Scielo RSS <![CDATA[South African Journal of Science]]> http://www.scielo.org.za/rss.php?pid=0038-235320130006&lang=en vol. 109 num. 11-12 lang. en <![CDATA[SciELO Logo]]> http://www.scielo.org.za/img/en/fbpelogp.gif http://www.scielo.org.za <![CDATA[<b>The DNA bill: Forensic science in the service of society</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600001&lng=en&nrm=iso&tlng=en <![CDATA[<b>Coordinated approaches to rehabilitating a river ecosystem invaded by alien plants and fish</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600002&lng=en&nrm=iso&tlng=en Large sums have been spent on controlling invasive alien species in South Africa over the past two decades, but documented accounts of successes are almost non-existent. This brief account describes progress with a coordinated pioneering project to simultaneously clear invasive alien trees and predatory alien fish from a degraded but ecologically important river ecosystem in the Cederberg region of the Western Cape Province, South Africa. Dense infestations of invasive Australian Acacia and Eucalyptus species were cleared over 2 years (2010-2012) from the riparian zone of the lower reaches of the Rondegat River. This clearance was followed by the local eradication of an alien fish, smallmouth bass Micropterus dolomieu, from the lower reaches of the river in February 2012 and March 2013 using the piscicide rotenone, so that native threatened fish species could re-colonise from the upper reaches of the river. Overall costs of the clearance and eradication amounted to nearly R4.5 million, and early indications are that the native riparian vegetation and fish are recovering well. The project illustrates several aspects of good practice: careful planning; close and enthusiastic collaboration between affected state and private landowners; public participation to address concerns; the simultaneous and coordinated application of mechanical, chemical and biological control of alien plants and chemical control of alien fish; and direction by qualified ecologists. Although it is too early to assess the long-term success, the exercise provides useful lessons for such projects elsewhere, and paves the way for the more widespread use of similar approaches in selected areas that are a priority for conservation. <![CDATA[<b>Research Briefs</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600003&lng=en&nrm=iso&tlng=en Large sums have been spent on controlling invasive alien species in South Africa over the past two decades, but documented accounts of successes are almost non-existent. This brief account describes progress with a coordinated pioneering project to simultaneously clear invasive alien trees and predatory alien fish from a degraded but ecologically important river ecosystem in the Cederberg region of the Western Cape Province, South Africa. Dense infestations of invasive Australian Acacia and Eucalyptus species were cleared over 2 years (2010-2012) from the riparian zone of the lower reaches of the Rondegat River. This clearance was followed by the local eradication of an alien fish, smallmouth bass Micropterus dolomieu, from the lower reaches of the river in February 2012 and March 2013 using the piscicide rotenone, so that native threatened fish species could re-colonise from the upper reaches of the river. Overall costs of the clearance and eradication amounted to nearly R4.5 million, and early indications are that the native riparian vegetation and fish are recovering well. The project illustrates several aspects of good practice: careful planning; close and enthusiastic collaboration between affected state and private landowners; public participation to address concerns; the simultaneous and coordinated application of mechanical, chemical and biological control of alien plants and chemical control of alien fish; and direction by qualified ecologists. Although it is too early to assess the long-term success, the exercise provides useful lessons for such projects elsewhere, and paves the way for the more widespread use of similar approaches in selected areas that are a priority for conservation. <![CDATA[<b>What is the research experience of young scientists in South Africa?</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600004&lng=en&nrm=iso&tlng=en The results of an online survey - the SAYAS Survey of Young Scientists that involved the participation of 1021 postgraduate students and postdoctoral fellows from tertiary institutions in South Africa - were released in a report launched in November 2013. In this commentary we highlight some of the key findings from the report: The Research Experience of Young Scientists in South Africa.¹ <![CDATA[<b>South Africa's Golden Gate Highlands National Park management plan: Critical reflections</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600005&lng=en&nrm=iso&tlng=en The Golden Gate Highlands National Park (GGHNP) is on the foothills of the Maluti Mountains and is the only national park in the eastern Free State Province of South Africa. The park is famous for its impressive sandstone formations.¹ It was established in 1963 for the purpose of protecting a pristine area with much emphasis on conserving the sandstone formations and the montane and Afro-Alpine grassland biome.² The GGHNP is situated in QwaQwa, which is well known for lacking sustainable development,³ and has been declared a Presidential Nodal Point because of high poverty, population growth and unemployment. These problems persist despite the fact that the park is the province's major tourist attraction. Previous research in and around the park has focused on geology, palaeontological finds, slope forms and the prominent lichen weathering,¹ and remarkably little has been done on the institutional framework and policy environment governing the management and conservation of park resources. The current park management plan was compiled in 2011. This plan provides the legal base for managing resources in the GGHNP. The absence of a comprehensive database on heritage sites complicates the park management process. Whilst remarkable progress has been made in zoning the park to establish a coherent spatial framework, more still needs to be done in using GIS to develop an Environmental Management System. Here we explore the extent to which the current institutional framework and policy initiatives in the management plan foster collaboration between community and national bodies, for purposes of enhancing conservation and the economic potential of heritage resources whilst broadening the scope for scientific research. The broad objective of the park management plan is to conserve biodiversity, with an emphasis on provision of an excellent learning platform, sustainable tourism opportunities and building of cooperation between stakeholders in order to promote local and regional economic development. <![CDATA[<b>Biodiversity</b>: <b>So much more than legs and leaves</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600006&lng=en&nrm=iso&tlng=en Microorganisms inhabit virtually every possible niche on Earth, including those at the outer envelope of survival. However, the focus of most conservation authorities and ecologists is the 'legs and leaves' side of biology -the 'macrobiology' that can be seen with the naked eye. There is little apparent concern for the preservation of microbial diversity, or of unique microbial habitats. Here we show examples of the astounding microbial diversity supported by South Africa's ecosystems and argue that because microbes constitute the vast majority of our planet's species they should be considered seriously in the future protection of our genetic resources. <![CDATA[<b>A review of <i>Kudoa</i>-induced myoliquefaction of marine fish species in South Africa and other countries</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600007&lng=en&nrm=iso&tlng=en Myoliquefaction of fish musculature results in customer quality complaints and in huge economic losses, especially with regard to Pacific hake (Merluccius productus), farm-reared Atlantic salmon (Salmo salar), South African pilchards (Sardinops ocellatus) and Cape snoek (Thyrsites atun). Myoliquefaction, or 'jelly flesh', is caused by proteolytic enzymes released by the marine myxosporean parasite, Kudoa thyrsites, after the death of the fish. Currently there are no fast methods of detection for this microscopic parasite, and because myoliquefaction is evident only after 38-56 h post-mortem, infected fish inevitably reach the processor and/or consumer. Several methods of detection have been investigated, but most of these methods are time-consuming and/or result in destruction of the fish, and are thus impractical for fishing vessels and fish processors. Limited research is available on possible means of destroying or inhibiting the post-mortem activity of the parasitic proteolytic enzyme. Means such as manipulating post-mortem pH and temperature control have been suggested; leaving opportunities for research into food technology applications such as cold-chain management and ionising radiation. <![CDATA[<b>Bridging disciplines to better elucidate the evolution of early <i>Homo sapiens</i> in southern Africa</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600008&lng=en&nrm=iso&tlng=en Elucidating the history of Homo sapiens has been a passion shared by many researchers spanning several decades. There are now overwhelming lines of evidence from genetic, archaeological, palaeoanthropological and, to some extent, palaeoenvironmental research, that place Africa as the region of origin of our species. The different fields of study use diverse types of data, and methods are subject to variances introduced by mutation rates, time estimates and/or sampling biases. All of these approaches have their respective shortcomings and error ranges and are accompanied by intense debate. Yet, it is timeous to review the most recent and salient highlights that the different approaches are contributing towards explaining our deep history and ancestry. It is, after all, one history, and consequently, there ought to be several convergent patterns between data sets. Our focus is to present an updated regional synthesis from each discipline for a specific window in time within the southern African context, namely between ~ 160 ka and 85 ka, and to speculate about possible connections between data sets for this period. Even though our focus is specific in time and space, it is not intended to consider southern Africa in isolation from the rest of Africa or to suggest a singular 'origins' locale for modern Homo sapiens. We hope that this integrated approach will stimulate discussions to include broader time periods within Africa and between continents. <![CDATA[<b>Prediction of soil distribution on two soilscapes in land type Dc17 east of Bloemfontein, South Africa</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600009&lng=en&nrm=iso&tlng=en The predictive nature of digital soil mapping makes it a labour- and cost-effective way of facilitating soil surveys. A digital elevation model was used to generate terrain attributes that can be used to infer the distribution of soil associations relative to the topography. Two study areas - Gladstone and Potsane -in the Free State Province of South Africa were considered. Slope, aspect, contour and plan curvature, topographic wetness index and topographic morphological unit were used to develop a model for predicting soil associations. Discriminant analysis was employed to develop the model. The model was trained on data obtained from Gladstone and validated on data from Gladstone and Potsane. Predicting soil form was unsatisfactory. Prediction done on soil associations, with soils grouped as deep, shallow and valley-bottom soils (criteria closely related to the suitability for in-field rainwater harvesting), achieved acceptable improvement in prediction accuracy. For Gladstone, when analysis was done using equal prior probability, accuracy percentages of 56.9%, 51.5% and 58.3% were found for calibration, cross-validation and areas suited to in-field rainwater harvesting, respectively. With prior probability set in accordance to sample frequency, the accuracy percentages were improved to 83.1%, 80.0% and 94.6%, respectively. In Potsane, the prediction accuracy percentage was low (38.23%) with equal prior probability but markedly improved (67.65%) when prior probability was similar to sample frequency. These results support the validity of the statement that the predictive nature of digital soil mapping makes it a labour- and cost-effective way of facilitating soil surveys. <![CDATA[<b>Spinning pipe gas lens aberrations along the axis and in the boundary layer</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600010&lng=en&nrm=iso&tlng=en When the walls of an open-ended horizontal steel pipe are heated before the pipe is rotated along its axis, the exchange of the expelled heated air with the incoming cooler air, sucked in along the axis, results in a medium capable of focusing a laser beam propagating along the pipe's axis - a spinning pipe gas lens. However, the interaction of the heated and cooler air generates local density fluctuations which generate aberrations on the laser beam wavefront. We present results for the characterisation of these aberrations using a Shack-Hartmann wavefront sensor. The measurements show that along the axis, rotating the pipe decreases y-tilt as a result of the removal of distortions caused by gravity, although there is an increase in higher-order aberrations. However, in the boundary layer, the dominant aberration is x-astigmatism which increases with rotation speed. The results are confirmed by the measurement of the beam quality factor which increases as a result of the increase in the size of the higher-order aberrations. The spinning pipe gas lens is a device which can be used to focus laser beams using air only, but, in the process, the air introduces distortions which reduce the quality of the beam. <![CDATA[<b>Growth-promoting effects of a seaweed concentrate at various pH and water hardness conditions</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600011&lng=en&nrm=iso&tlng=en Kelpak® - a liquid seaweed concentrate made from the kelp Ecklonia maxima (Osbeck) Papenfuss - is used as a natural biostimulant to promote rooting and improve yield in crops. Plant-soil environmental conditions and the chemistry of water used for irrigation may affect the efficiency of Kelpak. The effect of pH (pH 4.5, 6.5 and 8.5) and water hardness (200 mg/L and 400 mg/L Ca2+) on the growth-promoting ability of Kelpak was assessed using the mungbean rooting bioassay and in a pot trial with Swiss chard. Kelpak promoted rooting in all the treatments in the mungbean bioassay with maximum rooting generally achieved with 20% Kelpak. With 20% Kelpak, the addition of 200 mg/L and 400 mg/L Ca2+ decreased rooting at pH 4.5, increased rooting at pH 6.5 and did not affect rooting at pH 8.5. A similar trend was observed in the pot trial with Swiss chard: leaf and root (fresh weight) and pigment content (chl a, chl b and carotenoids) improved with the addition of 200 mg/L Ca2+ + 5% Kelpak at pH 6.5 or pH 8.5, while Kelpak was able to partially mask the negative effect of 200 mg/L Ca2+ at pH 4.5. These results suggest that while Kelpak is most effective in neutral pHs, it can be used to promote plant growth in a wide range of pH and water hardness conditions. <![CDATA[<b>Improved decision-making on irrigation farming in arid zones using a system dynamics model</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600012&lng=en&nrm=iso&tlng=en The Sandveld region in the Western Cape is a low rainfall area dominated by agricultural production using groundwater resources. The rise in agricultural production in the Sandveld has led to questions regarding the region's ecological sustainability. We developed a system dynamics model for the Sandveld system which captures land-use change, agricultural production, and groundwater abstraction and recharge. Using this model, we find little evidence that pressures on livelihoods result, either currently or in the immediate future, from ecological feedback effects. The model does indicate that the highest risks are associated with the financial viability of agriculture, in its present form, in the region. With lower margins, a drive towards economies of scale in agricultural production is more likely in the future. This process has had severe implications in some sectors already, with a 39% decrease in the number of potato producers in the Sandveld region between 2003 and 2009. These results highlight that an integrated approach to agricultural, economic and environmental management and planning is needed to capture the economic and ecological complexity and dynamics of the Sandveld system. <![CDATA[<b>Expression of defence-related genes against <i>Phytophthora cinnamomi</i> in five avocado rootstocks</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600013&lng=en&nrm=iso&tlng=en Avocado (Persea americana) - a major fruit crop worldwide - is threatened by root rot caused by Phytophthora cinnamomi. This pathogen is known to infect the plant via the feeder roots leading to branch dieback, and eventually tree mortality. While it is known that different avocado rootstocks have varying degrees of susceptibility to Phytophthora root rot, little research has been done on the avocado-Phytophthora interaction. In this study, transcript abundance levels of defence-related genes coding for phenylalanine ammonia-lyase, lipoxygenase, pathogenesis-related protein 5, endochitinase, gluthathionine S-transferase and metallothionein were characterised and compared among five rootstocks with varying susceptibility to root rot, after exposure to P cinnamomi. Root samples were collected at 0 h, 3 h, 6 h, 12 h, 24 h, 48 h and 72 h post-infection and transcript abundance of the defence-related genes was determined using quantitative real-time reverse transcription PCR. The results indicated the involvement of PR-5 and endochitinase in the defence response of all avocado rootstocks to P cinnamomi but these genes could not be directly linked to the observed phenotypic resistance. PR-5 and endochitinase were highly upregulated at 72 h post-infection. Differences in transcript abundance of phenylalanine ammonia-lyase and lipoxygenase genes were seen when comparing tolerant and less tolerant rootstocks, which may suggest that transcripts of these genes contribute to resistance. These data provide important insights into plant defence and into how different avocado rootstocks may exhibit increased resistance to infection by P. cinnamomi. <![CDATA[<b>A new look at demographic transformation for universities in South Africa</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600014&lng=en&nrm=iso&tlng=en We used our previously defined 'Equity Index' to determine the demographic profile of the 23 universities in South Africa's higher education sector. We undertook an analysis of the demographic profiles of both students and staff based on audited 2011 data from the Higher Education Management Information System. We also considered an equity-weighted research index. We show the general applicability of the Euclidean formula in calculating 230 equity indices within the university sector. All institutions in the country were ranked in these categories. These rankings are quite instructive as to the demographics of the sector, both nationally and for individual institutions. No university has reached the ideal Overall Equity Index of zero and none falls within a 5% tolerance of the national demographic data. Four groups of universities emerge: those with good equity indices and low research productivity; those with poor equity indices and low research productivity; those with poor equity indices and high research productivity; and, finally, those with good equity indices and high research productivity. This index is the first quantitative measure that can be incorporated into an analysis of transformation. The Equity Index adds an innovative 'new look' to the profile and differentiation of the South African higher education landscape, and should become an important policy tool in steering the system towards a notion of transformation that connects, rather than disconnects, equity, development and differentiation. The index may also become a useful universal measurement of equity in higher education (and other) systems globally. <![CDATA[<b>Isotopic ecology of fossil fauna from Olduvai Gorge at ca 1.8 Ma, compared with modern fauna</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600015&lng=en&nrm=iso&tlng=en Light stable isotope ratios (δ13C and δ18O) of tooth enamel have been widely used to determine the diets and water sources of fossil fauna. The carbon isotope ratios indicate whether the plants at the base of the food web used C3 or C4 photosynthetic pathways, while the oxygen isotope ratios indicate the composition of the local rainfall and whether the animals drank water or obtained it from plants. The contrasting diets of two early hominin species - Homo habilis and Paranthropus boisei - of ca 1.8 Ma (million years ago) in Tanzania were determined by means of stable carbon isotope analysis of their tooth enamel in a previous study. The diets of two specimens of P boisei, from Olduvai and Peninj, proved to be particularly unusual, because 80% of their carbon was derived from C4 plants. It was suggested that their diet consisted primarily of plants, with particular emphasis on papyrus, a C4 sedge. The dominance of C4 plants in the diet of P boisei is a finding supported in another study of 22 specimens from Kenya. The isotopic ecology and diets of fossil fauna that were present at the same time as the two fossil hominin species are described here, in order to provide a fuller understanding of their contrasting diets and of the moisture sources of their water intake. This information was then compared with the isotopic composition of modern fauna from the same region of Tanzania. The carbon isotope ratios for both fossil and modern specimens show that the habitats in which these faunal populations lived were quite similar - grassland or wooded grassland. They had enough bushes and trees to support a few species of browsers, but most of the animals were grazers or mixed feeders. The oxygen isotope ratios of the fossil and modern fauna were, however, very different, suggesting strongly that the source of moisture for the rain in the Olduvai region has changed during the past 1.8 million years. <![CDATA[<b>Molecular characterisation of <i>Mycoplasma gallisepticum</i> genotypes from chickens in Zimbabwe and South Africa</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532013000600016&lng=en&nrm=iso&tlng=en Mycoplasma gallisepticum is an economically important pathogen of poultry worldwide. Yet the characterisation of M. gallisepticum field strains present in southern Africa has not previously been reported. We characterised various M. gallisepticum genotypes within the region and highlight the unique differences between two genotypes found in South Africa and Zimbabwe. PCR targeting a partial region of the mgc2 gene was used to screen various poultry farms in South Africa and Zimbabwe for M. gallisepticum. Samples were characterised using multilocus gene-targeted sequencing. Portions of the surface protein encoding pvpA, gapA and mgc2 genes and the uncharacterised surface lipoprotein gene designated MGA_0319 were sequenced and analysed. Nucleotide sequences were compared to vaccine and reference strains as well as to strains from different countries. The South African genotype contained unique mgc2 and pvpA gene regions, while the Zimbabwean genotype proved to be even more distinct with unique gapA, mgc2 and pvpA gene regions. In addition, BLAST results showed high similarities in the partial mgc2 gene region between the South African and Zimbabwean genotypes and the 'atypical' Israeli RV-2 strain, suggesting a link in its epidemiology. These results also allow for improved control strategies for southern Africa, and the use of more effective vaccine strains.