Finite element modelling of a magma chamber surrounded by country-rock, with particular reference to the groundwater flow in sections of different permeability
- Authors: Remsing, Carmen
- Date: 2003 , 2013-05-23
- Subjects: Magmas , Groundwater flow
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5508 , http://hdl.handle.net/10962/d1007537 , Magmas , Groundwater flow
- Description: This thesis presents results of two-dimensional finite element modelling of a magma chamber surrounded by country-rock containing a section of high permeability. The high permeability section in the country-rock simulates structure that is predominant in controlling the groundwater convection pattern and resulting mineral deposits. The models have analogies in nature: for instance the gold mines in the Massif Central of France, the Pogo mine in Alaska and the Pilgrim's Rest gold field in South Africa. This is a complicated coupled system involving fluid flow and heat transfer under extreme conditions. The magma in the chamber convects and as it cools the heat liberated causes convection in the groundwater contained in the surrounding country-rock. This convection in turn affects the rate of liberation of heat from the magma. The software used for the modelling, FLOTRAN, is the computational fluid dynamics component of the commercial ANSYS package. The results obtained describe in detail the flow pattern in the magma chamber, the country-rock and high permeability section thereof. During the cooling of the magma chamber the groundwater convects more vigorously in the high permeability section than elsewhere, and a convection cell is seen forming within this region. This provides a mechanism for hydrothermal formation of valuable mineral deposits in the structure near a magma chamber. It is found that the relationship between the velocity of the flow in the cell and the temperature of the magma chamber is well represented by a first order linear differential equation, providing a simple understanding of this process, , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Date Issued: 2003
- Authors: Remsing, Carmen
- Date: 2003 , 2013-05-23
- Subjects: Magmas , Groundwater flow
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5508 , http://hdl.handle.net/10962/d1007537 , Magmas , Groundwater flow
- Description: This thesis presents results of two-dimensional finite element modelling of a magma chamber surrounded by country-rock containing a section of high permeability. The high permeability section in the country-rock simulates structure that is predominant in controlling the groundwater convection pattern and resulting mineral deposits. The models have analogies in nature: for instance the gold mines in the Massif Central of France, the Pogo mine in Alaska and the Pilgrim's Rest gold field in South Africa. This is a complicated coupled system involving fluid flow and heat transfer under extreme conditions. The magma in the chamber convects and as it cools the heat liberated causes convection in the groundwater contained in the surrounding country-rock. This convection in turn affects the rate of liberation of heat from the magma. The software used for the modelling, FLOTRAN, is the computational fluid dynamics component of the commercial ANSYS package. The results obtained describe in detail the flow pattern in the magma chamber, the country-rock and high permeability section thereof. During the cooling of the magma chamber the groundwater convects more vigorously in the high permeability section than elsewhere, and a convection cell is seen forming within this region. This provides a mechanism for hydrothermal formation of valuable mineral deposits in the structure near a magma chamber. It is found that the relationship between the velocity of the flow in the cell and the temperature of the magma chamber is well represented by a first order linear differential equation, providing a simple understanding of this process, , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Date Issued: 2003
From labour reserve to investment opportunity: economic development planning in the Mbashe Local Municipal area in the Eastern Cape
- Authors: Reynolds, John Hunter
- Date: 2003
- Subjects: Economic development -- South Africa -- Eastern Cape , Community development -- South Africa -- Eastern Cape , South Africa -- Economic policy , Planning -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSocSc
- Identifier: vital:3353 , http://hdl.handle.net/10962/d1007490 , Economic development -- South Africa -- Eastern Cape , Community development -- South Africa -- Eastern Cape , South Africa -- Economic policy , Planning -- South Africa -- Eastern Cape
- Description: Planning for economic development at the local level has become increasingly important in many countries of the world. South Africa is no exception and has had the local focus entrenched through constitutional provisions for developmental local government. This developmental approach has been intimately linked to, and influenced by, the broader legislative, policy and planning context within which the development challenges of post-Apartheid South Africa have been addressed. It has also been implemented in a context of far-reaching transformation of public institutions aimed, in the final analysis, at the effective functioning of three spheres of government. In this thesis, the Mbashe Local Municipal area is used as a case study for an examination of the linkages between economic development planning at the local, provincial and national levels. It is not a case study in the sense that an in-depth analysis of practice is undertaken; it is used rather as a lens through which the economic development planning activities of the three spheres of government are viewed. Its value as a lens lies in its location in the former Transkei, which is characterised by high levels of unemployment and poverty and low levels of service infrastructure, and in its status as one of the newly demarcated local municipalities in South Africa. Mbashe is a pilot site of the Promotion of Rural Livelihoods Programme, which has been linked to the Eastern Cape Province's Integrated Sustainable Rural Development Programme. It also includes one of the nodes of the Wild Coast Spatial Development Initiative, which has, since 1998, been promoted as a vehicle for economic development in the former Transkei. Research comprised extensive documentary research, individual interviews with key role players in the Mbashe Local Municipality, the Promotion of Rural Livelihoods Programme and the Wild Coast Spatial Development Initiative, and a group interview with members of the Local Economic Development Sub-Committee of the Mbashe Local Municipal Council. An attempt was made to understand the complex layers of policy and planning frameworks that guide planning at the national and provincial levels and within which local level economic development is situated, and to explore the responses that have been forged by agents within the Mbashe area. Key in this endeavour has been the initiatives developed under the guidance of the Mbashe Local Economic Development Sub-Committee. It is argued that the severe resource constraints faced within Mbashe, combined with limited knowledge of and participation in larger planning and resource mobilisation frameworks, lock Local Economic Development within the top-down and investmentled approaches, rather than the more integrated approach that is promoted in terms of legislation and that is required if poverty is to be addressed successfully. The limitations on state fiscal expenditure and the market-led approach to service provision and economic development, implemented in terms of South Africa's macroeconomic framework, combined with limited synchronisation of planning cycles in which integrated development planning at the local level is privileged, leave little scope for endogenous economic development at local level. There is scope for creative engagement with the interlocking local, provincial, national and continental economies by actively shifting resources in support of integrated, endogenous approaches. Such approaches could serve as counter-narratives to the dominance of neoliberalism and allow for the establishment of local economic development practice that addresses the needs of the poor and that builds integrated local economies under the control of democratic institutions. It is only with such a shifting of approach that economic development within Mbashe will shift the structural conditions that lock it into economic dependence and poverty.
- Full Text:
- Date Issued: 2003
- Authors: Reynolds, John Hunter
- Date: 2003
- Subjects: Economic development -- South Africa -- Eastern Cape , Community development -- South Africa -- Eastern Cape , South Africa -- Economic policy , Planning -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSocSc
- Identifier: vital:3353 , http://hdl.handle.net/10962/d1007490 , Economic development -- South Africa -- Eastern Cape , Community development -- South Africa -- Eastern Cape , South Africa -- Economic policy , Planning -- South Africa -- Eastern Cape
- Description: Planning for economic development at the local level has become increasingly important in many countries of the world. South Africa is no exception and has had the local focus entrenched through constitutional provisions for developmental local government. This developmental approach has been intimately linked to, and influenced by, the broader legislative, policy and planning context within which the development challenges of post-Apartheid South Africa have been addressed. It has also been implemented in a context of far-reaching transformation of public institutions aimed, in the final analysis, at the effective functioning of three spheres of government. In this thesis, the Mbashe Local Municipal area is used as a case study for an examination of the linkages between economic development planning at the local, provincial and national levels. It is not a case study in the sense that an in-depth analysis of practice is undertaken; it is used rather as a lens through which the economic development planning activities of the three spheres of government are viewed. Its value as a lens lies in its location in the former Transkei, which is characterised by high levels of unemployment and poverty and low levels of service infrastructure, and in its status as one of the newly demarcated local municipalities in South Africa. Mbashe is a pilot site of the Promotion of Rural Livelihoods Programme, which has been linked to the Eastern Cape Province's Integrated Sustainable Rural Development Programme. It also includes one of the nodes of the Wild Coast Spatial Development Initiative, which has, since 1998, been promoted as a vehicle for economic development in the former Transkei. Research comprised extensive documentary research, individual interviews with key role players in the Mbashe Local Municipality, the Promotion of Rural Livelihoods Programme and the Wild Coast Spatial Development Initiative, and a group interview with members of the Local Economic Development Sub-Committee of the Mbashe Local Municipal Council. An attempt was made to understand the complex layers of policy and planning frameworks that guide planning at the national and provincial levels and within which local level economic development is situated, and to explore the responses that have been forged by agents within the Mbashe area. Key in this endeavour has been the initiatives developed under the guidance of the Mbashe Local Economic Development Sub-Committee. It is argued that the severe resource constraints faced within Mbashe, combined with limited knowledge of and participation in larger planning and resource mobilisation frameworks, lock Local Economic Development within the top-down and investmentled approaches, rather than the more integrated approach that is promoted in terms of legislation and that is required if poverty is to be addressed successfully. The limitations on state fiscal expenditure and the market-led approach to service provision and economic development, implemented in terms of South Africa's macroeconomic framework, combined with limited synchronisation of planning cycles in which integrated development planning at the local level is privileged, leave little scope for endogenous economic development at local level. There is scope for creative engagement with the interlocking local, provincial, national and continental economies by actively shifting resources in support of integrated, endogenous approaches. Such approaches could serve as counter-narratives to the dominance of neoliberalism and allow for the establishment of local economic development practice that addresses the needs of the poor and that builds integrated local economies under the control of democratic institutions. It is only with such a shifting of approach that economic development within Mbashe will shift the structural conditions that lock it into economic dependence and poverty.
- Full Text:
- Date Issued: 2003
Genetic variation within two pulmonate limpet species, Siphonaria capensis and S. serrata along the South African coast
- Authors: Seaman, Jennifer Ann
- Date: 2003
- Subjects: Limpets -- South Africa Pulmonata Siphonaria Limpets -- Genetics
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5800 , http://hdl.handle.net/10962/d1006155
- Description: Dispersal rates are known to play a fundamental role in establishing the genetic structure found within a species. Dispersal in marine benthic invertebrates is largely dependent on life history strategy. The presence of pelagic larvae will potentially result in high dispersal within a species, while direct development limits dispersal. This study used two intertidal pulmonate limpet species to investigate the relationship between dispersal potential and genetic structure of populations. Siphonaria capensis produces benthic egg masses, which release pelagic larvae. These float in ocean currents before settling and metamorphosing into adults. S. serrata reproduces by direct development. The larvae hatch as completely metamorphosed juveniles after developing in an egg case not far from the parent. The high dispersal capacity of S. capensis pelagic larvae should result in high levels of within-population variation since individuals within a particular population may originate from several different populations. This should lead to high levels of gene flow along the coast and to low genetic differentiation among populations. On the other hand, the low dispersal potential of S. serrata should cause low levels of genetic variation within populations, as relatives will remain close to one another. Low levels of gene flow and high genetic differentiation among populations are expected in this species. In dealing with the relationship between life history strategy and population genetic structure in these two species, a series of indirect techniques was utilised. Multivariate analyses of the morphological variation within each species showed that variation in size was similar between the two species and largely governed by environmental factors. Variation in shell shape was largely under genetic control and supported the predictions made for each species. Variation in total proteins was relatively uninformative in terms of examining the differences between the two species. Allozyme analysis and mtDNA sequencing clearly showed differences between the species in terms of their population genetic structure. High levels of gene flow were found within S. capensis. This was strongly influenced by ocean currents, with the close inshore Agulhas current along the Transkei coast contributing to high levels of dispersal and hence gene flow. Low levels of gene flow occurred within S. serrata, resulting in low within-population variation and high among-population differentiation.
- Full Text:
- Date Issued: 2003
- Authors: Seaman, Jennifer Ann
- Date: 2003
- Subjects: Limpets -- South Africa Pulmonata Siphonaria Limpets -- Genetics
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5800 , http://hdl.handle.net/10962/d1006155
- Description: Dispersal rates are known to play a fundamental role in establishing the genetic structure found within a species. Dispersal in marine benthic invertebrates is largely dependent on life history strategy. The presence of pelagic larvae will potentially result in high dispersal within a species, while direct development limits dispersal. This study used two intertidal pulmonate limpet species to investigate the relationship between dispersal potential and genetic structure of populations. Siphonaria capensis produces benthic egg masses, which release pelagic larvae. These float in ocean currents before settling and metamorphosing into adults. S. serrata reproduces by direct development. The larvae hatch as completely metamorphosed juveniles after developing in an egg case not far from the parent. The high dispersal capacity of S. capensis pelagic larvae should result in high levels of within-population variation since individuals within a particular population may originate from several different populations. This should lead to high levels of gene flow along the coast and to low genetic differentiation among populations. On the other hand, the low dispersal potential of S. serrata should cause low levels of genetic variation within populations, as relatives will remain close to one another. Low levels of gene flow and high genetic differentiation among populations are expected in this species. In dealing with the relationship between life history strategy and population genetic structure in these two species, a series of indirect techniques was utilised. Multivariate analyses of the morphological variation within each species showed that variation in size was similar between the two species and largely governed by environmental factors. Variation in shell shape was largely under genetic control and supported the predictions made for each species. Variation in total proteins was relatively uninformative in terms of examining the differences between the two species. Allozyme analysis and mtDNA sequencing clearly showed differences between the species in terms of their population genetic structure. High levels of gene flow were found within S. capensis. This was strongly influenced by ocean currents, with the close inshore Agulhas current along the Transkei coast contributing to high levels of dispersal and hence gene flow. Low levels of gene flow occurred within S. serrata, resulting in low within-population variation and high among-population differentiation.
- Full Text:
- Date Issued: 2003
Geographical races of the honeybees (Apis Mellifera L.) of the Northern regions of Ethiopia
- Authors: Mohammed, Nuru Adgaba
- Date: 2003
- Subjects: Honeybee -- Ethiopia Honeybee -- Behavior -- Ethiopia Honeybee -- Ethiopia -- Morphology Honeybee -- Ecology -- Ethiopia
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5827 , http://hdl.handle.net/10962/d1007671
- Description: The ideal climatic conditions and diversity of floral resources allow Ethiopia to sustain millions of honeybee colonies. Beekeeping is widely practiced and plays a significant role in the livelihood of the farming community of the country. Despite this, information on the types of geographical races of honeybees, their behavioural characters and the related ecological factors are not established. In this work an attempt was made to characterise the honeybee populations of the northern parts of Ethiopia based on the analyses of morphological, behavioural and ecological characteristics. For morphological analysis, 155 honeybee colony samples from 31 localities were collected. 20 worker honeybees per colony sample totalled 3100 individual worker honeybees and thirteen morphological characters per bee, a total of 40 300 measurements were recorded following Ruttner's (1988) protocols. The behavioural characters such as reproductive swarming, migration, temperament and colony seasonal cycles were assessed based on survey work of a pre-structured questionnaire. Various univariate and multivariate statistical methods were employed to analyse the data. The principal components and step-wise linear discriminant analyses revealed the existence of four discrete morphoclusters or geographical races: A. m. jemenitica from eastern, northwestern and northern arid and semi-arid lowlands, A. m. scutellata from the western humid midlands, A. m. bandasii from sub-moist central highlands and A. m. monticola from the northern mountainous parts of the study areas. These different geographical races were found to be distinctively distributed in the different ecological parts of the study area. High intercolonial and intracolonial variances were observed in all localities, however particularly high values were obtained in areas of transitions between ecological zones indicating a region of gene flow or zones of hybridisation among the statistically defined populations. Such high variances were observed mostly in areas where A. m. jemenitica borders the other geographical races. Moreover. distinct behavioural variations were also noted among these geographical races. Generally. the highland and mountainous honeybees A. m. bandasii and A. m. monticola are relatively larger in body size. have less tendency to swarm. less inclination to migrate and are relatively gentle while the converse traits were noted for the lowlands and midlands honeybees A. m. jemenitica and A. m. scutellata. Both morphological and behavioural variations were highly correlated with environmental factors and the variations seem to be the result of long adaptation to the interrelated ecological factors in their respective areas. Variations in reproductive swarming periods were also noted among these honeybee populations as a result of variations in rainfall pattern. altitude and temperature in their respective ecological areas which are believed to alter the honeybee colonies' seasonal cycles and leads to partial temporal reproductive isolation among these different honeybee populations.
- Full Text:
- Date Issued: 2003
- Authors: Mohammed, Nuru Adgaba
- Date: 2003
- Subjects: Honeybee -- Ethiopia Honeybee -- Behavior -- Ethiopia Honeybee -- Ethiopia -- Morphology Honeybee -- Ecology -- Ethiopia
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5827 , http://hdl.handle.net/10962/d1007671
- Description: The ideal climatic conditions and diversity of floral resources allow Ethiopia to sustain millions of honeybee colonies. Beekeeping is widely practiced and plays a significant role in the livelihood of the farming community of the country. Despite this, information on the types of geographical races of honeybees, their behavioural characters and the related ecological factors are not established. In this work an attempt was made to characterise the honeybee populations of the northern parts of Ethiopia based on the analyses of morphological, behavioural and ecological characteristics. For morphological analysis, 155 honeybee colony samples from 31 localities were collected. 20 worker honeybees per colony sample totalled 3100 individual worker honeybees and thirteen morphological characters per bee, a total of 40 300 measurements were recorded following Ruttner's (1988) protocols. The behavioural characters such as reproductive swarming, migration, temperament and colony seasonal cycles were assessed based on survey work of a pre-structured questionnaire. Various univariate and multivariate statistical methods were employed to analyse the data. The principal components and step-wise linear discriminant analyses revealed the existence of four discrete morphoclusters or geographical races: A. m. jemenitica from eastern, northwestern and northern arid and semi-arid lowlands, A. m. scutellata from the western humid midlands, A. m. bandasii from sub-moist central highlands and A. m. monticola from the northern mountainous parts of the study areas. These different geographical races were found to be distinctively distributed in the different ecological parts of the study area. High intercolonial and intracolonial variances were observed in all localities, however particularly high values were obtained in areas of transitions between ecological zones indicating a region of gene flow or zones of hybridisation among the statistically defined populations. Such high variances were observed mostly in areas where A. m. jemenitica borders the other geographical races. Moreover. distinct behavioural variations were also noted among these geographical races. Generally. the highland and mountainous honeybees A. m. bandasii and A. m. monticola are relatively larger in body size. have less tendency to swarm. less inclination to migrate and are relatively gentle while the converse traits were noted for the lowlands and midlands honeybees A. m. jemenitica and A. m. scutellata. Both morphological and behavioural variations were highly correlated with environmental factors and the variations seem to be the result of long adaptation to the interrelated ecological factors in their respective areas. Variations in reproductive swarming periods were also noted among these honeybee populations as a result of variations in rainfall pattern. altitude and temperature in their respective ecological areas which are believed to alter the honeybee colonies' seasonal cycles and leads to partial temporal reproductive isolation among these different honeybee populations.
- Full Text:
- Date Issued: 2003
Holding on or letting go?: the resolution of grief in relation to two Xhosa rituals in South Africa
- Authors: Van Heerden, Gary Paul
- Date: 2003
- Subjects: South Africa -- Social life and customs , Death -- Social aspects -- South Africa , Mourning customs -- South Africa , Bereavement -- Psychological aspects , Bereavement -- South Africa -- Cross-cultural studies , Death -- South Africa -- Cross-cultural studies , Xhosa (African people) -- Rites and ceremonies , Xhosa (African people) -- Social life and customs , Animal sacrifice -- South Africa
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:3253 , http://hdl.handle.net/10962/d1016055
- Description: The dominant emphasis in Western models of bereavement is on the breaking of bonds with the deceased in order for healing to occur. Failure to let go often leads to a diagnosis of 'pathological grief'. This paper challenges the assumption that death invariably means that the bonds with the deceased have to be severed. Situating Western models of bereavement in a modernist context not only challenges the 'truth' claims of these models, but also facilitates a deconstruction of the elements that contribute to the emphasis on letting go. In contrast to these theories, two Xhosa rituals (umkhapho and umbuyiso) that seek to sustain the bond with the deceased person will be examined. Such rituals demonstrate that it is possible to both maintain the bond and for the bereaved person to move on with their lives. Despite different contexts, it will be argued that these Xhosa bereavement rituals have a contribution to make to Western models of bereavement and some implications for therapy will be explored.
- Full Text:
- Date Issued: 2003
- Authors: Van Heerden, Gary Paul
- Date: 2003
- Subjects: South Africa -- Social life and customs , Death -- Social aspects -- South Africa , Mourning customs -- South Africa , Bereavement -- Psychological aspects , Bereavement -- South Africa -- Cross-cultural studies , Death -- South Africa -- Cross-cultural studies , Xhosa (African people) -- Rites and ceremonies , Xhosa (African people) -- Social life and customs , Animal sacrifice -- South Africa
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:3253 , http://hdl.handle.net/10962/d1016055
- Description: The dominant emphasis in Western models of bereavement is on the breaking of bonds with the deceased in order for healing to occur. Failure to let go often leads to a diagnosis of 'pathological grief'. This paper challenges the assumption that death invariably means that the bonds with the deceased have to be severed. Situating Western models of bereavement in a modernist context not only challenges the 'truth' claims of these models, but also facilitates a deconstruction of the elements that contribute to the emphasis on letting go. In contrast to these theories, two Xhosa rituals (umkhapho and umbuyiso) that seek to sustain the bond with the deceased person will be examined. Such rituals demonstrate that it is possible to both maintain the bond and for the bereaved person to move on with their lives. Despite different contexts, it will be argued that these Xhosa bereavement rituals have a contribution to make to Western models of bereavement and some implications for therapy will be explored.
- Full Text:
- Date Issued: 2003
In defence of moral objectivity
- Authors: McKaiser, Eusebius
- Date: 2003 , 2013-05-23
- Subjects: Ethics , Objectivity
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:2740 , http://hdl.handle.net/10962/d1007599 , Ethics , Objectivity
- Description: This thesis examines the problem of moral objectivity, which is constituted by the ontological, epistemological and motivational challenges. It gradually develops an account of moral objectivity that has the dual function of dealing with the enemies of moral objectivity as well as giving a positive account of what moral objectivity is. It establishes these aims by arguing for the following theses. The first set of arguments show that relativist theories of ethics provide us with no forceful grounds for being sceptical about moral objectivity. The second set of arguments deepens the response to those who are sceptical about moral objectivity. It does so by showing in greater detail how rationality plays a substantive role in our practical deliberation, our notion of agency as well as our reactive attitudes. These arguments provide further reasons why we should have faith in the possibility of developing an adequate account of moral objectivity. The last set of arguments provides the positive account of moral objectivity. This positive account ends with the discussion of a paradigmatic moral fact that gives full expression (to the features of moral objectivity that have been articulated and defended.
- Full Text:
- Date Issued: 2003
- Authors: McKaiser, Eusebius
- Date: 2003 , 2013-05-23
- Subjects: Ethics , Objectivity
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:2740 , http://hdl.handle.net/10962/d1007599 , Ethics , Objectivity
- Description: This thesis examines the problem of moral objectivity, which is constituted by the ontological, epistemological and motivational challenges. It gradually develops an account of moral objectivity that has the dual function of dealing with the enemies of moral objectivity as well as giving a positive account of what moral objectivity is. It establishes these aims by arguing for the following theses. The first set of arguments show that relativist theories of ethics provide us with no forceful grounds for being sceptical about moral objectivity. The second set of arguments deepens the response to those who are sceptical about moral objectivity. It does so by showing in greater detail how rationality plays a substantive role in our practical deliberation, our notion of agency as well as our reactive attitudes. These arguments provide further reasons why we should have faith in the possibility of developing an adequate account of moral objectivity. The last set of arguments provides the positive account of moral objectivity. This positive account ends with the discussion of a paradigmatic moral fact that gives full expression (to the features of moral objectivity that have been articulated and defended.
- Full Text:
- Date Issued: 2003
Intelligent design and biology
- Authors: Ramsden, Sean
- Date: 2003
- Subjects: Hume, David, 1711-1776 , Darwin, Charles, 1809-1882 , Paley, William, 1743-1805 , Dembski, William A., 1960- , Behe, Michael J., 1952- , Evolution (Biology) , Probabilities , Naturalism , Intelligent design (Teleology)
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:2739 , http://hdl.handle.net/10962/d1007561 , Hume, David, 1711-1776 , Darwin, Charles, 1809-1882 , Paley, William, 1743-1805 , Dembski, William A., 1960- , Behe, Michael J., 1952- , Evolution (Biology) , Probabilities , Naturalism , Intelligent design (Teleology)
- Description: The thesis is that contrary to the received popular wisdom, the combination of David Hume's sceptical enquiry and Charles Darwin's provision of an alternative theoretical framework to the then current paradigm of natural theology did not succeed in defeating the design argument. I argue that William Paley's work best represented the status quo in the philosophy of biology circa 1800 and that with the logical mechanisms provided us by William Dembski in his seminal work on probability, there is a strong argument for thr work of Michael Behe to stand in a similar position today to that of Paley two centuries ago. The argument runs as follows: In Sections 1 and 2 of Chapter 1 I introduce the issues. In Section 3 I argue that William Paley's exposition of the design argument was archetypical of the natural theology school and that given Hume's already published criticism of the argument, Paley for one did not feel the design argument to be done for. I further argue in Section 4 that Hume in fact did no such thing and that neither did he see himself as having done so, but that the design argument was weak rather than fallacious. In Section 5 I outline the demise of natural theology as the dominant school of thought in the philosophy of biology, ascribing this to the rise of Darwinism and subsequently neo-Darwinism. I argue that design arguments were again not defeated but went into abeyance with the rise of a new paradigm associated with Darwinism, namely methodological naturalism. In Chapter 2 I advance the project by a discussion of William Dembski's formulation of design inferences, demonstrating their value in both everyday and technical usage. This is stated in Section 1. In Sections 2 and 3 I discuss Dembski's treatment of probability, whilst in Section 4 I examine Dembski's tying of different levels of probability to different mechanisms of explanation used in explicating the world. Section 5 is my analysis of the logic of the formal statement of the design argument according to Dembski. In Section 6 I encapsulate objections to Dembski. I conclude the chapter (with Section 7) by claiming that Dembski forwards a coherent model of design inferences that can be used in demonstrating that there is little difference between the way that Paley came to his conclusions two centuries ago and how modem philosophers of biology (such as I take Michael Behe to be, albeit that by profession he is a scientist) come to theirs when offering design explanations. Inference to the best explanation is demonstrated as lying at the crux of design arguments. In Chapter 3 I draw together the work of Michael Behe and Paley, showing through the mechanism of Dembski's work that they are closely related in many respects and that neither position is to be lightly dismissed. Section 1 introduces this. In Section 2 I introduce Behe's concept of irreducible complexity in the light of (functional) explanation. Section 3 is a detailed analysis of irreducible complexity. Section 4 raises and covers objections to Behe with the general theme being that (neo-) Darwinians beg the question against him. In Section 4 I apply the Dembskian mechanic directly to Behe's work. I argue that Behe does not quite meet the Dembskian criteria he needs to in order for his argument to stand as anything other than defeasible. However, in Section 5 I conclude by arguing that this is exactly what we are to expect from Behe's and similar theories, even within competing paradigms, in the philosophy of biology, given that inference to the best explanation is the logical lever therein at work. , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Date Issued: 2003
- Authors: Ramsden, Sean
- Date: 2003
- Subjects: Hume, David, 1711-1776 , Darwin, Charles, 1809-1882 , Paley, William, 1743-1805 , Dembski, William A., 1960- , Behe, Michael J., 1952- , Evolution (Biology) , Probabilities , Naturalism , Intelligent design (Teleology)
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:2739 , http://hdl.handle.net/10962/d1007561 , Hume, David, 1711-1776 , Darwin, Charles, 1809-1882 , Paley, William, 1743-1805 , Dembski, William A., 1960- , Behe, Michael J., 1952- , Evolution (Biology) , Probabilities , Naturalism , Intelligent design (Teleology)
- Description: The thesis is that contrary to the received popular wisdom, the combination of David Hume's sceptical enquiry and Charles Darwin's provision of an alternative theoretical framework to the then current paradigm of natural theology did not succeed in defeating the design argument. I argue that William Paley's work best represented the status quo in the philosophy of biology circa 1800 and that with the logical mechanisms provided us by William Dembski in his seminal work on probability, there is a strong argument for thr work of Michael Behe to stand in a similar position today to that of Paley two centuries ago. The argument runs as follows: In Sections 1 and 2 of Chapter 1 I introduce the issues. In Section 3 I argue that William Paley's exposition of the design argument was archetypical of the natural theology school and that given Hume's already published criticism of the argument, Paley for one did not feel the design argument to be done for. I further argue in Section 4 that Hume in fact did no such thing and that neither did he see himself as having done so, but that the design argument was weak rather than fallacious. In Section 5 I outline the demise of natural theology as the dominant school of thought in the philosophy of biology, ascribing this to the rise of Darwinism and subsequently neo-Darwinism. I argue that design arguments were again not defeated but went into abeyance with the rise of a new paradigm associated with Darwinism, namely methodological naturalism. In Chapter 2 I advance the project by a discussion of William Dembski's formulation of design inferences, demonstrating their value in both everyday and technical usage. This is stated in Section 1. In Sections 2 and 3 I discuss Dembski's treatment of probability, whilst in Section 4 I examine Dembski's tying of different levels of probability to different mechanisms of explanation used in explicating the world. Section 5 is my analysis of the logic of the formal statement of the design argument according to Dembski. In Section 6 I encapsulate objections to Dembski. I conclude the chapter (with Section 7) by claiming that Dembski forwards a coherent model of design inferences that can be used in demonstrating that there is little difference between the way that Paley came to his conclusions two centuries ago and how modem philosophers of biology (such as I take Michael Behe to be, albeit that by profession he is a scientist) come to theirs when offering design explanations. Inference to the best explanation is demonstrated as lying at the crux of design arguments. In Chapter 3 I draw together the work of Michael Behe and Paley, showing through the mechanism of Dembski's work that they are closely related in many respects and that neither position is to be lightly dismissed. Section 1 introduces this. In Section 2 I introduce Behe's concept of irreducible complexity in the light of (functional) explanation. Section 3 is a detailed analysis of irreducible complexity. Section 4 raises and covers objections to Behe with the general theme being that (neo-) Darwinians beg the question against him. In Section 4 I apply the Dembskian mechanic directly to Behe's work. I argue that Behe does not quite meet the Dembskian criteria he needs to in order for his argument to stand as anything other than defeasible. However, in Section 5 I conclude by arguing that this is exactly what we are to expect from Behe's and similar theories, even within competing paradigms, in the philosophy of biology, given that inference to the best explanation is the logical lever therein at work. , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Date Issued: 2003
Intercohort cannibalism and parturition-associated behaviour of captive-bred swordtail, Xiphophorus helleri (Pisces: Poeciliidae)
- Jones, Clifford Louis Wilshire
- Authors: Jones, Clifford Louis Wilshire
- Date: 2003
- Subjects: Poeciliidae -- Behavior Xiphophorus helleri Fish culture
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5351 , http://hdl.handle.net/10962/d1007812
- Description: Adult fish that belong to the family Poeciliidae cannibalise juveniles, both in the wild and under captive conditions, but this behaviour has only been partly investigated in the Poeciliidae in some of the commercially valuable species. The objective of the research is to develop an understanding of intercohort cannibalism and parturition-associated behaviour in captive-bred swordtail (Xiphophorus helleri), with applications to industry and future research of other poeciliids. Experiments investigating the effect of adult stocking density and sex ratio on the production of juveniles were used to determine if cannibalism occurs under culture conditions. The average rate of intercohort cannibalism ranged from (5.5 to 53.9%), and was positively density dependent and independent of sex ratio, indicating that males and females were probably equally cannibalistic. The highest number of juveniles (1725.7±141.4) produced per tank over 70 days was obtained from two males and eight females. To develop a better understanding of adult and juvenile behaviour during parturition, fish were observed under controlled laboratory conditions using video and behaviours such as attack (burst of speed by an adult in the direction of a juvenile), escape (avoidance of cannibalism after attack) and cannibalism (predation of a live juvenile by an adult), for example, were identified. Under laboratory conditions most young escaped in downward direction after attack (49%) and most utilised the refuge made that was made available. Furthermore, most attacks (62-65%) and cannibalism (57-84%) occurred at the bottom. Since the presence of refuge significantly increased the rate of juvenile survival under culture conditions, it was hypothesised that the rate of cannibalism could be reduced under farming conditions if juveniles were protected when they escaped downwards. This hypothesis was accepted as it was found that refuge at the bottom of the water column or the inclusion of a false-bottom reduced the rate of cannibalism by 49% and 72%, respectively. Similarly, the hypothesise that the rate of cannibalism could be reduced if juveniles where given protection when escaping sideways (32% of juveniles escaped sideways in the laboratory) was also accepted when tested under farm-scale conditions because a false-side reduced the rate of cannibalism by an average of 45%. Since males and females were equally responsible for cannibalising juveniles in the laboratory, it was hypothesised that the rate of cannibalism would decrease proportionately with the removal of males (Le. 20% of the cannibals) from the population; the removal of males under farming conditions resulted in a 19.5% reduction in the rate of cannibalism. Since older juveniles were better able to escape cannibalism than neonates and since adults habituate to stimuli that previously resulted in attack behaviour, it was hypothesised that the rate of cannibalism would remain unaffected by the length of time that juveniles were exposed to adults in the breeding tanks. This hypothesis was also accepted when tested under farm conditions. However, some hypotheses based on laboratory observations were not accepted. For example, a constant low light intensity did not appear to decrease the rate of cannibalism under farm conditions; also, the occurrence of dead and deformed juveniles went unnoticed in the laboratory, and under farm conditions, where adults did not have access to the bottom of the tank, 10% of the harvest consisted of dead and deformed juveniles. It is concluded that technologies, such as bottom-refuge or a false-side, that increase the size of the liveharvest and allow for the removal of potentially less viable offspring are recommended for the commercial production of poeciliids. The overall similarity of X. helleri behaviour between the laboratory experiments and the farm-scale trials suggests that the post-partum behaviour of X. helleri remains consistent under these different conditions; thus, behaviour under one set of conditions may be used to predict behaviour under other conditions. The application and significance of extrapolations to industry and future research of X. helleri and possibly other poeciliids were discussed and the most applicable laboratory observations with the highest extrapolation capacity were proposed. Furthermore, techniques were developed to aid industry and future researchers in making predictions relating to behaviour of X. helleri under different conditions based on laboratory observations. The results were used to develop a model indicating that selection pressures against cannibalism are not likely to exist at the rate of cannibalism observed here since the potential genetic gain through kin survival and inclusive fitness was shown to be greater than any potential genetiC loss experienced by a victim of cannibalism. The model was successfully tested under a range of social conditions. Other possible explanations for cannibalism in poeciliids, such as parental manipulation, nutritional advantages, opportunistic predation and the recovery of energy are discussed. It is suggested that the most likely proximate cause of cannibalism under captive conditions is opportunistic predation. The theory that cannibalism ensures that only viable genes of the victim are expressed, through inclusive fitness, is a possible ultimate cause of cannibalism, which may have been inherited from feral ancestors of captive-bred X. helleri.
- Full Text:
- Date Issued: 2003
- Authors: Jones, Clifford Louis Wilshire
- Date: 2003
- Subjects: Poeciliidae -- Behavior Xiphophorus helleri Fish culture
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5351 , http://hdl.handle.net/10962/d1007812
- Description: Adult fish that belong to the family Poeciliidae cannibalise juveniles, both in the wild and under captive conditions, but this behaviour has only been partly investigated in the Poeciliidae in some of the commercially valuable species. The objective of the research is to develop an understanding of intercohort cannibalism and parturition-associated behaviour in captive-bred swordtail (Xiphophorus helleri), with applications to industry and future research of other poeciliids. Experiments investigating the effect of adult stocking density and sex ratio on the production of juveniles were used to determine if cannibalism occurs under culture conditions. The average rate of intercohort cannibalism ranged from (5.5 to 53.9%), and was positively density dependent and independent of sex ratio, indicating that males and females were probably equally cannibalistic. The highest number of juveniles (1725.7±141.4) produced per tank over 70 days was obtained from two males and eight females. To develop a better understanding of adult and juvenile behaviour during parturition, fish were observed under controlled laboratory conditions using video and behaviours such as attack (burst of speed by an adult in the direction of a juvenile), escape (avoidance of cannibalism after attack) and cannibalism (predation of a live juvenile by an adult), for example, were identified. Under laboratory conditions most young escaped in downward direction after attack (49%) and most utilised the refuge made that was made available. Furthermore, most attacks (62-65%) and cannibalism (57-84%) occurred at the bottom. Since the presence of refuge significantly increased the rate of juvenile survival under culture conditions, it was hypothesised that the rate of cannibalism could be reduced under farming conditions if juveniles were protected when they escaped downwards. This hypothesis was accepted as it was found that refuge at the bottom of the water column or the inclusion of a false-bottom reduced the rate of cannibalism by 49% and 72%, respectively. Similarly, the hypothesise that the rate of cannibalism could be reduced if juveniles where given protection when escaping sideways (32% of juveniles escaped sideways in the laboratory) was also accepted when tested under farm-scale conditions because a false-side reduced the rate of cannibalism by an average of 45%. Since males and females were equally responsible for cannibalising juveniles in the laboratory, it was hypothesised that the rate of cannibalism would decrease proportionately with the removal of males (Le. 20% of the cannibals) from the population; the removal of males under farming conditions resulted in a 19.5% reduction in the rate of cannibalism. Since older juveniles were better able to escape cannibalism than neonates and since adults habituate to stimuli that previously resulted in attack behaviour, it was hypothesised that the rate of cannibalism would remain unaffected by the length of time that juveniles were exposed to adults in the breeding tanks. This hypothesis was also accepted when tested under farm conditions. However, some hypotheses based on laboratory observations were not accepted. For example, a constant low light intensity did not appear to decrease the rate of cannibalism under farm conditions; also, the occurrence of dead and deformed juveniles went unnoticed in the laboratory, and under farm conditions, where adults did not have access to the bottom of the tank, 10% of the harvest consisted of dead and deformed juveniles. It is concluded that technologies, such as bottom-refuge or a false-side, that increase the size of the liveharvest and allow for the removal of potentially less viable offspring are recommended for the commercial production of poeciliids. The overall similarity of X. helleri behaviour between the laboratory experiments and the farm-scale trials suggests that the post-partum behaviour of X. helleri remains consistent under these different conditions; thus, behaviour under one set of conditions may be used to predict behaviour under other conditions. The application and significance of extrapolations to industry and future research of X. helleri and possibly other poeciliids were discussed and the most applicable laboratory observations with the highest extrapolation capacity were proposed. Furthermore, techniques were developed to aid industry and future researchers in making predictions relating to behaviour of X. helleri under different conditions based on laboratory observations. The results were used to develop a model indicating that selection pressures against cannibalism are not likely to exist at the rate of cannibalism observed here since the potential genetic gain through kin survival and inclusive fitness was shown to be greater than any potential genetiC loss experienced by a victim of cannibalism. The model was successfully tested under a range of social conditions. Other possible explanations for cannibalism in poeciliids, such as parental manipulation, nutritional advantages, opportunistic predation and the recovery of energy are discussed. It is suggested that the most likely proximate cause of cannibalism under captive conditions is opportunistic predation. The theory that cannibalism ensures that only viable genes of the victim are expressed, through inclusive fitness, is a possible ultimate cause of cannibalism, which may have been inherited from feral ancestors of captive-bred X. helleri.
- Full Text:
- Date Issued: 2003
Investigation of the comparative cost-effectiveness of different strategies for the management of multidrug-resistant tuberculosis
- Authors: Rockcliffe, Nicole
- Date: 2003
- Subjects: Tuberculosis , Multidrug resistance , Tuberculosis -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3788 , http://hdl.handle.net/10962/d1003266 , Tuberculosis , Multidrug resistance , Tuberculosis -- Treatment
- Description: The tuberculosis epidemic is escalating in South Africa as well as globally. This escalation is exacerbated by the increasing prevalence of multidrug-resistant tuberculosis (MDRTB), which is defined by the World Health Organisation (WHO) as resistance of Mycobacteria to at least isoniazid and rifampicin. Multi-drug resistant tuberculosis is estimated to occur in 1-2% of newly diagnosed tuberculosis (TB) patients and in 4-8% of previously treated patients. MDRTB is both difficult and expensive to treat, costing up to 126 times that of drug-sensitive TB. Resource constrained countries such as South Africa often lack both the money and the infrastructure to treat this disease. The aim of this project was to determine whether the performance of a systematic review with subsequent economic modelling could influence the decision making process for policy makers. Data was gathered and an economic evaluation of MDRTB treatment was performed from the perspective of the South African Department of Health. Three treatment alternatives were identified: a protocol regimen of second line anti-tuberculosis agents, as recommended in the South African guidelines for MDRTB, an appropriate regimen designed for each patient according to the results of culture and drug susceptibility tests, and non-drug management. A decision-analysis model using DATA 3.0 by Treeage® was developed to estimate the costs of each alternative. Outcomes were measured in terms of cost alone as well as the ‘number of cases cured’ and the number of ‘years of life saved’ for patients dying, being cured or failing treatment. Drug, hospital and laboratory costs incurred using each alternative were included in the analysis. A sensitivity analysis was performed on all variables in order to identify threshold values that would change the outcome of the evaluation. Results of the decision analysis indicate that the individualised regimen was both the cheaper and more cost-effective regimen of the two active treatment options, and was estimated to cost R50 661 per case cured and R2 070 per year of life saved. The protocol regimen was estimated to cost R73 609 per case cured and R2 741 per year of life saved. The outcome of the decision analysis was sensitive to changes in some of the variables used to model the disease, particularly the daily cost of drugs, the length of time spent in hospital and the length of treatment received by those patients dying or failing treatment. This modelling exercise highlighted significant deficiencies in the quality of evidence on MDRTB management available to policy makers. Pragmatic choices based on operational and other logistic concerns may need to be reviewed when further information becomes available. A case can be made for the establishment of a national database of costing and efficacy information to guide future policy revisions of the South African MDRTB treatment programme, which is resource intensive and of only moderate efficacy. However, due to the widely disparate range of studies on which this evaluation was based, the outcome of the study may not be credible. In this case, the use of a systematic review with subsequent economic modelling could not validly influence policy-makers to change the decision that they made on the basis of drug availability.
- Full Text:
- Date Issued: 2003
- Authors: Rockcliffe, Nicole
- Date: 2003
- Subjects: Tuberculosis , Multidrug resistance , Tuberculosis -- Treatment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3788 , http://hdl.handle.net/10962/d1003266 , Tuberculosis , Multidrug resistance , Tuberculosis -- Treatment
- Description: The tuberculosis epidemic is escalating in South Africa as well as globally. This escalation is exacerbated by the increasing prevalence of multidrug-resistant tuberculosis (MDRTB), which is defined by the World Health Organisation (WHO) as resistance of Mycobacteria to at least isoniazid and rifampicin. Multi-drug resistant tuberculosis is estimated to occur in 1-2% of newly diagnosed tuberculosis (TB) patients and in 4-8% of previously treated patients. MDRTB is both difficult and expensive to treat, costing up to 126 times that of drug-sensitive TB. Resource constrained countries such as South Africa often lack both the money and the infrastructure to treat this disease. The aim of this project was to determine whether the performance of a systematic review with subsequent economic modelling could influence the decision making process for policy makers. Data was gathered and an economic evaluation of MDRTB treatment was performed from the perspective of the South African Department of Health. Three treatment alternatives were identified: a protocol regimen of second line anti-tuberculosis agents, as recommended in the South African guidelines for MDRTB, an appropriate regimen designed for each patient according to the results of culture and drug susceptibility tests, and non-drug management. A decision-analysis model using DATA 3.0 by Treeage® was developed to estimate the costs of each alternative. Outcomes were measured in terms of cost alone as well as the ‘number of cases cured’ and the number of ‘years of life saved’ for patients dying, being cured or failing treatment. Drug, hospital and laboratory costs incurred using each alternative were included in the analysis. A sensitivity analysis was performed on all variables in order to identify threshold values that would change the outcome of the evaluation. Results of the decision analysis indicate that the individualised regimen was both the cheaper and more cost-effective regimen of the two active treatment options, and was estimated to cost R50 661 per case cured and R2 070 per year of life saved. The protocol regimen was estimated to cost R73 609 per case cured and R2 741 per year of life saved. The outcome of the decision analysis was sensitive to changes in some of the variables used to model the disease, particularly the daily cost of drugs, the length of time spent in hospital and the length of treatment received by those patients dying or failing treatment. This modelling exercise highlighted significant deficiencies in the quality of evidence on MDRTB management available to policy makers. Pragmatic choices based on operational and other logistic concerns may need to be reviewed when further information becomes available. A case can be made for the establishment of a national database of costing and efficacy information to guide future policy revisions of the South African MDRTB treatment programme, which is resource intensive and of only moderate efficacy. However, due to the widely disparate range of studies on which this evaluation was based, the outcome of the study may not be credible. In this case, the use of a systematic review with subsequent economic modelling could not validly influence policy-makers to change the decision that they made on the basis of drug availability.
- Full Text:
- Date Issued: 2003
Isolation of antigenic peptides of Cowdria ruminantium and their encoding genes using a genome-derived phage display library
- Authors: Fehrsen, Jeanni
- Date: 2003
- Subjects: Bacteriophages -- Genetics Ruminants -- Diseases Heartwater
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3920 , http://hdl.handle.net/10962/d1003979
- Description: The development of new and effective vaccines and immunodiagnostic reagents requires the characterisation of antigenically relevant proteins and their interactions with the products of the immune system. Phage display technology was investigated as a means of elucidating some of the antigenic properties of the rickettsial parasite, Cowdria ruminantium (Cowdria). Randomly fragmented gene-derived libraries have been useful in elucidating viral and other epitopes, but only limited work has been done with entire genomes. A phage display library expressing a repertoire of Cowdria peptides was constructed. It was sufficiently large to represent the organism's genome, but lacked phages displaying peptides coded for by genes containing a Pvu II restriction enzyme site, including the one coding for the major antigenic protein 1 (MAP1). This was considered advantageous since MAP1 is immunodominant and has already been well characterised. Affinity selection with antibodies against Cowdria proteins other than MAP1 allowed several antibody-reactive peptides to be isolated. These selected sequences were placed in the context of the genome by screening a lambda bacteriophage library and by comparison with Cowdria DNA sequences. Apart from showing that antigenic mimics were present in the phage display library, six open reading frames encoding putative Cowdria proteins were identified. All had similarities to, or motifs in common with, membrane proteins and are thus likely to be exposed to the host's humoral immune system. Some of the proteins identified were larger than the antigens used to elicit the antibodies used for selection, probably as a result of the presence of cross-reactive epitopes. Despite limitations experienced when extending a fragmented-gene approach for epitope location to genomes, it was possible to identify an antigenic region on MAP1 by comparison with selected mimics. In addition, binding peptide sequences were identified with two monoclonal antibodies that had been raised against non-Cowdria antigens. An epitope on the VP7 protein of bluetongue virus was identified and peptides were found that reacted with a monoclonal antibody directed against malignant catarrhal fever virus. Thus, apart from being able to identify several potentially important Cowdria epitopes and genes, the fragmented-genome library holds promise as a universal reagent for identifying useful mimics.
- Full Text:
- Date Issued: 2003
- Authors: Fehrsen, Jeanni
- Date: 2003
- Subjects: Bacteriophages -- Genetics Ruminants -- Diseases Heartwater
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:3920 , http://hdl.handle.net/10962/d1003979
- Description: The development of new and effective vaccines and immunodiagnostic reagents requires the characterisation of antigenically relevant proteins and their interactions with the products of the immune system. Phage display technology was investigated as a means of elucidating some of the antigenic properties of the rickettsial parasite, Cowdria ruminantium (Cowdria). Randomly fragmented gene-derived libraries have been useful in elucidating viral and other epitopes, but only limited work has been done with entire genomes. A phage display library expressing a repertoire of Cowdria peptides was constructed. It was sufficiently large to represent the organism's genome, but lacked phages displaying peptides coded for by genes containing a Pvu II restriction enzyme site, including the one coding for the major antigenic protein 1 (MAP1). This was considered advantageous since MAP1 is immunodominant and has already been well characterised. Affinity selection with antibodies against Cowdria proteins other than MAP1 allowed several antibody-reactive peptides to be isolated. These selected sequences were placed in the context of the genome by screening a lambda bacteriophage library and by comparison with Cowdria DNA sequences. Apart from showing that antigenic mimics were present in the phage display library, six open reading frames encoding putative Cowdria proteins were identified. All had similarities to, or motifs in common with, membrane proteins and are thus likely to be exposed to the host's humoral immune system. Some of the proteins identified were larger than the antigens used to elicit the antibodies used for selection, probably as a result of the presence of cross-reactive epitopes. Despite limitations experienced when extending a fragmented-gene approach for epitope location to genomes, it was possible to identify an antigenic region on MAP1 by comparison with selected mimics. In addition, binding peptide sequences were identified with two monoclonal antibodies that had been raised against non-Cowdria antigens. An epitope on the VP7 protein of bluetongue virus was identified and peptides were found that reacted with a monoclonal antibody directed against malignant catarrhal fever virus. Thus, apart from being able to identify several potentially important Cowdria epitopes and genes, the fragmented-genome library holds promise as a universal reagent for identifying useful mimics.
- Full Text:
- Date Issued: 2003
Isolation, expression and purification of the hydantoin hydrolysing enzymes of agrobacterium tumefaciens
- Authors: Clark, Sally-Ann
- Date: 2003
- Subjects: Agrobacterium tumefaciens , Amino acids Hydantoin Enzymes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4140 , http://hdl.handle.net/10962/d1016233
- Description: The production of enantiomerically pure amino acids is of industrial importance as they are used in the synthesis of a number of pharmaceuticals, insecticides and herbicides and biologically active peptides and hormones. A number of microorganisms have been identified which possess hydantoin hydrolysing enzymes that stereoselectively convert racemic hydantoins into anantiomerically pure amino acids. Consequently these microorganisms and their enzymes are sought after as biocatalysts for the production of amino acids. The isolation of novel hydantoin hydrolising enzymes with unique or improved biocatalytic characteristics is of importance for the development of potential biocatalysts to be used in the production of enantiomerically pure amino acids. The genes encoding an N-carbamoyl-amino acid amidohydrolase, an enzyme involved in the hydrolysis of hydantoin, was isolated by screening a genomic DNA library of Agrobacterium tumefacience RU-AE01. Nucleotide sequence analysis of the region upstream of this gene revealed a fragment of a gene encoding the hydantoinase enzyme. I this study, a DNA probe consisting of the gene encoding the N-carbamoyl amino acid amidohydrolase, on a large enough fragment of the genomic DNA library which would allow for the simultaneous isolation the hydantoinase gene located upstream. Recombinant expression of the genes encoding hydantoin hydrolysing enzymes has been used to facilitate the production and purification of these enzymes for their use as biocatalysts. Two genes (ncaR1 and ncaR2) encoding different N-carbamoyl-amino acid amidohydrolases with distinct nucleotide and deduced amino acid sequences were isolated from the genome of A, tumefaciens RU-OR. In this study, the heterologous expression of ncaR1 and ncaR2 was explored. Investigation into the optimisation of the heterologous expression of ncaR1 showed that reducing the growth temperature of the recombinant E. coli producing NcaR1 resulted in a two-fold increase in N-carbamoyl-amino acid amidohydrolase activity and solubility. Furthermore, NcaR1 was produced with a C-terminal 6xHis tag, but NcaR1-6xHis did not possess N-carbamoyl amino acid amidohydrolase activity. Furthermore, purification of NcaR-6xHis under native conditions using affinity chromatography performed, and used for the production of antibodies.
- Full Text:
- Date Issued: 2003
- Authors: Clark, Sally-Ann
- Date: 2003
- Subjects: Agrobacterium tumefaciens , Amino acids Hydantoin Enzymes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4140 , http://hdl.handle.net/10962/d1016233
- Description: The production of enantiomerically pure amino acids is of industrial importance as they are used in the synthesis of a number of pharmaceuticals, insecticides and herbicides and biologically active peptides and hormones. A number of microorganisms have been identified which possess hydantoin hydrolysing enzymes that stereoselectively convert racemic hydantoins into anantiomerically pure amino acids. Consequently these microorganisms and their enzymes are sought after as biocatalysts for the production of amino acids. The isolation of novel hydantoin hydrolising enzymes with unique or improved biocatalytic characteristics is of importance for the development of potential biocatalysts to be used in the production of enantiomerically pure amino acids. The genes encoding an N-carbamoyl-amino acid amidohydrolase, an enzyme involved in the hydrolysis of hydantoin, was isolated by screening a genomic DNA library of Agrobacterium tumefacience RU-AE01. Nucleotide sequence analysis of the region upstream of this gene revealed a fragment of a gene encoding the hydantoinase enzyme. I this study, a DNA probe consisting of the gene encoding the N-carbamoyl amino acid amidohydrolase, on a large enough fragment of the genomic DNA library which would allow for the simultaneous isolation the hydantoinase gene located upstream. Recombinant expression of the genes encoding hydantoin hydrolysing enzymes has been used to facilitate the production and purification of these enzymes for their use as biocatalysts. Two genes (ncaR1 and ncaR2) encoding different N-carbamoyl-amino acid amidohydrolases with distinct nucleotide and deduced amino acid sequences were isolated from the genome of A, tumefaciens RU-OR. In this study, the heterologous expression of ncaR1 and ncaR2 was explored. Investigation into the optimisation of the heterologous expression of ncaR1 showed that reducing the growth temperature of the recombinant E. coli producing NcaR1 resulted in a two-fold increase in N-carbamoyl-amino acid amidohydrolase activity and solubility. Furthermore, NcaR1 was produced with a C-terminal 6xHis tag, but NcaR1-6xHis did not possess N-carbamoyl amino acid amidohydrolase activity. Furthermore, purification of NcaR-6xHis under native conditions using affinity chromatography performed, and used for the production of antibodies.
- Full Text:
- Date Issued: 2003
Judicial enforcement of socio-economic rights under the 1996 constitution : realising the vision of social justice
- Authors: Ngcukaitobi, T
- Date: 2003
- Subjects: South Africa. Constitution , South Africa. Bill of Rights , Civil rights -- South Africa , Human rights -- South Africa , South Africa -- Politics and government -- 1994- , South Africa -- Economic conditions -- 1991- , South Africa -- Social conditions -- 1994-
- Language: English
- Type: Thesis , Masters , LLM
- Identifier: vital:3689 , http://hdl.handle.net/10962/d1003204 , South Africa. Constitution , South Africa. Bill of Rights , Civil rights -- South Africa , Human rights -- South Africa , South Africa -- Politics and government -- 1994- , South Africa -- Economic conditions -- 1991- , South Africa -- Social conditions -- 1994-
- Description: Few legal developments in South Africa and elsewhere in the world in recent times have excited such controversy as the legal recognition of social and economic rights. South Africa has created a special place for itself in world affairs for being one of the countries that recognise socio-economic rights in a justiciable Bill of Rights. Partly this is in response to the appalling levels of poverty prevalent in the country which could potentially destabilise the new democracy. Improvement of the quality of life of every citizen is a crucial step in consolidating the constitutional democracy. The question that will face any court in giving effect to socio-economic rights is: how are these rights to be judicially enforced in a given context? The crux of this thesis lies in the resolution of this question. Firstly this thesis traces the philosophical foundations to the legal recognition of socio-economic rights. It is stated that the recognition of these rights in a justiciable bill of rights requires a conceptually sound understanding of the nature of obligations that these rights place on the state. It is emphasised that it is imperative that access to justice be facilitated to poor and vulnerable members of society for the realisation of the constitutional goal of addressing inequality. Particular concern and priority should in this context be given to women, children and the disabled. The study explores various judicial remedies and makes suggestions on new and innovative constitutional mechanisms for judicial enforcement of these rights. It is concluded that there is an important role to be played by civil society in giving meaningful effect to socio-economic rights.
- Full Text:
- Date Issued: 2003
- Authors: Ngcukaitobi, T
- Date: 2003
- Subjects: South Africa. Constitution , South Africa. Bill of Rights , Civil rights -- South Africa , Human rights -- South Africa , South Africa -- Politics and government -- 1994- , South Africa -- Economic conditions -- 1991- , South Africa -- Social conditions -- 1994-
- Language: English
- Type: Thesis , Masters , LLM
- Identifier: vital:3689 , http://hdl.handle.net/10962/d1003204 , South Africa. Constitution , South Africa. Bill of Rights , Civil rights -- South Africa , Human rights -- South Africa , South Africa -- Politics and government -- 1994- , South Africa -- Economic conditions -- 1991- , South Africa -- Social conditions -- 1994-
- Description: Few legal developments in South Africa and elsewhere in the world in recent times have excited such controversy as the legal recognition of social and economic rights. South Africa has created a special place for itself in world affairs for being one of the countries that recognise socio-economic rights in a justiciable Bill of Rights. Partly this is in response to the appalling levels of poverty prevalent in the country which could potentially destabilise the new democracy. Improvement of the quality of life of every citizen is a crucial step in consolidating the constitutional democracy. The question that will face any court in giving effect to socio-economic rights is: how are these rights to be judicially enforced in a given context? The crux of this thesis lies in the resolution of this question. Firstly this thesis traces the philosophical foundations to the legal recognition of socio-economic rights. It is stated that the recognition of these rights in a justiciable bill of rights requires a conceptually sound understanding of the nature of obligations that these rights place on the state. It is emphasised that it is imperative that access to justice be facilitated to poor and vulnerable members of society for the realisation of the constitutional goal of addressing inequality. Particular concern and priority should in this context be given to women, children and the disabled. The study explores various judicial remedies and makes suggestions on new and innovative constitutional mechanisms for judicial enforcement of these rights. It is concluded that there is an important role to be played by civil society in giving meaningful effect to socio-economic rights.
- Full Text:
- Date Issued: 2003
Language and value : the place of evaluation in linguistic theory
- Authors: Kilpert, Diana Mary
- Date: 2003
- Subjects: Linguistics -- Philosophy Systemic grammar Discourse analysis English language -- Standardization Linguistic analysis (Linguistics) Functionalism (Linguistics) Halliday, M. A. K. (Michael Alexander Kirkwood), 1925- Chomsky, Noam Labov, William Pinker, Steven, 1954- Harris, Roy, 1931-
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:2353 , http://hdl.handle.net/10962/d1002635
- Description: It is a central claim of modern linguistic theory that linguists do not prescribe, but describe language as it is, without pronouncing on correctness or judging one variety better than another. This attempt to exclude evaluation is motivated by a desire to be ' politically correct', which hinders objective analysis of language, and by an ill-advised imitation of the natural sciences, which obstructs the discipline's progress towards becoming a science in its own right. It involves linguists, as users of a valued variety, in self-deception and disingenuousness, distances them from the concerns of the ordinary language user, and betrays a failure to understand the involvement of social values in language, the nature of language itself, and the limits of linguistic science. On a wider scale, linguistics reflects society's devaluing and mechanisation of language. Despite growing concern expressed in the literature, and the incoherence that becomes apparent when linguists attempt to address social problems using a theory that regards language as an autonomous object, newcomers to the discipline continue to be taught that anti-prescriptivism is the natural corollary of a scientific approach to language. This thesis suggests that the way out of these difficulties is to rethink the meaning of ' theory' in linguistics. If we take the reflexivity of language seriously, building on M.A.K. Halliday's notion of 'linguistics as metaphor', we are reminded that a linguistic theory is made of language. Metalanguage must use the experiential and interpersonal meaning-making resources of everyday language. It follows that a linguistic theory cannot escape being evaluative, because evaluation is an inherent part of interpersonal meaning. If we fail to notice our own metalinguistic evaluation, this is because language disguises its evaluative meanings, or perhaps we are just not used to thinking of them as part of the grammar. To achieve clarity about the involvement of value in language, we need to turn our metalanguage back on itself - 'using the grammar to think with about the grammar' . Some ways of doing this are demonstrated here, turning the resources of systemic functional linguistics on linguists' own language. The circularity of this process should be seen not as a drawback but as a salutary reminder that linguistics is an interpretive rather than a discovery process. This knowledge should help us revalue language and make a place for evaluation in linguistic theory, paving the way for a socially responsible and productive linguistics.
- Full Text:
- Date Issued: 2003
- Authors: Kilpert, Diana Mary
- Date: 2003
- Subjects: Linguistics -- Philosophy Systemic grammar Discourse analysis English language -- Standardization Linguistic analysis (Linguistics) Functionalism (Linguistics) Halliday, M. A. K. (Michael Alexander Kirkwood), 1925- Chomsky, Noam Labov, William Pinker, Steven, 1954- Harris, Roy, 1931-
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:2353 , http://hdl.handle.net/10962/d1002635
- Description: It is a central claim of modern linguistic theory that linguists do not prescribe, but describe language as it is, without pronouncing on correctness or judging one variety better than another. This attempt to exclude evaluation is motivated by a desire to be ' politically correct', which hinders objective analysis of language, and by an ill-advised imitation of the natural sciences, which obstructs the discipline's progress towards becoming a science in its own right. It involves linguists, as users of a valued variety, in self-deception and disingenuousness, distances them from the concerns of the ordinary language user, and betrays a failure to understand the involvement of social values in language, the nature of language itself, and the limits of linguistic science. On a wider scale, linguistics reflects society's devaluing and mechanisation of language. Despite growing concern expressed in the literature, and the incoherence that becomes apparent when linguists attempt to address social problems using a theory that regards language as an autonomous object, newcomers to the discipline continue to be taught that anti-prescriptivism is the natural corollary of a scientific approach to language. This thesis suggests that the way out of these difficulties is to rethink the meaning of ' theory' in linguistics. If we take the reflexivity of language seriously, building on M.A.K. Halliday's notion of 'linguistics as metaphor', we are reminded that a linguistic theory is made of language. Metalanguage must use the experiential and interpersonal meaning-making resources of everyday language. It follows that a linguistic theory cannot escape being evaluative, because evaluation is an inherent part of interpersonal meaning. If we fail to notice our own metalinguistic evaluation, this is because language disguises its evaluative meanings, or perhaps we are just not used to thinking of them as part of the grammar. To achieve clarity about the involvement of value in language, we need to turn our metalanguage back on itself - 'using the grammar to think with about the grammar' . Some ways of doing this are demonstrated here, turning the resources of systemic functional linguistics on linguists' own language. The circularity of this process should be seen not as a drawback but as a salutary reminder that linguistics is an interpretive rather than a discovery process. This knowledge should help us revalue language and make a place for evaluation in linguistic theory, paving the way for a socially responsible and productive linguistics.
- Full Text:
- Date Issued: 2003
Locating the institution of traditional leadership within the institutional framework of South Africa's new democracy
- Authors: Mashele, Hlukanisa Prince
- Date: 2003
- Subjects: Tribal government -- South Africa , Political leadership -- South Africa , South Africa -- Politics and government -- 1994-
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:2858 , http://hdl.handle.net/10962/d1007512 , Tribal government -- South Africa , Political leadership -- South Africa , South Africa -- Politics and government -- 1994-
- Description: This study looks into the role of the institution of traditional leadership in post-apartheid South Africa. It seeks to critically engage the debate on how to locate the institution within the new politico-constitutional framework. This is done with the main objective of proposing an altemative to the current state of affairs vis-à-vis traditional leadership and governance in South Africa. In order to clear the ground, the study first deals with the important question of democracy in relation to the institution of traditional leadership. In this regard, the study unearthed that the institution of traditional leadership is fundamentally undemocratic in character, as it is largely based on heredity and devoid of principles of democracy such as equality, accountability, etc. In order to put matters into perspective the study also delves into the history of the institution of traditional leadership with the aim of getting to the role that traditional leaders played in various epochs of South Africa's political development. This investigation reveals that the denting of the integrity of the institution of traditional leadership began with the advent of colonialism and worsened by successive apartheid regimes. It is at these stages of development that the institution was subordinated to a higher authority that sought to use the institution as an instrument of domination and oppression of the black majority. Considering this role, it would seem that the place that the space that the institution occupies in the post-apartheid South African governance framework is a compromise. The institution plays an advisory role at all levels of government - with their houses in both national and provincial legislatures, whilst traditional leaders sit as ex-officio members on local councils. However, traditional leaders fiercely contest this position as, in their view, this limits their powers. The main argument of this study is that for traditional leaders to be given an advisory role in the current and future governance framework of the country is a step in the right direction, as that serves to insulate the institution from active politics. For that reason, the study recommends that the institution of traditional leadership should occupy a cultural space in society - meaning that it should be responsible for the preservation of African customs and culture. This, therefore, means that the institution is better-placed to advise government on cultural and customary aspects of development. Whilst playing this role, the institution of traditional leadership should also -be brought into line with democratic ways of governance.
- Full Text:
- Date Issued: 2003
- Authors: Mashele, Hlukanisa Prince
- Date: 2003
- Subjects: Tribal government -- South Africa , Political leadership -- South Africa , South Africa -- Politics and government -- 1994-
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:2858 , http://hdl.handle.net/10962/d1007512 , Tribal government -- South Africa , Political leadership -- South Africa , South Africa -- Politics and government -- 1994-
- Description: This study looks into the role of the institution of traditional leadership in post-apartheid South Africa. It seeks to critically engage the debate on how to locate the institution within the new politico-constitutional framework. This is done with the main objective of proposing an altemative to the current state of affairs vis-à-vis traditional leadership and governance in South Africa. In order to clear the ground, the study first deals with the important question of democracy in relation to the institution of traditional leadership. In this regard, the study unearthed that the institution of traditional leadership is fundamentally undemocratic in character, as it is largely based on heredity and devoid of principles of democracy such as equality, accountability, etc. In order to put matters into perspective the study also delves into the history of the institution of traditional leadership with the aim of getting to the role that traditional leaders played in various epochs of South Africa's political development. This investigation reveals that the denting of the integrity of the institution of traditional leadership began with the advent of colonialism and worsened by successive apartheid regimes. It is at these stages of development that the institution was subordinated to a higher authority that sought to use the institution as an instrument of domination and oppression of the black majority. Considering this role, it would seem that the place that the space that the institution occupies in the post-apartheid South African governance framework is a compromise. The institution plays an advisory role at all levels of government - with their houses in both national and provincial legislatures, whilst traditional leaders sit as ex-officio members on local councils. However, traditional leaders fiercely contest this position as, in their view, this limits their powers. The main argument of this study is that for traditional leaders to be given an advisory role in the current and future governance framework of the country is a step in the right direction, as that serves to insulate the institution from active politics. For that reason, the study recommends that the institution of traditional leadership should occupy a cultural space in society - meaning that it should be responsible for the preservation of African customs and culture. This, therefore, means that the institution is better-placed to advise government on cultural and customary aspects of development. Whilst playing this role, the institution of traditional leadership should also -be brought into line with democratic ways of governance.
- Full Text:
- Date Issued: 2003
Media and parliament in the Third Republic: a study of newspaper coverage of parliament by the Times of Zambia and the Post from January to November 2001
- Authors: Djokotoe-Gliguie, Edem K
- Date: 2003
- Subjects: Newspapers -- Zambia Mass media -- Political aspects -- Zambia Zambia -- Politics and government
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:3515 , http://hdl.handle.net/10962/d1007796
- Description: The press is credited with playing a central role in the consolidation of democracy by informing citizens, engaging them in the process of public decision making and governance and stimulating wide and inclusive debate on public matters. In emergent democracies like Zambia, the extent of the media's role as a public sphere, not to mention its impact, is not known. The study set out to investigate the extent of the press' public sphere role, particularly how Zambian newspapers report Parliament and how such coverage informs public opinion. It found that though the press covers Parliament, the nature of coverage does not empower newspaper readers with the kind of context, background and interpretation they would otherwise need to engage in public discourses on matters that affect them from an informed perspective. In the main, the role of the press in informing citizens is not fully realised, not only because uninformative character of coverage, but partly because of low literacy levels and the limited reach of local newspapers. It was against this background that the study recommended ways in which the Zambian press could re-focus its approach to parliamentary news coverage to make it more informational and more inclined towards playing a public sphere role, at least to the newspaper-reading public. Making parliamentary coverage an integrated newsroom function was the main recommendation. It provided the basis for suggesting a practical editorial option for the coverage of the legislature that accommodates the integration of context, background and interpretation into parliamentary news.
- Full Text:
- Date Issued: 2003
- Authors: Djokotoe-Gliguie, Edem K
- Date: 2003
- Subjects: Newspapers -- Zambia Mass media -- Political aspects -- Zambia Zambia -- Politics and government
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:3515 , http://hdl.handle.net/10962/d1007796
- Description: The press is credited with playing a central role in the consolidation of democracy by informing citizens, engaging them in the process of public decision making and governance and stimulating wide and inclusive debate on public matters. In emergent democracies like Zambia, the extent of the media's role as a public sphere, not to mention its impact, is not known. The study set out to investigate the extent of the press' public sphere role, particularly how Zambian newspapers report Parliament and how such coverage informs public opinion. It found that though the press covers Parliament, the nature of coverage does not empower newspaper readers with the kind of context, background and interpretation they would otherwise need to engage in public discourses on matters that affect them from an informed perspective. In the main, the role of the press in informing citizens is not fully realised, not only because uninformative character of coverage, but partly because of low literacy levels and the limited reach of local newspapers. It was against this background that the study recommended ways in which the Zambian press could re-focus its approach to parliamentary news coverage to make it more informational and more inclined towards playing a public sphere role, at least to the newspaper-reading public. Making parliamentary coverage an integrated newsroom function was the main recommendation. It provided the basis for suggesting a practical editorial option for the coverage of the legislature that accommodates the integration of context, background and interpretation into parliamentary news.
- Full Text:
- Date Issued: 2003
Mesozooplankton community structure and grazing impact in the polar frontal zone of the Southern Ocean
- Authors: Bernard, Kim Sarah
- Date: 2003
- Subjects: Zooplankton -- Antarctic Ocean , Copepoda -- Feeding and feeds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5731 , http://hdl.handle.net/10962/d1005417 , Zooplankton -- Antarctic Ocean , Copepoda -- Feeding and feeds
- Description: Mesozooplankton community structure and grazing impact in the Polar Frontal Zone (PFZ) of the Southern Ocean were investigated during two cruises of the South African National Antarctic Programme (SANAP), the Marion Offshore Ecosystem Variability Study I & II (MOEVS). During the first cruise (MOEVS I), a meso-scale oceanographic grid survey was conducted in the upstream region of the Prince Edward Islands (PEI) in austral autumn (April) 2001. Mesozooplankton samples, collected using a Bongo net (fitted with 200 and 300µm mesh nets) at depths between 200 and 300 m, were separated into three size fractions: 200-500 µm; 500-1000 µm; 1000-2000 µm by reverse filtration. Total surface (depth <5 m) chlorophyll-a (chl-a) concentration (measured fluorometrically) during the study ranged between 0.11 and 0.34 µg 1^(-1) and was always dominated by picophytoplankton (<2.0 µm). Total mesozooplankton abundance and biomass during the survey ranged between 49 and 1512 ind. m^(-3) and between 0.7 and 25 mg Dwt. m^(-3), respectively. Throughout the survey, the 200-500 µm class numerically dominated the mesozooplankton community, comprising an average of ~ 69% (SD = ± 12.3%). The dominant species in the 200-500 µm size fraction were the copepods Oithona similis, Calanus simillimus and Metridia lucens and the pteropod, Limacina retroversa. However, in terms of biomass, the 1000-2000 µm group was predominant, with dry weight values constituting an average of ~ 66% (SD = ± 10.2%). Biomass was dominated by carnivorous zooplankton, particularly the euphausiids, Euphausia vallentini and Thysanoessa vicina and the chaetognaths, Sagitta gazellae and Eukrohnia hamata. Three distinct groupings of stations were identified by multivariate analysis. The different station groupings identified reflect changes in the relative contributions of the rather than different species assemblages. During the second cruise (MOEVS II), conducted in April 2002 (austral autumn), mesozooplankton community structure and grazing impact were investigated at 13 stations in the west Indian sector of the PFZ. Total integrated chl-a biomass ranged between 11.17 and 28.34 mg chl-a m^(-2) and was always dominated by nano- and picophytoplankton (<20 µm). Throughout the study, small copepods, mainly Oithona similis and Ctenocalanus vanus, numerically dominated the mesozooplankton community comprising up to 85% (range 30 to 85%) of the total abundance. Grazing activity of the four most abundant copepods (O. similis, C. vanus, Calanus simillimus and Clausocalanus spp.), which comprised up to 93% of total mesozooplankton abundance, was investigated using the gut fluorescent technique. Results of gut fluorescence analyses indicated that C. simillimus, Clausocalanus spp. and Ctenocalanus vanus exhibited diel variability in gut pigments, with maximum values at various stages of the night. In contrast, O. similis did not demonstrate diel variation in gut pigment contents. Ingestion rates of the four copepods ranged from 23.23 to 1462.02 ng (pigm.) ind^(-1) day^(-1), depending on the species. The combined grazing impact of the four copepods, ranged between 1 and 36% of the phytoplankton standing stock per day, with the highest daily impact (~ 35.86%) occurring at stations in the vicinity of the Antarctic Polar Front. Among the copepods, O. similis and C. vanus were generally the most important consumers of phytoplankton biomass; together they were responsible for up to 89% (range 15 to 89%) of the total daily grazing impact. Carbon specific ingestion rates of the copepods varied between 42 and 320% body carbon per day, depending on the species. The study highlights the importance of small copepods in terms of both their significant contribution to total mesozooplankton numbers and their grazing impact on the phytoplankton standing stocks in the PFZ during austral autumn.
- Full Text:
- Date Issued: 2003
- Authors: Bernard, Kim Sarah
- Date: 2003
- Subjects: Zooplankton -- Antarctic Ocean , Copepoda -- Feeding and feeds
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5731 , http://hdl.handle.net/10962/d1005417 , Zooplankton -- Antarctic Ocean , Copepoda -- Feeding and feeds
- Description: Mesozooplankton community structure and grazing impact in the Polar Frontal Zone (PFZ) of the Southern Ocean were investigated during two cruises of the South African National Antarctic Programme (SANAP), the Marion Offshore Ecosystem Variability Study I & II (MOEVS). During the first cruise (MOEVS I), a meso-scale oceanographic grid survey was conducted in the upstream region of the Prince Edward Islands (PEI) in austral autumn (April) 2001. Mesozooplankton samples, collected using a Bongo net (fitted with 200 and 300µm mesh nets) at depths between 200 and 300 m, were separated into three size fractions: 200-500 µm; 500-1000 µm; 1000-2000 µm by reverse filtration. Total surface (depth <5 m) chlorophyll-a (chl-a) concentration (measured fluorometrically) during the study ranged between 0.11 and 0.34 µg 1^(-1) and was always dominated by picophytoplankton (<2.0 µm). Total mesozooplankton abundance and biomass during the survey ranged between 49 and 1512 ind. m^(-3) and between 0.7 and 25 mg Dwt. m^(-3), respectively. Throughout the survey, the 200-500 µm class numerically dominated the mesozooplankton community, comprising an average of ~ 69% (SD = ± 12.3%). The dominant species in the 200-500 µm size fraction were the copepods Oithona similis, Calanus simillimus and Metridia lucens and the pteropod, Limacina retroversa. However, in terms of biomass, the 1000-2000 µm group was predominant, with dry weight values constituting an average of ~ 66% (SD = ± 10.2%). Biomass was dominated by carnivorous zooplankton, particularly the euphausiids, Euphausia vallentini and Thysanoessa vicina and the chaetognaths, Sagitta gazellae and Eukrohnia hamata. Three distinct groupings of stations were identified by multivariate analysis. The different station groupings identified reflect changes in the relative contributions of the rather than different species assemblages. During the second cruise (MOEVS II), conducted in April 2002 (austral autumn), mesozooplankton community structure and grazing impact were investigated at 13 stations in the west Indian sector of the PFZ. Total integrated chl-a biomass ranged between 11.17 and 28.34 mg chl-a m^(-2) and was always dominated by nano- and picophytoplankton (<20 µm). Throughout the study, small copepods, mainly Oithona similis and Ctenocalanus vanus, numerically dominated the mesozooplankton community comprising up to 85% (range 30 to 85%) of the total abundance. Grazing activity of the four most abundant copepods (O. similis, C. vanus, Calanus simillimus and Clausocalanus spp.), which comprised up to 93% of total mesozooplankton abundance, was investigated using the gut fluorescent technique. Results of gut fluorescence analyses indicated that C. simillimus, Clausocalanus spp. and Ctenocalanus vanus exhibited diel variability in gut pigments, with maximum values at various stages of the night. In contrast, O. similis did not demonstrate diel variation in gut pigment contents. Ingestion rates of the four copepods ranged from 23.23 to 1462.02 ng (pigm.) ind^(-1) day^(-1), depending on the species. The combined grazing impact of the four copepods, ranged between 1 and 36% of the phytoplankton standing stock per day, with the highest daily impact (~ 35.86%) occurring at stations in the vicinity of the Antarctic Polar Front. Among the copepods, O. similis and C. vanus were generally the most important consumers of phytoplankton biomass; together they were responsible for up to 89% (range 15 to 89%) of the total daily grazing impact. Carbon specific ingestion rates of the copepods varied between 42 and 320% body carbon per day, depending on the species. The study highlights the importance of small copepods in terms of both their significant contribution to total mesozooplankton numbers and their grazing impact on the phytoplankton standing stocks in the PFZ during austral autumn.
- Full Text:
- Date Issued: 2003
Metal interactions with neural substrates and their role in neurodegeneration
- Authors: Lack, Barbara Anne
- Date: 2003
- Subjects: Nervous system -- Degeneration Neurotoxicology Chemical reactions Metals -- Physiological effect Melatonin -- Physiological effect
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4391 , http://hdl.handle.net/10962/d1005709
- Description: "Life" may be characterized as a controlled stationary flow equilibrium, maintained by energy consuming chemical reactions. The physiological functioning of these life systems include at least 28 of the elements isolated on the periodic table thus far, most of which are metals. However, as with Paracelsus Principle: "The dose makes the poison", there exists a definite link between metal levels, essential and toxic, and the onset of neurodegenerative diseases. The economic costs of brain dysfunction are enormous, but this pales in comparison to the staggering emotional toll on the victims themselves and their families. In an attempt to improve the understanding of the causes of neurodegeneration, this study focuses on one potential aspect: the possible link between metals and neurotransmitter homeostasis utilising a variety of electronanalytical techniques. Adsorptive cathodic stripping voltammetry was employed to investigate the binding affinities and complex formation of melatonin and its precursor serotonin with calcium, potassium, sodium, lithium and aluminium. The results showed that all the metals studied formed complexes with both pineal indoleamines. However, the stability and affmity of the ligands toward the various metals varied greatly. The study suggests a further role for melatonin, that of metalloregulator and possible metal detoxifier in the brain, the in vivo studies which followed will further substantiate this notion. This research additionally focused on the cholinergic system, in particular acetylcholine complex formation studies with mercury, lead, cadmium, copper and zinc using the adsorptive cathodic stripping voltammetry method. The formation and characterisation of a solid mercury-acetylcholine complex lent further strength to the in situ electrochemical complex formation observed. The results showed the preference of acetylcholine for environmentally toxic heavy metals (such as Cd²⁺) over those divalent cations that occur naturally in the body. The possible metalloregulatory role melatonin played in the three brain regIOns: cerebellum, cortex and corpus striatum of male Wistar rats was studied as an in vivo extension of the earlier in vitro studies. Anodic stripping voltammetry was employed to detect metal levels present. The results showed that daily injections of melatonin was responsible for significantly decreasing copper(I), cadmium(II) and lead(II) levels in various regions of the rat brain of those animals that had undergone a pinealectomy in comparison to the saline injected group having undergone the same treatment. Histological and electrochemical stripping techniques were applied to investigate the implications of high A1³⁺ levels in the brain regions, particularly the hippocampus. Melatonin showed signs of promise in indirect symptom alleviation and by significantly decreasing A1³⁺ levels in rats that had been dosed with melatonin prior to A1³⁺ treatments in comparison with the control groups. Finally a preliminary study outlining a method for the production of a calcium selective microelectrode was undertaken. Further work is still needed to optimise the microelectrode production as well as its possible applications. However, whilst the overall conclusions of this entire multidisciplinary study may indeed only be in effect one piece of a very large puzzle on neurodegenerative diseases, this piece will no doubt serve as a building block for further ideas and work in this field.
- Full Text:
- Date Issued: 2003
- Authors: Lack, Barbara Anne
- Date: 2003
- Subjects: Nervous system -- Degeneration Neurotoxicology Chemical reactions Metals -- Physiological effect Melatonin -- Physiological effect
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4391 , http://hdl.handle.net/10962/d1005709
- Description: "Life" may be characterized as a controlled stationary flow equilibrium, maintained by energy consuming chemical reactions. The physiological functioning of these life systems include at least 28 of the elements isolated on the periodic table thus far, most of which are metals. However, as with Paracelsus Principle: "The dose makes the poison", there exists a definite link between metal levels, essential and toxic, and the onset of neurodegenerative diseases. The economic costs of brain dysfunction are enormous, but this pales in comparison to the staggering emotional toll on the victims themselves and their families. In an attempt to improve the understanding of the causes of neurodegeneration, this study focuses on one potential aspect: the possible link between metals and neurotransmitter homeostasis utilising a variety of electronanalytical techniques. Adsorptive cathodic stripping voltammetry was employed to investigate the binding affinities and complex formation of melatonin and its precursor serotonin with calcium, potassium, sodium, lithium and aluminium. The results showed that all the metals studied formed complexes with both pineal indoleamines. However, the stability and affmity of the ligands toward the various metals varied greatly. The study suggests a further role for melatonin, that of metalloregulator and possible metal detoxifier in the brain, the in vivo studies which followed will further substantiate this notion. This research additionally focused on the cholinergic system, in particular acetylcholine complex formation studies with mercury, lead, cadmium, copper and zinc using the adsorptive cathodic stripping voltammetry method. The formation and characterisation of a solid mercury-acetylcholine complex lent further strength to the in situ electrochemical complex formation observed. The results showed the preference of acetylcholine for environmentally toxic heavy metals (such as Cd²⁺) over those divalent cations that occur naturally in the body. The possible metalloregulatory role melatonin played in the three brain regIOns: cerebellum, cortex and corpus striatum of male Wistar rats was studied as an in vivo extension of the earlier in vitro studies. Anodic stripping voltammetry was employed to detect metal levels present. The results showed that daily injections of melatonin was responsible for significantly decreasing copper(I), cadmium(II) and lead(II) levels in various regions of the rat brain of those animals that had undergone a pinealectomy in comparison to the saline injected group having undergone the same treatment. Histological and electrochemical stripping techniques were applied to investigate the implications of high A1³⁺ levels in the brain regions, particularly the hippocampus. Melatonin showed signs of promise in indirect symptom alleviation and by significantly decreasing A1³⁺ levels in rats that had been dosed with melatonin prior to A1³⁺ treatments in comparison with the control groups. Finally a preliminary study outlining a method for the production of a calcium selective microelectrode was undertaken. Further work is still needed to optimise the microelectrode production as well as its possible applications. However, whilst the overall conclusions of this entire multidisciplinary study may indeed only be in effect one piece of a very large puzzle on neurodegenerative diseases, this piece will no doubt serve as a building block for further ideas and work in this field.
- Full Text:
- Date Issued: 2003
Metallophthalocyanine derivatives as catalysts for the detection of sulphur dioxide, cyanide, nitrite and amino acids
- Authors: Thamae, Mamothibe Amelia
- Date: 2003
- Subjects: Cyanides Nitric oxide Electrochemistry Nitrites Suplhur dioxide Amino acids
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4295 , http://hdl.handle.net/10962/d1004542
- Description: Electrocatalytic reduction and oxidation of nitrite using cobalt phthalocyanine derivatives was studied. The detection limit of 1 x 10⁻¹° mol dm⁻³ was achieved when these molecules were employed as catalysts for nitrite detection. The mechanisms for nitrite catalysis were proposed. The position of the peripheral substituents on cobalt porphyrazines (related to cobalt phthalocyanines) affected the catalytic activity of these complexes. The highest activity for nitrite reduction was observed on the cobalt(II) 2,3-tetramethyltetrapyridinoporphyrazine ([CoTm-2,3-tppa]⁴⁺), with cobalt phthalocyanine showing the lowest activity, and the cobalt(II) 3,4- tetramethyltetrapyridinoporphyrazine ([CoTm-3,4-tppa]⁴⁺), showing intermediate behaviour. A mixture of a negatively charged cobalt(II) tetrasulfophthalocyanine ([Co¹¹TSPc]⁴⁻) and a positively charged [CoTm-3,4-tppa]⁴⁺ showed better activity for nitrite reduction than did the individual components. Cobalt porphyrazines lowered the potentials for nitrite reduction in that peaking was observed, as opposed to cobalt phthalocyanine, where only the increase in currents was observed without peaking. Using the cobalt phthalocyanine derivatives, nitrite can be reduced to ammonia with high current efficiency. A glassy carbon electrode modified with [Co¹¹TSPc]⁴⁻ was employed for the determination of nitrite. Nitrate had an insignificant effect on nitrite oxidation on these modified electrodes. Electrocatalytic determination of S0₂ was studied as a function of pH at a glassy carbon electrode modified with iron(II) tetrasulfophthalocaynine. It was found that depending on pH, S0₂.xH₂0, HS0₃⁻ and/or SO₃²⁻ are the main compounds in solution and that these compounds behave differently at the electrode surface. Detection limits ranging from 4.0 ± 0.1 x 10⁻⁵ to 7.5 ± 0.1 x 10⁻⁵ mol dm⁻³ depending on pH were observed. Similar results were obtained when cobalt(II) tetrasulfophthalocaynine was employed for S0₂ catalysis under the same experimental conditions. Cysteine and histidine determination using oxidation currents was performed on glassy carbon electrodes modified with [CoTm-3,4-tppa]⁴⁺ (represented as [CoTm-3,4-tppa]⁴⁺-GCE) in pH 7 Tris buffer. The detection limit of 1.0 x 10⁻⁵ mol dm⁻³ for cysteine and 2.24 x 10⁻⁷ mol dm⁻³ for histidine were obtained. Cyanide can be detected down to 1 x 10⁻¹¹ mol dm⁻³ using [CoTm-3,4-tppa]⁴⁺-GCE in pH 10.8 buffer. Cyanide and S0₂ coordinate to the [CoTSPc]⁴⁻ species. The coordination is accompanied by oxidation of the central Co(II) metal, forming a [Co¹¹¹CoTSPc]³⁻ species. The rate constants for cyanide coordination to the [Co¹¹TSPc]⁴⁻ complex are larger than those reported for the coordination of cyanide to FePc and RuPc complexes in non-aqueous media. Autoreduction of [Co¹¹Tmtppa]⁴⁺ occurred in the presence of either histidine or cysteine, with the formation of metal reduced species, [Co¹Tmtppa(-2)]³⁺. Nitric oxide and nitrite coordinate to the [Co¹¹Tmtppa]⁴⁺ species, without auto-reduction of this species, which was observed for cysteine or histidine. The use of [Co¹¹TSPc]⁴ resulted in improved rate of interaction with nitrite when compared to the [Co¹¹Tmtppa]⁴⁺ species.
- Full Text:
- Date Issued: 2003
- Authors: Thamae, Mamothibe Amelia
- Date: 2003
- Subjects: Cyanides Nitric oxide Electrochemistry Nitrites Suplhur dioxide Amino acids
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4295 , http://hdl.handle.net/10962/d1004542
- Description: Electrocatalytic reduction and oxidation of nitrite using cobalt phthalocyanine derivatives was studied. The detection limit of 1 x 10⁻¹° mol dm⁻³ was achieved when these molecules were employed as catalysts for nitrite detection. The mechanisms for nitrite catalysis were proposed. The position of the peripheral substituents on cobalt porphyrazines (related to cobalt phthalocyanines) affected the catalytic activity of these complexes. The highest activity for nitrite reduction was observed on the cobalt(II) 2,3-tetramethyltetrapyridinoporphyrazine ([CoTm-2,3-tppa]⁴⁺), with cobalt phthalocyanine showing the lowest activity, and the cobalt(II) 3,4- tetramethyltetrapyridinoporphyrazine ([CoTm-3,4-tppa]⁴⁺), showing intermediate behaviour. A mixture of a negatively charged cobalt(II) tetrasulfophthalocyanine ([Co¹¹TSPc]⁴⁻) and a positively charged [CoTm-3,4-tppa]⁴⁺ showed better activity for nitrite reduction than did the individual components. Cobalt porphyrazines lowered the potentials for nitrite reduction in that peaking was observed, as opposed to cobalt phthalocyanine, where only the increase in currents was observed without peaking. Using the cobalt phthalocyanine derivatives, nitrite can be reduced to ammonia with high current efficiency. A glassy carbon electrode modified with [Co¹¹TSPc]⁴⁻ was employed for the determination of nitrite. Nitrate had an insignificant effect on nitrite oxidation on these modified electrodes. Electrocatalytic determination of S0₂ was studied as a function of pH at a glassy carbon electrode modified with iron(II) tetrasulfophthalocaynine. It was found that depending on pH, S0₂.xH₂0, HS0₃⁻ and/or SO₃²⁻ are the main compounds in solution and that these compounds behave differently at the electrode surface. Detection limits ranging from 4.0 ± 0.1 x 10⁻⁵ to 7.5 ± 0.1 x 10⁻⁵ mol dm⁻³ depending on pH were observed. Similar results were obtained when cobalt(II) tetrasulfophthalocaynine was employed for S0₂ catalysis under the same experimental conditions. Cysteine and histidine determination using oxidation currents was performed on glassy carbon electrodes modified with [CoTm-3,4-tppa]⁴⁺ (represented as [CoTm-3,4-tppa]⁴⁺-GCE) in pH 7 Tris buffer. The detection limit of 1.0 x 10⁻⁵ mol dm⁻³ for cysteine and 2.24 x 10⁻⁷ mol dm⁻³ for histidine were obtained. Cyanide can be detected down to 1 x 10⁻¹¹ mol dm⁻³ using [CoTm-3,4-tppa]⁴⁺-GCE in pH 10.8 buffer. Cyanide and S0₂ coordinate to the [CoTSPc]⁴⁻ species. The coordination is accompanied by oxidation of the central Co(II) metal, forming a [Co¹¹¹CoTSPc]³⁻ species. The rate constants for cyanide coordination to the [Co¹¹TSPc]⁴⁻ complex are larger than those reported for the coordination of cyanide to FePc and RuPc complexes in non-aqueous media. Autoreduction of [Co¹¹Tmtppa]⁴⁺ occurred in the presence of either histidine or cysteine, with the formation of metal reduced species, [Co¹Tmtppa(-2)]³⁺. Nitric oxide and nitrite coordinate to the [Co¹¹Tmtppa]⁴⁺ species, without auto-reduction of this species, which was observed for cysteine or histidine. The use of [Co¹¹TSPc]⁴ resulted in improved rate of interaction with nitrite when compared to the [Co¹¹Tmtppa]⁴⁺ species.
- Full Text:
- Date Issued: 2003
Metallophthalocyanines as photocatalysts for transformation of chlorophenols and self-assembled monolayers for electrochemical detection of thiols and cyanides
- Authors: Ozoemena, Kenneth Ikechukwu
- Date: 2003
- Subjects: Electrochemistry Cyanides Thiols Chlorophenols Photocatalysis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4089 , http://hdl.handle.net/10962/d1007709
- Description: Photochemical properties of sulphonated phthalocyanine complexes of aluminium, zinc, tin and silicon, and octa-carboxyphthalocyanine complexes of aluminium and zinc have been investigated. These water-soluble metallophthalocyanine (MPc) complexes, especially the sulphonated aluminium and zinc phthalocyanines, were found to be good photosensitisers for the transformation of the toxic mono-, tri- and penta-chlorophenols in aqueous solutions. The efficiency of MPc sensitiser towards photo-transformation of chlorophenols depends on its effectiveness to generate singlet oxygen as well as its photostability. Octa-substituted thiol-derivatised phthalocyanine complexes of cobalt, iron and zinc were synthesized and their spectral and electrochemical properties investigated. The photochemical properties ofthe zinc phthalocyanine complexes in non-aqueous solutions were comparable to those in literature. Ultrathin films of the octasubstituted thiol-derivatised phthalocyanine complexes of cobalt, iron and zinc were, for the first time, immobilized onto gold electrodes using the self-assembling technique. Surface electrochemistry indicates that the ultrathin films are surface-confined self-assembled monolayer (SAM) species. Gold electrodes modified with the redox-active SAMs of cobalt and iron phthalocyanine complexes proved to be potential electrochemical sensors for the detection of thiols (L-cysteine, homocysteine and penicillamine) and thiocyanate in aqueous solutions (pH 4). The limits of detection for the thiols and thiocyanate were in the range of ∼ 10⁻⁷ and 10⁻⁶ mol dm⁻³, respectively. The modification process was reproducible and the modified electrodes showed good stability and, if stored in pH 4 buffer solutions, could be used for the analysis of thiols and thiocyanate for about a month without the need for recalibration. Etching of gold marred electrochemical detection of cyanide with the MPc-SAM-modified gold electrodes. Interestingly, however, kinetic and equilibria studies revealed strong interaction of octabutylthiophthalocyaninatoiron (II), FeOBTPc, with cyanide in both DMF and DMSO solutions.
- Full Text:
- Date Issued: 2003
- Authors: Ozoemena, Kenneth Ikechukwu
- Date: 2003
- Subjects: Electrochemistry Cyanides Thiols Chlorophenols Photocatalysis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4089 , http://hdl.handle.net/10962/d1007709
- Description: Photochemical properties of sulphonated phthalocyanine complexes of aluminium, zinc, tin and silicon, and octa-carboxyphthalocyanine complexes of aluminium and zinc have been investigated. These water-soluble metallophthalocyanine (MPc) complexes, especially the sulphonated aluminium and zinc phthalocyanines, were found to be good photosensitisers for the transformation of the toxic mono-, tri- and penta-chlorophenols in aqueous solutions. The efficiency of MPc sensitiser towards photo-transformation of chlorophenols depends on its effectiveness to generate singlet oxygen as well as its photostability. Octa-substituted thiol-derivatised phthalocyanine complexes of cobalt, iron and zinc were synthesized and their spectral and electrochemical properties investigated. The photochemical properties ofthe zinc phthalocyanine complexes in non-aqueous solutions were comparable to those in literature. Ultrathin films of the octasubstituted thiol-derivatised phthalocyanine complexes of cobalt, iron and zinc were, for the first time, immobilized onto gold electrodes using the self-assembling technique. Surface electrochemistry indicates that the ultrathin films are surface-confined self-assembled monolayer (SAM) species. Gold electrodes modified with the redox-active SAMs of cobalt and iron phthalocyanine complexes proved to be potential electrochemical sensors for the detection of thiols (L-cysteine, homocysteine and penicillamine) and thiocyanate in aqueous solutions (pH 4). The limits of detection for the thiols and thiocyanate were in the range of ∼ 10⁻⁷ and 10⁻⁶ mol dm⁻³, respectively. The modification process was reproducible and the modified electrodes showed good stability and, if stored in pH 4 buffer solutions, could be used for the analysis of thiols and thiocyanate for about a month without the need for recalibration. Etching of gold marred electrochemical detection of cyanide with the MPc-SAM-modified gold electrodes. Interestingly, however, kinetic and equilibria studies revealed strong interaction of octabutylthiophthalocyaninatoiron (II), FeOBTPc, with cyanide in both DMF and DMSO solutions.
- Full Text:
- Date Issued: 2003
Molecular characterization of the tetratricopeptide repeat-mediated interactions of murine stress-inducible protein 1 with major heat shock proteins
- Authors: Odunuga, Odutayo Odutola
- Date: 2003
- Subjects: Plants -- Effect of stress on Proteins -- Purification Electrophoresis Heat shock proteins
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4091 , http://hdl.handle.net/10962/d1007724
- Description: Murine stress-inducible protein 1 (mSTI1) is a co-chaperone that is homologous with the human heat shock protein 70 (Hsp70)/heat shock protein 90 (Hsp90)-organizing protein (Hop). The two proteins are homologues of the highly conserved stress-inducible protein 1 (STI1) family of co-chaperones. The STI1 proteins interact directly and simultaneously at some stage, with Hsp70 and Hsp90 in the formation of the hetero-multi-chaperone complexes that facilitate the folding of signal transducing kinases and functional maturation of steroid hormone receptors. The interactions of mSTI1 with both Hsp70 and Hsp90 is mediated by a versatile structural protein-protein interaction motif, the tetratricopeptide repeat (TPR). The TPR motif is a degenerate 34-amino acid sequence a-helical structural motif found in a significant number of functionally unrelated proteins. This study was aimed at characterizing the structural and functional determinants in the TPR domains of mSTI1 responsible for binding to and discriminating between Hsp70 and Hsp90. Guided by data from Hop's crystal structures and amino acid sequence alignment analyses, various biochemical techniques were used to both qualitatively and quantitatively characterize the contacts necessary for the N-terminal TPR domain (TPR1) of mSTI1 to bind to the C-terminal EEVD motif of heat shock cognate protein 70 (Hsc70) and to discriminate between Hsc70 and Hsp90. Substitutions in the first TPR motif of Lys⁸ or Asn¹² did not affect binding of mSTI1 to Hsc70, while double substitution of these residues abrogated binding. A substitution in the second TPR motif of Asn⁴³ lowered but did not abrogate binding. Similarly, a deletion in the second TPR motif coupled with a substitution of Lys⁸ or Asn¹² reduced but did not abrogate binding. Steady state fluorescence and circular dichroism spectroscopies revealed that the double substitution of Lys⁸ and Asn¹² resulted in perturbations of inter-domain interactions in mSTl1. Together these results suggest that mSTI1-Hsc70 interaction requires a network of electrostatic interactions not only between charged residues in the TPR1 domain of mSTI1 and the EEVD motif of Hsc70, but also outside the TPR1 domain. It is proposed that the electrostatic interactions in the first TPR motif collectively made by Lys⁸ and Asn¹² define part of the minimum interactions required for successful mSTI1-Hsc70 interaction. In the first central TPR domain (TPR1A), single substitution of Lys³°¹ was sufficient to abrogate the mSTI1-Hsp90 interaction. Using a truncated derivative of mSTI1 incapable of binding to Hsp90, residues predicted by crystallographic data to determine Hsp70 binding specificity were substituted in the TPR1 domain. The modified protein had reduced binding to Hsc70, but showed significant binding capacity for Hsp90. In contrast, topologically equivalent substitutions on a truncated derivative of mSTI1 incapable of binding to Hsc70 did not confer Hsc70 specificity on the TPR2A domain. These data suggest that binding of Hsc70 to the TPR1 domain is more specific than binding of Hsp90 to the TPR2A domain. In addition, residues C-terminal of helix A in the second TPR motif of mSTI1 were shown to be important in determining specific binding to Hsc70. Binding assays using surface plasmon resonance spectroscopy showed that the affinities of binding of mSTI1 to Hsc70 and Hsp90 were 2 μM and 1.5 μM respectively. Preliminary in vivo studies revealed differences in the dynamics of binding of endogenous and exogenous recombinant mSTI1 with Hsc70 and Hsp90. The outcome of this study poses serious implications for the mechanisms of mSTI1 interactions with Hsc70 and Hsp90 in the cell.
- Full Text:
- Date Issued: 2003
- Authors: Odunuga, Odutayo Odutola
- Date: 2003
- Subjects: Plants -- Effect of stress on Proteins -- Purification Electrophoresis Heat shock proteins
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4091 , http://hdl.handle.net/10962/d1007724
- Description: Murine stress-inducible protein 1 (mSTI1) is a co-chaperone that is homologous with the human heat shock protein 70 (Hsp70)/heat shock protein 90 (Hsp90)-organizing protein (Hop). The two proteins are homologues of the highly conserved stress-inducible protein 1 (STI1) family of co-chaperones. The STI1 proteins interact directly and simultaneously at some stage, with Hsp70 and Hsp90 in the formation of the hetero-multi-chaperone complexes that facilitate the folding of signal transducing kinases and functional maturation of steroid hormone receptors. The interactions of mSTI1 with both Hsp70 and Hsp90 is mediated by a versatile structural protein-protein interaction motif, the tetratricopeptide repeat (TPR). The TPR motif is a degenerate 34-amino acid sequence a-helical structural motif found in a significant number of functionally unrelated proteins. This study was aimed at characterizing the structural and functional determinants in the TPR domains of mSTI1 responsible for binding to and discriminating between Hsp70 and Hsp90. Guided by data from Hop's crystal structures and amino acid sequence alignment analyses, various biochemical techniques were used to both qualitatively and quantitatively characterize the contacts necessary for the N-terminal TPR domain (TPR1) of mSTI1 to bind to the C-terminal EEVD motif of heat shock cognate protein 70 (Hsc70) and to discriminate between Hsc70 and Hsp90. Substitutions in the first TPR motif of Lys⁸ or Asn¹² did not affect binding of mSTI1 to Hsc70, while double substitution of these residues abrogated binding. A substitution in the second TPR motif of Asn⁴³ lowered but did not abrogate binding. Similarly, a deletion in the second TPR motif coupled with a substitution of Lys⁸ or Asn¹² reduced but did not abrogate binding. Steady state fluorescence and circular dichroism spectroscopies revealed that the double substitution of Lys⁸ and Asn¹² resulted in perturbations of inter-domain interactions in mSTl1. Together these results suggest that mSTI1-Hsc70 interaction requires a network of electrostatic interactions not only between charged residues in the TPR1 domain of mSTI1 and the EEVD motif of Hsc70, but also outside the TPR1 domain. It is proposed that the electrostatic interactions in the first TPR motif collectively made by Lys⁸ and Asn¹² define part of the minimum interactions required for successful mSTI1-Hsc70 interaction. In the first central TPR domain (TPR1A), single substitution of Lys³°¹ was sufficient to abrogate the mSTI1-Hsp90 interaction. Using a truncated derivative of mSTI1 incapable of binding to Hsp90, residues predicted by crystallographic data to determine Hsp70 binding specificity were substituted in the TPR1 domain. The modified protein had reduced binding to Hsc70, but showed significant binding capacity for Hsp90. In contrast, topologically equivalent substitutions on a truncated derivative of mSTI1 incapable of binding to Hsc70 did not confer Hsc70 specificity on the TPR2A domain. These data suggest that binding of Hsc70 to the TPR1 domain is more specific than binding of Hsp90 to the TPR2A domain. In addition, residues C-terminal of helix A in the second TPR motif of mSTI1 were shown to be important in determining specific binding to Hsc70. Binding assays using surface plasmon resonance spectroscopy showed that the affinities of binding of mSTI1 to Hsc70 and Hsp90 were 2 μM and 1.5 μM respectively. Preliminary in vivo studies revealed differences in the dynamics of binding of endogenous and exogenous recombinant mSTI1 with Hsc70 and Hsp90. The outcome of this study poses serious implications for the mechanisms of mSTI1 interactions with Hsc70 and Hsp90 in the cell.
- Full Text:
- Date Issued: 2003