Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta Hemiptera).
- Owen, Christopher L, Marshall, David C, Wade, Elizabeth J, Meister, Russ, Goemans, Geert, Kunte, Krushnamegh, Moulds, Max, Hill, Kathy, Villet, Martin H, Pham, Thai-Hong, Kortyna, Michelle, Lemmon, Emily M, Lemmon, Alan R, Simon, Chris
- Authors: Owen, Christopher L , Marshall, David C , Wade, Elizabeth J , Meister, Russ , Goemans, Geert , Kunte, Krushnamegh , Moulds, Max , Hill, Kathy , Villet, Martin H , Pham, Thai-Hong , Kortyna, Michelle , Lemmon, Emily M , Lemmon, Alan R , Simon, Chris
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440749 , vital:73809 , https://doi.org/10.1093/sysbio/syac043
- Description: Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination.
- Full Text:
- Date Issued: 2022
- Authors: Owen, Christopher L , Marshall, David C , Wade, Elizabeth J , Meister, Russ , Goemans, Geert , Kunte, Krushnamegh , Moulds, Max , Hill, Kathy , Villet, Martin H , Pham, Thai-Hong , Kortyna, Michelle , Lemmon, Emily M , Lemmon, Alan R , Simon, Chris
- Date: 2022
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/440749 , vital:73809 , https://doi.org/10.1093/sysbio/syac043
- Description: Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination.
- Full Text:
- Date Issued: 2022
Making sense of climate change in a national curriculum
- Lotz-Sisitka, Heila, Mandikonza, Caleb, Misser, Shanu, Thomas, Kgomotso
- Authors: Lotz-Sisitka, Heila , Mandikonza, Caleb , Misser, Shanu , Thomas, Kgomotso
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/435193 , vital:73137 , ISBN 9781928502241 , https://library.oapen.org/handle/20.500.12657/64082
- Description: This chapter draws on three recent South African reviews of climate change education that have been undertaken by the authors: one in partnership with the United Nations Educational, Scientific and Cultural Organization (Unesco) and the South African National Biodiversity Institute (SANBI) in 2016 which produced a national case study on Climate Change Education in South Africa (Lotz-Sisitka and Mandikonza 2016); another that was undertaken for the Department of Environmental Affairs in 2018 for the Third National Communication on Climate Change for the United Nations Framework Convention for Climate Change (Lotz-Sisitka et al. 2018); 1 and a more recent review undertaken in the context of a research seminar series hosted by Rhodes University focusing on climate change education in South Africa (Lotz-Sisitka 2021). The chapter also draws on perspectives being developed in the Fundisa for Change Keep it Cool Project (VVOB/GreenMatter 2021) and from wider studies being undertaken for the international Monitoring and Evaluation of Climate Change Education programme (McKenzie 2020).
- Full Text:
- Date Issued: 2021
- Authors: Lotz-Sisitka, Heila , Mandikonza, Caleb , Misser, Shanu , Thomas, Kgomotso
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/435193 , vital:73137 , ISBN 9781928502241 , https://library.oapen.org/handle/20.500.12657/64082
- Description: This chapter draws on three recent South African reviews of climate change education that have been undertaken by the authors: one in partnership with the United Nations Educational, Scientific and Cultural Organization (Unesco) and the South African National Biodiversity Institute (SANBI) in 2016 which produced a national case study on Climate Change Education in South Africa (Lotz-Sisitka and Mandikonza 2016); another that was undertaken for the Department of Environmental Affairs in 2018 for the Third National Communication on Climate Change for the United Nations Framework Convention for Climate Change (Lotz-Sisitka et al. 2018); 1 and a more recent review undertaken in the context of a research seminar series hosted by Rhodes University focusing on climate change education in South Africa (Lotz-Sisitka 2021). The chapter also draws on perspectives being developed in the Fundisa for Change Keep it Cool Project (VVOB/GreenMatter 2021) and from wider studies being undertaken for the international Monitoring and Evaluation of Climate Change Education programme (McKenzie 2020).
- Full Text:
- Date Issued: 2021
Theorising Active Learning–A Historical Analysis
- Authors: Schudel, Ingrid J
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/435072 , vital:73128 , ISBN 9781928502241 , https://library.oapen.org/handle/20.500.12657/64082
- Description: There is no definitive or consensual Education for Sustainable Development (ESD) pedagogy but there is a suite of techniques which, if examined, will reveal similar features and principles. For example, in its ESD sourcebook, Unesco (2012) highlights pedagogies featuring question-orientated, analytical, critical and decisive skills, as well as relational pedagogies with features such as learner-centredness and participation. In its later Roadmap for Implementing the Global Action Programme for Education for Sustainable Development, Unesco calls for pedagogies that support the designing of ‘teaching and learning in an interactive, learner-centred way that enables exploratory, action-oriented and transformative learning’ (Unesco 2014: 12). An international collaborative group–ESD Expert-Net–highlighted the ‘active’ element of ESD arguing that ‘action’ or ‘doing’ elements of learning have traditionally been neglected, and that if ESD practice is to address local and global challenges ‘a strong action component’ is needed (Hoffmann and Rajeswari nd: 9). The notion of ‘active learning’has been of central interest in the Fundisa for Change project. This chapter describes its trajectory of development and use in South African ESD by outlining core features and principles for active learning. This is with a view to positioning the further chapters in this section of the book in relation to national and international research that has influenced the approach of Fundisa for Change. The chapter also serves to inform international interests in active learning.
- Full Text:
- Date Issued: 2021
- Authors: Schudel, Ingrid J
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/435072 , vital:73128 , ISBN 9781928502241 , https://library.oapen.org/handle/20.500.12657/64082
- Description: There is no definitive or consensual Education for Sustainable Development (ESD) pedagogy but there is a suite of techniques which, if examined, will reveal similar features and principles. For example, in its ESD sourcebook, Unesco (2012) highlights pedagogies featuring question-orientated, analytical, critical and decisive skills, as well as relational pedagogies with features such as learner-centredness and participation. In its later Roadmap for Implementing the Global Action Programme for Education for Sustainable Development, Unesco calls for pedagogies that support the designing of ‘teaching and learning in an interactive, learner-centred way that enables exploratory, action-oriented and transformative learning’ (Unesco 2014: 12). An international collaborative group–ESD Expert-Net–highlighted the ‘active’ element of ESD arguing that ‘action’ or ‘doing’ elements of learning have traditionally been neglected, and that if ESD practice is to address local and global challenges ‘a strong action component’ is needed (Hoffmann and Rajeswari nd: 9). The notion of ‘active learning’has been of central interest in the Fundisa for Change project. This chapter describes its trajectory of development and use in South African ESD by outlining core features and principles for active learning. This is with a view to positioning the further chapters in this section of the book in relation to national and international research that has influenced the approach of Fundisa for Change. The chapter also serves to inform international interests in active learning.
- Full Text:
- Date Issued: 2021
[A] girl from the village: totally unspoilt
- Authors: Naidu, Samantha
- Date: 2020
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/158057 , vital:40144 , ISBN 9781498591775
- Description: The South Asian women’s diaspora engages in spatio-temporal interactions and power differentials in a variety of narratives, articulating agency, multiplicities of belonging and culturally integrative practices, highlighting homing paradigms. The sense of alienness in a new homeland, rather in worldwide home places, triggers rethinking of diasporic conceptions and epistemes of individual and group histories, personal and collective experiences. Some of the questions that this anthology seeks to consider are: How do women from the South Asian diaspora represent cultural negotiations and alienness of the adopted homeland in various narratives? What are the themes/issues they select to portray their perceptions of foreignness? How do culture, history and politics intervene in their portrayal of lived experiences? How do they locate themselves in the matrix of foreignness and diaspora? The contributors to this anthology examine narratives depicting South Asian women, their complexly positioned voices, gesturing at the proliferating challenges and reflecting the grim realities of a globalized world.
- Full Text:
- Date Issued: 2020
- Authors: Naidu, Samantha
- Date: 2020
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/158057 , vital:40144 , ISBN 9781498591775
- Description: The South Asian women’s diaspora engages in spatio-temporal interactions and power differentials in a variety of narratives, articulating agency, multiplicities of belonging and culturally integrative practices, highlighting homing paradigms. The sense of alienness in a new homeland, rather in worldwide home places, triggers rethinking of diasporic conceptions and epistemes of individual and group histories, personal and collective experiences. Some of the questions that this anthology seeks to consider are: How do women from the South Asian diaspora represent cultural negotiations and alienness of the adopted homeland in various narratives? What are the themes/issues they select to portray their perceptions of foreignness? How do culture, history and politics intervene in their portrayal of lived experiences? How do they locate themselves in the matrix of foreignness and diaspora? The contributors to this anthology examine narratives depicting South Asian women, their complexly positioned voices, gesturing at the proliferating challenges and reflecting the grim realities of a globalized world.
- Full Text:
- Date Issued: 2020
Anger, Pain and the Body in the Public Sphere:
- Authors: Garman, Anthea
- Date: 2020
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/158459 , vital:40188 , ISBN 9781776145898
- Description: In this timely, original and sophisticated collection, writers from the Global South demonstrate that forms of publicness are multiple, mobile and varied. The notion that societies mediate issues through certain kinds of engagement is at the heart of imaginings of democracy and often centers on the ideal of the public sphere. But this imagined foundation of how we live collectively appears to have suffered a dramatic collapse across the world, with many democracies apparently unable to solve problems through talk – or even to agree on who speaks, in what ways and where. In the 10 essays in this timely, original and sophisticated collection, writers from southern Africa combine theoretical analysis with the examination of historical cases and contemporary developments to demonstrate that forms of publicness are multiple, mobile and varied. They propose new concepts and methodologies to analyse how public engagements work in society.
- Full Text:
- Date Issued: 2020
- Authors: Garman, Anthea
- Date: 2020
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/158459 , vital:40188 , ISBN 9781776145898
- Description: In this timely, original and sophisticated collection, writers from the Global South demonstrate that forms of publicness are multiple, mobile and varied. The notion that societies mediate issues through certain kinds of engagement is at the heart of imaginings of democracy and often centers on the ideal of the public sphere. But this imagined foundation of how we live collectively appears to have suffered a dramatic collapse across the world, with many democracies apparently unable to solve problems through talk – or even to agree on who speaks, in what ways and where. In the 10 essays in this timely, original and sophisticated collection, writers from southern Africa combine theoretical analysis with the examination of historical cases and contemporary developments to demonstrate that forms of publicness are multiple, mobile and varied. They propose new concepts and methodologies to analyse how public engagements work in society.
- Full Text:
- Date Issued: 2020
Building knowledge with theory: Unpacking complexity in doctoral writing
- Authors: Wilmot, Kirsten
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439480 , vital:73600 , https://www.ajol.info/index.php/cristal/article/view/203971
- Description: The use of theory to analyse and interpret empirical data is a valued practice in much social science doctoral research. A crucial aspect of this practice involves generating sophisticated theoretical understandings and critiques of phenomena in our social world. Despite the importance of theory, however, few concrete explanations of how to ‘theorise’exist in literature. This paper addresses this gap by demonstrating how a set of conceptual tools can be used to unpack what the craft of theorising looks like in explicit terms, and to reveal how this ability develops over time during the drafting process of dissertation writing. It does this by drawing on select texts from a successful doctoral dissertation, as well as an earlier draft version. In doing so, the paper provides an in-depth explanation of an essential process of doctoral research that is inherently known by many supervisors, yet seldom unpacked in explicit terms.
- Full Text:
- Date Issued: 2020
- Authors: Wilmot, Kirsten
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439480 , vital:73600 , https://www.ajol.info/index.php/cristal/article/view/203971
- Description: The use of theory to analyse and interpret empirical data is a valued practice in much social science doctoral research. A crucial aspect of this practice involves generating sophisticated theoretical understandings and critiques of phenomena in our social world. Despite the importance of theory, however, few concrete explanations of how to ‘theorise’exist in literature. This paper addresses this gap by demonstrating how a set of conceptual tools can be used to unpack what the craft of theorising looks like in explicit terms, and to reveal how this ability develops over time during the drafting process of dissertation writing. It does this by drawing on select texts from a successful doctoral dissertation, as well as an earlier draft version. In doing so, the paper provides an in-depth explanation of an essential process of doctoral research that is inherently known by many supervisors, yet seldom unpacked in explicit terms.
- Full Text:
- Date Issued: 2020
From the Booth to the Dock: 2018 elections in Zimbabwe and the elusive search for electoral integrity
- Mwonzora, Gift, Xaba, Mzingaye Brilliant
- Authors: Mwonzora, Gift , Xaba, Mzingaye Brilliant
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/159946 , vital:40358 , https://doi.org/10.1080/14662043.2020.1813457
- Description: The issue of presidential election petitions seems to be repeating itself with regularity in much of Africa, thus warranting the need for thorough analysis. Utilising the 2018 presidential election petition in Zimbabwe, the article examines whether electoral integrity and legitimacy can be derived from court-based action. Data for this article was gleaned from case law analysis, review of expert analysis from constitutional lawyers and election experts, video evidence, in-depth and critical reading of grey material. The article concludes that there are limitations in relying on litigation in seeking to realise electoral justice in much of Africa, including in Zimbabwe.
- Full Text:
- Date Issued: 2020
- Authors: Mwonzora, Gift , Xaba, Mzingaye Brilliant
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/159946 , vital:40358 , https://doi.org/10.1080/14662043.2020.1813457
- Description: The issue of presidential election petitions seems to be repeating itself with regularity in much of Africa, thus warranting the need for thorough analysis. Utilising the 2018 presidential election petition in Zimbabwe, the article examines whether electoral integrity and legitimacy can be derived from court-based action. Data for this article was gleaned from case law analysis, review of expert analysis from constitutional lawyers and election experts, video evidence, in-depth and critical reading of grey material. The article concludes that there are limitations in relying on litigation in seeking to realise electoral justice in much of Africa, including in Zimbabwe.
- Full Text:
- Date Issued: 2020
Geotourism, iconic landforms and island-style speciation patterns in National Parks of East Africa:
- Authors: Scoon, Roger N
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/158252 , vital:40166 , https://0-doi.org.wam.seals.ac.za/10.1007/s12371-020-00486-z
- Description: Many of the national parks in East Africa are equally as famous for their iconic landforms as they are for their diversity and concentrations of fauna and flora. The newly formed Ngorongoro-Lengai Geopark in northern Tanzania is the first geopark to be established in the region, but there is remarkable potential for geotourism in the majority of the national parks. The most spectacular landforms have been shaped by the East African Rift System. Formation of the two major rifts in the region, the Albertine Rift (or western branch) and the Gregory Rift (or eastern branch), was accompanied, or in some cases preceded, by extensive alkaline volcanism. The rifting and volcanism are primarily Late Cenozoic phenomenon that dissected and overprinted the older regional plateaus. Rifting impacted the regional drainage and captured major rivers, including the Victoria Nile.
- Full Text:
- Date Issued: 2020
- Authors: Scoon, Roger N
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/158252 , vital:40166 , https://0-doi.org.wam.seals.ac.za/10.1007/s12371-020-00486-z
- Description: Many of the national parks in East Africa are equally as famous for their iconic landforms as they are for their diversity and concentrations of fauna and flora. The newly formed Ngorongoro-Lengai Geopark in northern Tanzania is the first geopark to be established in the region, but there is remarkable potential for geotourism in the majority of the national parks. The most spectacular landforms have been shaped by the East African Rift System. Formation of the two major rifts in the region, the Albertine Rift (or western branch) and the Gregory Rift (or eastern branch), was accompanied, or in some cases preceded, by extensive alkaline volcanism. The rifting and volcanism are primarily Late Cenozoic phenomenon that dissected and overprinted the older regional plateaus. Rifting impacted the regional drainage and captured major rivers, including the Victoria Nile.
- Full Text:
- Date Issued: 2020
More than a century of biological control against invasive alien plants in South Africa: a synoptic view of what has been accomplished
- Hill, Martin P, Moran, Vincent C, Hoffmann, John H, Neser, Stefan, Zimmermann, Helmuth G, Simelane, David O, Klein, Hildegard, Zachariades, Costas, Wood, Alan R, Byrne, Marcus J, Paterson, Iain D, Martin, Grant D, Coetzee, Julie A
- Authors: Hill, Martin P , Moran, Vincent C , Hoffmann, John H , Neser, Stefan , Zimmermann, Helmuth G , Simelane, David O , Klein, Hildegard , Zachariades, Costas , Wood, Alan R , Byrne, Marcus J , Paterson, Iain D , Martin, Grant D , Coetzee, Julie A
- Date: 2020
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/176260 , vital:42679 , ISBN 978-3-030-32394-3 , 10.1007/978-3-030-32394-3
- Description: Invasive alien plant species negatively affect agricultural production, degrade conservation areas, reduce water supplies, and increase the intensity of wild fires. Since 1913, biological control agents ie plant-feeding insects, mites, and fungal pathogens, have been deployed in South Africa to supplement other management practices (herbicides and mechanical controls) used against these invasive plant species. We do not describe the biological control agent species.
- Full Text: false
- Date Issued: 2020
- Authors: Hill, Martin P , Moran, Vincent C , Hoffmann, John H , Neser, Stefan , Zimmermann, Helmuth G , Simelane, David O , Klein, Hildegard , Zachariades, Costas , Wood, Alan R , Byrne, Marcus J , Paterson, Iain D , Martin, Grant D , Coetzee, Julie A
- Date: 2020
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/176260 , vital:42679 , ISBN 978-3-030-32394-3 , 10.1007/978-3-030-32394-3
- Description: Invasive alien plant species negatively affect agricultural production, degrade conservation areas, reduce water supplies, and increase the intensity of wild fires. Since 1913, biological control agents ie plant-feeding insects, mites, and fungal pathogens, have been deployed in South Africa to supplement other management practices (herbicides and mechanical controls) used against these invasive plant species. We do not describe the biological control agent species.
- Full Text: false
- Date Issued: 2020
Plant Fibre Crafts Production, Trade and Income in Eswatini, Malawi and Zimbabwe
- Thondhlana, Gladman, Pullanikkatil, Deepa, Shackleton, Charlie M
- Authors: Thondhlana, Gladman , Pullanikkatil, Deepa , Shackleton, Charlie M
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/175936 , vital:42642 , https://doi.org/10.3390/f11080832 , https://doi.org/10.21504/RUR.c.5388470.v1
- Description: The production of plant fibre products is considered a promising pathway for contributing to people’s livelihoods particularly in developing countries, where economic options might be limited. However, there are limited comparative studies across countries on plant fibre products, making it difficult to examine how local and broader biophysical, socioeconomic, cultural and policy contexts influence craft production patterns in terms of primary plant resources used, products made and contributions to livelihoods. Using household surveys for data collection, this paper presents findings from a comparative analysis of plant fibre craft production and income in three southern African countries, Eswatini, Malawi and Zimbabwe.
- Full Text:
- Date Issued: 2020
- Authors: Thondhlana, Gladman , Pullanikkatil, Deepa , Shackleton, Charlie M
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/175936 , vital:42642 , https://doi.org/10.3390/f11080832 , https://doi.org/10.21504/RUR.c.5388470.v1
- Description: The production of plant fibre products is considered a promising pathway for contributing to people’s livelihoods particularly in developing countries, where economic options might be limited. However, there are limited comparative studies across countries on plant fibre products, making it difficult to examine how local and broader biophysical, socioeconomic, cultural and policy contexts influence craft production patterns in terms of primary plant resources used, products made and contributions to livelihoods. Using household surveys for data collection, this paper presents findings from a comparative analysis of plant fibre craft production and income in three southern African countries, Eswatini, Malawi and Zimbabwe.
- Full Text:
- Date Issued: 2020
Structural Characterization of Carbonic Anhydrase VIII and Effects of Missense Single Nucleotide Variations to Protein Structure and Function:
- Sanyanga, Taremekedzwa Allan, Tastan Bishop, Özlem
- Authors: Sanyanga, Taremekedzwa Allan , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/149670 , vital:38873 , https://doi.org/10.3390/ijms21082764
- Description: Human carbonic anhydrase 8 (CA-VIII) is an acatalytic isoform of the α -CA family. Though the protein cannot hydrate CO2, CA-VIII is essential for calcium (Ca2+) homeostasis within the body, and achieves this by allosterically inhibiting the binding of inositol 1,4,5-triphosphate (IP3) to the IP3 receptor type 1 (ITPR1) protein. However, the mechanism of interaction of CA-VIII to ITPR1 is not well understood. In addition, functional defects to CA-VIII due to non-synonymous single nucleotide polymorphisms (nsSNVs) result in Ca2+ dysregulation and the development of the phenotypes such as cerebellar ataxia, mental retardation and disequilibrium syndrome 3 (CAMRQ3). The pathogenesis of CAMRQ3 is also not well understood. The structure and function of CA-VIII was characterised, and pathogenesis of CAMRQ3 investigated. Structural and functional characterisation of CA-VIII was conducted through SiteMap and CPORT to identify potential binding site residues.
- Full Text:
- Date Issued: 2020
- Authors: Sanyanga, Taremekedzwa Allan , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/149670 , vital:38873 , https://doi.org/10.3390/ijms21082764
- Description: Human carbonic anhydrase 8 (CA-VIII) is an acatalytic isoform of the α -CA family. Though the protein cannot hydrate CO2, CA-VIII is essential for calcium (Ca2+) homeostasis within the body, and achieves this by allosterically inhibiting the binding of inositol 1,4,5-triphosphate (IP3) to the IP3 receptor type 1 (ITPR1) protein. However, the mechanism of interaction of CA-VIII to ITPR1 is not well understood. In addition, functional defects to CA-VIII due to non-synonymous single nucleotide polymorphisms (nsSNVs) result in Ca2+ dysregulation and the development of the phenotypes such as cerebellar ataxia, mental retardation and disequilibrium syndrome 3 (CAMRQ3). The pathogenesis of CAMRQ3 is also not well understood. The structure and function of CA-VIII was characterised, and pathogenesis of CAMRQ3 investigated. Structural and functional characterisation of CA-VIII was conducted through SiteMap and CPORT to identify potential binding site residues.
- Full Text:
- Date Issued: 2020
Unsustainable trade-offs: provisioning ecosystem services in rapidly changing Likangala River catchment in southern Malawi
- Pullanikkatil, Deepa, Mograbi, Penelope J, Palamuleni, Lobina, Ruhiiga, Tabukeli, Shackleton, Charlie M
- Authors: Pullanikkatil, Deepa , Mograbi, Penelope J , Palamuleni, Lobina , Ruhiiga, Tabukeli , Shackleton, Charlie M
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/176308 , vital:42683 , https://doi.org/10.1007/s10668-018-0240-x
- Description: Provisioning ecosystem services of the Likangala River Catchment in southern Malawi are important for livelihoods of those living there. Remote sensing, participatory mapping and focus group discussions were used to explore the spatio-temporal changes and trade-ofs in land-cover change from 1984 to 2013, and how that afects provisioning ecosystem services in the area. Communities derive a number of provisioning ecosystem services from the catchment. Forty-eight species of edible wild animals (including birds), 28 species of edible wild plants and fungi, 22 species of medicinal plants, construction materials, ornamental fowers, frewood, honey, gum, reeds and thatch/weaving grasses were derived from the catchment and used by local communities.
- Full Text:
- Date Issued: 2020
- Authors: Pullanikkatil, Deepa , Mograbi, Penelope J , Palamuleni, Lobina , Ruhiiga, Tabukeli , Shackleton, Charlie M
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/176308 , vital:42683 , https://doi.org/10.1007/s10668-018-0240-x
- Description: Provisioning ecosystem services of the Likangala River Catchment in southern Malawi are important for livelihoods of those living there. Remote sensing, participatory mapping and focus group discussions were used to explore the spatio-temporal changes and trade-ofs in land-cover change from 1984 to 2013, and how that afects provisioning ecosystem services in the area. Communities derive a number of provisioning ecosystem services from the catchment. Forty-eight species of edible wild animals (including birds), 28 species of edible wild plants and fungi, 22 species of medicinal plants, construction materials, ornamental fowers, frewood, honey, gum, reeds and thatch/weaving grasses were derived from the catchment and used by local communities.
- Full Text:
- Date Issued: 2020
A functional ontology for information systems
- Motara, Yusuf, M, Van der Schyff, Karl
- Authors: Motara, Yusuf, M , Van der Schyff, Karl
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/428936 , vital:72547 , https://hdl.handle.net/10520/EJC-1d75ba3e4a
- Description: The ontology of information systems — the way in which knowledge claims, and thus theories, are conceptualised and represented — is of particular importance in the information systems field, due to its reliance on relations between entities. This work proposes, demonstrates, and evaluates an alternative ontology for theory description which is arguably more powerful and more expressive than the dominant ontological model.
- Full Text:
- Date Issued: 2019
- Authors: Motara, Yusuf, M , Van der Schyff, Karl
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/428936 , vital:72547 , https://hdl.handle.net/10520/EJC-1d75ba3e4a
- Description: The ontology of information systems — the way in which knowledge claims, and thus theories, are conceptualised and represented — is of particular importance in the information systems field, due to its reliance on relations between entities. This work proposes, demonstrates, and evaluates an alternative ontology for theory description which is arguably more powerful and more expressive than the dominant ontological model.
- Full Text:
- Date Issued: 2019
Econo-Language Planning and Transformation in South Africa: From Localisation to Globalisation
- Authors: Kaschula, Russell H
- Date: 2019
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/174657 , vital:42498 , ISBN 9781108425346
- Description: This chapter seeks to create an understanding of the historical, sociopolitical and economic context within which language planning has taken place in South Africa (Alexander 1992). Furthermore, the extent to which government agencies and other stakeholder bodies have taken language planning into account when developing economic and development policies within the contemporary global reality will be assessed (Edozie 2004). Policies (if one can call them policies) such as the New Partnership for Africa’s Development (NEPAD), as well as the National Development Plan (NDP) in South Africa are analysed against the backdrop of language policy planning and implementation, to see if there are linkages between opportunity language planning on the ground (Antia 2017) and economic development. In other words does language planning create work opportunities through policy creation and implementation where our languages are seen as resources to be used appropriately in the market place?.
- Full Text:
- Date Issued: 2019
- Authors: Kaschula, Russell H
- Date: 2019
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/174657 , vital:42498 , ISBN 9781108425346
- Description: This chapter seeks to create an understanding of the historical, sociopolitical and economic context within which language planning has taken place in South Africa (Alexander 1992). Furthermore, the extent to which government agencies and other stakeholder bodies have taken language planning into account when developing economic and development policies within the contemporary global reality will be assessed (Edozie 2004). Policies (if one can call them policies) such as the New Partnership for Africa’s Development (NEPAD), as well as the National Development Plan (NDP) in South Africa are analysed against the backdrop of language policy planning and implementation, to see if there are linkages between opportunity language planning on the ground (Antia 2017) and economic development. In other words does language planning create work opportunities through policy creation and implementation where our languages are seen as resources to be used appropriately in the market place?.
- Full Text:
- Date Issued: 2019
Out of Africa?: a dated molecular phylogeny of the cicada tribe Platypleurini Schmidt (Hemiptera: Cicadidae), with a focus on African genera and the genus Platypleura Amyot and Audinet‐Serville
- Price, Benjamin W, Marshall, David C, Barker, Nigel P, Simon, Chris, Villet, Martin H
- Authors: Price, Benjamin W , Marshall, David C , Barker, Nigel P , Simon, Chris , Villet, Martin H
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140704 , vital:37911 , DOI: 10.1111/syen.12360
- Description: The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four-gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa.
- Full Text:
- Date Issued: 2019
- Authors: Price, Benjamin W , Marshall, David C , Barker, Nigel P , Simon, Chris , Villet, Martin H
- Date: 2019
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/140704 , vital:37911 , DOI: 10.1111/syen.12360
- Description: The Platypleurini is a large group of charismatic cicadas distributed from Cape Agulhas in South Africa, through tropical Africa, Madagascar, India and eastern Asia to Japan, with generic diversity concentrated in equatorial and southern Africa. This distribution suggests the possibility of a Gondwanan origin and dispersal to eastern Asia from Africa or India. We used a four-gene (three mitochondrial) molecular dataset, fossil calibrations and molecular clock information to explore the phylogenetic relationships of the platypleurine cicadas and the timing and geography of their diversification. The earliest splits in the tribe were found to separate forest genera in Madagascar and equatorial Africa from the main radiation, and all of the Asian/Indian species sampled formed a younger clade nested well within the African taxa.
- Full Text:
- Date Issued: 2019
Alternatives to Development in Africa:
- Authors: Matthews, Sally
- Date: 2018
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/142202 , vital:38058 , ISBN 9783319675091 , https://doi.org/10.1007/978-3-319-67510-7_7
- Description: Africa’s place in the world has been closely linked to the idea of development. Building on post-development theory’s critique of development, Matthews’ chapter asks whether and how we can move beyond development in Africa. She argues that contrary to the wishes of some post-development theorists, we cannot retrieve, discover, or create something that is purely not-development, entirely non-Western, and fully outside of coloniality. However, this does not mean that we ought to acquiesce in the face of the powerful discourses that have come to dominate the way in which we talk about Africa. The chapter tentatively explores some possible ways in which development can be both resisted and reappropriated in creative ways.
- Full Text:
- Date Issued: 2018
- Authors: Matthews, Sally
- Date: 2018
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/142202 , vital:38058 , ISBN 9783319675091 , https://doi.org/10.1007/978-3-319-67510-7_7
- Description: Africa’s place in the world has been closely linked to the idea of development. Building on post-development theory’s critique of development, Matthews’ chapter asks whether and how we can move beyond development in Africa. She argues that contrary to the wishes of some post-development theorists, we cannot retrieve, discover, or create something that is purely not-development, entirely non-Western, and fully outside of coloniality. However, this does not mean that we ought to acquiesce in the face of the powerful discourses that have come to dominate the way in which we talk about Africa. The chapter tentatively explores some possible ways in which development can be both resisted and reappropriated in creative ways.
- Full Text:
- Date Issued: 2018
Exploring grade 3 teachers’ resistance to ‘take up’progressive mathematics teaching roles
- Graven, Mellony, Westaway, Lise
- Authors: Graven, Mellony , Westaway, Lise
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69700 , vital:29568 , https://DOI: 10.1007/s13394-018-0237-7
- Description: This article addresses the question: Why teachers of mathematics have yet to ‘take up’ progressive roles? Drawing on the philosophy of critical realism and its methodological equivalent, social realism, we analyse interview and observation data of four grade 3 teachers, with the view to identifying the mechanisms conditioning the expression of teachers’ identities. In so doing, we show how post-apartheid changes in systemic roles of teachers create contradictory tensions for teachers as these bring their own mathematical learning and teaching experiences into contradiction with the new post-apartheid roles they are mandated to enact. We examine how this contradiction, together with beliefs about mathematics, pedagogy and learners, is expressed in the teaching of grade 3 mathematics. We maintain that the complementarity between teachers’ beliefs and old systemic roles provides an explanation for why teachers of grade 3 mathematics have yet to ‘take-up’ progressive roles. The implications point to the need for teacher development that creates enablers that lead to changes in classroom practices that align with policy-designated, progressive roles in teaching mathematics.
- Full Text:
- Date Issued: 2018
- Authors: Graven, Mellony , Westaway, Lise
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69700 , vital:29568 , https://DOI: 10.1007/s13394-018-0237-7
- Description: This article addresses the question: Why teachers of mathematics have yet to ‘take up’ progressive roles? Drawing on the philosophy of critical realism and its methodological equivalent, social realism, we analyse interview and observation data of four grade 3 teachers, with the view to identifying the mechanisms conditioning the expression of teachers’ identities. In so doing, we show how post-apartheid changes in systemic roles of teachers create contradictory tensions for teachers as these bring their own mathematical learning and teaching experiences into contradiction with the new post-apartheid roles they are mandated to enact. We examine how this contradiction, together with beliefs about mathematics, pedagogy and learners, is expressed in the teaching of grade 3 mathematics. We maintain that the complementarity between teachers’ beliefs and old systemic roles provides an explanation for why teachers of grade 3 mathematics have yet to ‘take-up’ progressive roles. The implications point to the need for teacher development that creates enablers that lead to changes in classroom practices that align with policy-designated, progressive roles in teaching mathematics.
- Full Text:
- Date Issued: 2018
Hepatitis C and HIV Coinfection in Developing Countries:
- Authors: Tastan Bishop, Özlem
- Date: 2018
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/148228 , vital:38721 , ISBN 9780128032343 , https://books.google.co.za/books?id=XSmlCgAAQBAJanddq=hepatitis+c+in+developing+countriesandsource=gbs_navlinks_s
- Description: Because of the common routes of transmission, hepatitis C virus (HCV) coinfection with HIV is frequent. Of the 36.6 million HIV-infected individuals worldwide, about 25% are also coinfected with HCV. Developing countries face the greatest burden of coinfection. HIV infection has been shown to have a significant impact on the progression of chronic HCV, with a higher risk of cirrhosis and hepatocellular carcinoma (HCC). Because of the improvements in the management and treatment of HIV/AIDS in resource-limited countries, HCV/HIV coinfection is becoming a significant clinical problem and a major cause of morbidity and mortality. HCV/HIV coinfection is characterized by aggressive hepatic fibrogenesis, incidence of cirrhosis, and HCC. HCC is currently a major cause for liver-related deaths in HIV patients. Viral eradication has been difficult to attain with interferon and ribavirin therapies. Novel therapies with direct-acting antiviral agents have been promising for this population. However, access to such expensive regimen is far beyond the capabilities of most resource-limited countries. Yet, studies lag behind those for HCV monoinfection.
- Full Text:
- Date Issued: 2018
- Authors: Tastan Bishop, Özlem
- Date: 2018
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/148228 , vital:38721 , ISBN 9780128032343 , https://books.google.co.za/books?id=XSmlCgAAQBAJanddq=hepatitis+c+in+developing+countriesandsource=gbs_navlinks_s
- Description: Because of the common routes of transmission, hepatitis C virus (HCV) coinfection with HIV is frequent. Of the 36.6 million HIV-infected individuals worldwide, about 25% are also coinfected with HCV. Developing countries face the greatest burden of coinfection. HIV infection has been shown to have a significant impact on the progression of chronic HCV, with a higher risk of cirrhosis and hepatocellular carcinoma (HCC). Because of the improvements in the management and treatment of HIV/AIDS in resource-limited countries, HCV/HIV coinfection is becoming a significant clinical problem and a major cause of morbidity and mortality. HCV/HIV coinfection is characterized by aggressive hepatic fibrogenesis, incidence of cirrhosis, and HCC. HCC is currently a major cause for liver-related deaths in HIV patients. Viral eradication has been difficult to attain with interferon and ribavirin therapies. Novel therapies with direct-acting antiviral agents have been promising for this population. However, access to such expensive regimen is far beyond the capabilities of most resource-limited countries. Yet, studies lag behind those for HCV monoinfection.
- Full Text:
- Date Issued: 2018
How are learning and training environments transforming with ESD
- O’Donoghue, R, Taylor, Jim, Venter, V
- Authors: O’Donoghue, R , Taylor, Jim , Venter, V
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/436718 , vital:73295 , ISBN 978-92-3-100244-1 , https://unesdoc.unesco.org/ark:/48223/pf0000261445
- Description: Action Area 2 of the Global Action Programme (GAP) on Edu-cation for Sustainable Development calls for the transformation of education and training environments1. This transformation can be interpreted in terms of changes in learning environ-ments brought about by the inclusion of ESD in education and training initiatives. This includes the integration of learning-led change found in whole-school approaches that emphasize in-clusive school governance, pedagogy and sustainable cam-pus management, as well as cooperation with partners and broader communities. These approaches are changing learn-ing environments in significant ways.
- Full Text:
- Date Issued: 2018
- Authors: O’Donoghue, R , Taylor, Jim , Venter, V
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/436718 , vital:73295 , ISBN 978-92-3-100244-1 , https://unesdoc.unesco.org/ark:/48223/pf0000261445
- Description: Action Area 2 of the Global Action Programme (GAP) on Edu-cation for Sustainable Development calls for the transformation of education and training environments1. This transformation can be interpreted in terms of changes in learning environ-ments brought about by the inclusion of ESD in education and training initiatives. This includes the integration of learning-led change found in whole-school approaches that emphasize in-clusive school governance, pedagogy and sustainable cam-pus management, as well as cooperation with partners and broader communities. These approaches are changing learn-ing environments in significant ways.
- Full Text:
- Date Issued: 2018
How to be or not to be? A critical dialogue on the limitations and opportunities of academic development in the current higher education context
- Behari-Leak, Kasturi, Chitanand, N, Padayachee, Kershree, Masehela, L, Vorster, Jo-Anne E, Ganas, Rieta, Merckel, Vanessa
- Authors: Behari-Leak, Kasturi , Chitanand, N , Padayachee, Kershree , Masehela, L , Vorster, Jo-Anne E , Ganas, Rieta , Merckel, Vanessa
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124217 , vital:35577 , https://hdl.handle.net/10520/EJC-13671ff578
- Description: In the tumultuous time we find ourselves, debates about pedagogy have taken centre stage once again. Concerns raised by the student protests of 2015 and 2016 have highlighted the urgent need to re-think traditional teaching, learning and assessment practices, as well as the development of decolonised and transformative curricula.Traditional notions of academic and professional development are now being tested and contested, insofar as they are able to respond to student challenges in appropriate, responsive, legitimate and relevant ways. As a professional organisation dedicated to supporting learning and teaching, the executive team of HELTASA responded to the challenge in this article by engaging with perspectives on the purpose, role and conceptualisation of academic development in the current decolonial moment in the South African Higher Education landscape. Critical processes that enable academics to engage, share thoughts and debate epistemological, pedagogical and methodological options to support students and academics are much needed. And the context and spirit in which these debates occur may be as important as the debates themselves.At its annual conference, the executive team facilitated a critical dialogue with conference delegates on the limitations and opportunities of AD in our current context. Given the diverse teaching and learning contexts and institutional differentiation in the sector, this article explores individual and collective theorised observations, reflections and experiences of the seven facilitators who led the CD. These reflections were analysed and discussed against the backdrop of AD as well as the affordances of CD as a participatory learning and engagement methodology. The findings showed that there is dire need to re-imagine, not only AD’s role but alternative forms of critical engagement in the sector.
- Full Text:
- Date Issued: 2018
- Authors: Behari-Leak, Kasturi , Chitanand, N , Padayachee, Kershree , Masehela, L , Vorster, Jo-Anne E , Ganas, Rieta , Merckel, Vanessa
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124217 , vital:35577 , https://hdl.handle.net/10520/EJC-13671ff578
- Description: In the tumultuous time we find ourselves, debates about pedagogy have taken centre stage once again. Concerns raised by the student protests of 2015 and 2016 have highlighted the urgent need to re-think traditional teaching, learning and assessment practices, as well as the development of decolonised and transformative curricula.Traditional notions of academic and professional development are now being tested and contested, insofar as they are able to respond to student challenges in appropriate, responsive, legitimate and relevant ways. As a professional organisation dedicated to supporting learning and teaching, the executive team of HELTASA responded to the challenge in this article by engaging with perspectives on the purpose, role and conceptualisation of academic development in the current decolonial moment in the South African Higher Education landscape. Critical processes that enable academics to engage, share thoughts and debate epistemological, pedagogical and methodological options to support students and academics are much needed. And the context and spirit in which these debates occur may be as important as the debates themselves.At its annual conference, the executive team facilitated a critical dialogue with conference delegates on the limitations and opportunities of AD in our current context. Given the diverse teaching and learning contexts and institutional differentiation in the sector, this article explores individual and collective theorised observations, reflections and experiences of the seven facilitators who led the CD. These reflections were analysed and discussed against the backdrop of AD as well as the affordances of CD as a participatory learning and engagement methodology. The findings showed that there is dire need to re-imagine, not only AD’s role but alternative forms of critical engagement in the sector.
- Full Text:
- Date Issued: 2018