"Is more, less?" : insect-insect interactions in a biological control context using water hyacinth as a model
- Weyl, Philip Sebastian Richard
- Authors: Weyl, Philip Sebastian Richard
- Date: 2012
- Subjects: Water hyacinth -- South Africa -- Eastern Cape , Water hyacinth -- Biological control -- South Africa -- Eastern Cape , Insects as biological pest control agents , Miridae -- South Africa -- Eastern Cape , Beetles -- South Africa -- Eastern Cape , Competition (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5724 , http://hdl.handle.net/10962/d1005410 , Water hyacinth -- South Africa -- Eastern Cape , Water hyacinth -- Biological control -- South Africa -- Eastern Cape , Insects as biological pest control agents , Miridae -- South Africa -- Eastern Cape , Beetles -- South Africa -- Eastern Cape , Competition (Biology)
- Description: Interactions between insects have been shown to be important regulators of population abundances and dynamics as well as drivers of spatial segregation and distribution. These are important aspects of the ecology of insects used in biological control and may have implications for the overall success of a particular programme. In the history of biological control there has been a tendency to release a suite of agents against a weed, which in some cases has increased the level of success, while in others little change has been observed. In most of these cases the implications of increasing the level of complexity of the system is not taken into account and there is little research on the effect of releasing another agent into the system. A brief meta-analysis was done on all the biological control programmes initiated in South Africa. Emphasis was placed on multi-species releases and the effects that overlapping niches were having on the number of agents responsible for the success of a programme. Where overlapping niches were present among agents released the number of agents responsible for success was lower than the number established. Water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach in South Africa has more arthropod agents released against it than anywhere else in the world, yet control has been variable. If the biology and host utilisation of all the agents against water hyacinth is considered, a definite overlap of niches is apparent in at least one life stage of all the agents. Therefore the probability of these insects interacting is high, especially if they are established at the same site in the field. Three of the insects released in South Africa have been selected to investigate possible interactions. They are Neochetina eichhorniae Warner, Neochetina bruchi Hustache and Eccritotarsus catarinensis (Carvalho). Y-tube olfactometer bioassays were used to measure responses of these insects to water hyacinth with prior feeding damage by either conspecifics or heterospecifics. This was done to determine whether olfactory cues played a role in host acceptability and avoidance of conspecifics or heterospecifics. The insects were given a choice between damaged and undamaged plants in various combinations. There was a significant preference for the undamaged plants when given a choice between undamaged and damaged plants. However when the insects were given a choice between two damaged plants there was no discrimination between heterospecific or conspecific damaged plants. This may indicate that there is little or no ecological cost for the insect to share a plant with other insects utilising a similar resource. Insect – insect interactions were investigated in a common garden plot experiment to measure the impact that pairwise combinations of the insect may have on their performance. There was a significant interaction between the mirid E. catarinensis and the weevil N. eichhorniae, with the weevil not performing as well when in combination with the mirid than when alone. Interestingly there was a negative interaction between the two weevil species when in combination, however it was impossible to determine which species was being affected if not both. None of the insects performed significantly better when in combination with another insect. A field study on Wriggleswade Dam in the Eastern Cape, South Africa was initiated to determine whether the relationship between the mirid E. catarinensis and the weevil N. eichhorniae could be determined in the field. The performance of the insects at the different sites in the field suggests that there was an interaction between the agents. This interaction did not limit the establishment of either insect at a site, but it did result in one insect dominating at a site over another. Interactions between the three species of insect tested in this thesis suggest that there are both negative and neutral relationships between them. A basic comparison between the insect performances from 15 sites around the country was done to determine if the spatial segregation observed in the field could be extrapolated to the natural South African situation. The interaction observed between N. eichhorniae and E. catarinensis does seem to extrapolate to the general South African situation where there is definite spatial segregation on a landscape level. The co–occurrence of the two Neochetina weevils at these sites suggests that the negative relationship observed between them in the common garden experiment does not extrapolate to the field. The results from this thesis suggest that the interactions between the agents tested would not limit establishment or have significant ramifications on performance. However, there may be spatial and temporal segregation of these species in the introduced range.
- Full Text:
- Date Issued: 2012
- Authors: Weyl, Philip Sebastian Richard
- Date: 2012
- Subjects: Water hyacinth -- South Africa -- Eastern Cape , Water hyacinth -- Biological control -- South Africa -- Eastern Cape , Insects as biological pest control agents , Miridae -- South Africa -- Eastern Cape , Beetles -- South Africa -- Eastern Cape , Competition (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5724 , http://hdl.handle.net/10962/d1005410 , Water hyacinth -- South Africa -- Eastern Cape , Water hyacinth -- Biological control -- South Africa -- Eastern Cape , Insects as biological pest control agents , Miridae -- South Africa -- Eastern Cape , Beetles -- South Africa -- Eastern Cape , Competition (Biology)
- Description: Interactions between insects have been shown to be important regulators of population abundances and dynamics as well as drivers of spatial segregation and distribution. These are important aspects of the ecology of insects used in biological control and may have implications for the overall success of a particular programme. In the history of biological control there has been a tendency to release a suite of agents against a weed, which in some cases has increased the level of success, while in others little change has been observed. In most of these cases the implications of increasing the level of complexity of the system is not taken into account and there is little research on the effect of releasing another agent into the system. A brief meta-analysis was done on all the biological control programmes initiated in South Africa. Emphasis was placed on multi-species releases and the effects that overlapping niches were having on the number of agents responsible for the success of a programme. Where overlapping niches were present among agents released the number of agents responsible for success was lower than the number established. Water hyacinth, Eichhornia crassipes (Martius) Solms-Laubach in South Africa has more arthropod agents released against it than anywhere else in the world, yet control has been variable. If the biology and host utilisation of all the agents against water hyacinth is considered, a definite overlap of niches is apparent in at least one life stage of all the agents. Therefore the probability of these insects interacting is high, especially if they are established at the same site in the field. Three of the insects released in South Africa have been selected to investigate possible interactions. They are Neochetina eichhorniae Warner, Neochetina bruchi Hustache and Eccritotarsus catarinensis (Carvalho). Y-tube olfactometer bioassays were used to measure responses of these insects to water hyacinth with prior feeding damage by either conspecifics or heterospecifics. This was done to determine whether olfactory cues played a role in host acceptability and avoidance of conspecifics or heterospecifics. The insects were given a choice between damaged and undamaged plants in various combinations. There was a significant preference for the undamaged plants when given a choice between undamaged and damaged plants. However when the insects were given a choice between two damaged plants there was no discrimination between heterospecific or conspecific damaged plants. This may indicate that there is little or no ecological cost for the insect to share a plant with other insects utilising a similar resource. Insect – insect interactions were investigated in a common garden plot experiment to measure the impact that pairwise combinations of the insect may have on their performance. There was a significant interaction between the mirid E. catarinensis and the weevil N. eichhorniae, with the weevil not performing as well when in combination with the mirid than when alone. Interestingly there was a negative interaction between the two weevil species when in combination, however it was impossible to determine which species was being affected if not both. None of the insects performed significantly better when in combination with another insect. A field study on Wriggleswade Dam in the Eastern Cape, South Africa was initiated to determine whether the relationship between the mirid E. catarinensis and the weevil N. eichhorniae could be determined in the field. The performance of the insects at the different sites in the field suggests that there was an interaction between the agents. This interaction did not limit the establishment of either insect at a site, but it did result in one insect dominating at a site over another. Interactions between the three species of insect tested in this thesis suggest that there are both negative and neutral relationships between them. A basic comparison between the insect performances from 15 sites around the country was done to determine if the spatial segregation observed in the field could be extrapolated to the natural South African situation. The interaction observed between N. eichhorniae and E. catarinensis does seem to extrapolate to the general South African situation where there is definite spatial segregation on a landscape level. The co–occurrence of the two Neochetina weevils at these sites suggests that the negative relationship observed between them in the common garden experiment does not extrapolate to the field. The results from this thesis suggest that the interactions between the agents tested would not limit establishment or have significant ramifications on performance. However, there may be spatial and temporal segregation of these species in the introduced range.
- Full Text:
- Date Issued: 2012
(L, M)-fuzzy topological spaces
- Authors: Matutu, Phethiwe Precious
- Date: 1992
- Subjects: Topological spaces , Fuzzy sets
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5410 , http://hdl.handle.net/10962/d1005224 , Topological spaces , Fuzzy sets
- Description: The objective of this thesis is to develop certain aspects of the theory of (L,M)-fuzzy topological spaces, where L and M are complete lattices (with additional conditions when necessary). We obtain results which are to a large extent analogous to results given in a series of papers of Šostak (where L = M = [0,1]) but not necessarily with analogous proofs. Often, our generalizations require a variety of techniques from lattice theory e.g. from continuity or complete distributive lattices.
- Full Text:
- Date Issued: 1992
- Authors: Matutu, Phethiwe Precious
- Date: 1992
- Subjects: Topological spaces , Fuzzy sets
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5410 , http://hdl.handle.net/10962/d1005224 , Topological spaces , Fuzzy sets
- Description: The objective of this thesis is to develop certain aspects of the theory of (L,M)-fuzzy topological spaces, where L and M are complete lattices (with additional conditions when necessary). We obtain results which are to a large extent analogous to results given in a series of papers of Šostak (where L = M = [0,1]) but not necessarily with analogous proofs. Often, our generalizations require a variety of techniques from lattice theory e.g. from continuity or complete distributive lattices.
- Full Text:
- Date Issued: 1992
A 150 MHz all sky survey with the Precision Array to Probe the Epoch of Reionization
- Authors: Chege, James Kariuki
- Date: 2020
- Subjects: Epoch of reionization -- Research , Astronomy -- Observations , Radio interferometers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117733 , vital:34556
- Description: The Precision Array to Probe the Epoch of Reionization (PAPER) was built to measure the redshifted 21 cm line of hydrogen from cosmic reionization. Such low frequency observations promise to be the best means of understanding the cosmic dawn; when the first galaxies in the universe formed, and also the Epoch of Reionization; when the intergalactic medium changed from neutral to ionized. The major challenges to these observations is the presence of astrophysical foregrounds that are much brighter than the cosmological signal. Here, I present an all-sky survey at 150 MHz obtained from the analysis of 300 hours of PAPER observations. Particular focus is given to the calibration and imaging techniques that need to deal with the wide field of view of a non-tracking instrument. The survey covers ~ 7000 square degrees of the southern sky. From a sky area of 4400 square degrees out of the total survey area, I extract a catalogue of sources brighter than 4 Jy whose accuracy was tested against the published GLEAM catalogue, leading to a fractional difference rms better than 20%. The catalogue provides an all-sky accurate model of the extragalactic foreground to be used for the calibration of future Epoch of Reionization observations and to be subtracted from the PAPER observations themselves in order to mitigate the foreground contamination.
- Full Text:
- Date Issued: 2020
- Authors: Chege, James Kariuki
- Date: 2020
- Subjects: Epoch of reionization -- Research , Astronomy -- Observations , Radio interferometers
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/117733 , vital:34556
- Description: The Precision Array to Probe the Epoch of Reionization (PAPER) was built to measure the redshifted 21 cm line of hydrogen from cosmic reionization. Such low frequency observations promise to be the best means of understanding the cosmic dawn; when the first galaxies in the universe formed, and also the Epoch of Reionization; when the intergalactic medium changed from neutral to ionized. The major challenges to these observations is the presence of astrophysical foregrounds that are much brighter than the cosmological signal. Here, I present an all-sky survey at 150 MHz obtained from the analysis of 300 hours of PAPER observations. Particular focus is given to the calibration and imaging techniques that need to deal with the wide field of view of a non-tracking instrument. The survey covers ~ 7000 square degrees of the southern sky. From a sky area of 4400 square degrees out of the total survey area, I extract a catalogue of sources brighter than 4 Jy whose accuracy was tested against the published GLEAM catalogue, leading to a fractional difference rms better than 20%. The catalogue provides an all-sky accurate model of the extragalactic foreground to be used for the calibration of future Epoch of Reionization observations and to be subtracted from the PAPER observations themselves in order to mitigate the foreground contamination.
- Full Text:
- Date Issued: 2020
A 22 GHz radio telescope
- Authors: Mutch, Laurence Ian
- Date: 1976
- Subjects: Radio telescopes , Paraboloid , Radio astronomy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5532 , http://hdl.handle.net/10962/d1012919
- Description: This thesis reports on the design, construction, testing and operation of the spectral line and continuum receivers built for the 22 GHz Radio Telescope. First results from 'the telescope were obtained and have been analysed to give an estimate of system efficiency. Tests have been performed on the front end and in particular on the 22 GHz mixer in order to determine the minimum detectable temperature. The Sun, Moon and major planets are sources suitable for antenna alignment and consequently a literature survey of emission at 22 GHz from elements of the Solar system has been made.
- Full Text:
- Date Issued: 1976
- Authors: Mutch, Laurence Ian
- Date: 1976
- Subjects: Radio telescopes , Paraboloid , Radio astronomy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5532 , http://hdl.handle.net/10962/d1012919
- Description: This thesis reports on the design, construction, testing and operation of the spectral line and continuum receivers built for the 22 GHz Radio Telescope. First results from 'the telescope were obtained and have been analysed to give an estimate of system efficiency. Tests have been performed on the front end and in particular on the 22 GHz mixer in order to determine the minimum detectable temperature. The Sun, Moon and major planets are sources suitable for antenna alignment and consequently a literature survey of emission at 22 GHz from elements of the Solar system has been made.
- Full Text:
- Date Issued: 1976
A 22 GHz water maser radiometer
- Authors: Nunn, Brian J
- Date: 1975
- Subjects: Masers , Radiometers
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5535 , http://hdl.handle.net/10962/d1012987
- Description: This thesis describes the properties of interstellar water maser sources, and other sources near 22 GHz. Calculations based on manufacturer's specifications of the 22 GHz mixer, which was to be used in a water radiometer, and on the size antenna aperture of the proposed antenna aperture, show the viability of constructing such a radiometer for spectral line and continuum work. Various sections of the radiometer were constructed, including the Cassegrain feed system and its support, an intermediate frequency amplifier and buffer, a timing control unit, and a data processor. These units are part of the radiometer, which is almost ready for observations of sources.
- Full Text:
- Date Issued: 1975
- Authors: Nunn, Brian J
- Date: 1975
- Subjects: Masers , Radiometers
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5535 , http://hdl.handle.net/10962/d1012987
- Description: This thesis describes the properties of interstellar water maser sources, and other sources near 22 GHz. Calculations based on manufacturer's specifications of the 22 GHz mixer, which was to be used in a water radiometer, and on the size antenna aperture of the proposed antenna aperture, show the viability of constructing such a radiometer for spectral line and continuum work. Various sections of the radiometer were constructed, including the Cassegrain feed system and its support, an intermediate frequency amplifier and buffer, a timing control unit, and a data processor. These units are part of the radiometer, which is almost ready for observations of sources.
- Full Text:
- Date Issued: 1975
A baculovirus-mediated expression system for the analysis of HaSV RNA packaging
- Authors: Mendes, Adriano
- Date: 2012
- Subjects: RNA , Baculoviruses , Helicoverpa armigera , Plasmids
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4025 , http://hdl.handle.net/10962/d1004085 , RNA , Baculoviruses , Helicoverpa armigera , Plasmids
- Description: The Helicoverpa armigera stunt virus (HaSV) is a member of a family of small nonenveloped (+) ssRNA insect viruses currently known as the Tetraviridae. This family is unique in terms of the T=4 quasi-symmetry of its capsid particles and the unusually narrow host range and tissue tropism. Assembly of tetraviral particles has been well characterised and involves the combination of 240 copies of a single capsid precursor protein (VCap) into a procapsid followed by autoproteolytic cleavage to yield the major (β) and minor (γ) capsid subunits within the mature particle. HaSV has two genomic RNAs, RNA 1 encoding the replicase and RNA 2 encoding VCap and p17, the ORF of which lies upstream of and overlaping with the 5’ end of the VCap ORF. Prior to this study, Vlok (2009) used a plasmid expression system to study RNA packaging in HaSV VLPs assembled in Spodoptera frugiperda 9 (Sf9) cells co-expressing p17 and VCap. The study showed that the p17 ORF was required for the packaging of RNA 2 during capsid assembly but it was unclear whether p17 expression was required for packaging. In addition, expression from the transfected plasmids was sub-optimal affecting both the yield of VLPs and the detection of p17. The aim of this study was to use the plasmid system to test whether p17 expression was required for plasmid-derived VLP RNA packaging and then develop a baculovirus-mediated system to test this hypothesis. By using a plasmid in which the start codon of p17 was mutated, it was shown that p17 expression was required for RNA 2 packaging into plasmid-VLPs. For the baculovirus system, four recombinant baculoviruses based upon the pFastBac Dual expression system, were constructed. These included Bac20, expressing wild type RNA 2, Bac21, RNA 2 with p17 silenced, Bac23, RNA 2 and p17 expressed on a separate transcript and Bac24, RNA 2 with p17 silenced plus p17 expressed on a separate transcript. Assembly of VLPs was more efficient using the baculovirus expression system and p17 expression was observed in cells infected with Bac20, Bac23 and Bac24, but not Bac21. In contrast to the plasmid-VLPs, bac-VLPs did not require p17 for the encapsidation of RNA 2. In addition to RNA 2, Bac23 and Bac24 packaged the p17 mRNA transcribed separately from RNA 2. This insinuated that bac-VLPs may be packaging RNA non-selectively. It was proposed that p17 may play a role in packaging in an RNA-limiting environment (plasmid system) but functioned differently when viral RNA was in excess (baculovirus system). This data points to the importance of developing a replication system for the analysis of the packaging pathways of these viruses and this study has laid down the foundations for such a system in which RNA 1 and RNA 2 can be introduced into a single cell by means of a single recombinant virus.
- Full Text:
- Date Issued: 2012
- Authors: Mendes, Adriano
- Date: 2012
- Subjects: RNA , Baculoviruses , Helicoverpa armigera , Plasmids
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4025 , http://hdl.handle.net/10962/d1004085 , RNA , Baculoviruses , Helicoverpa armigera , Plasmids
- Description: The Helicoverpa armigera stunt virus (HaSV) is a member of a family of small nonenveloped (+) ssRNA insect viruses currently known as the Tetraviridae. This family is unique in terms of the T=4 quasi-symmetry of its capsid particles and the unusually narrow host range and tissue tropism. Assembly of tetraviral particles has been well characterised and involves the combination of 240 copies of a single capsid precursor protein (VCap) into a procapsid followed by autoproteolytic cleavage to yield the major (β) and minor (γ) capsid subunits within the mature particle. HaSV has two genomic RNAs, RNA 1 encoding the replicase and RNA 2 encoding VCap and p17, the ORF of which lies upstream of and overlaping with the 5’ end of the VCap ORF. Prior to this study, Vlok (2009) used a plasmid expression system to study RNA packaging in HaSV VLPs assembled in Spodoptera frugiperda 9 (Sf9) cells co-expressing p17 and VCap. The study showed that the p17 ORF was required for the packaging of RNA 2 during capsid assembly but it was unclear whether p17 expression was required for packaging. In addition, expression from the transfected plasmids was sub-optimal affecting both the yield of VLPs and the detection of p17. The aim of this study was to use the plasmid system to test whether p17 expression was required for plasmid-derived VLP RNA packaging and then develop a baculovirus-mediated system to test this hypothesis. By using a plasmid in which the start codon of p17 was mutated, it was shown that p17 expression was required for RNA 2 packaging into plasmid-VLPs. For the baculovirus system, four recombinant baculoviruses based upon the pFastBac Dual expression system, were constructed. These included Bac20, expressing wild type RNA 2, Bac21, RNA 2 with p17 silenced, Bac23, RNA 2 and p17 expressed on a separate transcript and Bac24, RNA 2 with p17 silenced plus p17 expressed on a separate transcript. Assembly of VLPs was more efficient using the baculovirus expression system and p17 expression was observed in cells infected with Bac20, Bac23 and Bac24, but not Bac21. In contrast to the plasmid-VLPs, bac-VLPs did not require p17 for the encapsidation of RNA 2. In addition to RNA 2, Bac23 and Bac24 packaged the p17 mRNA transcribed separately from RNA 2. This insinuated that bac-VLPs may be packaging RNA non-selectively. It was proposed that p17 may play a role in packaging in an RNA-limiting environment (plasmid system) but functioned differently when viral RNA was in excess (baculovirus system). This data points to the importance of developing a replication system for the analysis of the packaging pathways of these viruses and this study has laid down the foundations for such a system in which RNA 1 and RNA 2 can be introduced into a single cell by means of a single recombinant virus.
- Full Text:
- Date Issued: 2012
A baseline survey of channel geomorphology with particular reference to the effects of sediment characteristics on ecosystem health in the Tsitsa River, Eastern Cape, South Africa
- Huchzermeyer, Nicholaus Heinrich
- Authors: Huchzermeyer, Nicholaus Heinrich
- Date: 2018
- Subjects: Fluvial geomorphology -- South Africa -- Eastern Cape , Stream health -- South Africa -- Eastern Cape , River sediments -- South Africa -- Eastern Cape , Watershed management -- South Africa -- Eastern Cape , Dams -- Environmental aspects -- South Africa -- Eastern Cape , Tsitsa River (South Africa) , Ntabelanga Dam (South Africa)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/58056 , vital:27040
- Description: Fluvial systems are dynamic systems in which variables in a catchment and river channel affect the morphology of river reaches. South African rivers are increasingly being exposed to stresses from a combination of factors, one of the most prevalent being the impacts of damming rivers which result in varying downstream sediment fluxes and flow regimes. The sediment load combined with flow characteristics for respective river channels provides the physical habitat for aquatic ecosystems. The damming of the Tsitsa River, through the construction of the Ntabelanga Dam, will change the overall downstream geomorphology. This creates an opportunity for research in the preconstruction window. The current condition of the Tsitsa River was monitored by completing a baseline survey of the channel geomorphology with specific reference to the influence of sediment on river habitats and ecosystem health. Five sites were established in variable reaches of the Tsitsa River, with Site 1 located above the proposed Ntabelanga Dam inundation and Sites 2-5 below the proposed dam wall. Each site included a range of features that can be monitored for their response to the dam. Physical variables, water quality and biota were monitored seasonally to note changes in habitat quality. A baseline survey of the present geomorphology and associated instream habitats of the selected reaches was set up by conducting cross-sectional surveys of channel topography, water slope surveys, discharge measurements and visual and quantitative assessments of substrate. Level loggers were installed at each site to collect continuous data on variations in depth and temperature. Monitoring surveys, in terms of fine sediment accumulation, were conducted to characterise dynamic habitat arrangements and macroinvertebrate community composition. A taxa related physical habitat score for the Tsitsa River was created. The relationship between water quality, physical and ecological characteristics of the Tsitsa River will aid further research in the area as well as create a better understanding of the influence of sediment on river habitats and ecosystem health. Monitoring sites can be used to monitor the impact of catchment-wide rehabilitation on river health prior to the dam being built. After dam construction, the top site above the dam inundation can still be used as a point to monitor the impact of catchment rehabilitation on ecosystem health in terms of fine sediment accumulation.
- Full Text:
- Date Issued: 2018
- Authors: Huchzermeyer, Nicholaus Heinrich
- Date: 2018
- Subjects: Fluvial geomorphology -- South Africa -- Eastern Cape , Stream health -- South Africa -- Eastern Cape , River sediments -- South Africa -- Eastern Cape , Watershed management -- South Africa -- Eastern Cape , Dams -- Environmental aspects -- South Africa -- Eastern Cape , Tsitsa River (South Africa) , Ntabelanga Dam (South Africa)
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/58056 , vital:27040
- Description: Fluvial systems are dynamic systems in which variables in a catchment and river channel affect the morphology of river reaches. South African rivers are increasingly being exposed to stresses from a combination of factors, one of the most prevalent being the impacts of damming rivers which result in varying downstream sediment fluxes and flow regimes. The sediment load combined with flow characteristics for respective river channels provides the physical habitat for aquatic ecosystems. The damming of the Tsitsa River, through the construction of the Ntabelanga Dam, will change the overall downstream geomorphology. This creates an opportunity for research in the preconstruction window. The current condition of the Tsitsa River was monitored by completing a baseline survey of the channel geomorphology with specific reference to the influence of sediment on river habitats and ecosystem health. Five sites were established in variable reaches of the Tsitsa River, with Site 1 located above the proposed Ntabelanga Dam inundation and Sites 2-5 below the proposed dam wall. Each site included a range of features that can be monitored for their response to the dam. Physical variables, water quality and biota were monitored seasonally to note changes in habitat quality. A baseline survey of the present geomorphology and associated instream habitats of the selected reaches was set up by conducting cross-sectional surveys of channel topography, water slope surveys, discharge measurements and visual and quantitative assessments of substrate. Level loggers were installed at each site to collect continuous data on variations in depth and temperature. Monitoring surveys, in terms of fine sediment accumulation, were conducted to characterise dynamic habitat arrangements and macroinvertebrate community composition. A taxa related physical habitat score for the Tsitsa River was created. The relationship between water quality, physical and ecological characteristics of the Tsitsa River will aid further research in the area as well as create a better understanding of the influence of sediment on river habitats and ecosystem health. Monitoring sites can be used to monitor the impact of catchment-wide rehabilitation on river health prior to the dam being built. After dam construction, the top site above the dam inundation can still be used as a point to monitor the impact of catchment rehabilitation on ecosystem health in terms of fine sediment accumulation.
- Full Text:
- Date Issued: 2018
A Bayesian approach to tilted-ring modelling of galaxies
- Authors: Maina, Eric Kamau
- Date: 2020
- Subjects: Bayesian statistical decision theory , Galaxies , Radio astronomy , TiRiFiC (Tilted Ring Fitting Code) , Neutral hydrogen , Spectroscopic data cubes , Galaxy parametrisation
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145783 , vital:38466
- Description: The orbits of neutral hydrogen (H I) gas found in most disk galaxies are circular and also exhibit long-lived warps at large radii where the restoring gravitational forces of the inner disk become weak (Spekkens and Giovanelli 2006). These warps make the tilted-ring model an ideal choice for galaxy parametrisation. Analysis software utilizing the tilted-ring-model can be grouped into two and three-dimensional based software. Józsa et al. (2007b) demonstrated that three dimensional based software is better suited for galaxy parametrisation because it is affected by the effect of beam smearing only by increasing the uncertainty of parameters but not with the notorious systematic effects observed for two-dimensional fitting techniques. TiRiFiC, The Tilted Ring Fitting Code (Józsa et al. 2007b), is a software to construct parameterised models of high-resolution data cubes of rotating galaxies. It uses the tilted-ring model, and with that, a combination of some parameters such as surface brightness, position angle, rotation velocity and inclination, to describe galaxies. TiRiFiC works by directly fitting tilted-ring models to spectroscopic data cubes and hence is not affected by beam smearing or line-of-site-effects, e.g. strong warps. Because of that, the method is unavoidable as an analytic method in future Hi surveys. In the current implementation, though, there are several drawbacks. The implemented optimisers search for local solutions in parameter space only, do not quantify correlations between parameters and cannot find errors of single parameters. In theory, these drawbacks can be overcome by using Bayesian statistics, implemented in Multinest (Feroz et al. 2008), as it allows for sampling a posterior distribution irrespective of its multimodal nature resulting in parameter samples that correspond to the maximum in the posterior distribution. These parameter samples can be used as well to quantify correlations and find errors of single parameters. Since this method employs Bayesian statistics, it also allows the user to leverage any prior information they may have on parameter values.
- Full Text:
- Date Issued: 2020
- Authors: Maina, Eric Kamau
- Date: 2020
- Subjects: Bayesian statistical decision theory , Galaxies , Radio astronomy , TiRiFiC (Tilted Ring Fitting Code) , Neutral hydrogen , Spectroscopic data cubes , Galaxy parametrisation
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/145783 , vital:38466
- Description: The orbits of neutral hydrogen (H I) gas found in most disk galaxies are circular and also exhibit long-lived warps at large radii where the restoring gravitational forces of the inner disk become weak (Spekkens and Giovanelli 2006). These warps make the tilted-ring model an ideal choice for galaxy parametrisation. Analysis software utilizing the tilted-ring-model can be grouped into two and three-dimensional based software. Józsa et al. (2007b) demonstrated that three dimensional based software is better suited for galaxy parametrisation because it is affected by the effect of beam smearing only by increasing the uncertainty of parameters but not with the notorious systematic effects observed for two-dimensional fitting techniques. TiRiFiC, The Tilted Ring Fitting Code (Józsa et al. 2007b), is a software to construct parameterised models of high-resolution data cubes of rotating galaxies. It uses the tilted-ring model, and with that, a combination of some parameters such as surface brightness, position angle, rotation velocity and inclination, to describe galaxies. TiRiFiC works by directly fitting tilted-ring models to spectroscopic data cubes and hence is not affected by beam smearing or line-of-site-effects, e.g. strong warps. Because of that, the method is unavoidable as an analytic method in future Hi surveys. In the current implementation, though, there are several drawbacks. The implemented optimisers search for local solutions in parameter space only, do not quantify correlations between parameters and cannot find errors of single parameters. In theory, these drawbacks can be overcome by using Bayesian statistics, implemented in Multinest (Feroz et al. 2008), as it allows for sampling a posterior distribution irrespective of its multimodal nature resulting in parameter samples that correspond to the maximum in the posterior distribution. These parameter samples can be used as well to quantify correlations and find errors of single parameters. Since this method employs Bayesian statistics, it also allows the user to leverage any prior information they may have on parameter values.
- Full Text:
- Date Issued: 2020
A best practice e-learning environment for software training
- Authors: Esterhuyse, Maxine Pier
- Date: 2017
- Subjects: Internet in education Computer-assisted instruction Web-based instruction -- Education
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/12165 , vital:27039
- Description: The incorporation of best practice in e-learning environments can increase the probability of success for companies and learners alike. By identifying and understanding the barriers that potential learners may face when interacting with e-learning products, the potential for e-learning failure may be alleviated. There are a variety of benefits that may be realised by companies incorporating e-learning opportunities into their management strategies. However, certain pedagogical principles, metrics and components need to be investigated and implemented in order for a corporate e-learning environment to be successful. The aim of this research is to prototype and evaluate a practical e-learning environment for software training (eLESTP) with e-learning components consisting of interactive learning objects that can guide the development and management of online training in the corporate context. The eLESTP is based on a theoretical contribution that is conceptualised in the form of an e-learning environment for software training (eLESTT). Hence, this study followed a research methodology that is appropriate for educational technologies, namely the Design-Based Research (DBR) methodology, which was applied in iterative cycles. Quantitative and qualitative data was collected by means of a case study, interviews, a focus group and survey. The proposed eLESTP underwent several iterations of feedback and improvement and the result is a real-world solution to the problem at hand. With the purpose of determining the success of corporate e-learning, the barriers and critical success factors for e-learning as well as evaluation criteria were explored. Interviews, a focus group and a survey were conducted in order to validate the investigated literature in a real-world context. Informal interviews enabled a better understanding of the organisational context of this study. The focus group was conducted with customers who were undergoing face-to-face training using conveyancing software developed by Korbitec. Many of the issues faced by learners identified in literature regarding e-learning in developing countries were identified by the participants from the case study. An e-learning survey was used to gather information regarding the intention of Korbitec’s customers to use e-learning as well as their satisfaction with using e-learning. From the survey, it was found that respondents were positive regarding intention to use and satisfaction toward e-learning usage. DBR Cycle 1: Problem Investigation and Proposal entailed the initial problem investigation by conducting a literature review, focus group and survey. DBR Cycle 2: Design Alternative 1 of this study involved a design alternative for eLESTP, namely Prototype 1. DBR Cycle 3: Design and Evaluate Alternative 2 involved the design and prototyping of Prototype 2 for eLESTP as well as the improvement of Prototype 2 through sub-cycles of testing and refinement. The suggestions for improvement were obtained from the relevant stakeholders at Korbitec who are content developers and subject-matter experts. The criteria used to evaluate the success of eLESTP, including its e-learning components, were synthesised and adapted from literature and a new set of evaluation criteria for e-learning environments in software training contexts was proposed. The evaluated eLESTP consists of the technology basis of the Modular Object Oriented Dynamic Learning Environment (Moodle), design guidelines for e-learning components, certification and competency-based training, pedagogical principles and best practice. Overall, eLESTP was positively received by various evaluator groups in formative and summative evaluations. The research results indicate that the use of an e-learning environment for software training purposes was useful and necessary. In support of this Masters dissertation, the following three conference papers have been published and presented at one local conference and two international conferences. In addition, an article has been published in an accredited journal: 1. IDIA 2015, Conference Paper – Zanzibar (Tanzania); 2. Conf-IRM 2016, Conference Paper – Cape Town (South Africa); 3. MCIS 2016, Conference Paper – Cyprus (Europe); and 4. IJIKM 2016, Journal Article.
- Full Text:
- Date Issued: 2017
- Authors: Esterhuyse, Maxine Pier
- Date: 2017
- Subjects: Internet in education Computer-assisted instruction Web-based instruction -- Education
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/12165 , vital:27039
- Description: The incorporation of best practice in e-learning environments can increase the probability of success for companies and learners alike. By identifying and understanding the barriers that potential learners may face when interacting with e-learning products, the potential for e-learning failure may be alleviated. There are a variety of benefits that may be realised by companies incorporating e-learning opportunities into their management strategies. However, certain pedagogical principles, metrics and components need to be investigated and implemented in order for a corporate e-learning environment to be successful. The aim of this research is to prototype and evaluate a practical e-learning environment for software training (eLESTP) with e-learning components consisting of interactive learning objects that can guide the development and management of online training in the corporate context. The eLESTP is based on a theoretical contribution that is conceptualised in the form of an e-learning environment for software training (eLESTT). Hence, this study followed a research methodology that is appropriate for educational technologies, namely the Design-Based Research (DBR) methodology, which was applied in iterative cycles. Quantitative and qualitative data was collected by means of a case study, interviews, a focus group and survey. The proposed eLESTP underwent several iterations of feedback and improvement and the result is a real-world solution to the problem at hand. With the purpose of determining the success of corporate e-learning, the barriers and critical success factors for e-learning as well as evaluation criteria were explored. Interviews, a focus group and a survey were conducted in order to validate the investigated literature in a real-world context. Informal interviews enabled a better understanding of the organisational context of this study. The focus group was conducted with customers who were undergoing face-to-face training using conveyancing software developed by Korbitec. Many of the issues faced by learners identified in literature regarding e-learning in developing countries were identified by the participants from the case study. An e-learning survey was used to gather information regarding the intention of Korbitec’s customers to use e-learning as well as their satisfaction with using e-learning. From the survey, it was found that respondents were positive regarding intention to use and satisfaction toward e-learning usage. DBR Cycle 1: Problem Investigation and Proposal entailed the initial problem investigation by conducting a literature review, focus group and survey. DBR Cycle 2: Design Alternative 1 of this study involved a design alternative for eLESTP, namely Prototype 1. DBR Cycle 3: Design and Evaluate Alternative 2 involved the design and prototyping of Prototype 2 for eLESTP as well as the improvement of Prototype 2 through sub-cycles of testing and refinement. The suggestions for improvement were obtained from the relevant stakeholders at Korbitec who are content developers and subject-matter experts. The criteria used to evaluate the success of eLESTP, including its e-learning components, were synthesised and adapted from literature and a new set of evaluation criteria for e-learning environments in software training contexts was proposed. The evaluated eLESTP consists of the technology basis of the Modular Object Oriented Dynamic Learning Environment (Moodle), design guidelines for e-learning components, certification and competency-based training, pedagogical principles and best practice. Overall, eLESTP was positively received by various evaluator groups in formative and summative evaluations. The research results indicate that the use of an e-learning environment for software training purposes was useful and necessary. In support of this Masters dissertation, the following three conference papers have been published and presented at one local conference and two international conferences. In addition, an article has been published in an accredited journal: 1. IDIA 2015, Conference Paper – Zanzibar (Tanzania); 2. Conf-IRM 2016, Conference Paper – Cape Town (South Africa); 3. MCIS 2016, Conference Paper – Cyprus (Europe); and 4. IJIKM 2016, Journal Article.
- Full Text:
- Date Issued: 2017
A biochemical study of the antidiabetic and anticogulant effects of Tulbaghia Violacea
- Authors: Davison, Candice
- Date: 2010
- Subjects: Medicinal plants -- South Africa , Diabetes -- Alternative treatment -- South Africa , Violaceae -- Therapeutic use -- South Africa , Anticoagulants (Medicine) , Plants -- Analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10311 , http://hdl.handle.net/10948/1523 , Medicinal plants -- South Africa , Diabetes -- Alternative treatment -- South Africa , Violaceae -- Therapeutic use -- South Africa , Anticoagulants (Medicine) , Plants -- Analysis
- Description: Secondary metabolites derived from plants, especially those used by traditional healers, are at the forefront of new drug development in combating diseases such as cancer and diabetes. Garlic is employed in indigenous medicine all over the world for the treatment of a variety of diseases. Dietary garlic has been recognized for its beneficial health effects. In particular, garlic consumption has been correlated with (i) reduction of risk factors for cardiovascular diseases and cancer, (ii) stimulation of immune function, (iii) enhanced detoxification of foreign compounds, (iv) hepatoprotection, (v) antimicrobial effects, (vi) antioxidant effects, and most importantly (vii) its hypoglycemic and anticoagulant properties. Due to these beneficial properties, garlic and its closely related genera which includes Tulbaghia violacea, may be useful as coadjuvant therapy in the treatment of type 2 diabetes and some of its physiological complications. The aim of this study was to determine if T. violacea has antidiabetic and anticoagulant properties. This was performed in vitro using both aqueous and organic extracts of the roots, leaves and bulbs. An organic extract was able to improve glucose-stimulated insulin secretion (GSIS) in INS-1 pancreatic β-cells and glucose uptake in Chang liver cells. The BO extract had no effect on the glucose uptake in 3T3-L1 an adipose cell line and reduced glucose utilisation in C2C12, a skeletal muscle cell line. Some of the properties displayed by T. violacea in this study are consistent with those found in similar studies with garlic extracts. It was observed that the BO extract increased the membrane potential and Glut-2 expression in INS-1 cells cultured at hyperglycemic levels, however, at normoglycemic levels a reduction was observed. The oxygen consumption increased at both glycemic levels due to treatment with the BO extract. Platelets were exposed to the extracts to determine their effects upon platelet aggregation, adhesion and protein secretion. Since the BO extract displayed the highest potential at inhibiting platelet aggregation and adhesion. A rat model was used in ex vivo studies to determine if the extract exhibited the same effect in a physiological model. It was noted that the BO extract exhibited a higher degree of inhibition on platelet aggregation and adhesion than the positive control, aspirin. The BO extract reduced clotting times in the prothrombin time (PT) test, but prolonged the clotting time in the actived partial thromboplastin time (APTT) assay in the ex vivo model; however, it had no affect on these clotting assays in the in vitro model using human blood. The BO extract increased the D-dimer and Fibrinogen-C levels in the in vitro model, but had no effect on the D-dimer concentrations and lowered the Fibrinogen-C levels in the ex vivo model. The active compounds in the extract remain to be elucidated.
- Full Text:
- Date Issued: 2010
- Authors: Davison, Candice
- Date: 2010
- Subjects: Medicinal plants -- South Africa , Diabetes -- Alternative treatment -- South Africa , Violaceae -- Therapeutic use -- South Africa , Anticoagulants (Medicine) , Plants -- Analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10311 , http://hdl.handle.net/10948/1523 , Medicinal plants -- South Africa , Diabetes -- Alternative treatment -- South Africa , Violaceae -- Therapeutic use -- South Africa , Anticoagulants (Medicine) , Plants -- Analysis
- Description: Secondary metabolites derived from plants, especially those used by traditional healers, are at the forefront of new drug development in combating diseases such as cancer and diabetes. Garlic is employed in indigenous medicine all over the world for the treatment of a variety of diseases. Dietary garlic has been recognized for its beneficial health effects. In particular, garlic consumption has been correlated with (i) reduction of risk factors for cardiovascular diseases and cancer, (ii) stimulation of immune function, (iii) enhanced detoxification of foreign compounds, (iv) hepatoprotection, (v) antimicrobial effects, (vi) antioxidant effects, and most importantly (vii) its hypoglycemic and anticoagulant properties. Due to these beneficial properties, garlic and its closely related genera which includes Tulbaghia violacea, may be useful as coadjuvant therapy in the treatment of type 2 diabetes and some of its physiological complications. The aim of this study was to determine if T. violacea has antidiabetic and anticoagulant properties. This was performed in vitro using both aqueous and organic extracts of the roots, leaves and bulbs. An organic extract was able to improve glucose-stimulated insulin secretion (GSIS) in INS-1 pancreatic β-cells and glucose uptake in Chang liver cells. The BO extract had no effect on the glucose uptake in 3T3-L1 an adipose cell line and reduced glucose utilisation in C2C12, a skeletal muscle cell line. Some of the properties displayed by T. violacea in this study are consistent with those found in similar studies with garlic extracts. It was observed that the BO extract increased the membrane potential and Glut-2 expression in INS-1 cells cultured at hyperglycemic levels, however, at normoglycemic levels a reduction was observed. The oxygen consumption increased at both glycemic levels due to treatment with the BO extract. Platelets were exposed to the extracts to determine their effects upon platelet aggregation, adhesion and protein secretion. Since the BO extract displayed the highest potential at inhibiting platelet aggregation and adhesion. A rat model was used in ex vivo studies to determine if the extract exhibited the same effect in a physiological model. It was noted that the BO extract exhibited a higher degree of inhibition on platelet aggregation and adhesion than the positive control, aspirin. The BO extract reduced clotting times in the prothrombin time (PT) test, but prolonged the clotting time in the actived partial thromboplastin time (APTT) assay in the ex vivo model; however, it had no affect on these clotting assays in the in vitro model using human blood. The BO extract increased the D-dimer and Fibrinogen-C levels in the in vitro model, but had no effect on the D-dimer concentrations and lowered the Fibrinogen-C levels in the ex vivo model. The active compounds in the extract remain to be elucidated.
- Full Text:
- Date Issued: 2010
A bioinorganic investigation of some metal complexes of the Schiff base, N,N'-bis(3-methoxysalicylaldimine)propan-2-ol
- Authors: Mopp, Estelle
- Date: 2010 , 2012-04-13
- Subjects: Schiff bases , Bioinorganic chemistry , Metal complexes , Transition metal complexes , Transition metals , Cancer -- Chemotherapy , Ligands -- Toxicity , Antineoplastic agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4413 , http://hdl.handle.net/10962/d1006768 , Schiff bases , Bioinorganic chemistry , Metal complexes , Transition metal complexes , Transition metals , Cancer -- Chemotherapy , Ligands -- Toxicity , Antineoplastic agents
- Description: This thesis includes the synthesis, characterisation, antioxidant and antimicrobial activities of Cu(II)-, Co(II)- and Co(III) complexes with N,N'-bis(3- methoxysalicylaldimine)propan-2-ol, 2-OH-oVANPN. The Schiff base ligand, 2-OHoVANPN, is derived from o-vanillin and 1,3-diaminopropan-2-ol. The o-vanillin condensed with 1,3-diaminopropan-2-ol in a 2:1 molar ratio yields this potential tetraor pentadentate ligand. The complexes synthesized are tetra (or penta or hexa) coordinated. Formation of the complexes is symbolized as follows:- MX₂ + 2-OH-oVANPN (2:1) -> [M(2-OH-oVANPN)Xn] + HnX MX₂ + 2-OH-oVANPN (2:1) -> [Mn(2-OH-oVANPN)OH] + H₂X₂ MX₂ + (o-vanillin : diaminopropanol) (1:1) -> [M(1:1)X₂] MX₂ + (o-vanillin : diaminopropanol) (1:1) -> [M₃(1:1)X₄] M = Cu(II), Co(II) or Co(III); X = Cl; n = 1, 2. Their structural features have been deduced from their elemental analytical data, IR spectral data, and electronic spectral data. With the exception of {Cu₃(C₁₁H₁₄N₂O₃)(Cl)₄(H₂O)₆}(A4), the Cu(II) complexes were monomeric with 2-OH-oVANPN acting as a tetradentate ligand. A binuclear Co(II) complex, [Co₂(C₁₉H₁₉N₂O₅)(OH)] (B1), was synthesised and the rest of the Co(II) and Co(III) complexes were monomeric with chloride ions coordinating to the metal centre in some cases. Electronic data suggest that the cobalt(II) complexes have octahedral geometries and the copper(II) complexes have square planar structures – Co(III) is likely to be octahedral. Thermal analyses, which included the copper-block-method for determining sublimation temperatures, revealed that some copper(II) and cobalt(II) complexes are hygroscopic and sublime at 200 °C and below. DSC analyses of the Cu(II) complexes gave exotherms around 300 °C for complexes K[Cu(C₁₉H₂₀N₂O₅)(OH)]·2H₂O (A1) and [Cu(C₁₁H15N₂O₃)(Cl)₂]·2H₂O (A2) and above 400 °C for [Cu(C₁₁H₁₆N₂O₃)(Cl)₂] (A3) and {Cu₃(C₁₁H₁₄N₂O₃)(Cl)₄(H₂O)₆} (A4). Antioxidant studies were carried out against the 2,2-diphenyl-1-picrylhydrazyl radical (DPPH·). The cobalt(II) complex, [Co₂(C₁₉H₁₉N₂O₅)(OH)] (B1), which was synthesized in the presence of KOH, had no antioxidant activity, whilst the other cobalt(II) complexes, [Co(C₁₇H₁₇N₂O₅(Cl))]·1½H₂O (B2), [Co(C₁₉H₂₂N₂O₅) (Cl)₂]·5½H₂O (B3) and [Co(C₁₉H₂₂N₂O₅)(Cl)₂]·5½H₂O (B4), which were synthesised in the absence of KOH, demonstrated antioxidant activity. The latter complexes are candidates for cancer cell line testing, while [Cu(C₁₁H₁₆N₂O₃)(Cl)₂] (A3), {Cu₃(C₁₁H₁₄N₂O₃)(Cl)₄(H₂O)₆} (A4), [Co(C₁₉H₂₁N₂O₅)(Cl)₂ ]·5H₂O (C2) and [Co(C₁₉H₂₀N₂O₅)(Cl)]·3H₂O (C3) may show anticancer activity through possible hydrolysis products. Most of the complexes synthesized displayed antimicrobial activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Aspergillus niger and Candida albicans. The results indicated that complexes [Cu(C₁₁H₁₆N₂O₃)(Cl)₂](A3), [Co(C₁₉H₂₂N₂O₅)(Cl)₂]·5½H₂O (B3) and [Co(C₁₉H₂₁N₂O₅)(Cl)₂ ]·5H₂O (C2) are active against the Gram-negative Ps. aeruginosa and that the ligand, 2-OH-oVANPN, did not have any activity. The same trend was observed with 2-OH-oVANPN, {Cu₃(C₁₁H₁₄N₂O₃)(Cl)4(H₂O)₆} (A4) and [Co(C₁₉H₂₀N₂O₅)(Cl)]·3H₂O (C3) against the Gram-positive S. aureus. As for activity against E. coli and C. albicans, some complexes showed more activity than the ligand. There is an observed trend here that the metal complexes are more active (toxic) than the corresponding ligand, which is in agreement with Tweedy’s chelation theory.
- Full Text:
- Date Issued: 2010
- Authors: Mopp, Estelle
- Date: 2010 , 2012-04-13
- Subjects: Schiff bases , Bioinorganic chemistry , Metal complexes , Transition metal complexes , Transition metals , Cancer -- Chemotherapy , Ligands -- Toxicity , Antineoplastic agents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4413 , http://hdl.handle.net/10962/d1006768 , Schiff bases , Bioinorganic chemistry , Metal complexes , Transition metal complexes , Transition metals , Cancer -- Chemotherapy , Ligands -- Toxicity , Antineoplastic agents
- Description: This thesis includes the synthesis, characterisation, antioxidant and antimicrobial activities of Cu(II)-, Co(II)- and Co(III) complexes with N,N'-bis(3- methoxysalicylaldimine)propan-2-ol, 2-OH-oVANPN. The Schiff base ligand, 2-OHoVANPN, is derived from o-vanillin and 1,3-diaminopropan-2-ol. The o-vanillin condensed with 1,3-diaminopropan-2-ol in a 2:1 molar ratio yields this potential tetraor pentadentate ligand. The complexes synthesized are tetra (or penta or hexa) coordinated. Formation of the complexes is symbolized as follows:- MX₂ + 2-OH-oVANPN (2:1) -> [M(2-OH-oVANPN)Xn] + HnX MX₂ + 2-OH-oVANPN (2:1) -> [Mn(2-OH-oVANPN)OH] + H₂X₂ MX₂ + (o-vanillin : diaminopropanol) (1:1) -> [M(1:1)X₂] MX₂ + (o-vanillin : diaminopropanol) (1:1) -> [M₃(1:1)X₄] M = Cu(II), Co(II) or Co(III); X = Cl; n = 1, 2. Their structural features have been deduced from their elemental analytical data, IR spectral data, and electronic spectral data. With the exception of {Cu₃(C₁₁H₁₄N₂O₃)(Cl)₄(H₂O)₆}(A4), the Cu(II) complexes were monomeric with 2-OH-oVANPN acting as a tetradentate ligand. A binuclear Co(II) complex, [Co₂(C₁₉H₁₉N₂O₅)(OH)] (B1), was synthesised and the rest of the Co(II) and Co(III) complexes were monomeric with chloride ions coordinating to the metal centre in some cases. Electronic data suggest that the cobalt(II) complexes have octahedral geometries and the copper(II) complexes have square planar structures – Co(III) is likely to be octahedral. Thermal analyses, which included the copper-block-method for determining sublimation temperatures, revealed that some copper(II) and cobalt(II) complexes are hygroscopic and sublime at 200 °C and below. DSC analyses of the Cu(II) complexes gave exotherms around 300 °C for complexes K[Cu(C₁₉H₂₀N₂O₅)(OH)]·2H₂O (A1) and [Cu(C₁₁H15N₂O₃)(Cl)₂]·2H₂O (A2) and above 400 °C for [Cu(C₁₁H₁₆N₂O₃)(Cl)₂] (A3) and {Cu₃(C₁₁H₁₄N₂O₃)(Cl)₄(H₂O)₆} (A4). Antioxidant studies were carried out against the 2,2-diphenyl-1-picrylhydrazyl radical (DPPH·). The cobalt(II) complex, [Co₂(C₁₉H₁₉N₂O₅)(OH)] (B1), which was synthesized in the presence of KOH, had no antioxidant activity, whilst the other cobalt(II) complexes, [Co(C₁₇H₁₇N₂O₅(Cl))]·1½H₂O (B2), [Co(C₁₉H₂₂N₂O₅) (Cl)₂]·5½H₂O (B3) and [Co(C₁₉H₂₂N₂O₅)(Cl)₂]·5½H₂O (B4), which were synthesised in the absence of KOH, demonstrated antioxidant activity. The latter complexes are candidates for cancer cell line testing, while [Cu(C₁₁H₁₆N₂O₃)(Cl)₂] (A3), {Cu₃(C₁₁H₁₄N₂O₃)(Cl)₄(H₂O)₆} (A4), [Co(C₁₉H₂₁N₂O₅)(Cl)₂ ]·5H₂O (C2) and [Co(C₁₉H₂₀N₂O₅)(Cl)]·3H₂O (C3) may show anticancer activity through possible hydrolysis products. Most of the complexes synthesized displayed antimicrobial activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Aspergillus niger and Candida albicans. The results indicated that complexes [Cu(C₁₁H₁₆N₂O₃)(Cl)₂](A3), [Co(C₁₉H₂₂N₂O₅)(Cl)₂]·5½H₂O (B3) and [Co(C₁₉H₂₁N₂O₅)(Cl)₂ ]·5H₂O (C2) are active against the Gram-negative Ps. aeruginosa and that the ligand, 2-OH-oVANPN, did not have any activity. The same trend was observed with 2-OH-oVANPN, {Cu₃(C₁₁H₁₄N₂O₃)(Cl)4(H₂O)₆} (A4) and [Co(C₁₉H₂₀N₂O₅)(Cl)]·3H₂O (C3) against the Gram-positive S. aureus. As for activity against E. coli and C. albicans, some complexes showed more activity than the ligand. There is an observed trend here that the metal complexes are more active (toxic) than the corresponding ligand, which is in agreement with Tweedy’s chelation theory.
- Full Text:
- Date Issued: 2010
A bitcoin framework : an alternative payment system for marginalized areas of South Africa using low-end mobile phones
- Authors: Dlamini, Nelisiwe Peaceness
- Date: 2016
- Subjects: Electronic funds transfers -- South Africa Bitcoin -- South Africa Mobile commerce -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/11884 , vital:39115
- Description: The emergence of the cryptocurrency Bitcoin, has invoked the need for developing financial systems that can be used to transfer digital value. This would serve as a solution to developing countries especially the challenged ones, when it comes to accommodating the financial needs of the disadvantaged people. Moreover, it facilitates access to financial services to allow them to transact with ease. Numerous companies have taken advantage of the prevalence of mobile phones and introduced financial platforms to provide financial inclusion to disadvantaged people. Financial institutions and Mobile Network Operators (MNO) have developed platforms such as cell phone banking services, mobile money, mobile wallets, and electronic wallets that can be used to provide affordable financial services. Although this is the case, alternative platforms that are affordable and accessible through mobile phones are still required. Therefore, this study proposes a Bitcoin framework that can be used as an alternative platform through low-end mobile phones to provide access to financial services to the disadvantaged people in marginalized areas. To prove the concept of the proposed Bitcoin framework, a Mobile Bitcoin Wallet System (MBWS) prototype was developed, which allows a person using a low-end mobile phone with no intervening technology such as Internet or Bluetooth, to access a Bitcoin wallet by sending a Short Message Service (SMS). This enables Bitcoin to be accessed more easily and affordably by the people. Thus the developed prototype conceptualizes an alternative payment system or a payment method that can augment the existing payment methods. The MBWS is evaluated to assess if it can offer the services that other platforms offer by being compared to a cell-phone banking service. It was deployed on a computer connected to the Internet to enable a connection to the Bitcoin network and access to the blockchain which records all the transactions that take place in Bitcoin. Although this system provides access to the Bitcoin wallet, for it to be applied to areas where people require an alternative payment system, it still needs to be enhanced for such use. This includes scaling the system and adding more functions to it.
- Full Text:
- Date Issued: 2016
- Authors: Dlamini, Nelisiwe Peaceness
- Date: 2016
- Subjects: Electronic funds transfers -- South Africa Bitcoin -- South Africa Mobile commerce -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10353/11884 , vital:39115
- Description: The emergence of the cryptocurrency Bitcoin, has invoked the need for developing financial systems that can be used to transfer digital value. This would serve as a solution to developing countries especially the challenged ones, when it comes to accommodating the financial needs of the disadvantaged people. Moreover, it facilitates access to financial services to allow them to transact with ease. Numerous companies have taken advantage of the prevalence of mobile phones and introduced financial platforms to provide financial inclusion to disadvantaged people. Financial institutions and Mobile Network Operators (MNO) have developed platforms such as cell phone banking services, mobile money, mobile wallets, and electronic wallets that can be used to provide affordable financial services. Although this is the case, alternative platforms that are affordable and accessible through mobile phones are still required. Therefore, this study proposes a Bitcoin framework that can be used as an alternative platform through low-end mobile phones to provide access to financial services to the disadvantaged people in marginalized areas. To prove the concept of the proposed Bitcoin framework, a Mobile Bitcoin Wallet System (MBWS) prototype was developed, which allows a person using a low-end mobile phone with no intervening technology such as Internet or Bluetooth, to access a Bitcoin wallet by sending a Short Message Service (SMS). This enables Bitcoin to be accessed more easily and affordably by the people. Thus the developed prototype conceptualizes an alternative payment system or a payment method that can augment the existing payment methods. The MBWS is evaluated to assess if it can offer the services that other platforms offer by being compared to a cell-phone banking service. It was deployed on a computer connected to the Internet to enable a connection to the Bitcoin network and access to the blockchain which records all the transactions that take place in Bitcoin. Although this system provides access to the Bitcoin wallet, for it to be applied to areas where people require an alternative payment system, it still needs to be enhanced for such use. This includes scaling the system and adding more functions to it.
- Full Text:
- Date Issued: 2016
A bulk and fraction-specific geochemical study of the origin of diverse high-grade hematitic iron ores from the Transvaal Supergroup, Northern Cape Province, South Africa
- Authors: Moloto, William
- Date: 2017
- Subjects: Iron ore -- South Africa -- Transvaal Supergroup , Hematite -- South Africa -- Transvaal Supergroup , Transvaal Supergroup (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/50546 , vital:25998
- Description: The Paleoproterozoic Transvaal Supergroup in the Northern Cape Province of South Africa is host to high-grade, Banded Iron Formation-hosted hematite iron-ore deposits and is the country’s most important source of iron to date. Previous studies suggest the origin of these iron ores to be ancient supergene, and that the ore forming process would have therefore pre-dated deposition of the basal Mapedi shales of the Olifansthoek Supergroup that unconformably overlies the Transvaal strata. The nature of the protolith to the ores has been suggested to be largely BIF of the Asbestos Hills Subgroup, and mainly the Kuruman BIF. The work presented in this thesis seeks to provide insights into the diversity of processes that are likely to have been involved during the genesis of these high-grade iron ores, in the context of constraining the pre-ore lithologies and the relative role of supergene-style, largely residual enrichment processes versus any possible metasomatic hydrothermal effects. This study had as primary focus the application of combined bulk and fraction-specific geochemical applications on representative iron-ore samples from four different localities in the Northern Cape Province, namely King/Khumani, Beeshoek, Heuninkranz and Hotazel. The collected samples show a variety of textures and also capture different pre-unconformity stratigraphic sections of BIF. The key objective was to assess whether the fraction-specific analytical results could provide any firm constraints for the origin of the ferrous and non-ferrous matrix fractions of the ores, namely whether they represent any combinations of protolith residue, allochtonously-introduced detritus or hydrothermally-derived material, and whether the results are comparable and consistent across all samples studied. In particular, constraints were sought as to whether the ore protolith was exclusively BIF or may potentially have contained at least a fraction of other lithologic types, such as shale; and whether there is sufficient evidence to support solely a supergene model for the ores or the data suggest other more epigenetic models of ore formation involving the action of hydrothermal fluids Bulk-rock geochemical analyses reveal the overwhelming dominance of Fe-oxide (as hematite) in all samples, at concentrations as high as 99 wt.% Fe2O3. Major and trace-element abundances of all samples were re-calculated assuming only iron addition from the postulated protolith (average BIF and shale), and the results revealed atypical enrichments in the iron ores by comparison to average BIF, and more shale-like relative abundances when normalised against the Post-Archaean Average Shale (PAAS). Specifically, BIF-normalised diagrams show relative enrichments by as much as 53-95% for Al2O3; 11-86% for TiO2; and 4-60% for P2O5. By contrast, PAAS-normalised values display enrichments of 1-3% for Al2O3, 0.2-3% for TiO2, and 3-13% for P2O5. Similar observations can be made for the greatest majority of trace elements when normalised against average BIF as compared to normalisation against PAAS. A suite of trace element that include alkali earths (e.g. Ba, Sr) and transition metals (e.g. Ni, Zn) show enrichments that are unrelated to the apparently detrital siliciclastic fraction of the ores, and are therefore linked to a possible hydrothermal input. Fraction-specific extractions were performed via the adaptation of existing dissolution protocols using oxalic acid (iron-oxide fraction) followed by HF digestion (silicate-fraction). The analyses of the produced aliquots using ICP-MS techniques, focused mainly on the REE abundances of the separated ferrous and non-ferrous matrix fractions and their comparisons to bulk-rock REE signatures. The results lend further support to the suggestion that the ore samples contain a predominant shale-like signal which does not directly compare to published REE signatures for supergene or hydrothermal BIF-hosted iron-ore deposits alike. The data therefore collectively point to a post-unconformity epigenetic hydrothermal event/s of iron ore-formation that would have exploited not only BIF but also shale as suitable pre-ore protolith.
- Full Text:
- Date Issued: 2017
- Authors: Moloto, William
- Date: 2017
- Subjects: Iron ore -- South Africa -- Transvaal Supergroup , Hematite -- South Africa -- Transvaal Supergroup , Transvaal Supergroup (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/50546 , vital:25998
- Description: The Paleoproterozoic Transvaal Supergroup in the Northern Cape Province of South Africa is host to high-grade, Banded Iron Formation-hosted hematite iron-ore deposits and is the country’s most important source of iron to date. Previous studies suggest the origin of these iron ores to be ancient supergene, and that the ore forming process would have therefore pre-dated deposition of the basal Mapedi shales of the Olifansthoek Supergroup that unconformably overlies the Transvaal strata. The nature of the protolith to the ores has been suggested to be largely BIF of the Asbestos Hills Subgroup, and mainly the Kuruman BIF. The work presented in this thesis seeks to provide insights into the diversity of processes that are likely to have been involved during the genesis of these high-grade iron ores, in the context of constraining the pre-ore lithologies and the relative role of supergene-style, largely residual enrichment processes versus any possible metasomatic hydrothermal effects. This study had as primary focus the application of combined bulk and fraction-specific geochemical applications on representative iron-ore samples from four different localities in the Northern Cape Province, namely King/Khumani, Beeshoek, Heuninkranz and Hotazel. The collected samples show a variety of textures and also capture different pre-unconformity stratigraphic sections of BIF. The key objective was to assess whether the fraction-specific analytical results could provide any firm constraints for the origin of the ferrous and non-ferrous matrix fractions of the ores, namely whether they represent any combinations of protolith residue, allochtonously-introduced detritus or hydrothermally-derived material, and whether the results are comparable and consistent across all samples studied. In particular, constraints were sought as to whether the ore protolith was exclusively BIF or may potentially have contained at least a fraction of other lithologic types, such as shale; and whether there is sufficient evidence to support solely a supergene model for the ores or the data suggest other more epigenetic models of ore formation involving the action of hydrothermal fluids Bulk-rock geochemical analyses reveal the overwhelming dominance of Fe-oxide (as hematite) in all samples, at concentrations as high as 99 wt.% Fe2O3. Major and trace-element abundances of all samples were re-calculated assuming only iron addition from the postulated protolith (average BIF and shale), and the results revealed atypical enrichments in the iron ores by comparison to average BIF, and more shale-like relative abundances when normalised against the Post-Archaean Average Shale (PAAS). Specifically, BIF-normalised diagrams show relative enrichments by as much as 53-95% for Al2O3; 11-86% for TiO2; and 4-60% for P2O5. By contrast, PAAS-normalised values display enrichments of 1-3% for Al2O3, 0.2-3% for TiO2, and 3-13% for P2O5. Similar observations can be made for the greatest majority of trace elements when normalised against average BIF as compared to normalisation against PAAS. A suite of trace element that include alkali earths (e.g. Ba, Sr) and transition metals (e.g. Ni, Zn) show enrichments that are unrelated to the apparently detrital siliciclastic fraction of the ores, and are therefore linked to a possible hydrothermal input. Fraction-specific extractions were performed via the adaptation of existing dissolution protocols using oxalic acid (iron-oxide fraction) followed by HF digestion (silicate-fraction). The analyses of the produced aliquots using ICP-MS techniques, focused mainly on the REE abundances of the separated ferrous and non-ferrous matrix fractions and their comparisons to bulk-rock REE signatures. The results lend further support to the suggestion that the ore samples contain a predominant shale-like signal which does not directly compare to published REE signatures for supergene or hydrothermal BIF-hosted iron-ore deposits alike. The data therefore collectively point to a post-unconformity epigenetic hydrothermal event/s of iron ore-formation that would have exploited not only BIF but also shale as suitable pre-ore protolith.
- Full Text:
- Date Issued: 2017
A case study of Bigodi Wetland Sanctuary as a community driven Community-Based Natural Resource Management initiative : maintaining livelihoods and wetland health
- Authors: Gosling, Amanda Karen
- Date: 2012
- Subjects: Wetland conservation -- Uganda , Wetland ecology -- Uganda , Natural resources management areas -- Uganda , Rural development -- Uganda
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4752 , http://hdl.handle.net/10962/d1007065 , Wetland conservation -- Uganda , Wetland ecology -- Uganda , Natural resources management areas -- Uganda , Rural development -- Uganda
- Description: Community-Based Natural Resource Management (CBNRM) is considered a win-win approach to reconcile conservation with natural resource use. CBNRM aims to accomplish conservation whilst prioritising development and contributing to poverty alleviation. This study analysed the different components of a CBNRM initiative, Bigodi Wetland Sanctuary (BWS), located in western Uganda. The study was carried out by interviewing the managing committee members (n= 8) as well as local households (n= 68) regarding the manner in which the project works, and the associated benefits and constraints. The main management issues recognised were a lack of monitoring and committee cohesiveness. The information gathered through the household survey enabled the calculation of the value of local livelihood options. This was done on the premise that conservation is better accepted when land users realise the economic value of natural resources. The average annual value of household livelihoods was represented by 30% crop production, 57% natural resource use, and 13% livestock. Lastly, wetland assessments were performed using the WET-Health and WET-EcoServices methodologies from the Wetland Management Series. These assessments indicated that the impacts of local livelihoods on the wetland were currently low but potential issues could arise with the increasing human population density. Ultimately, BWS presents both environmental and social costs and benefits. With a detailed and interdisciplinary method specific recommendations of improvement can be made to reduce such costs and further reconcile the conservation of Bigodi Wetland with local natural resource use..
- Full Text:
- Date Issued: 2012
- Authors: Gosling, Amanda Karen
- Date: 2012
- Subjects: Wetland conservation -- Uganda , Wetland ecology -- Uganda , Natural resources management areas -- Uganda , Rural development -- Uganda
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4752 , http://hdl.handle.net/10962/d1007065 , Wetland conservation -- Uganda , Wetland ecology -- Uganda , Natural resources management areas -- Uganda , Rural development -- Uganda
- Description: Community-Based Natural Resource Management (CBNRM) is considered a win-win approach to reconcile conservation with natural resource use. CBNRM aims to accomplish conservation whilst prioritising development and contributing to poverty alleviation. This study analysed the different components of a CBNRM initiative, Bigodi Wetland Sanctuary (BWS), located in western Uganda. The study was carried out by interviewing the managing committee members (n= 8) as well as local households (n= 68) regarding the manner in which the project works, and the associated benefits and constraints. The main management issues recognised were a lack of monitoring and committee cohesiveness. The information gathered through the household survey enabled the calculation of the value of local livelihood options. This was done on the premise that conservation is better accepted when land users realise the economic value of natural resources. The average annual value of household livelihoods was represented by 30% crop production, 57% natural resource use, and 13% livestock. Lastly, wetland assessments were performed using the WET-Health and WET-EcoServices methodologies from the Wetland Management Series. These assessments indicated that the impacts of local livelihoods on the wetland were currently low but potential issues could arise with the increasing human population density. Ultimately, BWS presents both environmental and social costs and benefits. With a detailed and interdisciplinary method specific recommendations of improvement can be made to reduce such costs and further reconcile the conservation of Bigodi Wetland with local natural resource use..
- Full Text:
- Date Issued: 2012
A case-control approach to assess variability in distribution of distance between transcription factor binding site and transcription start site
- Authors: Moos, Abdul Ragmaan
- Date: 2017
- Subjects: Transcription factors , Proteomics , Chromatin , Chromatin immunoprecipitation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5315 , vital:20808
- Description: Using the in-silico approach, with ENCODE ChIP-seq data for various transcription factors and different cell types; we systematically compared the distance between the transcription factor binding site (TFBS) and the transcription start (TSS). Our aim was to determine if the same transcription factor binds at a different position relative to the TSS in a normal and an abnormal cell type. We compare distribution of distance of binding sites from the TSS; to make description less verbose we call this “distance” where there is no possibility of confusion. We used a case-control methodology where the distance between the TFBS and the TSS in the normal, non-cancerous or untreated cell type is the control. The distance between the TFBS and the TSS in the cancerous or treated cell type is the case. We use the distance between the TFBS and the TSS in the control as the standard. We compared the distance between the TFBS and the TSS in the case and the control. If the distance between the TFBS and the TSS in the control was greater than the distance between the TFBS and the TSS in the case, we can infer the following. The transcription factor in the case binds closer to the TSS compared to the control. If the distance between the TFBS and the TSS in the control is smaller than the distance between the TFBS and the TSS in the case, we can infer the following. The TF in the case binds further away from the TSS compared to the control. Our method is a screening method whereby we compare ChIP-seq data to determine if there is a difference in the distribution distance between the TFBS and the TSS for normal and abnormal cell types. We used the R package ChIP-Enrich to compare the distribution of distance between ChIP-seq peak and the nearest TSS. ChIP-Enrich produces a histogram with the number of ChIP-seq peaks at a certain distance from the TSS. The results indicate for some transcription factors like GM12878-cMyc and K562-cMyc there is a difference between the distribution of distance between the TFBS and the nearest TSS. cMyc has more binding sites within a distance of 1kb from the TSS in GM12878 when compared to K562. GM12878-CTCF and K562-CTCF have slight differences when comparing their distribution of distance from the TSS. This means CTCF binds almost the same distance from the TSS in both GM12878 and K562. A549-gr treated with dexamethasone is interesting because with increase dose of dexamethasone the distribution of distance from the TSS changes as well.
- Full Text:
- Date Issued: 2017
- Authors: Moos, Abdul Ragmaan
- Date: 2017
- Subjects: Transcription factors , Proteomics , Chromatin , Chromatin immunoprecipitation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/5315 , vital:20808
- Description: Using the in-silico approach, with ENCODE ChIP-seq data for various transcription factors and different cell types; we systematically compared the distance between the transcription factor binding site (TFBS) and the transcription start (TSS). Our aim was to determine if the same transcription factor binds at a different position relative to the TSS in a normal and an abnormal cell type. We compare distribution of distance of binding sites from the TSS; to make description less verbose we call this “distance” where there is no possibility of confusion. We used a case-control methodology where the distance between the TFBS and the TSS in the normal, non-cancerous or untreated cell type is the control. The distance between the TFBS and the TSS in the cancerous or treated cell type is the case. We use the distance between the TFBS and the TSS in the control as the standard. We compared the distance between the TFBS and the TSS in the case and the control. If the distance between the TFBS and the TSS in the control was greater than the distance between the TFBS and the TSS in the case, we can infer the following. The transcription factor in the case binds closer to the TSS compared to the control. If the distance between the TFBS and the TSS in the control is smaller than the distance between the TFBS and the TSS in the case, we can infer the following. The TF in the case binds further away from the TSS compared to the control. Our method is a screening method whereby we compare ChIP-seq data to determine if there is a difference in the distribution distance between the TFBS and the TSS for normal and abnormal cell types. We used the R package ChIP-Enrich to compare the distribution of distance between ChIP-seq peak and the nearest TSS. ChIP-Enrich produces a histogram with the number of ChIP-seq peaks at a certain distance from the TSS. The results indicate for some transcription factors like GM12878-cMyc and K562-cMyc there is a difference between the distribution of distance between the TFBS and the nearest TSS. cMyc has more binding sites within a distance of 1kb from the TSS in GM12878 when compared to K562. GM12878-CTCF and K562-CTCF have slight differences when comparing their distribution of distance from the TSS. This means CTCF binds almost the same distance from the TSS in both GM12878 and K562. A549-gr treated with dexamethasone is interesting because with increase dose of dexamethasone the distribution of distance from the TSS changes as well.
- Full Text:
- Date Issued: 2017
A central enrichment-based comparison of two alternative methods of generating transcription factor binding motifs from protein binding microarray data
- Authors: Mahaye, Ntombikayise
- Date: 2013 , 2013-03-13
- Subjects: Transcription factors , Bioinformatics , Protein binding , Protein microarrays , Cell lines
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3890 , http://hdl.handle.net/10962/d1003049 , Transcription factors , Bioinformatics , Protein binding , Protein microarrays , Cell lines
- Description: Characterising transcription factor binding sites (TFBS) is an important problem in bioinformatics, since predicting binding sites has many applications such as predicting gene regulation. ChIP-seq is a powerful in vivo method for generating genome-wide putative binding regions for transcription factors (TFs). CentriMo is an algorithm that measures central enrichment of a motif and has previously been used as motif enrichment analysis (MEA) tool. CentriMo uses the fact that ChIP-seq peak calling methods are likely to be biased towards the centre of the putative binding region, at least in cases where there is direct binding. CentriMo calculates a binomial p-value representing central enrichment, based on the central bias of the binding site with the highest likelihood ratio. In cases where binding is indirect or involves cofactors, a more complex distribution of preferred binding sites may occur but, in many cases, a low CentriMo p-value and low width of maximum enrichment (about 100bp) are strong evidence that the motif in question is the true binding motif. Several other MEA tools have been developed, but they do not consider motif central enrichment. The study investigates the claim made by Zhao and Stormo (2011) that they have identified a simpler method than that used to derive the UniPROBE motif database for creating motifs from protein binding microarray (PBM) data, which they call BEEML-PBM (Binding Energy Estimation by Maximum Likelihood-PBM). To accomplish this, CentriMo is employed on 13 motifs from both motif databases. The results indicate that there is no conclusive difference in the quality of motifs from the original PBM and BEEML-PBM approaches. CentriMo provides an understanding of the mechanisms by which TFs bind to DNA. Out of 13 TFs for which ChIP-seq data is used, BEEML-PBM reports five better motifs and twice it has not had any central enrichment when the best PBM motif does. PBM approach finds seven motifs with better central enrichment. On the other hand, across all variations, the number of examples where PBM is better is not high enough to conclude that it is overall the better approach. Some TFs bind directly to DNA, some indirect or in combination with other TFs. Some of the predicted mechanisms are supported by literature evidence. This study further revealed that the binding specificity of a TF is different in different cell types and development stages. A TF is up-regulated in a cell line where it performs its biological function. The discovery of cell line differences, which has not been done before in any CentriMo study, is interesting and provides reasons to study this further.
- Full Text:
- Date Issued: 2013
- Authors: Mahaye, Ntombikayise
- Date: 2013 , 2013-03-13
- Subjects: Transcription factors , Bioinformatics , Protein binding , Protein microarrays , Cell lines
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3890 , http://hdl.handle.net/10962/d1003049 , Transcription factors , Bioinformatics , Protein binding , Protein microarrays , Cell lines
- Description: Characterising transcription factor binding sites (TFBS) is an important problem in bioinformatics, since predicting binding sites has many applications such as predicting gene regulation. ChIP-seq is a powerful in vivo method for generating genome-wide putative binding regions for transcription factors (TFs). CentriMo is an algorithm that measures central enrichment of a motif and has previously been used as motif enrichment analysis (MEA) tool. CentriMo uses the fact that ChIP-seq peak calling methods are likely to be biased towards the centre of the putative binding region, at least in cases where there is direct binding. CentriMo calculates a binomial p-value representing central enrichment, based on the central bias of the binding site with the highest likelihood ratio. In cases where binding is indirect or involves cofactors, a more complex distribution of preferred binding sites may occur but, in many cases, a low CentriMo p-value and low width of maximum enrichment (about 100bp) are strong evidence that the motif in question is the true binding motif. Several other MEA tools have been developed, but they do not consider motif central enrichment. The study investigates the claim made by Zhao and Stormo (2011) that they have identified a simpler method than that used to derive the UniPROBE motif database for creating motifs from protein binding microarray (PBM) data, which they call BEEML-PBM (Binding Energy Estimation by Maximum Likelihood-PBM). To accomplish this, CentriMo is employed on 13 motifs from both motif databases. The results indicate that there is no conclusive difference in the quality of motifs from the original PBM and BEEML-PBM approaches. CentriMo provides an understanding of the mechanisms by which TFs bind to DNA. Out of 13 TFs for which ChIP-seq data is used, BEEML-PBM reports five better motifs and twice it has not had any central enrichment when the best PBM motif does. PBM approach finds seven motifs with better central enrichment. On the other hand, across all variations, the number of examples where PBM is better is not high enough to conclude that it is overall the better approach. Some TFs bind directly to DNA, some indirect or in combination with other TFs. Some of the predicted mechanisms are supported by literature evidence. This study further revealed that the binding specificity of a TF is different in different cell types and development stages. A TF is up-regulated in a cell line where it performs its biological function. The discovery of cell line differences, which has not been done before in any CentriMo study, is interesting and provides reasons to study this further.
- Full Text:
- Date Issued: 2013
A chemical investigation of Tulbaghia Violacea
- Authors: Burton, Stephanie Gail
- Date: 1990
- Subjects: Liliaceae , Plants -- Analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4528 , http://hdl.handle.net/10962/d1015725
- Description: Tulbaghia violacea, a member of the family Alliaceae is indigenous to the Eastern Cape and is widely used as a herbal remedy for various febrile and gastro-enteric ailments, particularly in young children. Adverse effects, and even fatalities, have been reported following treatment with the plant extract. The project has involved synthesis of model compounds, chromatographic analysis of flavonoid and other constituents of the plant, and examination of the volatile components. Some fifteen flavones were synthesised as chromatographic models and in the course of this work, the development of a new method for synthesis of carboxylic anhydrides was completed. Use of the flavone standards permitted identification of the flavonols kaempferol and quercetin in hydrolysed glycosidic plant extracts. In addition, several sugars were identified, viz., D-glucose, D-fructose, L-arabinose and D-galactose as free sugars, and D-glucose, D-galactose , 1-rhamnose, D- fucose, D-xylose, 1-arabinose and D-fructose as glycosidic sugars, by g.l.c. and g. c. - m. s. analysis of derivatives of isolated sugar mixtures. The presence in the plant extracts of steroidal saponins was also demonstrated. The sulphur compounds, 2,4,5,7-tetrathiaoctane-2,2-dioxide and 2,4,5,7-tetrathiaoctane were isolated from the plant and characterised spectroscopically. This result, together with analysis of volatiles from the plant, has led to a proposal concerning the nature and origin of sulphur compounds in Tulbaghia violacea, showing close correlation with the sulphur compounds in Allium species. Investigation of the biological activity of Tulbaghia violacea extracts showed bacteriostatic activity, particularly of extracts which had not been heated, and which had been prepared from mature plants. Treatment of isolated smooth muscle preparations with Tulbaghia violacea extracts indicated the presence of a β-adrenergic agonist having an inhibitory effect on normal muscle contraction. The results of the investigations indicate that while there may be some basis for use of the plant as an antibacterial, or to treat colic, the adverse effects, caused possibly by the sulphur compounds and/or steroidal saponins present, may override the beneficial effects.
- Full Text:
- Date Issued: 1990
- Authors: Burton, Stephanie Gail
- Date: 1990
- Subjects: Liliaceae , Plants -- Analysis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4528 , http://hdl.handle.net/10962/d1015725
- Description: Tulbaghia violacea, a member of the family Alliaceae is indigenous to the Eastern Cape and is widely used as a herbal remedy for various febrile and gastro-enteric ailments, particularly in young children. Adverse effects, and even fatalities, have been reported following treatment with the plant extract. The project has involved synthesis of model compounds, chromatographic analysis of flavonoid and other constituents of the plant, and examination of the volatile components. Some fifteen flavones were synthesised as chromatographic models and in the course of this work, the development of a new method for synthesis of carboxylic anhydrides was completed. Use of the flavone standards permitted identification of the flavonols kaempferol and quercetin in hydrolysed glycosidic plant extracts. In addition, several sugars were identified, viz., D-glucose, D-fructose, L-arabinose and D-galactose as free sugars, and D-glucose, D-galactose , 1-rhamnose, D- fucose, D-xylose, 1-arabinose and D-fructose as glycosidic sugars, by g.l.c. and g. c. - m. s. analysis of derivatives of isolated sugar mixtures. The presence in the plant extracts of steroidal saponins was also demonstrated. The sulphur compounds, 2,4,5,7-tetrathiaoctane-2,2-dioxide and 2,4,5,7-tetrathiaoctane were isolated from the plant and characterised spectroscopically. This result, together with analysis of volatiles from the plant, has led to a proposal concerning the nature and origin of sulphur compounds in Tulbaghia violacea, showing close correlation with the sulphur compounds in Allium species. Investigation of the biological activity of Tulbaghia violacea extracts showed bacteriostatic activity, particularly of extracts which had not been heated, and which had been prepared from mature plants. Treatment of isolated smooth muscle preparations with Tulbaghia violacea extracts indicated the presence of a β-adrenergic agonist having an inhibitory effect on normal muscle contraction. The results of the investigations indicate that while there may be some basis for use of the plant as an antibacterial, or to treat colic, the adverse effects, caused possibly by the sulphur compounds and/or steroidal saponins present, may override the beneficial effects.
- Full Text:
- Date Issued: 1990
A clip composition case study of communal wool production in the Eastern Cape, South Africa
- Authors: Dreyer, Susanna Maria
- Date: 2019
- Subjects: Wool industry -- South Africa -- Eastern Cape , Wool -- South Africa -- Eastern Cape Sheep industry -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/39480 , vital:35265
- Description: Previous studies conducted on wool production in the communal areas of the Eastern Cape have concluded future research should focus on whether the observed differences in average wool price received between shearing sheds are due to differences in clip preparation (i.e. classing) or differences in the quality of the wool being produced (i.e. genetics).The objective of this study was to establish whether there are indeed geographical differences in the average wool price received by communal wool producers in the Eastern Cape and, if so, whether this difference in earnings is attributable to differences in the quality of wool produced and/or clip preparation. The current research explored eight years of wool production records of communal wool farmers (2009/10 to 2016/17) obtained from BKB, the largest wool broker in South Africa. Statistical analyses included descriptive statistics, analysis of variance, parametric tests (i.e. t-test) and multiple regression analysis. The conclusions drawn from this study are: that there are indeed statistically significant differences in the average wool price received between the different geographic areas of the Eastern Cape communal regions, and that the primary determining factor is wool quality, while clip preparation also plays an important but secondary role. The study identified specific geographic areas where developmental interventions are most critical, with specific emphasis on improving the genetic composition of the wool sheep flocks. Specific strategies are recommended, namely:Removing inferior-quality rams and replacing them with superior-quality rams to prevent any inferior nondescript rams from breeding and producing progeny; Replacing the inferior-quality nondescript ewes in specific areas with superior-quality ewes, and Improving the survival rate of lambs and thereby contributing towards expediting the rate of genetic improvement of the communal wool sheep flocks.
- Full Text:
- Date Issued: 2019
- Authors: Dreyer, Susanna Maria
- Date: 2019
- Subjects: Wool industry -- South Africa -- Eastern Cape , Wool -- South Africa -- Eastern Cape Sheep industry -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/39480 , vital:35265
- Description: Previous studies conducted on wool production in the communal areas of the Eastern Cape have concluded future research should focus on whether the observed differences in average wool price received between shearing sheds are due to differences in clip preparation (i.e. classing) or differences in the quality of the wool being produced (i.e. genetics).The objective of this study was to establish whether there are indeed geographical differences in the average wool price received by communal wool producers in the Eastern Cape and, if so, whether this difference in earnings is attributable to differences in the quality of wool produced and/or clip preparation. The current research explored eight years of wool production records of communal wool farmers (2009/10 to 2016/17) obtained from BKB, the largest wool broker in South Africa. Statistical analyses included descriptive statistics, analysis of variance, parametric tests (i.e. t-test) and multiple regression analysis. The conclusions drawn from this study are: that there are indeed statistically significant differences in the average wool price received between the different geographic areas of the Eastern Cape communal regions, and that the primary determining factor is wool quality, while clip preparation also plays an important but secondary role. The study identified specific geographic areas where developmental interventions are most critical, with specific emphasis on improving the genetic composition of the wool sheep flocks. Specific strategies are recommended, namely:Removing inferior-quality rams and replacing them with superior-quality rams to prevent any inferior nondescript rams from breeding and producing progeny; Replacing the inferior-quality nondescript ewes in specific areas with superior-quality ewes, and Improving the survival rate of lambs and thereby contributing towards expediting the rate of genetic improvement of the communal wool sheep flocks.
- Full Text:
- Date Issued: 2019
A collated digital, geological map database for the central Namaqua Province using geographical information system technology
- Authors: Holland, Henry
- Date: 1997
- Subjects: Geographic information systems , Namaqua Province (South Africa) -- Maps Databases , Geology Maps , Cartography
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4936 , http://hdl.handle.net/10962/d1005548 , Geographic information systems , Namaqua Province (South Africa) -- Maps Databases , Geology Maps , Cartography
- Description: The genlogy of the Namaqua Province is notoriously difficult to map and interpret due to polymetamorphic and multiple deformation events and limlted outcrop. Current maps of the Province reflect diverse interpretations of stratigraphy as a consequence of these difficulties. A Geographic Information System is essentially a digital database and a set of functions and procedures to capture, analyse and manipulate spatially related data. A GIS is therefore ideally suited to the study and analysis of maps. A digital map database was established, using modem GIS technology, to facilitate the collation of existing maps of an area in the Central Namaqua Province (CNP). This database is based on a lithological classification system similar to that used by Harris (1992), rather than on an interpretive stratigraphic model. In order to establish the database, existing geological maps were scanned into a GIS, and lines of outcrop and lithological contacts were digitised using a manual line following process, which is one of the functions native to a GIS. Attribute data were then attached to the resultant polygons. The attribute database consists of lithological, textural and mineralogical data, as well as stratigraphical classification data according to the South African Committee for Stratigraphy (SACS), correlative names assigned to units by the Precambrian Research Unit, the Geological Survey of South Africa, the Bushmanland Research group and the University of the Orange Free State. Other attribute data included in the database, are tectonic and absolute age information, and the terrane classification for the area. This database reflects the main objective of the project and also serves as a basis for further expansion of a geological GIS for the CNP. Cartographic and database capabilities of the GIS were employed to produce a collated lithological map of the CNP. A TNTmipsTM Spatial Manipulation Language routine was written to produce a database containing two fields linked to each polygon, one for lithology and one for a correlation probability factor. Correlation factors are calculated in this routine from three variables, namely the prominence a worker attached to a specific lithology within a unit or outcrop, the agreement amongst the various workers on the actual lithology present within an outcrop, and the correspondence between the source of the spatial element (mapped outcrop) and the source of the attribute data attached to it. Outcrops were displayed on the map according to the lithology with the highest correlation factor, providing a unique view of the spatial relationships and distribution patterns of lithological units in the CNP. A second map was produced indicating the correlation factors for lithologies within the CNP. Thematic maps are produced in a GIS by selecting spatial elements according to a set of criteria, usually based on the attribute database, and then displaying the elements as maps. Maps created by this process are known as customised maps, since users of the GIS can customise the selection and display of elements according to their needs. For instance, all outcrops of rock units containing particular lithologies of a given age occurring in a specific terrane can be displayed - either on screen or printed out as a map. The database also makes it possible to plot maps according to different stratigraphic classification systems. Areas where various workers disagree on the stratigraphic classification of units can be isolated, and displayed as separate maps in order to aid in the collation process. The database can assist SACS in identifying areas in the CNP where stratigraphic classification is still lacking or agreements on stratigraphic nomenclature have not yet been attained. More than one database can be attached to the spatial elements in a GIS, and the Namaqua-GIS can therefore be expanded to include geochemical, geophysical, economic, structural and geographical data. Other data on the area, such as more detailed maps, photographs and satellite images can be attached to the lithological map database in the correct spatial relationship. Another advantage of a GIS is the facility to continually update the database(s) as more information becomes available and/or as interpretation of the area is refined.
- Full Text:
- Date Issued: 1997
- Authors: Holland, Henry
- Date: 1997
- Subjects: Geographic information systems , Namaqua Province (South Africa) -- Maps Databases , Geology Maps , Cartography
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4936 , http://hdl.handle.net/10962/d1005548 , Geographic information systems , Namaqua Province (South Africa) -- Maps Databases , Geology Maps , Cartography
- Description: The genlogy of the Namaqua Province is notoriously difficult to map and interpret due to polymetamorphic and multiple deformation events and limlted outcrop. Current maps of the Province reflect diverse interpretations of stratigraphy as a consequence of these difficulties. A Geographic Information System is essentially a digital database and a set of functions and procedures to capture, analyse and manipulate spatially related data. A GIS is therefore ideally suited to the study and analysis of maps. A digital map database was established, using modem GIS technology, to facilitate the collation of existing maps of an area in the Central Namaqua Province (CNP). This database is based on a lithological classification system similar to that used by Harris (1992), rather than on an interpretive stratigraphic model. In order to establish the database, existing geological maps were scanned into a GIS, and lines of outcrop and lithological contacts were digitised using a manual line following process, which is one of the functions native to a GIS. Attribute data were then attached to the resultant polygons. The attribute database consists of lithological, textural and mineralogical data, as well as stratigraphical classification data according to the South African Committee for Stratigraphy (SACS), correlative names assigned to units by the Precambrian Research Unit, the Geological Survey of South Africa, the Bushmanland Research group and the University of the Orange Free State. Other attribute data included in the database, are tectonic and absolute age information, and the terrane classification for the area. This database reflects the main objective of the project and also serves as a basis for further expansion of a geological GIS for the CNP. Cartographic and database capabilities of the GIS were employed to produce a collated lithological map of the CNP. A TNTmipsTM Spatial Manipulation Language routine was written to produce a database containing two fields linked to each polygon, one for lithology and one for a correlation probability factor. Correlation factors are calculated in this routine from three variables, namely the prominence a worker attached to a specific lithology within a unit or outcrop, the agreement amongst the various workers on the actual lithology present within an outcrop, and the correspondence between the source of the spatial element (mapped outcrop) and the source of the attribute data attached to it. Outcrops were displayed on the map according to the lithology with the highest correlation factor, providing a unique view of the spatial relationships and distribution patterns of lithological units in the CNP. A second map was produced indicating the correlation factors for lithologies within the CNP. Thematic maps are produced in a GIS by selecting spatial elements according to a set of criteria, usually based on the attribute database, and then displaying the elements as maps. Maps created by this process are known as customised maps, since users of the GIS can customise the selection and display of elements according to their needs. For instance, all outcrops of rock units containing particular lithologies of a given age occurring in a specific terrane can be displayed - either on screen or printed out as a map. The database also makes it possible to plot maps according to different stratigraphic classification systems. Areas where various workers disagree on the stratigraphic classification of units can be isolated, and displayed as separate maps in order to aid in the collation process. The database can assist SACS in identifying areas in the CNP where stratigraphic classification is still lacking or agreements on stratigraphic nomenclature have not yet been attained. More than one database can be attached to the spatial elements in a GIS, and the Namaqua-GIS can therefore be expanded to include geochemical, geophysical, economic, structural and geographical data. Other data on the area, such as more detailed maps, photographs and satellite images can be attached to the lithological map database in the correct spatial relationship. Another advantage of a GIS is the facility to continually update the database(s) as more information becomes available and/or as interpretation of the area is refined.
- Full Text:
- Date Issued: 1997
A common analysis framework for simulated streaming-video networks
- Authors: Mulumba, Patrick
- Date: 2009
- Subjects: Computer networks -- Management , Streaming video , Mass media -- Technological innovations
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4590 , http://hdl.handle.net/10962/d1004828 , Computer networks -- Management , Streaming video , Mass media -- Technological innovations
- Description: Distributed media streaming has been driven by the combination of improved media compression techniques and an increase in the availability of bandwidth. This increase has lead to the development of various streaming distribution engines (systems/services), which currently provide the majority of the streaming media available throughout the Internet. This study aimed to analyse a range of existing commercial and open-source streaming media distribution engines, and classify them in such a way as to define a Common Analysis Framework for Simulated Streaming-Video Networks (CAFSS-Net). This common framework was used as the basis for a simulation tool intended to aid in the development and deployment of streaming media networks and predict the performance impacts of both network configuration changes, video features (scene complexity, resolution) and general scaling. CAFSS-Net consists of six components: the server, the client(s), the network simulator, the video publishing tools, the videos and the evaluation tool-set. Test scenarios are presented consisting of different network configurations, scales and external traffic specifications. From these test scenarios, results were obtained to determine interesting observations attained and to provide an overview of the different test specications for this study. From these results, an analysis of the system was performed, yielding relationships between the videos, the different bandwidths, the different measurement tools and the different components of CAFSS-Net. Based on the analysis of the results, the implications for CAFSS-Net highlighted different achievements and proposals for future work for the different components. CAFSS-Net was able to successfully integrate all of its components to evaluate the different streaming scenarios. The streaming server, client and video components accomplished their objectives. It is noted that although the video publishing tool was able to provide the necessary compression/decompression services, proposals for the implementation of alternative compression/decompression schemes could serve as a suitable extension. The network simulator and evaluation tool-set components were also successful, but future tests (particularly in low bandwidth scenarios) are suggested in order to further improve the accuracy of the framework as a whole. CAFSS-Net is especially successful with analysing high bandwidth connections with the results being similar to those of the physical network tests.
- Full Text:
- Date Issued: 2009
- Authors: Mulumba, Patrick
- Date: 2009
- Subjects: Computer networks -- Management , Streaming video , Mass media -- Technological innovations
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4590 , http://hdl.handle.net/10962/d1004828 , Computer networks -- Management , Streaming video , Mass media -- Technological innovations
- Description: Distributed media streaming has been driven by the combination of improved media compression techniques and an increase in the availability of bandwidth. This increase has lead to the development of various streaming distribution engines (systems/services), which currently provide the majority of the streaming media available throughout the Internet. This study aimed to analyse a range of existing commercial and open-source streaming media distribution engines, and classify them in such a way as to define a Common Analysis Framework for Simulated Streaming-Video Networks (CAFSS-Net). This common framework was used as the basis for a simulation tool intended to aid in the development and deployment of streaming media networks and predict the performance impacts of both network configuration changes, video features (scene complexity, resolution) and general scaling. CAFSS-Net consists of six components: the server, the client(s), the network simulator, the video publishing tools, the videos and the evaluation tool-set. Test scenarios are presented consisting of different network configurations, scales and external traffic specifications. From these test scenarios, results were obtained to determine interesting observations attained and to provide an overview of the different test specications for this study. From these results, an analysis of the system was performed, yielding relationships between the videos, the different bandwidths, the different measurement tools and the different components of CAFSS-Net. Based on the analysis of the results, the implications for CAFSS-Net highlighted different achievements and proposals for future work for the different components. CAFSS-Net was able to successfully integrate all of its components to evaluate the different streaming scenarios. The streaming server, client and video components accomplished their objectives. It is noted that although the video publishing tool was able to provide the necessary compression/decompression services, proposals for the implementation of alternative compression/decompression schemes could serve as a suitable extension. The network simulator and evaluation tool-set components were also successful, but future tests (particularly in low bandwidth scenarios) are suggested in order to further improve the accuracy of the framework as a whole. CAFSS-Net is especially successful with analysing high bandwidth connections with the results being similar to those of the physical network tests.
- Full Text:
- Date Issued: 2009