Taxonomic and trait-based responses of the orders Ephemeroptera, Plecoptera, Odonata, And Trichoptera (EPOT) to sediment stress in the Tsitsa River and its tributaries, Eastern Cape, South Africa
- Authors: Akamagwuna, Frank Chukwuzuoke
- Date: 2019
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/68082 , vital:29196
- Description: Increased urbanization and industrialisation due to human population growth and associated high demand for food have led to widespread disturbances of freshwater ecosystems and associated resources. A widely recognised consequence of these disturbances is the excessive delivery of sediments into the freshwater ecosystems, which severely affects the functioning and integrity of these systems.. The major water quality impairment in the Tsitsa River and its tributaries, situated in the Mzimvubu catchment in the Eastern Cape Province of South Africa, is known to be excessive sediment input. In this study, the application of macroinvertebrates taxonomic-based and trait-based approaches was used to assess the responses and vulnerability of Ephemeroptera, Plecoptera, Odonata and Trichoptera (EPOT) species to settled and suspended sediments stress in eight selected sampling sites in the Tsitsa River and its tributaries. The eight selected sites were Site 1 (Tsitsa upstream), Site 2 (Tsitsa downstream), Site 3 (Qurana tributary), Site 4 (Pot River upstream), Site 5 (Pot River downstream), Site 6 (Little Pot River), Site 7 (Millstream upstream) and Site 8 (Millstream downstream). The methods used in this study involved the analysis of water physico-chemical variables as well as sediment characteristics, derivation of five EPOT metrics, EPOT species-level taxonomic analysis, individual EPOT trait analysis and the development of a novel trait-based approach using a combination of traits. The sampling of EPOT taxa was done using the SASS5 protocols. Identification of EPOT was done to genus/species level and all data were subjected to relevant statistical analysis. The results of ecological categories derived for the physico-chemical variables generally indicated the ecological categories A and B, which was indicative of good water quality conditions. The result of sediment particle analysis revealed four distinct site groups: site group 1 (Tsitsa River upstream and Qurana tributary), site group 2 (Tsitsa River downstream and Millstream upstream), site group 3 (Pot River, both upstream and downstream, and Millstream downstream) and site group 4 (Little Pot River). The species-level taxonomic analysis of EPOT revealed that site group 1 was the most sediment-influenced sites whereas site group 4 was the least sediment-influenced. Species such as Paragopmhus sp., Aeshna sp. and Baetis sp. were considered sediment-tolerant with strong positive association with site group 1. The novel trait-based approach developed in this study proved useful in predicting the responses of EPOT species to sediment stress, and further discriminated between the study sites. The approach was used to group EPOT species into four vulnerability classes. The result showed that filter feeding EPOT species that have filamentous gills, preferring stone biotopes and feeding on detritus (FPOM) were mostly classified as highly vulnerable to sediment stress and indicated no significant association with the highly sediment-influenced site group 1. The TBA largely corresponded well to the predictions made with the relative abundance of the vulnerable class decreasing in the sediment-influenced sites compared to the tolerant and highly tolerant classes. Overall, the study revealed the importance of the complementary use of taxonomic and trait-based approaches to biomonitoring.
- Full Text:
- Date Issued: 2019
A pilot wide-field VLBI survey of the GOODS-North field
- Authors: Akoto-Danso, Alexander
- Date: 2019
- Subjects: Radio astronomy , Very long baseline interferometry , Radio interometers , Imaging systems in astronomy , Hubble Space Telescope (Spacecraft) -- Observations
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/72296 , vital:30027
- Description: Very Long Baseline Interferometry (VLBI) has significant advantages in disentangling active galactic nuclei (AGN) from star formation, particularly at intermediate to high-redshift due to its high angular resolution and insensitivity to dust. Surveys using VLBI arrays are only just becoming practical over wide areas with numerous developments and innovations (such as multi-phase centre techniques) in observation and data analysis techniques. However, fully automated pipelines for VLBI data analysis are based on old software packages and are unable to incorporate new calibration and imaging algorithms. In this work, the researcher developed a pipeline for VLBI data analysis which integrates a recent wide-field imaging algorithm, RFI excision, and a purpose-built source finding algorithm specifically developed for the 64kx64k wide-field VLBI images. The researcher used this novel pipeline to process 6% (~ 9 arcmin2 of the total 160 arcmin2) of the data from the CANDELS GOODS- North extragalactic field at 1.6 GHz. The milli-arcsec scale images have an average rms of a ~ 10 uJy/beam. Forty four (44) candidate sources were detected, most of which are at sub-mJy flux densities, having brightness temperatures and luminosities of >5x105 K and >6x1021 W Hz-1 respectively. This work demonstrates that automated post-processing pipelines for wide-field, uniform sensitivity VLBI surveys are feasible and indeed made more efficient with new software, wide-field imaging algorithms and more purpose-built source- finders. This broadens the discovery space for future wide-field surveys with upcoming arrays such as the African VLBI Network (AVN), MeerKAT and the Square Kilometre Array (SKA).
- Full Text:
- Date Issued: 2019
The influence of artificial light on the foraging efficiency and diet of insect eating bats
- Authors: Bailey, Lauren
- Date: 2019
- Subjects: Predation (Biology) , Bats -- Effect of light on , Bats -- Nutrition , Moths
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76376 , vital:30555
- Description: Artificial light may be altering the interactions between bats and moth prey. Unable to make use of bat evasion strategies around artificial light, eared moths are susceptible to exploitation by syntonic bats (using echolocation frequencies between 20-50 kHz within the hearing range of eared moths). Using a handheld plasma metabolite analyzer, I evaluated the foraging success of syntonic bats and rarer allotonic bats (using echolocation frequencies outside the hearing range of eared moths), in areas with artificial light and in areas of natural darkness. I used microscope diet analysis to determine whether bats were consuming more or fewer moths in areas with artificial light and in areas of natural darkness. Syntonic bats were more selective for moth prey under lit conditions, likely owing to a reduction in the ability of tympanate moths to evade bats. Moths increased in the diets of generalist syntonic bats (Pipistrellus hesperidus) foraging around artificial light sources. Some P. hesperidus individuals showed high β-hydroxybutyrate levels around lights, but there was no difference in β-hydroxybutyrate levels between lit and unlit conditions. There is insufficient evidence to reject the null hypothesis that the foraging success of syntonic bats is equivalent in lit vs unlit conditions. The foraging success and diets of allotonic bats, Rhinolophus capensis, appear to be negligibly impacted by artificial light on a small scale. My study emphasizes the need for a mechanistic understanding of the influence of artificial light on the foraging success of bat species. Bat-moth interactions may be influenced by other factors apart from the common assumption that increased refuelling rates will occur in syntonic species foraging on moths around artificial light.
- Full Text:
- Date Issued: 2019
A crowdsensing method for water resource monitoring in smart communities
- Authors: Banda, Clara Mloza
- Date: 2019
- Subjects: Data collection platforms
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/42449 , vital:36658
- Description: Crowdsensing aims to empower a large group of individuals to collect large amounts of data using their mobile devices, with the goal of sharing the collected data. Existing crowdsensing studies do not consider all the activities and methods of the crowdsensing process and the key success factors related to the process. Nor do they investigate the profile and behaviour of potential participants. The aim of this study was to design a crowdsensing method for water resource monitoring in smart communities. This study opted for an exploratory study using the Engaged Scholarship approach, which allows the study of complex real-world problems based on the different perspectives of key stakeholders. The proposed Crowdsensing Method considers the social, technical and programme design components. The study proposes a programme design for the Crowdsensing Methodwhich is crowdsensing ReferenceFrameworkthat includes Crowdsensing Processwith key success factors and guidelines that should be considered in each phase of the process. The method also uses the Theory of Planned Behaviour (TPB) to investigate citizens’intention to participate in crowdsensing for water resource monitoring and explores their attitudes, norms and perceived behavioural control on these intentions. Understanding the profiles of potential participants can assist with designing crowdsensing systems with appropriate incentive mechanisms to achieve adequate user participation and good service quality. A survey was conducted to validate the theoretical TB model in a real-world context. Regression and correlation analyses demonstrated that the attitudes, norms and perceived behavioural control can be used to predict participants’ intention to participate in crowdsensing for water resource monitoring. The survey results assisted with the development of an Incentive Mechanism as part of the Crowdsensing Method. This mechanism incorporates recruitment and incentive policies, as well as guidelines derived from the literature review and extant system analysis. The policies, called the OverSensepolicies, provide guidance for recruitment and rewarding of participants using the popular Stackelberg technique. The policies were evaluated using simulation experiments with a data set provided by the case study, the Nelson Mandela Bay Municipality. The results of the simulation experiments illustrated that the OverSenserecruitmentpolicycan reduce the computing resources required for the recruitment of participants and that the recruitment policy performs better than random or naïve recruitment policies. The proposed Crowdsensing Method was evaluated using an ecosystem of success factors for mobile-based interventions identified in the literature and the Crowdsensing Method adhered to a majority (90%) of the success factors. This study also contributes information systems design theory by proposing several sets of guidelines for crowdsensing projects and the development of crowdsensing systems. This study fulfils an identified need to study the applicability of crowdsensing for water resource monitoring and explores how a crowdsensing method can create a smart community.
- Full Text:
- Date Issued: 2019
The use of image processing to determine cell defects in polycrystalline solar modules
- Authors: Banda, Peter
- Date: 2019
- Subjects: Polycrystals
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/36573 , vital:33996
- Description: This research aims to use image processingtodetermine cell defects in polycrystalline solar modules. Image processing is a process of enhancing images for differentapplications. One domain that seems to not yet utilise the use of image processing, is photovoltaics. An increased use of fossil fuels is damaging the earth and a call to protect the earth has resulted in the emergence of pollutant-free technologies such as polycrystalline photovoltaic (PV) cells, which are connected to make up solar modules. However, defects often affect the performance of PV cells and consequently solar modules. Electroluminescence (EL) images are used to examine polycrystalline solar (PV) modules to determine if the modules are defective. The main research question that this research addressed is“How can an image processing technique be used to effectively identify defective polycrystalline PV cells from EL images of such cells?“. The experimental research methodology was used to address the main research question. The initial investigation into the problem revealed that certain sectors within industry, as well as the Physics Department at Nelson Mandela University(NMU), do not currently utiliseimage processing when examining EL images of solar modules. The current process is a tedious, manual process whereby solar modules are manually inspected. An analysis of the current processes enabled the identification of ways in which to automatically examine EL images of solar modules. An analysis of literatureprovided a better understanding of the different techniques that are used to examine solar modules, and it was identified how image processing can be applied to EL images. Further analysis of literatureprovided a better understanding of image processing and how image classification experiments using Deep Learning (DL) as an image processing technique can be used to address the main research question. The outcome of the experiments conducted in this research weredifferentadaptive models(LeNet, MobileNet, Xception)that can classify EL images of PV cellsaccording to known standardsused by the Physics Department at NMU. The known standards yielded four classes; normal, uncritical, critical and very critical, which were used for the classification of EL images of PV cells. The adaptive models were evaluated to obtain the precision, recall and F1–scoreof the models.The precession, recall, and F1–score were required to determine how effective the models were in identifying defective PV cells from EL images.The results indicated that an image processing technique canbe used to identify defective polycrystalline PV cells from EL images of such cells. However, further research needs to be conducted to improve the effectiveness of the adaptive models.
- Full Text:
- Date Issued: 2019
Development of a manual to train food handlers of the national school nutrition programme
- Authors: Barkhuizen, Kirsten Lyn
- Date: 2019
- Subjects: Food -- Safety measures
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/36559 , vital:33974
- Description: The study was conducted in order to develop a hygiene and food safety manual that can be used to train the food handlers of the National School Nutrition Programme. The co-operation of the Institute for International Medicine, Partnerships with Children, as part of the Health in Action Programme in this study, is appreciated. Food handlers of the National School Nutrition Programme in low socio-economic schools, in the Nelson Mandela Bay, in the Eastern Cape, were the population of the study. With many South Africans experiencing poverty and food insecurity, the National School Nutrition Programme aims to provide a social safety net and address short term hunger in children. However, challenges are faced regarding the implementation thereof, such as a lack of training of food handlers. This results in poor hygiene and food safety knowledge and behaviour. Subsequently, the risk of transmission of foodborne pathogens and the contamination of food rises. Foodborne illnesses are a major cause of morbidity and mortality, specifically in children, due to weak immune systems. Therefore, the study was conducted in order to develop and test a hygiene and food safety manual so that it can be made available to the South African Department of Education to be used by teachers in order to train the food handlers of the National School Nutrition Programme. The manual can then be used to train all newly recruited food handlers, and therefore ensure that school meals are safe to consume by learners.
- Full Text:
- Date Issued: 2019
Response of black wildebeest, a specialised grazer, to grass availability
- Authors: Barnardo, Toshka
- Date: 2019
- Subjects: Grasslands -- Research -- South Africa , Grassland ecology -- Research -- South Africa Food habits -- Research -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/30876 , vital:31192
- Description: The black wildebeest Connochaetes gnou, a southern African endemic largely confined to the Grassland biome, was used as a model species to assess the response of a specialised grazer to grass availability, as an indicator of habitat quality. The occurrence of animals in low-quality habitats may have detrimental effects on population performance and persistence. Robust techniques are therefore required to assess the response of animals to varying habitat quality, to ensure sustainability of populations and species. Black wildebeest habitat use was assessed in relation to grass availability and visibility, and faecal analysis was used to estimate variation in diet composition and quality, parasite loads, and faecal pellet dimensions, across a grass gradient. Grass consumption, diet quality, and faecal pellet size and weight of black wildebeest increased with increasing grass availability. While black wildebeest consumed up to 55% browse at grass-poor sites, they consistently preferred grasses, potentially resulting in an increased intake of low-quality grasses at grass-poor sites. This, combined with the increased intake of indigestible fibres in browse, may explain the observed trends in diet quality, which in turn may explain variation in faecal pellet size and weight (indicators of body size and weight). Furthermore, black wildebeest population trends within the study area suggest that populations in grass-poor habitats, outside their natural distribution range, may exhibit reduced population performance. These findings suggest that grass availability may be a useful indicator of habitat quality for specialised grazers. The study also provided an opportunity to explore the utility of various diet assessment techniques for estimating herbivore diet composition and quality. Caution should be applied when interpreting and comparing estimates of diet composition and quality that were estimated using different techniques, because different techniques may yield different diet estimates. The study also suggests that black wildebeest may switch to C3 grasses in the winter (as indicated by isotope analysis).
- Full Text:
- Date Issued: 2019
Targeted attack detection by means of free and open source solutions
- Authors: Bernardo, Louis F
- Date: 2019
- Subjects: Computer networks -- Security measures , Information technology -- Security measures , Computer security -- Management , Data protection
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92269 , vital:30703
- Description: Compliance requirements are part of everyday business requirements for various areas, such as retail and medical services. As part of compliance it may be required to have infrastructure in place to monitor the activities in the environment to ensure that the relevant data and environment is sufficiently protected. At the core of such monitoring solutions one would find some type of data repository, or database, to store and ultimately correlate the captured events. Such solutions are commonly called Security Information and Event Management, or SIEM for short. Larger companies have been known to use commercial solutions such as IBM's Qradar, Logrythm, or Splunk. However, these come at significant cost and arent suitable for smaller businesses with limited budgets. These solutions require manual configuration of event correlation for detection of activities that place the environment in danger. This usually requires vendor implementation assistance that also would come at a cost. Alternatively, there are open source solutions that provide the required functionality. This research will demonstrate building an open source solution, with minimal to no cost for hardware or software, while still maintaining the capability of detecting targeted attacks. The solution presented in this research includes Wazuh, which is a combination of OSSEC and the ELK stack, integrated with an Network Intrusion Detection System (NIDS). The success of the integration, is determined by measuring postive attack detection based on each different configuration options. To perform the testing, a deliberately vulnerable platform named Metasploitable will be used as a victim host. The victim host vulnerabilities were created specifically to serve as target for Metasploit. The attacks were generated by utilising Metasploit Framework on a prebuilt Kali Linux host.
- Full Text:
- Date Issued: 2019
The influence of briefing on Eastern Cape government project outcomes
- Authors: Binqela, Lukhanyo
- Date: 2019
- Subjects: Government projects -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44562 , vital:38128
- Description: South African Government projects are frequently completed with large cost overruns, extended schedules, quality concerns and an increase in emerging contractors making a significant loss in projects they undertake. The construction phase has been the focus of many studies on the causes of unfavourable project outcomes. However, the crucial stages in the construction process that influence the success of a project are the early ones. This is where major decisions that influence the features and form of a project occur. This study, which adopts a case study approach, aims to establish the influence of the brief development process on the outcome of Government projects in the Eastern Cape. Through the reviewed literature and primary data collection, the study aimed at establishing the influence of the brief that is utilised for a need analysis, to define a detailed scope of works, stakeholder engagement and the time management on Eastern Cape Government project outcomes. The Sarah Baartman district was the selected geographical scope of research. Five projects were selected; these included three schools, one emergency medical service facility and one office facility. The study revealed that Eastern Cape Government projects brief development is based on the client department 2013 Published Norms and Standards for state buildings and a need analysis for other stakeholders is not considered. The study further revealed that there is no stakeholder management in government projects; therefore, there is no stakeholder engagement plan during the brief development. The study further revealed that government time management is suboptimal because stakeholder needs are not realised. The research also found that Eastern Cape Government projects do not achieve stakeholder satisfaction and are delivered late. However, some Government projects are able to meet the desired quality and are within budget. The study thus proposes that the Eastern Cape Government projects need to adopt the dynamic brief development process and implement stakeholder management. The brief development process should be an ongoing process extending throughout the project life cycle responding in an innovative manner to emerging stakeholder requirements.
- Full Text:
- Date Issued: 2019
The influence of briefing on Eastern Cape government project outcomes
- Authors: Binqela, Lukhanyo
- Date: 2019
- Subjects: Project management -- South Africa -- Eastern Cape , Construction industry -- South Africa -- Eastern Cape Construction industry -- Management
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/44895 , vital:38186
- Description: South African Government projects are frequently completed with large cost overruns, extended schedules, quality concerns and an increase in emerging contractors making a significant loss in projects they undertake. The construction phase has been the focus of many studies on the causes of unfavourable project outcomes. However, the crucial stages in the construction process that influence the success of a project are the early ones. This is where major decisions that influence the features and form of a project occur. This study, which adopts a case study approach, aims to establish the influence of the brief development process on the outcome of Government projects in the Eastern Cape. Through the reviewed literature and primary data collection, the study aimed at establishing the influence of the brief that is utilised for a need analysis, to define a detailed scope of works, stakeholder engagement and the time management on Eastern Cape Government project outcomes. The Sarah Baartman district was the selected geographical scope of research. Five projects were selected; these included three schools, one emergency medical service facility and one office facility. The study revealed that Eastern Cape Government projects brief development is based on the client department 2013 Published Norms and Standards for state buildings and a need analysis for other stakeholders is not considered. The study further revealed that there is no stakeholder management in government projects; therefore, there is no stakeholder engagement plan during the brief development. The study further revealed that government time management is suboptimal because stakeholder needs are not realised. The research also found that Eastern Cape Government projects do not achieve stakeholder satisfaction and are delivered late. However, some Government projects are able to meet the desired quality and are within budget. The study thus proposes that the Eastern Cape Government projects need to adopt the dynamic brief development process and implement stakeholder management. The brief development process should be an ongoing process extending throughout the project life cycle responding in an innovative manner to emerging stakeholder requirements.
- Full Text:
- Date Issued: 2019
The cultivation of Gracilaria gracilis in the Swartkops estuary, South Africa
- Authors: Blewett, Alec
- Date: 2019
- Subjects: Gracilaria -- South Africa -- Port Elizabeth , Marine algae Algae -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/31446 , vital:31391
- Description: Gracilaria gracilis (Stackhouse) M. Steentoft, L. M. Irvine & W. F. Farnham is a species of red macroalgae which occurs naturally within the Swartkops Estuary in South Africa. Bunches of the species were inserted into the lay of ropes, which were then either suspended in the water column at the Tiger Bay Marina, or staked at the surface of the sediment in the mudflats where the initial material was harvested from. The first site was used for the suspended growth trial, while the second site was for the bottom grown trial. Both of the growth trials ran for the same time period, which was approximately three weeks per season. This study examined three facets of the G. gracilis material that was grown. The growth rate and biomass were recorded in order to examine the potential for the growth of the species on longlines within the estuary. Secondly, the crude nutritional content of the species was determined in order to assess its potential for use as an abalone feed, specifically the dry and ashed weights, and the protein, carbohydrate and lipid contents. Lastly, the cultivated biomass was examined in terms of its agar gel yield and properties, which included the gel strength and the gel –melting and –forming temperatures. The growth rates for the cultivated G. gracilis were poor, and the largest positive growth rate of 1.17 ± 3.2% was found in spring, for the bottom grown trial. This season also saw the only increase in biomass above that which was seeded onto the line, and the final average weight after 22 days was 354.28 ± 68.04 g. All other growth rates were negative, and biomass declined in both growth trials across all the seasons. The suspended growth trials showed more extreme declines, and were heavily contaminated with epiphytic material, while the bottom grown trial had more gradual decrease, and it is likely that conditions associated with the culture systems were not ideal. The largest percentage of protein was found in autumn, where the bottom grown trial had a value of 88 ± 2.32%. For all the seasons, the lipid content had an average percentage of 1.80 ± 0.75% for the bottom grown trial, while the suspended trial was very similar, and had a value of 1.74 ± 0.58%. The nutritional composition of the cultivated biomass was not found to be a good abalone feed in comparison to other studies in land-based aquaculture facilities. Agar characteristics extracted in the present study showed the greatest potential for use as a valuable economic resource. The native agar extracted from the cultivated material was very close to the standards set by United States Pharmacopeia for all the characteristics, and has the potential to possibly be improved further by using an alkali treatment.
- Full Text:
- Date Issued: 2019
Property price prediction: a model utilising sentiment analysis
- Authors: Botes, Rhys Cameron
- Date: 2019
- Subjects: Natural language processing (Computer science) , Computational linguistics Text processing (Computer science) Social networks
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/37117 , vital:34119
- Description: The increase in the use of social media has led many researchers and companies to investigate the potential uses of the data that is generated by these social media platforms. This research study investigates how the use of sentiment variables, obtained from the social media platform Twitter, can be used to augment housing transfer data in order to develop a predictive model. The Design Science Research (DSR) methodology was followed, guided by a Social Media Framework. Experimentation was required within the Design Cycle of the DSR methodology, which lead to the adoption of the Experimental Research methodology within this cycle. An initial literature review identified regression models for property price prediction. Through experimentation, Gradient Boosting regression was identified as an optimal regression model for this purpose. Thereafter a review of sentiment analysis models was conducted which resulted in the proposal of a CNN-LSTM model for the classification of Tweets. Initial experimentation conducted with this proposed model resulted in an obtained accuracy comparable to the top performing sentiment analysis models identified. A dataset obtained through SemEval, a series of evaluations of computational semantic analysis systems, was used for this phase. For the final experimentation, The CNN-LSTM model was used to obtain sentiment variables from Tweets that were collected from the Western Cape Province in 2017. This property dataset was augmented with the sentiment variables, after which experimentation was conducted by applying Gradient Boosting regression. The augmentation was done in two ways, either based on suburb pertaining to the property, or to the month in which the property was transferred. The results indicate that a model for Property Price Prediction Utilising Sentiment Analysis demonstrates a small improvement when suburb-based sentiment, obtained from Tweets with a minimum threshold per suburb, is utilised. An important finding was the fact that, when geo-coordinates are removed from the dataset, the sentiment variables replace them in the regression results, producing the same level as accuracy as when the coordinates are included.
- Full Text:
- Date Issued: 2019
Re-surveying the insectivorous bats of northern Kruger National Park, South Africa
- Authors: Brinkley, Erin Reed
- Date: 2019
- Subjects: Bats -- South Africa , Bats -- Behavior , Bats -- South Africa -- Ecology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/115697 , vital:34216
- Description: With over 1,300 known species, the order Chiroptera makes up about 20 percent of all mammalian species. Due to its sub-tropical climate, the northern part of Kruger National Park (KNP) in South Africa is believed to have the highest bat species richness in the country. However, the last comprehensive assessment of bat diversity in the region was conducted more than 30 years ago. In 2017 and 2018, I undertook the first detailed re-assessment of the bat communities of the northern KNP since the early 1980’s. I used both live-capture (harp traps and mist-netting) and acoustic technology (SM2 and SM4 Songmeters, Wildlife Acoustics. MA, USA) to sample bats at 24 sites across the northern region of KNP. Through live-capture (336 trapping hours), 155 bats representing 13 species from five families were recorded including Cloetis pervicali, which has never been recorded within the borders of the KNP before. The echolocation calls of all captured bats were recorded to develop a site-specific call reference library that was used (in combination with existing reference calls) as a guide for the identification of bat calls recorded using the acoustic detectors set across 24 sites (278 sampling nights). The acoustic monitoring identified 22 species from six families and two unknown sets of calls. Compared to the historical data of 40 documented species (collected over a 30-year period), the current survey (27 species) resulted in a lower species richness. However, this is likely due to the lower overall sampling effort during my survey. By re-surveying the bats of northern KNP, I have contributed towards an overall bat species inventory for this region. In addition, I have generated an important baseline dataset for the future monitoring of bat diversity across the KNP. Due to bats being important biological indicators, increased research on the various species and their behaviours is essential for improving our understanding of climate change effects as well as the overall health of the environment, especially in protected areas.
- Full Text:
- Date Issued: 2019
Sulphide textures and compositions associated with the hydrothermal/magmatic system of the Twangiza gold deposit (South Kivu, DRC)
- Authors: Busane, Emmanuel Aganze
- Date: 2019
- Subjects: Gold mines and mining -- Congo (Democratic Republic) , Geology -- Congo (Democratic Republic) , Hydrothermal alteration -- Congo (Democratic Republic) , Sulphide minerals -- Congo (Democratic Republic) , Gold ores -- Geology -- Congo (Democratic Republic) , Geochemistry -- Congo (Democratic Republic) , Twangiza Mine (Congo (Democratic Republic))
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/76588 , vital:30610
- Description: Twangiza mine is a gold deposit situated in the eastern Democratic Republic of Congo. The rock types at the Twangiza Mine consist of black shale, including carbonaceous mudstone and thin intercalated layers of siltstone, and feldspar-rich granitoid intrusive sills, referred to as albitite, folded into a major antiformal structure. The gold mineralization at the mine is commonly found associated with sulphides. The sulphide textures and compositions of mineralized and unmineralized samples of black shales, albitite sills and hydrothermal veins in the mine are considered for the understanding of the spatial association of gold with sulphides and gold mineralization history of the mine. The sulphides within the Twangiza mine consist of pyrite, arsenopyrite, pyrrhotite, chalcopyrite and rare cobaltite. The primary pyrite texture occurs in unmineralized black shale and is interpreted to be diagenetic. It consists of fine-grained anhedral pyrite crystals aggregating into spherical nodules and formed in replacement of organic material during the diagenesis process. The secondary pyrite textures resulted from the hydrothermal fluids activity and include (i) aggregates of annealed anhedral crystals into sulphide-rich lenses; (ii) elongated anhedral pyrite in the form of short stringers; (iii) fine-grained subhedral to euhedral pyrite randomly distributed within the rock matrix; (iv) euhedral zoned pyrite crystals occurring within veins; (v) aggregations of fine-grained anhedral pyrite, locally distributed in the matrix; (vi) abundant dissemination of fine-grained subhedral to anhedral pyrite crystals within the vein selvedge in the host rock; (vii) and coarse-grained massive pyrite bodies. The pyrite major elemental composition does not vary significantly in the different textures and sample types. The Fe content ranges from 44.57 to 46.40 wt. %, and the S content ranges from 53.75 to 55.25 wt. %. Pyrite from mineralized black shale and hydrothermal veins contains relatively higher concentrations of As (~ 1 wt. %) than pyrite from other sample types. The arsenopyrite commonly occurs as fine-grained anhedral crystals as inclusions within pyrite, medium-grained crystal intergrowing with pyrite and/or as coarse-grained massive arsenopyrite bodies in the massive sulphide veins. The arsenopyrite composition is uniform in all textural and sample type with Fe content ranging from 33.44 to 35.20 wt. %, S content ranging from 21.13 to 22.55 wt. % and As content ranging from 42.20 to 43.97 wt. %. In mineralized black shale and unmineralized black shale, the arsenopyrite shows, however, minor concentrations of Ni with 0.39 and 0.70 wt. % respectively. The pyrrhotite occurs as fine-grained anhedral patchy crystals randomly distributed within the rock matrix of unmineralized black shale and unmineralized granitoid, and / or as inclusions within pyrite in mineralized granitoid. The pyrrhotite shows a uniform composition in all samples and textural types, though minor concentrations of Ni (2.06 wt. %) content are reported in unmineralized granitoid. Chalcopyrite occurs as fine-grained crystals in inclusions within pyrite; and cobaltite occurs as rare fine-grained anhedral crystals occasionally disseminated in the albitite sill matrix. The chalcopyrite composition does not vary considerably in all sample and textural types, and cobaltite shows minor concentrations of Ni (4.55 wt. %) and Fe (3.45 wt. %). Native gold grains are commonly found associated with the secondary pyrite texture especially within the sulphide-rich lenses and in the massive sulphide veins, and are almost pure with ~97 wt. %. A Na-rich hydrothermal fluid from low-grade metamorphism associated with the E-W compressive tectonic event, which caused formation of the antiform structure which control the mineralization in the deposit area, led to the albitization of the deposit rocks and specially the alteration of the granitic assemblage to form albitite, and the deposition of aggregates of fine-grained anhedral crystals and growth and annealing of pyrite in sulphide-rich lenses. Afterward, the CO2-rich hydrothermal fluids influx circulated through reactivated structures, including quartz veins, and led to the precipitation of dolomite, ankerite, siderite and magnesite. They also led to the precipitation of pyrite of secondary textures as well as arsenopyrite, chalcopyrite and formation of pyrrhotite from the desulphurization of early pyrite. The CO2-rich hydrothermal fluids probably leached gold and other trace elements such as As, Co, etc. from the sedimentary host rocks and deposited them into suitable traps, such as the sulphide-rich lenses and massive sulphide bodies, preferably within the hinge zone of anticline axis constituting a hydrothermal fluid pathway.
- Full Text:
- Date Issued: 2019
Identifying methane emissions with isotopic and hydrochemical clues to their origin across selected areas of the Karoo Basin, South Africa
- Authors: Campbell, Richard Duncombe
- Date: 2019
- Subjects: Methane -- Environmental aspects -- South Africa , Atmospheric methane -- Environmental aspects -- South Africa , Groundwater -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/42218 , vital:36636
- Description: Currently, only sparse data exists on the methane emissions from the Main Karoo Basin, South Africa, where the potential discovery of vast quantities of unconventional natural gas from the black shales of the Whitehill Formation has sparked great interest in the prospect of hydraulic fracturing. In this study, a new infield methane quantification instrument (Picarro G2201-i) is used to identify freely emitted methane and more importantly collect stable carbon isotope ratios (δ13C-(CH4)g) that is used in obtaining information regarding the genetic origin and thermal maturity of the methane. Hydrochemical information (TOC, δ13C-TOC, 3H, δ18O, δ2H, and anions) were also scrutinised to assist in the determination of the origin of methane across the Karoo Basin. Twenty-one sites were investigated across four provinces in the Main Karoo Basin. Six of these sites are thermal springs, three are shallow boreholes (<100 m in depth), and twelve were Soekor (The Southern Oil Exploration Corporation)/deep boreholes (>1500 m). Of these 21 sites, 17 were suitable for either methane analysis or groundwater sampling, with four of the Soekor boreholes unsuitable. The presence of methane in groundwater and being freely emitted seems to be a common occurrence above the Main Karoo basin and of the 17 sites investigated, 14 had freely emitted methane emission. All but one of these sites had δ13C-(CH4)g signatures greater than -50 ‰, indicating a thermogenic origin. Combining the results obtained from the Picarro instrument with those compiled by Talma & Esterhuyse (2015), a higher resolution distribution map was created. The δ13C-CH4 signatures show patterning with a decreasing trend from the southern Karoo Basin to the north, which corresponds to the general decrease in thermal maturity of the Ecca shales (Whitehill Formation) northward across the Karoo Basin. The δ13C-(CH4)d results from a case study conducted by Eymold et al. (2018) differ significantly with the data collected in this study that included several of the same sampling locations. This is explained by a two phase partitioning (gas + water) that leads to the thermogenic endmember of methane being released in its free state (analysed by Picarro G2201-i) and microbial methane that is formed in situ remains dissolved in the water (analysed by Eymold et al. 2018). Soekor and deep sites; SA 1/66, KA 1/66, and KWV-1 that have direct pathways for methane migration from the Whitehill are deemed the best proxies to resolve the thermogenic endmember of methane, with δ13C-(CH4)g signatures of -26.32‰, 31.66‰, and -34.57‰, respectively. The hydrochemistry results suggests that that free methane emissions do not necessarily have to be associated with saline Cl- waters, as multiple sites have CH4 emissions with low salinities (Cl < 50 mg/L) and that methane in its free state can migrate to the surface due to buoyancy. The results also indicate that dolerite intrusions act as conduits for upward migration of groundwater from depth, but that the deep groundwater signatures proposed by Murray et al., (2015) are related to their different migration pathways and water-rock interactions rather than being representative of the deep formation waters. Using an initial assessment δ13C-CH4, TOC concentration [TOC] and the tritium (3H) values, where water samples that have 3H ≤ 1 TU, detectable TOC and δ13C-CH4 signatures > -50‰ could indicate hydraulic connectivity between the shallow aquifer and an organic/CH4 rich sedimentary layer, which may or may not be from the Whitehill Formation. However, this method for determining aquifer connectivity requires further investigations in the Karoo Basin context. The results obtained in this study add to the limited isotopic data of methane across the Karoo Basin and demonstrates the effectiveness of an infield identification of methane emissions using the Picarro G2201-i.
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- Date Issued: 2019
Substituent effects on the electrocatalytic activity of cobalt phthalocyanine in the presence of graphene quantum dots
- Authors: Centane, Sixolile Sibongiseni
- Date: 2019
- Subjects: Phthalocyanines , Quantum dots , Electrocatalysis , Electrochemistry
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67614 , vital:29121
- Description: The electrocatalytic activity of metallophthalocyanines derivatives is explored. Cobalt monocarboxyphenoxy phthalocyanine (1), cobalt tetracarboxyphenoxy phthalocyanine (2), cobalt tetraaminophenoxy phthalocyanine (3) and cobalt tris-(tert-butylphenoxy) monocarboxyphenoxy phthalocyanine (4) are the phthalocyanines employed in this work. The metallophthalocyanines were employed alone as well as in the presence of the carbon based graphene quantum dots. The electrocatalytic behaviour of functionalized GQDs is also explored herein. The catalytic processes studies were conducted on a glassy carbon electrode surface. Modification of the electrode was achieved by the adsorption method. The materials were adsorbed either alone, as premixed/covalently linked GQDs/Pc conjugates or sequentially. Sequentially adsorbed electrodes involved the phthalocyanines on top or beneath GQDs. Sequentially modified electrodes where the phthalocyanine had higher currents and low detection limits than when the phthalocyanine is underneath. Premixed conjugates showed better activity than the covalently formed conjugates. The nanomaterials synthesized and used in this work were characterized using transmission electron microscopy, UV-Vis spectroscopy, dynamic light scattering, Raman spectroscopy, X-ray diffraction, Atomic Force Microscopy and X-ray photoelectron spectroscopy. The modified electrodes were characterized using cyclic voltammetry and scanning electrochemical spectroscopy. The electrocatalytic activity of the modified electrodes towards the oxidation of hydrazine was evaluated using cyclic voltammetry and chronoamperometry. Superior catalytic activity was observed for the conjugates compared to that of the individual conjugates.
- Full Text:
- Date Issued: 2019
Biochemical characterization of the β-mannanase activity of Bacillus paralicheniformis SVD1
- Authors: Clarke, Matthew David
- Date: 2019
- Subjects: Mycobacterium avium paratuberculosis , Enzymes -- Biotechnology , Lignocellulose -- Biotechnology
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/67570 , vital:29112
- Description: Products produced via the enzymatic hydrolysis of lignocellulosic biomass, the most abundant renewable terrestrial source of carbon, can potentially replace a lot of the fuels and chemicals currently produced using non-renewable hydrocarbons. Mannan is a polysaccharide component of lignocellulose that is abundant in softwoods and legume seeds. Enzymatic hydrolysis of mannan by β-mannanases has various industrial applications, including use in biofuel and prebiotic mannooligosaccharide (MOS) production for the improvement of human and animal health. The industrial use of β-mannanases depends on their biochemical characteristics, such as their activity, stability and substrate specificity. Knowledge of their synergistic interactions with other enzymes is also useful for effective hydrolysis. Bacillus paralicheniformis SVD1 was used as a source for β-mannanases. The two mannanases of B. paralicheniformis SVD1 have not been biochemically characterized apart from minor characterization of crude β-mannanase activity. The protein sequences of the two β-mannanases, of glycosyl hydrolase family 5 and 26, have a 95% - 96% identity to the β-mannanases of B. licheniformis DSM13T (=ATCC14580T). These small protein sequence differences could lead to quite different biochemical characteristics. These mannanases were characterized as these enzymes may have industrially useful characteristics. To induce mannanase production, B. paralicheniformis SVD1 was cultured in broth containing the mannan substrate locust bean gum. Various growth curve parameters were measured over 72 h. Mannanase activity was the highest after 48 h of growth - this was the time at which mannanase activity was concentrated, using 3 kDa centrifugal filtration devices, for biochemical characterization of the crude activity. Zymography revealed that the crude concentrated mannanase fraction consisted of at least two mannanases with relative molecular weights (MWs) of 29.6 kDa and 33 kDa. This was smaller than expected – based on their theoretical molecular masses. Protease activity, which was detected in the broth, was probably the reason. There were two pH optima, pH 5.0 and pH 7.0, which also indicated the presence of two mannanases. The concentrated mannanase displayed characteristics that were expected of a B. paralicheniformis β-mannanase. The temperature optimum was 50°C and the activity loss was less than 7% at 50°C after 24 h. Substrate specificity assays revealed that there was predominantly mannanase activity present. Thin layer chromatography (TLC) analysis of mannan and MOS hydrolysis showed that mainly M2 and M3 MOS were produced; only MOS with a degree of polymerization of 4 or higher were hydrolyzed. Hydrolysis was minimal on mannoligosaccharides with galactose substituents. Activity and MOS production was the highest on soluble, low branched mannan substrates. The highest activity observed was on konjac glucomannan. Purification of the mannanase activity was then attempted using various methods. Ammonium sulfate precipitation, acetone precipitation, as well as centrifugal filtration device concentration was assessed for concentration of the mannanase activity.Concentration was not very successful due to low activity yields (≤ 20%). Anion exchange chromatography (AEC) and size exclusion chromatography (SEC) was used for purification. AEC gave good activity yield and fold purification, but SDS-PAGE analysis revealed the presence of many different proteins so further purification was necessary. SDS-PAGE analysis showed that there were only a few protein contaminants in the SEC fraction. However, the yield was too low to allow for biochemical characterization. The optimized purification procedure, which partially purified the mannanase activity, used 85% ammonium sulfate precipitation, followed by AEC. The fold purification was high (88.9) and the specific activity was 29.5 U.mg-1. A zymogram of the partially purified mannanase showed a mannanase active band with a MW of 40 - 41 kDa. A serine protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), was added during the purification steps. This indicated that the mannanase/s in the crude concentrate, without PMSF added, was hydrolyzed by serine protease activity. Native PAGE zymograms suggested that at least two different isoforms of mannanases were present. Additional purification would be required to determine the true characteristics of the mannanase/s. The biochemical characteristics of the crude and partially purified mannanases were similar. The pH optima of the partially purified mannanases were different; the pH optima were 6.0 and 9.0. The substrate specificities were similar, except that the partially purified mannanases displayed no cellulase and β-D-galactosidase activity, but showed a small amount of α-L-arabinase activity. The partially purified mannanase and a Cyamopsis tetragonolobus GH27 α-galactosidase synergistically hydrolyzed locust bean gum. The M50G50 combination displayed the highest extent of hydrolysis; after 24 h there was a 1.39 fold increase in reducing sugar release and the degree of synergy (DS) was 4.64. TLC analysis indicated that synergy increased the release of small MOS. These MOS could be useful as prebiotics. The synergy between the partially purified mannanase and the commercial cellulase mixture Cellic® CTec2 (Novozymes) on spent coffee grounds (SCG) was also determined. SCG is an abundant industrial waste product that has high mannan content. The SCG was pretreated using NaOH, and the monosaccharide, soluble phenolics and insoluble contents were determined. Glucose and mannose were the dominant monosaccharides in the SCG; the pretreated SCG contained 20.4% (w/w) glucose and 18.5% (w/w) mannose, respectively. The NaOH pretreatment improved mannanase hydrolysis of SCG. It resulted in the opening up and swelling of the SCG particles and removed some of the insoluble solids. The partially purified B. paralicheniformis SVD1 mannanase displayed no detectable activity on SCG, but showed synergy with CTec2, in terms of DS, on untreated and NaOH pretreated SCG. This is the first report of mannanasecellulase synergy on SCG; other studies found that increased hydrolysis was due to additive effects. The results obtained in this study are only an initial assessment of the biochemical properties of B. paralicheniformis SVD1 mannanase activity and its synergy with other enzymes. These results can be used to inform future studies.
- Full Text:
- Date Issued: 2019
The medicinal chemistry of selected halogenated diketopiperazines CYCLO(CIS-PRO-4F-PRO) and CYCLO(L-PHE-4I-VAL)
- Authors: Dakada, Vuyokazi
- Date: 2019
- Subjects: Medicinal plants , Drug development Cells -- Effect of drugs on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/39370 , vital:35221
- Description: Generally, peptides are selective and efficacious compounds; as a result, they are the best candidates for drug discovery and development. Most peptide-based drugs have been approved for clinical use. The 2,5-Diketopiperazines (DKPs), also known as cyclic dipeptides, are simple compounds which come from nature. Many DKPs are extracted from animals and plants. For example, cyclo(Proline(Pro)-Leucine(Leu)), cyclo(Proline-Valine(Val)), cyclo(Proline-Phenylalanine(Phe)) etc. In this study cyclo(cis-Proline(Pro)-4F-Proline(Pro)) and cyclo(L- Phenylalanine(Phe)-4I- Valine (Val)) were synthesized from their linear esters using a method modified by Milne et al. (1992). This method yielded good results. However, cyclo(L-Phe-4I-Val) degraded due to physicochemical stability attributes caused by hygroscopicity and photosensitivity. Quantitative analysis and evaluation of physicochemical properties of each dipeptide was achieved by using scanning electron microscopy, thermal analysis (differential scanning calorimetry and thermogravimetric analysis) and X-ray powder diffraction. To determine the purity of the cyclic dipeptide, high performance liquid chromatography and thin layer chromatography was used. The structural elucidation of the cyclic dipeptides was carried by employing infrared spectroscopy, mass spectrometry, nuclear magnetic resonance spectroscopy and, molecular modelling and computational chemistry. The aim of this research was to discover possible biological activity of cyclo(cis-Pro-4-F-Pro) and cyclo(L-Phe-4I-Val) with respect to their antimicrobial, anticancer, anti-diabetic and haematological effects. Cyclo(cis-Pro-4Fluoro-Pro) had no inhibitory effect on the antimicrobial strains tested, and cyclo(L-Phe-4Iodo-Val) could not be tested as the compound decomposed.
- Full Text:
- Date Issued: 2019
Categorising Network Telescope data using big data enrichment techniques
- Authors: Davis, Michael Reginald
- Date: 2019
- Subjects: Denial of service attacks , Big data , Computer networks -- Security measures
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/92941 , vital:30766
- Description: Network Telescopes, Internet backbone sampling, IDS and other forms of network-sourced Threat Intelligence provide researchers with insight into the methods and intent of remote entities by capturing network traffic and analysing the resulting data. This analysis and determination of intent is made difficult by the large amounts of potentially malicious traffic, coupled with limited amount of knowledge that can be attributed to the source of the incoming data, as the source is known only by its IP address. Due to the lack of commonly available tooling, many researchers start this analysis from the beginning and so repeat and re-iterate previous research as the bulk of their work. As a result new insight into methods and approaches of analysis is gained at a high cost. Our research approaches this problem by using additional knowledge about the source IP address such as open ports, reverse and forward DNS, BGP routing tables and more, to enhance the researcher's ability to understand the traffic source. The research is a BigData experiment, where large (hundreds of GB) datasets are merged with a two month section of Network Telescope data using a set of Python scripts. The result are written to a Google BigQuery database table. Analysis of the network data is greatly simplified, with questions about the nature of the source, such as its device class (home routing device or server), potential vulnerabilities (open telnet ports or databases) and location becoming relatively easy to answer. Using this approach, researchers can focus on the questions that need answering and efficiently address them. This research could be taken further by using additional data sources such as Geo-location, WHOIS lookups, Threat Intelligence feeds and many others. Other potential areas of research include real-time categorisation of incoming packets, in order to better inform alerting and reporting systems' configuration. In conclusion, categorising Network Telescope data in this way provides insight into the intent of the (apparent) originator and as such is a valuable tool for those seeking to understand the purpose and intent of arriving packets. In particular, the ability to remove packets categorised as non-malicious (e.g. those in the Research category) from the data eliminates a known source of `noise' from the data. This allows the researcher to focus their efforts in a more productive manner.
- Full Text:
- Date Issued: 2019
Modelling the structure and interactions of leukocyte integrins
- Authors: Dawson, Kyle-Richard
- Date: 2019
- Subjects: Proteins -- Structure , Molecular immunology Biochemistry
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/39392 , vital:35239
- Description: Heterodimeric transmembrane protein structure is complex and insufficient structural information exists, concerning leukocyte integrin proteins. To determine protein structure, homology modelling was conducted and modelling software was evaluated. Leukocyte integrin homologs were obtained from the PDB and models were generated using online servers and MODELLER. Template homologs were fewer in number and of lower quality in comparison to monomeric extracellular proteins. Models were docked using ClusPro, HADDOCK2.2 and AutoDock vina. Models were evaluated using PROSA, Verify-3D and PROSESS. Higher quality models were generated when using MODELLER to separately model monomeric subunits in three defined domain regions (extracellular, transmembrane and cytoplasmic). Template selection concerning these proteins is critical as an intricate relationship exists between model quality, template quality, template quantity, template resolution, target-template identity and template sequence coverage. Docking monomeric subunits was challenging when using ClusPro and the best ligand docking procedures were completed using AutoDock vina. PROSESS provided the most accurate evaluation of protein models, in comparison to PROSA and Verify-3D. These results indicate that although homology modelling is a powerful tool there is much room for improvement. Experimentally obtained templates should be expanded upon within the PDB and energy functions should cater for both monomeric and transmembrane heterodimeric proteins. Leukocyte integrins appear to adopt a closed conformation, which may still facilitate LDV ligand association within the α/β interface. The α3β1 integrin may interact with laminin-5 through the ELV sequence within the G-domain of the α laminin subunit
- Full Text:
- Date Issued: 2019