Scielo RSS <![CDATA[South African Journal of Science]]> http://www.scielo.org.za/rss.php?pid=0038-235320080001&lang=en vol. 104 num. 1-2 lang. en <![CDATA[SciELO Logo]]> http://www.scielo.org.za/img/en/fbpelogp.gif http://www.scielo.org.za <![CDATA[<b>Protein homology modelling and its use in South Africa</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100001&lng=en&nrm=iso&tlng=en Homology modelling is an important computational technique, within structural biology, to determine the 3D structure of proteins. It uses available high-resolution protein structures to produce a model of a protein of similar, but unknown, structure. We describe the essential steps in the process, and discuss the circumstances in which homology modelling is likely to lead to a useful result. Homology modelling plays a valuable role in drug design, and we illustrate this by one example, anti-SARS inhibitors. In South Africa, homology modelling has been applied to proteins that may be relevant for drug design in connection with diseases as well as in other potential industrial applications. The use to date has been limited, however, so this article aims to introduce this useful and cost-effective technique to a wider community. <![CDATA[<B>Prevalence of <I>Escherichia coli</I> O157 strains in cattle, pigs and humans in North West province, South Africa</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100002&lng=en&nrm=iso&tlng=en We have determined the prevalence of Escherichia coli O157 strains in cattle, pigs and humans. Eight hundred faecal samples were analysed, but only those isolates that satisfied all primary (oxidase and the triple sugar iron) and secondary identification criteria (API 20E) for E. coli are reported. A total of 294 E. coli isolates were further analysed for E. coli O157 characteristics by the slide agglutination test with E. coli O157-specific monovalent antiserum. Seventy-six E. coli O157 isolates were positively identified. In this group of isolates, the prevalence was higher in pigs (44-50%) than in cattle (5.4-20%) and humans (7.5%). Within the pig isolates, the prevalence was higher in the commercial (51%) than in the communal (44%) pigs. Similarly, the prevalence was higher in faeces from commercial (14-20%) than communal cattle (5.4%). This study highlights the need for correct hygiene, especially with commercial farming of cattle and pigs, and the processing of their products. Through this precaution, prevalence of E. coli O157 in farm animals can be minimized, preventing spread from animals to humans. <![CDATA[<B>How <U>not</U> to do research</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100003&lng=en&nrm=iso&tlng=en We have determined the prevalence of Escherichia coli O157 strains in cattle, pigs and humans. Eight hundred faecal samples were analysed, but only those isolates that satisfied all primary (oxidase and the triple sugar iron) and secondary identification criteria (API 20E) for E. coli are reported. A total of 294 E. coli isolates were further analysed for E. coli O157 characteristics by the slide agglutination test with E. coli O157-specific monovalent antiserum. Seventy-six E. coli O157 isolates were positively identified. In this group of isolates, the prevalence was higher in pigs (44-50%) than in cattle (5.4-20%) and humans (7.5%). Within the pig isolates, the prevalence was higher in the commercial (51%) than in the communal (44%) pigs. Similarly, the prevalence was higher in faeces from commercial (14-20%) than communal cattle (5.4%). This study highlights the need for correct hygiene, especially with commercial farming of cattle and pigs, and the processing of their products. Through this precaution, prevalence of E. coli O157 in farm animals can be minimized, preventing spread from animals to humans. <![CDATA[<B>Advancing the concepts of industrial ecology in South African institutions</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100004&lng=en&nrm=iso&tlng=en Industrial ecology seeks to apply the knowledge of systems in nature to the design and operation of industrial activities, to achieve integrated and sustainable relationships between the natural world and industry. Although the theoretical underpinning of the field corresponds in some ways to that of the emerging discipline of sustainability science, industrial ecology has evolved along two main directions that may be more practical for industry and policy-makers: 'eco-industrial parks' and islands of sustainability; and 'dematerialization-decarbonization' and the service economy. The opportunities and risks associated with applying the concepts of industrial ecology have been argued globally. This article provides an overview of how the concepts have already been applied to some extent in South Africa. We recommend how industrial ecology may be nurtured here, prioritizing areas where the field can be institutionalized. <![CDATA[<b>Alien reptiles and amphibians in South Africa</b>: <b>towards a pragmatic management strategy</b>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100005&lng=en&nrm=iso&tlng=en Biological invasions area a growing problem in South Africa. Many alien species have been introduced for various reasons and through multiple pathways over the past few centuries. Invasive alien reptiles and amphibians (herpetofauna) are not yet a major problem in the country. However, escalating difficulties with invasive species in these groups worldwide, and changing circumstances in South Africa, suggest a high risk of increased problems in the future. This paper reviews key issues pertaining to invasive alien herpetofauna worldwide and discusses how risk assessment can be used as part of an effective biosecurity strategy for South Africa. Nearly 300 species of alien herpetofauna have already been imported into the country via the pet trade and are being kept in captivity. There is a need to consider the potential threat of these species, and others still to be introduced, in line with practices in other countries where formal risk assessment policies are in place to separate potentially invasive species from those that are unlikely to be problematical. New legislation in South Africa seeks to regulate activities involving alien species, but exactly how this will be done has yet to be finalized. Each province in South Africa currently has its own legislation with different requirements; this causes many problems. Records of permit applications are also poor, complicating attempts to compile accurate inventories and to discern trends in imports and permit allocations. We define a pragmatic framework for dealing with alien reptiles and amphibians in South Africa. The framework identifies key issues facing the country and considers how the situation and advances elsewhere in the world can be used to set priorities. We propose that a risk assessment protocol be implemented for categorizing species as permissible or prohibited for import and trade. Accurate data are needed on the alien species already in South Africa. <![CDATA[<B>Southern African science in the year 1908</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100006&lng=en&nrm=iso&tlng=en Biological invasions area a growing problem in South Africa. Many alien species have been introduced for various reasons and through multiple pathways over the past few centuries. Invasive alien reptiles and amphibians (herpetofauna) are not yet a major problem in the country. However, escalating difficulties with invasive species in these groups worldwide, and changing circumstances in South Africa, suggest a high risk of increased problems in the future. This paper reviews key issues pertaining to invasive alien herpetofauna worldwide and discusses how risk assessment can be used as part of an effective biosecurity strategy for South Africa. Nearly 300 species of alien herpetofauna have already been imported into the country via the pet trade and are being kept in captivity. There is a need to consider the potential threat of these species, and others still to be introduced, in line with practices in other countries where formal risk assessment policies are in place to separate potentially invasive species from those that are unlikely to be problematical. New legislation in South Africa seeks to regulate activities involving alien species, but exactly how this will be done has yet to be finalized. Each province in South Africa currently has its own legislation with different requirements; this causes many problems. Records of permit applications are also poor, complicating attempts to compile accurate inventories and to discern trends in imports and permit allocations. We define a pragmatic framework for dealing with alien reptiles and amphibians in South Africa. The framework identifies key issues facing the country and considers how the situation and advances elsewhere in the world can be used to set priorities. We propose that a risk assessment protocol be implemented for categorizing species as permissible or prohibited for import and trade. Accurate data are needed on the alien species already in South Africa. <![CDATA[<B>Migration, mines and mores</B>: <B>the HIV epidemic in southern Africa</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100007&lng=en&nrm=iso&tlng=en The seriousness of the HIV epidemic in southern and eastern Africa has its roots in the 19th century-in the employment practices instituted on mines, farms and in cities, where millions of men have, ever since, lived apart from their families for the greater part of each year. This destruction of the family unit was a sociological disaster waiting for the arrival of HIV and is the source of many other social ills-not least the increasingly violent nature of South African society. In the short term we can promote HIV prevention measures such as male circumcision and condom use. In the medium term, we can hope that the many billions already spent on microbicide and vaccine research begin to pay dividends. In the long term, we need to change fundamentally the way that people live. <![CDATA[<B>Toxicity evaluation of synthetic food sweeteners by means of the Weaver Human Cell Test</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100008&lng=en&nrm=iso&tlng=en The seriousness of the HIV epidemic in southern and eastern Africa has its roots in the 19th century-in the employment practices instituted on mines, farms and in cities, where millions of men have, ever since, lived apart from their families for the greater part of each year. This destruction of the family unit was a sociological disaster waiting for the arrival of HIV and is the source of many other social ills-not least the increasingly violent nature of South African society. In the short term we can promote HIV prevention measures such as male circumcision and condom use. In the medium term, we can hope that the many billions already spent on microbicide and vaccine research begin to pay dividends. In the long term, we need to change fundamentally the way that people live. <![CDATA[<B>Decomposing populations</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100009&lng=en&nrm=iso&tlng=en A decomposed system of differential equations is one which can be conflated into a single scalar equation in one dependent variable that contains all of the dependent variables of the original system. We consider the first-order differential equations for four standard models of population growth and give examples chosen from a variety of applications. We also present methods of analysis for integrable systems. <![CDATA[<B>SERGE</B>: <B>a spatially explicit generator of local rainfall in southern Africa</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100010&lng=en&nrm=iso&tlng=en This article describes the features of SERGE, a stochastic, spatially explicit tool for the simulation of daily rainfall in arid environments. Rainfall data (either raw or produced by a rainfall generator) are frequently available on a daily basis but at low spatial resolution. Furthermore, although the rainfall characteristics of a given small area may vary little when averaged over the long term, rainfall does vary substantially on a daily time scale. It is exactly this short-term, small-scale variation that is of interest to modellers in many applications. A tool is needed therefore that generates spatio-temporal rainfall estimates based on only temporal data. To fill this gap, we developed SERGE using an ad hoc approach. Based on known characteristics of rainfall at a point, SERGE projects spatially homogeneous daily rainfall produced by a rainfall generator into spatially heterogeneous estimates by distributing clouds of fixed size and random position. Our algorithm preserves the long-term rainfall characteristics at each point, but introduces spatial autocorrelation of variable length. SERGE provides a simple and flexible tool for the simulation of spatio-temporal rainfall to be integrated into other models. SERGE is intended for modellers wanting to investigate the effect of spatially variable rainfall in their system. Given the importance of spatial variability in arid environments, this should be of interest to scientists in the fields of ecology, range management, agriculture, climate change, and hydrology. <![CDATA[<B>A five-day back trajectory climatology for Rukomechi research station (northern Zimbabwe) and the impact of large-scale atmospheric flows on concentrations of airborne coarse and fine particulate mass</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100011&lng=en&nrm=iso&tlng=en The climatology of slow and fast air mass transport towards Rukomechi research station in northern Zimbabwe (16.1°S, 29.4°E) is examined through an analysis of 5-day kinematic back trajectories arriving at 1180 m above ground level (~850 hPa) for the period 1994-99. The trajectories are computed daily by the HYSPLIT 4 model using the National Oceanic and Atmospheric Administration's re-analysed wind fields as input. Objective classification of trajectories into different flow regimes is done using a non-hierarchical cluster algorithm that is applied to all the trajectories at once, to examine the temporal and spatial characteristics. The synoptic-scale atmospheric circulation associated with each cluster was also studied. Four major transport corridors and seven large-scale flows were found to provide an indication of source regions of the air masses and transport pathways influencing Rukomechi. The dominant transport features include (1) the late dry season to wet season eastern air flows that contribute 35% of the total flow and which are driven by an anticyclone that wraps around the subcontinent and stretches into the Mozambique Channel, (2) the late wet season to dry season southeastern pathway that accounts for 44% of the total flow and is associated with the South Atlantic anticyclone and the tropical depression in the Indian Ocean, (3) the fast (11 m s-1) dry season southern flow (contributes 8%) that is driven by a continental anticyclone over South Africa coupled to a South Atlantic anticyclone, and (4) the north-northwesterly flow that contributes 6% to the total flow and is associated with the Intertropical Convergence Zone. A further, very slow (1.8 m s-1) flow regime, consisting of regionally re-circulated air results from regional differential heating at the surface. Concentrations of particulate mass, measured during 1994-2000 at the Rukomechi site, are shown to be significantly correlated with the occurrence of those seven large-scale flows, which have been identified by objective trajectory classification. High particulate mass concentrations are associated only with air masses carried along the fast easterly flow, the slow southeasterly flow and the southerly flow (dry season flows); low particulate mass concentrations are exclusively found with wet season flows. <![CDATA[<B>Antiplasmodial activities of some abietane diterpenes from the leaves of five <I>Plectranthus</I> species</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100012&lng=en&nrm=iso&tlng=en Seven known abietane diterpenes were isolated from five Plectranthus species, namely P. hadiensis, P. lucidus, P. ecklonii, P. purpuratus subsp. purpuratus and P. purpuratus subsp. tongaensis. The seven compounds were tested for their antiplasmodial activity and for their ability to inhibit β-haematin formation. Overall, they showed good activity (IC50 values ranging from 3.11 to 14.65 µM), with one compound being 62% as effective as chloroquine in inhibiting β-haematin formation. However, the cytotoxicity profile indicated a low degree of specificity towards the malaria parasite. When combined with quinine, three compounds interacted in an additive manner whereas one interacted synergistically. <![CDATA[<B>Optically stimulated luminescence dating at Rose Cottage Cave</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100013&lng=en&nrm=iso&tlng=en Six optically stimulated luminescence (OSL) dates are compared with stratigraphically associated 14C dates from Rose Cottage Cave. The OSL dates overlap the accepted 14C chronology except for one sample that overestimates the expected age by approximately 30%. A single-grain analysis demonstrates that the testing procedure for feldspar fails to reject single aliquots containing feldspar and the overestimate of age is attributed to this. Seven additional luminescence dates for the Middle Stone Age layers combined with the 14C chronology establish the terminal Middle Stone Age deposits at 27 000 years ago, while stone tool assemblages that are transitional between the Middle Stone Age and the Late Stone Age are dated to between 27 000 years and 20 000 years ago. Although there are inconsistencies in the Middle Stone Age dates, the results suggest that the Howiesons Poort at Rose Cottage Cave dates to between 70 000 years and 60 000 years ago. <![CDATA[<B>Fish bone sizes as estimators of standard lengths of three southern African freshwater species with application to archaeological samples</B>: <B>a preliminary investigation</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100014&lng=en&nrm=iso&tlng=en Estimating standard lengths (SL) from freshwater fish bones found in archaeological samples can provide information on the status of past fish populations, their exploitation and environmental conditions. The bones of three fish species were measured and tested against the SL to determine their accuracy as predictors. A limited number of bones proved useful to determine SL. The results were applied to the fish bones from an archaeological site in Lesotho, to determine the median and maximum size of the prehistoric fishes. Most of these were of breeding size, while the maximum sizes estimated appear to exceed those of current angling records. This study is limited by a small sample of modern fishes with a relatively restricted size range, but nonetheless provides useful insights into the size distribution of ancient fish populations in Lesotho. <![CDATA[<B>Effect of macromolecular crowding on the stability of monomeric glutaredoxin 2 and dimeric glutathione transferase A1-1</B>]]> http://www.scielo.org.za/scielo.php?script=sci_arttext&pid=S0038-23532008000100015&lng=en&nrm=iso&tlng=en The effect of macromolecular crowding on the structure and stability of monomeric glutaredoxin 2 (Grx2) and its homodimeric structural homologue human glutathione transferase A1-1 (hGST A1-1) was investigated using dextran 70 as crowding agent. Far-UV circular dichroism and fluorescence spectroscopic data indicated that repulsive steric interactions between the proteins and dextran (50-300 mg/ml) had little effect on the global structures of the native proteins. Urea-induced unfolding of both proteins was reversible (recoveries of >80%) at low dextran concentrations (&lt;100 mg/ml) but resulted in significant losses in refolding recoveries at higher levels of dextran, due to aggregation. The two-state global unfolding processes of Grx2 and hGST A1-1, as well as their m-values (unfolding cooperativity parameter), were unaffected by 100 mg/ml dextran, demonstrating the absence of specific intermolecular interactions between protein and crowder. Dextran at 100 mg/ml enhanced the stability of Grx2 and hGST A1-1 by 1.1 kcal/mol and 2.2 kcal/mol, respectively. Compaction of the unfolded states of both proteins is indicated by an increase in alpha-helical content and in the decreased solvent exposure of their tryptophan residues. The dextran-induced formation of compact states of urea-denatured Grx2 and hGST A1-1 is ascribed to steric excluded volume effects, which induce an entropic destabilization of expanded unfolded states, thereby shifting the equilibrium between native and unfolded states towards the native state. Quantitatively, however, the extent of stabilization of Grx2 is lower than that predicted by the equivalent hard particle model for the excluded volume effect of dextran on protein stability.