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Population genomics analysis of yellowfin tuna Thunnus albacares off South Africa reveals need for a shifted management boundary
No full textYellowfin tuna Thunnus albacares is a commercially and economically important fisheries species, which comprises the second largest component of South Africa’s catch of tuna and tuna-like species. Catches of the species off South Africa are treated as two discrete stocks by the two tuna Regional Fisheries Management Organisations (tRFMOs) under whose jurisdictions they fall. Individuals caught off the Western Cape, west of the boundary between the tRFMOs at 20°E, are included in assessment and management of the Atlantic Ocean yellowfin tuna stock by the International Commission for the Conservation of Atlantic Tunas (ICCAT), and those caught east of this boundary are assessed and managed as part of the Indian Ocean stock by the Indian Ocean Tuna Commission (IOTC). The boundary between these stocks is based on the confluence of the two oceans in this region and does not incorporate the population structure of species. For sustainable exploitation of fisheries resources, it is important that the definition of management stocks reflects species’ biological population structure; the fine-scale stock structure of yellowfin tuna off South Africa is therefore a research priority which this study aimed to address by means of population genomics analyses. Yellowfin tuna exhibit shallow genetic differentiation over wide geographic areas, and as such traditional population genetic approaches have limited power in resolving fishery significant population structure in the species. Herein, a population genomic approach was employed, specifically, genome-wide analysis of single nucleotide polymorphisms (SNPs) discovered using a next-generation DNA sequencing approach, to confer (i) increased statistical power to detect neutral structuring reflecting population connectivity patterns and (ii) signatures of local adaptation. The mitochondrial Control Region (mtDNA CR) was also sequenced to compare the resolving power of different approaches and to permit coalescent based analyses of the species evolutionary history in the region. Neutral SNP loci revealed significant structure within the dataset (Fst=0.0043; P<0.0001); partitioning of this differentiation within the dataset indicated significant differentiation between yellowfin tuna from the Western Cape and the Gulf of Guinea in the eastern Atlantic Ocean, with no significant differentiation between individuals from the Western Cape and Western Indian Ocean regions. This indicates two population units wherein there is a separation of the Gulf of Guinea from the remaining samples (Indian Ocean including Western Cape) that are largely derived from a single genetic population. This pattern was also supported by assignment tests. Positive outlier SNPs, exhibiting signatures of diversifying selection, suggest that individuals from these regions may be locally adapted, as well as demographically isolated. The mtDNA CR did not reveal any significant genetic structure among samples (Fst=0.0030; P=0.309), demonstrating the increased resolving power provided by population genomics approaches, but revealed signatures of historical demographic fluctuations associated with glacial cycles. Based on the findings of this study, it is suggested that yellowfin tuna caught off the Western Cape of South Africa are migrants from the Indian Ocean population, exhibiting significant genetic differentiation from the Atlantic Ocean Gulf of Guinea individuals, and should thus be included in the assessment and management of the Indian Ocean stock. It is therefore recommended that the boundary between the Atlantic and Indian Ocean yellowfin tuna stocks, under the mandates of ICCAT and the IOTC respectively, should be shifted to approximately 13.35°E to include all individuals caught in South African waters in the Indian Ocean stock.National Research Foundatio
The Association of HLA Class II Genetic and Expression Level Variation with response to the Hepatitis B Vaccine in South African laboratory workers
No full textThe hepatitis B virus (HBV) vaccine has contributed greatly to decreasing the HBV epidemic. However, it remains unclear why 5-10% of individuals do not mount an adequate antibody response. Previous studies have shown that genetic variation influences HBV vaccine response. Since such studies are lacking in South African individuals, we examined the associations between HBV vaccine response and genetic variation in HLA-DPB1, additional candidate genes and HLA-DPB1 expression levels in a South African cohort. HLA-DPA1 and -DPB1 allele typing was performed using Luminex technology, twenty-four candidate SNPs were typed by MassArray Analysis and HLA-DPB1 mRNA expression levels were measured by qPCR. HLA-DPB1*01:01, *04:01:01G and *09:01 and SNPs and haplotypes in IL1B, IL4, IL12B, IFNG and the HLA region were significantly associated with HBV vaccine response. A trend of lower HLA-DPB1 expression associating with better anti-HBs response was observed, although this was not significant. Response to the HBV vaccine is multi-genic but HLA-DP plays an important role.National Research Foundatio
Noninvasive measurement of dynamic correlations in spin systems
No full textNational Research Foundatio
Inhalable particulate systems for anti-tubercular drug delivery
No full textTuberculosis (TB) is a deadly infectious microbial disease that is currently dominating public health concerns. Among the pharmacological issues in the management of TB are the poor bioavailability of some anti-TB drugs, mostly due to the fast first-pass metabolism, and high drug load needed for combination therapy. These result in a lengthy treatment with several adverse effects causing decreased patient compliance. These factors often lead to the therapeutic failure and promote the development of drug resistant strains, justifying the urgent need for new therapeutic strategies. Liposomes are lipid-based particulate vehicles known to be the most clinically appointed drug carriers currently. Liposomal systems are reported to be rapidly engulfed by macrophages - where the mycobacterium often resides. This makes liposomes appropriate vehicles for targeted anti-TB drug delivery. Many research groups have reported the potential of liposomes systems to deliver anti-TB drugs. However, the costly formulation status of liposomes, due the use of expensive synthetic or highly purified natural phospholipids, is a limitation to the treatment of a poverty related infectious disease like TB. The aim of this study was to design and develop liposomes for pulmonary delivery of anti-TB drugs using crude soybean lecithin (CL) and its purirified version. CL is an FDA- approved naturally occurring phospholipid mixture that is quite cheap and readily available. Various liposome batches were prepared using a film hydration method and characterized by dynamic light scattering (DLS) and transmission electron microscopy (TEM). Liposomes composed of CL and cholesterol (Chol) in a 3:1 mass ratio were selected for drug encapsulation based on the following characteristics: polydispersity index (PDI, 0.28), mean particles sizes (PS, 502 nm) and zeta potential (ZP, -56 mV). Isoniazid (INH) was encapsulated as a model drug using a freeze-thaw loading technique and an HPLC method was validated for quantitative analysis. The physicochemical properties of INH-loaded liposomes were comprehensively investigated using thermal, microscopy and spectroscopic techniques. This formulation showed a high encapsulation efficiency (%EE) of 78%, much better than the liposomes made from purified lecithin, 20%. Other characteristics of INH- loaded liposomes, which make them attractive for pulmonary TB therapy, are presented in this dissertation. These include a controlled release of 50% of the encapsulated INH over 12 hours. Finally, rifampicin (RIF) was added as a hydrophobic model drug and several evaluations were conducted on these dual drug-loaded liposomes. Of particular interest, it was noted that the dual drug-loaded liposomes made of CL alone showed the highest %EE (59% for INH and 90% for RIF) compared to those containing Chol or those made of purified lecithin. Surprisingly, the average PS of the dual CL-based liposomes (1114 nm) was in the size range reported for optimum deep lung deposition and macrophage uptake. In addition, the mean ZP of these liposomes (-63 mV) seems to be favourable for their shelf stability and internalization by macrophages. Overall, these findings show that the dual CL-based liposomes developed would be promising for macrophage-targeting pulmonary delivery of anti-TB drugs.National Research Foundation (South Africa
A multilevel examination of the moderating role of diversity and tutorial language on intergroup contact in the first-year psychology tutorial programme at Stellenbosch University
No full textNational Research Foundatio
Aerosol trace metal concentration and dissolution characteristics from known dust emitters in southern Africa
No full textDust can be a source of micronutrients to surrounding areas such as oceans and terrestrial regions. The deposition of dust can provide trace elements to the open oceans, which can increase primary production and
ultimately remove carbon dioxide from the atmosphere, therefore reducing global warming. Previous remote
sensing studies have shown that southern African is a prominent dust emitting region and can potentially
provide micronutrients to oceanic regions which might be depleted in some bioactive trace elements. Hysplit
modeling software was used to estimate the long distance transport of dust emissions observed in southern
Africa between January 2005 and December 2008. The observations revealed that most of the dust emissions
occur during spring and winter seasons, with very little emissions in autumn. Most of the dust emissions tend
to travel off the Namibian coastline towards the north-west Africa regions and are mainly influenced by strong
south easterly trade winds. A strong air mass migrates towards the Indian Ocean and as far as the Australian
continent due to the effects of the westerlies. Fewer air masses travel towards the nutrient-limited regions of
the Atlantic Southern Ocean and central eastern Indian Ocean. The locations further north of the southern
Africa preferentially travel towards the north west Atlantic Ocean, because the westerlies are not strong enough
to transport air-masses towards the southern oceanic regions. This study also revealed that the prominent dust
emitting sites in southern Africa are two ephemeral rivers, Kuiseb and Omaruru River as well as two ephemeral
pans, the Etosha Pan in Namibia and Makgadikgadi Pan in Botswana. Emissions from these sources tend to
travel towards north west Atlantic Ocean and south east Indian Ocean, with the exception of the Etosha Pan,
which has emissions that travel towards the northern regions.
These emitters were investigated for particle size distribution, mineralogical characteristics and trace elemental
concentrations. The role of ephemeral rivers in southern Africa as potential sources of micronutrients to marine
environments has not been previously investigated extensively. Most previous studies focussed on the
ephemeral pans. Particle sizes can be an indicator of how far the sediments can potentially travel and of the
trace elemental solubility. Etosha Pan has the finest grain sizes, while the Makgadikgadi had the coarsest grain
size. Omaruru and Kuiseb River showed medium grain size variation. Our dissolution experiments showed,
however, that the dissolution of the sediments is mostly influenced by the mineralogy rather than the particle
sizes. The two pans appeared to be enriched in calcite, silica oxide and quartz, while the two rivers were more
enriched in kaolinite, quartz, illite and muscovite. High trace element solubility in the Etosha Pan is most
probably attributed to the high calcite content, which is highly soluble. A continuous flow through method
proved to be effective and inexpensive. This study is one of the few in southern Africa which aimed at
modelling the air mass pathways from dust emissions that have been observed instead of just creating
simulations. Our findings highlight the importance of additional studies to prove the dissolution and quality of
dust in dry regions as potential contributors to marine primary production.National Research Foundatio
Two new goatfishes of the genus Upeneus (Mullidae) from Australia and Indonesia
No full textTwo new goatfishes of the genus Upeneus (Mullidae) belonging to the putative japonicus species group are described and compared with congeneric species using a large set of meristic, morphometric and colour characters. Upeneus farnis n. sp. Uiblein & Peristiwady is described based on 14 adult specimens (> 65 mm SL) collected at the local fish market of Bitung, NE Sulawesi, Indonesia. Upeneus spottocaudalis n. sp. Uiblein & Gledhill is described based on 16 adult and seven subadult specimens (< 65 mm SL) specimens collected by trawling surveys off NE Australia and one non-type adult specimen collected off southern Indonesia. The new species differ from all other congenerics in the combination of dorsal-fin spine, pectoral-fin ray and gill raker numbers, body and head depth, length of head, snout, barbels and paired fins, height of anal and dorsal fins, eye size, and body, barbel and caudal-fin colour patterns. When compared in detail with the 12 other species of the japonicus group, Upeneus farnis n. sp. can be distinguished by smaller eyes, shallower anal and second dorsal fins, more pectoral-fin rays and gill rakers, and the lower caudal-fin lobe almost completely dark pigmented. Upeneus spottocaudalis n. sp. differs from the other japonicus-group species in larger eyes, higher second dorsal fin, pectoral fin shorter than pelvic fin, and presence of rounded, dark spots on the lower caudal-fin lobe. Subadults differ from adult U. spottocaudalis n. sp. mainly in longer pelvic fins. The high diversity of Upeneus species in relation to divergence in colour patterns and the need of further taxonomic exploration of the genus Upeneus is discussed
Uncovering a hidden diversity: two new species of Breviceps (Anura: Brevicipitidae) from northern KwaZulu-Natal, South Africa
No full textBreviceps carruthersi sp. nov. and Breviceps passmorei sp. nov. are described from northern KwaZulu-Natal. Both new species are distinguished from B. adspersus, B. mossambicus, B. poweri and B. cf. sopranus by substantial interspecific genetic divergence (> 6.8 uncorrected p-distance) in the mitochondrial 16S rRNA gene, differences in advertisement call structure and limited morphological variation. Breviceps carruthersi sp. nov. has a short, pulsatile call with minimal amplitude modulation and groups its calls. Breviceps passmorei sp. nov. differs significantly from B. adspersus and B. mossambicus in call duration and pulse number, but not in pulse rate or dominant frequency. For both new species morphological characters are of limited diagnostic value, necessitating a re-evaluation of the taxonomic status of populations currently assigned to B. adspersus and B. mossambicus in KwaZulu-Natal
Mental health care providers talk about suicide prevention among people with substance use disorders in South Africa
No full textNational Research Foundatio
Designing travel behaviour change interventions: a spatiotemporal perspective
No full textNational Research Foundatio