Allosteric pockets and dynamic residue network hubs of falcipain 2 in mutations including those linked to artemisinin resistance
- Okeke, Chiamaka J, Musyoka, Thommas M, Sheik Amamuddy, Olivier, Barozi, Victor, Tastan Bishop, Özlem
- Authors: Okeke, Chiamaka J , Musyoka, Thommas M , Sheik Amamuddy, Olivier , Barozi, Victor , Tastan Bishop, Özlem
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/476585 , vital:77939 , xlink:href="https://doi.org/10.1016/j.csbj.2021.10.011"
- Description: Continually emerging resistant strains of malarial parasites to current drugs present challenges. Understanding the underlying resistance mechanisms, especially those linked to allostery is, thus, highly crucial for drug design. This forms the main concern of the paper through a case study of falcipain 2 (FP-2) and its mutations, some of which are linked to artemisinin (ART) drug resistance. Here, we applied a variety of in silico approaches and tools that we developed recently, together with existing computational tools. This included novel essential dynamics and dynamic residue network (DRN) analysis algorithms. We identified six pockets demonstrating dynamic differences in the presence of some mutations. We observed striking allosteric effects in two mutant proteins. In the presence of M245I, a cryptic pocket was detected via a unique mechanism in which Pocket 2 fused with Pocket 6. In the presence of the A353T mutation, which is located at Pocket 2, the pocket became the most rigid among all protein systems analyzed. Pocket 6 was also highly stable in all cases, except in the presence of M245I mutation. The effect of ART linked mutations was more subtle, and the changes were at residue level. Importantly, we identified an allosteric communication path formed by four unique averaged BC hubs going from the mutated residue to the catalytic site and passing through the interface of three identified pockets. Collectively, we established and demonstrated that we have robust tools and a pipeline that can be applicable to the analysis of mutations.
- Full Text:
- Authors: Okeke, Chiamaka J , Musyoka, Thommas M , Sheik Amamuddy, Olivier , Barozi, Victor , Tastan Bishop, Özlem
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/476585 , vital:77939 , xlink:href="https://doi.org/10.1016/j.csbj.2021.10.011"
- Description: Continually emerging resistant strains of malarial parasites to current drugs present challenges. Understanding the underlying resistance mechanisms, especially those linked to allostery is, thus, highly crucial for drug design. This forms the main concern of the paper through a case study of falcipain 2 (FP-2) and its mutations, some of which are linked to artemisinin (ART) drug resistance. Here, we applied a variety of in silico approaches and tools that we developed recently, together with existing computational tools. This included novel essential dynamics and dynamic residue network (DRN) analysis algorithms. We identified six pockets demonstrating dynamic differences in the presence of some mutations. We observed striking allosteric effects in two mutant proteins. In the presence of M245I, a cryptic pocket was detected via a unique mechanism in which Pocket 2 fused with Pocket 6. In the presence of the A353T mutation, which is located at Pocket 2, the pocket became the most rigid among all protein systems analyzed. Pocket 6 was also highly stable in all cases, except in the presence of M245I mutation. The effect of ART linked mutations was more subtle, and the changes were at residue level. Importantly, we identified an allosteric communication path formed by four unique averaged BC hubs going from the mutated residue to the catalytic site and passing through the interface of three identified pockets. Collectively, we established and demonstrated that we have robust tools and a pipeline that can be applicable to the analysis of mutations.
- Full Text:
Bridging through “women’s work"
- Authors: Magadla, Siphokazi
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/298650 , vital:57724 , xlink:href="https://doi.org/10.1080/14616742.2020.1863158"
- Description: Bodomo’s bridge theory describes and predicts the long-term implications of African migrants’ activities and settlement in China. Drawing on research with African retail traders, university students, and corporate executives in China, I show that the bridge theory illuminates how African women and men rationalize their decisions to migrate to China within the context of the rise of Asia. Drawing on the literature regarding African women and work, I explain that structural economic conditions now force more Africans into economic sectors such as trade work that historically were dominated by African women. I demonstrate that African women’s roles as economic providers for their families and children in other sectors, such as university students and company executives, provide evidence of the continued “matricentric” nature of African households that rely on women’s economic productivity. I also examine the possibilities and limitations of building long-standing networks that shape African migrant settlement in China. I show that the historical theorization that characterizes global mobility as male – particularly regarding Africans – has contributed to the misrecognition of African women’s multiple activities in China.
- Full Text:
- Authors: Magadla, Siphokazi
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/298650 , vital:57724 , xlink:href="https://doi.org/10.1080/14616742.2020.1863158"
- Description: Bodomo’s bridge theory describes and predicts the long-term implications of African migrants’ activities and settlement in China. Drawing on research with African retail traders, university students, and corporate executives in China, I show that the bridge theory illuminates how African women and men rationalize their decisions to migrate to China within the context of the rise of Asia. Drawing on the literature regarding African women and work, I explain that structural economic conditions now force more Africans into economic sectors such as trade work that historically were dominated by African women. I demonstrate that African women’s roles as economic providers for their families and children in other sectors, such as university students and company executives, provide evidence of the continued “matricentric” nature of African households that rely on women’s economic productivity. I also examine the possibilities and limitations of building long-standing networks that shape African migrant settlement in China. I show that the historical theorization that characterizes global mobility as male – particularly regarding Africans – has contributed to the misrecognition of African women’s multiple activities in China.
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Knowledge of formal and informal regulations affecting wild plant foraging practices in urban spaces in South Africa
- Garekae, Hesekia, Shackleton, Charlie M
- Authors: Garekae, Hesekia , Shackleton, Charlie M
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/403221 , vital:69935 , xlink:href="https://doi.org/10.1016/j.forpol.2021.102659"
- Description: Although foraging wild plants is commonly perceived to be synonymous with rural areas, it is now increasingly recognized in urban areas. Notwithstanding, the regulations conditioning access to and rights to foraging in urban green spaces have seldom been examined. This study explored the formal and informal regulations governing access to and defining rights to forageable plant resources in the towns of Potchefstroom and Thabazimbi, South Africa. A random sample of 374 households was considered for the survey, complemented by in-depth interviews with 26 participants. Foraging occurred in a variety of public and private spaces, with the frequency of access differing with the type of space. The majority of the respondents were unaware of formal and informal regulations governing access to and use of urban landscapes. Recognizing foraging activities in urban landscapes is a fundamental step toward fostering active community involvement in the management and production of urban green spaces.
- Full Text:
- Authors: Garekae, Hesekia , Shackleton, Charlie M
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/403221 , vital:69935 , xlink:href="https://doi.org/10.1016/j.forpol.2021.102659"
- Description: Although foraging wild plants is commonly perceived to be synonymous with rural areas, it is now increasingly recognized in urban areas. Notwithstanding, the regulations conditioning access to and rights to foraging in urban green spaces have seldom been examined. This study explored the formal and informal regulations governing access to and defining rights to forageable plant resources in the towns of Potchefstroom and Thabazimbi, South Africa. A random sample of 374 households was considered for the survey, complemented by in-depth interviews with 26 participants. Foraging occurred in a variety of public and private spaces, with the frequency of access differing with the type of space. The majority of the respondents were unaware of formal and informal regulations governing access to and use of urban landscapes. Recognizing foraging activities in urban landscapes is a fundamental step toward fostering active community involvement in the management and production of urban green spaces.
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Prioritisation of targets for weed biological control I: a review of existing prioritisation schemes and development of a system for South Africa
- Downey, Paul O, Paterson, Iain D, Canavan, Kim N, Hill, Martin P
- Authors: Downey, Paul O , Paterson, Iain D , Canavan, Kim N , Hill, Martin P
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/417763 , vital:71484 , xlink:href="https://doi.org/10.1080/09583157.2021.1918636"
- Description: Biological control is widely utilised for the management of invasive alien plants (IAP). With the ever-increasing number of IAPs, it is important to prioritise targets for biocontrol in order to maximise the use of resources and the chances of success. This paper reviewed 12 previous systems developed to prioritise plant targets for biocontrol. The review underpins the selection of attributes and methodologies for the prioritisation of targets for biocontrol in South Africa. All of the previous systems are purpose-built and context-specific, so a new system is required for the South African setting. Previous prioritisation systems were assessed based on the attributes and methodology adopted. The attributes of previous systems were grouped into three sections, being (1) impact/importance of the target plant, (2) likelihood of achieving success, and (3) investment required. Nineteen attributes from previous systems are included in the new system, while nine were excluded due to a requirement for legislation and/or research, or because they conflicted with objectives of the new system in some way. Two methodological approaches were identified for how systems sourced information, either sourcing information through expert knowledge or the use of available literature and data. This information was then applied through either a quantitative or qualitative scoring method. A quantitative scoring method, with information sourced from available resources, was selected as the most appropriate methodology in the context of the new system for South Africa. This review streamlined the development and testing of the South African Biological Control Target Selection system.
- Full Text:
- Authors: Downey, Paul O , Paterson, Iain D , Canavan, Kim N , Hill, Martin P
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/417763 , vital:71484 , xlink:href="https://doi.org/10.1080/09583157.2021.1918636"
- Description: Biological control is widely utilised for the management of invasive alien plants (IAP). With the ever-increasing number of IAPs, it is important to prioritise targets for biocontrol in order to maximise the use of resources and the chances of success. This paper reviewed 12 previous systems developed to prioritise plant targets for biocontrol. The review underpins the selection of attributes and methodologies for the prioritisation of targets for biocontrol in South Africa. All of the previous systems are purpose-built and context-specific, so a new system is required for the South African setting. Previous prioritisation systems were assessed based on the attributes and methodology adopted. The attributes of previous systems were grouped into three sections, being (1) impact/importance of the target plant, (2) likelihood of achieving success, and (3) investment required. Nineteen attributes from previous systems are included in the new system, while nine were excluded due to a requirement for legislation and/or research, or because they conflicted with objectives of the new system in some way. Two methodological approaches were identified for how systems sourced information, either sourcing information through expert knowledge or the use of available literature and data. This information was then applied through either a quantitative or qualitative scoring method. A quantitative scoring method, with information sourced from available resources, was selected as the most appropriate methodology in the context of the new system for South Africa. This review streamlined the development and testing of the South African Biological Control Target Selection system.
- Full Text:
Rethinking the decolonial moment through collaborative practices at the International Library of African Music (ILAM), South Africa
- Watkins, Lee W, Madiba, Elijah M, McConnachie, Boudina E
- Authors: Watkins, Lee W , Madiba, Elijah M , McConnachie, Boudina E
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/480227 , vital:78409 , xlink:href="https://doi.org/10.1080/17411912.2021.1938628"
- Description: Until recently the International Library of African Music (ILAM) was at the receiving end of widespread criticisms because most of its collections were acquired through the colonial privilege of its founder, Hugh Tracey. Tracey recorded music and collected musical instruments in many countries of sub-Sahara Africa without following the rigorous ethical practices which are a necessary requirement for collectors these days. Since its establishment in 1954 until the early 2000s, moreover, ILAM had largely been inaccessible to black South Africans who comprise the majority of the population. Its presence, therefore, is complicated by a racist past associated with apartheid and a colonial past characterised by the misappropriation of the colonised's resources. In view of this history, ILAM had to shape a new reality which fell in line with calls and demands for decolonised practices such that the archive became an agent for transformation on numerous fronts. This series of articles describes the efforts undertaken by ILAM so that it could develop and implement policies which would place it at the vanguard of ethical archival practices on the continent. It is argued that the decolonial could be realised only through collaboration with entities which shared our interests in participatory and transformed archival practices.
- Full Text:
- Authors: Watkins, Lee W , Madiba, Elijah M , McConnachie, Boudina E
- Date: 2021
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/480227 , vital:78409 , xlink:href="https://doi.org/10.1080/17411912.2021.1938628"
- Description: Until recently the International Library of African Music (ILAM) was at the receiving end of widespread criticisms because most of its collections were acquired through the colonial privilege of its founder, Hugh Tracey. Tracey recorded music and collected musical instruments in many countries of sub-Sahara Africa without following the rigorous ethical practices which are a necessary requirement for collectors these days. Since its establishment in 1954 until the early 2000s, moreover, ILAM had largely been inaccessible to black South Africans who comprise the majority of the population. Its presence, therefore, is complicated by a racist past associated with apartheid and a colonial past characterised by the misappropriation of the colonised's resources. In view of this history, ILAM had to shape a new reality which fell in line with calls and demands for decolonised practices such that the archive became an agent for transformation on numerous fronts. This series of articles describes the efforts undertaken by ILAM so that it could develop and implement policies which would place it at the vanguard of ethical archival practices on the continent. It is argued that the decolonial could be realised only through collaboration with entities which shared our interests in participatory and transformed archival practices.
- Full Text:
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