Scielo RSS <![CDATA[South African Journal of Science]]> vol. 110 num. 9-10 lang. <![CDATA[SciELO Logo]]> <![CDATA[<b>Open sesame</b>]]> <![CDATA[<b>New possibilities for research on reef fish across the continental shelf of South Africa</b>]]> <![CDATA[<b><i>Excalfactoria</i></b><b> and a bird and word book to keep you warm</b>]]> <![CDATA[<b>Interdisciplinary mentoring in science</b>]]> <![CDATA[<b>Good news from the South: Biodiversity mainstreaming - A paradigm shift in conservation?</b>]]> <![CDATA[<b>Towards SunSmart school policies in South Africa</b>]]> <![CDATA[<b>Advances towards the development of a cloud-resolving model in South Africa</b>]]> Recent advances in supercomputing have made feasible the numerical integration of high-resolution cloud-resolving models (CRMs). CRMs are being used increasingly for high-resolution operational numerical weather prediction and for research purposes. We report on the development of a new CRM in South Africa. Two bulk microphysics parameterisation schemes were introduced to a dynamical core of a two-dimensional Non-hydrostatic σ-coordinate Model (NSM) developed in South Africa. The resulting CRM was used to simulate two 12-day periods and an 8-day period observed during the Tropical Oceans Global Atmosphere Coupled Ocean-Atmosphere Response Experiment. The response of the NSM to the large-scale forcing which occurred over the three periods, and which included both suppressed and active convection, was examined. The NSM is shown to be able to capture the differences in the three experiments and responds correctly to the large-scale forcing (i.e. it is able to distinguish between suppressed and active regimes). However, the model simulations are cooler and drier than the observations. We demonstrate progress made in the development of a CRM in South Africa, which can be used to study the attributes of convective rainfall over the region. <![CDATA[<b>IziNambuzane: IsiZulu names for insects</b>]]> We provide a tool for communicating about insects in isiZulu to facilitate research and knowledge sharing in the fields of indigenous knowledge, cultural entomology, environmental education and community extension involving isiZulu speakers. A total of 213 different names for 64 insect specimens were encountered among a sample of 67 respondents in 11 communities distributed across the province of KwaZulu-Natal, South Africa. This list includes 93 names that can be considered core isiZulu vocabulary and which are widely used to identify insects that are agriculturally, medically, domestically, culturally or ecologically common or significant. Substantial variation was found regarding the names for particular insects, especially between regions, suggesting dialectal differences between isiZulu speakers. Grammatical and social variation in names was also recorded. This study highlights interdisciplinary teamwork in the field of indigenous knowledge research and the influences affecting the standardisation of South African languages for technical and scientific work. <![CDATA[<b>Long bone cross-sectional geometric properties of Later Stone Age foragers and herder-foragers</b>]]> Diaphyseal cross-sectional geometry can be used to infer activity patterns in archaeological populations. We examined the cross-sectional geometric (CSG) properties of adult Later Stone Age (LSA) herder-forager long bones from the inland lower Orange River Valley of South Africa (n=5 m, 13 f). We then compared their CSG properties to LSA forager adults from the coastal fynbos (n=23 m, 14 f) and forest (n=17 m, 19 f) regions, building on a previous report (Stock and Pfeiffer, 2004). The periosteal mould method was used to quantify total subperiosteal area, torsional strength, bilateral asymmetry and diaphyseal circularity (Imax/Imin) at the mid-distal (35%) location of upper arms (humeri) and the mid-shaft (50%) location of upper legs (femora). Maximum humerus and femur lengths were similar among the three samples, suggesting that adult stature was similar in all three regions. When compared to the previous study, CSG property values obtained using the periosteal mould method correlated well, and there were no significant differences between data collected using the different methods. No statistically significant differences were found among the humerus or femur CSG properties from the different regions. This finding suggests that all individuals undertook similar volitional habitual activities in regard to their upper limbs, and also had similar degrees of terrestrial mobility. These results indicate relative behavioural homogeneity among LSA foragers and herder-foragers from South Africa. The small degree of regional variation apparent among the three samples may reflect local ecology and the subsistence demands affecting populations in these different regions. <![CDATA[<b>Open access in South Africa: A case study and reflections</b>]]> In this paper, we locate open access in the South African higher education research context where it is, distinctively, not shaped by the policy frameworks that are profoundly changing research dissemination behaviour in other parts of the world. We define open access and account for its rise by two quite different routes. We then present a case study of journal publishing at one South African university to identify existing journal publishing practices in terms of open access. This case provides the springboard for considering the implications - both positive and negative - of global open access trends for South African - and other - research and researchers. We argue that academics' engagement with open access and scholarly communication debates is in their interests as global networked researchers whose virtual identities and online scholarship are now a critical aspect of their professional engagement. <![CDATA[<b>Novel CYP2E1 haplotype identified in a South African cohort</b>]]> Alcohol abuse accounts for approximately 2.5 million deaths annually and is the third highest risk factor for disease and disability. Alcohol is metabolised by polymorphic enzymes and the status of an individual with respect to alcohol metabolising enzymes may have forensic relevance in post-mortems. Baseline frequencies of gene variants involved in alcohol metabolism need to be established to aid the identification of suitable population-specific polymorphisms to genotype during molecular autopsies. The principal alcohol metabolising enzymes include alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH) and cytochrome P450 2E1 (CYP2E1). Six single nucleotide polymorphisms (SNPs) - rs1229984G>A and rs2066702C>Tin ADH1B, rs671G>A in ALDH2, and rs3813867G>C, rs2031920C>T and rs6413432T>A in CYP2E1 - were genotyped in 150 individuals from four South African populations: Xhosa, Zulu, South African white and South African coloured. Allele frequencies for each SNP in the four population groups were 0-10% for rs1229984A, 2-12% for rs2066702T, 0-2% for rs671A, 1-4% for rs3813867C, 0-1% for rs2031920T and 3-15% for rs6413432A. Haplotype analysis revealed a novel combination of three SNPs in CYP2E1 whose effects on alcohol metabolism need further investigation. Establishment of baseline frequencies adds to our knowledge of genetic variation in alcohol metabolising enzymes and additional research is required to determine the functional significance of this novel CYP2E1 haplotype. <![CDATA[<b>Characterisation of <i>Mycosphaerella</i> species associated with pink spot on guava in South Africa</b>]]> Pink spot symptoms on guava fruit in the Lowveld region were in the past attributed to Colletotrichum gloeosporioides, but recently Mycosphaerella species were suggested to be part of a disease complex, including pink spot symptoms. During routine surveys of guava diseases in the Lowveld area of the Mpumalanga Province in South Africa, Mycosphaerella species were consistently isolated from guava fruit. Colletotrichum gloeosporioides was also retrieved, especially from older, bigger lesions. The Mycosphaerella isolates were compared based on their growth characteristics in culture and on DNA sequences of the internal transcribed spacer region, large subunit of the ribosomal DNA as well as the β-tubulin and translation elongation factor 1α gene regions. The phylogenetic analyses indicate that the isolates from the present study represent at least three species not previously reported on guavas. This report is therefore the first report of Mycosphaerella species associated with Psidium guajava in South Africa. <![CDATA[<b><i>Escherichia coli</i></b><b> with virulence factors and multidrug resistance in the Plankenburg River</b>]]> Escherichia coli is a natural inhabitant of the gut and E. coli levels in water are considered internationally to be an indication of faecal contamination. Although not usually pathogenic, E. coli has been linked to numerous foodborne disease outbreaks, especially those associated with fresh produce. One of the most common ways through which E. coli can be transferred onto fresh produce is if contaminated water is used for irrigation. In this study, a total of 81 confirmed E. coli strains were isolated from the Plankenburg River as part of three separate studies over 3 years. During sampling, E. coli levels in the river were above the accepted levels set by the World Health Organization and the South African Department of Water Affairs and Forestry for safe irrigation of fresh produce, which indicates that transfer of E. coli during irrigation is highly probable. Multiplex polymerase chain reaction screening for pathogenic gene sequences revealed one enteroaggregative positive strain and four enteropathogenic positive strains. The four enteropathogenic strains were also found to be resistant to three or more critically and highly important antibiotics and were therefore classified as multidrug resistant strains. These results show that E. coli with enteropathogenic potential and multiple antimicrobial resistance properties has persisted over time in the Plankenburg River. <![CDATA[<b>Trace element composition of two wild vegetables in response to soil-applied micronutrients</b>]]> Wild vegetables are an important commodity in the subsistence farming sector. They are considered to be rich in micronutrients and can therefore be used to overcome inadequate nutrition. However, research on micronutrients in wild vegetables remains limited and sporadic. In this study, we evaluated the responses of two wild vegetables - Corchorus olitorius and Amaranthus cruentus var. Arusha - to micronutrients added to the soil in comparison with a reference crop, Swiss chard (Beta vulgaris var. cicla). Swiss chard concentrated significantly (o<0.01) higher amounts of Cu, Zn and Mn in the leaves than did the wild vegetables. Variations in micronutrients among the vegetables were greater for Zn (72-363 mg/kg) and Mn (97.9-285.9 mg/kg) than for Cu (8.8-14 mg/kg). C. olitorius had the least capacity to concentrate Mn and Zn in the leaves. However, C. olitorius concentrated significantly more Fe (327 mg/kg) in the leaves than did A. cruentus (223 mg/kg) or B. vulgaris (295 mg/kg). The mean per cent S concentration in the leaves ranged from 0.26% in C. olitorius to 0.34% in A. cruentus and B. vulgaris. We conclude that the different vegetables had different abilities to concentrate Cu and Zn in the order B. vulgaris &gt; A. cruentus &gt; C. olitorius. These results seem to contradict the belief that wild vegetables have an inherent ability to concentrate mineral micronutrients in their tissues. <![CDATA[<b>Research governance and scientific knowledge production in The Gambia</b>]]> Public research institutions and scientists are principal actors in the production and transfer of scientific knowledge, technologies and innovations for application in industry as well for social and economic development. Based on the relevance of science and technology actors, the aim of this study was to identify and explain factors in research governance that influence scientific knowledge production and to contribute to empirical discussions on the impact levels of different governance models and structures. These discussions appear limited and mixed in the literature, although still are ongoing. No previous study has examined the possible contribution of the scientific committee model of research governance to scientific performance at the individual level of the scientist. In this context, this study contributes to these discussions, firstly, by suggesting that scientific committee structures with significant research steering autonomy could contribute not only directly to scientific output but also indirectly through moderating effects on research practices. Secondly, it is argued that autonomous scientific committee structures tend to play a better steering role than do management-centric models and structures of research governance. <![CDATA[<b>Tufa stromatolite ecosystems on the South African south coast</b>]]> Following the first description of living marine stromatolites along the South African east coast, new investigations along the south coast have revealed the occurrence of extensive fields of actively calcifying stromatolites. These stromatolites have been recorded at regular distances along a 200-km stretch of coastline, from Cape Recife in the east to the Storms River mouth in the west, with the highest density found between Schoenmakerskop and the Maitland River mouth. All active stromatolites are associated with freshwater seepage streams flowing from the dune cordon, which form rimstone dams and other accretions capable of retaining water in the supratidal platform. Resulting pools can reach a maximum depth of about 1 m and constitute a unique ecosystem in which freshwater and marine organisms alternate their dominance in response to vertical mixing and the balance between freshwater versus marine inflow. Although the factors controlling stromatolite growth are yet to be determined, nitrogen appears to be supplied mainly via the dune seeps. The epibenthic algal community within stromatolite pools is generally co-dominated by cyanobacteria and chlorophytes, with minimal diatom contribution. <![CDATA[<b>Prescription patterns of enzyme-containing products in South Africa over a 2-year period</b>]]> Enzymes are traded in five categories, namely medical (intervention), diagnostic (detection and quantification), molecular biology, biofuel and industrial. Therapeutic enzymes have been investigated for different uses, for example, for the treatment of genetic disorders, blood clotting disorders, cancer and infectious diseases and for burn debridement. No studies on the prescription of enzyme-containing products in South Africa could be found. Enzymes are classified in the Monthly Index of Medical Specialities under digestants, enzymes and fibrinolytics. The primary aim of this study was to investigate the prescription patterns and cost of enzyme-containing products in South Africa. A private health-care medicines claims database for 2010 and 2011 of approximately 4.5 million records was analysed retrospectively. Enzyme-containing products constituted a small percentage of medical insurance claims (only 0.02% of approximately 4.5 million claims for products and procedures), yet they were relatively expensive. A total of 906 products was prescribed at a cost of almost ZAR2 million over the 2 years. Hyaluronidase was the most frequently prescribed (60.04%), followed by pancreatin-containing products (34.66%). Pancreatin (lipase/ protease/amylase) is primarily used in the management of pancreatic exocrine insufficiency. The average cost per hyaluronidase prescription paid by the medical insurance schemes was ZAR280. Other enzyme-containing products prescribed were imiglucerase, alteplase and tenecteplase. Imiglucerase was overall the most expensive. Alteplase, tenecteplase and streptokinase are antithrombotic enzymes that are used in the treatment of acute myocardial infarction or ischaemic stroke. Streptokinase, regarded as the most affordable antithrombotic enzyme, was not prescribed during the period under study. With the growing opportunities for enzymes for therapeutics, the use of enzyme-containing products which are comparatively expensive require cost-effectiveness studies.