Faculty of Science (Research Outputs)

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    Batch and semi-continuous fermentation with Parageobacillus thermoglucosidasius DSM 6285 for H2 production
    (BMC, 2025) de Maayer, Pieter; Ardila, Magda S.; Aliyu, Habibu; Neumann, Anke
    Background 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.
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    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, Laurie
    The 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.
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    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.
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    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, Hannu
    Bolide 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.
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    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.
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    Confocal microscopy and molecular analyses reveal anal secretory apparatus in immatures and recover transcontinental Clade of Gall Mites (Eriophyoidea) from Tamarisks
    (MDPI, 2024-04) Sivu, Situngu; Chetverikov , Philipp E.; Ngubane-Ndhlovu, Nompumelelo P.; Elhalawan, Ashraf; Amrine, James
    Tamarisk is an invasive evergreen shrub native to arid regions of Africa and Eurasia and is considered a weed in some countries with dry climates. The complex of gall mites from tamarisks includes fourteen species from four genera of the family Eriophyidae. We reinvestigated the type species of the genus Dicruvasates, D. tamaricis from Egypt, described D. ngubani n. sp. from Tamarix usneoides from South Africa, and revised the generic concept of Dicruvasates. This genus possesses cuticular plates marking longitudinal opisthosomal ridges typical of various phyllocoptine genera, e.g., Echinacrus. We sequenced three genes of Dicruvasates and Phyllocoptes mites from Tamarix and Echinacrus from Frangula, combined our sequences with the data from GenBank, and performed single-gene phylogenetic analyses. All analyses inferred the following: (1) a transcontinental clade Tam comprising Dicruvasates + Aceria + Phyllocoptes from Tamarix; (2) Echinacrus distantly related to Dicruvasates, suggesting the homoplastic nature of the cuticular plates on the opisthosomal ridges, and (3) polyphyly of the genera Aceria and Phyllocoptes. We also investigated partially cleared specimens of Dicruvasates under CLSM and, for the first time, visualized a well-developed anal secretory apparatus (ASA) in the immatures of gall mites, which was previously shown to be a specialized system evolved in Eriophyoidea for silk production. We hypothesize that the ASA contributes to finding nymphs by conspecific males and advocate for the importance of the future molecular biology studies of gall mite silk for developing new methods for controlling mites based on the knowledge of their ecology, behavior, and silk gene genetics.
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    Temporal shifts in landscape connectivity for an ecosystem engineer, the roe deer, across a multiple-use landscape
    (Springer, 2018-04) Martin, Jodie; Vourc’h, Gwenae¨l; Bonnot, Nade`ge; Cargnelutti, Bruno; Chaval, Yannick; Lourte, Bruno; Goulard, Michel; Hoch, Thierry; Plantard, Olivier; Hewison, A. J. Mark; Morellet, Nicolas
    Context: Routine movements of large herbivores, often considered as ecosystem engineers, impact key ecological processes. Functional landscape connectivity for such species influences the spatial distribution of associated ecological services and disservices. Objectives: We studied how spatio-temporal variation in the risk-resource trade-off, generated by fluctuations in human activities and environmental conditions, influences the routine movements of roedeer across a heterogeneous landscape, generating shifts in functional connectivity at daily and seasonal time scales. Methods: We used GPS locations of 172 adult roedeer and step selection functions to infer landscape connectivity. In particular, we assessed the influence of six habitat features on fine scale movements across four biological seasons and three daily periods, based on variations in the risk-resource trade-off. Results: The influence of habitat features on roe deer movements was strongly dependent on proximity to refuge habitat, i.e. woodlands. Roe deer confined their movements to safe habitats during daytime and during the hunting season, when human activity is high.
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    Platinum-bearing chromite layers are caused by pressure reduction during magma ascent
    (Nature Research, 2018) Latypov, Rais; Costin, Gelu; Chistyakova, Sofya; Hunt, Emma J.; Mukherjee, Ria; Naldrett, Tony
    Platinum-bearing chromitites in mafic-ultramafic intrusions such as the Bushveld Complex are key repositories of strategically important metals for human society. Basaltic melts saturated in chromite alone are crucial to their generation, but the origin of such melts is controversial. One concept holds that they are produced by processes operating within the magma chamber, whereas another argues that melts entering the chamber were already saturated in chromite. Here we address the problem by examining the pressure-related changes in the topology of a Mg2SiO4–CaAl2Si2O8–SiO2–MgCr2O4 quaternary system and by thermodynamic modelling of crystallisation sequences of basaltic melts at 1–10 kbar pressures. We show that basaltic melts located adjacent to a so-called chromite topological trough in deep-seated reservoirs become saturated in chromite alone upon their ascent towards the Earth’s surface and subsequent cooling in shallow-level chambers. Large volumes of these chromite-only-saturated melts replenishing these chambers are responsible for monomineralic layers of massive chromitites with associated platinum-group elements.
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    Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data
    (BMC, 2018) Ceballos, Francisco C.; Hazelhurst, Scott; Ramsay, Michèle
    Background: Runs of Homozygosity (ROH) are genomic regions where identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits and diseases. ROH studies have predominantly exploited SNP array data, but are gradually moving to whole genome sequence (WGS) data as it becomes available. WGS data, covering more genetic variability, can add value to ROH studies, but require additional considerations during analysis. Results: Using SNP array and low coverage WGS data from 1885 individuals from 20 world populations, our aims were to compare ROH from the two datasets and to establish software conditions to get comparable results, thus providing guidelines for combining disparate datasets in joint ROH analyses. By allowing heterozygous SNPs per window, using the PLINK homozygosity function and non-parametric analysis, we were able to obtain non-significant differences in number ROH, mean ROH size and total sum of ROH between data sets using the different technologies for almost all populations. Conclusions: By allowing 3 heterozygous SNPs per ROH when dealing with WGS low coverage data, it is possible to establish meaningful comparisons between data using SNP array and WGS low coverage technologies.
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    Entanglement beating in free space through spin–orbit coupling
    (Springer Nature, 2018) Rosales-Guzmán, Carmelo; Denz, Cornelia; Otte, Eileen; Ndagano, Bienvenu; Forbes, Andrew
    It is well known that the entanglement of a quantum state is invariant under local unitary transformations. This rule dictates, for example, that the entanglement of internal degrees of freedom of a photon remains invariant during free-space propagation. Here, we outline a scenario in which this paradigm does not hold. Using local Bell states engineered from classical vector vortex beams with non-separable degrees of freedom, the so-called classically entangled states, we demonstrate that the entanglement evolves during propagation, oscillating between maximally entangled (purely vector) and product states (purely scalar). We outline the spin–orbit interaction behind these novel propagation dynamics and confirm the results experimentally, demonstrating spin–orbit coupling in paraxial beams. This demonstration highlights a hitherto unnoticed property of classical entanglement and simultaneously offers a device for the on-demand delivery of vector states to targets, for example, for dynamic laser materials processing, switchable resolution within stimulated emission depletion (STED) systems, and a tractor beam for entanglement.