Integrated computational approaches and tools for allosteric drug discovery:
- Amamuddy, Olivier S, Veldman, Wade, Manyumwa, Colleen, Khairallah, Afrah, Agajanian, Steve, Oluyemi, Odeyemi, Verkhivker, Gennady M, Tastan Bishop, Özlem
- Authors: Amamuddy, Olivier S , Veldman, Wade , Manyumwa, Colleen , Khairallah, Afrah , Agajanian, Steve , Oluyemi, Odeyemi , Verkhivker, Gennady M , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/163012 , vital:41004 , https://doi.org/10.3390/ijms21030847
- Description: Understanding molecular mechanisms underlying the complexity of allosteric regulation in proteins has attracted considerable attention in drug discovery due to the benefits and versatility of allosteric modulators in providing desirable selectivity against protein targets while minimizing toxicity and other side effects. The proliferation of novel computational approaches for predicting ligand–protein interactions and binding using dynamic and network-centric perspectives has led to new insights into allosteric mechanisms and facilitated computer-based discovery of allosteric drugs. Although no absolute method of experimental and in silico allosteric drug/site discovery exists, current methods are still being improved. As such, the critical analysis and integration of established approaches into robust, reproducible, and customizable computational pipelines with experimental feedback could make allosteric drug discovery more efficient and reliable. In this article, we review computational approaches for allosteric drug discovery and discuss how these tools can be utilized to develop consensus workflows for in silico identification of allosteric sites and modulators with some applications to pathogen resistance and precision medicine. The emerging realization that allosteric modulators can exploit distinct regulatory mechanisms and can provide access to targeted modulation of protein activities could open opportunities for probing biological processes and in silico design of drug combinations with improved therapeutic indices and a broad range of activities.
- Full Text:
- Date Issued: 2020
- Authors: Amamuddy, Olivier S , Veldman, Wade , Manyumwa, Colleen , Khairallah, Afrah , Agajanian, Steve , Oluyemi, Odeyemi , Verkhivker, Gennady M , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/163012 , vital:41004 , https://doi.org/10.3390/ijms21030847
- Description: Understanding molecular mechanisms underlying the complexity of allosteric regulation in proteins has attracted considerable attention in drug discovery due to the benefits and versatility of allosteric modulators in providing desirable selectivity against protein targets while minimizing toxicity and other side effects. The proliferation of novel computational approaches for predicting ligand–protein interactions and binding using dynamic and network-centric perspectives has led to new insights into allosteric mechanisms and facilitated computer-based discovery of allosteric drugs. Although no absolute method of experimental and in silico allosteric drug/site discovery exists, current methods are still being improved. As such, the critical analysis and integration of established approaches into robust, reproducible, and customizable computational pipelines with experimental feedback could make allosteric drug discovery more efficient and reliable. In this article, we review computational approaches for allosteric drug discovery and discuss how these tools can be utilized to develop consensus workflows for in silico identification of allosteric sites and modulators with some applications to pathogen resistance and precision medicine. The emerging realization that allosteric modulators can exploit distinct regulatory mechanisms and can provide access to targeted modulation of protein activities could open opportunities for probing biological processes and in silico design of drug combinations with improved therapeutic indices and a broad range of activities.
- Full Text:
- Date Issued: 2020
Impact of emerging mutations on the dynamic properties the SARS-CoV-2 main protease: an in silico investigation
- Amamuddy, Olivier S, Verkhivker, Gennady M, Tastan Bishop, Özlem
- Authors: Amamuddy, Olivier S , Verkhivker, Gennady M , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/163035 , vital:41006 , doi: 10.1021/acs.jcim.0c00634
- Description: The new coronavirus (SARS-CoV-2) is a global threat to world health and its economy. Its main protease (Mpro), which functions as a dimer, cleaves viral precursor proteins in the process of viral maturation. It is a good candidate for drug development owing to its conservation and the absence of a human homolog. An improved understanding of the protein behaviour can accelerate the discovery of effective therapies in order to reduce mortality. 100 ns all-atom molecular dynamics simulations of 50 homology modelled mutant Mpro dimers were performed at pH 7 from filtered sequences obtained from the GISAID database. Protease dynamics were analysed using RMSD, RMSF, Rg, the averaged betweenness centrality and geometry calculations. Domains from each Mpro protomer were found to generally have independent motions, while the dimer-stabilising N-finger region was found to be flexible in most mutants.
- Full Text:
- Date Issued: 2020
- Authors: Amamuddy, Olivier S , Verkhivker, Gennady M , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/163035 , vital:41006 , doi: 10.1021/acs.jcim.0c00634
- Description: The new coronavirus (SARS-CoV-2) is a global threat to world health and its economy. Its main protease (Mpro), which functions as a dimer, cleaves viral precursor proteins in the process of viral maturation. It is a good candidate for drug development owing to its conservation and the absence of a human homolog. An improved understanding of the protein behaviour can accelerate the discovery of effective therapies in order to reduce mortality. 100 ns all-atom molecular dynamics simulations of 50 homology modelled mutant Mpro dimers were performed at pH 7 from filtered sequences obtained from the GISAID database. Protease dynamics were analysed using RMSD, RMSF, Rg, the averaged betweenness centrality and geometry calculations. Domains from each Mpro protomer were found to generally have independent motions, while the dimer-stabilising N-finger region was found to be flexible in most mutants.
- Full Text:
- Date Issued: 2020
Impact of early pandemic stage mutations on molecular dynamics of SARS-CoV-2 Mpro:
- Amamuddy, Olivier S, Verkhivker, Gennady M, Tastan Bishop, Özlem
- Authors: Amamuddy, Olivier S , Verkhivker, Gennady M , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/162330 , vital:40835 , https://0-doi.org.wam.seals.ac.za/10.1021/acs.jcim.0c00634
- Description: A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease (Mpro), which is required for the proteolytic cleavage of viral precursor proteins, is a good candidate for drug development owing to its conservation and the absence of a human homolog. Improving our understanding of Mpro behavior can accelerate the discovery of effective therapies to reduce mortality. All-atom molecular dynamics (MD) simulations (100 ns) of 50 mutant Mpro dimers obtained from filtered sequences from the GISAID database were analyzed using root-mean-square deviation, root-mean-square fluctuation, Rg, averaged betweenness centrality, and geometry calculations.
- Full Text:
- Date Issued: 2020
- Authors: Amamuddy, Olivier S , Verkhivker, Gennady M , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/162330 , vital:40835 , https://0-doi.org.wam.seals.ac.za/10.1021/acs.jcim.0c00634
- Description: A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease (Mpro), which is required for the proteolytic cleavage of viral precursor proteins, is a good candidate for drug development owing to its conservation and the absence of a human homolog. Improving our understanding of Mpro behavior can accelerate the discovery of effective therapies to reduce mortality. All-atom molecular dynamics (MD) simulations (100 ns) of 50 mutant Mpro dimers obtained from filtered sequences from the GISAID database were analyzed using root-mean-square deviation, root-mean-square fluctuation, Rg, averaged betweenness centrality, and geometry calculations.
- Full Text:
- Date Issued: 2020
Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase:
- Amamuddy, Olivier S, Musyoka, Thommas M, Boateng, Rita A, Zabo, Sophakama, Tastan Bishop, Özlem
- Authors: Amamuddy, Olivier S , Musyoka, Thommas M , Boateng, Rita A , Zabo, Sophakama , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148869 , vital:38781 , https://doi.org/10.1016/j.csbj.2020.05.0099
- Description: Pyrazinamide (PZA) is the only first-line antitubercular drug active against latent Mycobacterium tuberculosis (Mtb). It is activated to pyrazinoic acid by the pncA-encoded pyrazinamidase enzyme (PZase). Despite the emergence of PZA drug resistance, the underlying mechanisms of resistance remain unclear. This study investigated part of these mechanisms by modelling a PZA-bound wild type and 82 mutant PZase structures before applying molecular dynamics (MD) with an accurate Fe2+ cofactor coordination geometry.
- Full Text:
- Date Issued: 2020
- Authors: Amamuddy, Olivier S , Musyoka, Thommas M , Boateng, Rita A , Zabo, Sophakama , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148869 , vital:38781 , https://doi.org/10.1016/j.csbj.2020.05.0099
- Description: Pyrazinamide (PZA) is the only first-line antitubercular drug active against latent Mycobacterium tuberculosis (Mtb). It is activated to pyrazinoic acid by the pncA-encoded pyrazinamidase enzyme (PZase). Despite the emergence of PZA drug resistance, the underlying mechanisms of resistance remain unclear. This study investigated part of these mechanisms by modelling a PZA-bound wild type and 82 mutant PZase structures before applying molecular dynamics (MD) with an accurate Fe2+ cofactor coordination geometry.
- Full Text:
- Date Issued: 2020
Understanding the Pyrimethamine drug resistance mechanism via combined molecular dynamics and dynamic residue network analysis:
- Amusengeri, Arnold, Tata, Rolland B, Tastan Bishop, Özlem
- Authors: Amusengeri, Arnold , Tata, Rolland B , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/163022 , vital:41005 , https://doi.org/10.3390/molecules25040904
- Description: In this era of precision medicine, insights into the resistance mechanism of drugs are integral for the development of potent therapeutics. Here, we sought to understand the contribution of four point mutations (N51I, C59R, S108N, and I164L) within the active site of the malaria parasite enzyme dihydrofolate reductase (DHFR) towards the resistance of the antimalarial drug pyrimethamine. Homology modeling was used to obtain full-length models of wild type (WT) and mutant DHFR. Molecular docking was employed to dock pyrimethamine onto the generated structures. Subsequent all-atom molecular dynamics (MD) simulations and binding free-energy computations highlighted that pyrimethamine’s stability and affinity inversely relates to the number of mutations within its binding site and, hence, resistance severity.
- Full Text:
- Date Issued: 2020
- Authors: Amusengeri, Arnold , Tata, Rolland B , Tastan Bishop, Özlem
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/163022 , vital:41005 , https://doi.org/10.3390/molecules25040904
- Description: In this era of precision medicine, insights into the resistance mechanism of drugs are integral for the development of potent therapeutics. Here, we sought to understand the contribution of four point mutations (N51I, C59R, S108N, and I164L) within the active site of the malaria parasite enzyme dihydrofolate reductase (DHFR) towards the resistance of the antimalarial drug pyrimethamine. Homology modeling was used to obtain full-length models of wild type (WT) and mutant DHFR. Molecular docking was employed to dock pyrimethamine onto the generated structures. Subsequent all-atom molecular dynamics (MD) simulations and binding free-energy computations highlighted that pyrimethamine’s stability and affinity inversely relates to the number of mutations within its binding site and, hence, resistance severity.
- Full Text:
- Date Issued: 2020
Macro-locational determinants and motive of Chinese foreign direct investment in Cameroon
- Authors: Andangnui, Quintabella
- Date: 2020
- Subjects: Investments, Foreign -- Cameroon , Investments, Chinese -- Cameroon , Corporations, Foreign -- Cameroon , Industrial location -- Cameroon
- Language: English
- Type: text , Thesis , Masters , MCom
- Identifier: http://hdl.handle.net/10962/163157 , vital:41014
- Description: This research falls under the general themes of macro-locational determinants and motives of Foreign Direct Investment (FDI) and the challenges faced by FDIs. Specifically, the research focuses on macro-locational determinants of FDI and the motives of Chinese FDI in Cameroon, and the challenges faced by Chinese FDI in Cameroon. This research is motivated by China’s interest in African countries as well as the reciprocal interest in Chinese FDI by African countries, especially Cameroon. While various FDI theories and previous empirical studies indicate that macro-locational determinants of FDI constitute a country’s principal comparative advantage to attract FDI, there is still no universally acceptable set of macro-locational determinants of FDI. Furthermore, some empirical studies assert that Chinese FDI does not follow conventional FDI theories or western approaches to FDI, especially when investing in African countries. It is suggested that some widely accepted macro-locational determinants of FDI are frequently ignored by Chinese FDI. While FDI theories identify four motives for FDI (resource-, market-, efficiency-, and strategic asset-seeking) as the main motives for investing in a foreign country, the motives for Chinese FDI, especially in Africa, have been questioned by some scholars, the media and politicians, due to the significant but seemingly counterintuitive investments made by Chinese state-owned FDI in politically unstable resource-rich African countries. Furthermore, differences in the motives of Chinese privately owned and state-owned firms identified in previous empirical studies have raised concerns, particularly regarding the motives of state-owned Chinese firms in Africa which suggest a stance of neo-colonialism by Chinese state-owned FDI. The research aims to identify the significant macro-locational determinants of Chinese FDI in Cameroon, to provide clarity on the motives of Chinese FDI and to identify the challenges faced by Chinese FDI in Cameroon. To achieve the aim of this research, hypothetical relationships based on FDI theory and previous empirical research were formulated between Chinese FDI and the proposed macro-locational determinants of FDI and the four identified motives of FDI. In this research, a positivist research paradigm using quantitative methods was followed. Accordingly, the research design and methodology was underpinned by the positivist paradigm. A descriptive and analytical survey methodology was utilised, using both primary and secondary data sources. Secondary data was collected from reliable and credible databases for the period 2004 to 2018 to generate a time series to test the hypothetical relationships pertaining to the macro-locational determinants of Chinese FDI in Cameroon. To test the hypothetical relationships pertaining to the motives of Chinese FDI and to identify the challenges of Chinese FDI in Cameroon, primary data was collected by means of a questionnaire using convenience and snowball sampling techniques. The validity of the findings on the macro-locational determinants of FDI was confirmed through unit root and cointegration tests. Confirmatory Factor Analysis (CFA) and Cronbach’s alpha coefficients were used to ensure the validity and reliability of the findings on the motives of FDI. To assess the hypothetical relationships on the motives for Chinese FDI, the hypothetical relationship on the macro-locational determinants of FDI was determined using Ordinary Least Square (OLS) regression, t-tests, one-way ANOVA, descriptive statistics and logistic regression. In addition, descriptive statistics were used to analyse the data on the challenges of Chinese FDI. The findings indicated that the main macro-locational determinants of Chinese FDI in Cameroon included market size, political risk, limited trade openness, real effective exchange rate, interest rate and human capital. The findings also indicated that market-seeking constitutes the main motive of privately owned Chinese FDI in Cameroon. The findings also indicated that the top four challenges faced by Chinese FDI in Cameroon include corruption, the ambiguity of the legal system of Cameroon, the difficulty to negotiate with government and privatisation officials and high levels of taxes. The findings of this research serve as a test of theory, given that they determine whether the macro-locational determinants identified from FDI theories are also significant macro-locational determinants of Chinese FDI. Furthermore, the findings have the potential to assist in policy formulation aimed at encouraging Chinese FDI into Cameroon. The findings could also assist the Cameroonian government to allocate national resources efficiently by prioritising identified macro-locational determinants. The findings provide clarity on the motives of Chinese FDI in Cameroon and could assist the government to negotiate better deals that may enable Cameroon to benefit optimally from Chinese FDI.
- Full Text:
- Date Issued: 2020
- Authors: Andangnui, Quintabella
- Date: 2020
- Subjects: Investments, Foreign -- Cameroon , Investments, Chinese -- Cameroon , Corporations, Foreign -- Cameroon , Industrial location -- Cameroon
- Language: English
- Type: text , Thesis , Masters , MCom
- Identifier: http://hdl.handle.net/10962/163157 , vital:41014
- Description: This research falls under the general themes of macro-locational determinants and motives of Foreign Direct Investment (FDI) and the challenges faced by FDIs. Specifically, the research focuses on macro-locational determinants of FDI and the motives of Chinese FDI in Cameroon, and the challenges faced by Chinese FDI in Cameroon. This research is motivated by China’s interest in African countries as well as the reciprocal interest in Chinese FDI by African countries, especially Cameroon. While various FDI theories and previous empirical studies indicate that macro-locational determinants of FDI constitute a country’s principal comparative advantage to attract FDI, there is still no universally acceptable set of macro-locational determinants of FDI. Furthermore, some empirical studies assert that Chinese FDI does not follow conventional FDI theories or western approaches to FDI, especially when investing in African countries. It is suggested that some widely accepted macro-locational determinants of FDI are frequently ignored by Chinese FDI. While FDI theories identify four motives for FDI (resource-, market-, efficiency-, and strategic asset-seeking) as the main motives for investing in a foreign country, the motives for Chinese FDI, especially in Africa, have been questioned by some scholars, the media and politicians, due to the significant but seemingly counterintuitive investments made by Chinese state-owned FDI in politically unstable resource-rich African countries. Furthermore, differences in the motives of Chinese privately owned and state-owned firms identified in previous empirical studies have raised concerns, particularly regarding the motives of state-owned Chinese firms in Africa which suggest a stance of neo-colonialism by Chinese state-owned FDI. The research aims to identify the significant macro-locational determinants of Chinese FDI in Cameroon, to provide clarity on the motives of Chinese FDI and to identify the challenges faced by Chinese FDI in Cameroon. To achieve the aim of this research, hypothetical relationships based on FDI theory and previous empirical research were formulated between Chinese FDI and the proposed macro-locational determinants of FDI and the four identified motives of FDI. In this research, a positivist research paradigm using quantitative methods was followed. Accordingly, the research design and methodology was underpinned by the positivist paradigm. A descriptive and analytical survey methodology was utilised, using both primary and secondary data sources. Secondary data was collected from reliable and credible databases for the period 2004 to 2018 to generate a time series to test the hypothetical relationships pertaining to the macro-locational determinants of Chinese FDI in Cameroon. To test the hypothetical relationships pertaining to the motives of Chinese FDI and to identify the challenges of Chinese FDI in Cameroon, primary data was collected by means of a questionnaire using convenience and snowball sampling techniques. The validity of the findings on the macro-locational determinants of FDI was confirmed through unit root and cointegration tests. Confirmatory Factor Analysis (CFA) and Cronbach’s alpha coefficients were used to ensure the validity and reliability of the findings on the motives of FDI. To assess the hypothetical relationships on the motives for Chinese FDI, the hypothetical relationship on the macro-locational determinants of FDI was determined using Ordinary Least Square (OLS) regression, t-tests, one-way ANOVA, descriptive statistics and logistic regression. In addition, descriptive statistics were used to analyse the data on the challenges of Chinese FDI. The findings indicated that the main macro-locational determinants of Chinese FDI in Cameroon included market size, political risk, limited trade openness, real effective exchange rate, interest rate and human capital. The findings also indicated that market-seeking constitutes the main motive of privately owned Chinese FDI in Cameroon. The findings also indicated that the top four challenges faced by Chinese FDI in Cameroon include corruption, the ambiguity of the legal system of Cameroon, the difficulty to negotiate with government and privatisation officials and high levels of taxes. The findings of this research serve as a test of theory, given that they determine whether the macro-locational determinants identified from FDI theories are also significant macro-locational determinants of Chinese FDI. Furthermore, the findings have the potential to assist in policy formulation aimed at encouraging Chinese FDI into Cameroon. The findings could also assist the Cameroonian government to allocate national resources efficiently by prioritising identified macro-locational determinants. The findings provide clarity on the motives of Chinese FDI in Cameroon and could assist the government to negotiate better deals that may enable Cameroon to benefit optimally from Chinese FDI.
- Full Text:
- Date Issued: 2020
Growth and photosynthetic responses of Acacia (Vachellia) seedlings to atmospheric CO2 increased from glacial to current concentrations: underlying mechanisms and ecological implications
- Authors: Anderson, Bruce Maurice
- Date: 2020
- Subjects: Acacia vachellia , Acacia vachellia -- Growth , Acacia -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/138182 , vital:37604
- Description: The African Acacia species Vachellia karroo, V. robusta, V. nilotica, and V. tortilis are some of the most invasive species implicated in bush encroachment and woody thickening of historically open savannas in southern Africa. This is partially explained by historic increases in atmospheric CO2 concentrations, which are proposed to have promoted the growth and survivorship of C3 tree seedlings relative to C4 grasses. However, the uniformity of CO2 responsiveness and differences among Vachellia species remain largely undetermined. Here we investigate the growth and photosynthetic responses of four Vachellia species, all implicated in woody encroachment, but originating from distinct climatic niches. Exposing these species to a range of sub-ambient CO2 concentrations (12 – 40 Pa) showed that V. karroo, V. robusta, V. nilotica and V. tortilis all responded strongly and fairly consistently to increasing CO2 concentrations, acting as a ‘functional type’ despite being selected from different geographic regions and having different climatic niches. Combined average net CO2 assimilation rates increased by 130% despite significant, but low levels of down-regulation and decreased stomatal conductance. The increased photosynthetic rates stimulated growth and biomass production in all compartments, with no significant differences in interspecific above and below ground allocation. Growth rates and dry biomass increased by 50% and 186%, respectively, while leaf level water use efficiency (ratio of net CO2 assimilation rate to transpiration rate) increased by an average of 218%. When this was scaled to the whole plant level, this stimulation was decreased to 80%. The decrease was the result of the CO2 stimulated increase in canopy areas, which increased leaf area for water loss. The seedlings’ total number of spinescent physical defenses, as well as the average mass and spine mass fraction also increased with rising CO2. These thicker spines could act as better deterrents against vertebrate browsers. Spine density was unchanged, however, showing that the increased spine numbers were associated with larger seedlings at higher CO2 rather than an increase in the number of spines per stem length. The stimulatory effects of increasing CO2 concentrations since the last glacial maximum and resultant increases in seedling growth and biomass are likely to have had important consequences for the survival and establishment of Acacia seedlings. Tolerance of drought and disturbance has been related to seedling size, hence stimulating the growth rate could confer disturbance tolerance and this tolerance would develop more rapidly with increasing CO2 concentrations. Furthermore, increased nitrogen and water use efficiency have the potential to support seedling establishment in environments where these resources would otherwise be limited at lower atmospheric CO2 concentrations. Resulting in a larger proportion of CO2 fertilization responsive woody seedlings surviving the seedling size classes, and persisting within historically open savannas. Where interspecific differences occurred they are likely to have arisen from adaptation to specific climates where these species are native and selection would have been driven by factors such climate, resource availability, levels of disturbance and competitive interactions. V. karroo had the highest growth rates and strong CO2 driven increases in biomass accumulation, despite having the lowest inherent photosynthetic rates. V. karroo also had the lowest increase in water use efficiency and high transpiration rates could potentially increase access to soil nutrients through mass flow. This species had the highest mean spine mass and showed significant increases in spine mass fraction at elevated CO2 concentrations, which may be important for deterring herbivores. V. robusta’s distribution to the mesic east coast of Africa suggests that water is an important limitation to its distribution. Hence, the CO2 stimulated increase in water use efficiency at both leaf and whole canopy level allows speculation that this may be an important driver of this species’ range expansion, which might continue if increasing levels of CO2 continue to promote water use efficiency. V. nilotica occupies a broad range of habitats, inhabiting large areas of the subtropics both north and south of the equator, with the strongest climatic correlates being the precipitation of the wettest quarter followed by high temperature seasonality. In response to increasing CO2, V. nilotica showed overall strong increases in growth, water use efficiency, and physical defenses. These responses may explain why V. nilotica has been such a successful encroacher in a broad range of habitats where limitations are likely to include multiple climatic factors and disturbances. V. tortilis has the widest distribution of all the species studied, covering broad ranges of Africa and only being excluded from the wettest parts of the equator and driest parts of the deserts. In these experiments this species showed the lowest biomass responsiveness to CO2, but had especially large increases in water use efficiency at both the leaf and canopy level. This may have been an important driver for this species’ encroachment into the more arid parts of its distribution, however this link will need to be verified with further experimentation.
- Full Text:
- Date Issued: 2020
- Authors: Anderson, Bruce Maurice
- Date: 2020
- Subjects: Acacia vachellia , Acacia vachellia -- Growth , Acacia -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/138182 , vital:37604
- Description: The African Acacia species Vachellia karroo, V. robusta, V. nilotica, and V. tortilis are some of the most invasive species implicated in bush encroachment and woody thickening of historically open savannas in southern Africa. This is partially explained by historic increases in atmospheric CO2 concentrations, which are proposed to have promoted the growth and survivorship of C3 tree seedlings relative to C4 grasses. However, the uniformity of CO2 responsiveness and differences among Vachellia species remain largely undetermined. Here we investigate the growth and photosynthetic responses of four Vachellia species, all implicated in woody encroachment, but originating from distinct climatic niches. Exposing these species to a range of sub-ambient CO2 concentrations (12 – 40 Pa) showed that V. karroo, V. robusta, V. nilotica and V. tortilis all responded strongly and fairly consistently to increasing CO2 concentrations, acting as a ‘functional type’ despite being selected from different geographic regions and having different climatic niches. Combined average net CO2 assimilation rates increased by 130% despite significant, but low levels of down-regulation and decreased stomatal conductance. The increased photosynthetic rates stimulated growth and biomass production in all compartments, with no significant differences in interspecific above and below ground allocation. Growth rates and dry biomass increased by 50% and 186%, respectively, while leaf level water use efficiency (ratio of net CO2 assimilation rate to transpiration rate) increased by an average of 218%. When this was scaled to the whole plant level, this stimulation was decreased to 80%. The decrease was the result of the CO2 stimulated increase in canopy areas, which increased leaf area for water loss. The seedlings’ total number of spinescent physical defenses, as well as the average mass and spine mass fraction also increased with rising CO2. These thicker spines could act as better deterrents against vertebrate browsers. Spine density was unchanged, however, showing that the increased spine numbers were associated with larger seedlings at higher CO2 rather than an increase in the number of spines per stem length. The stimulatory effects of increasing CO2 concentrations since the last glacial maximum and resultant increases in seedling growth and biomass are likely to have had important consequences for the survival and establishment of Acacia seedlings. Tolerance of drought and disturbance has been related to seedling size, hence stimulating the growth rate could confer disturbance tolerance and this tolerance would develop more rapidly with increasing CO2 concentrations. Furthermore, increased nitrogen and water use efficiency have the potential to support seedling establishment in environments where these resources would otherwise be limited at lower atmospheric CO2 concentrations. Resulting in a larger proportion of CO2 fertilization responsive woody seedlings surviving the seedling size classes, and persisting within historically open savannas. Where interspecific differences occurred they are likely to have arisen from adaptation to specific climates where these species are native and selection would have been driven by factors such climate, resource availability, levels of disturbance and competitive interactions. V. karroo had the highest growth rates and strong CO2 driven increases in biomass accumulation, despite having the lowest inherent photosynthetic rates. V. karroo also had the lowest increase in water use efficiency and high transpiration rates could potentially increase access to soil nutrients through mass flow. This species had the highest mean spine mass and showed significant increases in spine mass fraction at elevated CO2 concentrations, which may be important for deterring herbivores. V. robusta’s distribution to the mesic east coast of Africa suggests that water is an important limitation to its distribution. Hence, the CO2 stimulated increase in water use efficiency at both leaf and whole canopy level allows speculation that this may be an important driver of this species’ range expansion, which might continue if increasing levels of CO2 continue to promote water use efficiency. V. nilotica occupies a broad range of habitats, inhabiting large areas of the subtropics both north and south of the equator, with the strongest climatic correlates being the precipitation of the wettest quarter followed by high temperature seasonality. In response to increasing CO2, V. nilotica showed overall strong increases in growth, water use efficiency, and physical defenses. These responses may explain why V. nilotica has been such a successful encroacher in a broad range of habitats where limitations are likely to include multiple climatic factors and disturbances. V. tortilis has the widest distribution of all the species studied, covering broad ranges of Africa and only being excluded from the wettest parts of the equator and driest parts of the deserts. In these experiments this species showed the lowest biomass responsiveness to CO2, but had especially large increases in water use efficiency at both the leaf and canopy level. This may have been an important driver for this species’ encroachment into the more arid parts of its distribution, however this link will need to be verified with further experimentation.
- Full Text:
- Date Issued: 2020
Screening for small molecule modulators of Trypanosoma brucei Hsp70 chaperone activity based upon alcyonarian coral-derived natural products
- Andreassend, Sarah K, Bentley, Stephen, Blatch, Gregory L, Boshoff, Aileen, Keyzers, Robert A
- Authors: Andreassend, Sarah K , Bentley, Stephen , Blatch, Gregory L , Boshoff, Aileen , Keyzers, Robert A
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/426045 , vital:72309 , xlink:href="https://doi.org/10.3390/md18020081"
- Description: The Trypanosoma brucei Hsp70/J-protein machinery plays an essential role in survival, differentiation, and pathogenesis of the protozoan parasite, and is an emerging target against African Trypanosomiasis. This study evaluated a set of small molecules, inspired by the malonganenones and nuttingins, as modulators of the chaperone activity of the cytosolic heat inducible T. brucei Hsp70 and constitutive TbHsp70.4 proteins. The compounds were assessed for cytotoxicity on both the bloodstream form of T. b. brucei parasites and a mammalian cell line. The compounds were then investigated for their modulatory effect on the aggregation suppression and ATPase activities of the TbHsp70 proteins. A structure–activity relationship for the malonganenone-class of alkaloids is proposed based upon these results.
- Full Text:
- Date Issued: 2020
- Authors: Andreassend, Sarah K , Bentley, Stephen , Blatch, Gregory L , Boshoff, Aileen , Keyzers, Robert A
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/426045 , vital:72309 , xlink:href="https://doi.org/10.3390/md18020081"
- Description: The Trypanosoma brucei Hsp70/J-protein machinery plays an essential role in survival, differentiation, and pathogenesis of the protozoan parasite, and is an emerging target against African Trypanosomiasis. This study evaluated a set of small molecules, inspired by the malonganenones and nuttingins, as modulators of the chaperone activity of the cytosolic heat inducible T. brucei Hsp70 and constitutive TbHsp70.4 proteins. The compounds were assessed for cytotoxicity on both the bloodstream form of T. b. brucei parasites and a mammalian cell line. The compounds were then investigated for their modulatory effect on the aggregation suppression and ATPase activities of the TbHsp70 proteins. A structure–activity relationship for the malonganenone-class of alkaloids is proposed based upon these results.
- Full Text:
- Date Issued: 2020
Performance, functionalism and form in Ịzọn oral poety
- Authors: Armstrong, Imomotimi
- Date: 2020
- Subjects: Ijo (African people , Ijo language , Folk poetry, Ijo , Folk poetry -- Nigeria
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/140641 , vital:37906
- Description: Since the publication of Ruth Finnegan’s influential Oral Literature in Africa, way back in 1970, scholars have been paying earnest attention to oral traditions on the African continent. That seminal book pointed out to Africanist scholars the need to urgently collect and document the oral literatures of their various ethnic groups before they die out. However, it is the verbal arts of the major ethnic groups on the continent that very often benefit from this collection and documentation, as it were. Therefore, this study sought to examine the oral poetry of the Ịzọn, a minority ethnic nationality, located in the oil-rich Niger Delta region of Nigeria. The study employed unstructured interviews and participant observations to collect the data for the research. The transcribed and translated data was examined through three eclectic theories to the study of folklore: Russian formalism, performance and functionalism. The study found out that Ịzọn oral poetry is a combination of songs and one person’s praise chants. Moreover, it revealed that praise chanting is a recent practice amongst the Ịzọn that was introduced into Ịzọnland by Chief Adolphus Munamuna from the Yoruba of southwestern Nigeria. Furthermore, the study established that oral poetry plays important roles amongst the people. Besides, it ascertained that the performance of some sub-categories of the poetry is highly dramatic and theatrical. It also discovered that stylistic techniques such as formula, parallelism, proverb, ideophone, praise title, metaphor, repetition, alliteration, assonance, vowel lengthening, amongst others, give the poetry the quality of “literariness.” In addition, the study found out that the poetry, like oral poetry in other ethnic groups, demonstrates the three qualities of change, adaptability and survival. The study has contributed to existing scholarship on African oral traditions in the sense of collecting, documenting and generating awareness on Ịzọn oral poetry, most importantly pointing out the existence of praise chanting amongst a people who had no such culture and the conditions that gave rise to that practice.
- Full Text:
- Date Issued: 2020
- Authors: Armstrong, Imomotimi
- Date: 2020
- Subjects: Ijo (African people , Ijo language , Folk poetry, Ijo , Folk poetry -- Nigeria
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/140641 , vital:37906
- Description: Since the publication of Ruth Finnegan’s influential Oral Literature in Africa, way back in 1970, scholars have been paying earnest attention to oral traditions on the African continent. That seminal book pointed out to Africanist scholars the need to urgently collect and document the oral literatures of their various ethnic groups before they die out. However, it is the verbal arts of the major ethnic groups on the continent that very often benefit from this collection and documentation, as it were. Therefore, this study sought to examine the oral poetry of the Ịzọn, a minority ethnic nationality, located in the oil-rich Niger Delta region of Nigeria. The study employed unstructured interviews and participant observations to collect the data for the research. The transcribed and translated data was examined through three eclectic theories to the study of folklore: Russian formalism, performance and functionalism. The study found out that Ịzọn oral poetry is a combination of songs and one person’s praise chants. Moreover, it revealed that praise chanting is a recent practice amongst the Ịzọn that was introduced into Ịzọnland by Chief Adolphus Munamuna from the Yoruba of southwestern Nigeria. Furthermore, the study established that oral poetry plays important roles amongst the people. Besides, it ascertained that the performance of some sub-categories of the poetry is highly dramatic and theatrical. It also discovered that stylistic techniques such as formula, parallelism, proverb, ideophone, praise title, metaphor, repetition, alliteration, assonance, vowel lengthening, amongst others, give the poetry the quality of “literariness.” In addition, the study found out that the poetry, like oral poetry in other ethnic groups, demonstrates the three qualities of change, adaptability and survival. The study has contributed to existing scholarship on African oral traditions in the sense of collecting, documenting and generating awareness on Ịzọn oral poetry, most importantly pointing out the existence of praise chanting amongst a people who had no such culture and the conditions that gave rise to that practice.
- Full Text:
- Date Issued: 2020
Towards a capability maturity model for a cyber range
- Authors: Aschmann, Michael Joseph
- Date: 2020
- Subjects: Computer software -- Development , Computer security
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163142 , vital:41013
- Description: This work describes research undertaken towards the development of a Capability Maturity Model (CMM) for Cyber Ranges (CRs) focused on cyber security. Global cyber security needs are on the rise, and the need for attribution within the cyber domain is of particular concern. This has prompted major efforts to enhance cyber capabilities within organisations to increase their total cyber resilience posture. These efforts include, but are not limited to, the testing of computational devices, networks, and applications, and cyber skills training focused on prevention, detection and cyber attack response. A cyber range allows for the testing of the computational environment. By developing cyber events within a confined virtual or sand-boxed cyber environment, a cyber range can prepare the next generation of cyber security specialists to handle a variety of potential cyber attacks. Cyber ranges have different purposes, each designed to fulfil a different computational testing and cyber training goal; consequently, cyber ranges can vary greatly in the level of variety, capability, maturity and complexity. As cyber ranges proliferate and become more and more valued as tools for cyber security, a method to classify or rate them becomes essential. Yet while a universal criteria for measuring cyber ranges in terms of their capability maturity levels becomes more critical, there are currently very limited resources for researchers aiming to perform this kind of work. For this reason, this work proposes and describes a CMM, designed to give organisations the ability to benchmark the capability maturity of a given cyber range. This research adopted a synthesised approach to the development of a CMM, grounded in prior research and focused on the production of a conceptual model that provides a useful level of abstraction. In order to achieve this goal, the core capability elements of a cyber range are defined with their relative importance, allowing for the development of a proposed classification cyber range levels. An analysis of data gathered during the course of an expert review, together with other research, further supported the development of the conceptual model. In the context of cyber range capability, classification will include the ability of the cyber range to perform its functions optimally with different core capability elements, focusing on the Measurement of Capability (MoC) with its elements, namely effect, performance and threat ability. Cyber range maturity can evolve over time and can be defined through the Measurement of Maturity (MoM) with its elements, namely people, processes, technology. The combination of these measurements utilising the CMM for a CR determines the capability maturity level of a CR. The primary outcome of this research is the proposed level-based CMM framework for a cyber range, developed using adopted and synthesised CMMs, the analysis of an expert review, and the mapping of the results.
- Full Text:
- Date Issued: 2020
- Authors: Aschmann, Michael Joseph
- Date: 2020
- Subjects: Computer software -- Development , Computer security
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/163142 , vital:41013
- Description: This work describes research undertaken towards the development of a Capability Maturity Model (CMM) for Cyber Ranges (CRs) focused on cyber security. Global cyber security needs are on the rise, and the need for attribution within the cyber domain is of particular concern. This has prompted major efforts to enhance cyber capabilities within organisations to increase their total cyber resilience posture. These efforts include, but are not limited to, the testing of computational devices, networks, and applications, and cyber skills training focused on prevention, detection and cyber attack response. A cyber range allows for the testing of the computational environment. By developing cyber events within a confined virtual or sand-boxed cyber environment, a cyber range can prepare the next generation of cyber security specialists to handle a variety of potential cyber attacks. Cyber ranges have different purposes, each designed to fulfil a different computational testing and cyber training goal; consequently, cyber ranges can vary greatly in the level of variety, capability, maturity and complexity. As cyber ranges proliferate and become more and more valued as tools for cyber security, a method to classify or rate them becomes essential. Yet while a universal criteria for measuring cyber ranges in terms of their capability maturity levels becomes more critical, there are currently very limited resources for researchers aiming to perform this kind of work. For this reason, this work proposes and describes a CMM, designed to give organisations the ability to benchmark the capability maturity of a given cyber range. This research adopted a synthesised approach to the development of a CMM, grounded in prior research and focused on the production of a conceptual model that provides a useful level of abstraction. In order to achieve this goal, the core capability elements of a cyber range are defined with their relative importance, allowing for the development of a proposed classification cyber range levels. An analysis of data gathered during the course of an expert review, together with other research, further supported the development of the conceptual model. In the context of cyber range capability, classification will include the ability of the cyber range to perform its functions optimally with different core capability elements, focusing on the Measurement of Capability (MoC) with its elements, namely effect, performance and threat ability. Cyber range maturity can evolve over time and can be defined through the Measurement of Maturity (MoM) with its elements, namely people, processes, technology. The combination of these measurements utilising the CMM for a CR determines the capability maturity level of a CR. The primary outcome of this research is the proposed level-based CMM framework for a cyber range, developed using adopted and synthesised CMMs, the analysis of an expert review, and the mapping of the results.
- Full Text:
- Date Issued: 2020
Using Translanguaging in Higher Education to Empower Students' Voices and Enable Epistemological Becoming
- Asfour, Fouad-Martin, Ndabula, Yanela, Chakona, Gamuchirai, Mason, Paul, Oluwole, David O
- Authors: Asfour, Fouad-Martin , Ndabula, Yanela , Chakona, Gamuchirai , Mason, Paul , Oluwole, David O
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/425506 , vital:72251 , xlink:href="https://doi.org/10.29086/2519-5476/2020/sp31a4"
- Description: This article is based on research conducted by a group of plurilingual postgraduate students from different disciplines who facilitated writing groups at the Centre for Postgraduate Studies at Rhodes University over the past two years. It is based on self-reflective writing of language biographies and aims to raise attention about, and to open up a discussion on, the impact of social and personal language practices. We approach the role of language not only as complex interrogation of academic identity, but also as sense of embodied self, an active element in the formation of geo- and body-politics of knowledge which has been highlighted in recent literature focussing on translanguaging in education and decolonising the curricula of Higher Education. Following selfguided research, we engaged in a critical reflection on the use of home languages in education and consulted relevant literature that argues for the inclusion of translanguaging practices in Higher Education. Our research, therefore, focuses on new epistemologies afforded by a shift away from the monolingual habitus and from the concept of multilingualism towards plurilingualism and translanguaging. Our data suggests that a plurilingual approach towards teaching and learning in Higher Education can afford epistemological access to learners across faculties and disciplines in Higher Education, and we argue that the role of languages of tuition in curricula need to be strategically re-evaluated.
- Full Text:
- Date Issued: 2020
- Authors: Asfour, Fouad-Martin , Ndabula, Yanela , Chakona, Gamuchirai , Mason, Paul , Oluwole, David O
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/425506 , vital:72251 , xlink:href="https://doi.org/10.29086/2519-5476/2020/sp31a4"
- Description: This article is based on research conducted by a group of plurilingual postgraduate students from different disciplines who facilitated writing groups at the Centre for Postgraduate Studies at Rhodes University over the past two years. It is based on self-reflective writing of language biographies and aims to raise attention about, and to open up a discussion on, the impact of social and personal language practices. We approach the role of language not only as complex interrogation of academic identity, but also as sense of embodied self, an active element in the formation of geo- and body-politics of knowledge which has been highlighted in recent literature focussing on translanguaging in education and decolonising the curricula of Higher Education. Following selfguided research, we engaged in a critical reflection on the use of home languages in education and consulted relevant literature that argues for the inclusion of translanguaging practices in Higher Education. Our research, therefore, focuses on new epistemologies afforded by a shift away from the monolingual habitus and from the concept of multilingualism towards plurilingualism and translanguaging. Our data suggests that a plurilingual approach towards teaching and learning in Higher Education can afford epistemological access to learners across faculties and disciplines in Higher Education, and we argue that the role of languages of tuition in curricula need to be strategically re-evaluated.
- Full Text:
- Date Issued: 2020
New directions in Maritime and Fisheries Anthropology:
- Authors: Aswani, Shankar
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/179028 , vital:40101 , https://0-doi.org.wam.seals.ac.za/10.1111/aman.13380
- Description: Maritime and fisheries anthropology is a mixture of different themes couched under various theoretical frameworks that straddle the humanities and the sciences. In this subject survey, I explore different thematic and theoretical strands of maritime and fisheries anthropology and illustrate broader changes in this subdiscipline since around the mid‐1990s. I also review developing and future thematic and theoretical research frontiers, and discuss their potential contribution to a public and actionable anthropology/scholarship that can better inform fisheries management and conservation. This is important because in the twenty‐first century, coastal peoples are facing socioeconomic and environmental challenges that are increasingly becoming hazardous. To create a more actionable discipline, anthropology needs to be more accessible, inform innovation, and recapture a more pluralistic scholarship that champions interdisciplinary work. This will require the consilience between the humanities and natural sciences for studying human–marine interactions more broadly and for protecting the marine environment.
- Full Text:
- Date Issued: 2020
- Authors: Aswani, Shankar
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/179028 , vital:40101 , https://0-doi.org.wam.seals.ac.za/10.1111/aman.13380
- Description: Maritime and fisheries anthropology is a mixture of different themes couched under various theoretical frameworks that straddle the humanities and the sciences. In this subject survey, I explore different thematic and theoretical strands of maritime and fisheries anthropology and illustrate broader changes in this subdiscipline since around the mid‐1990s. I also review developing and future thematic and theoretical research frontiers, and discuss their potential contribution to a public and actionable anthropology/scholarship that can better inform fisheries management and conservation. This is important because in the twenty‐first century, coastal peoples are facing socioeconomic and environmental challenges that are increasingly becoming hazardous. To create a more actionable discipline, anthropology needs to be more accessible, inform innovation, and recapture a more pluralistic scholarship that champions interdisciplinary work. This will require the consilience between the humanities and natural sciences for studying human–marine interactions more broadly and for protecting the marine environment.
- Full Text:
- Date Issued: 2020
Detecting change in local ecological knowledge: An application of an index of taxonomic distinctness to an ethnoichthyological classification in the Solomon Islands
- Aswani, Shankar, Ferse, Sebastien C, Stäbler, Moritz, Chong-Montenegro, Carolina
- Authors: Aswani, Shankar , Ferse, Sebastien C , Stäbler, Moritz , Chong-Montenegro, Carolina
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/406521 , vital:70282 , xlink:href="https://doi.org/10.1016/j.ecolind.2020.106865"
- Description: The global accelerating loss of biodiversity is having immediate repercussions for ecosystems and human wellbeing, particularly in areas where people depend intimately on their natural environment for their livelihoods. Dovetailing this loss is the demise of local/traditional knowledge systems resulting from factors such as changing lifestyle and the transformation of local belief systems. While the importance of local ecological knowledge (LEK) for documentation of biodiversity and environmental change and development of management responses is well established, quantitative tools to analyze and systematically compare LEK are scarce. In this research, we analyze the complexity of local ecological knowledge used by respondents to classify locally-recognized marine species. We do so by applying a modified index of taxonomic distinctness to an ethnoichthyological classification in coastal communities in the Solomon Islands. In addition, we assess simple taxonomic diversity (richness in locally-recognized species names) by comparing taxonomies collected in 1992–1995 and 2014–2015. Results indicate that both endogenous (gender, age) and exogenous (proximity to market) factors have discernible effects on folk taxonomic knowledge in the region, with younger respondents and communities closer to a regional market center displaying a significantly lower richness of local species names. Folk taxonomic distinctness was significantly reduced closer to the regional market. The modified index of taxonomic distinctness applied in this research provides a useful tool to explore facets of local ecological knowledge in addition to simple richness of terms, and to compare across different regions and cultural backgrounds. Understanding changes in LEK is important because such knowledge enables communities who are highly dependent on living natural resources to harvest and manage resources more efficiently and also to detect and react to environmental change.
- Full Text:
- Date Issued: 2020
- Authors: Aswani, Shankar , Ferse, Sebastien C , Stäbler, Moritz , Chong-Montenegro, Carolina
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/406521 , vital:70282 , xlink:href="https://doi.org/10.1016/j.ecolind.2020.106865"
- Description: The global accelerating loss of biodiversity is having immediate repercussions for ecosystems and human wellbeing, particularly in areas where people depend intimately on their natural environment for their livelihoods. Dovetailing this loss is the demise of local/traditional knowledge systems resulting from factors such as changing lifestyle and the transformation of local belief systems. While the importance of local ecological knowledge (LEK) for documentation of biodiversity and environmental change and development of management responses is well established, quantitative tools to analyze and systematically compare LEK are scarce. In this research, we analyze the complexity of local ecological knowledge used by respondents to classify locally-recognized marine species. We do so by applying a modified index of taxonomic distinctness to an ethnoichthyological classification in coastal communities in the Solomon Islands. In addition, we assess simple taxonomic diversity (richness in locally-recognized species names) by comparing taxonomies collected in 1992–1995 and 2014–2015. Results indicate that both endogenous (gender, age) and exogenous (proximity to market) factors have discernible effects on folk taxonomic knowledge in the region, with younger respondents and communities closer to a regional market center displaying a significantly lower richness of local species names. Folk taxonomic distinctness was significantly reduced closer to the regional market. The modified index of taxonomic distinctness applied in this research provides a useful tool to explore facets of local ecological knowledge in addition to simple richness of terms, and to compare across different regions and cultural backgrounds. Understanding changes in LEK is important because such knowledge enables communities who are highly dependent on living natural resources to harvest and manage resources more efficiently and also to detect and react to environmental change.
- Full Text:
- Date Issued: 2020
Comprehensive data on the mechanical properties and biodegradation profile of polylactide composites developed for hard tissue repairs
- Aworinde, Abraham K, Adeosun, Samson O, Oyawale, Festus A, Emagbetere, Eyere, Ishola, Felix A, Olatunji, Obafemi, Akinlab, Stephen, Oyedepo, Sunday O, Ajayi, Oluseyi O, Akinlabi, Esther T
- Authors: Aworinde, Abraham K , Adeosun, Samson O , Oyawale, Festus A , Emagbetere, Eyere , Ishola, Felix A , Olatunji, Obafemi , Akinlab, Stephen , Oyedepo, Sunday O , Ajayi, Oluseyi O , Akinlabi, Esther T
- Date: 2020
- Subjects: Regeneration (Biology) , Vickers microhardness , Melt-blending technique
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/11260/3149 , vital:43158 , https://doi.org/10.1016/j.dib.2020.106107
- Description: Africa, the ancestral home of all modern humans, is the most informative continent for understanding the human genome and its contribution to complex disease. To better understand the genetics of schizophrenia, we studied the illness in the Xhosa population of South Africa, recruiting 909 cases and 917 age-, gender-, and residence-matched controls. Individuals with schizophrenia were significantly more likely than controls to harbor private, severely damaging mutations in genes that are critical to synaptic function, including neural circuitry mediated by the neurotransmitters glutamine, γ-aminobutyric acid, and dopamine. Schizophrenia is genetically highly heterogeneous, involving severe ultrarare mutations in genes that are critical to synaptic plasticity. The depth of genetic variation in Africa revealed this relationship with a moderate sample size and informed our understanding of the genetics of schizophrenia worldwide.
- Full Text:
- Date Issued: 2020
- Authors: Aworinde, Abraham K , Adeosun, Samson O , Oyawale, Festus A , Emagbetere, Eyere , Ishola, Felix A , Olatunji, Obafemi , Akinlab, Stephen , Oyedepo, Sunday O , Ajayi, Oluseyi O , Akinlabi, Esther T
- Date: 2020
- Subjects: Regeneration (Biology) , Vickers microhardness , Melt-blending technique
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/11260/3149 , vital:43158 , https://doi.org/10.1016/j.dib.2020.106107
- Description: Africa, the ancestral home of all modern humans, is the most informative continent for understanding the human genome and its contribution to complex disease. To better understand the genetics of schizophrenia, we studied the illness in the Xhosa population of South Africa, recruiting 909 cases and 917 age-, gender-, and residence-matched controls. Individuals with schizophrenia were significantly more likely than controls to harbor private, severely damaging mutations in genes that are critical to synaptic function, including neural circuitry mediated by the neurotransmitters glutamine, γ-aminobutyric acid, and dopamine. Schizophrenia is genetically highly heterogeneous, involving severe ultrarare mutations in genes that are critical to synaptic plasticity. The depth of genetic variation in Africa revealed this relationship with a moderate sample size and informed our understanding of the genetics of schizophrenia worldwide.
- Full Text:
- Date Issued: 2020
Between past and future: memory and mourning in the stories of Okwiri Oduor and Ndinda Kioko
- Authors: Awuor, Nicholas Amol
- Date: 2020
- Subjects: Women authors, Kenyan , Oduor, Okwiri -- The plea bargain , Oduor, Okwiri -- My father's head , Oduor, Okwiri -- Rag doll , Kioko, Ndinda -- Sometime before Maulidi , Kioko, Ndinda -- Some freedom dreams , Women and literature -- Africa , Bereavement -- Fiction , Culture in literature , Liberty in literature
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/161229 , vital:40608
- Description: This study investigates the literary activities of two emerging female Kenyan writers, Claudette Okwiri Oduor and Jacqueline Ndinda Kioko, both of whom are award-winning authors. Oduor won the 2014 Caine Prize for African Writing while Kioko bagged the Wasafiri New Writing Fiction Award 2017. It examines specifically how the writers deal with memory and mourning in negotiating between the past and future. I explore how their fictional and non-fictional narratives assist individuals and groups to confront loss, reconstruct new identities, and renegotiate belonging amidst personal and social upheaval. The fictional narratives at the centre of this research are Oduor’s “The Plea Bargain” (2011), “My Father’s Head” (2013) and “Rag Doll” (2014), and Kioko’s “Sometime Before Maulidi” (2014) and “Some Freedom Dreams” (2017). The study explores the themes of mental illness, existential crisis, and fragmentation, and considers bereavement, queer relationships, cultural freedom, and social recognition. The research further considers the active participation of these two writers in Kenya’s contemporary literary-cultural conversations, which span different genres and various media platforms, including blogs, YouTube clips, online magazines, and social media networks in dialogue with other writers. . I trace the significance of the literary-cultural link these authors have with their local, continental, and global counterparts in countries like Uganda, Nigeria, and South Africa. The link finds expression through their (in)direct association with some of the new online publishing outlets in Kenya like Jalada Africa, Enkare Review, and Kikwetu. More importantly, their shared participation in and association with such international awards and scholarships as the Commonwealth Short Story Prize, Kwani Trust Manuscript Project, and Miles Morland Foundation is integral in apprehending contemporary literary exchanges and multidirectional flows of publishing in Africa and beyond. I equally illustrate how mentorship of younger writers through local writers’ organisations and collectives like AMKA and Writivism help in the formation of an alternative canon other than the mainstream. The study affirms that the authors seem to transcend the boundaries of production and circulation by fluidly moving between electronic and non-electronic platforms, thus mimicking the memory production of remembering, repeating, and working through.
- Full Text:
- Date Issued: 2020
- Authors: Awuor, Nicholas Amol
- Date: 2020
- Subjects: Women authors, Kenyan , Oduor, Okwiri -- The plea bargain , Oduor, Okwiri -- My father's head , Oduor, Okwiri -- Rag doll , Kioko, Ndinda -- Sometime before Maulidi , Kioko, Ndinda -- Some freedom dreams , Women and literature -- Africa , Bereavement -- Fiction , Culture in literature , Liberty in literature
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/161229 , vital:40608
- Description: This study investigates the literary activities of two emerging female Kenyan writers, Claudette Okwiri Oduor and Jacqueline Ndinda Kioko, both of whom are award-winning authors. Oduor won the 2014 Caine Prize for African Writing while Kioko bagged the Wasafiri New Writing Fiction Award 2017. It examines specifically how the writers deal with memory and mourning in negotiating between the past and future. I explore how their fictional and non-fictional narratives assist individuals and groups to confront loss, reconstruct new identities, and renegotiate belonging amidst personal and social upheaval. The fictional narratives at the centre of this research are Oduor’s “The Plea Bargain” (2011), “My Father’s Head” (2013) and “Rag Doll” (2014), and Kioko’s “Sometime Before Maulidi” (2014) and “Some Freedom Dreams” (2017). The study explores the themes of mental illness, existential crisis, and fragmentation, and considers bereavement, queer relationships, cultural freedom, and social recognition. The research further considers the active participation of these two writers in Kenya’s contemporary literary-cultural conversations, which span different genres and various media platforms, including blogs, YouTube clips, online magazines, and social media networks in dialogue with other writers. . I trace the significance of the literary-cultural link these authors have with their local, continental, and global counterparts in countries like Uganda, Nigeria, and South Africa. The link finds expression through their (in)direct association with some of the new online publishing outlets in Kenya like Jalada Africa, Enkare Review, and Kikwetu. More importantly, their shared participation in and association with such international awards and scholarships as the Commonwealth Short Story Prize, Kwani Trust Manuscript Project, and Miles Morland Foundation is integral in apprehending contemporary literary exchanges and multidirectional flows of publishing in Africa and beyond. I equally illustrate how mentorship of younger writers through local writers’ organisations and collectives like AMKA and Writivism help in the formation of an alternative canon other than the mainstream. The study affirms that the authors seem to transcend the boundaries of production and circulation by fluidly moving between electronic and non-electronic platforms, thus mimicking the memory production of remembering, repeating, and working through.
- Full Text:
- Date Issued: 2020
"Knowing With": New Rhodes Board Navigates Collaboration, Intimacy, and Solidarity
- Baasch, Rachel M, Fọlárànmí, Stephen, Koide, Emi, Kakande, Angelo, Simbao, Ruth K
- Authors: Baasch, Rachel M , Fọlárànmí, Stephen , Koide, Emi , Kakande, Angelo , Simbao, Ruth K
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/147514 , vital:38645 , https://doi.org/10.1162/afar_a_00523
- Description: Rhodes University (or UCKAR), based in Makhanda, South Africa, joined the African Arts editorial consortium in 2016 and its first journal issue—vol. 50, no. 2—was published in 2017. Initially the board was run by Ruth Simbao, with the aim of developing collaborations with other scholars, particularly those based on the African continent and within the global south (Simbao 2017: 1). For the second Rhodes issue (Summer 2018), Simbao worked with Guest Board Member Amanda Tumusiime from Makerere University, and for the third Rhodes issue (Summer 2019) she collaborated with Stephen Folárànmí from Obáfémi Awólówò University, Ilé-Ifè, Nigeria, who at the time was a Postdoctoral Fellow at Rhodes.
- Full Text:
- Date Issued: 2020
- Authors: Baasch, Rachel M , Fọlárànmí, Stephen , Koide, Emi , Kakande, Angelo , Simbao, Ruth K
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/147514 , vital:38645 , https://doi.org/10.1162/afar_a_00523
- Description: Rhodes University (or UCKAR), based in Makhanda, South Africa, joined the African Arts editorial consortium in 2016 and its first journal issue—vol. 50, no. 2—was published in 2017. Initially the board was run by Ruth Simbao, with the aim of developing collaborations with other scholars, particularly those based on the African continent and within the global south (Simbao 2017: 1). For the second Rhodes issue (Summer 2018), Simbao worked with Guest Board Member Amanda Tumusiime from Makerere University, and for the third Rhodes issue (Summer 2019) she collaborated with Stephen Folárànmí from Obáfémi Awólówò University, Ilé-Ifè, Nigeria, who at the time was a Postdoctoral Fellow at Rhodes.
- Full Text:
- Date Issued: 2020
Dataset of experimental and adaptive neuro-fuzzy inference system (ANFIS) model prediction of R600a/MWCNT nanolubricant in a vapour compression system
- Babarinde, T O, Akinlabi, S A, Madyira, D M, Ekundayo, F M, Adedeji, P A
- Authors: Babarinde, T O , Akinlabi, S A , Madyira, D M , Ekundayo, F M , Adedeji, P A
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/11260/3248 , vital:43283 , https://www.sciencedirect.com/science/article/pii/S2352340920312105
- Description: This research paper assessed the performance of R600a with the base lubricant and Multi-walled Carbon Nanotube (MWCNT) nanolubricant at steady state. It describes the instruments required for measurement of the data parameter and its uncertainties, steps involved in preparing and replacing the MWCNT nanolubricant concentration with base lubricant in vapour compression refrigeration. The system’s temperature data was collected at the components inlets and outlets. Pressure data was also registered at the compressor outlet and inlet. The data was captured at 27 °C ambient temperature at an interval of 30 min for 300 min. The experiment includes the experimental data collection, Adaptive Neuro-Fuzzy Inference System (ANFIS) training and testing dataset. The use of ANFIS model is explained in predicting the efficiency of MWCNT nanolubricant in a vapour compression refrigerator system. The ANFIS model also provides statistical output measures such as Root Mean Square Error (RMSE) and Mean Absolute Deviation (MAD), Mean Absolute Percentage Error (MAPE), and determination coefficient (R2). The data is useful and important for replacing MWCNT nanolubricant with base lubricant in a vapour compression refrigeration system for researchers in the specialisation of energy-efficient materials in refrigeration. The data present can be reused for vapour compression refrigeration systems simulation and modelling.
- Full Text:
- Date Issued: 2020
- Authors: Babarinde, T O , Akinlabi, S A , Madyira, D M , Ekundayo, F M , Adedeji, P A
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/11260/3248 , vital:43283 , https://www.sciencedirect.com/science/article/pii/S2352340920312105
- Description: This research paper assessed the performance of R600a with the base lubricant and Multi-walled Carbon Nanotube (MWCNT) nanolubricant at steady state. It describes the instruments required for measurement of the data parameter and its uncertainties, steps involved in preparing and replacing the MWCNT nanolubricant concentration with base lubricant in vapour compression refrigeration. The system’s temperature data was collected at the components inlets and outlets. Pressure data was also registered at the compressor outlet and inlet. The data was captured at 27 °C ambient temperature at an interval of 30 min for 300 min. The experiment includes the experimental data collection, Adaptive Neuro-Fuzzy Inference System (ANFIS) training and testing dataset. The use of ANFIS model is explained in predicting the efficiency of MWCNT nanolubricant in a vapour compression refrigerator system. The ANFIS model also provides statistical output measures such as Root Mean Square Error (RMSE) and Mean Absolute Deviation (MAD), Mean Absolute Percentage Error (MAPE), and determination coefficient (R2). The data is useful and important for replacing MWCNT nanolubricant with base lubricant in a vapour compression refrigeration system for researchers in the specialisation of energy-efficient materials in refrigeration. The data present can be reused for vapour compression refrigeration systems simulation and modelling.
- Full Text:
- Date Issued: 2020
An octabrominated Sn (iv) tetraisopropylporphyrin as a photosensitizer dye for singlet oxygen biomedical applications
- Babu, Balaji, Mack, John, Nyokong, Tebello
- Authors: Babu, Balaji , Mack, John , Nyokong, Tebello
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/186679 , vital:44524 , xlink:href="https://doi.org/10.1039/D0DT01915A"
- Description: Two novel Sn(IV) tetraisopropylphenylporphyrins have been synthesized to explore the effect of octabromination at the β-pyrrole positions on their photophysical properties and photodynamic activity. The lower energy Q band of an octabrominated complex lies at 675 nm well within the therapeutic window. The octabrominated dye has a relatively high singlet oxygen quantum yield of 0.78 in DMF and exhibits favorable photodynamic activity against MCF-7 cells with an IC50 value of 10.7 μM and a 5.74 log reduction value (5 μM) towards S. aureus under illumination at 660 nm for 60 min with a Thorlabs M660L3 LED (280 mW cm−2).
- Full Text:
- Date Issued: 2020
- Authors: Babu, Balaji , Mack, John , Nyokong, Tebello
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/186679 , vital:44524 , xlink:href="https://doi.org/10.1039/D0DT01915A"
- Description: Two novel Sn(IV) tetraisopropylphenylporphyrins have been synthesized to explore the effect of octabromination at the β-pyrrole positions on their photophysical properties and photodynamic activity. The lower energy Q band of an octabrominated complex lies at 675 nm well within the therapeutic window. The octabrominated dye has a relatively high singlet oxygen quantum yield of 0.78 in DMF and exhibits favorable photodynamic activity against MCF-7 cells with an IC50 value of 10.7 μM and a 5.74 log reduction value (5 μM) towards S. aureus under illumination at 660 nm for 60 min with a Thorlabs M660L3 LED (280 mW cm−2).
- Full Text:
- Date Issued: 2020
Sn (iv) N-confused porphyrins as photosensitizer dyes for photodynamic therapy in the near IR region
- Babu, Balaji, Mack, John, Nyokong, Tebello
- Authors: Babu, Balaji , Mack, John , Nyokong, Tebello
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/186648 , vital:44521 , xlink:href="https://doi.org/10.1039/D0DT03296D"
- Description: The utility of Sn(IV) N-confused porphyrin (SnNCP) for use as photosensitizer dyes in photodynamic therapy is investigated. SnNCP has an unusually high singlet oxygen quantum yield of 0.72 in DMSO. IC50 values of 1.6 and 12.8 μM were obtained against MCF-7 cells upon irradiation with 660 and 780 nm LEDs.
- Full Text:
- Date Issued: 2020
Sn (iv) N-confused porphyrins as photosensitizer dyes for photodynamic therapy in the near IR region
- Authors: Babu, Balaji , Mack, John , Nyokong, Tebello
- Date: 2020
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/186648 , vital:44521 , xlink:href="https://doi.org/10.1039/D0DT03296D"
- Description: The utility of Sn(IV) N-confused porphyrin (SnNCP) for use as photosensitizer dyes in photodynamic therapy is investigated. SnNCP has an unusually high singlet oxygen quantum yield of 0.72 in DMSO. IC50 values of 1.6 and 12.8 μM were obtained against MCF-7 cells upon irradiation with 660 and 780 nm LEDs.
- Full Text:
- Date Issued: 2020
Non-aggregated lipophilic water-soluble tin porphyrins as photosensitizers for photodynamic therapy and photodynamic antimicrobial chemotherapy:
- Babu, Balaji, Soy, Rodah C, Mack, John, Nyokong, Tebello
- Authors: Babu, Balaji , Soy, Rodah C , Mack, John , Nyokong, Tebello
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/158241 , vital:40165 , DOI: 10.1039/d0nj01564d
- Description: Two readily synthesized water-soluble Sn(IV) porphyrins have been prepared with quaternized pyridyl nitrogens and 2-naphthalato trans-axial ligands. Methyl and hexyl groups were attached to the quaternized nitrogens to form lipophilic dyes with high singlet oxygen quantum yields (ca. 0.90) and unusually long triplet state lifetimes. The dyes exhibit good photodynamic activity against MCF-7 cells with IC50 values of 14.3 and 8.5 μM, respectively. The hexyl quaternized dye exhibited a 9.69 log reduction value (0.5 μM) towards S. aureus under illumination for 90 min (250 mW cm−2). The results demonstrate that this set of structural modification strategies for photosensitizer dyes merits further in depth study.
- Full Text:
- Date Issued: 2020
- Authors: Babu, Balaji , Soy, Rodah C , Mack, John , Nyokong, Tebello
- Date: 2020
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/158241 , vital:40165 , DOI: 10.1039/d0nj01564d
- Description: Two readily synthesized water-soluble Sn(IV) porphyrins have been prepared with quaternized pyridyl nitrogens and 2-naphthalato trans-axial ligands. Methyl and hexyl groups were attached to the quaternized nitrogens to form lipophilic dyes with high singlet oxygen quantum yields (ca. 0.90) and unusually long triplet state lifetimes. The dyes exhibit good photodynamic activity against MCF-7 cells with IC50 values of 14.3 and 8.5 μM, respectively. The hexyl quaternized dye exhibited a 9.69 log reduction value (0.5 μM) towards S. aureus under illumination for 90 min (250 mW cm−2). The results demonstrate that this set of structural modification strategies for photosensitizer dyes merits further in depth study.
- Full Text:
- Date Issued: 2020