Temperature-dependent performance and potential distribution of Pareuchaetes insulata, a biological control agent of Chromolaena odorata in South Africa
- Uyi, Osariyekemwen O, Zachariades, Costas, Hill, Martin P, McConnachie, Andrew J
- Authors: Uyi, Osariyekemwen O , Zachariades, Costas , Hill, Martin P , McConnachie, Andrew J
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/418067 , vital:71505 , xlink:href="https://doi.org/10.1007/s10526-016-9760-1"
- Description: Despite the release of about 1.9 million individuals of Pareuchaetes insulata (Walker) (Lepidoptera: Erebidae) in KwaZulu-Natal for the biological control of Chromolaena odorata (L.) King and Robinson (Asteraceae) in South Africa, the moth probably only established at one of the 30 release sites and its population level is generally low in the field. To determine whether climate incompatibility in South Africa is responsible for the poor performance of P. insulata, the effects of temperature on life-history traits were investigated under several constant temperatures. Although a degree-day model estimated between 3.9 and 10.0 generations of the moth per year in the weed’s invaded range, survival and fecundity declined while development time was prolonged at constant temperatures below 25 °C, indicating that both direct and indirect negative impacts of low winter temperatures, such as increased mortality, slow development and reduced fecundity as well as exposure to natural enemies, may partly explain the poor performance of P. insulata in South Africa.
- Full Text:
- Date Issued: 2016
- Authors: Uyi, Osariyekemwen O , Zachariades, Costas , Hill, Martin P , McConnachie, Andrew J
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/418067 , vital:71505 , xlink:href="https://doi.org/10.1007/s10526-016-9760-1"
- Description: Despite the release of about 1.9 million individuals of Pareuchaetes insulata (Walker) (Lepidoptera: Erebidae) in KwaZulu-Natal for the biological control of Chromolaena odorata (L.) King and Robinson (Asteraceae) in South Africa, the moth probably only established at one of the 30 release sites and its population level is generally low in the field. To determine whether climate incompatibility in South Africa is responsible for the poor performance of P. insulata, the effects of temperature on life-history traits were investigated under several constant temperatures. Although a degree-day model estimated between 3.9 and 10.0 generations of the moth per year in the weed’s invaded range, survival and fecundity declined while development time was prolonged at constant temperatures below 25 °C, indicating that both direct and indirect negative impacts of low winter temperatures, such as increased mortality, slow development and reduced fecundity as well as exposure to natural enemies, may partly explain the poor performance of P. insulata in South Africa.
- Full Text:
- Date Issued: 2016
The Bero Volcanic Complex: extension of the Paraná-Etendeka Igneous Province into SW Angola
- Marsh, Julian S, Swart, Roger S
- Authors: Marsh, Julian S , Swart, Roger S
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/60763 , vital:27827 , https://www.sciencedirect.com/science/article/pii/S0377027316304176
- Description: An extension of the Etendeka-Paraná Igneous Province into SW Angola occurs as minor basalt lavas, intrusive gabbro sheets, minor mafic dykes and thick sheets and lava flows (with minor pyroclastics) of quartz latite composition This suite crops out along the eastern margin of the Cretaceous Namibe Basin in SW Angola. The quartz latites from one locality have been referred to informally as the Giraul volcanics but the name ‘Giraul’ has previously been used for Cretaceous conglomerates. We propose the name Bero Volcanic Complex for this suite of intrusive and extrusive rocks on the basis that the full compositional range of this diverse suite crops out along the Rio Bero. Major and trace element compositions and Sr-, Nd-, and Pb-isotopic compositions indicate that the basalts and gabbros are equivalent to the high-Ti Khumib/Urubici and Pitanga types from the Etendeka and Paraná. The basalts underlie the quartz latites which are cut by mafic dykes some of which are compositionally equivalent to the Paranapanema lavas in the Paraná. Five different geochemical types of high-Ti quartz latite are recognised amongst the silicic volcanics, 3 of which have very close geochemical affinities to the Ventura, Sarusas, and Khoraseb types of the northern Etendeka. Their relative stratigraphic position in the Bero volcanic sequence is the same as in the Etendeka sequence and extend significantly the area over which these types were erupted. The two remaining types, Chinguau and High-Nb are not known from either the Etendeka or the Paraná provinces.
- Full Text:
- Date Issued: 2016
- Authors: Marsh, Julian S , Swart, Roger S
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/60763 , vital:27827 , https://www.sciencedirect.com/science/article/pii/S0377027316304176
- Description: An extension of the Etendeka-Paraná Igneous Province into SW Angola occurs as minor basalt lavas, intrusive gabbro sheets, minor mafic dykes and thick sheets and lava flows (with minor pyroclastics) of quartz latite composition This suite crops out along the eastern margin of the Cretaceous Namibe Basin in SW Angola. The quartz latites from one locality have been referred to informally as the Giraul volcanics but the name ‘Giraul’ has previously been used for Cretaceous conglomerates. We propose the name Bero Volcanic Complex for this suite of intrusive and extrusive rocks on the basis that the full compositional range of this diverse suite crops out along the Rio Bero. Major and trace element compositions and Sr-, Nd-, and Pb-isotopic compositions indicate that the basalts and gabbros are equivalent to the high-Ti Khumib/Urubici and Pitanga types from the Etendeka and Paraná. The basalts underlie the quartz latites which are cut by mafic dykes some of which are compositionally equivalent to the Paranapanema lavas in the Paraná. Five different geochemical types of high-Ti quartz latite are recognised amongst the silicic volcanics, 3 of which have very close geochemical affinities to the Ventura, Sarusas, and Khoraseb types of the northern Etendeka. Their relative stratigraphic position in the Bero volcanic sequence is the same as in the Etendeka sequence and extend significantly the area over which these types were erupted. The two remaining types, Chinguau and High-Nb are not known from either the Etendeka or the Paraná provinces.
- Full Text:
- Date Issued: 2016
The development of computational biology in South Africa: successes achieved and lessons learnt
- Mulder, Nicola J, Christoffels, Alan, De Oliveira, Tulio, Gamieldien, Junaid, Hazelhurst, Scott, Joubert, Fourie, Kumuthini, Judit, Pillay, Ché S, Snoep, Jacky L, Tastan Bishop, Özlem, Tiffin, Nicki
- Authors: Mulder, Nicola J , Christoffels, Alan , De Oliveira, Tulio , Gamieldien, Junaid , Hazelhurst, Scott , Joubert, Fourie , Kumuthini, Judit , Pillay, Ché S , Snoep, Jacky L , Tastan Bishop, Özlem , Tiffin, Nicki
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148347 , vital:38731 , DOI: 10.1371/journal.pcbi.1004395
- Description: Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.
- Full Text:
- Date Issued: 2016
- Authors: Mulder, Nicola J , Christoffels, Alan , De Oliveira, Tulio , Gamieldien, Junaid , Hazelhurst, Scott , Joubert, Fourie , Kumuthini, Judit , Pillay, Ché S , Snoep, Jacky L , Tastan Bishop, Özlem , Tiffin, Nicki
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148347 , vital:38731 , DOI: 10.1371/journal.pcbi.1004395
- Description: Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.
- Full Text:
- Date Issued: 2016
The effectiveness and impacts of subsidies to film industries
- Collins, Alan, Snowball, Jeanette D
- Authors: Collins, Alan , Snowball, Jeanette D
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68511 , vital:29273 , https://www.southafricanculturalobservatory.org.za/
- Description: Publisher version , Conference paper presented at the South African Cultural Observatory, First National Conference: Counting Culture, The Cultural and Creative Industries in National and International Context, 16-17 May 2016, The Boardwalk International Convention Centre, Nelson Mandela Bay.
- Full Text:
- Date Issued: 2016
- Authors: Collins, Alan , Snowball, Jeanette D
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68511 , vital:29273 , https://www.southafricanculturalobservatory.org.za/
- Description: Publisher version , Conference paper presented at the South African Cultural Observatory, First National Conference: Counting Culture, The Cultural and Creative Industries in National and International Context, 16-17 May 2016, The Boardwalk International Convention Centre, Nelson Mandela Bay.
- Full Text:
- Date Issued: 2016
The effects of silica based nanoparticles on the photophysicochemical properties, in vitro dark viability and photodynamic therapy study of zinc monocarboxyphenoxy phthalocyanine
- Oluwole, David O, Uddin, Imran, Prinsloo, Earl, Nyokong, Tebello
- Authors: Oluwole, David O , Uddin, Imran , Prinsloo, Earl , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/240371 , vital:50828 , xlink:href="https://doi.org/10.1016/j.jphotochem.2016.07.002"
- Description: Aminopropyl triethoxysilane functionalized core SiO2 and core/shell ZnO/SiO2 nanoparticles (NP) were covalently linked to zinc monocarboxyphenoxy phthalocyanine (ZnMCPPc, complex 1) via amide bond formation. The photophysicochemical behavior, in vitro dark viability and photodynamic therapy (PDT) activity against human breast adenocarcinoma cell line (MCF-7 cells) of the conjugates were studied. The nanoconjugates showed enhanced photophysicochemical behavior as compared to complex 1 alone. Complex 1 showed higher dark toxicity against MCF-7 cells when compared to the conjugates. In the dark, complex 1 accounted for less than 50% viable cells at 28.6 μg/mL and 57.1 μg/mL compared to the conjugates which accounted for more than 50% cell viability at these concentrations. The in vitro dark viability and PDT activity of complex 1 was reduced in the presence of these nanoparticles.
- Full Text:
- Date Issued: 2016
- Authors: Oluwole, David O , Uddin, Imran , Prinsloo, Earl , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/240371 , vital:50828 , xlink:href="https://doi.org/10.1016/j.jphotochem.2016.07.002"
- Description: Aminopropyl triethoxysilane functionalized core SiO2 and core/shell ZnO/SiO2 nanoparticles (NP) were covalently linked to zinc monocarboxyphenoxy phthalocyanine (ZnMCPPc, complex 1) via amide bond formation. The photophysicochemical behavior, in vitro dark viability and photodynamic therapy (PDT) activity against human breast adenocarcinoma cell line (MCF-7 cells) of the conjugates were studied. The nanoconjugates showed enhanced photophysicochemical behavior as compared to complex 1 alone. Complex 1 showed higher dark toxicity against MCF-7 cells when compared to the conjugates. In the dark, complex 1 accounted for less than 50% viable cells at 28.6 μg/mL and 57.1 μg/mL compared to the conjugates which accounted for more than 50% cell viability at these concentrations. The in vitro dark viability and PDT activity of complex 1 was reduced in the presence of these nanoparticles.
- Full Text:
- Date Issued: 2016
The good African society index
- Authors: Botha, Ferdi
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/396194 , vital:69157 , xlink:href="https://doi.org/10.1007/s11205-015-0891-z"
- Description: This paper constructs a Good Society Index for 45 African countries, termed the Good African Society Index (GASI). The GASI consists of nine main indexes: (1) economic sustainability, (2) democracy and freedom, (3) child well-being, (4) environment and infrastructure, (5) safety and security, (6) health and health systems, (7) integrity and justice, (8) education, and (9) social sustainability and social cohesion. Each component is split into four sub-components for a total of 36 indicators. Tunisia ranks highest on the GASI, followed by Cape Verde and Botswana. Chad has the lowest GASI score, followed by Central African Republic and Cote d’Ivoire. The GASI is strongly related to the 2012 Human Development Index and Fragile States Index, to a lesser extent, GNI per capita.
- Full Text:
- Date Issued: 2016
- Authors: Botha, Ferdi
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/396194 , vital:69157 , xlink:href="https://doi.org/10.1007/s11205-015-0891-z"
- Description: This paper constructs a Good Society Index for 45 African countries, termed the Good African Society Index (GASI). The GASI consists of nine main indexes: (1) economic sustainability, (2) democracy and freedom, (3) child well-being, (4) environment and infrastructure, (5) safety and security, (6) health and health systems, (7) integrity and justice, (8) education, and (9) social sustainability and social cohesion. Each component is split into four sub-components for a total of 36 indicators. Tunisia ranks highest on the GASI, followed by Cape Verde and Botswana. Chad has the lowest GASI score, followed by Central African Republic and Cote d’Ivoire. The GASI is strongly related to the 2012 Human Development Index and Fragile States Index, to a lesser extent, GNI per capita.
- Full Text:
- Date Issued: 2016
The GULLS project: a comparison of vulnerabilities across selected ocean hotspots and implications for adaptation to global change
- Cochrane, Kevern L, Hobday, Alistair J, Aswani, Shankar, Byfield, Val, Dutra, Leo X, Gasalla, Maria A, Haward, Marcus, Paytan, Adina, Pecl, Gretta T, Popova, Katya, Sainulabdeen, Shyam S, Savage, Candida, Sauer, Warwick H H, van Putten, Ingrid E, Visser, Natascha, TG Team
- Authors: Cochrane, Kevern L , Hobday, Alistair J , Aswani, Shankar , Byfield, Val , Dutra, Leo X , Gasalla, Maria A , Haward, Marcus , Paytan, Adina , Pecl, Gretta T , Popova, Katya , Sainulabdeen, Shyam S , Savage, Candida , Sauer, Warwick H H , van Putten, Ingrid E , Visser, Natascha , TG Team
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/422037 , vital:71906
- Description: The GULLS project, `Global learning for local solutions: Reducing vulnerability of marine-dependent coastal communities' has been underway since October 2014. The project has been investigating six regional `hotspots': marine areas experiencing rapid warming. These are south-east Australia, Brazil, India, Solomon Islands, South Africa, and the Mozambique Channel and Madagascar. Rapid warming could be expected to have social, cultural and economic impacts that could affect these countries in different ways and may already be doing so. GULLS has focused on contributing to assessing and reducing the vulnerability of coastal communities and other stakeholders dependent on marine resources and to facilitate adaptation to climate change and variability through an integrated and trans-disciplinary approach. It includes participants from Australia, Brazil, India, Madagascar, New Zealand, South Africa, the United Kingdom and the United States of America. The research programme has been divided into six inter-linked components: ocean models, biological and ecological sensitivity analyses, system models, social vulnerability, policy mapping, and communication and education. This presentation will provide a brief overview of each of these components and describe the benefits that have resulted from the collaborative and transdisciplinary approach of GULLS. Following the standard vulnerability elements of exposure, sensitivity and adaptive capacity, the vulnerabilities of coastal communities and other stakeholders dependent on marine resources in the five hotspots will be compared using a set of indicators derived and populated from results of the research programme. The implications of similarities and differences between the hotspots for adaptation planning and options will be described.
- Full Text:
- Date Issued: 2016
- Authors: Cochrane, Kevern L , Hobday, Alistair J , Aswani, Shankar , Byfield, Val , Dutra, Leo X , Gasalla, Maria A , Haward, Marcus , Paytan, Adina , Pecl, Gretta T , Popova, Katya , Sainulabdeen, Shyam S , Savage, Candida , Sauer, Warwick H H , van Putten, Ingrid E , Visser, Natascha , TG Team
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/422037 , vital:71906
- Description: The GULLS project, `Global learning for local solutions: Reducing vulnerability of marine-dependent coastal communities' has been underway since October 2014. The project has been investigating six regional `hotspots': marine areas experiencing rapid warming. These are south-east Australia, Brazil, India, Solomon Islands, South Africa, and the Mozambique Channel and Madagascar. Rapid warming could be expected to have social, cultural and economic impacts that could affect these countries in different ways and may already be doing so. GULLS has focused on contributing to assessing and reducing the vulnerability of coastal communities and other stakeholders dependent on marine resources and to facilitate adaptation to climate change and variability through an integrated and trans-disciplinary approach. It includes participants from Australia, Brazil, India, Madagascar, New Zealand, South Africa, the United Kingdom and the United States of America. The research programme has been divided into six inter-linked components: ocean models, biological and ecological sensitivity analyses, system models, social vulnerability, policy mapping, and communication and education. This presentation will provide a brief overview of each of these components and describe the benefits that have resulted from the collaborative and transdisciplinary approach of GULLS. Following the standard vulnerability elements of exposure, sensitivity and adaptive capacity, the vulnerabilities of coastal communities and other stakeholders dependent on marine resources in the five hotspots will be compared using a set of indicators derived and populated from results of the research programme. The implications of similarities and differences between the hotspots for adaptation planning and options will be described.
- Full Text:
- Date Issued: 2016
The influence of photoperiod on the reproductive physiology of the greater red musk shrew: Crocidura flavescens
- Hoole, C, McKechnie, Andrew E, Parker, Daniel M, Bennett, Nigel C
- Authors: Hoole, C , McKechnie, Andrew E , Parker, Daniel M , Bennett, Nigel C
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/70157 , vital:29626 , https://doi.org/10.1139/cjz-2015-0128
- Description: Photoperiodism involves the use of both absolute measures of day length and the direction in which day length is changing as a cue for regulating seasonal changes in physiology and behaviour so that birth and lactation coincide with optimal resource availability, increasing offspring survival. Induced ovulation and opportunistic breeding is often found in species that are predominantly solitary and territorial. In this study, the photoperiodic reproductive responses of male greater red musk shrews (Crocidura flavescens (I. Geoffroy Saint-Hilaire, 1827)) were investigated in the laboratory. The presence of spermatozoa regardless of the light cycle, suggest that although the shrews are photoresponsive, they may be capable of breeding throughout the year. Significantly greater testicular volume and eminiferous tubule diameter following exposure to a short day-light cycle suggests that these animals may have breeding peaks that correspond to short days. The presence of epidermal spines on the penis indicates that the shrew is likely also an induced ovulator. Flexible breeding patterns combined with induced ovulation affords this solitary species the greatest chance of reproductive success.
- Full Text:
- Date Issued: 2016
- Authors: Hoole, C , McKechnie, Andrew E , Parker, Daniel M , Bennett, Nigel C
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/70157 , vital:29626 , https://doi.org/10.1139/cjz-2015-0128
- Description: Photoperiodism involves the use of both absolute measures of day length and the direction in which day length is changing as a cue for regulating seasonal changes in physiology and behaviour so that birth and lactation coincide with optimal resource availability, increasing offspring survival. Induced ovulation and opportunistic breeding is often found in species that are predominantly solitary and territorial. In this study, the photoperiodic reproductive responses of male greater red musk shrews (Crocidura flavescens (I. Geoffroy Saint-Hilaire, 1827)) were investigated in the laboratory. The presence of spermatozoa regardless of the light cycle, suggest that although the shrews are photoresponsive, they may be capable of breeding throughout the year. Significantly greater testicular volume and eminiferous tubule diameter following exposure to a short day-light cycle suggests that these animals may have breeding peaks that correspond to short days. The presence of epidermal spines on the penis indicates that the shrew is likely also an induced ovulator. Flexible breeding patterns combined with induced ovulation affords this solitary species the greatest chance of reproductive success.
- Full Text:
- Date Issued: 2016
The interaction between graphene quantum dots grafted with polyethyleneimine and Au@ Ag nanoparticles
- Achadu, Ojodomo John, Uddin, Imran, Nyokong, Tebello
- Authors: Achadu, Ojodomo John , Uddin, Imran , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/188679 , vital:44775 , xlink:href="https://doi.org/10.1016/j.jphotochem.2016.03.016"
- Description: Graphene quantum dots grafted with polyethyleneimine (GQDs-PEI) and Au@Ag core-shell nanoparticles blend was demonstrated to be a novel biosensing nanoprobe for the rapid and highly sensitive detection of biothiols such as cysteine (Cys), homocysteine (Hcys) and glutathione (GSH). The fluorescence emission of GQDs-PEI was quenched efficiently upon interaction with Au@Ag core-shell nanoparticles. The quenched fluorescence emission of the GQDs-PEI was restored in the presence of the biothiols. The fluorimetric sensing is based on the strong affinity between the mercapto (SH) groups of the biothiols and the Au@Ag core-shell nanoparticles by which the interaction between GQDs-PEI and Au@Ag core-shell nanoparticles was disrupted with a consequent modulation (‘turn-on’) of the quenched GQDs-PEI emission. Thus, a new, simple, rapid and highly sensitive fluorescence nanoprobe for detecting biothiols has been developed in this work.
- Full Text:
- Date Issued: 2016
- Authors: Achadu, Ojodomo John , Uddin, Imran , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/188679 , vital:44775 , xlink:href="https://doi.org/10.1016/j.jphotochem.2016.03.016"
- Description: Graphene quantum dots grafted with polyethyleneimine (GQDs-PEI) and Au@Ag core-shell nanoparticles blend was demonstrated to be a novel biosensing nanoprobe for the rapid and highly sensitive detection of biothiols such as cysteine (Cys), homocysteine (Hcys) and glutathione (GSH). The fluorescence emission of GQDs-PEI was quenched efficiently upon interaction with Au@Ag core-shell nanoparticles. The quenched fluorescence emission of the GQDs-PEI was restored in the presence of the biothiols. The fluorimetric sensing is based on the strong affinity between the mercapto (SH) groups of the biothiols and the Au@Ag core-shell nanoparticles by which the interaction between GQDs-PEI and Au@Ag core-shell nanoparticles was disrupted with a consequent modulation (‘turn-on’) of the quenched GQDs-PEI emission. Thus, a new, simple, rapid and highly sensitive fluorescence nanoprobe for detecting biothiols has been developed in this work.
- Full Text:
- Date Issued: 2016
The limitations of current health literacy measures for use in developing countries:
- Authors: Dowse, Roslind
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/156607 , vital:40030 , DOI: 10.1080/17538068.2016.1147742
- Description: Health literacy measures have largely emanated from developed countries, reflecting the characteristics of their economies, populations, and health systems. In contrast, it is disconcerting that health literacy appears to be so under-researched in developing countries (DCs), despite the likelihood of inadequate health literacy being endemic. In this commentary, I highlight some challenges when using existing health literacy measures in DCs and conclude with a summary of considerations when using/developing a tool for these populations.
- Full Text:
- Date Issued: 2016
- Authors: Dowse, Roslind
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/156607 , vital:40030 , DOI: 10.1080/17538068.2016.1147742
- Description: Health literacy measures have largely emanated from developed countries, reflecting the characteristics of their economies, populations, and health systems. In contrast, it is disconcerting that health literacy appears to be so under-researched in developing countries (DCs), despite the likelihood of inadequate health literacy being endemic. In this commentary, I highlight some challenges when using existing health literacy measures in DCs and conclude with a summary of considerations when using/developing a tool for these populations.
- Full Text:
- Date Issued: 2016
The Malarial Exported PFA0660w Is an Hsp40 Co-Chaperone of PfHsp70-x
- Daniyan, Michael O, Boshoff, Aileen, Prinsloo, Earl, Pesce, Eva-Rachele, Blatch, Gregory L
- Authors: Daniyan, Michael O , Boshoff, Aileen , Prinsloo, Earl , Pesce, Eva-Rachele , Blatch, Gregory L
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66098 , vital:28901 , https://doi.org/10.1371/journal.pone.0148517
- Description: publisher version , Plasmodium falciparum, the human pathogen responsible for the most dangerous malaria infection, survives and develops in mature erythrocytes through the export of proteins needed for remodelling of the host cell. Molecular chaperones of the heat shock protein (Hsp) family are prominent members of the exportome, including a number of Hsp40s and a Hsp70. PFA0660w, a type II Hsp40, has been shown to be exported and possibly form a complex with PfHsp70-x in the infected erythrocyte cytosol. However, the chaperone properties of PFA0660w and its interaction with human and parasite Hsp70s are yet to be investigated. Recombinant PFA0660w was found to exist as a monomer in solution, and was able to significantly stimulate the ATPase activity of PfHsp70-x but not that of a second plasmodial Hsp70 (PfHsp70-1) or a human Hsp70 (HSPA1A), indicating a potential specific functional partnership with PfHsp70-x. Protein binding studies in the presence and absence of ATP suggested that the interaction of PFA0660w with PfHsp70-x most likely represented a co-chaperone/chaperone interaction. Also, PFA0660w alone produced a concentration-dependent suppression of rhodanese aggregation, demonstrating its chaperone properties. Overall, we have provided the first biochemical evidence for the possible role of PFA0660w as a chaperone and as co-chaperone of PfHsp70-x. We propose that these chaperones boost the chaperone power of the infected erythrocyte, enabling successful protein trafficking and folding, and thereby making a fundamental contribution to the pathology of malaria. , This work was supported by grants from the National Research Foundation (NRF) and Medical Research Council (MRC) of South Africa. The ProteOn XPR36 IAS was purchased from a National Nanotechnology Equipment Programme grant from the Department of Science and Technology and the NRF of South Africa. Michael O. Daniyan was a recipient of the Education Trust Fund (ETF) Academic Staff Training and Development (AST and D) scholarship of Obafemi Awolowo University, Ile-Ife, Nigeria and a Rhodes University Council research bursary
- Full Text:
- Date Issued: 2016
- Authors: Daniyan, Michael O , Boshoff, Aileen , Prinsloo, Earl , Pesce, Eva-Rachele , Blatch, Gregory L
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66098 , vital:28901 , https://doi.org/10.1371/journal.pone.0148517
- Description: publisher version , Plasmodium falciparum, the human pathogen responsible for the most dangerous malaria infection, survives and develops in mature erythrocytes through the export of proteins needed for remodelling of the host cell. Molecular chaperones of the heat shock protein (Hsp) family are prominent members of the exportome, including a number of Hsp40s and a Hsp70. PFA0660w, a type II Hsp40, has been shown to be exported and possibly form a complex with PfHsp70-x in the infected erythrocyte cytosol. However, the chaperone properties of PFA0660w and its interaction with human and parasite Hsp70s are yet to be investigated. Recombinant PFA0660w was found to exist as a monomer in solution, and was able to significantly stimulate the ATPase activity of PfHsp70-x but not that of a second plasmodial Hsp70 (PfHsp70-1) or a human Hsp70 (HSPA1A), indicating a potential specific functional partnership with PfHsp70-x. Protein binding studies in the presence and absence of ATP suggested that the interaction of PFA0660w with PfHsp70-x most likely represented a co-chaperone/chaperone interaction. Also, PFA0660w alone produced a concentration-dependent suppression of rhodanese aggregation, demonstrating its chaperone properties. Overall, we have provided the first biochemical evidence for the possible role of PFA0660w as a chaperone and as co-chaperone of PfHsp70-x. We propose that these chaperones boost the chaperone power of the infected erythrocyte, enabling successful protein trafficking and folding, and thereby making a fundamental contribution to the pathology of malaria. , This work was supported by grants from the National Research Foundation (NRF) and Medical Research Council (MRC) of South Africa. The ProteOn XPR36 IAS was purchased from a National Nanotechnology Equipment Programme grant from the Department of Science and Technology and the NRF of South Africa. Michael O. Daniyan was a recipient of the Education Trust Fund (ETF) Academic Staff Training and Development (AST and D) scholarship of Obafemi Awolowo University, Ile-Ife, Nigeria and a Rhodes University Council research bursary
- Full Text:
- Date Issued: 2016
The network society: A model for computing infrastructure in South African schools
- Siebörger, Ingrid, Terzoli, Alfredo
- Authors: Siebörger, Ingrid , Terzoli, Alfredo
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/430651 , vital:72706 , 10.1109/ISTAFRICA.2016.7530673
- Description: Worldwide computers are being used in schools for, amongst other things, developing the knowledge and skills required for citizens to be able to operate within the 21st Century Information Age. Realising the potential of technology in uplifting the lives of its citizens the South Afri-can government has proposed the National Broadband Plan (SA Con-nect). However, unfortunately this plan only addresses the networking aspect of Information Communication Technologies (ICTs). In this pa-per we investigate appropriate Information Technologies for schools in the light of SA Connect, and propose a model for the computing infra-structure required in South African schools in order to support access to and adoption of technology and networks. This model is based on our multi-year experimentation in the Siyakhula Living Lab.
- Full Text:
- Date Issued: 2016
- Authors: Siebörger, Ingrid , Terzoli, Alfredo
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/430651 , vital:72706 , 10.1109/ISTAFRICA.2016.7530673
- Description: Worldwide computers are being used in schools for, amongst other things, developing the knowledge and skills required for citizens to be able to operate within the 21st Century Information Age. Realising the potential of technology in uplifting the lives of its citizens the South Afri-can government has proposed the National Broadband Plan (SA Con-nect). However, unfortunately this plan only addresses the networking aspect of Information Communication Technologies (ICTs). In this pa-per we investigate appropriate Information Technologies for schools in the light of SA Connect, and propose a model for the computing infra-structure required in South African schools in order to support access to and adoption of technology and networks. This model is based on our multi-year experimentation in the Siyakhula Living Lab.
- Full Text:
- Date Issued: 2016
The optical limiting of blue and green ytterbium double-decker phthalocyanines in solution and in poly (acrylic acid) as thin films
- Sekhosana, Kutloana E, Nyokong, Tebello
- Authors: Sekhosana, Kutloana E , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/188585 , vital:44767 , xlink:href="https://doi.org/10.1016/j.ica.2016.05.026"
- Description: Bis{1(4), 8(11), 15(18), 22(25)-tetra(4-tert-butylphenoxy)phthalocyaninato} ytterbium(III) (2a) (the green form) was synthesized and reduced to form 2b (the blue form). Nonlinear optical parameters for complex 2 in green and blue forms were determined using the Z-scan technique and the values of third-order imaginary susceptibility (Im[χ(3)]) and second-order hyperpolarizability (γ) of the order of 10−9 (for 2b) and 10−27 esu, respectively, were obtained in solution. In poly(acrylic acid) as a thin film, complex 2a showed extremely high Im[χ(3)] and γ values of the order 10−8 and 10−25 respectively. A low optical limiting threshold value of 0.075 J cm−2 was obtained for the thin film 2a.
- Full Text:
- Date Issued: 2016
- Authors: Sekhosana, Kutloana E , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/188585 , vital:44767 , xlink:href="https://doi.org/10.1016/j.ica.2016.05.026"
- Description: Bis{1(4), 8(11), 15(18), 22(25)-tetra(4-tert-butylphenoxy)phthalocyaninato} ytterbium(III) (2a) (the green form) was synthesized and reduced to form 2b (the blue form). Nonlinear optical parameters for complex 2 in green and blue forms were determined using the Z-scan technique and the values of third-order imaginary susceptibility (Im[χ(3)]) and second-order hyperpolarizability (γ) of the order of 10−9 (for 2b) and 10−27 esu, respectively, were obtained in solution. In poly(acrylic acid) as a thin film, complex 2a showed extremely high Im[χ(3)] and γ values of the order 10−8 and 10−25 respectively. A low optical limiting threshold value of 0.075 J cm−2 was obtained for the thin film 2a.
- Full Text:
- Date Issued: 2016
The photobleaching of the free and encapsulated metallic phthalocyanine and its effect on the photooxidation of simple molecules
- Fanchiotti, Brenda Gomes, Machado, Marcella Piffer Zamprogno, de Paula, Letícia Camilato, Durmuş, Mahmut, Nyokong, Tebello, da Silva, Gonçalves, da Silva, André Romero
- Authors: Fanchiotti, Brenda Gomes , Machado, Marcella Piffer Zamprogno , de Paula, Letícia Camilato , Durmuş, Mahmut , Nyokong, Tebello , da Silva, Gonçalves , da Silva, André Romero
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/239687 , vital:50755 , xlink:href="https://doi.org/10.1016/j.jphotobiol.2016.10.007"
- Description: The photobleaching of an unsubstituted phthalocyanine (gallium(III) phthalocyanine chloride (GaPc)) and a substituted phthalocyanine (1,4-(tetrakis[4-(benzyloxy)phenoxy]phthalocyaninato) indium(III) chloride (InTBPPc)) was monitored for the free photosensitizers and for the phthalocyanines encapsulated into nanoparticles of PEGylated poly(D,L-lactide-co-glycolide) (PLGA-PEG). Phosphate-buffered solutions (PBS) and organic solutions of the free GaPc or the free InTBPPc, and suspensions of each encapsulated photosensitizer (2–15 μmol/L) were irradiated using a laser diode of 665 nm with a power of 1–104 mW and a light dose of 7.5 J/cm2. The relative absorbance (RA) of the free GaPc dissolved in 1-methyl-2-pyrrolidone (MP) decreased 8.4 times when the laser power increased from 1 mW to 104 mW. However, the free or encapsulated GaPc did not suffer the photobleaching in PBS solution. The RA values decreased 2.4 times and 22.2 times for the free InTBPPc dissolved in PBS solution and in dimethylformamide (DMF), respectively, but the encapsulated InTBPPc was only photobleached when the laser power was 104 mW at 8 μmol/L. The increase of the free GaPc concentration favored the photobleaching in MP until 8 μmol/L while the increase from 2 μmol/L to 5 μmol/L reduced the photodegradation in PBS solution. However, the photobleaching of the free InTBPPc in DMF or in PBS solution, and of each encapsulated photosensitizer was not influenced by increasing the concentration. The influence of the photobleaching on the capability of the free and encapsulated GaPc and InTBPPc to photooxidate the simple molecules was investigated monitoring the fluorescence of dimethylanthracene (DMA) and the tryptophan (Trp). Free InTBPPc was 2.0 and 1.8 times faster to photooxidate the DMA and Trp than it was the free GaPc, but the encapsulated GaPc was 3.4 times more efficient to photooxidize the Trp than it was the encapsulated InTBPPc due to the photodegradation suffered by the encapsulated InTBPPc. The participation of the singlet oxygen was confirmed with the sodium azide in the photobleaching of all free and encapsulated photosensitizer, and in the photooxidation of the DMA and Trp. The asymmetry of InTBPPc increased the solubility of the free compound, decreasing the aggregation state of the photosensitizer and favoring the photobleaching process. The encapsulation shows capability in decreasing the photobleaching of both photosensitizers but the confocal micrographs showed that the increase of the solubility favored the InTBPPc photobleaching during the acquisition of optical cross section. A novel low-symmetry A3B-type phthalocyanine annelated with a pyrazino[2,3-f]phenanthroline ring system and substituted with six solubilizing diisopropylphenoxy-groups (1) was synthesized by metalfree DBU-promoted cross-condensation of diiminoisoindolines derived from 4,5- bis(diisopropylphenoxy)phthalonitrile and pyrazino[2,3-f][1,10]phenanthroline-2,3-dicarbonitrile. The use of these particular precursors affords A3B phthalocyanine in 15% yield, while cross-condensation of the corresponding dinitriles yields only trace amounts of the target compound. Comparative studies of the A3B-type phthalocyanine and its symmetrical octa(diisopropylphenoxy)-substituted counterpart 2 reveal striking differences in the Q band regions of their UVevisible absorption (UVeVis) spectra, which could be readily rationalized through a comparison with calculated TD-DFT spectra. Since 1 can have two NH-tautomers with equivalent and non-equivalent NH-groups, and DFT calculations predict that the former tautomer is only 2.3 kcal/mol more stable than the latter one, a comprehensive analysis of 13C NMR spectra was carried out through the application of 1 He13C HMBC and HSQC techniques. It demonstrated that only the tautomer with equivalent NH-groups is present in solution.
- Full Text:
- Date Issued: 2016
- Authors: Fanchiotti, Brenda Gomes , Machado, Marcella Piffer Zamprogno , de Paula, Letícia Camilato , Durmuş, Mahmut , Nyokong, Tebello , da Silva, Gonçalves , da Silva, André Romero
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/239687 , vital:50755 , xlink:href="https://doi.org/10.1016/j.jphotobiol.2016.10.007"
- Description: The photobleaching of an unsubstituted phthalocyanine (gallium(III) phthalocyanine chloride (GaPc)) and a substituted phthalocyanine (1,4-(tetrakis[4-(benzyloxy)phenoxy]phthalocyaninato) indium(III) chloride (InTBPPc)) was monitored for the free photosensitizers and for the phthalocyanines encapsulated into nanoparticles of PEGylated poly(D,L-lactide-co-glycolide) (PLGA-PEG). Phosphate-buffered solutions (PBS) and organic solutions of the free GaPc or the free InTBPPc, and suspensions of each encapsulated photosensitizer (2–15 μmol/L) were irradiated using a laser diode of 665 nm with a power of 1–104 mW and a light dose of 7.5 J/cm2. The relative absorbance (RA) of the free GaPc dissolved in 1-methyl-2-pyrrolidone (MP) decreased 8.4 times when the laser power increased from 1 mW to 104 mW. However, the free or encapsulated GaPc did not suffer the photobleaching in PBS solution. The RA values decreased 2.4 times and 22.2 times for the free InTBPPc dissolved in PBS solution and in dimethylformamide (DMF), respectively, but the encapsulated InTBPPc was only photobleached when the laser power was 104 mW at 8 μmol/L. The increase of the free GaPc concentration favored the photobleaching in MP until 8 μmol/L while the increase from 2 μmol/L to 5 μmol/L reduced the photodegradation in PBS solution. However, the photobleaching of the free InTBPPc in DMF or in PBS solution, and of each encapsulated photosensitizer was not influenced by increasing the concentration. The influence of the photobleaching on the capability of the free and encapsulated GaPc and InTBPPc to photooxidate the simple molecules was investigated monitoring the fluorescence of dimethylanthracene (DMA) and the tryptophan (Trp). Free InTBPPc was 2.0 and 1.8 times faster to photooxidate the DMA and Trp than it was the free GaPc, but the encapsulated GaPc was 3.4 times more efficient to photooxidize the Trp than it was the encapsulated InTBPPc due to the photodegradation suffered by the encapsulated InTBPPc. The participation of the singlet oxygen was confirmed with the sodium azide in the photobleaching of all free and encapsulated photosensitizer, and in the photooxidation of the DMA and Trp. The asymmetry of InTBPPc increased the solubility of the free compound, decreasing the aggregation state of the photosensitizer and favoring the photobleaching process. The encapsulation shows capability in decreasing the photobleaching of both photosensitizers but the confocal micrographs showed that the increase of the solubility favored the InTBPPc photobleaching during the acquisition of optical cross section. A novel low-symmetry A3B-type phthalocyanine annelated with a pyrazino[2,3-f]phenanthroline ring system and substituted with six solubilizing diisopropylphenoxy-groups (1) was synthesized by metalfree DBU-promoted cross-condensation of diiminoisoindolines derived from 4,5- bis(diisopropylphenoxy)phthalonitrile and pyrazino[2,3-f][1,10]phenanthroline-2,3-dicarbonitrile. The use of these particular precursors affords A3B phthalocyanine in 15% yield, while cross-condensation of the corresponding dinitriles yields only trace amounts of the target compound. Comparative studies of the A3B-type phthalocyanine and its symmetrical octa(diisopropylphenoxy)-substituted counterpart 2 reveal striking differences in the Q band regions of their UVevisible absorption (UVeVis) spectra, which could be readily rationalized through a comparison with calculated TD-DFT spectra. Since 1 can have two NH-tautomers with equivalent and non-equivalent NH-groups, and DFT calculations predict that the former tautomer is only 2.3 kcal/mol more stable than the latter one, a comprehensive analysis of 13C NMR spectra was carried out through the application of 1 He13C HMBC and HSQC techniques. It demonstrated that only the tautomer with equivalent NH-groups is present in solution.
- Full Text:
- Date Issued: 2016
Towards malicious network activity mitigation through subnet reputation analysis
- Herbert, Alan, Irwin, Barry V W
- Authors: Herbert, Alan , Irwin, Barry V W
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/427799 , vital:72463 , https://www.researchgate.net/profile/Barry-Ir-win/publication/327622788_Towards_Malicious_Network_Activity_Mitigation_through_Subnet_Reputation_Analysis/links/5b9a1a88458515310583fda6/Towards-Malicious-Network-Activity-Mitigation-through-Subnet-Reputation-Analysis.pdf
- Description: Analysis technologies that focus on partial packet rather than full packet analysis have shown promise in detection of malicious activity on net-works. NetFlow is one such emergent protocol that is used to log net-work flows through summarizing key features of them. These logs can then be exported to external NetFlow sinks and proper configuration can see effective bandwidth bottleneck mitigation occurring on net-works. Furthermore, each NetFlow source node is configurable with its own unique ID number. This feature enables a system that knows where a NetFlow source node ID number resides physically to say which network flows are occurring from which physical locations irre-spective of the IP addresses involved in these network flows.
- Full Text:
- Date Issued: 2016
- Authors: Herbert, Alan , Irwin, Barry V W
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/427799 , vital:72463 , https://www.researchgate.net/profile/Barry-Ir-win/publication/327622788_Towards_Malicious_Network_Activity_Mitigation_through_Subnet_Reputation_Analysis/links/5b9a1a88458515310583fda6/Towards-Malicious-Network-Activity-Mitigation-through-Subnet-Reputation-Analysis.pdf
- Description: Analysis technologies that focus on partial packet rather than full packet analysis have shown promise in detection of malicious activity on net-works. NetFlow is one such emergent protocol that is used to log net-work flows through summarizing key features of them. These logs can then be exported to external NetFlow sinks and proper configuration can see effective bandwidth bottleneck mitigation occurring on net-works. Furthermore, each NetFlow source node is configurable with its own unique ID number. This feature enables a system that knows where a NetFlow source node ID number resides physically to say which network flows are occurring from which physical locations irre-spective of the IP addresses involved in these network flows.
- Full Text:
- Date Issued: 2016
Transcription factor motif quality assessment requires systematic comparative analysis
- Kibet, Cabel K, Machanick, Philip
- Authors: Kibet, Cabel K , Machanick, Philip
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439366 , vital:73570 , https://f1000research.com/articles/4-1429
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Date Issued: 2016
- Authors: Kibet, Cabel K , Machanick, Philip
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439366 , vital:73570 , https://f1000research.com/articles/4-1429
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Date Issued: 2016
Transcription factor motif quality assessment requires systematic comparative analysis [version 2; referees: 2 approved]
- Kibet, Caleb K, Machanick, Philip
- Authors: Kibet, Caleb K , Machanick, Philip
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61169 , vital:27987 , http://dx.doi.org/10.12688/f1000research.7408.2
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Date Issued: 2016
- Authors: Kibet, Caleb K , Machanick, Philip
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61169 , vital:27987 , http://dx.doi.org/10.12688/f1000research.7408.2
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Date Issued: 2016
Two in one: cryptic species discovered in biological control agent populations using molecular data and crossbreeding experiments
- Paterson, Iain D, Mangan, Rose, Downie, Douglas A, Coetzee, Julie A, Hill, Martin P, Burke, Ashley M, Downey, Paul O, Henry, Thomas J, Compton, Stephen G
- Authors: Paterson, Iain D , Mangan, Rose , Downie, Douglas A , Coetzee, Julie A , Hill, Martin P , Burke, Ashley M , Downey, Paul O , Henry, Thomas J , Compton, Stephen G
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/424877 , vital:72191 , xlink:href="https://doi.org/10.1002/ece3.2297"
- Description: There are many examples of cryptic species that have been identified through DNA-barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.
- Full Text:
- Date Issued: 2016
- Authors: Paterson, Iain D , Mangan, Rose , Downie, Douglas A , Coetzee, Julie A , Hill, Martin P , Burke, Ashley M , Downey, Paul O , Henry, Thomas J , Compton, Stephen G
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/424877 , vital:72191 , xlink:href="https://doi.org/10.1002/ece3.2297"
- Description: There are many examples of cryptic species that have been identified through DNA-barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.
- Full Text:
- Date Issued: 2016
Unpacking Pandora’s box: Understanding and categorising ecosystem disservices for environmental management and human wellbeing
- Shackleton, Charlie M, Ruwanza, Sheunesu, Sinasson Sanni, Gisele, Bennett, S, De Lacy, Peter, Modipa, Rebone D, Mtati, Nosiseko, Sachikonye, Mwazvita T B, Thondhlana, Gladman
- Authors: Shackleton, Charlie M , Ruwanza, Sheunesu , Sinasson Sanni, Gisele , Bennett, S , De Lacy, Peter , Modipa, Rebone D , Mtati, Nosiseko , Sachikonye, Mwazvita T B , Thondhlana, Gladman
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/182113 , vital:43801 , xlink:href="https://doi.org/10.1007/s10021-015-9952-z"
- Description: Research into the benefits that ecosystems contribute to human wellbeing has multiplied over the last few years following from the seminal contributions of the international Millennium Ecosystem Assessment. In comparison, the fact that some ecosystem goods and services undermine or harm human wellbeing has been seriously overlooked. These negative impacts have become known as ecosystem disservices. The neglect of ecosystem disservices is problematic because investments into the management or reduction of ecosystem disservices may yield better outcomes for human wellbeing, or at a lower investment, than management of ecosystem services. Additionally, management to optimise specific ecosystem services may simultaneously exacerbate associated disservices. We posit that one reason for the neglect of ecosystem disservices from the discourse and policy debates around ecosystems and human wellbeing is because there is no widely accepted definition or typology of ecosystem disservices. Here, we briefly examine current understandings of the term ecosystem disservices and offer a definition and a working typology to help generate debate, policy and management options around ecosystem disservices. We differentiate ecosystem disservices from natural hazards and social hazards, consider some of their inherent properties and then classify them into six categories. A variety of examples are used to illustrate the different types of, and management strategies to, ecosystem disservices.
- Full Text:
- Date Issued: 2016
- Authors: Shackleton, Charlie M , Ruwanza, Sheunesu , Sinasson Sanni, Gisele , Bennett, S , De Lacy, Peter , Modipa, Rebone D , Mtati, Nosiseko , Sachikonye, Mwazvita T B , Thondhlana, Gladman
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/182113 , vital:43801 , xlink:href="https://doi.org/10.1007/s10021-015-9952-z"
- Description: Research into the benefits that ecosystems contribute to human wellbeing has multiplied over the last few years following from the seminal contributions of the international Millennium Ecosystem Assessment. In comparison, the fact that some ecosystem goods and services undermine or harm human wellbeing has been seriously overlooked. These negative impacts have become known as ecosystem disservices. The neglect of ecosystem disservices is problematic because investments into the management or reduction of ecosystem disservices may yield better outcomes for human wellbeing, or at a lower investment, than management of ecosystem services. Additionally, management to optimise specific ecosystem services may simultaneously exacerbate associated disservices. We posit that one reason for the neglect of ecosystem disservices from the discourse and policy debates around ecosystems and human wellbeing is because there is no widely accepted definition or typology of ecosystem disservices. Here, we briefly examine current understandings of the term ecosystem disservices and offer a definition and a working typology to help generate debate, policy and management options around ecosystem disservices. We differentiate ecosystem disservices from natural hazards and social hazards, consider some of their inherent properties and then classify them into six categories. A variety of examples are used to illustrate the different types of, and management strategies to, ecosystem disservices.
- Full Text:
- Date Issued: 2016
Was Myriophyllum spicatum L.(Haloragaceae) recently introduced to South Africa from Eurasia?
- Weyl, Philip S, Thum, RA, Moody, ML, Newman, RM, Coetzee, Julie A
- Authors: Weyl, Philip S , Thum, RA , Moody, ML , Newman, RM , Coetzee, Julie A
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/425463 , vital:72242 , xlink:href="https://doi.org/10.1016/j.aquabot.2015.09.003"
- Description: There is debate over the native or exotic status of Myriophyllum spicatum L. (Haloragaceae) in South Africa, which has important implications for developing and implementing management strategies. The aim of this study was to determine if M. spicatum was recently introduced from Eurasia by reconstructing the genetic relationships between South African and Eurasian M. spicatum using both a nuclear ribosomal (ITS1-5.8S-ITS2-26S) and a chloroplast intron (trnQ-rps16) sequence from 40 populations. For both these DNA markers, the South African populations were distinct from Eurasian populations, but always stemmed from a European origin. The data suggest that South African and European M. spicatum share a common ancestor, however the divergence of both markers are characteristic of a long period of isolation rather than a recent introduction from Europe. The genetic data from this study suggest that M. spicatum has not been introduced recently, but is most likely a native component of the South African flora.
- Full Text:
- Date Issued: 2016
- Authors: Weyl, Philip S , Thum, RA , Moody, ML , Newman, RM , Coetzee, Julie A
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/425463 , vital:72242 , xlink:href="https://doi.org/10.1016/j.aquabot.2015.09.003"
- Description: There is debate over the native or exotic status of Myriophyllum spicatum L. (Haloragaceae) in South Africa, which has important implications for developing and implementing management strategies. The aim of this study was to determine if M. spicatum was recently introduced from Eurasia by reconstructing the genetic relationships between South African and Eurasian M. spicatum using both a nuclear ribosomal (ITS1-5.8S-ITS2-26S) and a chloroplast intron (trnQ-rps16) sequence from 40 populations. For both these DNA markers, the South African populations were distinct from Eurasian populations, but always stemmed from a European origin. The data suggest that South African and European M. spicatum share a common ancestor, however the divergence of both markers are characteristic of a long period of isolation rather than a recent introduction from Europe. The genetic data from this study suggest that M. spicatum has not been introduced recently, but is most likely a native component of the South African flora.
- Full Text:
- Date Issued: 2016