Forecasting solar cycle 24 using neural networks
- Authors: Uwamahoro, Jean
- Date: 2009
- Subjects: Solar cycle , Neural networks (Computer science) , Ionosphere , Ionospheric electron density , Ionospheric forecasting , Solar thermal energy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5468 , http://hdl.handle.net/10962/d1005253 , Solar cycle , Neural networks (Computer science) , Ionosphere , Ionospheric electron density , Ionospheric forecasting , Solar thermal energy
- Description: The ability to predict the future behavior of solar activity has become of extreme importance due to its effect on the near-Earth environment. Predictions of both the amplitude and timing of the next solar cycle will assist in estimating the various consequences of Space Weather. Several prediction techniques have been applied and have achieved varying degrees of success in the domain of solar activity prediction. These techniques include, for example, neural networks and geomagnetic precursor methods. In this thesis, various neural network based models were developed and the model considered to be optimum was used to estimate the shape and timing of solar cycle 24. Given the recent success of the geomagnetic precusrsor methods, geomagnetic activity as measured by the aa index is considered among the main inputs to the neural network model. The neural network model developed is also provided with the time input parameters defining the year and the month of a particular solar cycle, in order to characterise the temporal behaviour of sunspot number as observed during the last 10 solar cycles. The structure of input-output patterns to the neural network is constructed in such a way that the network learns the relationship between the aa index values of a particular cycle, and the sunspot number values of the following cycle. Assuming January 2008 as the minimum preceding solar cycle 24, the shape and amplitude of solar cycle 24 is estimated in terms of monthly mean and smoothed monthly sunspot number. This new prediction model estimates an average solar cycle 24, with the maximum occurring around June 2012 [± 11 months], with a smoothed monthly maximum sunspot number of 121 ± 9.
- Full Text:
- Authors: Uwamahoro, Jean
- Date: 2009
- Subjects: Solar cycle , Neural networks (Computer science) , Ionosphere , Ionospheric electron density , Ionospheric forecasting , Solar thermal energy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5468 , http://hdl.handle.net/10962/d1005253 , Solar cycle , Neural networks (Computer science) , Ionosphere , Ionospheric electron density , Ionospheric forecasting , Solar thermal energy
- Description: The ability to predict the future behavior of solar activity has become of extreme importance due to its effect on the near-Earth environment. Predictions of both the amplitude and timing of the next solar cycle will assist in estimating the various consequences of Space Weather. Several prediction techniques have been applied and have achieved varying degrees of success in the domain of solar activity prediction. These techniques include, for example, neural networks and geomagnetic precursor methods. In this thesis, various neural network based models were developed and the model considered to be optimum was used to estimate the shape and timing of solar cycle 24. Given the recent success of the geomagnetic precusrsor methods, geomagnetic activity as measured by the aa index is considered among the main inputs to the neural network model. The neural network model developed is also provided with the time input parameters defining the year and the month of a particular solar cycle, in order to characterise the temporal behaviour of sunspot number as observed during the last 10 solar cycles. The structure of input-output patterns to the neural network is constructed in such a way that the network learns the relationship between the aa index values of a particular cycle, and the sunspot number values of the following cycle. Assuming January 2008 as the minimum preceding solar cycle 24, the shape and amplitude of solar cycle 24 is estimated in terms of monthly mean and smoothed monthly sunspot number. This new prediction model estimates an average solar cycle 24, with the maximum occurring around June 2012 [± 11 months], with a smoothed monthly maximum sunspot number of 121 ± 9.
- Full Text:
Geomagnetically induced current characteristics in southern Africa
- Authors: Ngwira, Chigomezyo Mudala
- Date: 2009
- Subjects: Magnetic Observatory (South African Council for Scientific and Industrial Research) Geomagnetism -- Africa,Southern Computer networks -- Africa, Southern Magnetospheric currents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5469 , http://hdl.handle.net/10962/d1005254
- Description: Geomagnetically induced currents (GICs), resulting from adverse space weather, have been demonstrated to cause damage to power transformers at mid-latitudes. There is growing concern over possible GIC effects in the Southern African network due to its long power lines. Previous efforts to model the electric field associated with GICs in the Southern Africa region used a uniform ground conductivity model. In an effort to improve the modelling of GICs, GIC data together with Hermanus Magnetic Observatory geomagnetic field data were used to obtain a multilayered ground conductivity model. This process requires a definition of the network coefficients, which are then used in subsequent calculations. This study shows that GIC computed with the new network coefficients and the multilayered ground conductivity model improves the accuracy of GIC modelling. Then GIC statistics are derived based on the recordings of the geomagnetic field at Hermanus, the new network coefficients and ground conductivity model. The geoelectric field is modelled using the plane wave method. The properties of the geomagnetic field, their time derivatives and local geomagnetic indices were investigated to determine their characteristics in relation to the GIC. The pattern of the time derivatives of the horizontal geomagnetic field closely follow the rate of change of the north-south geomagnetic component rather than the east-west component. The correlation between the GIC and the local geomagnetic field indices was also investigated. The results show that there is a higher correlation between the GIC and the east-west components of the geomagnetic local indices than between the GIC and the north-south components. This corresponds very well with the orientation of the power lines feeding the power transformers at the South African Grassridge electrical substation GIC site. Thus, the geoelectric field driving the GIC at Grassridge is north-south oriented. Further, it is shown that the geomagnetic observation sites have a strong directional preference with respect to the Grassridge GIC site.
- Full Text:
- Authors: Ngwira, Chigomezyo Mudala
- Date: 2009
- Subjects: Magnetic Observatory (South African Council for Scientific and Industrial Research) Geomagnetism -- Africa,Southern Computer networks -- Africa, Southern Magnetospheric currents
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5469 , http://hdl.handle.net/10962/d1005254
- Description: Geomagnetically induced currents (GICs), resulting from adverse space weather, have been demonstrated to cause damage to power transformers at mid-latitudes. There is growing concern over possible GIC effects in the Southern African network due to its long power lines. Previous efforts to model the electric field associated with GICs in the Southern Africa region used a uniform ground conductivity model. In an effort to improve the modelling of GICs, GIC data together with Hermanus Magnetic Observatory geomagnetic field data were used to obtain a multilayered ground conductivity model. This process requires a definition of the network coefficients, which are then used in subsequent calculations. This study shows that GIC computed with the new network coefficients and the multilayered ground conductivity model improves the accuracy of GIC modelling. Then GIC statistics are derived based on the recordings of the geomagnetic field at Hermanus, the new network coefficients and ground conductivity model. The geoelectric field is modelled using the plane wave method. The properties of the geomagnetic field, their time derivatives and local geomagnetic indices were investigated to determine their characteristics in relation to the GIC. The pattern of the time derivatives of the horizontal geomagnetic field closely follow the rate of change of the north-south geomagnetic component rather than the east-west component. The correlation between the GIC and the local geomagnetic field indices was also investigated. The results show that there is a higher correlation between the GIC and the east-west components of the geomagnetic local indices than between the GIC and the north-south components. This corresponds very well with the orientation of the power lines feeding the power transformers at the South African Grassridge electrical substation GIC site. Thus, the geoelectric field driving the GIC at Grassridge is north-south oriented. Further, it is shown that the geomagnetic observation sites have a strong directional preference with respect to the Grassridge GIC site.
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Human-river relationships in the Kat River catchment and the implications for integrated water resource management (IWRM) : an exploraratory study
- Authors: Birkholz, Sharon Alice
- Date: 2009
- Subjects: Aquatic ecology -- South Africa -- Kat River , Rivers -- South Africa -- Kat River -- Sociological aspects , Rivers -- South Africa -- Kat River , Water supply -- South Africa -- Kat River -- Management , Human ecology -- South Africa -- Kat River , Stream ecology -- South Africa -- Kat River
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: vital:4838 , http://hdl.handle.net/10962/d1005514
- Description: Through out this study ‘relational scenarios’ were seen as the possible outcomes of the expression of human-river relationships in a catchment. Working within Inglis’s (2008, pg. 10) comment that ‘the Human World Relationship is expressed through a person’s views and behaviour towards the natural world, which can be either constructive or destructive’, two relational scenarios were selected to represent these two predicted outcomes of human-environment (or in the case of this thesis human-river) relationships: IWRM, seen as constructive and mutually beneficial to both the social and ecological system, and the Tragedy of the Commons, seen as destructive and parasitic in nature. In respect to this assertion, a conceptual framework or model was developed and used to guide the inductive process of this research. Through a social survey (administered via semi-structured interviews) of stakeholders (water-users) in the Kat River Catchment, Eastern Cape, South Africa, social attitudes towards the Kat River were explored. These attitudes were considered as variables that relate to the expression of ‘Human World Relationships’ namely ‘values and behaviour’ (Inglis, 2008, pg. 10). The findings of this thesis confirm that attitudes are influential components of human-river relationships in the Kat River Catchment. It was observed from the findings that the attitudes individuals have towards the Kat River have the potential to influence the ways people interact with the River and its associated resources, and are in turn influenced by the condition of the River and connections people have or make with the River within their daily lives. Such relationships in turn affect the management of the River and its water resources and influence how individuals approach water-related issues and undertake the associated activities. Given this understanding it was then proposed that attitudes could provide information that enables the prediction of likely ‘relational scenarios’ (IWRM or the Tragedy of the Commons) in a catchment. The findings appear to support this proposal, and three main attitude groups (utilitarian, associative and dissociative) were identified and used to further the discussion into how this knowledge could be used in predicting possible relational scenarios based on human-river relationships. Further exploration of the identified attitude groups suggested that these variables are significantly influenced by environmental ethics and place attachment (present in the community) and a series of guiding frameworks were developed to facilitate the exploration of the attitude groups relative to these concepts. The frameworks were generated from the hypothesis that knowledge of attitude groups in a catchment, in connection with the relative degrees to which moral values and worldviews are expressed, could provide insight into the readiness of a catchment system for the implementation of IWRM and/or the facilitative steps needed to shift the influence of unfavourable attitude groups (i.e. dissociative attitudes). Such steps would most likely involve extensive educational, awareness and capacity building programs. Finally, given the above theoretical frameworks, inductively developed from the findings of the social survey and related literature, the conceptual model was reevaluated and extended to include the thesis findings and hypotheses. It is suggested that in a catchment where there is a balance between the expression of utilitarian and associative attitude groups, then there is a high probability of finding present evidence of mutually beneficial human-river relationships already in play, as well as ‘fertile soil’ for the promotion of IWRM and philosophies and skills that generate such relationships. Alternatively in an area with a strong expression of dissociative attitudes, it is more likely to find evidence of destructive, more parasitic-like relationships being expressed, and a lack of commitment and interest in being involved in changing the status quo. It is likely that where both associative and dissociative attitudes are present there will be an overlap of elements of both scenarios – a situation that is probable in most catchments – depending on the strength of expression of either attitude group the balance will shift (be shifting) between the two relational scenarios.
- Full Text:
- Authors: Birkholz, Sharon Alice
- Date: 2009
- Subjects: Aquatic ecology -- South Africa -- Kat River , Rivers -- South Africa -- Kat River -- Sociological aspects , Rivers -- South Africa -- Kat River , Water supply -- South Africa -- Kat River -- Management , Human ecology -- South Africa -- Kat River , Stream ecology -- South Africa -- Kat River
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: vital:4838 , http://hdl.handle.net/10962/d1005514
- Description: Through out this study ‘relational scenarios’ were seen as the possible outcomes of the expression of human-river relationships in a catchment. Working within Inglis’s (2008, pg. 10) comment that ‘the Human World Relationship is expressed through a person’s views and behaviour towards the natural world, which can be either constructive or destructive’, two relational scenarios were selected to represent these two predicted outcomes of human-environment (or in the case of this thesis human-river) relationships: IWRM, seen as constructive and mutually beneficial to both the social and ecological system, and the Tragedy of the Commons, seen as destructive and parasitic in nature. In respect to this assertion, a conceptual framework or model was developed and used to guide the inductive process of this research. Through a social survey (administered via semi-structured interviews) of stakeholders (water-users) in the Kat River Catchment, Eastern Cape, South Africa, social attitudes towards the Kat River were explored. These attitudes were considered as variables that relate to the expression of ‘Human World Relationships’ namely ‘values and behaviour’ (Inglis, 2008, pg. 10). The findings of this thesis confirm that attitudes are influential components of human-river relationships in the Kat River Catchment. It was observed from the findings that the attitudes individuals have towards the Kat River have the potential to influence the ways people interact with the River and its associated resources, and are in turn influenced by the condition of the River and connections people have or make with the River within their daily lives. Such relationships in turn affect the management of the River and its water resources and influence how individuals approach water-related issues and undertake the associated activities. Given this understanding it was then proposed that attitudes could provide information that enables the prediction of likely ‘relational scenarios’ (IWRM or the Tragedy of the Commons) in a catchment. The findings appear to support this proposal, and three main attitude groups (utilitarian, associative and dissociative) were identified and used to further the discussion into how this knowledge could be used in predicting possible relational scenarios based on human-river relationships. Further exploration of the identified attitude groups suggested that these variables are significantly influenced by environmental ethics and place attachment (present in the community) and a series of guiding frameworks were developed to facilitate the exploration of the attitude groups relative to these concepts. The frameworks were generated from the hypothesis that knowledge of attitude groups in a catchment, in connection with the relative degrees to which moral values and worldviews are expressed, could provide insight into the readiness of a catchment system for the implementation of IWRM and/or the facilitative steps needed to shift the influence of unfavourable attitude groups (i.e. dissociative attitudes). Such steps would most likely involve extensive educational, awareness and capacity building programs. Finally, given the above theoretical frameworks, inductively developed from the findings of the social survey and related literature, the conceptual model was reevaluated and extended to include the thesis findings and hypotheses. It is suggested that in a catchment where there is a balance between the expression of utilitarian and associative attitude groups, then there is a high probability of finding present evidence of mutually beneficial human-river relationships already in play, as well as ‘fertile soil’ for the promotion of IWRM and philosophies and skills that generate such relationships. Alternatively in an area with a strong expression of dissociative attitudes, it is more likely to find evidence of destructive, more parasitic-like relationships being expressed, and a lack of commitment and interest in being involved in changing the status quo. It is likely that where both associative and dissociative attitudes are present there will be an overlap of elements of both scenarios – a situation that is probable in most catchments – depending on the strength of expression of either attitude group the balance will shift (be shifting) between the two relational scenarios.
- Full Text:
Investigating the enzymatic mechanism of platinum nanoparticle synthesis in sulfate-reducing bacteria
- Authors: Riddin, Tamsyn Louise
- Date: 2009
- Subjects: Platinum , Nanoparticles , Sulfate-reducing bacteria
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3965 , http://hdl.handle.net/10962/d1004024 , Platinum , Nanoparticles , Sulfate-reducing bacteria
- Description: Efforts to discover an efficient yet environmentally friendly mode of metal nanoparticle (NP) synthesis are increasing rapidly. A ‘green’ route that avoids the high costs, toxic wastes and complicated protocols associated with chemical synthesis methods is therefore highly sought after. A biologically based protocol will provide the possibility of gaining control over the mechanism merely by manipulating the experimental conditions of the system. Given that the properties of nanoparticles are highly dependant on the morphology of the particles themselves, this mechanistic control will provide significant industrial advantages with regards to tailoring specific properties of the nanoparticles produced. The key objectives of this study were to: a) determine whether a consortium of sulfate-reducing bacteria was capable of platinum nanoparticle synthesis, b) elucidate the bioreductive, enzymatic mechanism responsible, and c) attempt to control the morphologies of the particles produced. A consortium of sulfate-reducing bacteria (SRB), isolated from sewage sludge, was used in these investigations due to the advantages a consortium provides in comparison to pure cultures. The syntrophic relationships established within the constituent species not only prevent the growth of contaminant microbes, but increases the oxygen-tolerance of the system as a whole. The sulfate-reducing consortium was shown to possess an aerobic mechanism for Pt(IV) reduction which, though different from the anaerobic bioreductive mechanism previously identified in literature, did not require an exogenous electron donor. It was demonstrated that the Pt(IV) ion becomes reduced to Pt(0) via a two-cycle mechanism involving Pt(II) as the intermediate. Further investigation elucidated the reduction of Pt(IV) to Pt(II) to be dependant on a novel Pt(IV) reductase which becomes upregulated in the presence of Cu(II), while the reduction of Pt(II) to Pt(0) occurred by means of a periplasmic hydrogenase. To our knowledge, this is the first time a coupled mechanism for Pt(IV) reduction by micro-organisms has been proposed. A cell-free, crude protein solution from the consortium produced both geometric and irregular platinum nanoparticles. The wavelength of 334 nm was chosen as a nonquantitative indicator of Pt(0) nanoparticle formation over time. The optimum conditions for nanoparticle synthesis were pH 9.0, 65 ˚C and 0.75 mM Pt(IV) as H2PtCl6 salt. In the absence of a buffer a Pt(IV) concentration > 1 mM resulted in the precipitation of protein-nanoparticle bioconjugates, due to unfavourable acidic conditions. This demonstrated that the nanoparticles were binding to and becoming stabilised by general protein in the cell-free solution. Upon addition of a sodium-bicarbonate buffer, a general increase in Pt(IV) reduction to Pt(II) was observed. The addition of the buffer also resulted in an unexplained change in particle morphology and for this reason was not used in subsequent investigations. Polyvinylpyrrolidone (PVP) was shown to compromise the reduction rate of the Pt(IV) ion by SRB cells. The presence of extracellular NP’s was suggested by the colour of the supernatant turning brown and the A334 increasing over time. Attempts to visualise the particles by transmission electron microscopy (TEM) resulted in an unexpected phenomenon where nanoparticles could be observed to form dynamically upon irradiation by the electron beam. Extended irradiation by the electron beam also resulted in structural changes of the particles occurring during observation. An increase in temperature was shown to increase the reduction rate which in turn resulted in particles decreasing in size. The starting pH was shown to have a significant effect on the reduction rate and particle morphology although specific trends could not be identified. In conclusion, the cell-soluble extract from the sulfate-reducing consortium investigated, is capable of Pt(0) nanoparticle synthesis. Precise control over the particle morphology was not attained although the mechanism was further clarified and optimal conditions for nanoparticle synthesis were determined.
- Full Text:
- Authors: Riddin, Tamsyn Louise
- Date: 2009
- Subjects: Platinum , Nanoparticles , Sulfate-reducing bacteria
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3965 , http://hdl.handle.net/10962/d1004024 , Platinum , Nanoparticles , Sulfate-reducing bacteria
- Description: Efforts to discover an efficient yet environmentally friendly mode of metal nanoparticle (NP) synthesis are increasing rapidly. A ‘green’ route that avoids the high costs, toxic wastes and complicated protocols associated with chemical synthesis methods is therefore highly sought after. A biologically based protocol will provide the possibility of gaining control over the mechanism merely by manipulating the experimental conditions of the system. Given that the properties of nanoparticles are highly dependant on the morphology of the particles themselves, this mechanistic control will provide significant industrial advantages with regards to tailoring specific properties of the nanoparticles produced. The key objectives of this study were to: a) determine whether a consortium of sulfate-reducing bacteria was capable of platinum nanoparticle synthesis, b) elucidate the bioreductive, enzymatic mechanism responsible, and c) attempt to control the morphologies of the particles produced. A consortium of sulfate-reducing bacteria (SRB), isolated from sewage sludge, was used in these investigations due to the advantages a consortium provides in comparison to pure cultures. The syntrophic relationships established within the constituent species not only prevent the growth of contaminant microbes, but increases the oxygen-tolerance of the system as a whole. The sulfate-reducing consortium was shown to possess an aerobic mechanism for Pt(IV) reduction which, though different from the anaerobic bioreductive mechanism previously identified in literature, did not require an exogenous electron donor. It was demonstrated that the Pt(IV) ion becomes reduced to Pt(0) via a two-cycle mechanism involving Pt(II) as the intermediate. Further investigation elucidated the reduction of Pt(IV) to Pt(II) to be dependant on a novel Pt(IV) reductase which becomes upregulated in the presence of Cu(II), while the reduction of Pt(II) to Pt(0) occurred by means of a periplasmic hydrogenase. To our knowledge, this is the first time a coupled mechanism for Pt(IV) reduction by micro-organisms has been proposed. A cell-free, crude protein solution from the consortium produced both geometric and irregular platinum nanoparticles. The wavelength of 334 nm was chosen as a nonquantitative indicator of Pt(0) nanoparticle formation over time. The optimum conditions for nanoparticle synthesis were pH 9.0, 65 ˚C and 0.75 mM Pt(IV) as H2PtCl6 salt. In the absence of a buffer a Pt(IV) concentration > 1 mM resulted in the precipitation of protein-nanoparticle bioconjugates, due to unfavourable acidic conditions. This demonstrated that the nanoparticles were binding to and becoming stabilised by general protein in the cell-free solution. Upon addition of a sodium-bicarbonate buffer, a general increase in Pt(IV) reduction to Pt(II) was observed. The addition of the buffer also resulted in an unexplained change in particle morphology and for this reason was not used in subsequent investigations. Polyvinylpyrrolidone (PVP) was shown to compromise the reduction rate of the Pt(IV) ion by SRB cells. The presence of extracellular NP’s was suggested by the colour of the supernatant turning brown and the A334 increasing over time. Attempts to visualise the particles by transmission electron microscopy (TEM) resulted in an unexpected phenomenon where nanoparticles could be observed to form dynamically upon irradiation by the electron beam. Extended irradiation by the electron beam also resulted in structural changes of the particles occurring during observation. An increase in temperature was shown to increase the reduction rate which in turn resulted in particles decreasing in size. The starting pH was shown to have a significant effect on the reduction rate and particle morphology although specific trends could not be identified. In conclusion, the cell-soluble extract from the sulfate-reducing consortium investigated, is capable of Pt(0) nanoparticle synthesis. Precise control over the particle morphology was not attained although the mechanism was further clarified and optimal conditions for nanoparticle synthesis were determined.
- Full Text:
Mariculture as a means to add value to the east coast rock lobster Panulirus homarus rubellus subsistence fishery : a physiological approach to define transport and growout protocols for wild caught juveniles
- Authors: Kemp, J O G
- Date: 2009
- Subjects: Lobster fisheries -- South Africa , Lobster culture -- South Africa , Lobsters -- Growth -- South Africa , Mariculture -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5299 , http://hdl.handle.net/10962/d1005144
- Description: In a context of declining capture fisheries and public pressure for greater access to marine resources, marine aquaculture is receiving increasing interest from the South African government as a means to increase the diversity of economic activities in coastal regions, thereby providing employment and reducing poverty. The east coast rock lobster Panulirus homarus rubellus is currently harvested by subsistence fisherman along the former Transkei coastline of south-east South Africa and presents a possible opportunity for ongrowing wild juvenile lobsters in culture facilities. Lack of compliance coupled with poor enforcement of the minimum size limit (65 mm carapace length) has resulted in the ongoing harvest of undersize size lobsters by subsistence fishers. Generally, fishers either consume these undersize lobsters or sell them to tourists for low prices. In line with international trends in rock lobster aquaculture, interest has subsequently arisen in the possibilities of ongrowing these undersize lobsters as a means of adding value to the P. h rubellus resource for subsistence fishers. The aim of this physiological study was to assess the biological feasibility of harvesting, transporting and culturing wild caught juvenile lobsters, thereby provide empirical data to inform the development of suitable transport and culture protocols. The experimental objectives were to asses the effect of temperature on growth and survival of P. h. rubellus, as well as the effects of a suite of extrinsic and intrinsic factors on ammonia excretion and oxygen consumption. Juvenile lobsters were collected by hand from near-shore reefs (2-15 m depth) off Mdumbi in the former Transkei, Eastern Cape Province and transported by road (7 hours) to the Port Alfred Marine Research Laboratory where they were held in a recirculating culture system. The effect of temperature over a range of 9.7 °C (18.9±0.7 to 28.6±1.5 °C) on the growth and survival of juvenile P. h. rubellus fed a diet of fresh mussel flesh was investigated. Specific growth rate (SGR) was significantly different between temperatures (p = 0.01), with the highest values recorded for the 24 °C and 28 °C treatments. There was no significant difference in moult increment (MI) between temperatures, however, intermoult period (IMP) differed significantly between temperatures (p = 0.0015) with mean IMP lowest at 24 °C, although not significantly different from the means of the 26 °C and 28 °C treatments. IMP was highest at 19 °C and 21 °C. Apparent feed intake was significantly different between treatments (p < 0.0001) and exhibited a strong positive correlation with increasing temperature. Food conversion ratio (FCR) differed significantly between temperatures (p = 0.02) with 24 °C exhibiting the most efficient FCR. The results for growth rate and food conversion efficiency suggested that 24 °C is optimal for the growout of juvenile P. h. rubellus. In the second study, the effect of body weight, emersion, daily rhythm, feeding and ambient ammonia on the total ammonia nitrogen (TAN) excretion rate was investigated. Body weight (n = 16, range of 16.8 – 322 g) was positively correlated to daytime TAN excretion rate (mg h⁻¹). Re-immersion after one hour emersion in a moist environment was characterized by a significant increase in TAN excretion rate for the first hour compared to pre-immersion levels. The amount of TAN excreted during this period was as expected if basal TAN excretion rates were maintained during emersion. TAN excretion rates returned to pre-emersion levels by the end of the second hour. There was no evidence of a daily rhythm in TAN excretion rate for P. h. rubellus. TAN excretion rates were elevated following feeding. An initial peak in TAN excretion rate after seven hours (7.58 times pre-feeding rate) was followed by a smaller peak after 13 hours (6.69 times pre-feeding rate). TAN excretion rate dropped to levels not significantly different from pre-feeding levels after 23 hours and consistently returned to pre-feeding levels after 42 hours. The TAN excretion rates of lobster exposed for two hours to an ambient TAN concentration of 1.02±0.10 mg l⁻¹ and 2.3± 0.2 mg l⁻¹ were not significantly different from TAN excretion rates recorded at low ambient water TAN prior to exposure. Exposure to an ambient TAN concentration of 4.45±0.78 mg l⁻¹ had a significant effect on the TAN excretion rate, with pronounced ammonia uptake occurring for all animals at this concentration. The third study investigated the effects of body weight, diurnal rhythm, feeding and emersion on lobster oxygen consumption. Body weight was positively correlated to both standard and active oxygen consumption (mg O2 h⁻¹) while body weight was negatively correlated to mass-specific standard oxygen uptake (mg O2 g⁻¹ h⁻¹). Diurnal rhythm exhibited a strong effect on the lobsters oxygen consumption, with average night time values 67% greater than those recorded during the day. This was related to activity driven by intrinsic nocturnal foraging behaviour. Feeding resulted in a classic specific dynamic action (SDA) response, with postprandial oxygen consumption increasing to a peak before decreasing gradually to preprandial levels. Emersion resulted in a significant increase in oxygen consumption, with lobsters rapidly recovering to pre-emersion levels after four hours. Results from these studies suggest that the capture, transport and culture of juvenile P. h. rubellus is biologically feasible. Empirical data generated were used to provide recommendations regarding species optimised transport and culture protocols. A purge time of 48 hours before transport is suggested to ensure that ammonia excretion and oxygen consumption are at basal levels. Furthermore, emersed transport for a period of one hour is characterised by rapid recovery upon re-immersion. In order to prevent the accumulation of stressors, it is suggested that consecutive periods of emersion are interjected with recovery periods (five hours) in water to allow the removal of accumulated ammonia and repayment of the oxygen debt incurred. The recorded ammonia rates indicate that a biological filter size of 4.8 m³ is recommended for 1000 kg of fed lobsters in a culture situation, although this can be reduced considerably if lobsters are being held without feeding (0.72 m³). A flow rate of 112 l kg⁻¹ h⁻¹ is required to meet the metabolic requirements of lobsters. Bottlenecks to the viable commercial culture of P. h. rubellus, and the ability of this practice to provide the socio-economic benefits that were envisioned, are discussed.
- Full Text:
- Authors: Kemp, J O G
- Date: 2009
- Subjects: Lobster fisheries -- South Africa , Lobster culture -- South Africa , Lobsters -- Growth -- South Africa , Mariculture -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5299 , http://hdl.handle.net/10962/d1005144
- Description: In a context of declining capture fisheries and public pressure for greater access to marine resources, marine aquaculture is receiving increasing interest from the South African government as a means to increase the diversity of economic activities in coastal regions, thereby providing employment and reducing poverty. The east coast rock lobster Panulirus homarus rubellus is currently harvested by subsistence fisherman along the former Transkei coastline of south-east South Africa and presents a possible opportunity for ongrowing wild juvenile lobsters in culture facilities. Lack of compliance coupled with poor enforcement of the minimum size limit (65 mm carapace length) has resulted in the ongoing harvest of undersize size lobsters by subsistence fishers. Generally, fishers either consume these undersize lobsters or sell them to tourists for low prices. In line with international trends in rock lobster aquaculture, interest has subsequently arisen in the possibilities of ongrowing these undersize lobsters as a means of adding value to the P. h rubellus resource for subsistence fishers. The aim of this physiological study was to assess the biological feasibility of harvesting, transporting and culturing wild caught juvenile lobsters, thereby provide empirical data to inform the development of suitable transport and culture protocols. The experimental objectives were to asses the effect of temperature on growth and survival of P. h. rubellus, as well as the effects of a suite of extrinsic and intrinsic factors on ammonia excretion and oxygen consumption. Juvenile lobsters were collected by hand from near-shore reefs (2-15 m depth) off Mdumbi in the former Transkei, Eastern Cape Province and transported by road (7 hours) to the Port Alfred Marine Research Laboratory where they were held in a recirculating culture system. The effect of temperature over a range of 9.7 °C (18.9±0.7 to 28.6±1.5 °C) on the growth and survival of juvenile P. h. rubellus fed a diet of fresh mussel flesh was investigated. Specific growth rate (SGR) was significantly different between temperatures (p = 0.01), with the highest values recorded for the 24 °C and 28 °C treatments. There was no significant difference in moult increment (MI) between temperatures, however, intermoult period (IMP) differed significantly between temperatures (p = 0.0015) with mean IMP lowest at 24 °C, although not significantly different from the means of the 26 °C and 28 °C treatments. IMP was highest at 19 °C and 21 °C. Apparent feed intake was significantly different between treatments (p < 0.0001) and exhibited a strong positive correlation with increasing temperature. Food conversion ratio (FCR) differed significantly between temperatures (p = 0.02) with 24 °C exhibiting the most efficient FCR. The results for growth rate and food conversion efficiency suggested that 24 °C is optimal for the growout of juvenile P. h. rubellus. In the second study, the effect of body weight, emersion, daily rhythm, feeding and ambient ammonia on the total ammonia nitrogen (TAN) excretion rate was investigated. Body weight (n = 16, range of 16.8 – 322 g) was positively correlated to daytime TAN excretion rate (mg h⁻¹). Re-immersion after one hour emersion in a moist environment was characterized by a significant increase in TAN excretion rate for the first hour compared to pre-immersion levels. The amount of TAN excreted during this period was as expected if basal TAN excretion rates were maintained during emersion. TAN excretion rates returned to pre-emersion levels by the end of the second hour. There was no evidence of a daily rhythm in TAN excretion rate for P. h. rubellus. TAN excretion rates were elevated following feeding. An initial peak in TAN excretion rate after seven hours (7.58 times pre-feeding rate) was followed by a smaller peak after 13 hours (6.69 times pre-feeding rate). TAN excretion rate dropped to levels not significantly different from pre-feeding levels after 23 hours and consistently returned to pre-feeding levels after 42 hours. The TAN excretion rates of lobster exposed for two hours to an ambient TAN concentration of 1.02±0.10 mg l⁻¹ and 2.3± 0.2 mg l⁻¹ were not significantly different from TAN excretion rates recorded at low ambient water TAN prior to exposure. Exposure to an ambient TAN concentration of 4.45±0.78 mg l⁻¹ had a significant effect on the TAN excretion rate, with pronounced ammonia uptake occurring for all animals at this concentration. The third study investigated the effects of body weight, diurnal rhythm, feeding and emersion on lobster oxygen consumption. Body weight was positively correlated to both standard and active oxygen consumption (mg O2 h⁻¹) while body weight was negatively correlated to mass-specific standard oxygen uptake (mg O2 g⁻¹ h⁻¹). Diurnal rhythm exhibited a strong effect on the lobsters oxygen consumption, with average night time values 67% greater than those recorded during the day. This was related to activity driven by intrinsic nocturnal foraging behaviour. Feeding resulted in a classic specific dynamic action (SDA) response, with postprandial oxygen consumption increasing to a peak before decreasing gradually to preprandial levels. Emersion resulted in a significant increase in oxygen consumption, with lobsters rapidly recovering to pre-emersion levels after four hours. Results from these studies suggest that the capture, transport and culture of juvenile P. h. rubellus is biologically feasible. Empirical data generated were used to provide recommendations regarding species optimised transport and culture protocols. A purge time of 48 hours before transport is suggested to ensure that ammonia excretion and oxygen consumption are at basal levels. Furthermore, emersed transport for a period of one hour is characterised by rapid recovery upon re-immersion. In order to prevent the accumulation of stressors, it is suggested that consecutive periods of emersion are interjected with recovery periods (five hours) in water to allow the removal of accumulated ammonia and repayment of the oxygen debt incurred. The recorded ammonia rates indicate that a biological filter size of 4.8 m³ is recommended for 1000 kg of fed lobsters in a culture situation, although this can be reduced considerably if lobsters are being held without feeding (0.72 m³). A flow rate of 112 l kg⁻¹ h⁻¹ is required to meet the metabolic requirements of lobsters. Bottlenecks to the viable commercial culture of P. h. rubellus, and the ability of this practice to provide the socio-economic benefits that were envisioned, are discussed.
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Molecular and biochemical analysis of the diet of the black rhinoceros
- Authors: Kgopa, Ananias Hodi
- Date: 2009 , 2013-07-15
- Subjects: Black rhinoceros -- South Africa -- Eastern Cape , Browse (Animal food) -- South Africa -- Eastern Cape -- Analysis , Black rhinoceros -- Manure -- Analysis , Phenols , Antioxidants , Plant ecology -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4064 , http://hdl.handle.net/10962/d1004721 , Black rhinoceros -- South Africa -- Eastern Cape , Browse (Animal food) -- South Africa -- Eastern Cape -- Analysis , Black rhinoceros -- Manure -- Analysis , Phenols , Antioxidants , Plant ecology -- South Africa -- Eastern Cape
- Description: The black rhinoceros, Diceros bicornis, is listed as critically endangered. The black rhinoceros population in the Great Fish River Reserve (GFRR) has increased steadily to a current estimate of one hundred animals since the re-introduction of four animals in 1986. In an effort to contribute to the effective conservation and management of this species, dietary composition was studied in the medium Portulcaria thicket vegetation of the GFRR. This study used a molecular approach to determine the diet of the black rhinoceros of the GFRR by sequencing the ribulose bisphosphate carboxylase large subunit (rbcL) gene in plants and dung. Twenty-three plant species were collected from the reserve, and 802 bp of the rbcL gene were sequenced. These plant sequences were used as a reference database for the identification of plant sequences generated from black rhinoceros dung. Initial studies investigated the amplification, cloning and sequencing of DNA extracted from the dung samples which indicated the viability of the molecular approach. Thereafter, dung generated rbcL DNA was analyzed by GS FLX sequencing. Of the plant sequences identified by comparison to the GenBank database, Carissa bispinosa was the most prevalent. The study further characterized the antioxidant activities and phenolic content of plants eaten by the black rhinoceros using four different assays. Phyllanthus verrucosus, Putterlickia pyracantha, Maytenus capitata, Euclea undulata and Ozoroa mucrunata consistently had high antioxidant activities when assayed against 2,2-azinobis (3-ethyl benzothiazolium-6-sulfonic acid) (ABTSʹ⁺), 2,2-diphenyl-1-picrylhydrazyl (DPPHʹ), and ferric reducing antioxidant potentials (FRAP) and phenolic content when evaluated using the Folin-Ciocalteu assay. The majority of plants investigated showed low antioxidant potentials and low phenolic content. The extent to which antioxidants influenced the browse selection by the black rhinoceros remains inconclusive.
- Full Text:
- Authors: Kgopa, Ananias Hodi
- Date: 2009 , 2013-07-15
- Subjects: Black rhinoceros -- South Africa -- Eastern Cape , Browse (Animal food) -- South Africa -- Eastern Cape -- Analysis , Black rhinoceros -- Manure -- Analysis , Phenols , Antioxidants , Plant ecology -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4064 , http://hdl.handle.net/10962/d1004721 , Black rhinoceros -- South Africa -- Eastern Cape , Browse (Animal food) -- South Africa -- Eastern Cape -- Analysis , Black rhinoceros -- Manure -- Analysis , Phenols , Antioxidants , Plant ecology -- South Africa -- Eastern Cape
- Description: The black rhinoceros, Diceros bicornis, is listed as critically endangered. The black rhinoceros population in the Great Fish River Reserve (GFRR) has increased steadily to a current estimate of one hundred animals since the re-introduction of four animals in 1986. In an effort to contribute to the effective conservation and management of this species, dietary composition was studied in the medium Portulcaria thicket vegetation of the GFRR. This study used a molecular approach to determine the diet of the black rhinoceros of the GFRR by sequencing the ribulose bisphosphate carboxylase large subunit (rbcL) gene in plants and dung. Twenty-three plant species were collected from the reserve, and 802 bp of the rbcL gene were sequenced. These plant sequences were used as a reference database for the identification of plant sequences generated from black rhinoceros dung. Initial studies investigated the amplification, cloning and sequencing of DNA extracted from the dung samples which indicated the viability of the molecular approach. Thereafter, dung generated rbcL DNA was analyzed by GS FLX sequencing. Of the plant sequences identified by comparison to the GenBank database, Carissa bispinosa was the most prevalent. The study further characterized the antioxidant activities and phenolic content of plants eaten by the black rhinoceros using four different assays. Phyllanthus verrucosus, Putterlickia pyracantha, Maytenus capitata, Euclea undulata and Ozoroa mucrunata consistently had high antioxidant activities when assayed against 2,2-azinobis (3-ethyl benzothiazolium-6-sulfonic acid) (ABTSʹ⁺), 2,2-diphenyl-1-picrylhydrazyl (DPPHʹ), and ferric reducing antioxidant potentials (FRAP) and phenolic content when evaluated using the Folin-Ciocalteu assay. The majority of plants investigated showed low antioxidant potentials and low phenolic content. The extent to which antioxidants influenced the browse selection by the black rhinoceros remains inconclusive.
- Full Text:
Movement bahaviour of three South African inshore sparid species in rocky intertidal and shallow subtidal habitats
- Authors: Watt-Pringle, Peter Andrew
- Date: 2009
- Subjects: Sparidae -- South Africa , Diplodus , Sparodon Durbanensis , Fisheries -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5302 , http://hdl.handle.net/10962/d1005147 , Sparidae -- South Africa , Diplodus , Sparodon Durbanensis , Fisheries -- South Africa
- Description: This study investigated the movement behaviour of three inshore South African sparids – blacktail (Diplodus sargus capensis), zebra (Diplodus cervinus hottentotus) and white musselcracker (Sparodon durbanensis), popular inshore fishery species caught in appreciable numbers along much of the South African coast. The first study component examined movements of juveniles in a rocky intertidal nursery area at Schoenmakerskop near Port Elizabeth. Juveniles in a single gully were tagged with Visible Implant Elastomer (VIE) and resighted at the study site on snorkelling gear over a seven-month period. Tagged zebra and musselcracker displayed limited movement between potential low tide refuges, being observed repeatedly in the same gully over the full duration of the study. However, blacktail displayed greater movements and were seen infrequently in the later period of the study, probably having undergone an ontogenetic habitat shift to subtidal areas. There was evidence that blacktail maintain use of their intertidal nursery over high tide, during which the other two species moved into shallower areas adjacent to their low tide refuge. The results of three national tagging programs were analysed to determine the movement patterns of adolescent and adult fishes. The coast-wide ORI-WWF National Voluntary Tagging Program and two dedicated research programs in marine protected areas (MPAs) at De Hoop MPA and Tsitsikamma National Park (TNP) recorded few large-scale movements of tagged adult blacktail, zebra and juvenile musselcracker. High spatial-resolution data from the TNP suggested movements were usually on scales far smaller than one km. Together with long periods at liberty for many recaptured individuals, this suggests these fishes are longterm residents of small home range areas. However, tagged musselcracker over 600 mm forklength (adults) were observed to make large-scale movements, including some in excess of 800 km from Eastern Cape to KwaZulu-Natal waters. Predominantly eastward movements of adults recaptured during the spawning season indicate seasonal spawning migrations that occur in different regions of the coast. These enable the use of prevailing oceanographic currents to disperse eggs and larvae to suitable rocky nursery habitat. The third component of this study made use of high-resolution data on the temporal and spatial distribution of catches by scientific angling in the TNP to examine the daily activity patterns of the study species in relation to diel and tidal cycles, and habitat use. Blacktail capture probability was correlated with the diurnal light cycle, with peaks close to twilight suggesting elevated crepuscular foraging activity. Catches of blacktail, zebra and small musselcracker were correlated with the tidal cycle, foraging peaking over high tide periods. All three species used shallow inshore habitats extensively for foraging, blacktail showing a preference for sandy areas, while zebra and small musselcracker preferred shallow reef. Capture probability of larger musselcracker, however, was unrelated to habitat, possibly evidence of increasing area and habitat use with an ontogenetic change in diet. The lifetime movement patterns of these three species are discussed in relation to conservation measures and their management in South African fisheries. Restricted movement throughout post-settlement life for blacktail and zebra, and during the juvenile phase for musselcracker, makes local populations vulnerable to overexploitation. At present, MPAs probably play an important role in protecting local blacktail and zebra populations from overexploitation, and limited post-settlement movements mean the degree of larval dispersal between protected and adjacent areas will likely determine the effectiveness of MPAs in enhancing fisheries for these species. By contrast, MPAs likely provide recruits to fisheries for musselcracker during ontogenetic movements and dispersal from MPAs during spawning migrations. MPAs only offer partial protection to adult musselcracker populations in the spawning season, but this could nevertheless be significant under high levels of exploitation.
- Full Text:
- Authors: Watt-Pringle, Peter Andrew
- Date: 2009
- Subjects: Sparidae -- South Africa , Diplodus , Sparodon Durbanensis , Fisheries -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5302 , http://hdl.handle.net/10962/d1005147 , Sparidae -- South Africa , Diplodus , Sparodon Durbanensis , Fisheries -- South Africa
- Description: This study investigated the movement behaviour of three inshore South African sparids – blacktail (Diplodus sargus capensis), zebra (Diplodus cervinus hottentotus) and white musselcracker (Sparodon durbanensis), popular inshore fishery species caught in appreciable numbers along much of the South African coast. The first study component examined movements of juveniles in a rocky intertidal nursery area at Schoenmakerskop near Port Elizabeth. Juveniles in a single gully were tagged with Visible Implant Elastomer (VIE) and resighted at the study site on snorkelling gear over a seven-month period. Tagged zebra and musselcracker displayed limited movement between potential low tide refuges, being observed repeatedly in the same gully over the full duration of the study. However, blacktail displayed greater movements and were seen infrequently in the later period of the study, probably having undergone an ontogenetic habitat shift to subtidal areas. There was evidence that blacktail maintain use of their intertidal nursery over high tide, during which the other two species moved into shallower areas adjacent to their low tide refuge. The results of three national tagging programs were analysed to determine the movement patterns of adolescent and adult fishes. The coast-wide ORI-WWF National Voluntary Tagging Program and two dedicated research programs in marine protected areas (MPAs) at De Hoop MPA and Tsitsikamma National Park (TNP) recorded few large-scale movements of tagged adult blacktail, zebra and juvenile musselcracker. High spatial-resolution data from the TNP suggested movements were usually on scales far smaller than one km. Together with long periods at liberty for many recaptured individuals, this suggests these fishes are longterm residents of small home range areas. However, tagged musselcracker over 600 mm forklength (adults) were observed to make large-scale movements, including some in excess of 800 km from Eastern Cape to KwaZulu-Natal waters. Predominantly eastward movements of adults recaptured during the spawning season indicate seasonal spawning migrations that occur in different regions of the coast. These enable the use of prevailing oceanographic currents to disperse eggs and larvae to suitable rocky nursery habitat. The third component of this study made use of high-resolution data on the temporal and spatial distribution of catches by scientific angling in the TNP to examine the daily activity patterns of the study species in relation to diel and tidal cycles, and habitat use. Blacktail capture probability was correlated with the diurnal light cycle, with peaks close to twilight suggesting elevated crepuscular foraging activity. Catches of blacktail, zebra and small musselcracker were correlated with the tidal cycle, foraging peaking over high tide periods. All three species used shallow inshore habitats extensively for foraging, blacktail showing a preference for sandy areas, while zebra and small musselcracker preferred shallow reef. Capture probability of larger musselcracker, however, was unrelated to habitat, possibly evidence of increasing area and habitat use with an ontogenetic change in diet. The lifetime movement patterns of these three species are discussed in relation to conservation measures and their management in South African fisheries. Restricted movement throughout post-settlement life for blacktail and zebra, and during the juvenile phase for musselcracker, makes local populations vulnerable to overexploitation. At present, MPAs probably play an important role in protecting local blacktail and zebra populations from overexploitation, and limited post-settlement movements mean the degree of larval dispersal between protected and adjacent areas will likely determine the effectiveness of MPAs in enhancing fisheries for these species. By contrast, MPAs likely provide recruits to fisheries for musselcracker during ontogenetic movements and dispersal from MPAs during spawning migrations. MPAs only offer partial protection to adult musselcracker populations in the spawning season, but this could nevertheless be significant under high levels of exploitation.
- Full Text:
Phenolic compounds in water and the implications for rapid detection of indicator micro-organisms using ß-D-Galactosidase and ß-D-Glucuronidase
- Authors: Abboo, Sagaran
- Date: 2009
- Subjects: Water -- Purification -- Biological treatment , Pollutants -- Biodegradation , Phenol , Organic water pollutants , Water quality biological assessment , Water -- Pollution
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3978 , http://hdl.handle.net/10962/d1004037 , Water -- Purification -- Biological treatment , Pollutants -- Biodegradation , Phenol , Organic water pollutants , Water quality biological assessment , Water -- Pollution
- Description: Faecal contamination in water is detected using appropriate microbial models such as total coliforms, faecal coliforms and E. coli. Βeta-D-Galactosidase (β-GAL) and Beta-D-glucuronidase (β-GUD) are two marker enzymes that are used to test for the presence of total coliforms and E. coli in water samples, respectively. Various assay methods have been developed using chromogenic and fluorogenic substrates. In this study, the chromogenic substrates chlorophenol red β-D-galactopyranoside (CPRG) for β-GAL and p-nitrophenyl-β-D-galactopyranoside (PNPG) for β-GUD were used. Potential problems associated with this approach include interference from other organisms present in the environment (e.g. plants, algae and other bacteria), as well as the presence of certain chemicals, such as phenolic compounds in water. Phenolic compounds are present in the aquatic environment due to their extensive industrial applications. The USA Enviromental Protection Agency (EPA) lists 11 Priority Pollutant Phenols (PPP) due to their high level of toxicity. This study investigated the interfering effects of the eleven PPP found in water on the enzyme activities of both the β-GAL and β-GUD enzyme assays. The presence of these PPP in the β-GAL and β-GUD enzyme assays showed that over and underestimation of activity may occur due to inhibition or activation of these enzymes. Three types of inhibition to enzyme activities were identified from double reciprocal Lineweaver-Burk plots. The inhibition constants (Ki) were determined for all inhibitory phenolic compounds from appropriate secondary plots. Furthermore, this study presented a validated reverse phase high performance liquid chromatography (RP-HPLC) method, developed for the simultaneous detection, separation and determination of all eleven phenolic compounds found in the environment. This method demonstrated good linearity, reproducibility, accuracy and sensitivity. Environmental water samples were collected from rivers, streams, industrial sites and wastewater treatment plant effluent. These samples were extracted and concentrated using a solid phase extraction (SPE) procedure prior to analysis employing the newly developed HPLC method in this study. Seasonal variations on the presence of the PPP in the environment were observed at certain collection sites. The concentrations found were between 0.033 μg/ml for 2,4-dinitrophenol in a running stream to 0.890 mg/ml for pentachlorophenol from an tannery industrial site. These concentrations of phenolic compounds found in these environments were able to interfere with the β-GAL and β-GUD enzyme assays.
- Full Text:
- Authors: Abboo, Sagaran
- Date: 2009
- Subjects: Water -- Purification -- Biological treatment , Pollutants -- Biodegradation , Phenol , Organic water pollutants , Water quality biological assessment , Water -- Pollution
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3978 , http://hdl.handle.net/10962/d1004037 , Water -- Purification -- Biological treatment , Pollutants -- Biodegradation , Phenol , Organic water pollutants , Water quality biological assessment , Water -- Pollution
- Description: Faecal contamination in water is detected using appropriate microbial models such as total coliforms, faecal coliforms and E. coli. Βeta-D-Galactosidase (β-GAL) and Beta-D-glucuronidase (β-GUD) are two marker enzymes that are used to test for the presence of total coliforms and E. coli in water samples, respectively. Various assay methods have been developed using chromogenic and fluorogenic substrates. In this study, the chromogenic substrates chlorophenol red β-D-galactopyranoside (CPRG) for β-GAL and p-nitrophenyl-β-D-galactopyranoside (PNPG) for β-GUD were used. Potential problems associated with this approach include interference from other organisms present in the environment (e.g. plants, algae and other bacteria), as well as the presence of certain chemicals, such as phenolic compounds in water. Phenolic compounds are present in the aquatic environment due to their extensive industrial applications. The USA Enviromental Protection Agency (EPA) lists 11 Priority Pollutant Phenols (PPP) due to their high level of toxicity. This study investigated the interfering effects of the eleven PPP found in water on the enzyme activities of both the β-GAL and β-GUD enzyme assays. The presence of these PPP in the β-GAL and β-GUD enzyme assays showed that over and underestimation of activity may occur due to inhibition or activation of these enzymes. Three types of inhibition to enzyme activities were identified from double reciprocal Lineweaver-Burk plots. The inhibition constants (Ki) were determined for all inhibitory phenolic compounds from appropriate secondary plots. Furthermore, this study presented a validated reverse phase high performance liquid chromatography (RP-HPLC) method, developed for the simultaneous detection, separation and determination of all eleven phenolic compounds found in the environment. This method demonstrated good linearity, reproducibility, accuracy and sensitivity. Environmental water samples were collected from rivers, streams, industrial sites and wastewater treatment plant effluent. These samples were extracted and concentrated using a solid phase extraction (SPE) procedure prior to analysis employing the newly developed HPLC method in this study. Seasonal variations on the presence of the PPP in the environment were observed at certain collection sites. The concentrations found were between 0.033 μg/ml for 2,4-dinitrophenol in a running stream to 0.890 mg/ml for pentachlorophenol from an tannery industrial site. These concentrations of phenolic compounds found in these environments were able to interfere with the β-GAL and β-GUD enzyme assays.
- Full Text:
Photosynthetic and evolutionary determinants of the response of selected C3 and C4 (NADP-ME) grasses to fire
- Authors: Martin, Tarryn
- Date: 2009
- Subjects: Photosynthesis , Carbon -- Metabolism , Grasses -- Adaptation , Plants -- Effect of fires on , Grasses -- Research , Grasses -- Physiology , Grasses -- Evolution , Grasslands -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4211 , http://hdl.handle.net/10962/d1003780 , Photosynthesis , Carbon -- Metabolism , Grasses -- Adaptation , Plants -- Effect of fires on , Grasses -- Research , Grasses -- Physiology , Grasses -- Evolution , Grasslands -- Research
- Description: Species possess characteristics that are considered adapted to burning and these allow them to outcompete species and dominate in fire prone environments. It has therefore been proposed that fire might have played a critical role in the observed expansion of the grasslands, during the late Miocene. The aim of this study was (i) to investigate whether plant response to fire was a result of physiology or (ii) whether it was due to phylogenetic history. This was achieved by doing a pair-wise comparison between Panicoideae (and Panicoideae) and non-Panicoideae (Danthonioideae and Aristidoideae) species. Pre-fire characteristics, that would enhance fire frequency and assist with plant recovery after burning, were compared across phylogenies and photosynthetic type. Post fire plant recovery was then followed in a field and pot comparison which examined the re-growth of the leaf canopy area, leaf mass, above-ground biomass and the cost of this to the below-ground biomass. The pre-fire characteristics showed both a photosynthetic and phylogenetic response. It was found that the species showed a greater canopy death during winter and had a lower moisture content than the species. These characteristics would potentially contribute towards a larger fuel load in the species. However, the comparison of the dead standing biomass at the end of winter and the below-ground biomass, showed a phylogenetic response with the Panicoideae having a proportionally larger dead standing biomass and below-ground biomass than the non-Panicoideae. These results suggest that not only did the Panicoideae have a larger potential fuel load but that they also shunted carbon below-ground, enabling a fast recovery after being burned. The post-fire results were more strongly determined by phylogeny than by photosynthetic type. The Panicoideae recovered faster and more completely than the non-Panicoideae grasses, possibly contributing to their success and expansion under conditions of increased fire frequency. Although recovery of the and Panicoideae were similar, frequently burnt grasslands are dominated by the Panicoideae. Hence, this dominance cannot be explained by differences in their fire responses and may be determined by the post-fire environmental conditions that potentially advantage species possessing the photosynthetic pathway. Panicoideae dominance is limited to mesic environments where fire is the likely driver of grassland expansion while more arid environments are dominated by non-Panicoideae species. Representative species from these non-Panicoid subfamilies showed poor recovery after fire. This suggests that factors other than fire were the likely drivers of these xeric grassland expansions. The ability of these subfamilies, and particularly the species, to cope with drought remains a likely selective mechanism that requires further research.
- Full Text:
- Authors: Martin, Tarryn
- Date: 2009
- Subjects: Photosynthesis , Carbon -- Metabolism , Grasses -- Adaptation , Plants -- Effect of fires on , Grasses -- Research , Grasses -- Physiology , Grasses -- Evolution , Grasslands -- Research
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4211 , http://hdl.handle.net/10962/d1003780 , Photosynthesis , Carbon -- Metabolism , Grasses -- Adaptation , Plants -- Effect of fires on , Grasses -- Research , Grasses -- Physiology , Grasses -- Evolution , Grasslands -- Research
- Description: Species possess characteristics that are considered adapted to burning and these allow them to outcompete species and dominate in fire prone environments. It has therefore been proposed that fire might have played a critical role in the observed expansion of the grasslands, during the late Miocene. The aim of this study was (i) to investigate whether plant response to fire was a result of physiology or (ii) whether it was due to phylogenetic history. This was achieved by doing a pair-wise comparison between Panicoideae (and Panicoideae) and non-Panicoideae (Danthonioideae and Aristidoideae) species. Pre-fire characteristics, that would enhance fire frequency and assist with plant recovery after burning, were compared across phylogenies and photosynthetic type. Post fire plant recovery was then followed in a field and pot comparison which examined the re-growth of the leaf canopy area, leaf mass, above-ground biomass and the cost of this to the below-ground biomass. The pre-fire characteristics showed both a photosynthetic and phylogenetic response. It was found that the species showed a greater canopy death during winter and had a lower moisture content than the species. These characteristics would potentially contribute towards a larger fuel load in the species. However, the comparison of the dead standing biomass at the end of winter and the below-ground biomass, showed a phylogenetic response with the Panicoideae having a proportionally larger dead standing biomass and below-ground biomass than the non-Panicoideae. These results suggest that not only did the Panicoideae have a larger potential fuel load but that they also shunted carbon below-ground, enabling a fast recovery after being burned. The post-fire results were more strongly determined by phylogeny than by photosynthetic type. The Panicoideae recovered faster and more completely than the non-Panicoideae grasses, possibly contributing to their success and expansion under conditions of increased fire frequency. Although recovery of the and Panicoideae were similar, frequently burnt grasslands are dominated by the Panicoideae. Hence, this dominance cannot be explained by differences in their fire responses and may be determined by the post-fire environmental conditions that potentially advantage species possessing the photosynthetic pathway. Panicoideae dominance is limited to mesic environments where fire is the likely driver of grassland expansion while more arid environments are dominated by non-Panicoideae species. Representative species from these non-Panicoid subfamilies showed poor recovery after fire. This suggests that factors other than fire were the likely drivers of these xeric grassland expansions. The ability of these subfamilies, and particularly the species, to cope with drought remains a likely selective mechanism that requires further research.
- Full Text:
Phylogeography and epifauna of two intertidal seaweeds on the coast of South Africa
- Authors: Mmonwa, Lucas Kolobe
- Date: 2009
- Subjects: Phylogeography -- South Africa , Marine algae -- South Africa , Red algae -- South Africa , Gelidium -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5738 , http://hdl.handle.net/10962/d1005424 , Phylogeography -- South Africa , Marine algae -- South Africa , Red algae -- South Africa , Gelidium -- South Africa
- Description: Southern African biogeographic boundaries delimit the phylogeographic distribution of some coastal and estuarine invertebrates. This study investigated the impact of these boundaries on the phylogeographic distribution of two intertidal red seaweeds, Gelidium pristoides and Hypnea spicifera using the mitochondrial Cox2-3 spacer and the nuclear ITS1 regions. G. pristoides spores have short distance-dispersal, while long distance-dispersal is more likely in H. spicifera via spores and drifting fertile thallus fragments. Both markers revealed a south-western and south-eastern lineage within G. pristoides but the breaks between lineages do not coincide with any recognised biogeographic limits. The Cox2-3 spacer revealed a boundary between the two lineages at the Alexandria Coastal Dunefield (ACD) and ITS1 at the Gamtoos-Van Stadens Dunefields (GVD) which is approximately 80km west of the ACD. The minor difference between the two markers regarding location of the phylogeographic boundary is probably due to the dating differences between the two dunefields. The ACD as developed currently is superimposed on the ancient dunefields which formed during the Pleistocene, coinciding with the Cox2-3 spacer sequences divergence which dates back 500,000 - 580,000 years. The GVD formed during the Holocene (6,500 - 4,000 years ago), coinciding with the ITS1 sequences divergence which dates 4,224 - 4,928 years ago. Thus, these phylogeographic boundaries probably appeared without the influence of biogeographic boundaries, but rather due to the lack of suitable habitat in the dunefields, coupled with short dispersal-distances of the spores. Analysis of the ITS1 and Cox2-3 spacer regions in H. spicifera revealed that the species is characterized by uniform genetic structure along the coastline. This reflects the species`s potential for long range expansion as it inhabits both the intertidal and subtidal zones; and this presumably leads to high gene flow among populations. The ITS1 sequences showed minimal genetic variation of one substitution between the gametophyte and tetrasporophyte generations within H. spicifera. This suggests the predominance of asexual reproduction, which reduces gene flow and fixes alleles between generations. ANOSIM and Bray-Curtis cluster analyses showed scale-dependant variation in the abundances of epifauna (mainly amphipod, isopod, mollusc and polychaete species) on G. pristoides. At small local (within site) and large (among sites) scales, there were weak and no structure in epifaunal abundances respectively. However, at larger, biogeographic scales, samples from the same biogeographic region tended to be clustered together. Thus, there was a group containing predominantly south coast samples and a group containing east coast samples mixed with the remaining south coast samples. Such scale-dependant variation in epifaunal abundances is probably due to the effects of factors driving species richness at small local (within site) scales (e.g. wave exposure, seaweed biomass) and at larger, biogeographic scales (e.g. surface sea temperature). Moreover, at very small (individual samples) scales; there was no correlation between epifauna composition and genotype of the seaweed. Seaweed samples characterized by distinct ITS1 or Cox2-3 spacer sequences did not show any significant differences in epifaunal composition. Although the distributional pattern of the epifaunal community observed at large biogeographic scale is not clear, it seems to be associated with the biogeographic regions. However, phylogeographic distribution of Gelidium pristoides is not connected to biogeographic regions. Thus, at larger, biogeographic scales, there is no correlation between phylogeographic distribution of G. pristoides and distribution of the associated fauna
- Full Text:
- Authors: Mmonwa, Lucas Kolobe
- Date: 2009
- Subjects: Phylogeography -- South Africa , Marine algae -- South Africa , Red algae -- South Africa , Gelidium -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5738 , http://hdl.handle.net/10962/d1005424 , Phylogeography -- South Africa , Marine algae -- South Africa , Red algae -- South Africa , Gelidium -- South Africa
- Description: Southern African biogeographic boundaries delimit the phylogeographic distribution of some coastal and estuarine invertebrates. This study investigated the impact of these boundaries on the phylogeographic distribution of two intertidal red seaweeds, Gelidium pristoides and Hypnea spicifera using the mitochondrial Cox2-3 spacer and the nuclear ITS1 regions. G. pristoides spores have short distance-dispersal, while long distance-dispersal is more likely in H. spicifera via spores and drifting fertile thallus fragments. Both markers revealed a south-western and south-eastern lineage within G. pristoides but the breaks between lineages do not coincide with any recognised biogeographic limits. The Cox2-3 spacer revealed a boundary between the two lineages at the Alexandria Coastal Dunefield (ACD) and ITS1 at the Gamtoos-Van Stadens Dunefields (GVD) which is approximately 80km west of the ACD. The minor difference between the two markers regarding location of the phylogeographic boundary is probably due to the dating differences between the two dunefields. The ACD as developed currently is superimposed on the ancient dunefields which formed during the Pleistocene, coinciding with the Cox2-3 spacer sequences divergence which dates back 500,000 - 580,000 years. The GVD formed during the Holocene (6,500 - 4,000 years ago), coinciding with the ITS1 sequences divergence which dates 4,224 - 4,928 years ago. Thus, these phylogeographic boundaries probably appeared without the influence of biogeographic boundaries, but rather due to the lack of suitable habitat in the dunefields, coupled with short dispersal-distances of the spores. Analysis of the ITS1 and Cox2-3 spacer regions in H. spicifera revealed that the species is characterized by uniform genetic structure along the coastline. This reflects the species`s potential for long range expansion as it inhabits both the intertidal and subtidal zones; and this presumably leads to high gene flow among populations. The ITS1 sequences showed minimal genetic variation of one substitution between the gametophyte and tetrasporophyte generations within H. spicifera. This suggests the predominance of asexual reproduction, which reduces gene flow and fixes alleles between generations. ANOSIM and Bray-Curtis cluster analyses showed scale-dependant variation in the abundances of epifauna (mainly amphipod, isopod, mollusc and polychaete species) on G. pristoides. At small local (within site) and large (among sites) scales, there were weak and no structure in epifaunal abundances respectively. However, at larger, biogeographic scales, samples from the same biogeographic region tended to be clustered together. Thus, there was a group containing predominantly south coast samples and a group containing east coast samples mixed with the remaining south coast samples. Such scale-dependant variation in epifaunal abundances is probably due to the effects of factors driving species richness at small local (within site) scales (e.g. wave exposure, seaweed biomass) and at larger, biogeographic scales (e.g. surface sea temperature). Moreover, at very small (individual samples) scales; there was no correlation between epifauna composition and genotype of the seaweed. Seaweed samples characterized by distinct ITS1 or Cox2-3 spacer sequences did not show any significant differences in epifaunal composition. Although the distributional pattern of the epifaunal community observed at large biogeographic scale is not clear, it seems to be associated with the biogeographic regions. However, phylogeographic distribution of Gelidium pristoides is not connected to biogeographic regions. Thus, at larger, biogeographic scales, there is no correlation between phylogeographic distribution of G. pristoides and distribution of the associated fauna
- Full Text:
Polymers, catalysts and nanostructures a hybrid approach to biomolecule detection
- Authors: Frith, Kelly-Anne
- Date: 2009
- Subjects: Polymers , Nanostructured materials , Biomolecules , Tryptophan , Melatonin , Electrodes , Electrochemistry , Tryptophan oxygenase
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3980 , http://hdl.handle.net/10962/d1004039 , Polymers , Nanostructured materials , Biomolecules , Tryptophan , Melatonin , Electrodes , Electrochemistry , Tryptophan oxygenase
- Description: The main goals in electroanalytical sensing are towards improved sensitivity and selectivity, or specificity, of an analyte. There are several approaches to achieving these goals with the main approach being modification of an electrode surface with synthetic or natural catalysts (enzymes), polymers and also utilisation of nanostructured materials. At present, there is a strong movement towards hybrid sensing which couple different properties of two or more surface modification approaches. In this thesis, a range of these surface modifications were explored for analysis and detection of two main analytes: the amino acid, tryptophan (Trp); and, the neurotransmitter, dopamine (DA). Specifically, this thesis aimed to utilise these methods to enhance the sensitivity and selectivity for Trp over an interferent, the indoleamine, melatonin (Mel); and, DA over the vitamin, ascorbic acid (AA). For Trp detection, immobilisation of an enzyme, Tryptophanase (Trpase) resulted in poor selectivity for the analyte. However, enhanced sensitivity and selectivity was achieved through pH manipulation of the electrolyte medium at a Nafion®-modified electrode surface for both Trp and Mel. At pH 3.0, the Mel and Trp anodic peak potentials were sufficiently resolved allowing for an LOD of 1.60 and 1.62 nM,respectively, and permitting the accurate analysis of Trp in a dietary supplement containing Mel. Multi-walled carbon nanotubes (MWCNTs) suspended in Nafion® exhibited further increases in the signal responses of these analytes at pH 3.0 and 7.4 with minimal change in the resolution of the anodic peaks. A lower sensitivity was, therefore, observed at the Nafion® and MWCNT modified electrode compared to the Nafion®-modified electrode at pH 3.0 with LODs of 0.59 and 0.80 nM exhibited for Trp and Mel, respectively. Enhanced selectivity for Trp in the presence of Mel can be achieved with MWCNTs in the presence of metallotetrasulphonated phthalocyanines (MTSPcs) particularly at pH 3.0, owing to cation exchange effects. However, the lack of sensitivity towards Trp, and even Mel, at this CoTSPc and MWCNT modified electrode remains a drawback. For DA, detection at the MWCNT and Nafion® surface resulted in improved sensitivity over that of both the bare electrode (613.0 nM) and the Nafion® modified electrode (1045.1 nM) with a calculated LOD of 133.9 nM at this layer. Furthermore, improvements in the selectivity of DA were achieved at the Nafion® and MWCNT modified electrode as exclusion of AA (150 μM) was achieved. At the MWCNT and CoTSPc surface, AA was excluded up to 130 μM with sensitivity for DA extending as low as 14.3 nM, far greater than observed for Trp and Mel. These concentrations are well within physiological concentration ranges and represent the most significant solution yet in terms of AA exclusion and enhanced sensitivity for DA. An examination of the surface layering by impedance spectroscopy and atomic force microscopy indicates that the success of the hybrid sensor utilising CoTSPc and MWCNTs lay in improved dispersion of MWCNTs and improved electron transfer kinetics, facilitated by the net charge of the materials present. This thesis, thus, showed the utility of a judicious selection of synthetic and biological catalysts, polymers and carbon nanomaterials towards a hybrid approach to the electrochemical sensing of Trp, Mel, DA and AA with focus on sensitivity and selectivity of these analytes.
- Full Text:
- Authors: Frith, Kelly-Anne
- Date: 2009
- Subjects: Polymers , Nanostructured materials , Biomolecules , Tryptophan , Melatonin , Electrodes , Electrochemistry , Tryptophan oxygenase
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3980 , http://hdl.handle.net/10962/d1004039 , Polymers , Nanostructured materials , Biomolecules , Tryptophan , Melatonin , Electrodes , Electrochemistry , Tryptophan oxygenase
- Description: The main goals in electroanalytical sensing are towards improved sensitivity and selectivity, or specificity, of an analyte. There are several approaches to achieving these goals with the main approach being modification of an electrode surface with synthetic or natural catalysts (enzymes), polymers and also utilisation of nanostructured materials. At present, there is a strong movement towards hybrid sensing which couple different properties of two or more surface modification approaches. In this thesis, a range of these surface modifications were explored for analysis and detection of two main analytes: the amino acid, tryptophan (Trp); and, the neurotransmitter, dopamine (DA). Specifically, this thesis aimed to utilise these methods to enhance the sensitivity and selectivity for Trp over an interferent, the indoleamine, melatonin (Mel); and, DA over the vitamin, ascorbic acid (AA). For Trp detection, immobilisation of an enzyme, Tryptophanase (Trpase) resulted in poor selectivity for the analyte. However, enhanced sensitivity and selectivity was achieved through pH manipulation of the electrolyte medium at a Nafion®-modified electrode surface for both Trp and Mel. At pH 3.0, the Mel and Trp anodic peak potentials were sufficiently resolved allowing for an LOD of 1.60 and 1.62 nM,respectively, and permitting the accurate analysis of Trp in a dietary supplement containing Mel. Multi-walled carbon nanotubes (MWCNTs) suspended in Nafion® exhibited further increases in the signal responses of these analytes at pH 3.0 and 7.4 with minimal change in the resolution of the anodic peaks. A lower sensitivity was, therefore, observed at the Nafion® and MWCNT modified electrode compared to the Nafion®-modified electrode at pH 3.0 with LODs of 0.59 and 0.80 nM exhibited for Trp and Mel, respectively. Enhanced selectivity for Trp in the presence of Mel can be achieved with MWCNTs in the presence of metallotetrasulphonated phthalocyanines (MTSPcs) particularly at pH 3.0, owing to cation exchange effects. However, the lack of sensitivity towards Trp, and even Mel, at this CoTSPc and MWCNT modified electrode remains a drawback. For DA, detection at the MWCNT and Nafion® surface resulted in improved sensitivity over that of both the bare electrode (613.0 nM) and the Nafion® modified electrode (1045.1 nM) with a calculated LOD of 133.9 nM at this layer. Furthermore, improvements in the selectivity of DA were achieved at the Nafion® and MWCNT modified electrode as exclusion of AA (150 μM) was achieved. At the MWCNT and CoTSPc surface, AA was excluded up to 130 μM with sensitivity for DA extending as low as 14.3 nM, far greater than observed for Trp and Mel. These concentrations are well within physiological concentration ranges and represent the most significant solution yet in terms of AA exclusion and enhanced sensitivity for DA. An examination of the surface layering by impedance spectroscopy and atomic force microscopy indicates that the success of the hybrid sensor utilising CoTSPc and MWCNTs lay in improved dispersion of MWCNTs and improved electron transfer kinetics, facilitated by the net charge of the materials present. This thesis, thus, showed the utility of a judicious selection of synthetic and biological catalysts, polymers and carbon nanomaterials towards a hybrid approach to the electrochemical sensing of Trp, Mel, DA and AA with focus on sensitivity and selectivity of these analytes.
- Full Text:
Predictability of Geomagnetically Induced Currents using neural networks
- Authors: Lotz, Stefan
- Date: 2009
- Subjects: Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5483 , http://hdl.handle.net/10962/d1005269 , Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Description: It is a well documented fact that Geomagnetically Induced Currents (GIC’s) poses a significant threat to ground-based electric conductor networks like oil pipelines, railways and powerline networks. A study is undertaken to determine the feasibility of using artificial neural network models to predict GIC occurrence in the Southern African power grid. The magnitude of an induced current at a specific location on the Earth’s surface is directly related to the temporal derivative of the geomagnetic field (specifically its horizontal components) at that point. Hence, the focus of the problem is on the prediction of the temporal variations in the horizontal geomagnetic field (@Bx/@t and @By/@t). Artificial neural networks are used to predict @Bx/@t and @By/@t measured at Hermanus, South Africa (34.27◦ S, 19.12◦ E) with a 30 minute prediction lead time. As input parameters to the neural networks, insitu solar wind measurements made by the Advanced Composition Explorer (ACE) satellite are used. The results presented here compare well with similar models developed at high-latitude locations (e.g. Sweden, Finland, Canada) where extensive GIC research has been undertaken. It is concluded that it would indeed be feasible to use a neural network model to predict GIC occurrence in the Southern African power grid, provided that GIC measurements, powerline configuration and network parameters are made available.
- Full Text:
- Authors: Lotz, Stefan
- Date: 2009
- Subjects: Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5483 , http://hdl.handle.net/10962/d1005269 , Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Description: It is a well documented fact that Geomagnetically Induced Currents (GIC’s) poses a significant threat to ground-based electric conductor networks like oil pipelines, railways and powerline networks. A study is undertaken to determine the feasibility of using artificial neural network models to predict GIC occurrence in the Southern African power grid. The magnitude of an induced current at a specific location on the Earth’s surface is directly related to the temporal derivative of the geomagnetic field (specifically its horizontal components) at that point. Hence, the focus of the problem is on the prediction of the temporal variations in the horizontal geomagnetic field (@Bx/@t and @By/@t). Artificial neural networks are used to predict @Bx/@t and @By/@t measured at Hermanus, South Africa (34.27◦ S, 19.12◦ E) with a 30 minute prediction lead time. As input parameters to the neural networks, insitu solar wind measurements made by the Advanced Composition Explorer (ACE) satellite are used. The results presented here compare well with similar models developed at high-latitude locations (e.g. Sweden, Finland, Canada) where extensive GIC research has been undertaken. It is concluded that it would indeed be feasible to use a neural network model to predict GIC occurrence in the Southern African power grid, provided that GIC measurements, powerline configuration and network parameters are made available.
- Full Text:
Protein secondary structure prediction using neural networks and support vector machines
- Authors: Tsilo, Lipontseng Cecilia
- Date: 2009
- Subjects: Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5569 , http://hdl.handle.net/10962/d1002809 , Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Description: Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), and coil (C). For NN we use Resilient Backpropagation training with and without early stopping. We use NN with either no hidden layer or with one hidden layer with 1,2,...,40 hidden neurons. For SVM we use a Gaussian kernel with parameter fixed at = 0.1 and varying cost parameters C in the range [0.1,5]. 10- fold cross-validation is used to obtain overall estimates for the probability of making a correct prediction. Our experiments indicate for NN and SVM that the different binary classifiers have varying accuracies: from 69% correct predictions for coils vs. non-coil up to 80% correct predictions for stand vs. non-strand. It is further demonstrated that NN with no hidden layer or not more than 2 hidden neurons in the hidden layer are sufficient for better predictions. For SVM we show that the estimated accuracies do not depend on the value of the cost parameter. As a major result, we will demonstrate that the accuracy estimates of NN and SVM binary classifiers cannot distinguish. This contradicts a modern belief in bioinformatics that SVM outperforms other predictors.
- Full Text:
- Authors: Tsilo, Lipontseng Cecilia
- Date: 2009
- Subjects: Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5569 , http://hdl.handle.net/10962/d1002809 , Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Description: Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), and coil (C). For NN we use Resilient Backpropagation training with and without early stopping. We use NN with either no hidden layer or with one hidden layer with 1,2,...,40 hidden neurons. For SVM we use a Gaussian kernel with parameter fixed at = 0.1 and varying cost parameters C in the range [0.1,5]. 10- fold cross-validation is used to obtain overall estimates for the probability of making a correct prediction. Our experiments indicate for NN and SVM that the different binary classifiers have varying accuracies: from 69% correct predictions for coils vs. non-coil up to 80% correct predictions for stand vs. non-strand. It is further demonstrated that NN with no hidden layer or not more than 2 hidden neurons in the hidden layer are sufficient for better predictions. For SVM we show that the estimated accuracies do not depend on the value of the cost parameter. As a major result, we will demonstrate that the accuracy estimates of NN and SVM binary classifiers cannot distinguish. This contradicts a modern belief in bioinformatics that SVM outperforms other predictors.
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Purification and characterization of fructosyltransferase for the synthesis of short-chain fructo-oligosaccharides and investigation into thier anti-carcinogenic properties
- Authors: Nemukula, Aluwani
- Date: 2009
- Subjects: Oligosaccharides , Polygalacturonase , Aspergillus , Fructose , Inulin , Cancer -- Prevention , Cancer -- Research , Carcinogens , High performance liquid chromatography
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3927 , http://hdl.handle.net/10962/d1003986 , Oligosaccharides , Polygalacturonase , Aspergillus , Fructose , Inulin , Cancer -- Prevention , Cancer -- Research , Carcinogens , High performance liquid chromatography
- Description: There is a growing attention in the synthesis of fructo-oligosaccharides (FOS) due to their excellent bio-functional and health-promoting properties. The current production processes are limited to chemical hydrolysis reactions of plant extracts, which are often associated with several drawbacks. In this study, fructosyltransferase (FTase) and polygalacturonase (PGase) activities, present in a commercial enzyme preparation (Pectinex® Ultra SP-L) sourced from Aspergillus aculeatus, have been separated and fully purified by anion-exchange and sizeexclusion chromatography. The FTase possesses fructosyl transfer activity for FOS synthesis and the PGase has pectin hydrolytic activity. Fructosyltransferase is a single-band protein with a molecular weight of 85 kDa, whereas PGase is a distinct protein of 40 kDa. The temperature and pH optima of FTase were 60 ºC and 6.0, with a half-life of 8 h; while that for PGase were 40 ºC and 6.0, respectively. FTase was slightly inhibited in the presence of Ni²⁺, Mg²⁺ and urea; but PGase was more susceptible to divalent ions such as Ca²⁺, Mg²⁺ and Mn²⁺. The kinetic parameters (Km and Vmax) of FTase for the hydrolysis of β-(2→1) linkages from sucrose were 752.3 mM and 120.5 μmol.min⁻¹.mL⁻¹, respectively; whereas the same parameters for pectin hydrolysis by PGase were 13.0 mg.mL⁻¹ and 263 μmol.min-1.mL⁻¹, respectively. The purified FTase was able to transfer fructosyl residues from sucrose, synthesizing the corresponding chains of FOS. PGase was relatively stable at 40 ºC (t½ > 3 h), depolymerizing the pectin backbone while releasing the inulins from within the chicory roots. Analysis of various mixtures of FOS by mass spectrometry, HPLC and ¹H-NMR was undertaken. Results indicated that MS with electrospray ionization and ¹H-NMR are capable of providing relative quantitative data of the FOS present in the mixtures. The pharmaceutical effects of various sc-FOS (0.5%, v/v) and SCFA (0.3%, v/v) on certain bacterial enzymes (β-glucuronidase, urease and β-glucosidase) associated with the formation of carcinogens were also studied. These enzyme activities were not directly influenced by the sc-FOS, but were found to be remarkably decreased by SCFA, pointing toward the prebiotic effect of FOS in intestinal microflora modulation.
- Full Text:
- Authors: Nemukula, Aluwani
- Date: 2009
- Subjects: Oligosaccharides , Polygalacturonase , Aspergillus , Fructose , Inulin , Cancer -- Prevention , Cancer -- Research , Carcinogens , High performance liquid chromatography
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3927 , http://hdl.handle.net/10962/d1003986 , Oligosaccharides , Polygalacturonase , Aspergillus , Fructose , Inulin , Cancer -- Prevention , Cancer -- Research , Carcinogens , High performance liquid chromatography
- Description: There is a growing attention in the synthesis of fructo-oligosaccharides (FOS) due to their excellent bio-functional and health-promoting properties. The current production processes are limited to chemical hydrolysis reactions of plant extracts, which are often associated with several drawbacks. In this study, fructosyltransferase (FTase) and polygalacturonase (PGase) activities, present in a commercial enzyme preparation (Pectinex® Ultra SP-L) sourced from Aspergillus aculeatus, have been separated and fully purified by anion-exchange and sizeexclusion chromatography. The FTase possesses fructosyl transfer activity for FOS synthesis and the PGase has pectin hydrolytic activity. Fructosyltransferase is a single-band protein with a molecular weight of 85 kDa, whereas PGase is a distinct protein of 40 kDa. The temperature and pH optima of FTase were 60 ºC and 6.0, with a half-life of 8 h; while that for PGase were 40 ºC and 6.0, respectively. FTase was slightly inhibited in the presence of Ni²⁺, Mg²⁺ and urea; but PGase was more susceptible to divalent ions such as Ca²⁺, Mg²⁺ and Mn²⁺. The kinetic parameters (Km and Vmax) of FTase for the hydrolysis of β-(2→1) linkages from sucrose were 752.3 mM and 120.5 μmol.min⁻¹.mL⁻¹, respectively; whereas the same parameters for pectin hydrolysis by PGase were 13.0 mg.mL⁻¹ and 263 μmol.min-1.mL⁻¹, respectively. The purified FTase was able to transfer fructosyl residues from sucrose, synthesizing the corresponding chains of FOS. PGase was relatively stable at 40 ºC (t½ > 3 h), depolymerizing the pectin backbone while releasing the inulins from within the chicory roots. Analysis of various mixtures of FOS by mass spectrometry, HPLC and ¹H-NMR was undertaken. Results indicated that MS with electrospray ionization and ¹H-NMR are capable of providing relative quantitative data of the FOS present in the mixtures. The pharmaceutical effects of various sc-FOS (0.5%, v/v) and SCFA (0.3%, v/v) on certain bacterial enzymes (β-glucuronidase, urease and β-glucosidase) associated with the formation of carcinogens were also studied. These enzyme activities were not directly influenced by the sc-FOS, but were found to be remarkably decreased by SCFA, pointing toward the prebiotic effect of FOS in intestinal microflora modulation.
- Full Text:
Restoration of degraded subtropical thickets in the Baviaanskloof Megareserve, South Africa: the role of carbon stocks and Portulacaria afra survivorship
- Authors: Powell, Michael John
- Date: 2009
- Subjects: Portulacaria afra -- South Africa -- Eastern Cape , Portulacaceae -- South Africa -- Eastern Cape , Biodiversity conservation -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Shrubs -- South Africa -- Eastern Cape , Succulent plants -- South Africa -- Eastern Cape , Baviaanskloof (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4764 , http://hdl.handle.net/10962/d1007164 , Portulacaria afra -- South Africa -- Eastern Cape , Portulacaceae -- South Africa -- Eastern Cape , Biodiversity conservation -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Shrubs -- South Africa -- Eastern Cape , Succulent plants -- South Africa -- Eastern Cape , Baviaanskloof (South Africa)
- Description: The semi-arid forms of subtropical thicket in the Eastern and Western Cape have been heavily degraded through unsustainable pastoralism over the last century or more. The degraded areas exhibit a significant loss of above-ground and belowground carbon stocks, and consequently provide an opportunity for restoration through the formal and informal carbon markets. A prerequisite for the attainment of carbon credits is to ensure sound carbon stock baselines prior to effecting restoration. I report on the carbon stocks (including sub-pools) for a number of intact subtropical thicket types, as well as the differentials between the intact and degraded states (including the sub-pools). Total carbon stocks (TCS in t C ha⁻¹) for intact vegetation (to a soil depth 0–25 cm), ranged from 87.73±6.51 to 70.64±17.24. For degraded vegetation (including old lands), TCS (t C ha⁻¹) ranged from 34.05±3.61 to 21.03±2.70. For all vegetation types, the differentials in TCS along the degradation gradient (0–25 cm) are highly significant and strengthen the possibility for carbon credit financing to catalyse the restoration of the degraded semi-arid subtropical thickets. This study has shown a mean loss of 57.23 t C ha⁻¹ in Baviaanskloof spekboom thickets, when measured to a soil depth of 25 cm. Portulacaria afra is a key species within the semi-arid subtropical thickets, being a canopy dominant and a driver of soil nutrient status, but has been largely lost from the degraded landscapes. Degraded semi-arid subtropical thicket vegetation lacks regeneration via seedling recruitment; restoration therefore requires the manual replanting of P. afra using cut truncheons. Survivorship trials were undertaken infield in 2005 to establish restoration protocols for P. afra, with survivorship being recorded in 2006 and 2008. Overall survivorship for all treatments was found to be 43.2±2.8% in 2006, dropping to 35.8±2.7% in 2008. Planting posture (flat or upright) showed the most significant results of all the factors tested in 2006 and 2008. Micro-damming also influenced survivorship in that micro-damming was associated with marginally higher survivorship (47.4 ±2.0% with damming vs. 39.1±1.5% without damming in 2006, and 39.3±1.9% vs. 32.3±1.5% in 2008). Higher planting density only showed a significant positive impact on survivorship in 2008. Neither stem diameter nor clumping significantly affected degree of survival. A key finding in the study has been the non-static nature of P. afra truncheon survivorship, even after being well established (three years since planting). The results from the study will guide the restoration protocols for the restoration of degraded subtropical thickets, where P. afra requires replanting.
- Full Text:
- Authors: Powell, Michael John
- Date: 2009
- Subjects: Portulacaria afra -- South Africa -- Eastern Cape , Portulacaceae -- South Africa -- Eastern Cape , Biodiversity conservation -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Shrubs -- South Africa -- Eastern Cape , Succulent plants -- South Africa -- Eastern Cape , Baviaanskloof (South Africa)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4764 , http://hdl.handle.net/10962/d1007164 , Portulacaria afra -- South Africa -- Eastern Cape , Portulacaceae -- South Africa -- Eastern Cape , Biodiversity conservation -- South Africa -- Eastern Cape , Plant conservation -- South Africa -- Eastern Cape , Shrubs -- South Africa -- Eastern Cape , Succulent plants -- South Africa -- Eastern Cape , Baviaanskloof (South Africa)
- Description: The semi-arid forms of subtropical thicket in the Eastern and Western Cape have been heavily degraded through unsustainable pastoralism over the last century or more. The degraded areas exhibit a significant loss of above-ground and belowground carbon stocks, and consequently provide an opportunity for restoration through the formal and informal carbon markets. A prerequisite for the attainment of carbon credits is to ensure sound carbon stock baselines prior to effecting restoration. I report on the carbon stocks (including sub-pools) for a number of intact subtropical thicket types, as well as the differentials between the intact and degraded states (including the sub-pools). Total carbon stocks (TCS in t C ha⁻¹) for intact vegetation (to a soil depth 0–25 cm), ranged from 87.73±6.51 to 70.64±17.24. For degraded vegetation (including old lands), TCS (t C ha⁻¹) ranged from 34.05±3.61 to 21.03±2.70. For all vegetation types, the differentials in TCS along the degradation gradient (0–25 cm) are highly significant and strengthen the possibility for carbon credit financing to catalyse the restoration of the degraded semi-arid subtropical thickets. This study has shown a mean loss of 57.23 t C ha⁻¹ in Baviaanskloof spekboom thickets, when measured to a soil depth of 25 cm. Portulacaria afra is a key species within the semi-arid subtropical thickets, being a canopy dominant and a driver of soil nutrient status, but has been largely lost from the degraded landscapes. Degraded semi-arid subtropical thicket vegetation lacks regeneration via seedling recruitment; restoration therefore requires the manual replanting of P. afra using cut truncheons. Survivorship trials were undertaken infield in 2005 to establish restoration protocols for P. afra, with survivorship being recorded in 2006 and 2008. Overall survivorship for all treatments was found to be 43.2±2.8% in 2006, dropping to 35.8±2.7% in 2008. Planting posture (flat or upright) showed the most significant results of all the factors tested in 2006 and 2008. Micro-damming also influenced survivorship in that micro-damming was associated with marginally higher survivorship (47.4 ±2.0% with damming vs. 39.1±1.5% without damming in 2006, and 39.3±1.9% vs. 32.3±1.5% in 2008). Higher planting density only showed a significant positive impact on survivorship in 2008. Neither stem diameter nor clumping significantly affected degree of survival. A key finding in the study has been the non-static nature of P. afra truncheon survivorship, even after being well established (three years since planting). The results from the study will guide the restoration protocols for the restoration of degraded subtropical thickets, where P. afra requires replanting.
- Full Text:
Salinity induced physiological responses in juvenile dusky kob, Argyrosomus japonicus (Sciaenidae)
- Authors: Bernatzeder, Andrea Katinka
- Date: 2009
- Subjects: Osmoregulation , Argyrosomus -- Effects of salt on -- South Africa , Sciaenidae -- Effects of salt on -- South Africa , Argyrosomus -- Physiology , Sciaenidae -- Physiology , Fishes -- Physiology , Biological control systems , Marine ecology -- South Africa , Fishery management -- South Africa , Mariculture -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5318 , http://hdl.handle.net/10962/d1005163 , Osmoregulation , Argyrosomus -- Effects of salt on -- South Africa , Sciaenidae -- Effects of salt on -- South Africa , Argyrosomus -- Physiology , Sciaenidae -- Physiology , Fishes -- Physiology , Biological control systems , Marine ecology -- South Africa , Fishery management -- South Africa , Mariculture -- South Africa
- Description: Fisheries management regulations for dusky kob Argyrosomus japonicus, an important commercial and recreational fisheries species, have failed and the stock is considered collapsed. It is important to take an ecosystems approach to management which includes understanding the effect of environmental factors on recruitment, abundance and distribution. The distribution of early juveniles (20-150 mm TL) in the wild appears to be restricted to the upper reaches of estuaries at salinities below 5 psu. Food availability could not explain the distribution of early juveniles. The aim of this study was to investigate the role of salinity on the distribution of early juvenile dusky kob (<150 mm TL) by examining physiological responses of juveniles exposed to a range of salinities under laboratory conditions. The hypothesis was that the physiological functioning of early juveniles would be optimised at the reduced salinities which they naturally occur at. The objectives of this study were to investigate the effect of salinity on: i) plasma osmolality; ii) growth, food conversion ratio and condition factor; and iii) gill histology with emphasis on chloride cell size and number. A preliminary study was undertaken to determine whether the use of 2-phenoxyethanol had an effect on plasma osmolality. Juveniles pithed prior to blood sampling were used as the control. Plasma osmolality was not affected by exposure or duration of exposure (2, 4, 6, 8, 10 min) to 2-phenoxyethanol. The ability of teleosts to regulate plasma osmolality over a wide range of salinities indicates their degree of ‘physiological euryhalinity’. Plasma osmolality of juveniles exposed to 5, 12 and 35 psu was measured every two weeks over a total of six weeks. Although juveniles were able to regulate plasma osmolality over the duration of the experiment, plasma osmolality at 5 and 12 psu was significantly lower than in fish maintained at 35 psu. Growth is used as an indicator of the relative energy used for osmoregulation at different salinities, as the energy used for osmoregulation becomes unavailable for growth. A nineweek growth experiment was conducted on juveniles exposed to 5, 12 and 35 psu. Juveniles grew and survived at all three salinities. However, growth of juveniles at 5 psu was significantly lower than at 12 and 35 psu. Other than a significantly greater weight gain at 35 psu relative to 12 psu, there was no significant difference in specific growth and length gain between juveniles at 12 and 35 psu. Food conversion ratio and condition factor at 12 and 35 psu were not significantly different, but food conversion ratio and condition factor at 5 psu was significantly greater and lower than at 35 psu respectively. In fish, gills are considered the major organ involved in osmoregulation. Within the gills, chloride cells are the predominant site of ion exchange which is driven by the Na⁺, K⁺- ATPase enzyme. Gill samples of juveniles exposed to 5, 12 and 35 psu for six weeks were examined histologically using light microscopy. Chloride cells of juveniles maintained at 5 psu were significantly more abundant than in juveniles at 12 and 35 psu. Chloride cells of juveniles at 5 psu were significantly larger than in juveniles kept at 12 psu, but not significantly different to those of juveniles kept at 35 psu. The ability of the juvenile fish to regulate plasma osmolality indicates that they are 'physiologically euryhaline', but the reduced growth and proliferation of chloride cells at 5 psu suggests that energy expenditure for osmoregulation is increased at hypoosmotic salinities. Salinity induced physiological responses could therefore not explain the natural distribution of early juvenile dusky kob and it is proposed that other environmental factors (e.g. temperature) are also important. It is also hypothesised that the high conductivity of an estuary in South Africa, to which our understanding is limited, may negate the effect of reduced salinity. Although freshwater input into estuaries is an important factor, further investigations to explain the distribution and abundance of early juveniles is required to make management recommendations. Dusky kob is also becoming an increasingly popular aquaculture species in South Africa. In this regard, early juvenile dusky kob can be grown at salinities as low as 12 psu without negatively affecting growth and production.
- Full Text:
- Authors: Bernatzeder, Andrea Katinka
- Date: 2009
- Subjects: Osmoregulation , Argyrosomus -- Effects of salt on -- South Africa , Sciaenidae -- Effects of salt on -- South Africa , Argyrosomus -- Physiology , Sciaenidae -- Physiology , Fishes -- Physiology , Biological control systems , Marine ecology -- South Africa , Fishery management -- South Africa , Mariculture -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5318 , http://hdl.handle.net/10962/d1005163 , Osmoregulation , Argyrosomus -- Effects of salt on -- South Africa , Sciaenidae -- Effects of salt on -- South Africa , Argyrosomus -- Physiology , Sciaenidae -- Physiology , Fishes -- Physiology , Biological control systems , Marine ecology -- South Africa , Fishery management -- South Africa , Mariculture -- South Africa
- Description: Fisheries management regulations for dusky kob Argyrosomus japonicus, an important commercial and recreational fisheries species, have failed and the stock is considered collapsed. It is important to take an ecosystems approach to management which includes understanding the effect of environmental factors on recruitment, abundance and distribution. The distribution of early juveniles (20-150 mm TL) in the wild appears to be restricted to the upper reaches of estuaries at salinities below 5 psu. Food availability could not explain the distribution of early juveniles. The aim of this study was to investigate the role of salinity on the distribution of early juvenile dusky kob (<150 mm TL) by examining physiological responses of juveniles exposed to a range of salinities under laboratory conditions. The hypothesis was that the physiological functioning of early juveniles would be optimised at the reduced salinities which they naturally occur at. The objectives of this study were to investigate the effect of salinity on: i) plasma osmolality; ii) growth, food conversion ratio and condition factor; and iii) gill histology with emphasis on chloride cell size and number. A preliminary study was undertaken to determine whether the use of 2-phenoxyethanol had an effect on plasma osmolality. Juveniles pithed prior to blood sampling were used as the control. Plasma osmolality was not affected by exposure or duration of exposure (2, 4, 6, 8, 10 min) to 2-phenoxyethanol. The ability of teleosts to regulate plasma osmolality over a wide range of salinities indicates their degree of ‘physiological euryhalinity’. Plasma osmolality of juveniles exposed to 5, 12 and 35 psu was measured every two weeks over a total of six weeks. Although juveniles were able to regulate plasma osmolality over the duration of the experiment, plasma osmolality at 5 and 12 psu was significantly lower than in fish maintained at 35 psu. Growth is used as an indicator of the relative energy used for osmoregulation at different salinities, as the energy used for osmoregulation becomes unavailable for growth. A nineweek growth experiment was conducted on juveniles exposed to 5, 12 and 35 psu. Juveniles grew and survived at all three salinities. However, growth of juveniles at 5 psu was significantly lower than at 12 and 35 psu. Other than a significantly greater weight gain at 35 psu relative to 12 psu, there was no significant difference in specific growth and length gain between juveniles at 12 and 35 psu. Food conversion ratio and condition factor at 12 and 35 psu were not significantly different, but food conversion ratio and condition factor at 5 psu was significantly greater and lower than at 35 psu respectively. In fish, gills are considered the major organ involved in osmoregulation. Within the gills, chloride cells are the predominant site of ion exchange which is driven by the Na⁺, K⁺- ATPase enzyme. Gill samples of juveniles exposed to 5, 12 and 35 psu for six weeks were examined histologically using light microscopy. Chloride cells of juveniles maintained at 5 psu were significantly more abundant than in juveniles at 12 and 35 psu. Chloride cells of juveniles at 5 psu were significantly larger than in juveniles kept at 12 psu, but not significantly different to those of juveniles kept at 35 psu. The ability of the juvenile fish to regulate plasma osmolality indicates that they are 'physiologically euryhaline', but the reduced growth and proliferation of chloride cells at 5 psu suggests that energy expenditure for osmoregulation is increased at hypoosmotic salinities. Salinity induced physiological responses could therefore not explain the natural distribution of early juvenile dusky kob and it is proposed that other environmental factors (e.g. temperature) are also important. It is also hypothesised that the high conductivity of an estuary in South Africa, to which our understanding is limited, may negate the effect of reduced salinity. Although freshwater input into estuaries is an important factor, further investigations to explain the distribution and abundance of early juveniles is required to make management recommendations. Dusky kob is also becoming an increasingly popular aquaculture species in South Africa. In this regard, early juvenile dusky kob can be grown at salinities as low as 12 psu without negatively affecting growth and production.
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Studies towards the synthesis of novel tridentate ligands for use in ruthenium metathesis catalysts
- Authors: Millward, Tanya
- Date: 2009
- Subjects: Ligands , Catalysis , Metathesis (Chemistry) , Ruthenium , Complex compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4360 , http://hdl.handle.net/10962/d1005025 , Ligands , Catalysis , Metathesis (Chemistry) , Ruthenium , Complex compounds
- Description: This work has focussed on the preparation of a variety of tridentate ligands, designed to form ruthenium complexes as potential metathesis catalysts. Various approaches to the tridentate, malonate-tethered imidazolidine system have been investigated, and a promising route to accessing ligands of this type is discussed. A tridentate malonate-tethered pyridine ligand has been successfully prepared and its dithallium salt has been accessed by hydrolysis with thallium carbonate; approaches to a longer-chain analogue have also been investigated. A thallium pyridine-2,6- dicarboxylate ligand has been has been successfully prepared, as have a range of pyridine diamine ligands, with various alkyl and aromatic substituents on the amine donor atoms. Preliminary investigations into the potential of these compounds as ligands for alkylidene ruthenium complexes are reported using molecular modelling techniques. The geometries and steric energies of the ligands and their corresponding complexes have been analysed, and results obtained from two different software packages are compared. Finally, some preliminary complexation studies have been undertaken.
- Full Text:
- Authors: Millward, Tanya
- Date: 2009
- Subjects: Ligands , Catalysis , Metathesis (Chemistry) , Ruthenium , Complex compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4360 , http://hdl.handle.net/10962/d1005025 , Ligands , Catalysis , Metathesis (Chemistry) , Ruthenium , Complex compounds
- Description: This work has focussed on the preparation of a variety of tridentate ligands, designed to form ruthenium complexes as potential metathesis catalysts. Various approaches to the tridentate, malonate-tethered imidazolidine system have been investigated, and a promising route to accessing ligands of this type is discussed. A tridentate malonate-tethered pyridine ligand has been successfully prepared and its dithallium salt has been accessed by hydrolysis with thallium carbonate; approaches to a longer-chain analogue have also been investigated. A thallium pyridine-2,6- dicarboxylate ligand has been has been successfully prepared, as have a range of pyridine diamine ligands, with various alkyl and aromatic substituents on the amine donor atoms. Preliminary investigations into the potential of these compounds as ligands for alkylidene ruthenium complexes are reported using molecular modelling techniques. The geometries and steric energies of the ligands and their corresponding complexes have been analysed, and results obtained from two different software packages are compared. Finally, some preliminary complexation studies have been undertaken.
- Full Text:
Synthesis and electrochemistry of octapentylthio phthalocyanine complexes of manganese, titanium and vanadium
- Authors: Mbambisa, Gcineka
- Date: 2009
- Subjects: Electrochemistry , Phthalocyanines -- Synthesis , Manganese , Titanium , Vanadium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4368 , http://hdl.handle.net/10962/d1005033 , Electrochemistry , Phthalocyanines -- Synthesis , Manganese , Titanium , Vanadium
- Description: Synthesis of new thio derivatised Pcs with manganese, titanium and vanadium as a central metal is reported. The complexes synthesised were characterised using spectroscopic and electrochemical means. The complexes displayed interesting spectroscopic properties with absorption of the Q band being observed in the near infrared region. These complexes have unusual colours for MPc complexes, with purple or red colour being observed in solution. Interesting electrochemical properties were observed, with rare observation of the MnIV/MnIII redox couple. There was observation of oxidation peaks for the pentylthio derivatised Pc with titanium as the central metal; this is unusual since for reported thio derivatives based on TiPc, no oxidation was observed. The vanadium based Pc showed an interesting spectrum for the first ring based reduction. The absorption spectrum obtained for the 1st reduction of the vanadium complex using spectroelectrochemistry would normally indicate a metal based process but comparing with literature it was concluded that it is a ring based reduction process. Generally all the MPc complexes formed a well ordered stable monolayer on the gold electrode. Electrocatalytic studies using L-cysteine revealed that the SAM based on manganese (III) octapentylthio phthalocyanine (AcOMnOPTPc) was the most effective since it catalyses L-cysteine at much lower oxidation potentials and it is also much more stable.
- Full Text:
- Authors: Mbambisa, Gcineka
- Date: 2009
- Subjects: Electrochemistry , Phthalocyanines -- Synthesis , Manganese , Titanium , Vanadium
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4368 , http://hdl.handle.net/10962/d1005033 , Electrochemistry , Phthalocyanines -- Synthesis , Manganese , Titanium , Vanadium
- Description: Synthesis of new thio derivatised Pcs with manganese, titanium and vanadium as a central metal is reported. The complexes synthesised were characterised using spectroscopic and electrochemical means. The complexes displayed interesting spectroscopic properties with absorption of the Q band being observed in the near infrared region. These complexes have unusual colours for MPc complexes, with purple or red colour being observed in solution. Interesting electrochemical properties were observed, with rare observation of the MnIV/MnIII redox couple. There was observation of oxidation peaks for the pentylthio derivatised Pc with titanium as the central metal; this is unusual since for reported thio derivatives based on TiPc, no oxidation was observed. The vanadium based Pc showed an interesting spectrum for the first ring based reduction. The absorption spectrum obtained for the 1st reduction of the vanadium complex using spectroelectrochemistry would normally indicate a metal based process but comparing with literature it was concluded that it is a ring based reduction process. Generally all the MPc complexes formed a well ordered stable monolayer on the gold electrode. Electrocatalytic studies using L-cysteine revealed that the SAM based on manganese (III) octapentylthio phthalocyanine (AcOMnOPTPc) was the most effective since it catalyses L-cysteine at much lower oxidation potentials and it is also much more stable.
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Synthesis and photophysical properties of antimony and lead phthalocyanines
- Modibane, Kwena Desmond, Guest
- Authors: Modibane, Kwena Desmond , Guest
- Date: 2009 , 2009-02-27
- Subjects: Phthalocyanines , Photochemistry , Antimony compounds , Lead compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4370 , http://hdl.handle.net/10962/d1005035 , Phthalocyanines , Photochemistry , Antimony compounds , Lead compounds
- Description: This work hereby presents the synthesis, spectroscopic and photophysical properties of newly synthesized lead (PbPc) and antimony (SbPc) phthalocyanines. The complexes are either unsubstituted or substituted at the peripheral and non-peripheral positions with phenoxy, 4-t-butylphenoxy and 4-benzyloxyphenoxy groups. The photophysical properties of these complexes were studied in dimethylsulfoxide, dimethylformamide, toluene, tetrahydrofuran and chloroform as solvents. The fluorescence spectra for PbPc complexes were different to that of the excitation spectra due to demetallation upon excitation. On the other hand, the excitation spectra of oxidized antimony (Sb(V)Pc) derivatives were found to be similar to absorption spectra. High triplet quantum yields for PbPc and SbPc complexes ranging from 0.70 to 0.86, low triplet lifetimes (20–60 μs in DMSO, while they were <10 μs in the rest of the solvents) and low fluorescence quantum yields were observed and is attributed to the presence of heavy atoms (Pb and Sb ions). The nonlinear optical properties of PbPc complexes were studied in dimethylsulfoxide. The optical limiting threshold intensity (Ilim) for the PbPc derivatives were calculated and ranged from 2.1 to 6.8 W/cm2. The photodegradation studies of the PbPc and SbPc complexes synthesized showed that then are stable.
- Full Text:
- Authors: Modibane, Kwena Desmond , Guest
- Date: 2009 , 2009-02-27
- Subjects: Phthalocyanines , Photochemistry , Antimony compounds , Lead compounds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4370 , http://hdl.handle.net/10962/d1005035 , Phthalocyanines , Photochemistry , Antimony compounds , Lead compounds
- Description: This work hereby presents the synthesis, spectroscopic and photophysical properties of newly synthesized lead (PbPc) and antimony (SbPc) phthalocyanines. The complexes are either unsubstituted or substituted at the peripheral and non-peripheral positions with phenoxy, 4-t-butylphenoxy and 4-benzyloxyphenoxy groups. The photophysical properties of these complexes were studied in dimethylsulfoxide, dimethylformamide, toluene, tetrahydrofuran and chloroform as solvents. The fluorescence spectra for PbPc complexes were different to that of the excitation spectra due to demetallation upon excitation. On the other hand, the excitation spectra of oxidized antimony (Sb(V)Pc) derivatives were found to be similar to absorption spectra. High triplet quantum yields for PbPc and SbPc complexes ranging from 0.70 to 0.86, low triplet lifetimes (20–60 μs in DMSO, while they were <10 μs in the rest of the solvents) and low fluorescence quantum yields were observed and is attributed to the presence of heavy atoms (Pb and Sb ions). The nonlinear optical properties of PbPc complexes were studied in dimethylsulfoxide. The optical limiting threshold intensity (Ilim) for the PbPc derivatives were calculated and ranged from 2.1 to 6.8 W/cm2. The photodegradation studies of the PbPc and SbPc complexes synthesized showed that then are stable.
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The conservation and management of freshwater fishes in the Greater Addo Elephant National Park
- Authors: Traas, Graham Ronald Louis
- Date: 2009
- Subjects: Addo Elephant National Park (South Africa) , Freshwater fishes -- South Africa -- Eastern Cape , Fishery conservation -- South Africa -- Eastern Cape , Fishery management -- South Africa -- Eastern Cape , Estuarine fishes -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5247 , http://hdl.handle.net/10962/d1005090 , Addo Elephant National Park (South Africa) , Freshwater fishes -- South Africa -- Eastern Cape , Fishery conservation -- South Africa -- Eastern Cape , Fishery management -- South Africa -- Eastern Cape , Estuarine fishes -- South Africa -- Eastern Cape
- Description: Freshwater fish are the most imperilled vertebrate group with a high projected extinction rate. In general, the world's freshwater ichthyofauna is in a poor state and is threatened by habitat destruction, pollution, the effects of alien species, damming, water extraction and overfishing. Within South Africa, legislation supporting the conservation of aquatic habitats and its associated fauna is strong, but there is a lack of capacity and poor co-ordination between agencies responsible for the conservation and management. The Greater Addo Elephant National Park (GAENP) includes the upper catchments of five of the Sundays River tributaries. Since the optimal method of conserving freshwater aquatic biota is to conserve the headwaters of either the river or its tributaries, there is an opportunity to conserve the native ichthyofauna of the Sundays River system. The principal objective of this thesis was, therefore, to provide information pertinent to the conservation and management of the fishes in the Sundays River system. Sixteen species of freshwater and estuarine fish were sampled, of which eight were alien. Species composition in each of the rivers, with the exception of the Kabouga River, had changed significantly from previous studies. The distribution ranges of several indigenous species had reduced, while those of some alien species was increased. Two species not previously recorded, Labeo capensis and Gambusia affinis, were sampled. Alien species were sampled from all the tributaries. Diversity indices and community assemblage models were identified as approaches for monitoring the ichthyofauna in this species depauperate system. Diversity indices were not recommended for use as a monitoring tool, as they provided insufficient detail on community composition and structure. A modified depletion estimator was applied to multiple pass electrofishing data to determine the effects of various physico-chemical variables on the absolute abundance of Pseudobarbus afer, an endangered species. Pseudobarbus afer density was found to be positively correlated to the presence of boulders. Where P. afer were present, they were abundant. Of the total sampled catch, 21.8% was comprised of alien fishes. Clarias gariepinus was the most successful invader having penetrated all but one of the tributaries. Micropterus salmoides changed the species composition of the Wit River significantly through predation, and is potentially the most dangerous of the alien species in the Sundays River system, capable of extirpating a population of P. afer in as little as three days. Only one man-made barrier to the upstream migration of alien fishes was present on the tributaries, and several addition barriers are required to safeguard the populations of indigenous fish in the headwaters of these tributaries. Several management and conservation tools are presented and discussed, including river rehabilitation, translocation, eradication of alien species, erection of barrier weirs and captive breeding programmes. Public awareness and education is stressed because without support from the communities surrounding the GAENP, management plans for conservation of the indigenous ichthyofauna will, in all likelihood, fail.
- Full Text:
- Authors: Traas, Graham Ronald Louis
- Date: 2009
- Subjects: Addo Elephant National Park (South Africa) , Freshwater fishes -- South Africa -- Eastern Cape , Fishery conservation -- South Africa -- Eastern Cape , Fishery management -- South Africa -- Eastern Cape , Estuarine fishes -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5247 , http://hdl.handle.net/10962/d1005090 , Addo Elephant National Park (South Africa) , Freshwater fishes -- South Africa -- Eastern Cape , Fishery conservation -- South Africa -- Eastern Cape , Fishery management -- South Africa -- Eastern Cape , Estuarine fishes -- South Africa -- Eastern Cape
- Description: Freshwater fish are the most imperilled vertebrate group with a high projected extinction rate. In general, the world's freshwater ichthyofauna is in a poor state and is threatened by habitat destruction, pollution, the effects of alien species, damming, water extraction and overfishing. Within South Africa, legislation supporting the conservation of aquatic habitats and its associated fauna is strong, but there is a lack of capacity and poor co-ordination between agencies responsible for the conservation and management. The Greater Addo Elephant National Park (GAENP) includes the upper catchments of five of the Sundays River tributaries. Since the optimal method of conserving freshwater aquatic biota is to conserve the headwaters of either the river or its tributaries, there is an opportunity to conserve the native ichthyofauna of the Sundays River system. The principal objective of this thesis was, therefore, to provide information pertinent to the conservation and management of the fishes in the Sundays River system. Sixteen species of freshwater and estuarine fish were sampled, of which eight were alien. Species composition in each of the rivers, with the exception of the Kabouga River, had changed significantly from previous studies. The distribution ranges of several indigenous species had reduced, while those of some alien species was increased. Two species not previously recorded, Labeo capensis and Gambusia affinis, were sampled. Alien species were sampled from all the tributaries. Diversity indices and community assemblage models were identified as approaches for monitoring the ichthyofauna in this species depauperate system. Diversity indices were not recommended for use as a monitoring tool, as they provided insufficient detail on community composition and structure. A modified depletion estimator was applied to multiple pass electrofishing data to determine the effects of various physico-chemical variables on the absolute abundance of Pseudobarbus afer, an endangered species. Pseudobarbus afer density was found to be positively correlated to the presence of boulders. Where P. afer were present, they were abundant. Of the total sampled catch, 21.8% was comprised of alien fishes. Clarias gariepinus was the most successful invader having penetrated all but one of the tributaries. Micropterus salmoides changed the species composition of the Wit River significantly through predation, and is potentially the most dangerous of the alien species in the Sundays River system, capable of extirpating a population of P. afer in as little as three days. Only one man-made barrier to the upstream migration of alien fishes was present on the tributaries, and several addition barriers are required to safeguard the populations of indigenous fish in the headwaters of these tributaries. Several management and conservation tools are presented and discussed, including river rehabilitation, translocation, eradication of alien species, erection of barrier weirs and captive breeding programmes. Public awareness and education is stressed because without support from the communities surrounding the GAENP, management plans for conservation of the indigenous ichthyofauna will, in all likelihood, fail.
- Full Text: