Faculty of Science (Research Outputs)
Permanent URI for this communityhttps://hdl.handle.net/10539/38025
Browse
46 results
Search Results
Item Draft genome sequence of the fungal pathogen Penicillium expansum (PPRI25879) isolated in South Africa(Elsevier, 2025-02) Chan, Wai Yin; Rauwane, Molemi; Figlan, Sandiswa; Ntushelo, KhayalethuObjectives: Penicillium expansum, a necrotrophic plant pathogen with a wide range of fruit hosts, is an important causal agent of blue mold rot. The fruit business suffers significant financial losses because of blue mold rot that occurs during fruit storage, transportation, and sale. The objective of this work was to generate a high-quality draft genome assembly of P. expansum, which will contribute to enhancing the management of blue mold, especially in stone and pome fruits, including grapes, by improving our understanding of the epidemiology of the pathogen and its interactions with the host. Data description: Here, we describe the genome sequence of Penicillium expansum isolate PPRI25879, one of the most virulent strains isolated from grapes in South Africa. Sequencing reads from P. expansum produced approximately 3.5 Gb. The assembly generated a draft genome of size 32.1 Mb, consisting of 1648 contigs, with an N50 of 508 KB. Examination of the genome completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the draft genome carries 97.9% of the 746 genes in the Eurotiomycetes_odb10 database. The draft genome sequence will allow improved genomic comparisons among the most important pathogens belonging to the Penicillium genus, with the aim of improving our knowledge of their plant-pathogen interactions, population biology, and control.Item Deep-crustal layered mafic complexes in the Mesoproterozoic oceanic-arc of the Tugela Terrane, South Africa(Elsevier, 2025-03) Wilson, Allan H.Layered mafic intrusions are important in understanding the generation of continental crust in oceanic arcs. The Mesoproterozoic (c. 1200 Ma) Tugela Terrane in southeast South Africa is made up of a series of thrust slices of varied rock-types purported to have been derived in oceanic arcs prior to accretion onto the southern margin of the Archean Kaapvaal Craton. They are not ophiolites. Mafic intrusions in two adjacent thrust slices are known as the Tugela Rand and Mambula Complexes. Both intrusions are intensely layered on scales of centimetres to several tens of metres but clear cyclic units are not apparent and crystal fractionation is limited indicating these were open systems with magma chamber through-flow. Tugela Rand is made up of dominantly olivine-bearing rocks ranging from dunite and pyroxenite to gabbro. In contrast, Mambula is dominantly gabbroic with only rare olivine-bearing rocks and is more evolved with layers of titaniferous-magnetite. Primary magmatic structures in both complexes include graded bedding, slumping and erosion features. Relatively high pressure of formation is indicated by the aluminous nature of the pyroxenes and corona textures by reaction between plagioclase and olivine. Chromitites in Tugela Rand range from massive to podiform with the rare orbicular variety indicating complex controls on chromite accretion. They include the high-Al compositional variety. There are no other similar chromitite occurrences in South Africa. The complexes, together with their enclosing rock-types, draw striking parallels with the lower arc crust observed in the late Cretaceous Kohistan arc complex in NE Pakistan. The Tugela Rand Complex shares many similarities with the Chilas Complex in that terrane, while the Mambula Complex is considered to be a more evolved derivative of the same magma. This study shows that generation of juvenile continental crust formation in mature island arc systems may have been firmly established by the Mesoproterozoic.Item Spatio-temporal trends in daily precipitation extremes over the Enkangala escarpment of South Africa: 1961–2021(Springer, 2025-02) Abubakar, Hadisu Bello; Scholes, Mary C.; Engelbrecht, Francois A.The Intergovernmental Panel on Climate Change in its Sixth Assessment Report reported that increases in extreme weather events can already be detected in every region in the world. For eastern southern Africa the report provides evidence of an increasing trend in extreme precipitation events, but more research is needed to understand how this change is manifesting over regions as diverse as South Africa’s eastern escarpment and northern Mozambique. This study evaluates the trends in extreme precipitation over the Enkangala Escarpment, part of South Africa’s eastern escarpment, over the period 1961 to 2021. Daily precipitation data covering 22 stations with fewer than 10% missing values over 61 years were obtained from the South African Weather Service. A total of twelve extreme events precipitation indices were computed using the ClimPACT2 package, and a time series trend analysis was performed using the Trend Free Whitening Mann Kendal test and a field significance test. The results indicate significant increasing trends in nine out of the twelve extreme events indices that were investigated. The three indices which have shown significant decreasing trends include Consecutive Wet days (CWD) at (0.03 day/year total annual rainfall (PRCPTOT) (0.61 mm/decade) and the annual count of days when precipitation≥10 mm (R10mm) of 0.32 days/decade. Indices such Rx1 days, Rx3 days and Rx5 days exhibited increasing trends of 0.2 days/decade each. Other indices with an increasing trend are CDD (3.6 day/decade), R20mm (0.2 days/decade) and R30mm (0.2 days/decade). The R95p (11.2 mm/decade) and R99p (6.0 mm/decade) indices, and Simple Daily Intensity Index(0.4 mm/decade) also exhibit positive trends over the study period. Overall the analysis is indicative of a change in the nature of rainfall over the Enkangala escarpment of South Africa, with annual rainfall totals, the number of consecutive wet days and the frequency of events with smaller thresholds such as 10 mm/day decreasing, but with extreme events of larger thresholds occurring more frequently. That is, when it rains, it tends to rain more intensely than in the past. The use of a field significance test was useful to formalise when relatively small but spatially homogeneous trends detected at separate weather stations yield statistical significance. The findings of the paper are relevant to decision and policy in multiple of socio-economic sectors active in South Africa’s eastern escarpment.Item A Technique to Solve a Parabolic Equation by Point Symmetries that Incorporate Initial Data(Springer, 2025-03) Jamal, Sameerah; Maphanga, RivoningoIn this paper, we show how transformation techniques coupled with a convolution integral can be used to solve a generalised option-pricing model, including the Black–Scholes model. Such equations are parabolic and the special convolutions are extremely involved as they arise from an initial value problem. New symmetries are derived to obtain solutions through an application of the invariant surface condition. The main outcome is that the point symmetries are effective in producing exact solutions that satisfy a given initial condition, such as those represented by a call-option.Item The synergetic effect of drought and land use changes on Ethiopian Rift Valley Northwestern Escarpment livelihood systems(Springer, 2025-02) Gidey, Eskinder; Mhangara, Paidamwoyo; Nasir, Jemal; Zeleke, Tesfaye; Assefa, Engdawork; Kahsay, Shishay; Birhane, EmiruClimate change has significantly impacted smallholder farmers in developing countries, where most livelihoods rely on rain-fed agricultural systems. The Northwestern Escarpment of the Ethiopian Rift Valley (NEERV) is among Ethiopia’s most drought-vulnerable areas and is highly affected by land use and land cover change (LULCC). This study aimed to analyze the synergistic impacts of drought and LULCC in the three major livelihood zones (LZs) of NEERV between 1983 and 2019. The study used socioeconomic, climatic, and earth observation datasets. Utilizing a mix of socioeconomic, climatic, and earth observation datasets, this paper investigated the combined effects of these factors on three major livelihood zones: Alagie-Ofla (ALOFLZ), Tsirare catchment (TCLZ), and Raya Valley (RVLZ). The analysis revealed significant rainfall variability, with annual fluctuations between 31 and 50% and seasonal variations ranging from 39 to 99%. This variability has contributed to frequent drought occurrences, with intervals of approximately 2.13 years in ALOFLZ, 2.2 years in TCLZ, and 2.13 years in RVLZ. There has been a notable increase in cultivated and built-up areas across all zones. The study found that drought and LULCC have severely impacted agricultural productivity and local ecosystems, with the most pronounced effects observed in RVLZ, TCLZ, and ALOFLZ. The findings highlight a critical need for integrated approaches to manage and monitor the synergistic impacts of drought and LULCC. The study underscores the importance of enhancing drought and LULCC monitoring systems to improve resilience and adaptability in vulnerable regions. The research contributes to a deeper understanding of how these intertwined factors exacerbate environmental and socioeconomic challenges, offering valuable insights into policy and management strategies for mitigating their effects. Recommendations include enhancing the current drought and LULCC monitoring systems to improve predictions and mitigation efforts, thus bolstering resilience and adaptability among affected communities.Item Batch and semi-continuous fermentation with Parageobacillus thermoglucosidasius DSM 6285 for H2 production(BMC, 2025) de Maayer, Pieter; Ardila, Magda S.; Aliyu, Habibu; Neumann, AnkeBackground Parageobacillus thermoglucosidasius is a facultatively anaerobic thermophile that is able to produce hydrogen (H2) gas from the oxidation of carbon monoxide through the water–gas shift reaction when grown under anaerobic conditions. The water–gas shift (WGS) reaction is driven by a carbon monoxide dehydrogenase– hydrogenase enzyme complex. Previous experiments exploring hydrogenogenesis with P. thermoglucosidasius have relied on batch fermentations comprising defned media compositions and gas atmospheres. This study evaluated the efects of a semi-continuous feeding strategy on hydrogenogenesis. Results A batch and two semi-continuous fermentations, with feeding of the latter fresh media (with glucose) in either 24 h or 48 h intervals were undertaken and H2 production, carbon monoxide dehydrogenase (CODH) activity, and metabolite consumption/production were monitored throughout. Maximum H2 production rates (HPR) of 0.14 and 0.3 mmol min−1, were observed for the batch and the semi-continuous fermentations, respectively. Daily feeding attained stable H2 production for 7 days, while feeding every 48 h resulted in high variations in H2 production. CODH enzyme activity correlated with H2 production, with a maximum of 1651 U mL−1 on day 14 with the 48 h feeding strategy, while CODH activity remained relatively constant throughout the fermentation process with the 24 h feeding strategy. Conclusions The results emphasize the signifcance of a semi-continuous glucose-containing feed for attaining stable hydrogen production with P. thermoglucosidasius. The semi-continuous fermentations achieved a 46% higher HPR than the batch fermentation. The higher HPRs achieved with both semi-continuous fermentations imply that this approach could enhance the biohydrogen platform. However, optimizing the feeding interval is pivotal to ensuring stable hydrogen production.Item New modern and Pleistocene fossil micromammal assemblages from Swartkrans, South Africa: Paleobiodiversity, taphonomic, and environmental context(Elsevier, 2024-03) Steininger, Christine; Clarke, Ronald J.; Caruana, Matthew V.; Kuman, Kathleen; Pickering, Travis Rayne; Linchamps, Pierre; Stoetzel, Emmanuelle; Amberny, LaurieThe oldest deposit at the hominin-bearing cave of Swartkrans, South Africa, is the Lower Bank of Member 1, dated to ca. 2.2 million years ago. Excavations of this unit have produced a diverse and extensive mammalian fossil record, including Paranthropus robustus and early Homo fossils, along with numerous Oldowan stone tools. The present study focuses on the taxonomic analysis of the micromammalian fossil assemblage obtained from recent excavations of the Lower Bank, conducted between 2005 and 2010, as part of the Swartkrans Paleoanthropological Research Project. The taxonomic composition of this assemblage is dominated by Mystromys, a rodent indicative of grassland environments. Taphonomic analysis indicates an accumulation of prey by Tyto alba (Barn owl) or a related species. Environments inferred from this evidence reflect an open landscape primarily covered by grassland vegetation, but they also feature components of wooded areas, rocky outcrops, and the proximity of a river. The Swartkrans fossil assemblage is compared with Cooper's D (dated to ca. 1.4 Ma) and a modern coprocoenosis of Bubo africanus (spotted eagle-owl) collected within the Swartkrans cave for taxonomic, taphonomic, and paleoecological perspectives. Contrasting fossil and modern micromammalian data provide a better understanding of accumulation processes and facilitate a diachronic reconstruction of changes in climate and landscape evolution. Issues regarding paleoenvironmental reconstruction methodologies based on micromammals are also discussed.Item Developing a density functional theory model of glassy carbon via carbon defect induction and relaxation(Elsevier, 2025-01) Falch, A.; Meerholz, K.; van Sittert, C.G.C.E.Glassy Carbon (GC) is a non-graphitising carbon known for its thermal stability, conductivity, and resistance to chemical attack, making it valuable in industrial and scientific applications, especially as an electrode substrate in catalysis research. Despite its widespread use, GC’s precise structural characteristics is unclear due to synthesis variability. This study developed and validated a computational model to simulate GC’s structure. Starting from the R3-carbon allotrope, density functional theory calculations were used to construct a representative GC model, incorporating induced defects to mimic its structural imperfections. Multiple GC slab models were created for comparative analysis. Validation involved comparing theoretical X-ray diffraction data with published data, confirming the model’s accuracy in representing the GC’s structure. The model showed high correlation with existing models, particularly those by Jurkiewicz et al., emphasizing the effect of formation temperature on GC’s structural evolution. These findings enhance the understanding of GC’s structural complexities, providing a solid foundation for future research and applications in material science, especially for robust and conductive substrates used in electrocatalysis.Item Evidence for igneous differentiation in Sudbury Igneous Complex and impact-driven evolution of terrestrial planet proto-crusts(Nature Research, 2019-01) Latypov, Rais; Chistyakova, Sofya; Grieve, Richard; Huhma, HannuBolide impact is a ubiquitous geological process in the Solar System, which produced craters and basins filled with impact melt sheets on the terrestrial planets. However, it remains controversial whether these sheets were able to undergo large-scale igneous differentiation, or not. Here, we report on the discovery of large discrete bodies of melanorites that occur throughout almost the entire stratigraphy of the 1.85-billion-year-old Sudbury Igneous Complex (SIC) – the best exposed impact melt sheet on Earth – and use them to reaffirm that conspicuous norite-gabbro-granophyre stratigraphy of the SIC is produced by fractional crystallization of an originally homogeneous impact melt of granodioritic composition. This implies that more ancient and compositionally primitive Hadean impact melt sheets on the Earth and other terrestrial planets also underwent large-volume igneous differentiation. The near-surface differentiation of these giant impact melt sheets may therefore have contributed to the evolution and lithological diversity of the proto-crust on terrestrial planets.Item The Miocene primate Pliobates is a pliopithecoid(Nature Research, 2024-04) Amélie Beaudet; Zanolli, Clément; Urciuoli, Alessandro; Almécija, Sergio; Fortuny, Josep; Robles, Josep M.; Bouchet, Florian; Moyà-Solà, Salvador; Alba, David M.The systematic status of the small-bodied catarrhine primate Pliobates cataloniae, from the Miocene (11.6 Ma) of Spain, is controversial because it displays a mosaic of primitive and derived features compared with extant hominoids (apes and humans). Cladistic analyses have recovered Pliobates as either a stem hominoid or as a pliopithecoid stem catarrhine (i.e., preceding the cercopithecoid–hominoid divergence). Here, we describe additional dental remains of P. cataloniae from another locality that display unambiguous synapomorphies of crouzeliid pliopithecoids. Our cladistic analyses support a close phylogenetic link with poorly-known small crouzeliids from Europe based on (cranio)dental characters but recover pliopithecoids as stem hominoids when postcranial characters are included. We conclude that Pliobates is a derived stem catarrhine that shows postcranial convergences with modern apes in the elbow and wrist joints—thus clarifying pliopithecoid evolution and illustrating the plausibility of independent acquisition of postcranial similarities between hylobatids and hominids.