect to NX DOM AIN behavior captured across the dataset. These findings outlined the cost of DNS miseonfiguration as well as highlighting instances of NXDOMAIN generation through malicious practice. With respect to DNS abuses, original research with respect to long-term scanning generated as a result of amplification attack activity on the greater Internet is presented. Many instances of amplification domain scans were captured during the packet capture, and an attempt is made to correlate that activity temporally with known amplification attack reports. The final area that this thesis deals with is the relatively new field of Bitflipping and Bitsquatting, delivering results on bitflip detection and evaluation over the course of the entire dataset. The detection methodology is outlined, and the final results are compared to findings given in recent bitflip literature.
- Full Text:
Active Layer Dynamics at Four Borehole Sites in Western Dronning Maud Land, Antarctica
- Authors: Kotzé, Camilla
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4894 , http://hdl.handle.net/10962/d1021295
- Description: Permafrost and active layer dynamics in the Antarctic play an important role within terrestrial landscapes and ecosystems and as a climate change indicator. However, they remain less thoroughly researched than their Northern-Hemispheric counterpart. Despite advancements made by ANTPAS on the permafrost and active layer monitoring network in the Antarctic, observational gaps still exist. Western Dronning Maud Land (WDML) has been identified as one of these gaps, necessitating further research on permafrost dynamics and the influence of climate parameters thereon. Such elucidation is critical to both the cryospheric and life sciences. Variations in the surface climate of Antarctica can be seen as a result of inter-annual variations in atmospheric circulation, enhancing permafrost degradation and active layer thickening which directly affects soil processes, such as sorting and cryoturbation. Ground temperatures from four permafrost boreholes from WDML were analysed from 2007 to 2014. The study sites exhibit seasonal freezing, periglacial landforms, and altitudinal variation, ranging between ca. 450masl to ca. 1300masl. Using ground thermal regime and regional climate data, the spatial and temporal variability of the active layer in the Ahlmannryggen and Jutulsessen areas of WDML were characterised. 137 Cs tracing has revealed that the active layer and associated landforms have been active over the past half century. Further results show that active layer depths at each site vary inter-annually and are particularly influenced by snow cover, altitude and distance to the ice-shelf. Moreover, a correlation between the SAO (Semi-Annual Oscillation) and measured ground temperatures was found, principally during the transitional season of the SAO in May and September. The relationship between climate and ground thermal regimes, especially the influence of teleconnections thereon, is essential to improving the understanding of permafrost dynamics and landform morphology in continental Antarctica.
- Full Text:
- Authors: Kotzé, Camilla
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4894 , http://hdl.handle.net/10962/d1021295
- Description: Permafrost and active layer dynamics in the Antarctic play an important role within terrestrial landscapes and ecosystems and as a climate change indicator. However, they remain less thoroughly researched than their Northern-Hemispheric counterpart. Despite advancements made by ANTPAS on the permafrost and active layer monitoring network in the Antarctic, observational gaps still exist. Western Dronning Maud Land (WDML) has been identified as one of these gaps, necessitating further research on permafrost dynamics and the influence of climate parameters thereon. Such elucidation is critical to both the cryospheric and life sciences. Variations in the surface climate of Antarctica can be seen as a result of inter-annual variations in atmospheric circulation, enhancing permafrost degradation and active layer thickening which directly affects soil processes, such as sorting and cryoturbation. Ground temperatures from four permafrost boreholes from WDML were analysed from 2007 to 2014. The study sites exhibit seasonal freezing, periglacial landforms, and altitudinal variation, ranging between ca. 450masl to ca. 1300masl. Using ground thermal regime and regional climate data, the spatial and temporal variability of the active layer in the Ahlmannryggen and Jutulsessen areas of WDML were characterised. 137 Cs tracing has revealed that the active layer and associated landforms have been active over the past half century. Further results show that active layer depths at each site vary inter-annually and are particularly influenced by snow cover, altitude and distance to the ice-shelf. Moreover, a correlation between the SAO (Semi-Annual Oscillation) and measured ground temperatures was found, principally during the transitional season of the SAO in May and September. The relationship between climate and ground thermal regimes, especially the influence of teleconnections thereon, is essential to improving the understanding of permafrost dynamics and landform morphology in continental Antarctica.
- Full Text:
An assessment of the efficiency and effectiveness of the Working for Water NBAL mapping, contract teams and clearing of Acacia mearnsii
- Authors: Modipa, Rebone Dineo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3192 , vital:20383
- Description: Working for Water (WfW) works to fulfil their dual mandate of protecting ecosystem services and creating employment opportunities for poor communities. There have been many successes but evidence is increasing regarding the inefficiencies at project and site scales. The study was undertaken in the Eastern Cape, South Africa, at a farm called Ann’s Villa situated in the Kommadagga valley, at the foot of the northern side of the Zuurberg pass. The study sought to assess the efficiency of the WfW mapping of natural biological aliens (NBAL), of contract teams and the effectiveness of the clearing methods employed to clear Acacia mearnsii. To achieve this, WfW mapping was analysed, contract team dynamics of the different task groups were observed and assessed and various Acacia mearnsii and indigenous plant variables were measured pre-and post-clearing of A. mearnsii. The first key finding was that overall the WfW NBAL mapping was inaccurate, with WfW A. mearnsii percentage cover (cover) estimations significantly over-estimated. Acacia mearnsii cover over-estimations resulted in fruitless expenditure as contracts were more expensive than necessary. Cover under-estimations also led to the inability to fulfill contractual obligations and the subsequent halting of the clearing of a large portion the study area. It was recommended that the NBAL mapping as well as the cover estimations of NBALs be conducted more rigorously, with expert assistance where skills are lacking, to avoid the associated fruitless expenditure. The second key finding was that WfW contract teams were largely inefficient, as a result of waiting, stemming from the lack of continuity in work. There was a strong positive relationship between subgroup chainsaw operator (CO) to stacker ratio and subgroup CO to stacker efficiency ratio. These inefficiencies meant that a mean of 58±67% of the total money spent per team resulted in fruitless expenditure. It was recommend that contract teams be organised to promote the continuity of work and that the current high stacker to CO ratios be reversed to increase efficiency and reduce fruitless expenditures. The third key finding was that overall the WfW methods of clearing A. mearnsii were 95% effective with a 90% removal success. The last key finding was that initial clearing operations had a largely insignificant impact on indigenous plant biodiversity. It was recommended that post-clearing inspection of quality control is conducted more rigorously and that penalties be implemented to deter contract teams from cutting indigenous species.
- Full Text:
- Authors: Modipa, Rebone Dineo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3192 , vital:20383
- Description: Working for Water (WfW) works to fulfil their dual mandate of protecting ecosystem services and creating employment opportunities for poor communities. There have been many successes but evidence is increasing regarding the inefficiencies at project and site scales. The study was undertaken in the Eastern Cape, South Africa, at a farm called Ann’s Villa situated in the Kommadagga valley, at the foot of the northern side of the Zuurberg pass. The study sought to assess the efficiency of the WfW mapping of natural biological aliens (NBAL), of contract teams and the effectiveness of the clearing methods employed to clear Acacia mearnsii. To achieve this, WfW mapping was analysed, contract team dynamics of the different task groups were observed and assessed and various Acacia mearnsii and indigenous plant variables were measured pre-and post-clearing of A. mearnsii. The first key finding was that overall the WfW NBAL mapping was inaccurate, with WfW A. mearnsii percentage cover (cover) estimations significantly over-estimated. Acacia mearnsii cover over-estimations resulted in fruitless expenditure as contracts were more expensive than necessary. Cover under-estimations also led to the inability to fulfill contractual obligations and the subsequent halting of the clearing of a large portion the study area. It was recommended that the NBAL mapping as well as the cover estimations of NBALs be conducted more rigorously, with expert assistance where skills are lacking, to avoid the associated fruitless expenditure. The second key finding was that WfW contract teams were largely inefficient, as a result of waiting, stemming from the lack of continuity in work. There was a strong positive relationship between subgroup chainsaw operator (CO) to stacker ratio and subgroup CO to stacker efficiency ratio. These inefficiencies meant that a mean of 58±67% of the total money spent per team resulted in fruitless expenditure. It was recommend that contract teams be organised to promote the continuity of work and that the current high stacker to CO ratios be reversed to increase efficiency and reduce fruitless expenditures. The third key finding was that overall the WfW methods of clearing A. mearnsii were 95% effective with a 90% removal success. The last key finding was that initial clearing operations had a largely insignificant impact on indigenous plant biodiversity. It was recommended that post-clearing inspection of quality control is conducted more rigorously and that penalties be implemented to deter contract teams from cutting indigenous species.
- Full Text:
An assessment of the invasion state and fisheries suitability in four dams and a natural lake in the Western Cape, South Africa
- Authors: Dredge, Brendon Neville
- Date: 2016
- Subjects: Introduced organisms Fishery management -- South Africa -- Western Cape Fishes -- Conservation -- South Africa -- Western Cape Introduced fishes -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69114 , vital:29391
- Description: Despite more than a century of introductions, fish invasions are poorly understood in South Africa. This thesis aims to: (1) provide baseline information on the fish fauna in five inland water bodies (four dams: Theewaterskloof, Clanwilliam, Quaggaskloof, and Voelvlei and a natural lake, Groenvlei) in the Western Cape; (2) determine which species were established and provide a baseline of abundance and size structure for monitoring and, (3) make preliminary recommendations for a fishery. First, criteria for determining establishment were developed by undertaking a full biological assessment of bluegill Lepomis macrochirus, a data-poor species in South Africa. This included the assessment of growth rate using validated estimates of age derived from otoliths in two dams (Clanwilliam Dam: Lt=335.9(1−eo.113(t+1.06)); Groenvlei: Lt=287.2(1-e−0.171(t+0.54)). Length at 50% maturity was similar for males (146 mmFL) and females (147 mmFL). Length frequency analysis combined with data on the age and growth and reproduction demonstrated that established populations of bluegill contained several age cohorts as well as mature and juvenile fishes. A meta-analysis was conducted to: (1) compile a list of initial stocking dates for all alien fishes in each waterbody and (2) use angler tournament data to assess for additional species and persistence over time. Data from the meta-analysis was combined with ichthyological survey data to determine establishment success. These data demonstrated that nine non-native species had established in the five water bodies. Clanwilliam Dam had the largest number (7) of non-native species established, Groenvlei (5) and Theewaterskloof, Brandvlei and Voelvlei the lowest with four species. The state of invasion of each species in the province showed that all nine species are categorised as invasive. This information on establishment was then integrated into a framework for rapidly determining what type of fishery would be most suitable for the 5 waterbodies. Potential yield was estimated using morphoedaphic models, were 260 t/yr for Theewaterskloof Dam, 93 t/yr for Voelvlei, 81 t/yr for Brandvlei, 59 t/yr for Groenvlei and 55 t/yr for Groenvlei. The CPUE for Groenvlei was the highest in gill nets with 1.32 ± 1.94 kg/h, then Voelvlei 1.05 ± 1.34 kg/h followed by Brandvlei (0.84 ± 1.48 kg/h), Clanwilliam (0.71 ± 1.55 kg/h) and lastly Theewaterskloof (0.36 ± 0.41 kg/h). Only Theewaterskloof could produce in excess of 100 t/yr but less than 400 t/yr of fish making it suitable for a small scale fishery. The CPUE values of Theewaterskloof were the lowest and a gill net fishery on this water body may not produce sufficient fish for the fishery. All water bodies had a high recreational angling usage, the opening of a small scale fishery could be detrimental to this industry. Subsistence and recreational anglers should be promoted with the possibility of a long line industry targeting Clarias gariepinus.
- Full Text:
- Authors: Dredge, Brendon Neville
- Date: 2016
- Subjects: Introduced organisms Fishery management -- South Africa -- Western Cape Fishes -- Conservation -- South Africa -- Western Cape Introduced fishes -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69114 , vital:29391
- Description: Despite more than a century of introductions, fish invasions are poorly understood in South Africa. This thesis aims to: (1) provide baseline information on the fish fauna in five inland water bodies (four dams: Theewaterskloof, Clanwilliam, Quaggaskloof, and Voelvlei and a natural lake, Groenvlei) in the Western Cape; (2) determine which species were established and provide a baseline of abundance and size structure for monitoring and, (3) make preliminary recommendations for a fishery. First, criteria for determining establishment were developed by undertaking a full biological assessment of bluegill Lepomis macrochirus, a data-poor species in South Africa. This included the assessment of growth rate using validated estimates of age derived from otoliths in two dams (Clanwilliam Dam: Lt=335.9(1−eo.113(t+1.06)); Groenvlei: Lt=287.2(1-e−0.171(t+0.54)). Length at 50% maturity was similar for males (146 mmFL) and females (147 mmFL). Length frequency analysis combined with data on the age and growth and reproduction demonstrated that established populations of bluegill contained several age cohorts as well as mature and juvenile fishes. A meta-analysis was conducted to: (1) compile a list of initial stocking dates for all alien fishes in each waterbody and (2) use angler tournament data to assess for additional species and persistence over time. Data from the meta-analysis was combined with ichthyological survey data to determine establishment success. These data demonstrated that nine non-native species had established in the five water bodies. Clanwilliam Dam had the largest number (7) of non-native species established, Groenvlei (5) and Theewaterskloof, Brandvlei and Voelvlei the lowest with four species. The state of invasion of each species in the province showed that all nine species are categorised as invasive. This information on establishment was then integrated into a framework for rapidly determining what type of fishery would be most suitable for the 5 waterbodies. Potential yield was estimated using morphoedaphic models, were 260 t/yr for Theewaterskloof Dam, 93 t/yr for Voelvlei, 81 t/yr for Brandvlei, 59 t/yr for Groenvlei and 55 t/yr for Groenvlei. The CPUE for Groenvlei was the highest in gill nets with 1.32 ± 1.94 kg/h, then Voelvlei 1.05 ± 1.34 kg/h followed by Brandvlei (0.84 ± 1.48 kg/h), Clanwilliam (0.71 ± 1.55 kg/h) and lastly Theewaterskloof (0.36 ± 0.41 kg/h). Only Theewaterskloof could produce in excess of 100 t/yr but less than 400 t/yr of fish making it suitable for a small scale fishery. The CPUE values of Theewaterskloof were the lowest and a gill net fishery on this water body may not produce sufficient fish for the fishery. All water bodies had a high recreational angling usage, the opening of a small scale fishery could be detrimental to this industry. Subsistence and recreational anglers should be promoted with the possibility of a long line industry targeting Clarias gariepinus.
- Full Text:
An assessment of the small-scale fisheries in the Kogelberg district of the Western Cape, South Africa
- Authors: Jordan, Tia
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/997 , vital:20011
- Description: Small-scale fisheries play a critical role in communities by contributing to food security, poverty alleviation and source of income. The study focused on the Kleinmond small-scale fishery and estimated the current economic value of the fishery as well as exploring the potential for increasing this and also whether it is being used in a way that ensures sustainable harvesting of the marine resources. It was important to evaluate the ecological, economic and social dimensions of the fishing community in order to address the problems currently facing the community. The study draws on previous research done in the Kleinmond area. Data were collected to update and complement previous research and addresses current research. In order to investigate the fisheries catch contribution in the area, data were obtained from the Department of Agriculture, Forestry and Fisheries. Three different questionnaires were developed and conducted in face-to-face formal and informal interviews with the various stakeholders (n=42) in the value-chain. Interviews were also conducted telephonically with other stakeholders and a focus group was formed to supplement previous available data. Simple economic models were developed for the fisheries working from the Kleinmond harbour, which were used to estimate the gross and net economic value of catches for individual right-holders, as well as the Kleinmond area as a whole. The economic models used in this study showed that the West Coast rock lobster Jasus lalandii, fishery was the primary source of income for small-scale fishers. This was due to the rock lobsters being sold to the export market as a high-valued commodity, whereas the linefish were sold to the local market as a lower-valued commodity. However, linefish were found to be more of a commodity to the community as a portion would be retained for personal consumption. The linefishers were concerned in that over the past couple of years, snoek Thrysites atun have been absent the Kleinmond area, resulting in and the fishing effort shifting to a resident species Cape bream Pachymetopon blochii. Whereas West Coast rock lobster were considered to be harvested sustainably under the current total allowable catch strategy, there was concern for the future of the fishery because of the occurrence of illegal fishing, both locally and nationally. Small-scale fisheries in the Kleinmond community are largely dependent on fishing resources, even though the industry is only marginally profitable. Future management measures should concentrate on optimising the value-chain to provide both sustainability for the resources and improve the livelihoods of the community.
- Full Text:
- Authors: Jordan, Tia
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/997 , vital:20011
- Description: Small-scale fisheries play a critical role in communities by contributing to food security, poverty alleviation and source of income. The study focused on the Kleinmond small-scale fishery and estimated the current economic value of the fishery as well as exploring the potential for increasing this and also whether it is being used in a way that ensures sustainable harvesting of the marine resources. It was important to evaluate the ecological, economic and social dimensions of the fishing community in order to address the problems currently facing the community. The study draws on previous research done in the Kleinmond area. Data were collected to update and complement previous research and addresses current research. In order to investigate the fisheries catch contribution in the area, data were obtained from the Department of Agriculture, Forestry and Fisheries. Three different questionnaires were developed and conducted in face-to-face formal and informal interviews with the various stakeholders (n=42) in the value-chain. Interviews were also conducted telephonically with other stakeholders and a focus group was formed to supplement previous available data. Simple economic models were developed for the fisheries working from the Kleinmond harbour, which were used to estimate the gross and net economic value of catches for individual right-holders, as well as the Kleinmond area as a whole. The economic models used in this study showed that the West Coast rock lobster Jasus lalandii, fishery was the primary source of income for small-scale fishers. This was due to the rock lobsters being sold to the export market as a high-valued commodity, whereas the linefish were sold to the local market as a lower-valued commodity. However, linefish were found to be more of a commodity to the community as a portion would be retained for personal consumption. The linefishers were concerned in that over the past couple of years, snoek Thrysites atun have been absent the Kleinmond area, resulting in and the fishing effort shifting to a resident species Cape bream Pachymetopon blochii. Whereas West Coast rock lobster were considered to be harvested sustainably under the current total allowable catch strategy, there was concern for the future of the fishery because of the occurrence of illegal fishing, both locally and nationally. Small-scale fisheries in the Kleinmond community are largely dependent on fishing resources, even though the industry is only marginally profitable. Future management measures should concentrate on optimising the value-chain to provide both sustainability for the resources and improve the livelihoods of the community.
- Full Text:
An erosion and sediment delivery model for semi-arid catchments
- Authors: Bryson, Louise Kay
- Date: 2016
- Subjects: Sedimentation and deposition , Erosion , Watershed management -- South Africa , Water-supply -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:6056 , http://hdl.handle.net/10962/d1020331
- Description: Sedimentation has become a significant environmental threat in South Africa as it intensifies water management problems in the water-scarce semi-arid regions of the country. As South Africa already allocates 98% of available water, the loss of storage capacity in reservoirs and degraded water quality has meant that a reliable water supply is compromised. The overall aim of this thesis was to develop a catchment scale model that represents the sediment dynamics of semi-arid regions of South Africa as a simple and practically applicable tool for water resource managers. Development of a conceptual framework for the model relied on an understanding of both the sediment dynamics of South African catchments and applicable modelling techniques. Scale was an issue in both cases as most of our understanding of the physical processes of runoff generation and sediment transport has been derived from plot scale studies. By identifying defining properties of semi-arid catchments it was possible to consider how temporal and spatial properties at higher levels emerged from properties at lower levels. These properties were effectively represented by using the Pitman rainfall-runoff model disaggregated to a daily timescale, the Modified Universal Soil Loss Equation (MUSLE) model incorporating probability function theory and through the representation of sediment storages across a semi-distributed catchment. The model was tested on two small and one large study catchment in the Karoo, South Africa, with limited observed data. Limitations to the model were found to be the large parameter data set and the dominance of structural constraints with an increase in catchment size. The next steps in model development will require a reduction of the parameter data set and an inclusion of an in-stream component for sub-catchments at a larger spatial scale. The model is applicable in areas such as South Africa where water resource managers need a simple model at the catchment scale in order to make decisions. This type of model provides a simple representation of the stochastic nature of erosion and sediment delivery over large spatial and temporal scales.
- Full Text:
- Authors: Bryson, Louise Kay
- Date: 2016
- Subjects: Sedimentation and deposition , Erosion , Watershed management -- South Africa , Water-supply -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:6056 , http://hdl.handle.net/10962/d1020331
- Description: Sedimentation has become a significant environmental threat in South Africa as it intensifies water management problems in the water-scarce semi-arid regions of the country. As South Africa already allocates 98% of available water, the loss of storage capacity in reservoirs and degraded water quality has meant that a reliable water supply is compromised. The overall aim of this thesis was to develop a catchment scale model that represents the sediment dynamics of semi-arid regions of South Africa as a simple and practically applicable tool for water resource managers. Development of a conceptual framework for the model relied on an understanding of both the sediment dynamics of South African catchments and applicable modelling techniques. Scale was an issue in both cases as most of our understanding of the physical processes of runoff generation and sediment transport has been derived from plot scale studies. By identifying defining properties of semi-arid catchments it was possible to consider how temporal and spatial properties at higher levels emerged from properties at lower levels. These properties were effectively represented by using the Pitman rainfall-runoff model disaggregated to a daily timescale, the Modified Universal Soil Loss Equation (MUSLE) model incorporating probability function theory and through the representation of sediment storages across a semi-distributed catchment. The model was tested on two small and one large study catchment in the Karoo, South Africa, with limited observed data. Limitations to the model were found to be the large parameter data set and the dominance of structural constraints with an increase in catchment size. The next steps in model development will require a reduction of the parameter data set and an inclusion of an in-stream component for sub-catchments at a larger spatial scale. The model is applicable in areas such as South Africa where water resource managers need a simple model at the catchment scale in order to make decisions. This type of model provides a simple representation of the stochastic nature of erosion and sediment delivery over large spatial and temporal scales.
- Full Text:
An insight into the profile characteristics and technical batting skill of adolescent cricket players
- Authors: Clark, Matthew Edward
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2838 , vital:20331
- Description: Background: Current traditional cricket practices incorporate the use of a netted-off pitch to provide cricket players the opportunity to hone their skills with bat and ball. The lack of ecological validity of these training environments results in the absence of important task and environmental constraints which influences the manner in which the sport is played. Objectives: The purpose of the current research was two-fold: firstly, it aimed to establish a profile database of adolescent cricket players in the Eastern Cape province of South Africa; and secondly, it aimed to investigate the efficacy of a constraints-led training intervention on skill development in adolescent cricket batsmen. Methods: Study I required 90 participants (u13: n = 40; u15: n = 50) to perform measures pertaining to anthropometric, morphological, flexibility and physical performance characteristics. This included stature, mass, body composition, limb length, flexibility, agility, and power measures. Study II was a case-control study (u15: n = 24), whereby the experimental group (n = 12) was exposed to a constraints-led batting protocol during the course of the cricket season. The objective of the protocol was to encourage the manipulation of the ball around the playing field. Pre- and post-intervention measures were performed using a batting skills test, which assessed batsmen’s capability to manipulate the ball to various areas of the playing field. Results: Study I revealed significant differences (p <0.0001) in stature, mass, limb length and power variables when comparing the u15 age group with the u13 age group. No differences were recorded for agility. The u13 age group had greater linear correlations for the variables of interest compared to the u15 age group. Study II revealed no differences in technical skill between the experimental group and the control (p <0.315).. The tests also revealed that adolescent batsmen favoured hitting deliveries through the extra-cover scoring zone. The third-man and fine-leg scoring zones were least preferred to hit deliveries through. A number of limitations to the study design resulted in the inability to determine the efficacy of a constraints-led batting protocol on skill development in an adolescent batting cohort. Conclusion: The results of study I indicated that the onset of puberty played an important role in the measures and performances between the u13 and u15 age groups. The results of study II indicated that adolescent batsmen are not adept at manipulating the ball around the field. Recommendations are provided for both studies.
- Full Text:
- Authors: Clark, Matthew Edward
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2838 , vital:20331
- Description: Background: Current traditional cricket practices incorporate the use of a netted-off pitch to provide cricket players the opportunity to hone their skills with bat and ball. The lack of ecological validity of these training environments results in the absence of important task and environmental constraints which influences the manner in which the sport is played. Objectives: The purpose of the current research was two-fold: firstly, it aimed to establish a profile database of adolescent cricket players in the Eastern Cape province of South Africa; and secondly, it aimed to investigate the efficacy of a constraints-led training intervention on skill development in adolescent cricket batsmen. Methods: Study I required 90 participants (u13: n = 40; u15: n = 50) to perform measures pertaining to anthropometric, morphological, flexibility and physical performance characteristics. This included stature, mass, body composition, limb length, flexibility, agility, and power measures. Study II was a case-control study (u15: n = 24), whereby the experimental group (n = 12) was exposed to a constraints-led batting protocol during the course of the cricket season. The objective of the protocol was to encourage the manipulation of the ball around the playing field. Pre- and post-intervention measures were performed using a batting skills test, which assessed batsmen’s capability to manipulate the ball to various areas of the playing field. Results: Study I revealed significant differences (p <0.0001) in stature, mass, limb length and power variables when comparing the u15 age group with the u13 age group. No differences were recorded for agility. The u13 age group had greater linear correlations for the variables of interest compared to the u15 age group. Study II revealed no differences in technical skill between the experimental group and the control (p <0.315).. The tests also revealed that adolescent batsmen favoured hitting deliveries through the extra-cover scoring zone. The third-man and fine-leg scoring zones were least preferred to hit deliveries through. A number of limitations to the study design resulted in the inability to determine the efficacy of a constraints-led batting protocol on skill development in an adolescent batting cohort. Conclusion: The results of study I indicated that the onset of puberty played an important role in the measures and performances between the u13 and u15 age groups. The results of study II indicated that adolescent batsmen are not adept at manipulating the ball around the field. Recommendations are provided for both studies.
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An investigation into the interaction effects of simultaneous physical and cognitive task execution on performance, perceptual and physical responses
- Authors: Ross, Natalie
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3562 , vital:20525
- Description: Many modern day work environments require some degree of dual tasking, particularly the simultaneous performance of cognitive jobs alongside physical activity. The nature of such tasks is often job dependent and may require cognitive functions such as perception, decision making, memory, or response selection/execution in conjunction to task specific physical requirements. Previous research has indicated a possible relationship between concurrent physical and cognitive demands and task performance, safety and efficiency. However, this research is limited and inconsistent. The current study aimed to identify the interaction, if any, between concurrent physical and mental demands, and determine the impact of sensory modality and stage of information processing on this interaction, with specific focus on the performance, perceptual and physical responses during different types of cognitive tasks performed concurrently with a lifting task. 20 (10 male, 10 female) Rhodes University students participated in this study. Each participant performed 9 test conditions - a physical lifting task, a visual and an auditory memory task, and a visual and an auditory decision making task in isolation, as well as the lifting task concurrently with each of these cognitive tasks. Performance was recorded via accuracy and work output of cognitive tasks and the number of lifts for each condition. Perceptual measures were obtained via the Borg RPE and Subjective Workload Assessment Technique. Spinal kinematics were measured using the Lumbar Motion Monitor, while muscle activity of the Erector Spinae, Rectus Abdominis, Rectus Femoris and Biceps Femoris muscles were recorded using the Biometrix Data Logger surface EMG equipment. Mean results were analysed using a dependent T-test to observe any general interaction, and a Two-way ANOVA for the impact of sensory modality and stage of processing. Individual responses were also considered to gain better understanding of both intra and inter-human variability under the various test conditions. Results showed a significant decrease in cognitive performance, increased perception of physical effort, time pressure, mental effort and psychological stress under simultaneous physical and mental demands, while no significant differences in physical responses were observed. Further observations included increased dual-task interference during visual and decision-making tasks when combined with physical demands compared to that of auditory and memory tasks respectively. Individual responses showed large variability between individuals indicating the presence of positive, negative and non-responders to concurrent physical and mental demands. Results therefore imply an individual specific interaction between concurrent physical and mental demands that may or may not be detrimental to worker productivity, job error, injury rates and worker well-being, and that the type of cognitive task performed may impact this interaction.
- Full Text:
- Authors: Ross, Natalie
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3562 , vital:20525
- Description: Many modern day work environments require some degree of dual tasking, particularly the simultaneous performance of cognitive jobs alongside physical activity. The nature of such tasks is often job dependent and may require cognitive functions such as perception, decision making, memory, or response selection/execution in conjunction to task specific physical requirements. Previous research has indicated a possible relationship between concurrent physical and cognitive demands and task performance, safety and efficiency. However, this research is limited and inconsistent. The current study aimed to identify the interaction, if any, between concurrent physical and mental demands, and determine the impact of sensory modality and stage of information processing on this interaction, with specific focus on the performance, perceptual and physical responses during different types of cognitive tasks performed concurrently with a lifting task. 20 (10 male, 10 female) Rhodes University students participated in this study. Each participant performed 9 test conditions - a physical lifting task, a visual and an auditory memory task, and a visual and an auditory decision making task in isolation, as well as the lifting task concurrently with each of these cognitive tasks. Performance was recorded via accuracy and work output of cognitive tasks and the number of lifts for each condition. Perceptual measures were obtained via the Borg RPE and Subjective Workload Assessment Technique. Spinal kinematics were measured using the Lumbar Motion Monitor, while muscle activity of the Erector Spinae, Rectus Abdominis, Rectus Femoris and Biceps Femoris muscles were recorded using the Biometrix Data Logger surface EMG equipment. Mean results were analysed using a dependent T-test to observe any general interaction, and a Two-way ANOVA for the impact of sensory modality and stage of processing. Individual responses were also considered to gain better understanding of both intra and inter-human variability under the various test conditions. Results showed a significant decrease in cognitive performance, increased perception of physical effort, time pressure, mental effort and psychological stress under simultaneous physical and mental demands, while no significant differences in physical responses were observed. Further observations included increased dual-task interference during visual and decision-making tasks when combined with physical demands compared to that of auditory and memory tasks respectively. Individual responses showed large variability between individuals indicating the presence of positive, negative and non-responders to concurrent physical and mental demands. Results therefore imply an individual specific interaction between concurrent physical and mental demands that may or may not be detrimental to worker productivity, job error, injury rates and worker well-being, and that the type of cognitive task performed may impact this interaction.
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An investigation into the prevalence and growth of phishing attacks against South African financial targets
- Authors: Lala, Darshan Magan
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3157 , vital:20379
- Description: Phishing in the electronic communications medium is the act of sending unsolicited email messages with the intention of masquerading as a reputed business. The objective is to deceive the recipient into divulging personal and sensitive information such as bank account details, credit card numbers and passwords. Attacks against financial services are the most common types of targets for scammers. Phishing attacks in South Africa have cost businesses and consumers substantial amounts of financial loss. This research investigated existing literature to understand the basic concepts of email, phishing, spam and how these fit together. The research also looks into the increasing growth of phishing worldwide and in particular against South African targets. A quantitative study is performed and reported on; this involves the study and analysis of phishing statistics in a data set provided by the South African Anti-Phishing Working Group. The data set contains phishing URL information, country code where the site has been hosted, targeted company name, IP address information and timestamp of the phishing site. The data set contains 161 different phishing targets. The research primarily focuses on the trend in phishing attacks against six South African based financial institutions, but also correlates this with the overall global trend using statistical analysis. The results from the study of the data set are compared to existing statistics and literature regarding the prevalence and growth of phishing in South Africa. The question that this research answers is whether or not the prevalence and growth of phishing in South Africa correlates with the global trend in phishing attacks. The findings indicate that certain correlations exist between some of the South African phishing targets and global phishing trends.
- Full Text:
- Authors: Lala, Darshan Magan
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3157 , vital:20379
- Description: Phishing in the electronic communications medium is the act of sending unsolicited email messages with the intention of masquerading as a reputed business. The objective is to deceive the recipient into divulging personal and sensitive information such as bank account details, credit card numbers and passwords. Attacks against financial services are the most common types of targets for scammers. Phishing attacks in South Africa have cost businesses and consumers substantial amounts of financial loss. This research investigated existing literature to understand the basic concepts of email, phishing, spam and how these fit together. The research also looks into the increasing growth of phishing worldwide and in particular against South African targets. A quantitative study is performed and reported on; this involves the study and analysis of phishing statistics in a data set provided by the South African Anti-Phishing Working Group. The data set contains phishing URL information, country code where the site has been hosted, targeted company name, IP address information and timestamp of the phishing site. The data set contains 161 different phishing targets. The research primarily focuses on the trend in phishing attacks against six South African based financial institutions, but also correlates this with the overall global trend using statistical analysis. The results from the study of the data set are compared to existing statistics and literature regarding the prevalence and growth of phishing in South Africa. The question that this research answers is whether or not the prevalence and growth of phishing in South Africa correlates with the global trend in phishing attacks. The findings indicate that certain correlations exist between some of the South African phishing targets and global phishing trends.
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An investigation into the use of intuitive control interfaces and distributed processing for enhanced three dimensional sound localization
- Authors: Hedges, M L
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2992 , vital:20350
- Description: This thesis investigates the feasibility of using gestures as a means of control for localizing three dimesional (3D) sound sources in a distributed immersive audio system. A prototype system was implemented and tested which uses state of the art technology to achieve the stated goals. A Windows Kinect is used for gesture recognition which translates human gestures into control messages by the prototype system, which in turn performs actions based on the recognized gestures. The term distributed in the context of this system refers to the audio processing capacity. The prototype system partitions and allocates the processing load between a number of endpoints. The reallocated processing load consists of the mixing of audio samples according to a specification. The endpoints used in this research are XMOS AVB endpoints. The firmware on these endpoints were modified to include the audio mixing capability which was controlled by a state of the art audio distribution networking standard, Ethernet AVB. The hardware used for the implementation of the prototype system is relatively cost efficient in comparison to professional audio hardware, and is also commercially available for end users. The successful implementation and results from user testing of the prototype system demonstrates how it is a feasible option for recording the localization of a sound source. The ability to partition the processing provides a modular approach to building immersive sound systems. This removes the constraint of a centralized mixing console with a predetermined speaker configuration.
- Full Text:
- Authors: Hedges, M L
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2992 , vital:20350
- Description: This thesis investigates the feasibility of using gestures as a means of control for localizing three dimesional (3D) sound sources in a distributed immersive audio system. A prototype system was implemented and tested which uses state of the art technology to achieve the stated goals. A Windows Kinect is used for gesture recognition which translates human gestures into control messages by the prototype system, which in turn performs actions based on the recognized gestures. The term distributed in the context of this system refers to the audio processing capacity. The prototype system partitions and allocates the processing load between a number of endpoints. The reallocated processing load consists of the mixing of audio samples according to a specification. The endpoints used in this research are XMOS AVB endpoints. The firmware on these endpoints were modified to include the audio mixing capability which was controlled by a state of the art audio distribution networking standard, Ethernet AVB. The hardware used for the implementation of the prototype system is relatively cost efficient in comparison to professional audio hardware, and is also commercially available for end users. The successful implementation and results from user testing of the prototype system demonstrates how it is a feasible option for recording the localization of a sound source. The ability to partition the processing provides a modular approach to building immersive sound systems. This removes the constraint of a centralized mixing console with a predetermined speaker configuration.
- Full Text:
An investigation into the use of intuitive control interfaces and distributed processing for enhanced three dimensional sound localization
- Authors: Hedges, Mitchell Lawrence
- Date: 2016
- Subjects: Human-computer interaction , Acoustic localization , Sound -- Equipment and supplies , Acoustical engineering , Surround-sound systems , Wireless sensor nodes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4724 , http://hdl.handle.net/10962/d1020615
- Description: This thesis investigates the feasibility of using gestures as a means of control for localizing three dimensional (3D) sound sources in a distributed immersive audio system. A prototype system was implemented and tested which uses state of the art technology to achieve the stated goals. A Windows Kinect is used for gesture recognition which translates human gestures into control messages by the prototype system, which in turn performs actions based on the recognized gestures. The term distributed in the context of this system refers to the audio processing capacity. The prototype system partitions and allocates the processing load between a number of endpoints. The reallocated processing load consists of the mixing of audio samples according to a specification. The endpoints used in this research are XMOS AVB endpoints. The firmware on these endpoints were modified to include the audio mixing capability which was controlled by a state of the art audio distribution networking standard, Ethernet AVB. The hardware used for the implementation of the prototype system is relatively cost efficient in comparison to professional audio hardware, and is also commercially available for end users. the successful implementation and results from user testing of the prototype system demonstrates how it is a feasible option for recording the localization of a sound source. The ability to partition the processing provides a modular approach to building immersive sound systems. This removes the constraint of a centralized mixing console with a predetermined speaker configuration.
- Full Text:
- Authors: Hedges, Mitchell Lawrence
- Date: 2016
- Subjects: Human-computer interaction , Acoustic localization , Sound -- Equipment and supplies , Acoustical engineering , Surround-sound systems , Wireless sensor nodes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4724 , http://hdl.handle.net/10962/d1020615
- Description: This thesis investigates the feasibility of using gestures as a means of control for localizing three dimensional (3D) sound sources in a distributed immersive audio system. A prototype system was implemented and tested which uses state of the art technology to achieve the stated goals. A Windows Kinect is used for gesture recognition which translates human gestures into control messages by the prototype system, which in turn performs actions based on the recognized gestures. The term distributed in the context of this system refers to the audio processing capacity. The prototype system partitions and allocates the processing load between a number of endpoints. The reallocated processing load consists of the mixing of audio samples according to a specification. The endpoints used in this research are XMOS AVB endpoints. The firmware on these endpoints were modified to include the audio mixing capability which was controlled by a state of the art audio distribution networking standard, Ethernet AVB. The hardware used for the implementation of the prototype system is relatively cost efficient in comparison to professional audio hardware, and is also commercially available for end users. the successful implementation and results from user testing of the prototype system demonstrates how it is a feasible option for recording the localization of a sound source. The ability to partition the processing provides a modular approach to building immersive sound systems. This removes the constraint of a centralized mixing console with a predetermined speaker configuration.
- Full Text:
An investigation of the aquatic macroinvertebrate fauna of the southern Great Escarpment (South Africa): insights from ecological and genetic studies
- Authors: Taylor, Chantal Lee
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4275 , http://hdl.handle.net/10962/d1020839
- Description: Biological diversity in freshwater biomes is vital to maintain healthy, functioning ecosystems with resilience to disturbance and the impacts of climate change. Freshwater ecosystems provide essential resources to life on Earth. However, as increasing pressure is being placed on the environment by human population growth, the quality of freshwater resources and the health of these ecosystems are at risk. Mountain streams provide an important source of water and are usually less affected by anthropogenic stressors, compared to lowland freshwaters. These montane streams are therefore of important conservation value and due to their untransformed nature serve as ideal ecosystems for biodiversity studies and as reference sites for studies on environmental change. This study explores aquatic macroinvertebrate biodiversity of the southern Great Escarpment in South Africa. Species assemblages and the environmental variables of each site were sampled from first order streams across five different mountain blocks along the Great Escarpment. Additionally, mitochondrial DNA of three mayfly species (Afroptilum sudafricanum, Demoreptus natalensis and Demoreptus capensis), commonly occurring in the study area, was analysed to compare the genetic diversity between habitat specialist and habitat generalist species. A total of 2 595 macroinvertebrate specimens from 47 families and 86 species were collected with several interesting and potentially new species being discovered. Partitioned diversity analyses indicate that macroinvertebrate diversity varies across mountain blocks. Multivariate analyses indicate that differences in assemblages could be attributed to differences in environmental variables between sites, particularly water velocity, total dissolved solids and salinity. As these environmental variables reflect of the topography of the sites, differences in species assemblages was attributed to difference in topography and therefore biotopes present. Habitat-restricted mayfly species (D. natalensis and D. capensis), occur in distinct populations confined to mountains blocks. Isolation-by-distance analyses further emphasis that these species are genetically restricted by their habitat preference for mountain streams. In contrast, A. sudafricanum, a habitat generalist, showed no indication of genetic structure due to location or distance. Possible cryptic taxa and new species were identified within A. sudafricanum and Dermoreptus respectively. This study provides an important contribution to the baseline data of freshwater macroinvertebrate diversity for the southern Great Escarpment region and provides insights into the considerable genetic diversity of selected aquatic taxa across this region.
- Full Text:
- Authors: Taylor, Chantal Lee
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4275 , http://hdl.handle.net/10962/d1020839
- Description: Biological diversity in freshwater biomes is vital to maintain healthy, functioning ecosystems with resilience to disturbance and the impacts of climate change. Freshwater ecosystems provide essential resources to life on Earth. However, as increasing pressure is being placed on the environment by human population growth, the quality of freshwater resources and the health of these ecosystems are at risk. Mountain streams provide an important source of water and are usually less affected by anthropogenic stressors, compared to lowland freshwaters. These montane streams are therefore of important conservation value and due to their untransformed nature serve as ideal ecosystems for biodiversity studies and as reference sites for studies on environmental change. This study explores aquatic macroinvertebrate biodiversity of the southern Great Escarpment in South Africa. Species assemblages and the environmental variables of each site were sampled from first order streams across five different mountain blocks along the Great Escarpment. Additionally, mitochondrial DNA of three mayfly species (Afroptilum sudafricanum, Demoreptus natalensis and Demoreptus capensis), commonly occurring in the study area, was analysed to compare the genetic diversity between habitat specialist and habitat generalist species. A total of 2 595 macroinvertebrate specimens from 47 families and 86 species were collected with several interesting and potentially new species being discovered. Partitioned diversity analyses indicate that macroinvertebrate diversity varies across mountain blocks. Multivariate analyses indicate that differences in assemblages could be attributed to differences in environmental variables between sites, particularly water velocity, total dissolved solids and salinity. As these environmental variables reflect of the topography of the sites, differences in species assemblages was attributed to difference in topography and therefore biotopes present. Habitat-restricted mayfly species (D. natalensis and D. capensis), occur in distinct populations confined to mountains blocks. Isolation-by-distance analyses further emphasis that these species are genetically restricted by their habitat preference for mountain streams. In contrast, A. sudafricanum, a habitat generalist, showed no indication of genetic structure due to location or distance. Possible cryptic taxa and new species were identified within A. sudafricanum and Dermoreptus respectively. This study provides an important contribution to the baseline data of freshwater macroinvertebrate diversity for the southern Great Escarpment region and provides insights into the considerable genetic diversity of selected aquatic taxa across this region.
- Full Text:
An investigation on the effect of Russian wheat aphid (Diuraphis noxia Kurdjumov) population growth and feeding damage on selected barley (Hordeum vulgare L.) cultivars under ambient and elevated CO2
- Authors: Sacranie, Sattar Farouk
- Date: 2016
- Subjects: Russian wheat aphid -- Research -- South Africa Barley -- Disease and pest resistance -- South Africa Callose Aphids
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/50311 , vital:25975
- Description: The Russian wheat aphid (RWA) (Diuraphis noxia Kurdjumov) is a major pest of cultivated small grains. It is particularly devastating because of is high reproductive rate which results in the growth of large populations which become damaging to its host plants. Development of resistant barley (Hordeum vulgare L.) cultivars is complicated as resistance is polygenic. As a result, the industry remains at risk now that the RWA has spread throughout South Africa. It has, as recently as, 2013, been identified in the SW Cape, which was previously geographically isolated. This is South Africa‟s principle barley growing region. Now a potentially huge problem exists. Therefore, it is imperative that an alternative to pesticide use is found. Testing potential innate resistance in barley cultivars is thus, critical. In this thesis, I present data on four barely cultivars where I have examined their resistance/ lack of resistance to three known RWA biotypes, RWASA1, RWASA2 and RWASA3. The barley varieties used were two economically important South African malt barley cultivars (S5 and SSG 564) along with two potentially RWA resistant Afghan accessions (CIho 4125 and CIho 4159). The RWA biotype population growth rates on each of the plants were determined over a 14 day period. The aim was to establish baseline data of the effects of RWA population growth on the host plants under ambient CO2 (380 – 400 ppm) conditions. The extent of RWA feeding damage was investigated at the cell level by examining saliva deposition and cell disruption using Transmission Electron Microscopy; at the tissue/vascular level using fluorescence microscopy, to determine the extent of callose formation; at a whole leaf level by recording percent chlorosis and leaf roll; and finally, at a whole plant level by measuring biomass loss.The experiments were repeated under elevated CO2 (450 ppm) to model any changes in RWA/plant interaction with respect to future climate change. The effects of an elevated CO2 environment and RWA feeding on host plant foliar N and C:N ratio were compared to ambient CO2 conditions, to provide a clearer picture of the potential nutrient drain that a feeding RWA colony exacts on its host. Of the varieties tested, the CIho accessions performed better than the two SA barley cultivars as the CIho accessions appeared to express a mild antibiosis resistance response as RWA populations, particularly those of RWASA1, were smaller than those observed on either S5 or SSG 564. In addition, less damage was evident in the two CIho accessions due to RWA feeding. II RWASA2 was the most virulent of the three RWA biotypes tested, followed by RWASA3 while RWASA1 was the least virulent. Under elevated CO2 conditions, RWA feeding damage was exacerbated but the trend of biotype virulence remained the same. Higher aphid population sizes were recorded under elevated CO2, meant that even the more resistant CIho accessions were overcome by the increased demand made by the larger aphid colonies on the host plants. The % foliar N data showed that under elevated CO2 aphid-free control plants had increased N levels in their leaves. Increased “food” supply (as shown by the increased N levels) therefore allowed significantly larger aphid populations to develop on the plants exposed to elevated CO2, due to improved nutrient status of the phloem sap taken up by RWA. The knock-on effect of a higher aphid population was increased cell disruption as a result of extensive probing, extensive formations of wound callose, with the result that phloem damage impeded nutrient flow through the vascular tissues which contributed to chlorosis and (eventually plant) death. The major conclusion from this study is that even a mild CO2 elevation resulted in an increase aphid population which may pose a severe and very real threat to a barley crop. Therefore, without effort to identify and deploy resistant barley cultivars, it could well be possible that future barley cultivation in South Africa may no longer be viable.
- Full Text:
- Authors: Sacranie, Sattar Farouk
- Date: 2016
- Subjects: Russian wheat aphid -- Research -- South Africa Barley -- Disease and pest resistance -- South Africa Callose Aphids
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/50311 , vital:25975
- Description: The Russian wheat aphid (RWA) (Diuraphis noxia Kurdjumov) is a major pest of cultivated small grains. It is particularly devastating because of is high reproductive rate which results in the growth of large populations which become damaging to its host plants. Development of resistant barley (Hordeum vulgare L.) cultivars is complicated as resistance is polygenic. As a result, the industry remains at risk now that the RWA has spread throughout South Africa. It has, as recently as, 2013, been identified in the SW Cape, which was previously geographically isolated. This is South Africa‟s principle barley growing region. Now a potentially huge problem exists. Therefore, it is imperative that an alternative to pesticide use is found. Testing potential innate resistance in barley cultivars is thus, critical. In this thesis, I present data on four barely cultivars where I have examined their resistance/ lack of resistance to three known RWA biotypes, RWASA1, RWASA2 and RWASA3. The barley varieties used were two economically important South African malt barley cultivars (S5 and SSG 564) along with two potentially RWA resistant Afghan accessions (CIho 4125 and CIho 4159). The RWA biotype population growth rates on each of the plants were determined over a 14 day period. The aim was to establish baseline data of the effects of RWA population growth on the host plants under ambient CO2 (380 – 400 ppm) conditions. The extent of RWA feeding damage was investigated at the cell level by examining saliva deposition and cell disruption using Transmission Electron Microscopy; at the tissue/vascular level using fluorescence microscopy, to determine the extent of callose formation; at a whole leaf level by recording percent chlorosis and leaf roll; and finally, at a whole plant level by measuring biomass loss.The experiments were repeated under elevated CO2 (450 ppm) to model any changes in RWA/plant interaction with respect to future climate change. The effects of an elevated CO2 environment and RWA feeding on host plant foliar N and C:N ratio were compared to ambient CO2 conditions, to provide a clearer picture of the potential nutrient drain that a feeding RWA colony exacts on its host. Of the varieties tested, the CIho accessions performed better than the two SA barley cultivars as the CIho accessions appeared to express a mild antibiosis resistance response as RWA populations, particularly those of RWASA1, were smaller than those observed on either S5 or SSG 564. In addition, less damage was evident in the two CIho accessions due to RWA feeding. II RWASA2 was the most virulent of the three RWA biotypes tested, followed by RWASA3 while RWASA1 was the least virulent. Under elevated CO2 conditions, RWA feeding damage was exacerbated but the trend of biotype virulence remained the same. Higher aphid population sizes were recorded under elevated CO2, meant that even the more resistant CIho accessions were overcome by the increased demand made by the larger aphid colonies on the host plants. The % foliar N data showed that under elevated CO2 aphid-free control plants had increased N levels in their leaves. Increased “food” supply (as shown by the increased N levels) therefore allowed significantly larger aphid populations to develop on the plants exposed to elevated CO2, due to improved nutrient status of the phloem sap taken up by RWA. The knock-on effect of a higher aphid population was increased cell disruption as a result of extensive probing, extensive formations of wound callose, with the result that phloem damage impeded nutrient flow through the vascular tissues which contributed to chlorosis and (eventually plant) death. The major conclusion from this study is that even a mild CO2 elevation resulted in an increase aphid population which may pose a severe and very real threat to a barley crop. Therefore, without effort to identify and deploy resistant barley cultivars, it could well be possible that future barley cultivation in South Africa may no longer be viable.
- Full Text:
Assessing estuarine nursery habitats for Cape Stumpnose (Rhabdosargus holubi), (Pisces: Sparidae) in a warm-temperate estuary in the Eastern Cape, South Africa
- Authors: Leslie, Timothy David
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3178 , vital:20381
- Description: The nursery role hypothesis provides an approach for assessing the nursery function of habitat types within estuaries. This study attempted to assess the nursery value of the dominant estuarine habitats in the Bushmans Estuary for Rhabdosargus holubi (Steindachner 1881) by analysing habitat complexity, relative abundance and behaviour of R. holubi and using stomach contents analysis and dietary diatom composition as indicative of feeding habitat. Structural habitat complexity was assessed in Zostera capensis (Setchell) seagrass and Spartina maritima (Curtis Fernald) salt marsh by sampling above-ground stem density and length, and total cover per unit area (Ct/At). Dimensionless habitat complexity indices such as the interstitial spatial index (ISI) at three magnifications and fractal geometry at two magnifications were used to further analyse habitat complexity. Above-ground biomass (P<0.05) in each season and canopy height (P<0.001) were significantly higher in salt marsh than in seagrass whilst stem density was significantly higher in seagrass than in salt marsh in each season (P<0.001). Each dimensionless index indicated that complexity is notably higher in seagrass than in the salt marsh. Using dimensionless indices that analyse complexity at different spatial scales provided a better analysis of habitat complexity than canopy height and biomass as it allowed for direct comparisons between habitat types. Underwater video cameras were deployed in seagrass, salt marsh and sand flat habitats to assess the relative abundance and behaviour of R. holubi. The relative abundance of R. holubi was significantly higher in seagrass than salt marsh and sand flats, whilst the behaviour of R. holubi indicated a high degree of habitat use in structured habitats and a low degree of habitat use in unstructured sand flat habitats. This indicated that not only are juvenile R. holubi a vegetation-associated species, but also a species that prefers seagrass to salt marsh.
- Full Text:
- Authors: Leslie, Timothy David
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3178 , vital:20381
- Description: The nursery role hypothesis provides an approach for assessing the nursery function of habitat types within estuaries. This study attempted to assess the nursery value of the dominant estuarine habitats in the Bushmans Estuary for Rhabdosargus holubi (Steindachner 1881) by analysing habitat complexity, relative abundance and behaviour of R. holubi and using stomach contents analysis and dietary diatom composition as indicative of feeding habitat. Structural habitat complexity was assessed in Zostera capensis (Setchell) seagrass and Spartina maritima (Curtis Fernald) salt marsh by sampling above-ground stem density and length, and total cover per unit area (Ct/At). Dimensionless habitat complexity indices such as the interstitial spatial index (ISI) at three magnifications and fractal geometry at two magnifications were used to further analyse habitat complexity. Above-ground biomass (P<0.05) in each season and canopy height (P<0.001) were significantly higher in salt marsh than in seagrass whilst stem density was significantly higher in seagrass than in salt marsh in each season (P<0.001). Each dimensionless index indicated that complexity is notably higher in seagrass than in the salt marsh. Using dimensionless indices that analyse complexity at different spatial scales provided a better analysis of habitat complexity than canopy height and biomass as it allowed for direct comparisons between habitat types. Underwater video cameras were deployed in seagrass, salt marsh and sand flat habitats to assess the relative abundance and behaviour of R. holubi. The relative abundance of R. holubi was significantly higher in seagrass than salt marsh and sand flats, whilst the behaviour of R. holubi indicated a high degree of habitat use in structured habitats and a low degree of habitat use in unstructured sand flat habitats. This indicated that not only are juvenile R. holubi a vegetation-associated species, but also a species that prefers seagrass to salt marsh.
- Full Text:
Bayesian accelerated life tests: exponential and Weibull models
- Authors: Izally, Sharkay Ruwade
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3003 , vital:20351
- Description: Reliability life testing is used for life data analysis in which samples are tested under normal conditions to obtain failure time data for reliability assessment. It can be costly and time consuming to obtain failure time data under normal operating conditions if the mean time to failure of a product is long. An alternative is to use failure time data from an accelerated life test (ALT) to extrapolate the reliability under normal conditions. In accelerated life testing, the units are placed under a higher than normal stress condition such as voltage, current, pressure, temperature, to make the items fail in a shorter period of time. The failure information is then transformed through an accelerated model commonly known as the time transformation function, to predict the reliability under normal operating conditions. The power law will be used as the time transformation function in this thesis. We will first consider a Bayesian inference model under the assumption that the underlying life distribution in the accelerated life test is exponentially distributed. The maximal data information (MDI) prior, the Ghosh Mergel and Liu (GML) prior and the Jeffreys prior will be derived for the exponential distribution. The propriety of the posterior distributions will be investigated. Results will be compared when using these non-informative priors in a simulation study by looking at the posterior variances. The Weibull distribution as the underlying life distribution in the accelerated life test will also be investigated. The maximal data information prior will be derived for the Weibull distribution using the power law. The uniform prior and a mixture of Gamma and uniform priors will be considered. The propriety of these posteriors will also be investigated. The predictive reliability at the use-stress will be computed for these models. The deviance information criterion will be used to compare these priors. As a result of using a time transformation function, Bayesian inference becomes analytically intractable and Markov Chain Monte Carlo (MCMC) methods will be used to alleviate this problem. The Metropolis-Hastings algorithm will be used to sample from the posteriors for the exponential model in the accelerated life test. The adaptive rejection sampling method will be used to sample from the posterior distributions when the Weibull model is considered.
- Full Text:
- Authors: Izally, Sharkay Ruwade
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3003 , vital:20351
- Description: Reliability life testing is used for life data analysis in which samples are tested under normal conditions to obtain failure time data for reliability assessment. It can be costly and time consuming to obtain failure time data under normal operating conditions if the mean time to failure of a product is long. An alternative is to use failure time data from an accelerated life test (ALT) to extrapolate the reliability under normal conditions. In accelerated life testing, the units are placed under a higher than normal stress condition such as voltage, current, pressure, temperature, to make the items fail in a shorter period of time. The failure information is then transformed through an accelerated model commonly known as the time transformation function, to predict the reliability under normal operating conditions. The power law will be used as the time transformation function in this thesis. We will first consider a Bayesian inference model under the assumption that the underlying life distribution in the accelerated life test is exponentially distributed. The maximal data information (MDI) prior, the Ghosh Mergel and Liu (GML) prior and the Jeffreys prior will be derived for the exponential distribution. The propriety of the posterior distributions will be investigated. Results will be compared when using these non-informative priors in a simulation study by looking at the posterior variances. The Weibull distribution as the underlying life distribution in the accelerated life test will also be investigated. The maximal data information prior will be derived for the Weibull distribution using the power law. The uniform prior and a mixture of Gamma and uniform priors will be considered. The propriety of these posteriors will also be investigated. The predictive reliability at the use-stress will be computed for these models. The deviance information criterion will be used to compare these priors. As a result of using a time transformation function, Bayesian inference becomes analytically intractable and Markov Chain Monte Carlo (MCMC) methods will be used to alleviate this problem. The Metropolis-Hastings algorithm will be used to sample from the posteriors for the exponential model in the accelerated life test. The adaptive rejection sampling method will be used to sample from the posterior distributions when the Weibull model is considered.
- Full Text:
Beta decay of 100/400 Zr produced in neutron-induced fission of natural uranium
- Authors: Kamoto, Thokozani
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3024 , vital:20353
- Description: Fission fragments, produced by neutron bombardment of natural uranium at the Physics Department, Jyväskylä, Finland, are studied in this work. The data had been sorted into 25 Y — y coincidence matrices which were then analysed. In this work we aimed to identify the fission products using Y-Y coincidence analysis and then study the beta-decay of some of the fission products. Sixteen fission products ranging from A = 94 to A = 136 were identified. Out of these fission products beta decay of the A = 100 (100/40 Zr – 100/41 Nb – 100/42 Mo) chain was studied in greater detail. We have also studied the variation of the relative intensities as a function of time of the 159-, 528-, 600-, 768-, 928- and 1502-keV Y-rav lines in 100/42 Mo and the profiles of the relative intensities have been modelled with the variation of the activity of 100/41 Nb against time. Configuration assignments of 100 Zr and 100/42 Mo are discussed.
- Full Text:
- Authors: Kamoto, Thokozani
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3024 , vital:20353
- Description: Fission fragments, produced by neutron bombardment of natural uranium at the Physics Department, Jyväskylä, Finland, are studied in this work. The data had been sorted into 25 Y — y coincidence matrices which were then analysed. In this work we aimed to identify the fission products using Y-Y coincidence analysis and then study the beta-decay of some of the fission products. Sixteen fission products ranging from A = 94 to A = 136 were identified. Out of these fission products beta decay of the A = 100 (100/40 Zr – 100/41 Nb – 100/42 Mo) chain was studied in greater detail. We have also studied the variation of the relative intensities as a function of time of the 159-, 528-, 600-, 768-, 928- and 1502-keV Y-rav lines in 100/42 Mo and the profiles of the relative intensities have been modelled with the variation of the activity of 100/41 Nb against time. Configuration assignments of 100 Zr and 100/42 Mo are discussed.
- Full Text:
Bio-prospecting a Soil Metagenomic Library for Carbohydrate Active Esterases
- Authors: Shezi, Ntombifuthi
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4172 , http://hdl.handle.net/10962/d1021266
- Description: Lignocellulosic biomass is a promising renewable resource on earth. Plant biomass contains fermentable sugars and other moieties that can be converted to biofuels or other chemicals. Enzymatic hydrolysis of these biopolymers is significant in the liberation of sugars for fermentation into desired products. Owing to its complex structure, synergistic action of enzymes is required for its degradation. Enzymes that are involved in biomass degradation include cellulases, hemicellulases and the accessory enzymes acetyl xylan esterases and ferulic acid esterases. Ferulic acid esterases (FAEs, EC 3.1.1.73), represent a subclass of carboxylester hydrolases (EC 3.1.1.-) that catalyse the release of hydroxycinnamic acids (such as ferulic acid, p-coumaric, ferulic, sinapic and caffeic acid) that are generally found esterified to polysaccharides, such as arabinoxylans. Hydroxycinnamic acids have widespread potential applications due to their antimicrobial, photoprotectant and antioxidant properties, as well as their use as flavour precursors. Therefore, this interesting group of FAEs has a potentially wide variety of applications in agriculture, food and pharmaceutical industries. In the search for novel biocatalysts, metagenomics is considered as an alternative approach to conventional microbe screening, therefore, searching for novel biocatalysts from a soil metagenome that harbours a unique diversity of biocatalyst is significant. The aim of this study was to extract DNA from soil associated with cattle manure and construct a soil metagenomic library using a fosmid based plasmid vector and subsequently functionally screen for ferulic acid esterases using ethyl ferulate as a model substrate. A total of 59 recombinant fosmids conferring ferulic acid esterase phenotypes were identified (Hit rate 1:3122) and the two fosmids that consistently showed high FAE activities were selected for further study. Following nucleotide sequencing and translational analysis, two fae encoding open reading frames (FAE9 and FAE27) of approximately 274 and 322 aa, respectively, were identified. The amino acid sequence of the two ORFs contained a classical conserved esterase/lipase G-x-S-x-G sequence motif. The two genes (fae9 and fae27) were successfully expressed in Escherichia coli BL21 (DE3) and the purified enzymes exhibited respective temperature optima of 50 °C and 40 °C, and respective pH optima of 6.0 and 7.0. Further biochemical characterisation showed that FAE9 and FAE27 have high substrate specificity, following the fact that EFA is the preferred substrate for FAE9 (kcat/Km value of 128 s−1.mM-1) and also the preferred substrate for FAE27 (kcat/Km value of 137 s−1.mM-1). This work proves that soil is a valuable environmental source for novel esterase screening through functional based metagenomic approach. Therefore, this method may be used to screen for other valuable enzymes from environmental sources using inexpensive natural sources to encourage the screening of specific enzymes. Biochemistry of the two isolated enzymes makes these enzymes to be useful in industrial applications due to broad substrate activity that could replace the specialised enzymes to complete plant biomass degradation.
- Full Text:
- Authors: Shezi, Ntombifuthi
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4172 , http://hdl.handle.net/10962/d1021266
- Description: Lignocellulosic biomass is a promising renewable resource on earth. Plant biomass contains fermentable sugars and other moieties that can be converted to biofuels or other chemicals. Enzymatic hydrolysis of these biopolymers is significant in the liberation of sugars for fermentation into desired products. Owing to its complex structure, synergistic action of enzymes is required for its degradation. Enzymes that are involved in biomass degradation include cellulases, hemicellulases and the accessory enzymes acetyl xylan esterases and ferulic acid esterases. Ferulic acid esterases (FAEs, EC 3.1.1.73), represent a subclass of carboxylester hydrolases (EC 3.1.1.-) that catalyse the release of hydroxycinnamic acids (such as ferulic acid, p-coumaric, ferulic, sinapic and caffeic acid) that are generally found esterified to polysaccharides, such as arabinoxylans. Hydroxycinnamic acids have widespread potential applications due to their antimicrobial, photoprotectant and antioxidant properties, as well as their use as flavour precursors. Therefore, this interesting group of FAEs has a potentially wide variety of applications in agriculture, food and pharmaceutical industries. In the search for novel biocatalysts, metagenomics is considered as an alternative approach to conventional microbe screening, therefore, searching for novel biocatalysts from a soil metagenome that harbours a unique diversity of biocatalyst is significant. The aim of this study was to extract DNA from soil associated with cattle manure and construct a soil metagenomic library using a fosmid based plasmid vector and subsequently functionally screen for ferulic acid esterases using ethyl ferulate as a model substrate. A total of 59 recombinant fosmids conferring ferulic acid esterase phenotypes were identified (Hit rate 1:3122) and the two fosmids that consistently showed high FAE activities were selected for further study. Following nucleotide sequencing and translational analysis, two fae encoding open reading frames (FAE9 and FAE27) of approximately 274 and 322 aa, respectively, were identified. The amino acid sequence of the two ORFs contained a classical conserved esterase/lipase G-x-S-x-G sequence motif. The two genes (fae9 and fae27) were successfully expressed in Escherichia coli BL21 (DE3) and the purified enzymes exhibited respective temperature optima of 50 °C and 40 °C, and respective pH optima of 6.0 and 7.0. Further biochemical characterisation showed that FAE9 and FAE27 have high substrate specificity, following the fact that EFA is the preferred substrate for FAE9 (kcat/Km value of 128 s−1.mM-1) and also the preferred substrate for FAE27 (kcat/Km value of 137 s−1.mM-1). This work proves that soil is a valuable environmental source for novel esterase screening through functional based metagenomic approach. Therefore, this method may be used to screen for other valuable enzymes from environmental sources using inexpensive natural sources to encourage the screening of specific enzymes. Biochemistry of the two isolated enzymes makes these enzymes to be useful in industrial applications due to broad substrate activity that could replace the specialised enzymes to complete plant biomass degradation.
- Full Text:
Biology and ecology of Glossogobius callidus (Smith 1937) in irrigation impoundments in the Sundays River Valley of the Eastern Cape
- Authors: Mofu, Lubabalo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1136 , vital:20023
- Description: The River Goby Glossogobius callidus (Smith, 1937) is a native abundant fish in both freshwater and estuarine habitats in the Cape Fold Ecoregion, yet little information is available on its life-history. This study aims to contribute to knowledge on the age and growth, reproductive biology and the diet and feeding habits of G. callidus in irrigation impoundments. Glossogobius callidus was sampled monthly from August 2013 till March 2015; from the irrigation ponds in the Sundays River Valley, Eastern Cape Province, South Africa. To determine sex, gonads were visually assessed under a dissecting microscope to confirm the sex based on the shape of the urogenital papillae. Fish were then dissected to confirm sex and gonads were categorised into five macroscopic stages which were histologically validated. Microscopic stages of gonadal development were discerned based on nuclear and cytoplasmic characteristics of the oocyte or sperm. Ovaries and sperms were assigned stages based on the most advanced type of oocyte present. In total 2054 fishes ranging in length from 21.1 mm to 137.2 mm TL were sampled. The sex ratio (1.1 males: 1 females) did not differ from unity (x2 = 0.027, df = 1, p = 0.87). Length at 50% maturity (Lm) was 70 mm TL females and 72 mm TL for males. Spawning season was mid-spring and mid-summer and mean ± S.D absolute fecundity was estimated at 1028.2 ± 131.7 ova/fish. Relative fecundity (number of vitellogenic oocytes per gram of eviscerated fish mass) were estimated at 50 ± 18 ova/fish gram. Otoliths from 560 fish were used for ageing. Growth zone deposition rate was validated using edge analysis. As a unimodal periodic regression model best described the temporal proportion of opaque zone deposition on the edge of otoliths over a one-year period, growth zone deposition rate was validated as annual. The oldest female fish was a 4-year old 84.4 mm TL fish and the oldest male was a 7-year old 100.5 mm TL fish. The length-at-age for the entire population of 560 G. callidus provided von Bertalanffy parameters of Lt = 92 (1 - e -0.58(t + 0.4)) mm TL for the entire population, Lt = 70 (1 - e -1.8 (t + 0.06)) mm TL for males and Lt = 65 (1 - e -1.8 (t + 0.05)) mm TL for females. Converting length at maturity to age at maturity demonstrated that G. callidus attained maturity at an age of 2-years. Growth performance described using the phi-prime index showed that G. callidus had lower growth performance compared to the invasive Neogobius melanostomus. Using age structure, natural mortality was estimated at 1.31 yr-1 using catch curve analysis. Diet of G. callidus comprised of ten taxonomic groups. Among these, aquatic invertebrates were the most diverse group but while relative contribution of the dietary components varied across all size classes and seasons, the key prey items were consistently found in all size classes. These were Diptera, Hemiptera, Trichoptera, Odonata, Cladocera, Copepoda, Hydracarina, Amphipoda, Crustacea, and Mollusca. While dietary differences were observed between the size classes and throughout the seasons, G. callidus can be regarded as a generalist feeder preying on an array of different species. Given its abundance and diet, I suggest that G. callidus contribute considerably to the invertebrate predation pressure in these artificial aquatic environments in an arid region. In summary, medium fecundity, fast growth, moderate maturity, and a generalist feeding behaviour demonstrate that G. callidus is an equilibrium life strategist. In comparison with other species, the life-history traits of G. callidus from irrigation impoundments resemble those of other freshwater goby species, some of which are global invaders.
- Full Text:
- Authors: Mofu, Lubabalo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1136 , vital:20023
- Description: The River Goby Glossogobius callidus (Smith, 1937) is a native abundant fish in both freshwater and estuarine habitats in the Cape Fold Ecoregion, yet little information is available on its life-history. This study aims to contribute to knowledge on the age and growth, reproductive biology and the diet and feeding habits of G. callidus in irrigation impoundments. Glossogobius callidus was sampled monthly from August 2013 till March 2015; from the irrigation ponds in the Sundays River Valley, Eastern Cape Province, South Africa. To determine sex, gonads were visually assessed under a dissecting microscope to confirm the sex based on the shape of the urogenital papillae. Fish were then dissected to confirm sex and gonads were categorised into five macroscopic stages which were histologically validated. Microscopic stages of gonadal development were discerned based on nuclear and cytoplasmic characteristics of the oocyte or sperm. Ovaries and sperms were assigned stages based on the most advanced type of oocyte present. In total 2054 fishes ranging in length from 21.1 mm to 137.2 mm TL were sampled. The sex ratio (1.1 males: 1 females) did not differ from unity (x2 = 0.027, df = 1, p = 0.87). Length at 50% maturity (Lm) was 70 mm TL females and 72 mm TL for males. Spawning season was mid-spring and mid-summer and mean ± S.D absolute fecundity was estimated at 1028.2 ± 131.7 ova/fish. Relative fecundity (number of vitellogenic oocytes per gram of eviscerated fish mass) were estimated at 50 ± 18 ova/fish gram. Otoliths from 560 fish were used for ageing. Growth zone deposition rate was validated using edge analysis. As a unimodal periodic regression model best described the temporal proportion of opaque zone deposition on the edge of otoliths over a one-year period, growth zone deposition rate was validated as annual. The oldest female fish was a 4-year old 84.4 mm TL fish and the oldest male was a 7-year old 100.5 mm TL fish. The length-at-age for the entire population of 560 G. callidus provided von Bertalanffy parameters of Lt = 92 (1 - e -0.58(t + 0.4)) mm TL for the entire population, Lt = 70 (1 - e -1.8 (t + 0.06)) mm TL for males and Lt = 65 (1 - e -1.8 (t + 0.05)) mm TL for females. Converting length at maturity to age at maturity demonstrated that G. callidus attained maturity at an age of 2-years. Growth performance described using the phi-prime index showed that G. callidus had lower growth performance compared to the invasive Neogobius melanostomus. Using age structure, natural mortality was estimated at 1.31 yr-1 using catch curve analysis. Diet of G. callidus comprised of ten taxonomic groups. Among these, aquatic invertebrates were the most diverse group but while relative contribution of the dietary components varied across all size classes and seasons, the key prey items were consistently found in all size classes. These were Diptera, Hemiptera, Trichoptera, Odonata, Cladocera, Copepoda, Hydracarina, Amphipoda, Crustacea, and Mollusca. While dietary differences were observed between the size classes and throughout the seasons, G. callidus can be regarded as a generalist feeder preying on an array of different species. Given its abundance and diet, I suggest that G. callidus contribute considerably to the invertebrate predation pressure in these artificial aquatic environments in an arid region. In summary, medium fecundity, fast growth, moderate maturity, and a generalist feeding behaviour demonstrate that G. callidus is an equilibrium life strategist. In comparison with other species, the life-history traits of G. callidus from irrigation impoundments resemble those of other freshwater goby species, some of which are global invaders.
- Full Text:
Calibration and wide field imaging with PAPER: a catalogue of compact sources
- Authors: Philip, Liju
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2397 , vital:20285
- Description: Observations of the redshifted 21 cm HI line promise to be a formidable tool for cosmology, allowing the investigation of the end of the so-called dark ages, when the first galaxies formed, and the subsequent Epoch of Reionization when the intergalactic medium transitioned from neutral to ionized. Such observations are plagued by foreground emission which is a few orders of magnitude brighter than the 21 cm line. In this thesis I analyzed data from the Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER) in order to improve the characterization of the extragalactic foreground component. I derived a catalogue of unresolved radio sources down to a 5 Jy flux density limit at 150 MHz and derived their spectral index distribution using literature data at 408 MHz. I implemented advanced techniques to calibrate radio interferometric data that led to a few percent accuracy on the flux density scale of the derived catalogue. This work, therefore, represents a further step towards creating an accurate, global sky model that is crucial to improve calibration of Epoch of Reionization observations.
- Full Text:
- Authors: Philip, Liju
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2397 , vital:20285
- Description: Observations of the redshifted 21 cm HI line promise to be a formidable tool for cosmology, allowing the investigation of the end of the so-called dark ages, when the first galaxies formed, and the subsequent Epoch of Reionization when the intergalactic medium transitioned from neutral to ionized. Such observations are plagued by foreground emission which is a few orders of magnitude brighter than the 21 cm line. In this thesis I analyzed data from the Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER) in order to improve the characterization of the extragalactic foreground component. I derived a catalogue of unresolved radio sources down to a 5 Jy flux density limit at 150 MHz and derived their spectral index distribution using literature data at 408 MHz. I implemented advanced techniques to calibrate radio interferometric data that led to a few percent accuracy on the flux density scale of the derived catalogue. This work, therefore, represents a further step towards creating an accurate, global sky model that is crucial to improve calibration of Epoch of Reionization observations.
- Full Text: