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 pattern-richness of graphical passwords
- Vorster, Johannes, Van Heerden, Renier, Irwin, Barry V W
- Authors: Vorster, Johannes , Van Heerden, Renier , Irwin, Barry V W
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68322 , vital:29238 , https://doi.org/10.1109/ISSA.2016.7802931
- Description: Publisher version , Conventional (text-based) passwords have shown patterns such as variations on the username, or known passwords such as “password”, “admin” or “12345”. Patterns may similarly be detected in the use of Graphical passwords (GPs). The most significant such pattern - reported by many researchers - is hotspot clustering. This paper qualitatively analyses more than 200 graphical passwords for patterns other than the classically reported hotspots. The qualitative analysis finds that a significant percentage of passwords fall into a small set of patterns; patterns that can be used to form attack models against GPs. In counter action, these patterns can also be used to educate users so that future password selection is more secure. It is the hope that the outcome from this research will lead to improved behaviour and an enhancement in graphical password security.
- Full Text: false
- Date Issued: 2016
- Authors: Vorster, Johannes , Van Heerden, Renier , Irwin, Barry V W
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68322 , vital:29238 , https://doi.org/10.1109/ISSA.2016.7802931
- Description: Publisher version , Conventional (text-based) passwords have shown patterns such as variations on the username, or known passwords such as “password”, “admin” or “12345”. Patterns may similarly be detected in the use of Graphical passwords (GPs). The most significant such pattern - reported by many researchers - is hotspot clustering. This paper qualitatively analyses more than 200 graphical passwords for patterns other than the classically reported hotspots. The qualitative analysis finds that a significant percentage of passwords fall into a small set of patterns; patterns that can be used to form attack models against GPs. In counter action, these patterns can also be used to educate users so that future password selection is more secure. It is the hope that the outcome from this research will lead to improved behaviour and an enhancement in graphical password security.
- Full Text: false
- 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
Thermoluminescence of kunzite: a study of kinetic processes and dosimetry characteristics
- Ogundare, F O, Alatishe, M A, Chithambo, Makaiko L, Costin, G
- Authors: Ogundare, F O , Alatishe, M A , Chithambo, Makaiko L , Costin, G
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124701 , vital:35650 , https://doi.org/10.1016/j.nimb.2016.02.059
- Description: Since the use of natural minerals for dating and dose reconstruction using luminescence techniques is well-established and always of interest, we present thermoluminescence characteristics of kunzite, a gem variety of spodumene. The chemical composition of the sample was determined using an Electron Probe MicroAnalyzer.
- Full Text: false
- Date Issued: 2016
- Authors: Ogundare, F O , Alatishe, M A , Chithambo, Makaiko L , Costin, G
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124701 , vital:35650 , https://doi.org/10.1016/j.nimb.2016.02.059
- Description: Since the use of natural minerals for dating and dose reconstruction using luminescence techniques is well-established and always of interest, we present thermoluminescence characteristics of kunzite, a gem variety of spodumene. The chemical composition of the sample was determined using an Electron Probe MicroAnalyzer.
- Full Text: false
- Date Issued: 2016
Time-resolved luminescence from quartz: an overview of contemporary developments and applications
- Chithambo, Makaiko L, Pagonis, Vasilis, Ankjærgaard, Christina
- Authors: Chithambo, Makaiko L , Pagonis, Vasilis , Ankjærgaard, Christina
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124743 , vital:35658 , https://doi.org/10.1016/j.physb.2015.10.014
- Description: Time-resolved optical stimulation of luminescence has become established as a key method for measurement of optically stimulated luminescence from quartz, feldspar and α-Al2O3:C, all materials of interest in dosimetry. The aim of time-resolved optical stimulation is to separate in time the stimulation and emission of luminescence. The luminescence is stimulated from a sample using a brief light pulse and the emission monitored during stimulation in the presence of scattered stimulating light or after pulsing, over photomultiplier noise only. Although the use of the method in retrospective dosimetry has been somewhat limited, the technique has been successfully applied to study mechanisms in the processes leading up to luminescence emission. The main means for this has been the temperature dependence of the luminescence intensity as well as the luminescence lifetimes determined from time-resolved luminescence spectra. In this paper we review some key developments in theory and applications to quartz including methods of evaluating lifetimes, techniques of evaluating kinetic parameters using both the dependence of luminescence intensity and lifetime on measurement temperature, and of lifetimes on annealing temperature. We then provide an overview of some notable applications such as separation of quartz signals from a quartz–feldspar admixture and the utility of the dynamic throughput, a measure of luminescence measured as a function of the pulse width. The paper concludes with some suggestions of areas where further exploration would advance understanding of dynamics of luminescence in quartz and help address some outstanding problems in its application.
- Full Text: false
- Date Issued: 2016
- Authors: Chithambo, Makaiko L , Pagonis, Vasilis , Ankjærgaard, Christina
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124743 , vital:35658 , https://doi.org/10.1016/j.physb.2015.10.014
- Description: Time-resolved optical stimulation of luminescence has become established as a key method for measurement of optically stimulated luminescence from quartz, feldspar and α-Al2O3:C, all materials of interest in dosimetry. The aim of time-resolved optical stimulation is to separate in time the stimulation and emission of luminescence. The luminescence is stimulated from a sample using a brief light pulse and the emission monitored during stimulation in the presence of scattered stimulating light or after pulsing, over photomultiplier noise only. Although the use of the method in retrospective dosimetry has been somewhat limited, the technique has been successfully applied to study mechanisms in the processes leading up to luminescence emission. The main means for this has been the temperature dependence of the luminescence intensity as well as the luminescence lifetimes determined from time-resolved luminescence spectra. In this paper we review some key developments in theory and applications to quartz including methods of evaluating lifetimes, techniques of evaluating kinetic parameters using both the dependence of luminescence intensity and lifetime on measurement temperature, and of lifetimes on annealing temperature. We then provide an overview of some notable applications such as separation of quartz signals from a quartz–feldspar admixture and the utility of the dynamic throughput, a measure of luminescence measured as a function of the pulse width. The paper concludes with some suggestions of areas where further exploration would advance understanding of dynamics of luminescence in quartz and help address some outstanding problems in its application.
- Full Text: false
- 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
Trophic interactions in an austral temperate ephemeral pond inferred using stable isotope analysis
- Dalu, Tatenda, Weyl, Olaf L F, Froneman, P William, Wasserman, Ryan J
- Authors: Dalu, Tatenda , Weyl, Olaf L F , Froneman, P William , Wasserman, Ryan J
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68022 , vital:29185 , https://doi.org/10.1007/s10750-015-2533-5
- Description: Publisher version , Ephemeral ponds are vulnerable aquatic habitats which are difficult to protect given their dynamic nature and sensitivity to degradation during dry periods. Little information is available on these habitats in austral regions, with almost no information on food-web structure and complexity. The study aimed to assess trophic interactions among dominant organisms in an ephemeral pond food web, and investigate the importance of autochthonous and allochthonous carbon, using 13C and 15N isotopes. Results of the investigation suggest that the food web comprised four trophic levels, with the top predators being Notonectids (Notonecta sp.) and diving beetles (Cybister tripunctatus (Olivier)). Intermediary trophic levels comprised zooplankton (daphniids and copepodids), macroinvertebrates (e.g. micronectids and molluscs) and tadpoles. Generalist feeders dominated the higher trophic levels (>3) with specialists comprising the lower trophic levels (≤3). The consumers preferred autochthonous fine particulate organic matter, epiphyton and submerged macrophyte organic matter sources over allochthonous sources. Autochthonous organic matter was transferred to the food web via zooplankton and select macroinvertebrates including Micronecta sp. and Physa sp. The food-web structure within the pond appeared to reflect the secondary stage of trophic structural complexity in the evolution of ephemeral ponds over the course of their hydro-period.
- Full Text: false
- Date Issued: 2016
- Authors: Dalu, Tatenda , Weyl, Olaf L F , Froneman, P William , Wasserman, Ryan J
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68022 , vital:29185 , https://doi.org/10.1007/s10750-015-2533-5
- Description: Publisher version , Ephemeral ponds are vulnerable aquatic habitats which are difficult to protect given their dynamic nature and sensitivity to degradation during dry periods. Little information is available on these habitats in austral regions, with almost no information on food-web structure and complexity. The study aimed to assess trophic interactions among dominant organisms in an ephemeral pond food web, and investigate the importance of autochthonous and allochthonous carbon, using 13C and 15N isotopes. Results of the investigation suggest that the food web comprised four trophic levels, with the top predators being Notonectids (Notonecta sp.) and diving beetles (Cybister tripunctatus (Olivier)). Intermediary trophic levels comprised zooplankton (daphniids and copepodids), macroinvertebrates (e.g. micronectids and molluscs) and tadpoles. Generalist feeders dominated the higher trophic levels (>3) with specialists comprising the lower trophic levels (≤3). The consumers preferred autochthonous fine particulate organic matter, epiphyton and submerged macrophyte organic matter sources over allochthonous sources. Autochthonous organic matter was transferred to the food web via zooplankton and select macroinvertebrates including Micronecta sp. and Physa sp. The food-web structure within the pond appeared to reflect the secondary stage of trophic structural complexity in the evolution of ephemeral ponds over the course of their hydro-period.
- Full Text: false
- 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
Two new species of Xosopsaltria Kirkaldy, 1904, with a key to the species of South African pygmy bladder cicadas (Hemiptera Cicadidae Cicadettinae Tettigomyiini)
- Sanborn, Allen F, Villet, Martin H
- Authors: Sanborn, Allen F , Villet, Martin H
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/441274 , vital:73873 , https://mapress.com/zt/article/view/zootaxa.4092.2.3
- Description: Two species, Xosopsaltria brachyptera n. sp. and Xosopsaltria vitripennis n. sp., are described as new. Notes on their biology and a key to the South African pygmy bladder cicadas are also provided.
- Full Text:
- Date Issued: 2016
- Authors: Sanborn, Allen F , Villet, Martin H
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/441274 , vital:73873 , https://mapress.com/zt/article/view/zootaxa.4092.2.3
- Description: Two species, Xosopsaltria brachyptera n. sp. and Xosopsaltria vitripennis n. sp., are described as new. Notes on their biology and a key to the South African pygmy bladder cicadas are also provided.
- 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
Validation of the periodicity of growth zone formation in the otoliths of four fish species from the Upper Zambezi ecoregion, southern Africa
- Taylor, Geraldine C, Peel, Richard A, Weyl, Olaf L F, Hay, Clinton J
- Authors: Taylor, Geraldine C , Peel, Richard A , Weyl, Olaf L F , Hay, Clinton J
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443414 , vital:74116 , https://hdl.handle.net/10520/EJC196537
- Description: In the Upper Zambezi and Okavango ecoregions, Brycinus lateralis, Hepsetus cuvieri, Schilbe intermedius and Serranochromis macrocephalus are important in subsistence fisheries, while S. intermedius and S. macrocephalus are often caught in commercial catches. Despite their importance, there is little information on their age and growth and age validation. Growth zone deposition rate in otoliths of B. lateralis, H. cuvieri, S. intermedius and S. macrocephalus was validated as annual using edge analysis in this study. Annual deposition of growth zones was corroborated by a fluorochrome marking experiment. Both methods demonstrated that one growth zone was deposited annually. Edge analysis demonstrated that the highest proportion of opaque zones was detected between August and December, most likely as a result of slow growth during lower temperature water during the preceding winter. With growth zone deposition validated as annual, future research should focus on determining the growth, maturity and mortality rates of these species, parameters which are important for their management.
- Full Text:
- Date Issued: 2016
- Authors: Taylor, Geraldine C , Peel, Richard A , Weyl, Olaf L F , Hay, Clinton J
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/443414 , vital:74116 , https://hdl.handle.net/10520/EJC196537
- Description: In the Upper Zambezi and Okavango ecoregions, Brycinus lateralis, Hepsetus cuvieri, Schilbe intermedius and Serranochromis macrocephalus are important in subsistence fisheries, while S. intermedius and S. macrocephalus are often caught in commercial catches. Despite their importance, there is little information on their age and growth and age validation. Growth zone deposition rate in otoliths of B. lateralis, H. cuvieri, S. intermedius and S. macrocephalus was validated as annual using edge analysis in this study. Annual deposition of growth zones was corroborated by a fluorochrome marking experiment. Both methods demonstrated that one growth zone was deposited annually. Edge analysis demonstrated that the highest proportion of opaque zones was detected between August and December, most likely as a result of slow growth during lower temperature water during the preceding winter. With growth zone deposition validated as annual, future research should focus on determining the growth, maturity and mortality rates of these species, parameters which are important for their management.
- Full Text:
- Date Issued: 2016
Was Myriophyllum spicatum L.(Haloragaceae) recently introduced to South Africa from Eurasia?
- Weyl, Philip S R, Thum, R A, Moody, M L, Newman, R M, Coetzee, Julie A
- Authors: Weyl, Philip S R , Thum, R A , Moody, M L , Newman, R M , 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 R , Thum, R A , Moody, M L , Newman, R M , 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
Water footprint assessment of citrus production in South Africa: A case study of the Lower Sundays River Valley
- Munro, Samantha A, Fraser, Gavin C G, Snowball, Jeanette D, Pahlow, Markus
- Authors: Munro, Samantha A , Fraser, Gavin C G , Snowball, Jeanette D , Pahlow, Markus
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69240 , vital:29463 , https://doi.org/10.1016/j.jclepro.2016.06.142
- Description: Water footprint assessment is a developing method that is being increasingly applied to quantify water use, prioritise reductions, assess sustainability and provide information to achieve sustainable, efficient, and equitable water use. The objectives of this paper were to conduct a water footprint assessment of primary citrus production within the Lower Sundays River Valley in South Africa using local, high-resolution data and to examine indicators (water scarcity, pollution, efficiency, productivity and access) to determine the sustainability of blue, green and grey water footprints of a wet, dry and average year. Lemons were found to have the lowest blue and combined green-blue water footprint per ton of production across all climatic years, followed by soft citrus, valencias and navels. Valencias had the lowest, and navels the highest grey WF (relating to inorganic nitrogen). Lemons, despite their high crop water and fertiliser requirements, were regarded more economically efficient in comparison to valencias, soft citrus and navels, in that they provided higher net income and more employment hours per m3 of water in comparison to other citrus crops. In an average season, lemons generated approximately 39% more income per m3 of water than navels, despite navels being the dominant cultivar. Blue water consumption for citrus in the catchment was calculated to be 58.7 Mm3 for an average season and 89.2 Mm3 for a dry season. Due to an inter-basin transfer scheme, no physical water scarcity occurred, and both environmental and basic human needs are met. Water pollution levels related to nitrogen however, exceeded the assimilative capacity of the run-off in dry years. The area also experiences institutional and infrastructural scarcity and 14% of the population do not have access to piped water. Stakeholders and governments may use the results of water footprint assessments to determine the status of river basins, make evaluations for future water usage and the potential impacts of expanding agriculture and different management strategies. Including environmental and socio-economic indicators will also improve the integrity of water footprint assessments.
- Full Text: false
- Date Issued: 2016
- Authors: Munro, Samantha A , Fraser, Gavin C G , Snowball, Jeanette D , Pahlow, Markus
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69240 , vital:29463 , https://doi.org/10.1016/j.jclepro.2016.06.142
- Description: Water footprint assessment is a developing method that is being increasingly applied to quantify water use, prioritise reductions, assess sustainability and provide information to achieve sustainable, efficient, and equitable water use. The objectives of this paper were to conduct a water footprint assessment of primary citrus production within the Lower Sundays River Valley in South Africa using local, high-resolution data and to examine indicators (water scarcity, pollution, efficiency, productivity and access) to determine the sustainability of blue, green and grey water footprints of a wet, dry and average year. Lemons were found to have the lowest blue and combined green-blue water footprint per ton of production across all climatic years, followed by soft citrus, valencias and navels. Valencias had the lowest, and navels the highest grey WF (relating to inorganic nitrogen). Lemons, despite their high crop water and fertiliser requirements, were regarded more economically efficient in comparison to valencias, soft citrus and navels, in that they provided higher net income and more employment hours per m3 of water in comparison to other citrus crops. In an average season, lemons generated approximately 39% more income per m3 of water than navels, despite navels being the dominant cultivar. Blue water consumption for citrus in the catchment was calculated to be 58.7 Mm3 for an average season and 89.2 Mm3 for a dry season. Due to an inter-basin transfer scheme, no physical water scarcity occurred, and both environmental and basic human needs are met. Water pollution levels related to nitrogen however, exceeded the assimilative capacity of the run-off in dry years. The area also experiences institutional and infrastructural scarcity and 14% of the population do not have access to piped water. Stakeholders and governments may use the results of water footprint assessments to determine the status of river basins, make evaluations for future water usage and the potential impacts of expanding agriculture and different management strategies. Including environmental and socio-economic indicators will also improve the integrity of water footprint assessments.
- Full Text: false
- Date Issued: 2016
Ways of belonging: meanings of “Nature” among Xhosa-speaking township residents in South Africa
- Cocks, Michelle L, Alexander, Jamie K, Mogano, Lydia, Vetter, Susan M
- Authors: Cocks, Michelle L , Alexander, Jamie K , Mogano, Lydia , Vetter, Susan M
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66021 , vital:28877 , https://doi.org/10.2993/0278-0771-36.4.820
- Description: publisher version , The concept of biocultural diversity, originally used to describe indigenous people and their ways of using and managing natural resources, has more recently been applied within the urban context to understand the variability of interactions between humans and nature. Significant progress has been made internationally in acknowledging the need to preserve and maintain green spaces in urban environments. Current efforts to address the need for greening urban areas in South Africa primarily focus on the establishment and maintenance of botanical gardens and parks as well as various green belts within the urban landscape. South Africa's urban areas are overwhelmingly shaped by the historical segregation of space and stark disparities in wealth. The distribution, quality, and extent of urban green spaces reflect this. Many township dwellers do not have access to these amenities and their interactions with nature are thus usually constrained to access to municipal commonages. This article explores how areas of natural vegetation in municipal commonages on the outskirts of urban centers in South Africa continue to offer places of cultural, spiritual, and restorative importance to Xhosa-speaking township dwellers. A case study from Grahamstown, an urban center in the Eastern Cape with a population of around 80,000, illustrates how ability to access and move through such places contributes to people's well-being, identity formation, and shared heritage. A case is made for adopting a biocultural diversity approach to spatial planning and urban development within the South African context.
- Full Text: false
- Date Issued: 2016
- Authors: Cocks, Michelle L , Alexander, Jamie K , Mogano, Lydia , Vetter, Susan M
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66021 , vital:28877 , https://doi.org/10.2993/0278-0771-36.4.820
- Description: publisher version , The concept of biocultural diversity, originally used to describe indigenous people and their ways of using and managing natural resources, has more recently been applied within the urban context to understand the variability of interactions between humans and nature. Significant progress has been made internationally in acknowledging the need to preserve and maintain green spaces in urban environments. Current efforts to address the need for greening urban areas in South Africa primarily focus on the establishment and maintenance of botanical gardens and parks as well as various green belts within the urban landscape. South Africa's urban areas are overwhelmingly shaped by the historical segregation of space and stark disparities in wealth. The distribution, quality, and extent of urban green spaces reflect this. Many township dwellers do not have access to these amenities and their interactions with nature are thus usually constrained to access to municipal commonages. This article explores how areas of natural vegetation in municipal commonages on the outskirts of urban centers in South Africa continue to offer places of cultural, spiritual, and restorative importance to Xhosa-speaking township dwellers. A case study from Grahamstown, an urban center in the Eastern Cape with a population of around 80,000, illustrates how ability to access and move through such places contributes to people's well-being, identity formation, and shared heritage. A case is made for adopting a biocultural diversity approach to spatial planning and urban development within the South African context.
- Full Text: false
- Date Issued: 2016
What lies beneath: exploring the deeper purposes of feedback on student writing through considering disciplinary knowledge and knowers
- Van Heerden, Martina, Clarence, Sherran, Bharuthram, Sharita
- Authors: Van Heerden, Martina , Clarence, Sherran , Bharuthram, Sharita
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/59856 , vital:27669 , https://doi.org/10.1080/02602938.2016.1212985
- Description: Feedback plays an integral role in students’ learning and development, as it is often the only personal communication that students have with tutors or lecturers about their own work. Yet, in spite of its integral role in student learning, there is disagreement between how students and tutors or lecturers perceive the pedagogic purpose of feedback. Central to this disagreement is the role that feedback has to play in ensuring that students produce the ‘right’ kinds of knowledge, and become the ‘right’ kinds of knowers within their disciplines. This paper argues that, in order to find common ground between students and tutors or lecturers on what feedback is for, and how to both give and use it effectively, we need to conceptualise disciplinary knowledge and knowers anew. We offer, as a useful starting point, the Specialisation dimension of Legitimation Code Theory as both practical theory and methodological tool for exploring knowledge and knowers in English Studies and Law as two illustrative cases. The paper concludes that this analysis offers lecturers and tutors a fresh understanding of the disciplinary knowledge and knower structures they work within and, relatedly, a clearer view of the work their feedback needs to do within these.
- Full Text: false
- Date Issued: 2016
- Authors: Van Heerden, Martina , Clarence, Sherran , Bharuthram, Sharita
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/59856 , vital:27669 , https://doi.org/10.1080/02602938.2016.1212985
- Description: Feedback plays an integral role in students’ learning and development, as it is often the only personal communication that students have with tutors or lecturers about their own work. Yet, in spite of its integral role in student learning, there is disagreement between how students and tutors or lecturers perceive the pedagogic purpose of feedback. Central to this disagreement is the role that feedback has to play in ensuring that students produce the ‘right’ kinds of knowledge, and become the ‘right’ kinds of knowers within their disciplines. This paper argues that, in order to find common ground between students and tutors or lecturers on what feedback is for, and how to both give and use it effectively, we need to conceptualise disciplinary knowledge and knowers anew. We offer, as a useful starting point, the Specialisation dimension of Legitimation Code Theory as both practical theory and methodological tool for exploring knowledge and knowers in English Studies and Law as two illustrative cases. The paper concludes that this analysis offers lecturers and tutors a fresh understanding of the disciplinary knowledge and knower structures they work within and, relatedly, a clearer view of the work their feedback needs to do within these.
- Full Text: false
- Date Issued: 2016
Why a contextual approach to professional development?
- Leibowitz, B L, Vorster, Jo-Anne, Ndebele, C
- Authors: Leibowitz, B L , Vorster, Jo-Anne , Ndebele, C
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61288 , vital:28009 , https://journals.co.za/content/journal/10520/EJC-4ad93ec2a
- Description: One of the peculiarities of the literature on academic professional development with regard to teaching is its a-political nature. It pays insufficient attention to issues of equity, and to how privilege, geographical location, class and ethnicity influence the way that staff in higher education learn to teach. This is surprising, or paradoxical, given the strong world-wide concern for widening participation and student success in higher education. The approaches towards professional academic development have been dominated by literature from the global North, which does not take into account conditions in resource-constrained environments. We contend that literature from these Southern environments enrich the international body of literature. Thus there is a need for scholarly writing on learning to teach in higher education, which takes a specifically social, contextual and relational approach and which considers these within resource-rich as well as resource-constrained environments.
- Full Text:
- Date Issued: 2016
- Authors: Leibowitz, B L , Vorster, Jo-Anne , Ndebele, C
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61288 , vital:28009 , https://journals.co.za/content/journal/10520/EJC-4ad93ec2a
- Description: One of the peculiarities of the literature on academic professional development with regard to teaching is its a-political nature. It pays insufficient attention to issues of equity, and to how privilege, geographical location, class and ethnicity influence the way that staff in higher education learn to teach. This is surprising, or paradoxical, given the strong world-wide concern for widening participation and student success in higher education. The approaches towards professional academic development have been dominated by literature from the global North, which does not take into account conditions in resource-constrained environments. We contend that literature from these Southern environments enrich the international body of literature. Thus there is a need for scholarly writing on learning to teach in higher education, which takes a specifically social, contextual and relational approach and which considers these within resource-rich as well as resource-constrained environments.
- Full Text:
- Date Issued: 2016