Phylogenetics and historical biogeography of the Teloganodidae (Ephemeroptera)
- Pereira da Conceicoa, Lyndall Louise
- Authors: Pereira da Conceicoa, Lyndall Louise
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64900 , vital:28629
- Description: The Teloganodidae are a mayfly family endemic to the southwestern Cape (South Africa), with relatives in Madagascar and Asia. Like many other aquatic invertebrates in Africa, they have been considerably understudied. Research into biodiversity and biogeography allows an understanding of the earth’s biota, producing knowledge which can be used to develop strategies to preserve and monitor this biota. Mismanagement of water systems places biodiversity of river fauna under an ever-increasing extinction threat. This investigation explores rivers in under-collected areas to determine how well teloganodids have been represented in the literature, with four genera and five species described at the onset of this study. A lectotype for Lestagella penicillata Barnard (1940) has been elected and described in detail, setting “benchmark” characters for future descriptions. Standard DNA sequencing methods provide portions of three mitochondrial genes; cytochrome oxidase subunit I (COI), small subunit ribosomal 16S RNA (16S), 12S ribosomal DNA (12S) and two nuclear genes, Histone 3 (H3) and 28S ribosomal DNA (28S) for up to 255 specimens. Fore and hind wings of 79 teloganodid adults were used to examine phylogenetic signal and evolutionary divergence using geometric morphometrics. A multi-faceted approach is used to investigate relationships between clades and the effects of deep-time climatic and landform changes which have influenced the diversity and distribution seen today. Tree (Bayesian Inference and Maximum Likelihood) and network (parsimony) phylogenies, ancestral reconstruction, historical biogeography and wingevolution of the Teloganodidae are investigated. Species tree analyses discovered 27 species and six genera. Distinct lineages are restricted to catchments, and strong phylogeographic structure was found within most genera. Southern African Teloganodidae are shown to have originated in the Cretaceous, with divergence and dispersal of lineages depended on their established locality at the time of tectonic events (uplift) and climatic changes (sea level regressions and transgressions). Geographic clines in wing-shape of Lestagella across its range imply evolutionary adaptations to specific catchment landscape and environment. A detailed analysis of biodiversity has many valuable contributions, from directing future research, understanding adaptive processes, fine-tuning phylogeographical and evolutionary hypotheses, to improving management and conservation decisions in order to preserve endemic biodiversity hotspots.
- Full Text:
- Authors: Pereira da Conceicoa, Lyndall Louise
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/64900 , vital:28629
- Description: The Teloganodidae are a mayfly family endemic to the southwestern Cape (South Africa), with relatives in Madagascar and Asia. Like many other aquatic invertebrates in Africa, they have been considerably understudied. Research into biodiversity and biogeography allows an understanding of the earth’s biota, producing knowledge which can be used to develop strategies to preserve and monitor this biota. Mismanagement of water systems places biodiversity of river fauna under an ever-increasing extinction threat. This investigation explores rivers in under-collected areas to determine how well teloganodids have been represented in the literature, with four genera and five species described at the onset of this study. A lectotype for Lestagella penicillata Barnard (1940) has been elected and described in detail, setting “benchmark” characters for future descriptions. Standard DNA sequencing methods provide portions of three mitochondrial genes; cytochrome oxidase subunit I (COI), small subunit ribosomal 16S RNA (16S), 12S ribosomal DNA (12S) and two nuclear genes, Histone 3 (H3) and 28S ribosomal DNA (28S) for up to 255 specimens. Fore and hind wings of 79 teloganodid adults were used to examine phylogenetic signal and evolutionary divergence using geometric morphometrics. A multi-faceted approach is used to investigate relationships between clades and the effects of deep-time climatic and landform changes which have influenced the diversity and distribution seen today. Tree (Bayesian Inference and Maximum Likelihood) and network (parsimony) phylogenies, ancestral reconstruction, historical biogeography and wingevolution of the Teloganodidae are investigated. Species tree analyses discovered 27 species and six genera. Distinct lineages are restricted to catchments, and strong phylogeographic structure was found within most genera. Southern African Teloganodidae are shown to have originated in the Cretaceous, with divergence and dispersal of lineages depended on their established locality at the time of tectonic events (uplift) and climatic changes (sea level regressions and transgressions). Geographic clines in wing-shape of Lestagella across its range imply evolutionary adaptations to specific catchment landscape and environment. A detailed analysis of biodiversity has many valuable contributions, from directing future research, understanding adaptive processes, fine-tuning phylogeographical and evolutionary hypotheses, to improving management and conservation decisions in order to preserve endemic biodiversity hotspots.
- Full Text:
Phylogenetics of the keratin-feeding beetle family Trogidae (Coleoptera: Scarabaeoidea)
- Authors: Strümpher, Werner Petrus
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/1232 , vital:20037
- Description: Trogidae constitute a monophyletic and biologically unique family within the Scarabaeoidea, being the only keratinophagous group in its superfamily. Traditionally, the family has been divided into three distinctive genera, Omorgus Erichson, Polynoncus Burmeister, and Trox Fabricius. Although the taxonomy of the group is relatively well studied, recently changes to the existing classification have been proposed without the family as currently constituted being subjected to phylogenetic analyses. In this study I present the first molecular phylogeny for this cosmopolitan family, based on three partially sequenced gene regions: 16SrRNA, 18S rRNA and 28S rRNA domain 2. Analyses resolved relationships between and within genera and subgenera that are largely congruent with existing taxonomic hypotheses based on morphology. I recovered four well-supported radiations: Polynoncus, Omorgus, Holarctic Trox and Afrotropical Phoberus. One of the more surprising results was the monophyly of Phoberus. Based on the evidence, I propose reinstating the genus Phoberus to accommodate all Afrotropical (including Madagascan endemic) species. The results re-emphasise the validity of Scholtz’s (1986a) classification system for the genus Omorgusand its subgeneraand provide evidence of an African origin for Madagascan trogids. Divergence analysis was able to date the major events for the origin of extant lineages of Trogidae. The subsequent diversification of the major lineages is largely attributed to Pangaean and Gondwanan vicariance events in the Mid-Jurassic and early Late Cretaceous, respectively. The separation of the landmasses resulted in the evolution of four distinct groups: Omorgus, Polynoncus, Trox and Phoberus. The monophyletic subgenus Phoberus MacLeay is of particular interest; about one-third (14 of 40) of the species in the Afrotropical region have lost the ability to fly. To gain insights into the evolution of flightlessness in this clade, phylogenetic relationships among species were inferred using molecular sequence data. Four partial sequences of four genes (COI, 16S, 18S and 28S domain 2) were obtained for 27 species, covering all of the recognised species-groups. Estimated times of divergence were based on published mutation rates for COI. The results recovered eight monophyletic lineages, supporting the morphology-based subdivisions of the genus. Flightlessness evolved at least five times within the subgenus. There is no strong support for the re-acquisition of functional wings once they are lost. Diversification, and the present relictual distributions, in African Phoberus can be linked to climatic and geological events associated with the Miocene and Pliocene Climate Optimum in southern Africa. The evolution of flightlessness in Phoberus is consistent with the habitat stability hypothesis. All flightless species occupy refugial areas with relatively long-term environmental stability. Phoberus is a promising model group for studying evolutionary trends relating to flightlessness, speciation and biogeography. Flightlessness is a counterintuitive evolutionary development, given the many advantages of flight. To interpret the diversification in the flightless Phoberus capensis Scholtz, the phylogenetic relationships among several populations of P. capensis are investigated. Phylogenetic relationships among populations were inferred using molecular sequence data that suggested three distinct evolutionary lineages, which was also supported by morphological characters. Divergence time estimates suggest a Pliocene-Pleistocene diversification. Based on these results, it is suggested that P. capensis experienced climatically-driven allopatric speciation with sheltered Afrotemperate forests and high mountain peaks serving as important refugia in response to climatic exacerbations. The P. capensis complex thus represents a speciation process in which flight-restricted populations evolved in close allopatry, possibly as recently as the Pleistocene. Two of the three divergent and geographically distinct lineages are described as novel species. This study represents the most recent comprehensive work on the Trogidae. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. Trogidae are formally divided into two subfamilies, Omorginae and Troginae. The subgenus Phoberus is restored to genus rank to include all the Afrotropical species, and Afromorgus is confirmed at subgeneric rank. The genus Madagatrox is synonymised with Phoberus.
- Full Text:
- Authors: Strümpher, Werner Petrus
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/1232 , vital:20037
- Description: Trogidae constitute a monophyletic and biologically unique family within the Scarabaeoidea, being the only keratinophagous group in its superfamily. Traditionally, the family has been divided into three distinctive genera, Omorgus Erichson, Polynoncus Burmeister, and Trox Fabricius. Although the taxonomy of the group is relatively well studied, recently changes to the existing classification have been proposed without the family as currently constituted being subjected to phylogenetic analyses. In this study I present the first molecular phylogeny for this cosmopolitan family, based on three partially sequenced gene regions: 16SrRNA, 18S rRNA and 28S rRNA domain 2. Analyses resolved relationships between and within genera and subgenera that are largely congruent with existing taxonomic hypotheses based on morphology. I recovered four well-supported radiations: Polynoncus, Omorgus, Holarctic Trox and Afrotropical Phoberus. One of the more surprising results was the monophyly of Phoberus. Based on the evidence, I propose reinstating the genus Phoberus to accommodate all Afrotropical (including Madagascan endemic) species. The results re-emphasise the validity of Scholtz’s (1986a) classification system for the genus Omorgusand its subgeneraand provide evidence of an African origin for Madagascan trogids. Divergence analysis was able to date the major events for the origin of extant lineages of Trogidae. The subsequent diversification of the major lineages is largely attributed to Pangaean and Gondwanan vicariance events in the Mid-Jurassic and early Late Cretaceous, respectively. The separation of the landmasses resulted in the evolution of four distinct groups: Omorgus, Polynoncus, Trox and Phoberus. The monophyletic subgenus Phoberus MacLeay is of particular interest; about one-third (14 of 40) of the species in the Afrotropical region have lost the ability to fly. To gain insights into the evolution of flightlessness in this clade, phylogenetic relationships among species were inferred using molecular sequence data. Four partial sequences of four genes (COI, 16S, 18S and 28S domain 2) were obtained for 27 species, covering all of the recognised species-groups. Estimated times of divergence were based on published mutation rates for COI. The results recovered eight monophyletic lineages, supporting the morphology-based subdivisions of the genus. Flightlessness evolved at least five times within the subgenus. There is no strong support for the re-acquisition of functional wings once they are lost. Diversification, and the present relictual distributions, in African Phoberus can be linked to climatic and geological events associated with the Miocene and Pliocene Climate Optimum in southern Africa. The evolution of flightlessness in Phoberus is consistent with the habitat stability hypothesis. All flightless species occupy refugial areas with relatively long-term environmental stability. Phoberus is a promising model group for studying evolutionary trends relating to flightlessness, speciation and biogeography. Flightlessness is a counterintuitive evolutionary development, given the many advantages of flight. To interpret the diversification in the flightless Phoberus capensis Scholtz, the phylogenetic relationships among several populations of P. capensis are investigated. Phylogenetic relationships among populations were inferred using molecular sequence data that suggested three distinct evolutionary lineages, which was also supported by morphological characters. Divergence time estimates suggest a Pliocene-Pleistocene diversification. Based on these results, it is suggested that P. capensis experienced climatically-driven allopatric speciation with sheltered Afrotemperate forests and high mountain peaks serving as important refugia in response to climatic exacerbations. The P. capensis complex thus represents a speciation process in which flight-restricted populations evolved in close allopatry, possibly as recently as the Pleistocene. Two of the three divergent and geographically distinct lineages are described as novel species. This study represents the most recent comprehensive work on the Trogidae. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. Trogidae are formally divided into two subfamilies, Omorginae and Troginae. The subgenus Phoberus is restored to genus rank to include all the Afrotropical species, and Afromorgus is confirmed at subgeneric rank. The genus Madagatrox is synonymised with Phoberus.
- Full Text:
Physicochemical and antimicrobial photodynamic chemotherapy of unsymmetrical indium phthalocyanines alone or in the presence of magnetic nanoparticles
- Osifeko, Olawale L, Uddin, Imran, Mashazi, Philani N, Nyokong, Tebello
- Authors: Osifeko, Olawale L , Uddin, Imran , Mashazi, Philani N , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/189121 , vital:44818 , xlink:href="https://doi.org/10.1039/C5NJ01922B"
- Description: An AB3 type photosensitiser, consisting of 4-pyridylsulfanyl units (denoted as B3) and one aminophenoxy (denoted as A) group (complex 3) was synthesized. Complex 3 was then quaternized to form complex 4. The aminophenoxy substituent of complex 3 was used for the formation of the amide linkage with the carboxylic functionalised magnetic nanoparticles. Complexes 3 and 4 and their conjugates with magnetic nanoparticles were then used for photodynamic antimicrobial chemotherapy on E. coli. The cationic photosensitiser 4 showed a high efficiency for photodynamic antimicrobial chemotherapy at a very low concentration compared to its conjugate on E. coli.
- Full Text:
- Authors: Osifeko, Olawale L , Uddin, Imran , Mashazi, Philani N , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/189121 , vital:44818 , xlink:href="https://doi.org/10.1039/C5NJ01922B"
- Description: An AB3 type photosensitiser, consisting of 4-pyridylsulfanyl units (denoted as B3) and one aminophenoxy (denoted as A) group (complex 3) was synthesized. Complex 3 was then quaternized to form complex 4. The aminophenoxy substituent of complex 3 was used for the formation of the amide linkage with the carboxylic functionalised magnetic nanoparticles. Complexes 3 and 4 and their conjugates with magnetic nanoparticles were then used for photodynamic antimicrobial chemotherapy on E. coli. The cationic photosensitiser 4 showed a high efficiency for photodynamic antimicrobial chemotherapy at a very low concentration compared to its conjugate on E. coli.
- Full Text:
Pitched
- Authors: Du Plessis, Jana
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:6002 , http://hdl.handle.net/10962/d1021209
- Description: Pitched is a novella made up of short stories. It is about breaking in, breaking down and breaking out of the advertising industry. My protagonist loves and hates this confusing world she lives in. She is tough but also emotional and anxious, often trapped between her strong desires and her strong morality. She finds herself both attracted to and repulsed by the people who inhabit this world - sexy wolf-like men, and prickly female execs alike. I have been inspired by the work of Lidia Yuknavitch, Kate Zambreno, Michelle Tea and Chris Kraus to create a universal woman I can identify with.
- Full Text:
- Authors: Du Plessis, Jana
- Date: 2016
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:6002 , http://hdl.handle.net/10962/d1021209
- Description: Pitched is a novella made up of short stories. It is about breaking in, breaking down and breaking out of the advertising industry. My protagonist loves and hates this confusing world she lives in. She is tough but also emotional and anxious, often trapped between her strong desires and her strong morality. She finds herself both attracted to and repulsed by the people who inhabit this world - sexy wolf-like men, and prickly female execs alike. I have been inspired by the work of Lidia Yuknavitch, Kate Zambreno, Michelle Tea and Chris Kraus to create a universal woman I can identify with.
- Full Text:
Planning adaptation to climate change in fast-warming marine regions with seafood-dependent coastal communities
- Hobday, Alistair J, Cochrane, Kevern L, Howard, James, Aswani, Shankar, Byfield, Val, Duggan, Greg, Duna, Elethu, Dutra, Leo X C, Frusher, Stewart D, Fulton, Elizabeth A, Gammage, Louise, Gasalla, Maria A, Griffiths, Chevon, Guissamulo, Almeida, Haward, Marcus, Jarre, Astrid, Jennings, Sarah M, Jordan, Tia, Joyner, Jessica, Ramani, Narayana K, Shanmugasundaram, Swathi L P, Malherbe, Willem, Ortega-Cisneros, Kelly, Paytan, Adina, Pecl, Gretta T, Plagányi, Éva E, Popova, Ekaterina E, Razafindrainibe, Haja, Roberts, Michael J, Rohit, Prathiba, Sainulabdeen, Shyam S, Sauer, Warwick H H, Valappil, Sathianandan T, Zacharia, Paryiappanal U, Van Putten, E Ingrid
- Authors: Hobday, Alistair J , Cochrane, Kevern L , Howard, James , Aswani, Shankar , Byfield, Val , Duggan, Greg , Duna, Elethu , Dutra, Leo X C , Frusher, Stewart D , Fulton, Elizabeth A , Gammage, Louise , Gasalla, Maria A , Griffiths, Chevon , Guissamulo, Almeida , Haward, Marcus , Jarre, Astrid , Jennings, Sarah M , Jordan, Tia , Joyner, Jessica , Ramani, Narayana K , Shanmugasundaram, Swathi L P , Malherbe, Willem , Ortega-Cisneros, Kelly , Paytan, Adina , Pecl, Gretta T , Plagányi, Éva E , Popova, Ekaterina E , Razafindrainibe, Haja , Roberts, Michael J , Rohit, Prathiba , Sainulabdeen, Shyam S , Sauer, Warwick H H , Valappil, Sathianandan T , Zacharia, Paryiappanal U , Van Putten, E Ingrid
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125675 , vital:35806 , https://doi.10.1007/s11160-016-9419-0
- Description: Many coastal communities rely on living marine resources for livelihoods and food security. These resources are commonly under stress from overfishing, pollution, coastal development and habitat degradation. Climate change is an additional stressor beginning to impact coastal systems and communities, but may also lead to opportunities for some species and the people they sustain. We describe the research approach for a multi-country project, focused on the southern hemisphere, designed to contribute to improving fishing community adaptation efforts by characterizing, assessing and predicting the future of coastal-marine food resources, and codeveloping adaptation options through the provision and sharing of knowledge across fast-warming marine regions (i.e. marine ‘hotspots’). These hotspots represent natural laboratories for observing change and concomitant human adaptive responses, and for developing adaptation options and management strategies. Focusing on adaptation options and strategies for enhancing coastal resilience at the local level will contribute to capacity building and local empowerment in order to minimise negative outcomes and take advantage of opportunities arising from climate change. However, developing comparative approaches across regions that differ in political institutions, socio-economic community demographics, resource dependency and research capacity is challenging. Here, we describe physical, biological, social and governance tools to allow hotspot comparisons, and several methods to evaluate and enhance interactions within a multi-nation research team. Strong partnerships within and between the focal regions are critical to scientific and political support for development of effective approaches to reduce future vulnerability. Comparing these hotspot regions will enhance local adaptation responses and generate outcomes applicable to other regions.
- Full Text:
- Authors: Hobday, Alistair J , Cochrane, Kevern L , Howard, James , Aswani, Shankar , Byfield, Val , Duggan, Greg , Duna, Elethu , Dutra, Leo X C , Frusher, Stewart D , Fulton, Elizabeth A , Gammage, Louise , Gasalla, Maria A , Griffiths, Chevon , Guissamulo, Almeida , Haward, Marcus , Jarre, Astrid , Jennings, Sarah M , Jordan, Tia , Joyner, Jessica , Ramani, Narayana K , Shanmugasundaram, Swathi L P , Malherbe, Willem , Ortega-Cisneros, Kelly , Paytan, Adina , Pecl, Gretta T , Plagányi, Éva E , Popova, Ekaterina E , Razafindrainibe, Haja , Roberts, Michael J , Rohit, Prathiba , Sainulabdeen, Shyam S , Sauer, Warwick H H , Valappil, Sathianandan T , Zacharia, Paryiappanal U , Van Putten, E Ingrid
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125675 , vital:35806 , https://doi.10.1007/s11160-016-9419-0
- Description: Many coastal communities rely on living marine resources for livelihoods and food security. These resources are commonly under stress from overfishing, pollution, coastal development and habitat degradation. Climate change is an additional stressor beginning to impact coastal systems and communities, but may also lead to opportunities for some species and the people they sustain. We describe the research approach for a multi-country project, focused on the southern hemisphere, designed to contribute to improving fishing community adaptation efforts by characterizing, assessing and predicting the future of coastal-marine food resources, and codeveloping adaptation options through the provision and sharing of knowledge across fast-warming marine regions (i.e. marine ‘hotspots’). These hotspots represent natural laboratories for observing change and concomitant human adaptive responses, and for developing adaptation options and management strategies. Focusing on adaptation options and strategies for enhancing coastal resilience at the local level will contribute to capacity building and local empowerment in order to minimise negative outcomes and take advantage of opportunities arising from climate change. However, developing comparative approaches across regions that differ in political institutions, socio-economic community demographics, resource dependency and research capacity is challenging. Here, we describe physical, biological, social and governance tools to allow hotspot comparisons, and several methods to evaluate and enhance interactions within a multi-nation research team. Strong partnerships within and between the focal regions are critical to scientific and political support for development of effective approaches to reduce future vulnerability. Comparing these hotspot regions will enhance local adaptation responses and generate outcomes applicable to other regions.
- Full Text:
Plasmodium falciparum Hep1 is required to prevent the self aggregation of PfHsp70-3
- Nyakundi, David O, Vuko, Loyiso A M, Bentley, Stephen J, Hoppe, Heinrich C, Blatch, Gregory L, Boshoff, Aileen
- Authors: Nyakundi, David O , Vuko, Loyiso A M , Bentley, Stephen J , Hoppe, Heinrich C , Blatch, Gregory L , Boshoff, Aileen
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66109 , vital:28903 , https://doi.org/10.1371/journal.pone.0156446
- Description: publisher version , The majority of mitochondrial proteins are encoded in the nucleus and need to be imported from the cytosol into the mitochondria, and molecular chaperones play a key role in the efficient translocation and proper folding of these proteins in the matrix. One such molecular chaperone is the eukaryotic mitochondrial heat shock protein 70 (Hsp70); however, it is prone to self-aggregation and requires the presence of an essential zinc-finger protein, Hsp70-escort protein 1 (Hep1), to maintain its structure and function. PfHsp70-3, the only Hsp70 predicted to localize in the mitochondria of P. falciparum, may also rely on a Hep1 orthologue to prevent self-aggregation. In this study, we identified a putative Hep1 orthologue in P. falciparum and co-expression of PfHsp70-3 and PfHep1 enhanced the solubility of PfHsp70-3. PfHep1 suppressed the thermally induced aggregation of PfHsp70-3 but not the aggregation of malate dehydrogenase or citrate synthase, thus showing specificity for PfHsp70-3. Zinc ions were indeed essential for maintaining the function of PfHep1, as EDTA chelation abrogated its abilities to suppress the aggregation of PfHsp70-3. Soluble and functional PfHsp70-3, acquired by co-expression with PfHep-1, will facilitate the biochemical characterisation of this particular Hsp70 protein and its evaluation as a drug target for the treatment of malaria. , This work was funded by grants from the National Research Foundation (NRF); grant number 87663 and Deutsche Forschungsgemeinschaft (DFG); grant number LI 402/14-1. D.O.N. is the recipient of academic development and training funds from Mwenge Catholic University, Moshi, Tanzania. S.J.B. is the recipient of an NRF Doctoral Innovation Scholarship.
- Full Text:
- Authors: Nyakundi, David O , Vuko, Loyiso A M , Bentley, Stephen J , Hoppe, Heinrich C , Blatch, Gregory L , Boshoff, Aileen
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66109 , vital:28903 , https://doi.org/10.1371/journal.pone.0156446
- Description: publisher version , The majority of mitochondrial proteins are encoded in the nucleus and need to be imported from the cytosol into the mitochondria, and molecular chaperones play a key role in the efficient translocation and proper folding of these proteins in the matrix. One such molecular chaperone is the eukaryotic mitochondrial heat shock protein 70 (Hsp70); however, it is prone to self-aggregation and requires the presence of an essential zinc-finger protein, Hsp70-escort protein 1 (Hep1), to maintain its structure and function. PfHsp70-3, the only Hsp70 predicted to localize in the mitochondria of P. falciparum, may also rely on a Hep1 orthologue to prevent self-aggregation. In this study, we identified a putative Hep1 orthologue in P. falciparum and co-expression of PfHsp70-3 and PfHep1 enhanced the solubility of PfHsp70-3. PfHep1 suppressed the thermally induced aggregation of PfHsp70-3 but not the aggregation of malate dehydrogenase or citrate synthase, thus showing specificity for PfHsp70-3. Zinc ions were indeed essential for maintaining the function of PfHep1, as EDTA chelation abrogated its abilities to suppress the aggregation of PfHsp70-3. Soluble and functional PfHsp70-3, acquired by co-expression with PfHep-1, will facilitate the biochemical characterisation of this particular Hsp70 protein and its evaluation as a drug target for the treatment of malaria. , This work was funded by grants from the National Research Foundation (NRF); grant number 87663 and Deutsche Forschungsgemeinschaft (DFG); grant number LI 402/14-1. D.O.N. is the recipient of academic development and training funds from Mwenge Catholic University, Moshi, Tanzania. S.J.B. is the recipient of an NRF Doctoral Innovation Scholarship.
- Full Text:
Plasmodium falciparum Hsp70-z, an Hsp110 homologue, exhibits independent chaperone activity and interacts with Hsp70-1 in a nucleotide-dependent fashion
- Ziningwa, Tawanda, Achilonu, Ikechukwu, Hoppe, Heinrich C, Prinsloo, Earl, Dirr, Heinrich W, Shonhai, Addmore
- Authors: Ziningwa, Tawanda , Achilonu, Ikechukwu , Hoppe, Heinrich C , Prinsloo, Earl , Dirr, Heinrich W , Shonhai, Addmore
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/431765 , vital:72802 , xlink:href="https://doi.org/10.1007/s12192-016-0678-4"
- Description: The role of molecular chaperones, among them heat shock proteins (Hsps), in the development of malaria parasites has been well documented. Hsp70s are molecular chaperones that facilitate protein folding. Hsp70 proteins are composed of an N-terminal nucleotide binding domain (NBD), which confers them with ATPase activity and a Cterminal substrate binding domain (SBD). In the ADPbound state, Hsp70 possesses high affinity for substrate and releases the folded substrate when it is bound to ATP. The two domains are connected by a conserved linker segment. Hsp110 proteins possess an extended lid segment, a feature that distinguishes them from canonical Hsp70s.
- Full Text:
- Authors: Ziningwa, Tawanda , Achilonu, Ikechukwu , Hoppe, Heinrich C , Prinsloo, Earl , Dirr, Heinrich W , Shonhai, Addmore
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/431765 , vital:72802 , xlink:href="https://doi.org/10.1007/s12192-016-0678-4"
- Description: The role of molecular chaperones, among them heat shock proteins (Hsps), in the development of malaria parasites has been well documented. Hsp70s are molecular chaperones that facilitate protein folding. Hsp70 proteins are composed of an N-terminal nucleotide binding domain (NBD), which confers them with ATPase activity and a Cterminal substrate binding domain (SBD). In the ADPbound state, Hsp70 possesses high affinity for substrate and releases the folded substrate when it is bound to ATP. The two domains are connected by a conserved linker segment. Hsp110 proteins possess an extended lid segment, a feature that distinguishes them from canonical Hsp70s.
- Full Text:
Politics at a distance from the state: radical, South African and Zimbabwean praxis today
- Helliker, Kirk D, Van der Walt, Lucien
- Authors: Helliker, Kirk D , Van der Walt, Lucien
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/71364 , vital:29837 , https://doi.org/10.1080/02589001.2016.1240792
- Description: For decades, most anti-capitalist and anti-imperialist movements identified radical social transformation with the capture of state power. The collapse of supposedly enabling states led recently to a crisis of left and working class politics. But this has also opened space for the rediscovery of society-centred, anti-capitalist modes of bottom-up change, labelled as ‘at a distance’ politics. These modes have registered important successes in practice, such as the Zapatistas in Mexico, and have involved strands of anarchism and syndicalism, and autonomist Marxism. This article, an introduction to a collection of papers emerging from a 2012 conference of academics and activists in South Africa, aims to help articulate an understanding of social transformation from below that has been analytically and politically side-lined not only in South Africa (and Zimbabwe), but globally. In doing so, it provides a preliminary attempt to map and create a dialogue between three major positions within the broad category of ‘at a distance’ politics.
- Full Text: false
- Authors: Helliker, Kirk D , Van der Walt, Lucien
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/71364 , vital:29837 , https://doi.org/10.1080/02589001.2016.1240792
- Description: For decades, most anti-capitalist and anti-imperialist movements identified radical social transformation with the capture of state power. The collapse of supposedly enabling states led recently to a crisis of left and working class politics. But this has also opened space for the rediscovery of society-centred, anti-capitalist modes of bottom-up change, labelled as ‘at a distance’ politics. These modes have registered important successes in practice, such as the Zapatistas in Mexico, and have involved strands of anarchism and syndicalism, and autonomist Marxism. This article, an introduction to a collection of papers emerging from a 2012 conference of academics and activists in South Africa, aims to help articulate an understanding of social transformation from below that has been analytically and politically side-lined not only in South Africa (and Zimbabwe), but globally. In doing so, it provides a preliminary attempt to map and create a dialogue between three major positions within the broad category of ‘at a distance’ politics.
- Full Text: false
Population assessment and feeding ecology of brown hyenas (hyaena brunnea) in Mountain Zebra National Park, Eastern Cape, South Africa
- Authors: Comley, Jessica
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2862 , vital:20336
- Description: The development of many small (<400 km2), enclosed game reserves in the Eastern Cape Province of South Africa over the past 25 years has contributed greatly to the conservation of large carnivores. However, the brown hyena (Hyaena brunnea) is one of the least studied large carnivores in South Africa. Nevertheless, the reintroduction of this species (n=3 in 2008) into Mountain Zebra National Park (MZNP) provided the perfect opportunity to broaden our understanding of the role that this carnivore plays in an enclosed system. Camera trap data was collected for just over a year from April 2014 to April 2015 and brown hyena density estimates were calculated using spatially explicit capture-recapture analysis. Left-side images of brown hyenas were used in the analysis and 12 individuals were positively identified. The best model to estimate brown hyena density included a road covariate and estimated brown hyena density to be 6-10 individuals/100 km2 (an absolute abundance of between 12 and 21 individuals), which is higher than densities calculated for brown hyenas in other arid, open systems. In, addition, brown hyena scat samples were collected over a five year period from April 2011 to June 2015 and standard techniques for scat analysis were used to identify prey items. Cheetah (Acinonyx jubatus) and lion (Panthera leo) kill site data were used to investigate the impacts of these species on the diet of brown hyenas. Before the release of lions brown hyenas predominantly scavenged on medium-sized mammals, which was what the cheetahs mainly killed. However, after the release of the lions, brown hyenas predominantly scavenged on large mammals, which was what the lions primarily killed. The results from my study indicate that brown hyenas are most likely reaching high densities in enclosed systems, due to increased scavenging opportunities provided by other large predators. The rapid increase of brown hyena densities from small founder populations in enclosed reserves could result in inbreeding. Therefore, in order to successfully conserve brown hyenas and other large carnivores in South Africa, continual post-release monitoring and possible implementation of meta-population management schemes is required.
- Full Text:
- Authors: Comley, Jessica
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/2862 , vital:20336
- Description: The development of many small (<400 km2), enclosed game reserves in the Eastern Cape Province of South Africa over the past 25 years has contributed greatly to the conservation of large carnivores. However, the brown hyena (Hyaena brunnea) is one of the least studied large carnivores in South Africa. Nevertheless, the reintroduction of this species (n=3 in 2008) into Mountain Zebra National Park (MZNP) provided the perfect opportunity to broaden our understanding of the role that this carnivore plays in an enclosed system. Camera trap data was collected for just over a year from April 2014 to April 2015 and brown hyena density estimates were calculated using spatially explicit capture-recapture analysis. Left-side images of brown hyenas were used in the analysis and 12 individuals were positively identified. The best model to estimate brown hyena density included a road covariate and estimated brown hyena density to be 6-10 individuals/100 km2 (an absolute abundance of between 12 and 21 individuals), which is higher than densities calculated for brown hyenas in other arid, open systems. In, addition, brown hyena scat samples were collected over a five year period from April 2011 to June 2015 and standard techniques for scat analysis were used to identify prey items. Cheetah (Acinonyx jubatus) and lion (Panthera leo) kill site data were used to investigate the impacts of these species on the diet of brown hyenas. Before the release of lions brown hyenas predominantly scavenged on medium-sized mammals, which was what the cheetahs mainly killed. However, after the release of the lions, brown hyenas predominantly scavenged on large mammals, which was what the lions primarily killed. The results from my study indicate that brown hyenas are most likely reaching high densities in enclosed systems, due to increased scavenging opportunities provided by other large predators. The rapid increase of brown hyena densities from small founder populations in enclosed reserves could result in inbreeding. Therefore, in order to successfully conserve brown hyenas and other large carnivores in South Africa, continual post-release monitoring and possible implementation of meta-population management schemes is required.
- Full Text:
Possible futures for science and engineering education
- Blackie, Margaret A L, Le Roux, Kate, McKenna, Sioux
- Authors: Blackie, Margaret A L , Le Roux, Kate , McKenna, Sioux
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66796 , vital:28994 , ISSN 1573-174X , https://doi.org/10.1007/s10734-015-9962-y
- Description: Publisher version , From Introduction: The understanding that the science, engineering, technology and mathematics disciplines (STEM) have a significant and directly causal role to play in economic productivity and innovation has driven an increased focus on these fields in higher education. Innovation in this context is a shorthand for the harnessing of the knowledge economy and the provision of products with novel significant ‘added value’. The assumption in both developed and developing economies alike is that STEM will drive national growth (World Bank 2002; UNESCO 2009), and this impacts on demands that universities provide competent graduates in sufficient numbers. However, exactly what ‘competency’ might mean in this context is open to debate.
- Full Text: false
- Authors: Blackie, Margaret A L , Le Roux, Kate , McKenna, Sioux
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66796 , vital:28994 , ISSN 1573-174X , https://doi.org/10.1007/s10734-015-9962-y
- Description: Publisher version , From Introduction: The understanding that the science, engineering, technology and mathematics disciplines (STEM) have a significant and directly causal role to play in economic productivity and innovation has driven an increased focus on these fields in higher education. Innovation in this context is a shorthand for the harnessing of the knowledge economy and the provision of products with novel significant ‘added value’. The assumption in both developed and developing economies alike is that STEM will drive national growth (World Bank 2002; UNESCO 2009), and this impacts on demands that universities provide competent graduates in sufficient numbers. However, exactly what ‘competency’ might mean in this context is open to debate.
- Full Text: false
Post-apartheid nostalgia and the sadomasochistic pleasures of archival art
- Authors: Nsele, Zamansele
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/458648 , vital:75758 , https://hdl.handle.net/10520/EJC199624
- Description: The burgeoning genre of archival art practice in post-apartheid South Africa has catalysed the evocation of nostalgia in abundance. The archive has been at the centre of numerous exhibitions in contemporary art. This paper explores the meaning of an emerging nostalgic turn in post-apartheid South Africa. The discussion considers the pleasure afforded by the sentimentality underpinning nostalgia and attends to the manner in which nostalgia coheres with the creative and aesthetic techniques of archival art. Scopophilia and the covert function of the sadomasochistic gaze are outlined. It is suggested that such acts of retrieval and repetition generally override ethical considerations in part because they unfold from the realm of the unconscious. The paper draws on psychoanalysis by way of Frantz Fanon.
- Full Text:
- Authors: Nsele, Zamansele
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/458648 , vital:75758 , https://hdl.handle.net/10520/EJC199624
- Description: The burgeoning genre of archival art practice in post-apartheid South Africa has catalysed the evocation of nostalgia in abundance. The archive has been at the centre of numerous exhibitions in contemporary art. This paper explores the meaning of an emerging nostalgic turn in post-apartheid South Africa. The discussion considers the pleasure afforded by the sentimentality underpinning nostalgia and attends to the manner in which nostalgia coheres with the creative and aesthetic techniques of archival art. Scopophilia and the covert function of the sadomasochistic gaze are outlined. It is suggested that such acts of retrieval and repetition generally override ethical considerations in part because they unfold from the realm of the unconscious. The paper draws on psychoanalysis by way of Frantz Fanon.
- Full Text:
Post-apartheid nostalgia and the sadomasochistic pleasures of archival art:
- Authors: Nsele, Zamansele
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/145598 , vital:38450 , DOI : 10.4314/eia.v43i3.6
- Description: The burgeoning genre of archival art practice in post-apartheid South Africa has catalysed the evocation of nostalgia in abundance. The archive has been at the centre of numerous exhibitions in contemporary art. This paper explores the meaning of an emerging nostalgic turn in post-apartheid South Africa. The discussion considers the pleasure afforded by the sentimentality underpinning nostalgia and attends to the manner in which nostalgia coheres with the creative and aesthetic techniques of archival art. Scopophilia and the covert function of the sadomasochistic gaze are outlined. It is suggested that such acts of retrieval and repetition generally override ethical considerations in part because they unfold from the realm of the unconscious. The paper draws on psychoanalysis by way of Frantz Fanon.
- Full Text:
- Authors: Nsele, Zamansele
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/145598 , vital:38450 , DOI : 10.4314/eia.v43i3.6
- Description: The burgeoning genre of archival art practice in post-apartheid South Africa has catalysed the evocation of nostalgia in abundance. The archive has been at the centre of numerous exhibitions in contemporary art. This paper explores the meaning of an emerging nostalgic turn in post-apartheid South Africa. The discussion considers the pleasure afforded by the sentimentality underpinning nostalgia and attends to the manner in which nostalgia coheres with the creative and aesthetic techniques of archival art. Scopophilia and the covert function of the sadomasochistic gaze are outlined. It is suggested that such acts of retrieval and repetition generally override ethical considerations in part because they unfold from the realm of the unconscious. The paper draws on psychoanalysis by way of Frantz Fanon.
- Full Text:
Potential benefits and experienced challenges of small household biogas-digesters for rural households
- Authors: Langley, Kyle Anthony
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4789 , http://hdl.handle.net/10962/d1021268
- Description: Access to renewable energy supplies is a critical foundation for sustainable development and poverty alleviation. Anaerobic biogas-digesters also referred to as bio-digesters, have been identified as one of the leading technologies with regards to assisting in improving energy access for remote rural areas that still remain dependent upon biomass usage. This thesis assesses the potential feasibility of bio-digesters for rural households in South Africa by focusing on the experiences of a remote and rural community in Eastern Cape. A standardised survey was used to capture household details and energy use patterns of households with 180 interviews being conducted. Field observations were also conducted on the five bio-digesters installed in the community over a three month period. Despite the predominance of electrification in the community, households were heavily reliant upon biomass in the form of fuelwood and cattle dung to supplement their energy needs. Households supplemented their energy usage with alternative energy sources such as LPG gas and paraffin, especially during periods when electricity was unavailable or deemed too expensive. Initial knowledge of bio-digester technology in the community was non-existent, however with the installation of bio-digesters within the targeted villages, social learning was observed. Despite low temperatures bio-digesters continued to function throughout the study period, though malfunctions did occur and gas production did not reach optimal levels. Primary challenges encountered were the lack of financial subsidies for wide-spread adoption; the limited technical capacity of the community to conduct repairs and minimal gas production due to a build-up of ligneous materials within the gas chamber of the bio-digesters. Bio-digesters were found to provide significant benefits for households and further studies into maximising their effectiveness for rural South African households are recommended.
- Full Text:
- Authors: Langley, Kyle Anthony
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4789 , http://hdl.handle.net/10962/d1021268
- Description: Access to renewable energy supplies is a critical foundation for sustainable development and poverty alleviation. Anaerobic biogas-digesters also referred to as bio-digesters, have been identified as one of the leading technologies with regards to assisting in improving energy access for remote rural areas that still remain dependent upon biomass usage. This thesis assesses the potential feasibility of bio-digesters for rural households in South Africa by focusing on the experiences of a remote and rural community in Eastern Cape. A standardised survey was used to capture household details and energy use patterns of households with 180 interviews being conducted. Field observations were also conducted on the five bio-digesters installed in the community over a three month period. Despite the predominance of electrification in the community, households were heavily reliant upon biomass in the form of fuelwood and cattle dung to supplement their energy needs. Households supplemented their energy usage with alternative energy sources such as LPG gas and paraffin, especially during periods when electricity was unavailable or deemed too expensive. Initial knowledge of bio-digester technology in the community was non-existent, however with the installation of bio-digesters within the targeted villages, social learning was observed. Despite low temperatures bio-digesters continued to function throughout the study period, though malfunctions did occur and gas production did not reach optimal levels. Primary challenges encountered were the lack of financial subsidies for wide-spread adoption; the limited technical capacity of the community to conduct repairs and minimal gas production due to a build-up of ligneous materials within the gas chamber of the bio-digesters. Bio-digesters were found to provide significant benefits for households and further studies into maximising their effectiveness for rural South African households are recommended.
- Full Text:
Predators of aerial insects and riparian cross-boundary trophic dynamics: web-building spiders, dragonflies and damselflies
- Authors: Chari, Lenin Dzibakwe
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/55791 , vital:26734
- Description: This thesis characterises the cross-boundary trophic interactions of a relatively small model ecosystem, the Kowie River (Eastern Cape of South Africa), to explore their epistemic implications for systems ecology. Using web-building spiders and odonates (dragonflies and damselflies) as model organisms, I sought to investigate whether the diets of predators of aerial insects could be used to assess the strength of the trophic connectivity between freshwater and terrestrial systems in relation to variables such as stream width, distance from the river and aquatic insect emergence rates and abundances. Predator diet composition was determined by using a combination of diet analysis tools: direct observations of cross-subsidies, naturally-abundant stable (carbon and nitrogen) isotope analysis and fatty acid analysis. I also sought to reveal feeding niches and guilds among riparian aerial predators and investigate how the environment influenced predators’ access to aquatic prey subsidies. As emergent aquatic insect abundances decreased with an increase in distance from the river, and increased with stream width and seasonal changes from winter to summer, stable isotope and fatty acid analyses revealed distinct changes in web-building spider diet composition. Examination of the fatty acid eicosapentaenoic acid, a component commonly used as an indicator of consumer reliance on aquatic nutritional subsidies, showed that aquatic subsidies extended further inland at the wider sections of the river. Spiders and odonates at the wider sections of the Kowie River generally received more subsidies (56 – 70%) than those at the narrower sections (25 – 60%). When terrestrial insect biomass was distinctly low in winter, the benefit of aquatic subsidisation to spiders was relatively lower at the narrower sections of the Kowie River relative to the wide sections. As such, riparian areas adjacent to wide parts of the river were more likely to support larger populations of aerial predators than those at the narrow sections. Apart from the diet changes across time and space, there was evidence of inter-specific niche partitioning in both spiders and odonates, but no differences were observed between males and females of the same species. Results showed odonates of different sizes and hunting strategies had separate dietary niches, hence varied access to aquatic nutritional subsidies. The larger odonate taxa that frequently foraged mid-air had more varied diets and relied less on aquatic emergent insects than the smaller odonates that foraged from perches near the river. There was also evidence of niche partitioning amongst the spiders, as those that built horizontal webs captured more aquatic insects (40 – 78%) than the vertical orb-web builders (20 – 66%). This study showed that the nature and extent of trophic cross-boundary linkages in riparian areas largely depended on the availability of subsidies that varied seasonally and spatially. The width of the stream and seasonal variability emerged as important predictors of emergent insect abundances/biomasses that influenced predator feeding niches. The high mobility of odonates made their reliance on aquatic nutritional subsidies different from the less mobile spiders. The link between the width of the river and the extent of trophic connectivity has implications for riparian area management and definition of riparian buffer zones. However, the variation in diet niches amongst terrestrial consumers makes the results area-specific, and more studies are required that incorporate additional terrestrial predators in other fluvial systems so that we can make some generalizations on the dynamics of riparian trophic cross-boundary links.
- Full Text:
- Authors: Chari, Lenin Dzibakwe
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/55791 , vital:26734
- Description: This thesis characterises the cross-boundary trophic interactions of a relatively small model ecosystem, the Kowie River (Eastern Cape of South Africa), to explore their epistemic implications for systems ecology. Using web-building spiders and odonates (dragonflies and damselflies) as model organisms, I sought to investigate whether the diets of predators of aerial insects could be used to assess the strength of the trophic connectivity between freshwater and terrestrial systems in relation to variables such as stream width, distance from the river and aquatic insect emergence rates and abundances. Predator diet composition was determined by using a combination of diet analysis tools: direct observations of cross-subsidies, naturally-abundant stable (carbon and nitrogen) isotope analysis and fatty acid analysis. I also sought to reveal feeding niches and guilds among riparian aerial predators and investigate how the environment influenced predators’ access to aquatic prey subsidies. As emergent aquatic insect abundances decreased with an increase in distance from the river, and increased with stream width and seasonal changes from winter to summer, stable isotope and fatty acid analyses revealed distinct changes in web-building spider diet composition. Examination of the fatty acid eicosapentaenoic acid, a component commonly used as an indicator of consumer reliance on aquatic nutritional subsidies, showed that aquatic subsidies extended further inland at the wider sections of the river. Spiders and odonates at the wider sections of the Kowie River generally received more subsidies (56 – 70%) than those at the narrower sections (25 – 60%). When terrestrial insect biomass was distinctly low in winter, the benefit of aquatic subsidisation to spiders was relatively lower at the narrower sections of the Kowie River relative to the wide sections. As such, riparian areas adjacent to wide parts of the river were more likely to support larger populations of aerial predators than those at the narrow sections. Apart from the diet changes across time and space, there was evidence of inter-specific niche partitioning in both spiders and odonates, but no differences were observed between males and females of the same species. Results showed odonates of different sizes and hunting strategies had separate dietary niches, hence varied access to aquatic nutritional subsidies. The larger odonate taxa that frequently foraged mid-air had more varied diets and relied less on aquatic emergent insects than the smaller odonates that foraged from perches near the river. There was also evidence of niche partitioning amongst the spiders, as those that built horizontal webs captured more aquatic insects (40 – 78%) than the vertical orb-web builders (20 – 66%). This study showed that the nature and extent of trophic cross-boundary linkages in riparian areas largely depended on the availability of subsidies that varied seasonally and spatially. The width of the stream and seasonal variability emerged as important predictors of emergent insect abundances/biomasses that influenced predator feeding niches. The high mobility of odonates made their reliance on aquatic nutritional subsidies different from the less mobile spiders. The link between the width of the river and the extent of trophic connectivity has implications for riparian area management and definition of riparian buffer zones. However, the variation in diet niches amongst terrestrial consumers makes the results area-specific, and more studies are required that incorporate additional terrestrial predators in other fluvial systems so that we can make some generalizations on the dynamics of riparian trophic cross-boundary links.
- Full Text:
Prediction of protein secondary structure using binary classificationtrees, naive Bayes classifiers and the Logistic Regression Classifier
- Eldud Omer, Ahmed Abdelkarim
- Authors: Eldud Omer, Ahmed Abdelkarim
- Date: 2016
- Subjects: Bayesian statistical decision theory , Logistic regression analysis , Biostatistics , Proteins -- Structure
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5581 , http://hdl.handle.net/10962/d1019985
- Description: The secondary structure of proteins is predicted using various binary classifiers. The data are adopted from the RS126 database. The original data consists of protein primary and secondary structure sequences. The original data is encoded using alphabetic letters. These data are encoded into unary vectors comprising ones and zeros only. Different binary classifiers, namely the naive Bayes, logistic regression and classification trees using hold-out and 5-fold cross validation are trained using the encoded data. For each of the classifiers three classification tasks are considered, namely helix against not helix (H/∼H), sheet against not sheet (S/∼S) and coil against not coil (C/∼C). The performance of these binary classifiers are compared using the overall accuracy in predicting the protein secondary structure for various window sizes. Our result indicate that hold-out cross validation achieved higher accuracy than 5-fold cross validation. The Naive Bayes classifier, using 5-fold cross validation achieved, the lowest accuracy for predicting helix against not helix. The classification tree classifiers, using 5-fold cross validation, achieved the lowest accuracies for both coil against not coil and sheet against not sheet classifications. The logistic regression classier accuracy is dependent on the window size; there is a positive relationship between the accuracy and window size. The logistic regression classier approach achieved the highest accuracy when compared to the classification tree and Naive Bayes classifiers for each classification task; predicting helix against not helix with accuracy 77.74 percent, for sheet against not sheet with accuracy 81.22 percent and for coil against not coil with accuracy 73.39 percent. It is noted that it is easier to compare classifiers if the classification process could be completely facilitated in R. Alternatively, it would be easier to assess these logistic regression classifiers if SPSS had a function to determine the accuracy of the logistic regression classifier.
- Full Text:
- Authors: Eldud Omer, Ahmed Abdelkarim
- Date: 2016
- Subjects: Bayesian statistical decision theory , Logistic regression analysis , Biostatistics , Proteins -- Structure
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5581 , http://hdl.handle.net/10962/d1019985
- Description: The secondary structure of proteins is predicted using various binary classifiers. The data are adopted from the RS126 database. The original data consists of protein primary and secondary structure sequences. The original data is encoded using alphabetic letters. These data are encoded into unary vectors comprising ones and zeros only. Different binary classifiers, namely the naive Bayes, logistic regression and classification trees using hold-out and 5-fold cross validation are trained using the encoded data. For each of the classifiers three classification tasks are considered, namely helix against not helix (H/∼H), sheet against not sheet (S/∼S) and coil against not coil (C/∼C). The performance of these binary classifiers are compared using the overall accuracy in predicting the protein secondary structure for various window sizes. Our result indicate that hold-out cross validation achieved higher accuracy than 5-fold cross validation. The Naive Bayes classifier, using 5-fold cross validation achieved, the lowest accuracy for predicting helix against not helix. The classification tree classifiers, using 5-fold cross validation, achieved the lowest accuracies for both coil against not coil and sheet against not sheet classifications. The logistic regression classier accuracy is dependent on the window size; there is a positive relationship between the accuracy and window size. The logistic regression classier approach achieved the highest accuracy when compared to the classification tree and Naive Bayes classifiers for each classification task; predicting helix against not helix with accuracy 77.74 percent, for sheet against not sheet with accuracy 81.22 percent and for coil against not coil with accuracy 73.39 percent. It is noted that it is easier to compare classifiers if the classification process could be completely facilitated in R. Alternatively, it would be easier to assess these logistic regression classifiers if SPSS had a function to determine the accuracy of the logistic regression classifier.
- Full Text:
Preference for C4 shade grasses increases hatchling performance in the butterfly, Bicyclus safitza
- Nokelainen, Ossi, Ripley, Bradford Sherman, Van Bergen, Erik, Osborne, Colin P, Brakefield, Paul M
- Authors: Nokelainen, Ossi , Ripley, Bradford Sherman , Van Bergen, Erik , Osborne, Colin P , Brakefield, Paul M
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61424 , vital:28025 , http://onlinelibrary.wiley.com/doi/10.1002/ece3.2235/full
- Description: The Miocene radiation of C4 grasses under high-temperature and low ambient CO2 levels occurred alongside the transformation of a largely forested landscape into savanna. This inevitably changed the host plant regime of herbivores, and the simultaneous diversification of many consumer lineages, including Bicyclus butterflies in Africa, suggests that the radiations of grasses and grazers may be evolutionary linked. We examined mechanisms for this plant–herbivore interaction with the grass-feeding Bicyclus safitza in South Africa. In a controlled environment, we tested oviposition preference and hatchling performance on local grasses with C3 or C4 photosynthetic pathways that grow either in open or shaded habitats. We predicted preference for C3 plants due to a hypothesized lower processing cost and higher palatability to herbivores. In contrast, we found that females preferred C4 shade grasses rather than either C4 grasses from open habitats or C3 grasses. The oviposition preference broadly followed hatchling performance, although hatchling survival was equally good on C4 or C3 shade grasses. This finding was explained by leaf toughness; shade grasses were softer than grasses from open habitats. Field monitoring revealed a preference of adults for shaded habitats, and stable isotope analysis of field-sampled individuals confirmed their preference for C4 grasses as host plants. Our findings suggest that plant–herbivore interactions can influence the direction of selection in a grass-feeding butterfly. Based on this work, we postulate future research to test whether these interactions more generally contribute to radiations in herbivorous insects via expansions into new, unexploited ecological niches.
- Full Text:
- Authors: Nokelainen, Ossi , Ripley, Bradford Sherman , Van Bergen, Erik , Osborne, Colin P , Brakefield, Paul M
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61424 , vital:28025 , http://onlinelibrary.wiley.com/doi/10.1002/ece3.2235/full
- Description: The Miocene radiation of C4 grasses under high-temperature and low ambient CO2 levels occurred alongside the transformation of a largely forested landscape into savanna. This inevitably changed the host plant regime of herbivores, and the simultaneous diversification of many consumer lineages, including Bicyclus butterflies in Africa, suggests that the radiations of grasses and grazers may be evolutionary linked. We examined mechanisms for this plant–herbivore interaction with the grass-feeding Bicyclus safitza in South Africa. In a controlled environment, we tested oviposition preference and hatchling performance on local grasses with C3 or C4 photosynthetic pathways that grow either in open or shaded habitats. We predicted preference for C3 plants due to a hypothesized lower processing cost and higher palatability to herbivores. In contrast, we found that females preferred C4 shade grasses rather than either C4 grasses from open habitats or C3 grasses. The oviposition preference broadly followed hatchling performance, although hatchling survival was equally good on C4 or C3 shade grasses. This finding was explained by leaf toughness; shade grasses were softer than grasses from open habitats. Field monitoring revealed a preference of adults for shaded habitats, and stable isotope analysis of field-sampled individuals confirmed their preference for C4 grasses as host plants. Our findings suggest that plant–herbivore interactions can influence the direction of selection in a grass-feeding butterfly. Based on this work, we postulate future research to test whether these interactions more generally contribute to radiations in herbivorous insects via expansions into new, unexploited ecological niches.
- Full Text:
Presentation and representation of environmental problems and problem-solving methods and processes in the Grade 10 Geography syllabus: a Namibian case study
- Authors: Zokka, Herman Kankara
- Date: 2016
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: vital:2074 , http://hdl.handle.net/10962/d1021253
- Description: Environmental issues in Namibia are considered to be one of the major threats to the lives of the Namibian people (Namibia. Ministry of National Planning Commission [MNPC], 2004). This study explored problem solving as one of the teaching methods used in Grade 10 Geography syllabuses as a response to such environmental issues/risks. Geography provides learners with an understanding of the issues and risks in their world that need to be addressed in order to improve the quality of their lives and health of their environment. This study focused on how environmental problems and problem-solving methods are presented in the Namibian Grade 10 Geography syllabus and how these are represented and implemented through teacher intentionality and practice. The theoretical framework for this study was informed by two theories namely risk society and social constructivism. This study was conducted at three schools in the Rundu circuit in the Kavango region and one teacher was involved in the study at each school. This study was conducted within an interpretive research tradition and was qualitative in nature. The study used document analysis, focus group discussion and classroom observation as data generation methods. The findings of the study reveal that the complexity of environmental issues is highlighted in the syllabus and in teachers’ intentionality and practice. The findings also show that a limited variety of teaching methods were used in problem solving strategies. The study also found that problem solving was influenced by different constructivist learning principles. The study further found that limited numbers of problem-solving steps were used in the process of problem solving. The study concludes by calling for further research into problem solving strategies. This can be done to empower Geography teachers to use more complex problem solving strategies to deepen problem solving and to engage problems in more depth.
- Full Text:
- Authors: Zokka, Herman Kankara
- Date: 2016
- Language: English
- Type: Thesis , Masters , MEd
- Identifier: vital:2074 , http://hdl.handle.net/10962/d1021253
- Description: Environmental issues in Namibia are considered to be one of the major threats to the lives of the Namibian people (Namibia. Ministry of National Planning Commission [MNPC], 2004). This study explored problem solving as one of the teaching methods used in Grade 10 Geography syllabuses as a response to such environmental issues/risks. Geography provides learners with an understanding of the issues and risks in their world that need to be addressed in order to improve the quality of their lives and health of their environment. This study focused on how environmental problems and problem-solving methods are presented in the Namibian Grade 10 Geography syllabus and how these are represented and implemented through teacher intentionality and practice. The theoretical framework for this study was informed by two theories namely risk society and social constructivism. This study was conducted at three schools in the Rundu circuit in the Kavango region and one teacher was involved in the study at each school. This study was conducted within an interpretive research tradition and was qualitative in nature. The study used document analysis, focus group discussion and classroom observation as data generation methods. The findings of the study reveal that the complexity of environmental issues is highlighted in the syllabus and in teachers’ intentionality and practice. The findings also show that a limited variety of teaching methods were used in problem solving strategies. The study also found that problem solving was influenced by different constructivist learning principles. The study further found that limited numbers of problem-solving steps were used in the process of problem solving. The study concludes by calling for further research into problem solving strategies. This can be done to empower Geography teachers to use more complex problem solving strategies to deepen problem solving and to engage problems in more depth.
- Full Text:
Principled, pragmatic revitalisation of catchment management forums in South Africa
- Munnik, Victor, Burt, Jane C, Price, Leigh, Barnes, Garth, Ashe, Bryan, Motloung, Sysman
- Authors: Munnik, Victor , Burt, Jane C , Price, Leigh , Barnes, Garth , Ashe, Bryan , Motloung, Sysman
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/436743 , vital:73298 , ISBN 978-1-4312-0831-9 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/TT%20682-17.pdf
- Description: There are many views on Catchment Management Forums (CMFs). They are seen as places for enthusiastic participation, communities of practice in the making, and crucial to the devo-lution of water management to local stakeholders. They are also seen as exhausted, toothless talk shops, unrepresenta-tive, undemocratic, haunts of the privileged, ignored by officials and a waste of time.
- Full Text:
- Authors: Munnik, Victor , Burt, Jane C , Price, Leigh , Barnes, Garth , Ashe, Bryan , Motloung, Sysman
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/436743 , vital:73298 , ISBN 978-1-4312-0831-9 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/TT%20682-17.pdf
- Description: There are many views on Catchment Management Forums (CMFs). They are seen as places for enthusiastic participation, communities of practice in the making, and crucial to the devo-lution of water management to local stakeholders. They are also seen as exhausted, toothless talk shops, unrepresenta-tive, undemocratic, haunts of the privileged, ignored by officials and a waste of time.
- Full Text:
Principles of Control Protocol Design and Implementation
- Eales, Andrew, Foss, Richard
- Authors: Eales, Andrew , Foss, Richard
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/426801 , vital:72392 , https://www.aes.org/e-lib/online/browse.cfm?elib=18238
- Description: Control protocols are used within audio networks to manage both audio streams and networked audio devices. A number of control protocols for audio devices have been recently developed, including the AES standards AES64-2012 and AES70-2015. Despite these developments, an ontology of control protocol design and implementation does not exist. This paper proposes design and implementation heuristics for control protocols. Different categories of control protocol design and implementation heuristics are presented and the implications of individual heuristics are discussed. These heuristics allow the features provided by different control protocols to be compared and evaluated and provide guidelines for future control protocol development.
- Full Text:
- Authors: Eales, Andrew , Foss, Richard
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/426801 , vital:72392 , https://www.aes.org/e-lib/online/browse.cfm?elib=18238
- Description: Control protocols are used within audio networks to manage both audio streams and networked audio devices. A number of control protocols for audio devices have been recently developed, including the AES standards AES64-2012 and AES70-2015. Despite these developments, an ontology of control protocol design and implementation does not exist. This paper proposes design and implementation heuristics for control protocols. Different categories of control protocol design and implementation heuristics are presented and the implications of individual heuristics are discussed. These heuristics allow the features provided by different control protocols to be compared and evaluated and provide guidelines for future control protocol development.
- Full Text:
Purification and characterization of β-mannanase from Aspergillus terreus and its applicability in depolymerization of mannans and saccharification of lignocellulosic biomass
- Soni, Hemant, Rawat, Hemant Kumar, Kango, Naveen
- Authors: Soni, Hemant , Rawat, Hemant Kumar , Kango, Naveen
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66167 , vital:28912 , https://doi.org/10.1007/s13205-016-0454-2
- Description: publisher version , Aspergillus terreus FBCC 1369 was grown in solid-state culture under statistically optimized conditions. β-Mannanase was purified to apparent homogeneity by ultrafiltration, anion exchange and gel filtration chromatography. A purification factor of 10.3-fold was achieved, with the purified enzyme exhibiting specific activity of 53 U/mg protein. The purified β-mannanase was optimally active at pH 7.0 and 70 °C and displayed stability over a broad pH range of 4.0–8.0 and a 30 min half-life at 80 °C. The molecular weight of β-mannanase was calculated as ~49 kDa by SDS-PAGE. The enzyme exhibited K m and V maxvalues of 5.9 mg/ml and 39.42 µmol/ml/min, respectively. β-Mannanase activity was stimulated by β-mercaptoethanol and strongly inhibited by Hg2+. The β-Mannanase did not hydrolyze mannobiose and mannotriose, but only mannotetraose liberating mannose and mannotriose. This indicated that at least four mannose residues were required for catalytic activity. Oligosaccharide with a degree of polymerization (DP) three was the predominant product in the case of locust bean gum (16.5 %) and guar gum (15.8 %) hydrolysis. However, the enzyme liberated DP4 oligosaccharide (24 %) exclusively from konjac gum. This property can be exploited in oligosaccharides production with DP 3–4. β-Mannanase hydrolyzed pretreated lignocelluloses and liberated reducing sugars (% theoretical yield) from copra meal (30 %). This property is an important factor for the bioconversion of the biomass.
- Full Text: false
- Authors: Soni, Hemant , Rawat, Hemant Kumar , Kango, Naveen
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66167 , vital:28912 , https://doi.org/10.1007/s13205-016-0454-2
- Description: publisher version , Aspergillus terreus FBCC 1369 was grown in solid-state culture under statistically optimized conditions. β-Mannanase was purified to apparent homogeneity by ultrafiltration, anion exchange and gel filtration chromatography. A purification factor of 10.3-fold was achieved, with the purified enzyme exhibiting specific activity of 53 U/mg protein. The purified β-mannanase was optimally active at pH 7.0 and 70 °C and displayed stability over a broad pH range of 4.0–8.0 and a 30 min half-life at 80 °C. The molecular weight of β-mannanase was calculated as ~49 kDa by SDS-PAGE. The enzyme exhibited K m and V maxvalues of 5.9 mg/ml and 39.42 µmol/ml/min, respectively. β-Mannanase activity was stimulated by β-mercaptoethanol and strongly inhibited by Hg2+. The β-Mannanase did not hydrolyze mannobiose and mannotriose, but only mannotetraose liberating mannose and mannotriose. This indicated that at least four mannose residues were required for catalytic activity. Oligosaccharide with a degree of polymerization (DP) three was the predominant product in the case of locust bean gum (16.5 %) and guar gum (15.8 %) hydrolysis. However, the enzyme liberated DP4 oligosaccharide (24 %) exclusively from konjac gum. This property can be exploited in oligosaccharides production with DP 3–4. β-Mannanase hydrolyzed pretreated lignocelluloses and liberated reducing sugars (% theoretical yield) from copra meal (30 %). This property is an important factor for the bioconversion of the biomass.
- Full Text: false