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:
- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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.
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- Date Issued: 2016
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:
- Date Issued: 2016
Classical and quantum picture of the interior of two-dimensional black holes
- Authors: Shawa, Mark
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3629 , vital:20531
- Description: A quantum-mechanical description of black holes would represent the final step in our understanding of the nature of space-time. However, any progress towards that end is usually foiled by persistent space-time singularities that exist at the center of black holes. From the four-dimensional point of view, black holes seem to resist quantization. Under highly symmetric conditions, all higher-dimensional black holes are two-dimensional. Unlike their higher-dimensional counterparts, two dimensional black holes may not resist quantization. A non-trivial description of gravity in two dimensions is not possible using Einstein’s theory of gravity alone. However, we may still arrive at a consistent description of gravity by introducing a scalar field known as the dilaton. In this thesis, we study both the classical and quantum aspects of the interior of two-dimensional black holes using a generalized dilaton-gravity theory. Classically, we will find that the interior of most two-dimensional black holes is not much different from that of four-dimensional black holes. But by introducing quantized matter into the theory, the fluctuations in space-time will give a different picture of the structure of interior of black holes. Using a low-energy effective field theory, we will show that it is indeed possible to identify quantum modes in the interior of black holes and perform quantum-mechanical calculations near the singularity.
- Full Text:
- Date Issued: 2016
Comparative analysis of existing pipelines for assessment of arbuscular mycorrhizal fungal biodiversity in natural and commercial rooibos (aspalathus linearis) and honeybush (cyclopia intermedia) soil samples
- Authors: De Wit, Hermina Johanna
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2915 , vital:20342
- Full Text:
- Date Issued: 2016
Controls on the distribution of manganese in banded iron-formations (BIF) of the palaeoproterozoic transvaal supergroup, South Africa
- Authors: Fryer, Lindi
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2926 , vital:20343
- Description: The 2.65 to 2.05 Ga Transvaal Supergroup comprises one of the best-preserved and largely continuous successions in the world of Banded Iron-Formation (BIF), a chemical sedimentary rock composed of fine (mm to cm scale) interbanded iron-rich and iron-poor bands, developed atop the Archaean Kaapvaal Craton of southern Africa. The Transvaal BIF sequence contains at its upper stratigraphic part, an intriguing interlayered BIF-Mn association, namely the Hotazel Formation in the Kalahari Manganese Field, which constitutes the largest land-based manganese deposit on record. The genesis of the Hotazel deposits, and their exact significance in terms of atmosphere-hydrosphere-biosphere evolution, remain as elusive as they are challenging. In this thesis, an attempt is made to illuminate the origin and diagenesis of the Hotazel Formation and its post-depositional hydrothermal modification, through a highresolution geochemical study of the narrowest of the three BIF-Mn sedimentary cycles present in the Hotazel stratigraphy. This approach is coupled with a preliminary geochemical study of the distribution of Mn in older BIF of the Transvaal Supergroup as well (Kuruman and Griquatown Formations), so as to test recent models that causally link all BIFs in the Transvaal Supergroup under a common and evolving palaeo-environment of deposition. The results indicate that the cyclic deposition of the Hotazel BIF and enveloped Mn-rich sediments would have taken place in a stratified basin with a well-developed chemocline in terms of the vertical distributions of Mn and Fe, much like recent anoxic stratified basins such as the Orca Basin in the Gulf of Mexico. The increased Mn abundances as Mn-bearing ferrous carbonates in the upper part of the Griquatown BIF predating the Hotazel strata, also seems to lend support to the notion that the two BIFs are temporally interlinked as part of a broader sedimentary continuum. Finally, the largely conservative behaviour of Mn and associated elements during hydrothermal alteration of the Hotazel rocks is re-assessed, and renewed emphasis is placed on the possibility that brine metasomatism may have been a key factor in Mn redistribution and residual enrichment.
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- Date Issued: 2016
Cosmological structure formation using spectral methods
- Authors: Funcke, Michelle
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2969 , vital:20348
- Description: Numerical simulations are becoming an increasingly important tool for understanding the growth and development of structure in the universe. Common practice is to discretize the space-time using physical variables. The discreteness is embodied by considering the dynamical variables as fields on a fixed spatial and time resolution, or by constructing the matter fields by a large number of particles which interact gravitationally (N-body methods). Recognizing that the physical quantities of interest are related to the spectrum of perturbations, we propose an alternate discretization in the frequency domain, using standard spectral methods. This approach is further aided by periodic boundary conditions which allows a straightforward decomposition of variables in a Fourier basis. Fixed resources require a high-frequency cut-off which lead to aliasing effects in non-linear equations, such as the ones considered here. This thesis describes the implementation of a 3D cosmological model based on Newtonian hydrodynamic equations in an expanding background. Initial data is constructed as a spectrum of perturbations, and evolved in the frequency domain using a pseudo-spectral evolution scheme and an explicit Runge-Kutta time integrator. The code is found to converge for both linear and non-linear evolutions, and the convergence rate is determined. The correct growth rates expected from analytical calculations are recovered in the linear case. In the non-linear model, we observe close correspondence with linear growth and are able to monitor the growth on features associated with the non-linearity. High-frequency aliasing effects were evident in the non-linear evolutions, leading to a study of two potential resolutions to this problem: a boxcar filter which adheres to“Orszag’s two thirds rule” and an exponential window function, the exponential filter suggested by Hou and Li [1], and a shifted version of the exponential filter suggested, which has the potential to alleviate high frequency- ripples resulting from the Gibbs’ phenomenon. We found that the filters were somewhat successful at reducing aliasing effects but that the Gibbs’ phenomenon could not be entirely removed by the choice of filters.
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- Date Issued: 2016
Detecting derivative malware samples using deobfuscation-assisted similarity analysis
- Authors: Wrench, Peter Mark
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/383 , vital:19954
- Description: The overwhelming popularity of PHP as a hosting platform has made it the language of choice for developers of Remote Access Trojans (RATs or web shells) and other malicious software. These shells are typically used to compromise and monetise web platforms by providing the attacker with basic remote access to the system, including _le transfer, command execution, network reconnaissance, and database connectivity. Once infected, compromised systems can be used to defraud users by hosting phishing sites, performing Distributed Denial of Service attacks, or serving as anonymous platforms for sending spam or other malfeasance. The vast majority of these threats are largely derivative, incorporating core capabilities found in more established RATs such as c99 and r57. Authors of malicious software routinely produce new shell variants by modifying the behaviours of these ubiquitous RATs, either to add desired functionality or to avoid detection by signature-based detection systems. Once these modified shells are eventually identified (or additional functionality is required), the process of shell adaptation begins again. The end result of this iterative process is a web of separate but related shell variants, many of which are at least partially derived from one of the more popular and influential RATs. In response to the problem outlined above, the author set out to design and implement a system capable of circumventing common obfuscation techniques and identifying derivative malware samples in a given collection. To begin with, a decoder component was developed to syntactically deobfuscate and normalise PHP code by detecting and reversing idiomatic obfuscation constructs, and to apply uniform formatting conventions to all system inputs. A unified malware analysis framework, called Viper, was then extended to create a modular similarity analysis system comprised of individual feature extraction modules, modules responsible for batch processing, a matrix module for comparing sample features, and two visualisation modules capable of generating visual representations of shell similarity. The principal conclusion of the research was that the deobfuscation performed by the decoder component prior to analysis dramatically improved the observed levels of similarity between test samples. This in turn allowed the modular similarity analysis system to identify derivative clusters (or families) within a large collection of shells more accurately. Techniques for isolating and re-rendering these clusters were also developed and demonstrated to be effective at increasing the amount of detail available for evaluating the relative magnitudes of the relationships within each cluster.
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- Date Issued: 2016