Chronotype and PERIOD3 Variable Number Tandem Repeat Polymorphism in Individual Sports Athletes

A link between diurnal preference and a variable number tandem-repeat (VNTR) polymorphism in the PERIOD3 gene (PER3) has been demonstrated: the longer PER3⁵ and shorter PER3⁴ alleles with preferences for mornings and evenings, respectively. As many competitive events in South Africa for individual athletes are scheduled for the early mornings, we hypothesized that this might favor those athletes with a preference for morning activities. Self-selected white, male cyclists (CYC, n = 125), runners (RUN, n = 120) and Ironman triathletes (IM, n = 287) of European descent were compared with a control population of active, non-competitive individuals (CON, n = 96). The chronotypes of all CYC, RUN and CON participants and a sub-sample of the IM group (n = 49) were assessed using the Horne–Östberg Morningness–Eveningness Questionnaire, and the PER3 VNTR genotype for each participant was determined. The athlete groups contained more morning-type individuals than the CON group (CYC: 72%, n = 90; RUN: 67%, n = 80; IM: 59%, n = 29; CON: 41%, n = 39; p < .001). The prevalence of the PER3⁵ allele was greater in the athlete groups (CYC: 61%, n = 152; RUN: 58%, n = 132; IM: 56%, n = 324; CON: 38%, n = 76; p < .001), and more athletes were genotyped as PER3^5/5 than CON individuals (CYC: 41%, n = 51; RUN: 23%, n = 26; IM: 28%, n = 81, CON: 9%, n = 8; p < .001). A strong relationship between chronotype and PER3 VNTR genotype was observed (p < .001). Finally, the time of day at which the athletes preferred to train was related to their chronotype (p < .001). This is the first study of its kind in a South African sporting population, and the results have not yet been replicated. These data suggest that white males of European descent participating in individual endurance sports in South Africa are more likely to be morning types. Furthermore, the PER3 VNTR may be one of the factors contributing to this observation. (Author correspondence: laura.roden@uct.ac.za)     

South African rock art

The total number of rock art sites in South Africa certainly is in excess of 30,000. Collectively, they include well over a million images. However, fewer than 10,000 sites are listed on official databases. One reason for the lack of documentation is the high cost of establishing and maintaining recording programs. There is also a low level of public interest in rock art because both the art and the history of indigenous peoples have been neglected in school and university curricula. Matters are improving: At least one postgraduate university course dedicated to rock art will be offered at the University of the Witwatersrand beginning in 1999. Moreover, the gradual inclusion of cultural resources in heritage conservation and management programs is continuing. The significance of the oversight in the past is magnified if we consider the fragility of the art and the potential wealth of information it holds for understanding the evolution of South African society over the past 30,000 years. Rock art is an irreplaceable historical archive of extraordinary value. Although no one would dispute that this art must survive intact into the next millennium, research into its meaning is equally important if we are to convince the public that the art is worth saving. It is in this latter field that South African researchers have made a significant contribution to rock art studies in the past three decades.     

Association Study of a Variable-Number Tandem Repeat Polymorphism in the Clock Gene PERIOD3 and Chronotype in Norwegian University Students

Circadian rhythms are endogenously generated cycles involving physiological parameters, such as core body temperature, hormone levels, blood pressure, sleep, and metabolism, with a period length of around 24?h. The circadian clock in mammals is regulated by a set of clock genes that are functionally linked together, and polymorphisms in clock genes could be associated with differences in circadian rhythms. A variable-number tandem repeat (VNTR) in the human clock gene PERIOD3 (PER3) has been suggested to correlate with a morning (lark) versus evening (owl) chronotype as well as with the circadian rhythm sleep disorder “delayed sleep phase disorder” (DSPD). The authors examined 432 healthy Norwegian university students in search of further support for an association between the PER3 polymorphism and diurnal preference. The Horne-Östberg Morningness-Eveningness Questionnaire (MEQ) and Preferences Scale (PS) were used to evaluate subjective chronotype. DNA samples were genotyped with respect to the 4-repeat and 5-repeat alleles of the VNTR PER3 polymorphism, and the genotype distribution was 192 (4-4), 191 (4-5), and 49 (5-5). The authors estimated that the power to detect an association of the 4-allele with preference for morningness or eveningness was 75%. The authors found no association between the PER3 clock gene and chronotype, indicating that the proposed role of PER3 needs further clarification. (Author correspondence: teresa.osland@med.uib.no)     

Volatile constituents and antimicrobial activities of nine South African liverwort species

The volatile constituents of nine liverworts species (Asterella marginata, Dumortiera hirsuta, Fossombronia swaziensis, Marchantia pappeana, Marchantia polymorpha subsp. ruderalis, Pallavicinia lyellii, Plagiochasma rupestre, Riccia albolimbata and Symphyogyna podophylla) from South Africa were determined by gas chromatography. Where possible the volatile constituents identified were compared to those reported for the same species from other countries. Among the analysed liverworts, the chemical compositions of A. marginata, F. swaziensis, M. pappeana, and R. albolimbata are reported for the first time. Each of the analysed liverwort species produced its own characteristic components. Thujopsanes, chamigranes and cuparanes were found to be the most characteristic components of M. polymorpha subsp. ruderalis. The presence of dumortane-type sesquiterpenoids in D. hirsuta indicated that this species is similar in chemistry to an Argentinean sample. This is one of only a handful of reports on the presence of this sesquiterpene-type in liverworts. Simple thallose liverworts, S. podophylla and P. lyellii, were characterized by the presence of labdane-type diterpenoids. In addition, the antimicrobial activities of chloroform:methanol (1:1) extracts of the liverworts were evaluated against several important human pathogens using the serial dilution assay. Four of the liverwort species were active against Pseudomonas aeruginosa with MIC values ranging from 0.50 to 1.0 mg/mL. Some activity (MIC value of 1.0 mg/mL) was also recorded for the crude extracts of P. lyellii and M. pappeana against Escherichia coli. The extract of S. podophylla displayed the best activity towards the yeast Cryptococcus neoformans (MIC = 1.0 mg/mL). Although approximately 300 liverwort species occur in southern Africa, a Scopus search confirmed that this is the first report of the volatile profiles and biological properties of species from the region.     

South African populations of Littorina rudis

Littorina rudis was collected from stands of Spartina capensis in saltmarsh habitats within Langebaan and knysna lagoon, Cape Province. It was absent from rocky sores and from saltmarshes east of Knysna. The shell, radular and penial morphology are described. L. rudis from both localities bore tessellated colour patterns similar to those of British saltmarsh ecotypes. The Knysna population contained individuals with a unique amber background colour. The shells from Knysna and Langebaan were very thin in accordance with the sheltered habitats. The number of embryos carried in the brood puch was similar in both countries. Sexual maturity was attained at about 4 mm shell length; the male and female modal sizes were 4.9 mm and 5.1 mm respectively at Langebaan. No. published records were found for L. rudis in South West Africa. Some possible origins of the South African L. rudis populations are discussed.     

South African Museums and the Creation of a New National Identity

Museums are important sites of national cultural production, collective memory making, and the construction of national narratives. Contemporary South Africa is a particularly interesting place to study these processes. With the demise of apartheid, South Africa faces the difficult challenge of creating a new national identity that incorporates an examination of past oppression yet leaves the way open for building a national identity that incorporates all its diverse groups. The museums reviewed below, the Robben Island Prison Museum, the District Six Museum in Capetown, and the Kwa Muhle local history museum in Durban all make important contributions to this process.     

The biology of Dendropoma corallinaceum and Serpulorbis natalensis, two South African vermetid gastropods

D. corallinacewn forms sheet-like colonies at Mean Low Water (MLW) on exposed rocky shores: S. natalensis forms loose aggregations under stones below MLW in more sheltered situations. Both species released young from July— December. D. corallinaceun has single embryos in capsules brooded free in the mantle cavity; S. natalensis has 20–40 embryos per capsule, the latter being attached to the roof of the shell and hanging through a dorsal slit in the mantle. The morphology of the crawling young is similar in both species, resembling adult errant prosobranchs. D. corallinaceum has a stouter, more streamlined protoconch than S. natalensis correlated with the more turbulent water of its habitat. The crawling young secrete a sticky mucous trail for adhesion to the substratum. They are strongly photopositive until settlement. D. corallinaceum can settle within 24 hours but may delay settlement to 4–5 days if suitable substrata are absent. Metamorphosis is complete 2 days after settlement. D. corallinaceum prefer to settle on Lithothamnion which is easily eroded by the radula to provide a groove for rapid, firm attachments to the substratum. Both species feed from mucous nets, S. natalensis having a slower feeding rhythm commensurate with its larger size. Contiguous pairs of S. natalensis have synchronised feeding rhythms, probably to reduce mutual net robbing. Particles are also filtered out of suspension; many particles are rejected in the pseudofaeces but some are ingested. D. corallinaceum and S. natalensis have many similar ecologically equivalent species throughout the warm temperate and tropical seas of the world.     

On the genetic interrelationships of South African Negroes

This study addresses the comparative genetic interrelationships between South African Negro groups. For this the genetic distances between seven ethnically defined Negro subsamples (total of 998 individuals) based on 24 genetic loci/polymorphisms are calculated by applying standard distance formulae. These computations offer an opportunity to evaluate the different polymorphisms in terms of their effects on the genetic distances. The genetic interrelationships thus computed are illustrated by way of dendrograms and are discussed in terms of their comparative significance. It follows from the findings that the Ndebele, Northern Sotho (Pedi), and Tswana form a closely related subcluster and that the Zulu and Swazi as well as the Venda and Shangana-Tsonga form two additional, more distant, subclusters. These results are discussed and tentatively interpreted against the background of the reported Khoisan admixture of the populations concerned as well as their ethnological history. The data are also compared to those derived from metric and dermatoglyphic studies. It is concluded that whereas there is some agreement between these categories of variation (genetic, metric, and dermatoglyphic) as far as the comparative evaluation of South African Negro groups is concerned, there also are discrepancies. These conclusions need to be explained in terms of evolutionary mechanisms (such as historic origins, hybridization, natural selection, and genetic drift) in order to obtain a more consistent and comprehensive comparative picture of the physical anthropology of southern African populations.     

The oral susceptibility of South African field populations of Culicoides to African horse sickness virus

Twenty‐two isolates of African horse sickness virus (AHSV), representing its distinct serotypes, geographical and historical origins, were fed to three populations of South African livestock‐associated Culicoides spp. (Diptera, Ceratopogonidae). Infective blood meals included 12 recent isolates, nine historical reference strains and one live attenuated vaccine strain serotype 7 (AHSV‐7) of the virus. Field‐collected midges were fed through a chicken‐skin membrane on sheep blood spiked with one of the viruses, which concentrations ranged from 5.4 to 8.8 log₁₀TCID₅₀/mL of blood. After 10 days incubation at 23.5°C, AHSV was isolated from 11 Culicoides species. Standard in vitro passaging of AHSV‐7, used for the preparation of live attenuated vaccine, did not reduce its ability to infect Culicoides species. Virus recovery rates in orally infected Culicoides midges differed significantly between species and populations, serotypes, isolates and seasons. Significant variations in oral susceptibility recorded in this study emphasize a complex inter‐relationship between virus and vector, which is further influenced by multiple intrinsic and extrinsic factors. As it is not possible to standardize all these factors under laboratory conditions, conclusive assessment of the role of field‐collected Culicoides midges in the transmission of orbiviruses remains problematic. Nevertheless, results of this study suggest the potential for multi‐vector transmission of AHSV virus in South Africa.     

Taxonomic patterns of bleaching within a South African coral assemblage

In 1998, the Indian Ocean coral reefs suffered a severe and extensive mass bleaching event. The thermal tolerances of corals were exceeded and their photosynthetic symbionts (zooxanthellae) lost. Mortalities of up to 90% were recorded on the reefs of Seychelles, Maldives, Kenya and Tanzania. South African coral reefs were among the few that largely escaped the 1998 mass bleaching event, but may be threatened in the future if global warming increases. This study assessed the extent of coral bleaching and partial recovery at Sodwana Bay, South Africa during 2000 and 2001. Bleaching levels in this study varied over the course of a year, which suggested that seasonally varying parameters such as sea temperature were the most likely cause of bleaching. Bleaching levels were highest at the shallowest site. However, these bleaching levels were very low in comparison with those of reefs elsewhere in the Indian Ocean. The greater volume of water over the relatively deeper reefs of Sodwana Bay may have protected the reefs from severe bleaching. Field measurements on the three reefs indicated that, although the reefs at Sodwana Bay are still healthy, bleaching increased from <1% in 1998 to 5–10% in 2002. Bleaching occurred in 26 coral genera. The Alcyonacea were highly susceptible to bleaching, especially Sarcophyton sp. Among the hard corals, Montipora spp. were the species most susceptible to bleaching. The sensitivity of these genera to early and slight increases in temperature suggests that they can forewarn of a possible greater bleaching event. In contrast, the coral genera Turbinaria and Stylophora were most resistant to bleaching.     

Genetic diversity of two African and sixteen South American populations determined on the basis of six hypervariable loci

A total of 582 individuals (1,164 chromosomes) from two African, eight African-derived South American, five South American Amerindian, and three Brazilian urban populations were studied at four variable number of tandem repeat (VNTR) and two short tandem repeat (STR) hypervariable loci. These two sets of loci did not show distinct allele profiles, which might be expected if different processes promoted their molecular differentiation. The two African groups showed little difference between them, and their intrapopulational variation was similar to those obtained in the African-derived South American communities. The latter showed different degrees of interpopulation variability, despite the fact that they presented almost identical average degrees of non-African admixture. The F_ST single locus estimates differed in the five sets of populations, probably due to genetic drift, indicating the need to consider population structure in the evaluation of their total variability. A high interpopulational diversity was found among Amerindian populations in relation to Brazilian African-derived isolated communities. This is probably a consequence of the differences in the patterns of gene flow and genetic drift that each of these semi-isolated groups experienced. Am J Phys Anthropol 109:425–437, 1999. © 1999 Wiley-Liss, Inc.     

Desire Work: Producing Heterosexuality in South African Pentecostal Gay Men

Gay men in Cape Town, South Africa joined a Pentecostal ministry in an attempt to produce what they understood as ‘natural’ heterosexual attraction. In this article, I explore how these gay men try to form new selves through what I call ‘desire work’, or physical and emotional micropractices and discipline. Desire is not ‘natural’, but it is produced through a multitude of engagements with cultural norms, public life, political economies, and social forces. New selves are built through concerted bodily changes and comportment [Mahmood, Saba. 2005. Politics of Piety: The Islamic Revival and the Feminist Subject. Princeton, NJ: Princeton University Press], and although gay Pentecostal men shared this process, their success was limited. I understand desire work as a response to a larger context in which many Pentecostals are disaffected with the post-apartheid government and withdraw from politics as a result. Their fears of the uncertainties of democracy pushed them to engage in optimistic fantasies of heterosexual lives, which were not often realised [Berlant, Lauren Gail. 2011. Cruel Optimism. Durham, NC: Duke University Press].     

Orphanhood and fertility in young adults: Evidence from South Africa

I study the relation between orphanhood and fertility patterns in young adults using a longitudinal survey from the city of Cape Town, South Africa. The data set combines two survey waves with a year-by-year life history calendar that records key outcomes (e.g., schooling, work, fertility). It also provides information on so-called ‘parental investments’ (time and material support), family background, and literacy and numeracy test scores. I find that orphans exhibit significantly higher rates of teenage pregnancy. In particular, teenage motherhood is 19% points more likely among (female) orphans. These results suggest that orphanhood may leave a long-lasting ‘imprint’ in terms of premature fertility, especially in teenage females.     

Nonomuraea candida sp. nov., a new species from South African soil

A novel actinomycete, strain HMC10^T, was isolated from a soil sample taken from the banks of the Gamka River in the Swartberg Nature Reserve, Western Cape Province, South Africa. Strain HMC10^T was identified as a member of the genus Nonomuraea by a polyphasic approach. Strain HMC10^T could be differentiated from other members of the genus Nonomuraea on the basis of physiology and 16S rRNA gene sequence analysis. DNA-DNA hybridization further differentiated strain HMC10^T from its nearest phylogenetic neighbour, Nonomuraea turkmeniaca NRRL B-16246^T (4.5 ± 3.8% DNA relatedness). Strain HMC10^T exhibited weak antibiosis against Mycobacterium aurum A+, but none against Mycobacterium tuberculosis H37Rv^T. The name Nonomuraea candida is proposed, with the type strain HMC10^T (= DSM 45086^T = NRRL B-24552^T). The GenBank accession number for the 16S rRNA gene sequence of Nonomuraea candida HMC10^T is DQ285421.     

Biomass and production estimates of a fish community in a small South African estuary

The fish community of the small (17·5 ha) intermittently open East Kleinemonde estuary was sampled between 1994 and 1997 to estimate population size, standing stock, growth and productivity. The estuarine-spawning species were numerically more abundant ( n c . 750 000) but due to their small size contributed only 11·7% to the total biomass. The total annual productivity of all fishes in the estuary ( n c . 890 000), with a standing stock of 28·44 g m ⁻², was calculated at 55·89 g m⁻² year⁻¹. The small sparid Rhabdosargus holubi with a production estimate of 41·35 g m⁻² year⁻¹ accounted for <74% of the total fish production in this estuary.     

Sustainable dive ecotourism on a South African coral reef

SCUBA ecotourism provides economic support for local human communities and for conservation. Such support should be sustainable and as ecologically non-destructive as possible to its coral reef foundation. In recent years, the major increase in SCUBA activity has become a significant consideration at some locations. Among these are the South African coral reefs at Sodwana Bay, which receive 80 000 dives per year. Between May 1998 and January 1999, assessments using line-intercept and belt transects showed that 5.9% of hard corals and 4.0% of soft corals were damaged from various causes, while only 0.02% of the hard corals were dead. Of the 222 diver contacts observed, only 1.63% produced instant and visually-clear damage, with no measurable decline in overall coral reef health. Direct observations on 89 recreational divers showed that photographers made damaging contacts on nine out of ten dives, while novice divers made one such contact per six dives, moderately experienced divers about once every 14 dives, and very experienced divers about once every 123 dives. Increased time lapsed since the last dive increased diver damage by novices. We calculated that the 80 000 dives were equivalent to 1 m² of reef receiving 2.3 diver contacts per year. Acropora austera was by far the most significantly damaged coral, with one out of four branches broken per year. But as this species accounted for only 0.2% of reef benthos cover, this impact was not representative of overall reef health. This heavy species-specific impact makes A. austera a good bio-monitor.     

Carpal fusions in children of four South African populations

The incidence of carpal fusions was determined from radiographs of both hands of 2,250 Pretoria schoolchildren aged 72 to 191 months. The group included White, Negro, Coloured and Indian subjects. Of the many possible varieties of carpal fusion, only lunato-triquetral fusion and capitate-hamate fusion were encountered. No examples of lunato-triquetral fusion were encountered in children less than ten years of age. In Pretoria Negroes aged 10 to 15 years, the incidence of lunato-triquetral synostosis is 4.57%, while Pretoria Coloureds show an incidence of 1.51%. This type of fusion was not noted in the White or Indian populations. Two examples of capitate-hamate synostosis were encountered in Pretoria Negroes. The available evidence suggests that these two varieties of carpal fusion may be added to the list of discrete traits varying in frequency from population to population and probably reflecting different underlying gene frequencies. No significant sex difference in incidence of lunato-triquetral fusion was noted in the present study. Lunato-triquetral fusion is about twice as commonly bilateral as unilateral in occurrence.     

Grazing and landscape controls on nitrogen availability across 330 South African savanna sites

The availability of nitrogen (N) is an important determinant of ecosystem and community dynamics for grasslands and savannas, influencing factors such as biomass productivity, plant and herbivore composition, and losses of N to waters and the atmosphere. To better understand the controls over N availability at landscape to regional scales, we quantified a range of plant and soil characteristics at each of 330 sites in three regions of South Africa: Kruger National Park (KNP), private game reserves adjacent to KNP (private protected areas – PPAs) and Hluhluwe‐iMfolozi Park (HiP). In comparing regions and sites within regions, grazing appeared to have a strong influence on N availability. Sites in the PPAs adjacent to KNP as well as sodic and alluvial sites in general typically had the highest N availability. The high N availability of these sites was not generally associated with greater potential N mineralization, but instead with less grass biomass and more forb biomass that indicated greater grazing pressure. Whereas sodic sites had a long history of high N availability as evidenced by their high soil δ¹⁵N, the greater N availability in the PPAs over the two parks appeared to be relatively recent. Grazer biomass, average potential mineralization rates and grass biomass for HiP were greater than KNP, yet there were no differences in N availability as indexed by soil and foliar δ¹⁵N between sites in the two parks. Although the short‐term increase in N availability in PPAs is not necessarily deleterious, it is uncertain whether current productivity levels in those ecosystems is sustainable. With differences in management causing herbivore biomass to be 150% greater in the PPAs than the adjacent KNP, changes in plant communities and nitrogen cycling might lead to long‐term degradation of these ecosystems, their ability to sustain herbivore populations, and also serve as an economic resource for the region.     

Fire and the chemistry of a South African mountain stream

The effects of a late-summer prescribed burn on the chemistry of a second-order mountain stream in the south-western Cape, South Africa, were investigated. Nitrate concentrations in stream water were significantly higher during the winter of the post-burn year. Increased concentrations of chloride, bicarbonate, polyphenols and potassium and decreased sodium concentrations were also recorded. Concentrations of ammonium, phosphate, calcium, magnesium, total dissolved solids and hydrogen ions were not significantly affected by the burn. Ionic export from the catchment was generally greater in the post-burn year. Apart from nitrate, however, values probably lie within the natural range of year-to-year variation. It is predicted that enhanced losses of nitrate will decrease progressively with the recovery of the vegetation and the re-establishment of soil/plant nutrient cycles. Atmospheric losses of nutrients in smoke were unquantified, but may be of more significance to site productivity than losses through surface runoff, which, in the case of nitrogen, appear to be compensated by precipitation inputs.