MD-TASK: a software suite for analyzing molecular dynamics trajectories
- Brown, David K, Penkler, David L, Amamuddy, Olivier S, Ross, Caroline J, Atilgan, Ali R, Atilgan, Canan, Tastan Bishop, Özlem
- Authors: Brown, David K , Penkler, David L , Amamuddy, Olivier S , Ross, Caroline J , Atilgan, Ali R , Atilgan, Canan , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125138 , vital:35735 , https://doi.10.1093/bioinformatics/btx349
- Description: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories.
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- Authors: Brown, David K , Penkler, David L , Amamuddy, Olivier S , Ross, Caroline J , Atilgan, Ali R , Atilgan, Canan , Tastan Bishop, Özlem
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125138 , vital:35735 , https://doi.10.1093/bioinformatics/btx349
- Description: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories.
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Application of Baylis-Hillman methodology in the direct construction of chromone derivatives
- Faridoon, H, Olomola, Temitope O, Klein, Rosalyn, Kaye, Perry T
- Authors: Faridoon, H , Olomola, Temitope O , Klein, Rosalyn , Kaye, Perry T
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442488 , vital:73992 , https://doi.org/10.1016/j.tet.2015.11.039
- Description: Pyridinium chlorochromate oxidation of Baylis-Hillman-derived tert-butyl 2H-chromene-3-carboxylates affords chromone-3-carboxylate esters, providing the first application of Baylis-Hillman methodology in a direct and convenient three-step synthesis of chromone derivatives.
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- Authors: Faridoon, H , Olomola, Temitope O , Klein, Rosalyn , Kaye, Perry T
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442488 , vital:73992 , https://doi.org/10.1016/j.tet.2015.11.039
- Description: Pyridinium chlorochromate oxidation of Baylis-Hillman-derived tert-butyl 2H-chromene-3-carboxylates affords chromone-3-carboxylate esters, providing the first application of Baylis-Hillman methodology in a direct and convenient three-step synthesis of chromone derivatives.
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Employment and diversity in the cultural and creative industries in South Africa: research note
- Authors: Snowball, Jeanette D
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/71493 , vital:29858 , https://hdl.handle.net/10520/EJC188591
- Description: The publication of Richard Florida's (2002) The Rise of the Creative Class marked a growing international interest in the creative economy. There are several ways of understanding the creative economy, often divided into the cultural and creative industries. Cultural industries are those whose major outputs have some symbolic value, such as fine arts, film and craft, jewelry design, publishing and fashion. Creative industries are defined more broadly as those that have knowledge as their major input. In addition to cultural goods and services, these include things like software design and internet services. UNESCO (2009) provides guidelines for defining the cultural and creative industries and the ways in which they can be measured, but there is currently no international consensus. Nor is there likely to be, since different countries will have very different levels of involvement and focus that may shape what information is useful, for example, for shaping policy.
- Full Text: false
- Authors: Snowball, Jeanette D
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/71493 , vital:29858 , https://hdl.handle.net/10520/EJC188591
- Description: The publication of Richard Florida's (2002) The Rise of the Creative Class marked a growing international interest in the creative economy. There are several ways of understanding the creative economy, often divided into the cultural and creative industries. Cultural industries are those whose major outputs have some symbolic value, such as fine arts, film and craft, jewelry design, publishing and fashion. Creative industries are defined more broadly as those that have knowledge as their major input. In addition to cultural goods and services, these include things like software design and internet services. UNESCO (2009) provides guidelines for defining the cultural and creative industries and the ways in which they can be measured, but there is currently no international consensus. Nor is there likely to be, since different countries will have very different levels of involvement and focus that may shape what information is useful, for example, for shaping policy.
- Full Text: false
Ericoid fungal inoculation of blueberry under commercial production in South Africa
- Bizabani, Christine, Fontenla, Sonia, Dames, Joanna F
- Authors: Bizabani, Christine , Fontenla, Sonia , Dames, Joanna F
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/448610 , vital:74746 , https://doi.org/10.1016/j.scienta.2016.06.029
- Description: Ericoid mycorrhizal (ERM) fungi are known to enhance growth of plants belonging to the Ericaceae family. However, the outcomes of root-fungal associations in this family are influenced by several factors such as soil nutrient status, climatic conditions, host variety and fungal partner. The aim of this study was (i) to determine whether symbiotic fungal structures form in roots of Misty (Vaccinium corymbosum) and Brightwell (V. ashei) blueberry varieties, following inoculation with Leohumicola, Oidiodendron maius and Meliniomyces fungal species, and (ii) evaluate inoculation effects on the growth of blueberry varieties. The study was conducted for 60 weeks under commercial production conditions at Amathole Berries, Sutterheim, South Africa. All three fungi were isolated from Erica plants growing naturally in Albany Centre of Endemism of South Africa. All ERM formed mycorrhizal structures characteristic of typical ericoid colonisation in the roots of both Misty and Brightwell. However, percentage colonisation was low. The highest colonisation percentage, 20.4%, was observed in Misty inoculated with Oidiodendron maius. Colonisation was significantly different compared to un-inoculated controls in the Misty variety. In both varieties inoculated with either Leohumicola or Meliniomyces did not improve (p > 0.05) shoot growth and biomass. All fungal species improved root biomass in Misty but not in Brightwell. This indicates that ERM inoculation may potentially benefit plant of Misty and that responses to ERM inoculation vary between blueberry varieties.
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- Authors: Bizabani, Christine , Fontenla, Sonia , Dames, Joanna F
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/448610 , vital:74746 , https://doi.org/10.1016/j.scienta.2016.06.029
- Description: Ericoid mycorrhizal (ERM) fungi are known to enhance growth of plants belonging to the Ericaceae family. However, the outcomes of root-fungal associations in this family are influenced by several factors such as soil nutrient status, climatic conditions, host variety and fungal partner. The aim of this study was (i) to determine whether symbiotic fungal structures form in roots of Misty (Vaccinium corymbosum) and Brightwell (V. ashei) blueberry varieties, following inoculation with Leohumicola, Oidiodendron maius and Meliniomyces fungal species, and (ii) evaluate inoculation effects on the growth of blueberry varieties. The study was conducted for 60 weeks under commercial production conditions at Amathole Berries, Sutterheim, South Africa. All three fungi were isolated from Erica plants growing naturally in Albany Centre of Endemism of South Africa. All ERM formed mycorrhizal structures characteristic of typical ericoid colonisation in the roots of both Misty and Brightwell. However, percentage colonisation was low. The highest colonisation percentage, 20.4%, was observed in Misty inoculated with Oidiodendron maius. Colonisation was significantly different compared to un-inoculated controls in the Misty variety. In both varieties inoculated with either Leohumicola or Meliniomyces did not improve (p > 0.05) shoot growth and biomass. All fungal species improved root biomass in Misty but not in Brightwell. This indicates that ERM inoculation may potentially benefit plant of Misty and that responses to ERM inoculation vary between blueberry varieties.
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On luminescence stimulated from deep traps using thermally-assisted time-resolved optical stimulation in α-Al2O3: C
- Nyirenda, Angel N, Chithambo, Makaiko L, Polymeris, G S
- Authors: Nyirenda, Angel N , Chithambo, Makaiko L , Polymeris, G S
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124627 , vital:35639 , https://doi.org/10.1016/j.radmeas.2016.01.016
- Description: We report a study of charge transfer mechanisms of electrons stimulated optically from very deep traps, also known as donor traps, in α-Al2O3:C. The investigations were carried out using thermally-assisted time-resolved optical stimulation, thermoluminescence and by way of residual thermoluminescence from the main electron trap. When the charges are optically stimulated from the deep traps, they are redistributed via the conduction band to the main electron trap and the shallow trap from where they are optically or thermally released for recombination at luminescence centres. The luminescence is strongly quenched at high measurement temperature as evident by very short luminescence lifetimes at these temperatures. The main peak due to residual thermoluminescence is located at a higher temperature than the conventional main peak.
- Full Text: false
- Authors: Nyirenda, Angel N , Chithambo, Makaiko L , Polymeris, G S
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124627 , vital:35639 , https://doi.org/10.1016/j.radmeas.2016.01.016
- Description: We report a study of charge transfer mechanisms of electrons stimulated optically from very deep traps, also known as donor traps, in α-Al2O3:C. The investigations were carried out using thermally-assisted time-resolved optical stimulation, thermoluminescence and by way of residual thermoluminescence from the main electron trap. When the charges are optically stimulated from the deep traps, they are redistributed via the conduction band to the main electron trap and the shallow trap from where they are optically or thermally released for recombination at luminescence centres. The luminescence is strongly quenched at high measurement temperature as evident by very short luminescence lifetimes at these temperatures. The main peak due to residual thermoluminescence is located at a higher temperature than the conventional main peak.
- Full Text: false
SEAmester – South Africa’s first class afloat
- Ansorge, Isabelle J, Brundrit, Geoff, Brundrit, Jean, Dorrington, Rosemary A, Fawcett, Sarah, Gammon, David, Henry, Tahlia, Hermes, Juliet, Hölscher, Beate, d’Hotman, Jethan, Meiklejohn, Ian, Morris, Tammy, Pinto, Izidine, Du Plessis, Marcel, Roman, Raymond, Saunders, Clinton, Shabangu, Fannie W, De Vos, Marc, Walker, David R, Louw, Gavin
- Authors: Ansorge, Isabelle J , Brundrit, Geoff , Brundrit, Jean , Dorrington, Rosemary A , Fawcett, Sarah , Gammon, David , Henry, Tahlia , Hermes, Juliet , Hölscher, Beate , d’Hotman, Jethan , Meiklejohn, Ian , Morris, Tammy , Pinto, Izidine , Du Plessis, Marcel , Roman, Raymond , Saunders, Clinton , Shabangu, Fannie W , De Vos, Marc , Walker, David R , Louw, Gavin
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/65539 , vital:28808 , https://doi.org/10.17159/sajs.2016/a0171
- Description: publisher version , From Introduction: Marine science is a highly competitive environment. The need to improve the cohort of South African postgraduates, who would be recognised both nationally and internationally for their scientific excellence, is crucial. It is possible to attract students early on in their careers to this discipline via cutting-edge science, technology and unique field experiences. Through the engagement of students with real-life experiences such as SEAmester, universities supporting marine science postgraduate degree programmes can attract a sustainable throughput of numerically proficient students. By achieving a more quantitative and experienced input into our postgraduate degree programmes, we will, as a scientific community, greatly improve our long-term capabilities to accurately measure, model and predict the impacts of current climate change scenarios. The short-term goal is to attract and establish a cohort of proficient marine and atmospheric science graduates who will contribute to filling the capacity needs of South African marine science as a whole. The SEAmester programme, by involving researchers from across all the relevant disciplines and tertiary institutions, provides an opportunity to build a network of collaborative teaching within the marine field. In doing so, these researchers will foster and strengthen new and current collaborations between historically white and black universities (Figure 1). The long-term objective of SEAmester is to build critical mass within the marine sciences to ensure sustained growth of human capacity in marine science in South Africa – aligning closely with the current DST Research and Development strategies and the Operation Phakisa Oceans Economy initiative.
- Full Text:
- Authors: Ansorge, Isabelle J , Brundrit, Geoff , Brundrit, Jean , Dorrington, Rosemary A , Fawcett, Sarah , Gammon, David , Henry, Tahlia , Hermes, Juliet , Hölscher, Beate , d’Hotman, Jethan , Meiklejohn, Ian , Morris, Tammy , Pinto, Izidine , Du Plessis, Marcel , Roman, Raymond , Saunders, Clinton , Shabangu, Fannie W , De Vos, Marc , Walker, David R , Louw, Gavin
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/65539 , vital:28808 , https://doi.org/10.17159/sajs.2016/a0171
- Description: publisher version , From Introduction: Marine science is a highly competitive environment. The need to improve the cohort of South African postgraduates, who would be recognised both nationally and internationally for their scientific excellence, is crucial. It is possible to attract students early on in their careers to this discipline via cutting-edge science, technology and unique field experiences. Through the engagement of students with real-life experiences such as SEAmester, universities supporting marine science postgraduate degree programmes can attract a sustainable throughput of numerically proficient students. By achieving a more quantitative and experienced input into our postgraduate degree programmes, we will, as a scientific community, greatly improve our long-term capabilities to accurately measure, model and predict the impacts of current climate change scenarios. The short-term goal is to attract and establish a cohort of proficient marine and atmospheric science graduates who will contribute to filling the capacity needs of South African marine science as a whole. The SEAmester programme, by involving researchers from across all the relevant disciplines and tertiary institutions, provides an opportunity to build a network of collaborative teaching within the marine field. In doing so, these researchers will foster and strengthen new and current collaborations between historically white and black universities (Figure 1). The long-term objective of SEAmester is to build critical mass within the marine sciences to ensure sustained growth of human capacity in marine science in South Africa – aligning closely with the current DST Research and Development strategies and the Operation Phakisa Oceans Economy initiative.
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South Africa in the Antarctic Circumnavigation Expedition: a multi-institutional and interdisciplinary scientific project
- Halo, Issufo, Dorrington, Rosemary A, Bornman, Thomas G, De Villiers, Stephanie, Fawcett, Sarah
- Authors: Halo, Issufo , Dorrington, Rosemary A , Bornman, Thomas G , De Villiers, Stephanie , Fawcett, Sarah
- Date: 2016
- Language: English
- Type: article
- Identifier: http://hdl.handle.net/10962/65428 , vital:28790 , https://doi.org/10.17159/sajs.2016/a0173
- Description: publisher version , The polar regions are more critically affected by climate change than any other region on our planet.1,2 On the Antarctic continent and in its surrounding oceans, the effects of climate change are likely to be dramatic,3 and include largescale catastrophic ice melt, loss of habitat and biodiversity, and global sea level rise. The ‘Southern Ocean’ refers to the region where Atlantic, Indian and Pacific Ocean waters come together to encircle Antarctica. These waters connect the different ocean basins by linking the shallow and deep limbs of the global ocean current system (‘overturning circulation’) and play a critical role in storing and distributing heat and carbon dioxide (CO2 ). The Southern Ocean thus regulates not only the climate of the Antarctic, but of the entire earth system.1,4 By extension, the capacity of the global ocean to ameliorate earth’s changing climate is strongly controlled by the Southern Ocean. Marine phytoplankton (microscopic plants inhabiting the sunlit upper ocean) convert CO2 (an inorganic form of carbon) dissolved in surface waters into organic carbon through photosynthesis. This organic carbon fuels upper trophic levels such as fish, mammals and birds, and a portion sinks into the deep ocean where it remains stored for hundreds to thousands of years. This mechanism, which lowers the atmospheric concentration of CO2 , is termed the ‘biological pump’.5 The efficiency of the global ocean’s biological pump is currently limited by the Southern Ocean, where the macronutrients (nitrate and phosphate) required for photosynthesis are never fully consumed in surface waters. In theory, increased consumption of these nutrients could drive higher organic carbon removal to the deep ocean, enhancing the oceanic uptake of atmospheric CO2 . Indeed, more complete consumption of Southern Ocean nutrients is a leading hypothesis for the decrease in atmospheric CO2 that characterised the ice ages.6 Despite the global importance of the Southern Ocean, knowledge of the controls on and interactions among the physical, chemical and biological processes operating in Antarctic ecosystems is limited, largely because of a scarcity of in-situ observational data, compounded by the challenge of integrating siloed scientific fields. Given predictions that diverse aspects of Southern Ocean physics and carbon biogeochemistry are likely to change in the coming decades, a transdisciplinary approach to studying Antarctic systems is critical.
- Full Text:
- Authors: Halo, Issufo , Dorrington, Rosemary A , Bornman, Thomas G , De Villiers, Stephanie , Fawcett, Sarah
- Date: 2016
- Language: English
- Type: article
- Identifier: http://hdl.handle.net/10962/65428 , vital:28790 , https://doi.org/10.17159/sajs.2016/a0173
- Description: publisher version , The polar regions are more critically affected by climate change than any other region on our planet.1,2 On the Antarctic continent and in its surrounding oceans, the effects of climate change are likely to be dramatic,3 and include largescale catastrophic ice melt, loss of habitat and biodiversity, and global sea level rise. The ‘Southern Ocean’ refers to the region where Atlantic, Indian and Pacific Ocean waters come together to encircle Antarctica. These waters connect the different ocean basins by linking the shallow and deep limbs of the global ocean current system (‘overturning circulation’) and play a critical role in storing and distributing heat and carbon dioxide (CO2 ). The Southern Ocean thus regulates not only the climate of the Antarctic, but of the entire earth system.1,4 By extension, the capacity of the global ocean to ameliorate earth’s changing climate is strongly controlled by the Southern Ocean. Marine phytoplankton (microscopic plants inhabiting the sunlit upper ocean) convert CO2 (an inorganic form of carbon) dissolved in surface waters into organic carbon through photosynthesis. This organic carbon fuels upper trophic levels such as fish, mammals and birds, and a portion sinks into the deep ocean where it remains stored for hundreds to thousands of years. This mechanism, which lowers the atmospheric concentration of CO2 , is termed the ‘biological pump’.5 The efficiency of the global ocean’s biological pump is currently limited by the Southern Ocean, where the macronutrients (nitrate and phosphate) required for photosynthesis are never fully consumed in surface waters. In theory, increased consumption of these nutrients could drive higher organic carbon removal to the deep ocean, enhancing the oceanic uptake of atmospheric CO2 . Indeed, more complete consumption of Southern Ocean nutrients is a leading hypothesis for the decrease in atmospheric CO2 that characterised the ice ages.6 Despite the global importance of the Southern Ocean, knowledge of the controls on and interactions among the physical, chemical and biological processes operating in Antarctic ecosystems is limited, largely because of a scarcity of in-situ observational data, compounded by the challenge of integrating siloed scientific fields. Given predictions that diverse aspects of Southern Ocean physics and carbon biogeochemistry are likely to change in the coming decades, a transdisciplinary approach to studying Antarctic systems is critical.
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The role of entomopathogenic fungi in the control of citrus pests in South Africa: cause for optimism
- Coombes, Candice A, Chartier-Fizgerald, Veronique, Wiblin, Danielle, Dames, Joanna F, Hill, Martin P, Moore, Sean D
- Authors: Coombes, Candice A , Chartier-Fizgerald, Veronique , Wiblin, Danielle , Dames, Joanna F , Hill, Martin P , Moore, Sean D
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/453480 , vital:75257 , ISBN 978-1-83768-091-7 , https://iobc-wprs.org/product/the-role-of-entomopathogenic-fungi-in-the-control-of-citrus-pests-in-south-africa-cause-for-optimism/
- Description: Citrus is a highly productive crop in South Africa, but it is damaged by a number of pests that result in yield loss and have the potential to limit market access. Maximum residue limits (MRLs) imposed by importing countries have driven the need for alternative control technologies, including the use of entomopathogenic fungi (EPF). Bioprospecting in citrus orchards and seven years of bioassay trials identified Beauveria bassiana G Ar 17 B3 and Metarhizium anisopliae G 11 3 L6 and FCM Ar 23 B3 as the most virulent fungal isolates. Preliminary trials with these three fungi against the arboreal pests, California red scale, Aonidiella aurantii (Maskell), citrus mealybug, Planococcus citri (Risso) and citrus thrips, Scirtothrips aurantii Faure, have been promising. False codling moth (FCM), Thaumatotibia leucotreta (Meyrick) is the most important citrus pest in South Africa and while considerable research has been conducted on controlling the insect on the tree, the soil borne stages of this insect have largely been ignored. After laboratory bioassays, the three fungal isolates were taken to field trials. All three isolates persisted for at least six months after application to the soil. A large scale field trial, showed that although all three isolates reduced FCM infestation, isolate B. bassiana G Ar 17 B3 performed best, recording a consistent 80% reduction in FCM infestation throughout the trial period. The results of nearly 10 years of research on the potential of EPFs in the control of citrus pests in South Africa are certainly cause for optimism.
- Full Text:
- Authors: Coombes, Candice A , Chartier-Fizgerald, Veronique , Wiblin, Danielle , Dames, Joanna F , Hill, Martin P , Moore, Sean D
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/453480 , vital:75257 , ISBN 978-1-83768-091-7 , https://iobc-wprs.org/product/the-role-of-entomopathogenic-fungi-in-the-control-of-citrus-pests-in-south-africa-cause-for-optimism/
- Description: Citrus is a highly productive crop in South Africa, but it is damaged by a number of pests that result in yield loss and have the potential to limit market access. Maximum residue limits (MRLs) imposed by importing countries have driven the need for alternative control technologies, including the use of entomopathogenic fungi (EPF). Bioprospecting in citrus orchards and seven years of bioassay trials identified Beauveria bassiana G Ar 17 B3 and Metarhizium anisopliae G 11 3 L6 and FCM Ar 23 B3 as the most virulent fungal isolates. Preliminary trials with these three fungi against the arboreal pests, California red scale, Aonidiella aurantii (Maskell), citrus mealybug, Planococcus citri (Risso) and citrus thrips, Scirtothrips aurantii Faure, have been promising. False codling moth (FCM), Thaumatotibia leucotreta (Meyrick) is the most important citrus pest in South Africa and while considerable research has been conducted on controlling the insect on the tree, the soil borne stages of this insect have largely been ignored. After laboratory bioassays, the three fungal isolates were taken to field trials. All three isolates persisted for at least six months after application to the soil. A large scale field trial, showed that although all three isolates reduced FCM infestation, isolate B. bassiana G Ar 17 B3 performed best, recording a consistent 80% reduction in FCM infestation throughout the trial period. The results of nearly 10 years of research on the potential of EPFs in the control of citrus pests in South Africa are certainly cause for optimism.
- Full Text:
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