Scielo RSS <![CDATA[South African Journal of Science]]> vol. 111 num. 7-8 lang. en <![CDATA[SciELO Logo]]> <![CDATA[<b>An investment in knowledge....producing new interest</b>]]> <![CDATA[<b>Plantation forestry and invasive pines in the Cape Floristic Region: Towards conflict resolution</b>]]> <![CDATA[<b>Neville Alexander: History, politics and the language question</b>]]> <![CDATA[<b>Lessons for eye health practitioners</b>]]> <![CDATA[<b>Intellectual property rights in Africa: The way ahead</b>]]> <![CDATA[<b>Memoirs of an ichthyologist</b>]]> <![CDATA[<b>Shakespeare, plants, and chemical analysis of early 17th century clay 'tobacco' pipes from Europe</b>]]> <![CDATA[<b>Fly ash composting to improve fertiliser value - A review</b>]]> South Africa is increasingly reliant upon coal-fired power stations for electricity generation. Fly ash, a byproduct of coal combustion, contains a high total content of essential plant nutrients such as phosphorus, as well as heavy metals. If the plant nutrient bio-availability in fly ash could be improved, and the toxic element content reduced, fly ash could contribute significantly as a fertiliser source in South African agriculture. In this review, we summarise up-to-date information on the soil fertility and detoxification benefits of fly ash composting, and identify information gaps in this regard. We discuss scientific studies on the potential of fly ash based composts to supply plant nutrients and to contaminate the environment. We also explore the roles of earthworms and microorganisms in improving the decomposition process, and hence the fertiliser value of fly ash composts. Although much progress has been made, further research efforts are required to optimise microbial and earthworm activity in the decomposition process, which could further enhance nutrient supply benefits and reduce toxic elements at higher fly ash incorporation rates. <![CDATA[<b>A review of quantitative studies of South African youth resilience: Some gaps</b>]]> Resilience (positive adjustment to hardship) relies on a socioecologically facilitated process in which individuals navigate towards, and negotiate for, health-promoting resources, and their social ecology, in return, provides support in culturally aligned ways (Ungar, Trauma Violence & Abuse 2013;14(3):255-266). In the light of international critiques of the conceptualisation and measurement of resilience, the aim of this study was to systematically review quantitative studies of South African youth resilience in order to consider to what extent such studies failed to address documented critique (Luthar et al., Child Development 2000;71(3):543-562). We argue that, for the most part, quantitative studies of South African youth resilience did not mirror international developments of understanding resilience as a complex socioecologically facilitated process. Furthermore, the majority of reviewed studies lacked a culturally or contextually sound measurement and contained conflicting operationalisations of resilience-related constructs. Essentially, the results of this study call for quantitative studies that will statistically explain the complex dynamic resilience-supporting transactions between South African youth and their contexts and guide mental health practitioners and service providers towards more precise explanations and promotion of resilience in South African youth. <![CDATA[<b>Pancreatic islet regeneration: Therapeutic potential, unknowns and controversy</b>]]> Glucose homeostasis in mammals is primarily maintained by the insulin-secreting β-cells contained within pancreas-resident islets of Langerhans. Gross disruption of this glucose regulation as a result of pancreatic dysfunction frequently results in diabetes, which is currently a major health concern in South Africa, as well as globally. For many years, researchers have realised that the pancreas, and specifically the islets of Langerhans, have a regenerative capacity, as islet mass has frequently been shown to increase following induced pancreatic injury. Given that gross β-cell loss contributes significantly to the pathogenesis of both type 1 and type 2 diabetes, endogenous pancreatic islet regeneration has been investigated extensively as a potential β-cell replacement therapy for diabetes. From the extensive research conducted on pancreatic regeneration, opposing findings and opinions have arisen as to how, and more recently even if, pancreatic regeneration occurs following induced injury. In this review, we outline and discuss the three primary mechanisms by which pancreatic regeneration is proposed to occur: neogenesis, β-cell replication and transdifferentiation. We further explain some of the advanced techniques used in pancreatic regeneration research, and conclude that despite the technologically advanced research tools available to researchers today, the mechanisms governing pancreatic regeneration may remain elusive until more powerful techniques are developed to allow for real-time, live-cell assessment of morphology and gene expression within the pancreas. <![CDATA[<b>Using satellite data to identify and track intense thunderstorms in South and southern Africa</b>]]> To issue warnings of thunderstorms, which have the potential for severe weather elements such as heavy rainfall and hail, is a task of all weather services. In data sparse regions, where there is no or limited access to expensive observation systems, satellite data can provide very useful information for this purpose. The Nowcasting Satellite Application Facility in Europe developed software to identify and track rapidly developing thunderstorms (RDT) using data from the geostationary Meteosat Second Generation satellite. The software was installed in South Africa and tested over the South African as well as the southern African domain. The RDT product was validated by means of 20 case studies. Over the South African region, validation was done by means of visual comparison to radar images as well as in a quantitative manner against the occurrence of lightning. Visual comparisons between the RDT product and images from satellite data as well as the occurrence of heavier rainfall were done over areas outside South Africa. Good correlations were found between the identified storms and the occurrence of lightning over South Africa. Visual comparisons indicated that the RDT software can be useful over the southern African domain, where lightning and radar data are not available. Very encouraging results were obtained in the 20 case studies. The RDT software can be a valuable tool for general and aviation forecasters to warn the public of pending severe weather, especially in areas where other data sources are absent or not adequate. <![CDATA[<b>Allele frequencies of <i>AVPR1A </i>and <i>MAOA </i>in the Afrikaner population</b>]]> The Afrikaner population was founded mainly by European immigrants that arrived in South Africa from 1652. However, female slaves from Asia and Africa and local KhoeSan women may have contributed as much as 7% to this population's genes. We quantified variation at two tandem repeats to see if this historical founder effect and/or admixture could be detected. The two loci were chosen because they are in the promoters of genes of neurotransmitters that are known to be correlated with social behaviour. Specifically, arginine vasopressin receptor 1A's (AVPR1A) RS3 locus has been shown to correlate with age of sexual onset and happiness in monogamous relationships while the tandem repeat in the promoter of the monoamine oxidase A (MAOA) gene correlates with reactive aggression. The Afrikaner population contained more AVPR1A RS3 alleles than other Caucasoid populations, potentially reflecting a history of admixture. Even though Afrikaners have one of the lowest recorded non-paternity rates in the world, the population did not differ at AVPR1A RS3 locus form other European populations, suggesting a non-genetic explanation, presumably religion, for the low non-paternity rate. By comparing population allele-frequency spectra it was found that different studies have confused AVPR1A RS3 alleles and we make some suggestions to rectify these mistakes in future studies. While MAOA allele frequencies differed between racial groups, the Afrikaner population showed no evidence of admixture. In fact, Afrikaners had more 4-repeat alleles than other populations of European origin, not fewer. The 4-repeat allele may have been selected for during colonisation. <![CDATA[<b>Long-term changes and variability in rainfall and streamflow in Luvuvhu River Catchment, South Africa</b>]]> We investigated long-term changes and variability in daily rainfall and streamflow in the Luvuvhu River Catchment, South Africa. Changes and variability in rainfall and streamflow impact on available water resources and the allocation of these resources. Daily rainfall data for six stations and daily streamflow data for four stations for the period 1920/1921-2005/2006 were grouped into cycles of 5 and 10 years. Daily means and standard deviations were computed for each cycle. Standard deviation was used to define the rainfall and streamflow variability. Linear regression was used to compute trends in 5- and 10-year average rainfall and streamflow and their standard deviations. Paired two-tailed t-tests (significance level of 0.05) were carried out to verify the spatial variability of rainfall and streamflow in the study area. Mann-Kendall and linear regression were used to determine trend analyses based on long-term annual rainfall and streamflow data. All but two rainfall stations showed decreasing trends in 5- and 10-year mean rainfall; 10-year mean daily rainfall showed decadal rainfall fluctuations. Contrasting trends were observed in 5- and 10-year mean streamflow, indicating that other factors such as anthropogenic activities and impoundments could be impacting on streamflow. Trend directions identified from Mann-Kendall and linear regression analyses of long-term annual rainfall and streamflow were similar to those identified by linear regression of 5- and 10-year mean daily rainfall. Results of paired two-tailed t-tests verified the spatial variability of rainfall and streamflow in the study area. We have shown that the variability of rainfall and streamflow has increased in the Luvuvhu River Catchment over the 86-year study period. <![CDATA[<b>Evidence for climate-induced range shift in <i>Brachystegia </i>(miombo) woodland</b>]]> Brachystegia spiciformis Benth. is the dominant component of miombo, the sub-tropical woodlands which cover 2.7 million km² of south-central Africa and which is coincident with the largest regional centre of endemism in Africa. However, pollen records from the genus Brachystegia suggest that miombo has experienced rapid range retraction (~450 km) from its southernmost distributional limit over the past 6000 years. This abrupt biological response created an isolated (by ~200 km) and incomparable relict at the trailing population edge in northeast South Africa. These changes in miombo population dynamics may have been triggered by minor natural shifts in temperature and moisture regimes. If so, B. spiciformis is likely to be especially responsive to present and future anthropogenic climate change. This rare situation offers a unique opportunity to investigate climatic determinants of range shift at the trailing edge of a savanna species. A niche modelling approach was used to produce present-day and select future B. spiciformis woodland ecological niche models. In keeping with recent historical range shifts, further ecological niche retraction of between 30.6% and 47.3% of the continuous miombo woodland in Zimbabwe and southern Mozambique is predicted by 2050. Persistence of the existing relict under future climate change is plausible, but range expansion to fragmented refugia in northeast South Africa is unlikely. As Brachystegia woodland and associated biota form crucial socio-economic and biodiversity components of savannas in southern Africa, their predicted further range retraction is of concern. <![CDATA[<b>Towards polarisation-encoded quantum key distribution in optical fibre networks</b>]]> Quantum key distribution - a process that encodes digital information - often utilises fibre optic technologies for commercial applications. Fibre provides the benefit of a dark channel as well as the convenience of independence of a line-of-sight connection between the sender and receiver. In order to implement quantum key distribution protocols utilising polarisation encoding, the birefringence effects of fibre must be compensated for. Birefringence is caused by manufacturing impurities in the fibre or a change in environmental conditions and results in a rotation of the state of polarisation of light as it is propagated through the fibre. With dynamic environmental conditions, the birefringence effects should be monitored with a test signal at regular time intervals so that the polarisation of each photon can be appropriately compensated to its original state. Orthogonal states are compensated simultaneously, but most protocols, such as BB84 and B92, require non-orthogonal basis sets. Instead of using a compensator for each basis, the presented scheme fixes the polarisation controller onto the plane on the Poincaré that passes through both bases, compensating both non-orthogonal bases simultaneously. <![CDATA[<b>A multiphysics simulation of a fluorine electrolysis cell</b>]]> We modelled a laboratory-scale fluorine reactor which employed fully coupled, fundamental electron, heat, mass and momentum transfer (two-phase) equations to deliver a transient simulation. Hydrodynamic quasi-steady-state results were produced for the current density, electric field, temperature, reactive species concentration, gas and liquid velocity profiles as well as gas fraction distribution within the reactor. Simulation results were verified by modelling and comparing models from published works on similar reactors, as the laboratory-scale reactor is still in construction phase. Comparisons were favourable. <![CDATA[<b>Predictive modelling of wetland occurrence in KwaZulu-Natal, South Africa</b>]]> The global trend of transformation and loss of wetlands through conversion to other land uses has deleterious effects on surrounding ecosystems, and there is a resultant increasing need for the conservation and preservation of wetlands. Improved mapping of wetland locations is critical to achieving objective regional conservation goals, which depends on accurate spatial knowledge. Current approaches to mapping wetlands through the classification of satellite imagery typically under-represents actual wetland area; the importance of ancillary data in improving accuracy in mapping wetlands is therefore recognised. In this study, we compared two approaches - Bayesian networks and logistic regression - to predict the likelihood of wetland occurrence in KwaZulu-Natal, South Africa. Both approaches were developed using the same data set of environmental surrogate predictors. We compared and verified model outputs using an independent test data set, with analyses including receiver operating characteristic curves and area under the curve (AUC). Both models performed similarly (AUC>0.84), indicating the suitability of a likelihood approach for ancillary data for wetland mapping. Results indicated that high wetland probability areas in the final model outputs correlated well with known wetland systems and wetland-rich areas in KwaZulu-Natal. We conclude that predictive models have the potential to improve the accuracy of wetland mapping in South Africa by serving as valuable ancillary data. <![CDATA[<b>Climate change trends and environmental impacts in the Makonde Communal Lands, Zimbabwe</b>]]> During the last century, climate has increasingly become variable and changeable, with significant deviations from the observed normal averages, which often leads to disruptive consequences to ecosystems and livelihoods. Climate change induced environmental challenges are viewed to be particularly severe to economically challenged tropical societies including the Zimbabwean rural communities. We sought to determine local level climate change trends and associated biophysical implications in the Makonde Communal Lands of Zimbabwe. Our findings suggest that there has been significant climate change in the Makonde Communal Lands since 1962. The climate change observed has induced the deterioration of ecosystem productivity, diversity and services, to the detriment of human livelihoods. We provide insights into how to better understand local level dynamics between climate change and local ecosystem goods and services as the basis of livelihood in marginalised rural communities. Among the key reasons for concern about impacts of anthropogenic activities on climate is the fact that changing climate has direct impacts on the biophysical world, which in turn is a vital asset for human livelihoods, economies and general well-being. <![CDATA[<b>Relationships between student throughput variables and properties</b>]]> Many different models have been designed to describe the plethora of factors that influence student throughput and success and how these factors affect throughput system variables and properties. System variables include headcounts (H) and successful credits (S) of throughput systems; some examples of system properties are the percentage of the new student intake graduating annually, and the average number of years to graduate or to drop out of a degree. However, no past study has defined the analytical relationships between these variables and properties from a process perspective - which was the purpose of this study. Three simple analytical equations were derived for 4-year degrees, and then geometrically interpreted. The behaviour of a simplified throughput system can be described by the position of a point in the admissible region of the H-S plane, with each point relating to a specific set of system properties. The successful credits ratio (S/H) is shown to be the ideal process efficiency ratio for throughput systems. The results were also extended to degrees of shorter duration. The behaviour of real throughput systems is broadly found to be similar to the behaviour of simplified throughput systems. In this study, only the mathematical foundations for the general relationships between throughput properties and throughput variables for a degree were established. The way in which this mathematical basis finds application in practice is illustrated for a few selected cases only, because of the specific focus of this paper. <![CDATA[<b>Directed genetic modification of African horse sickness virus by reverse genetics</b>]]> African horse sickness virus (AHSV), a member of the Orbivirus genus in the family Reoviridae, is an arthropod-transmitted pathogen that causes a devastating disease in horses with a mortality rate greater than 90%. Fundamental research on AHSV and the development of safe, efficacious vaccines could benefit greatly from an uncomplicated genetic modification method to generate recombinant AHSV. We demonstrate that infectious AHSV can be recovered by transfection of permissive mammalian cells with transcripts derived in vitro from purified AHSV core particles. These findings were expanded to establish a genetic modification system for AHSV that is based on transfection of the cells with a mixture of purified core transcripts and a synthetic T7 transcript. This approach was applied successfully to recover a directed cross-serotype reassortant AHSV and to introduce a marker sequence into the viral genome. The ability to manipulate the AHSV genome and engineer specific mutants will increase understanding of AHSV replication and pathogenicity, as well as provide a tool for generating designer vaccine strains. <![CDATA[<b>In-vitro effects of garlic extracts on pathogenic fungi <i>Botrytis cinerea, Penicillium expansum </i>and <i>Neofabraea alba</i></b>]]> The antifungal activity of garlic extracts applied directly and through volatile release was tested against the growth of postharvest pathogens Botrytis cinerea, Penicillium expansum and Neofabraea alba. Mycelial growth of B. cinerea and P expansum was inhibited by aqueous and ethanol dilutions on garlic extract amended media (direct method) in a dose-response manner. The aqueous dilution was more effective than the ethanol dilution. Both dilutions inhibited mycelial growth of N. alba to a similar extent but no trend in data was noted across the concentration range. Calculated EC50 values indicated that 13.36% and 8.09% aqueous dilutions could be used to inhibit growth of B. cinerea and P. expansum, respectively; however, values generated for N. alba either bordered on or exceeded the concentration range. The volatile vapour application of garlic was able to inhibit mycelial growth and spore germination of all pathogens at concentrations as low as 20%. Gas chromatography-mass spectrometry analysis showed that 85.95% of compounds present in the garlic sample belonged to a sulphur or sulphur-derived group. Allicin, the active component of garlic, was not found; however, breakdown products of allicin were present in high amounts. Overall, the antifungal activity of garlic extracts for the control of B. cinerea and P. expansum was confirmed. Further investigations into the antifungal effect of garlic extracts on N. alba is required, although garlic volatiles seem to be effective. This report is the first of antifungal activity of garlic extracts against N. alba - the causal agent of bull's eye rot, one of the major diseases of apples. <![CDATA[<b>Multiplexed CRISPR/Cas9 genome editing increases the efficacy of homologous-dependent repair of donor sequences in mammalian cells</b>]]> Efficient and robust genome editing tools and strategies allow for specific and exact genetic changes to be captured in model systems, thereby accelerating both forward and reverse genetics studies. The development of CRISPR/Cas9 as a facile designer nuclease toolset has allowed for defined genetic modifications to be efficiently made through homology-directed repair of targeted DNA double-stranded breaks (DSBs) using exogenous repair templates. However, traditional single DSB strategies are still relatively inefficient as the short gene conversion tracts of mammalian cell systems limit the extent of achievable gene alteration from the DSB site. In order to improve on the inefficiency, we devised a dual cut strategy, which relies on reconstituting entire deleted gene fragments to precisely modify extensive gene regions of interest. Using the CRISPR/Cas9 system, we were able to introduce targeted deletions and repair of the endogenous KRAS gene locus in cell culture. The use of two simultaneous DSBs can be employed for efficient application of homology-directed repair with a large dsDNA donor sequence, thereby improving the efficacy of deriving cells with a desired gene editing outcome. In conclusion, a multiplexed CRISPR/Cas9 editing strategy represents an efficient tool for the editing of complex, heterologous sequence tracts.