Faculty of Science

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The Faculty of Science is respected within South Africa, Africa and the world arena as a knowledge-partner of note that builds on the scientific, technological and intellectual capacity of Africa and plays an active role in the development of South African society. The faculty is placed in the top 300 within the category Natural Sciences of the QS World University Ranking list.

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1-tert-Butyl 2-ethyl 5-bromo-3-(thiophen-2-ylcarbonyl)-1H-indole-1,2-dicarboxylate
(International Union of Crystallography, 2013-01-16) Hassam, Mohammad; Smith, Vincent J.
ENGLISH ABSTRACT: In the title compound, C21H20BrNO5S, the thiophene group is located above the mean plane of the indole ring and displays rotational disorder (i.e. rotation through 180). The site occupancy of the major component is 0.902 (2), while that of the minor component is 0.098 (2). In the crystal, pairs of weak C—HO interactions link the molecules into centrosymmetric dimers.
11-ketotestosterone and 11-ketodihydrotestosterone in castration resistant prostate cancer : potent androgens which can no longer be ignored
(Public Library of Science, 2016) Pretorius, Elzette; Africander, Donita J.; Vlok, Mare; Perkins, Meghan S.; Quanson, Jonathan; Storbeck, Karl-Heinz
Dihydrotestosterone (DHT) is regarded as the most potent natural androgen and is implicated in the development and progression of castration resistant prostate cancer (CRPC). Under castrate conditions, DHT is produced from the metabolism of the adrenal androgen precursors, DHEA and androstenedione. Recent studies have shown that the adrenal steroid 11β-hydroxyandrostenedione (11OHA4) serves as the precursor to the androgens 11-ketotestosterone (11KT) and 11-ketodihydrotestosterone (11KDHT). In this study we comprehensively assess the androgenic activity of 11KT and 11KDHT. This is the first study, to our knowledge, to show that 11KT and 11KDHT, like T and DHT, are potent and efficacious agonists of the human androgen receptor (AR) and induced both the expression of representative AR-regulated genes as well as cellular proliferation in the androgen dependent prostate cancer cell lines, LNCaP and VCaP. Proteomic analysis revealed that 11KDHT regulated the expression of more AR-regulated proteins than DHT in VCaP cells, while in vitro conversion assays showed that 11KT and 11KDHT are metabolized at a significantly lower rate in both LNCaP and VCaP cells when compared to T and DHT, respectively. Our findings show that 11KT and 11KDHT are bona fide androgens capable of inducing androgen-dependant gene expression and cell growth, and that these steroids have the potential to remain active longer than T and DHT due to the decreased rate at which they are metabolised. Collectively, our data demonstrates that 11KT and 11KDHT likely play a vital, but overlooked, role in the development and progression of CRPC.
11β-Hydroxyandrostenedione returns to the steroid arena : biosynthesis, metabolism and function
(MDPI, 2013-10) Bloem, Liezl M.; Storbeck, Karl-Heinz; Schloms, Lindie; Swart, Amanda C.
The biological significance of 11β-hydroxyandrostenedione (11OHA4) has eluded researchers for the past six decades. It is now known that 11OHA4 is biosynthesized in the androgen arm of the adrenal steroidogenesis pathway and subsequently metabolized by steroidogenic enzymes in vitro, serving as precursor to recognized and novel androgenic steroids. These in vitro findings extend beyond the adrenal, suggesting that 11OHA4 could be metabolized in steroid-responsive peripheral tissues, as is the case for androgen precursor metabolites of adrenal origin. The significance thereof becomes apparent when considering that the metabolism of 11OHA4 in LNCaP androgen dependent prostate cancer cells yields androgenic steroid metabolites. It is thus possible that 11OHA4 may be metabolized to yield ligands for steroid receptors in not only the prostate but also in other steroid-responsive tissues. Future investigations of 11OHA4 may therefore characterize it as a vital steroid with far-reaching physiological consequences. An overview of the research on 11OHA4 since its identification in 1953 will be presented, with specific focus on the most recent works that have advanced our understanding of its biological role, thereby underscoring its relevance in health and disease.
A 195Pt Nuclear magnetic resonance and molecular dynamics computer simulation study of the solvation of simple platinum (IV) chlorido complex anions in water and water-miscible solvent mixtures
(2017-03) Engelbrecht, Leon de Villiers; Koch, Klaus R.; Stellenbosch University. Faculty of Science. Dept. of Chemistry and Polymer Science.
ENGLISH ABSTRACT: A combined 195Pt NMR spectroscopy and Molecular Dynamics (MD) computer simulation study of the solvation of the octahedral Pt(IV) complex [PtCl6]2‒ in binary mixtures of water and the fully water-miscible organic solvents methanol, 2-methoxyethanol and 1,2-dimethoxyethane has been carried out. A recent 195Pt NMR chemical shift-trends study indicated a preferential solvation of the aforementioned platinum complex by the organic solvent component in such solvent mixtures. The solvent dependence of the intrinsic 1Δ195Pt(37/35Cl) NMR isotope shifts of [PtCl6]2‒ in pure solvents indicate a slight increase in magnitude ~7 ppb in the order water < methanol < 2-methoxyethanol < 1,2-dimethoxyethane. In selected equimolar binary mixtures of water and organic solvents, 1Δ195Pt(37/35Cl) is found to be similar in magnitude to that in the pure organic solvents, supporting the proposed preferential solvation of the platinum complex. 195Pt NMR T1 spin relaxation times and pulsed gradient spin echo (PGSE) translational diffusion measurements were performed for [PtCl6]2‒ in selected solvents and binary mixtures. The results were interpreted in the context of hydrodynamic continuum models of molecular diffusion; while these were found to be not strictly appropriate, the rotational and translational dynamics results appear to be notionally consistent with the preferential solvation phenomenon as indicated. A series of classical MD computer simulations were performed for [PtCl6]2‒ in these equimolar binary solvent mixtures, using a recently revised force field developed by Naidoo et al. The results using the standard force field indicate a strong preference for water in the primary solvation shell region of the complex in all solvent mixtures studied. A similar result is obtained for [PtCl4]2‒ in an equimolar water‒methanol mixture. Simulations were repeated with ionic charges scaled according to the recently developed Molecular Dynamics in Electronic Continuum (MDEC) theory, which is intended to account for the dielectric screening of charges in condensed phases. In these MDEC simulations, a significant reduction in the contribution of water to the primary solvation shells of both complexes is observed; this is particularly evident in the solvation shell of [PtCl6]2‒ in mixtures of water with 2-methoxyethanol and 1,2-dimethoxyethane, for which a strong preferential solvation by the organic components has been indicated. Dynamic properties were also computed from MD trajectories, and are qualitatively consistent with experimental trends, but deviate due to the solvent model combination. Finally, an interpretation of the fascinating 35/37Cl and 16/18O isotope-induced fine structure in the 195Pt NMR spectra of complexes of the type [PtCln(OH)6‒n]2‒, n = 0‒5, is presented, based on the expected trans-influence series of ligands for Pt(IV) OH‒ > Cl‒ > H2O in aqueous solution.
36 Chlorine isotope systematics in saline groundwater in the Buffels River Valley
(Stellenbosch : Stellenbosch University, 2018-03) Van Gend, Jani; Miller, Jodie A.; Clarke, Catherine E.; Stellenbosch University. Faculty of Science. Dept. of Earth Sciences.
ENGLISH ABSTRACT: It is typical for coastal aquifers in arid regions to be affected by salinisation, populations in these areas that rely upon groundwater resources are often directly afflicted by this phenomenon. Large parts of the western coast of South Africa are affected by variably saline groundwater as a result of varying degrees of salinisation, primarily driven by evaporative processes. Initial stable δ2H and δ18O isotopic investigations suggest rainfall and groundwaters carry evaporative signatures, further investigation has suggested that there are other significant salt contributors in the region, although these sources and pathways are poorly constrained. One such alternate salt source may arise from paleo-termite mounds, called heuweltjies, that are found in areas along the west coast. These structures typically consist of salt- and nutrient-rich sediments and the recorded sediment EC values for these structures are an order of magnitude higher than that of the adjacent interheuweltjies. Furthermore, sediment EC values of heuweltjies increase with depth and the difference between deep and shallow EC values in heuweltjies are between 1000 and 3000 μS/cm, with the deeper samples having the higher EC value. The possibility of heuweltjie salts entering the groundwater system and contributing to groundwater salinisation in this area has not been investigated as yet. The town of Buffels Rivier in the western region of the Northern Cape has limited surface water resources and is dependent on local groundwater for subsistence. For this reason, it is an ideal site to investigate these atypical salinisation drivers. In order to effectively isolate the additional salt sources, several geochemical, isotopic and geophysical methods were implemented. Highly variable soil and groundwater EC values were observed in the field area. Furthermore, 36Cl isotope ratios together with noble gas data provides some evidence that aquifer mixing occurs. This is further evidenced by the spatial discontinuity in groundwater 87Sr/86Sr ratios. The geology of this area consist of basement granite gneisses and the contribution of rock salt to the groundwater cannot be excluded. 87Sr/86Sr ratios in groundwater in the Buffels River Valley are elevated, ranging between 0.73030 and 0.78240, which is typically associated with the water-rock interaction granitic rocks. The extent of the salt contribution from the various systems in the Buffels River Valley is still not fully understood but it is evident that conventional, semi-arid salinisation through evaporation is not the only driver in this regional system.
3D numerical techniques for determining the foot of a continental slope
(Stellenbosch : Stellenbosch University, 2004-12) Pantland, Nicolette Ariana; Van Vuuren, J. H.; Stellenbosch University. Faculty of Science. Dept. of Mathematical Sciences.
ENGLISH ABSTRACT: The United Nations Convention on the Law of the Sea (UNCLOS) provides an opportunity for qualifying coastal signatory states to claim extended maritime estate. The opportunity to claim rests on the precept that in certain cases a continental shelf extends beyond the traditionally demarcated two hundred nautical mile (200M) Exclusive Economic Zone (EEZ) mark. In these cases a successful claim results in states having sovereign rights to the living and non-living resources of the seabed and subsoil, as well as the sedentary species, of the area claimed. Where the continental shelf extends beyond the 200M mark, the Foot of the Continental Slope (FoS) has to be determined as one of the qualifying criteria. Article 76 of UNCLOS de nes the FoS as ". . . the point of maximum change in the gradient at its base." Currently Caris Lots is the most widely used software which incorporates public domain data to determine the FoS as a step towards defining the offshore extent of an extended continental shelf. In this software, existing methods to compute the FoS are often subjective, typically involving an operator choosing the best perceived foot point during consideration of a two dimensional profile of the continental slope. These foot points are then joined by straight lines to form the foot line to be used in the desk top study (feasibility study). The purpose of this thesis is to establish a semi-automated and mathematically based three dimensional method for determination of the FoS using South African data as a case study. Firstly, a general background of UNCLOS is given (with emphasis on Article 76), including a brief discussion of the geological factors that influence the characteristics of a continental shelf and thus factors that could influence the determination of the FoS. Secondly, a mathematical method for determination of the surfaces of extremal curvature (on three dimensional data), originally proposed by Vanicek and Ou in 1994, is detailed and applied to two smooth, hypothetical sample surfaces. A discussion of the bathymetric data to be used for application introduces the factors to be taken into account when using extensive survey data as well as methods to process the raw data for use. The method is then applied to two sets of gridded bathymetric data of differing resolution for four separate regions around the South African coast. The ridges formed on the resulting surfaces of maximum curvature are then traced in order to obtain a foot line definition for each region and each resolution. The results obtained from application of the method are compared with example foot points provided by the subjective two dimensional method of computation within the Caris Lots software suite. A comparison of the results for the different resolutions of data is included to provide insight as to the effectiveness of the method with differing spatial coarseness of data. Finally, an indication of further work is provided in the conclusion to this thesis, in the form of a number of recommendations for possible adaptations of the mathematical and tracing methods, and improvements thereof.
3D position estimation of sports players through multi-view tracking
(Stellenbosch : University of Stellenbosch, 2010-12) Vos, Robert (Robbie); Brink, Willie; Herbst, Ben; University of Stellenbosch. Faculty of Science. Dept. of Mathematical Sciences.
ENGLISH ABSTRACT: Extracting data from video streams and using the data to better understand the observed world allows many systems to automatically perform tasks that ordinarily needed to be completed by humans. One such problem with a wide range of applications is that of detecting and tracking people in a video sequence. This thesis looks speci cally at the problem of estimating the positions of players on a sports eld, as observed by a multi-view camera setup. Previous attempts at solving the problem are discussed, after which the problem is broken down into three stages: detection, 2D tracking and 3D position estimation. Possible solutions to each of the problems are discussed and compared to one another. Motion detection is found to be a fast and e ective solution to the problem of detecting players in a single view. Tracking players in 2D image coordinates is performed by implementing a hierarchical approach to the particle lter. The hierarchical approach is chosen as it improves the computational complexity without compromising on accuracy. Finally 3D position estimation is done by multiview, forward projection triangulation. The components are combined to form a full system that is able to nd and locate players on a sports eld. The overall system that is developed is able to detect, track and triangulate player positions. The components are tested individually and found to perform well. By combining the components and introducing feedback between them the results of the individual components as well as those of the overall system are improved.
A 3D Virtual Environment Development Platform for ASD Therapy Tools
(Stellenbosch : University of Stellenbosch, 2009-12) Chamberlain, Morne Edward; Van Zijl, L.; University of Stellenbosch. Faculty of Science. Dept. of Mathematical Sciences. Computer Science.
ENGLISH ABSTRACT: The aim of this thesis is to develop a generic 3D virtual environment development platform for autism spectrum disorder (ASD) therapy tools. The potential of using computerised therapy tools for ASD therapy is well known. However, the development of such tools is expensive and time-consuming, and is language and culture speci c. This work intends to alleviate these problems. The design of the platform is based on known game engine designs, but adapted for the requirements of ASD therapy tools. It supports standard features such as 3D rendering, animation and audio output. Speci c features, aimed at ASD therapy tools and educational games, included in our engine are: replays, data capturing, remote monitoring over a network and language localisation. We also implemented an input hardware abstraction layer to allow support for non-standard input peripherals in the future, without modifying existing game implementations. Furthermore, to separate the development of games and tools from the engine, we include wrapper libraries in our engine for Lua and Java. We successfully developed our engine and implemented a number of prototype therapy tools and educational games. These implementations confirmed that the engine works as expected. Some of these programs are currently in use at a local primary school.
4-Aza-Podophyllotoxins: synthesis and use as anti-cancer agents
(Stellenbosch : Stellenbosch University, 2020-03) Gould, Khaya TImothy; Van Otterlo, Willem A. L.; Blackie, Margaret; Stellenbosch University. Faculty of Science. Dept. of Chemistry and Polymer Science.
ENGLISH ABSTRACT: Podophyllotoxins, and their derivatives, have shown significant anti-proliferative properties. Etoposide and other semi-synthetic analogues, such as teniposide, have been successfully employed as clinical anti-cancer agents. 4-Aza-podophyllotoxins, which are structurally simplified synthetic analogues of podophyllotoxin, have been successfully synthesised and have shown comparable biological activity to the naturally occurring (-) podophyllotoxin. To further investigate the method of inhibition of this class of compounds, which have been reported to act as either tubulin inhibitors or topoisomerase II poisons, two libraries of 4-aza-podophyllotoxin analogues were synthesised. The biological test results from the first library of analogues was used to inform the synthesis of a second library of compounds. The first library contains a diverse group of twelve 4-aza- podophylltoxin analogues, six with differences in the 4N- position. Half of these compounds were modelled after etoposide, and half modelled after the naturally-occurring (-)-podophyllotoxin. This was achieved through N- functionalization of the starting material, an aniline, prior to its use in a multicomponent reaction with tetronic acid and a functionalized benzaldehyde. The second library of four compounds was generated using an azide alkyne cycloaddition to modify two alkyne-containing compounds from the first library. The first library has shown IC50 values of nano-molar concentrations (125-250 nM) against a WHCO1 oesophageal cell line assay. A small structure activity relationship from these biological results was obtained.
4-Benzyloxylonchocarpin and muracatanes A-C from Ranunculus muricatus L. and their biological effects
(MDPI, 2020-11-17) Hussain, Hidayat; Ali, Iftikhar; Wang, Daijie; Mamadalieva, Nilufar Z.; Hussain, Wahid; Csuk, Rene; Loesche, Anne; Fischer, Lucie; Staerk, Dan; Anam, Syariful; AlZain, Mashail N.; Mushtaq, Maria; Ul-Haq, Zaheer; Ullah, Riaz; Noman, Omar M.; Abbas, Ghulam; Green, Ivan R.
ENGLISH ABSTRACT: Ranunculus muricatus L. is a spiny fruit buttercup that is used in various traditional medicinal systems. In the current investigation of R. muricatus, the new chalcone 4-benzyloxylonchocarpin (1), the new anthraquinone muracatanes A (2), the new-to-nature anthraquinone muracatanes B (3), and the new naphthalene analog muracatanes C (4) were isolated, in addition to the three previously reported compounds, 4-methoxylonchocarpin (5), β-sitosterol (6), and β-sitosterol β-D-glucopyranoside (7). Their structures were elucidated using 1D (1H and 13C) and 2D (COSY, HSQC, and HMBC) NMR spectroscopy and HR-ESI-MS. Chalcone 1 showed potent acetylcholinesterase inhibitory effects with Ki of 5.39 µM and Ki′ of 3.54 µM, but none of the isolated compounds showed inhibitory activity towards butyrylcholinesterase. Anthraquinone 3 illustrated α-glucosidase inhibitory effects with IC50-values of 164.46 ± 83.04 µM. Compound 5 displayed moderate cytotoxic activity towards ovarian carcinoma (A2780, IC50 = 25.4 µM), colorectal adenocarcinoma (HT29, IC50 = 20.2 µM), breast cancer (MCF7, IC50 = 23.7 µM), and thyroid carcinoma (SW1736, IC50 = 26.2 µM) while it was inactive towards pharynx carcinoma (FaDu: IC50 > 30 µM).
50 years of Emmonsia disease in humans : the dramatic emergence of a cluster of novel fungal pathogens
(Public Library of Science, 2015) Schwartz, Ilan S.; Kenyon, Chris; Feng, Peiying; Govender, Nelesh P.; Dukik, Karolina; Sigler, Lynne; Jiang, Yanping; Stielow, J. Benjamin; Munoz, Jose F.; Cuomo, Christina A.; Botha, Alfred; Stchigel, Alberto M.; De Hoog, G. Sybren
New species of Emmonsia-like fungi, with phylogenetic and clinical similarities to Blastomyces and Histoplasma, have emerged as causes of systemic human mycoses worldwide. They differ from classical Emmonsia species by producing a thermally-dependent, yeast-like phase rather than adiaspores, and by causing disseminated infections, predominantly in immunocompromised patients and often with high case-fatality rates. Such differences will be important for clinicians to consider in diagnosis and patient management, and for microbiologists who may encounter these fungi with increasing frequency.
59Co NMR, a tool for the study of the structure, reactivity and supramolecular chemistry of Co(III) complexes derived from a series of N-alkyl-N-alkyl(aryl)-N’-acyl(aroyl)thioureas
(Stellenbosch : Stellenbosch University, 2020, 2020-03) Barnard, Ilse; Koch, Klaus Robert; Gerber, Wilhelmus Jacobus; Stellenbosch University. Faculty of Science. Dept. of Chemistry and Polymer Science.
ENGLISH ABSTRACT: A large library of Co(III) complexes, derived from selected monopodal and bipodal N,N- dialkyl-N’-acyl(aroyl)thioureas, have been synthesized and characterized. These ligands form tris(chelated) complexes in the thermodynamically more stable fac geometry with the cobalt metal. The monopodal ligands, and their corresponding Co(III) complexes, were separated into two groups based on the two R substituents of the C(S)-NRR’ function. The first group were named the symmetrically substituted acylthiourea derivatives, where R = R’. Due to the increased stability provided by the chelate effect as well as the selective population of the lower-energy d-orbitals, such complexes are generally expected to be kinetically stable in solution. Nonetheless, the ‘symmetrical’ Co(III) complexes were utilized for the study of the unexpected, slow and spontaneous ligand exchange reaction between non-identical homoleptic pairs of low-spin d⁶ octahedral fac-[Co(LA-κS,O)3] and fac-[Co(LB-κS,O)3] complexes in organic solvents. The exchange reaction between these complexes result in mixtures of their corresponding heteroleptic fac-[Co(LA-κS,O)2(LB-κS,O)] and fac-[Co(LA-κS,O)(LB-κS,O)2] complexes in solution. This discovery was followed by a quantitative determination of the ligand exchange equilibria as well as a relative rate study, as a function of temperature, of the reaction using rp-HPLC. It was then established that the high chemical shift sensitivity of ⁵⁹Co NMR is a powerful tool for the easy characterization of the Co(III) complexes derived from symmetrically substituted acylthioureas in solution. The utility of ⁵⁹Co NMR as a spectroscopic tool was exemplified after utilizing this technique for further additional studies of factors shown to dramatically affect the relative rate of ligand exchange in these complexes, specifically light and solvent. The second group of monopodal acylthiourea ligands investigated were named the asymmetrically substituted acylthioureas, where R ≠ R’. The partial double bond character in the C-N bond of the C(S)-NRR’ function results in the E,Z configurational isomerism of these ligands in solution. The isomerism is expressed as duplicate resonances in the ¹H NMR spectra of the uncoordinated ‘asymmetrical’ acylthiourea ligands. The Z to E isomer ratio varies depending on the two R and R’ substituents of the thiourea moiety. Notably, the isomerism in the uncoordinated ligands is passed on to the Co(III) chelates after coordination. As for the symmetrically substituted acylthiourea Co(III) complexes, we find that the ⁵⁹Co NMR chemical shift is very sensitive to the structure of the asymmetrical fac-[Co(Lⁿ-κS,O)3] complexes in solution. Significantly, the presence of the four, theoretically possible, fac- [Co(EEE-Lⁿ-κS,O)3], fac-[Co(EEZ-Lⁿ-κS,O)3], fac-[Co(EZZ-Lⁿ-κS,O)3] and fac-[Co(ZZZ-Lⁿ- κS,O)3] isomers is readily observable by means of ⁵⁹Co NMR, which shows four well-resolved resonances. From the relative peak integrals of the ⁵⁹Co NMR peaks, a semi-quantitative estimate of the relative amounts of the configurational isomers in solution was possible, although assignment of the isomers is not trivial. The assignment of the ⁵⁹Co peaks to each of the EEE, EEZ, EZZ and ZZZ configurational isomers of the asymmetrical fac-[Co(Lⁿ-κS,O)3] complexes were based on the relative E/Z ratio of the uncoordinated ligands, which was established from their ¹H NMR spectra. However, this assignment assumes that the relative E/Z ratio does not vary significantly during coordination to cobalt and remains therefore ambiguous. The distribution of the EEE, EEZ, EZZ and ZZZ configurational isomers was shown to be dependent on the solvent used during the analyses. Moreover, we evaluated the temperature needed to lift the barrier to rotation in the C-N bond of the coordinated ligands. Finally, the ⁵⁹Co NMR trends of several complexes isolated for single crystal X-ray diffraction analysis were complemented by DFT linear transit calculations of their configurational isomers. Finally, we investigate the interesting coordination chemistry of the well-ordered and multinuclear coordination systems of the bipodal acylthiourea analogues, namely aroylbis(N,N-dialkylthioureas). Two ligands were selected for this purpose, including isophthaloylbis(N,N-diethylthiourea) and a bipodal ligand with a modified aromatic spacer derived from catechol. These were utilized as pre-programmed chelating ligands to form metallamacrocyclic octahedral facial Cobalt(III) complexes via self-assembly. The latter catechol-spaced ligand was used for the synthesis of a number of oligometallic Co(III) complexes by one-pot reactions of the ligand, Co³⁺ and a variety of monovalent cations, to form metallacryptates of type {M⁺ ⊂ [Co2(L-κS,O))3]}(PF6), M⁺ = K⁺, Rb⁺, Cs⁺ and NH4+. A significant discovery, owing to the unique sensitivity of the ⁵⁹Co nucleus, was the instrumental role ⁵⁹Co NMR played in our attempt to characterize the metallacryptates and to determine their conditional stabilities in solution. This was achieved by way of several biphasic exchange experiments of cations between an aqueous and non-aqueous phase. This is a novel discovery that has allowed for the study of various factors shown to effect the stability of the metallacryptates in solution.
A fully dissociated compound of plant origin for inflammatory gene repression
(PNAS, 2005-11) De Bosscher, Karolien; Van den Berghe, Wim; Beck, Ilse M. E.; Van Molle, Wim; Hennuyer, Nathalie; Hapgood, Janet; Liber, Claude; Staels, Bart; Louw, Ann; Haegeman, Guy
The identification of selective glucocorticoid receptor (GR) modifiers, which separate transactivation and transrepression properties, represents an important research goal for steroid pharmacology. Although the gene-activating properties of GR are mainly associated with undesirable side effects, its negative interference with the activity of transcription factors, such as NF-κB, greatly contributes to its antiinflammatory and immune-suppressive capacities. In the present study, we found that Compound A (CpdA), a plant-derived phenyl aziridine precursor, although not belonging to the steroidal class of GR-binding ligands, does mediate gene-inhibitory effects by activating GR. We demonstrate that CpdA exerts an antiinflammatory potential by down-modulating TNF-induced proinflammatory gene expression, such as IL-6 and E-selectin, but, interestingly, does not at all enhance glucocorticoid response element-driven genes or induce GR binding to glucocorticoid response element-dependent genes in vivo. We further show that the specific gene-repressive effect of CpdA depends on the presence of functional GR, displaying a differential phosphorylation status with CpdA as compared with dexamethasone treatment. The antiinflammatory mechanism involves both a reduction of the in vivo DNA-binding activity of p65 as well as an interference with the transactivation potential of NF-κB. Finally, we present evidence that CpdA is as effective as dexamethasone in counter-acting acute inflammation in vivo and does not cause a hyperglycemic side effect. Taken together, this compound may be a lead compound of a class of antiinflammatory agents with fully dissociated properties and might thus hold great potential for therapeutic use. © 2005 by The National Academy of Sciences of the USA.
A study on the reversible photo-induced isomerisation of platinum(II) and palladium(II) complexes of the N,N-dialkyl-N’-acyl(aroyl)thioureas with reversed-phase HPLC separation from related rhodium(III), ruthenium(III) and iridium(III) complexes
(Stellenbosch : Stellenbosch University, 2014-04) Nkabyo, Henry Ane; Koch, Klaus R.; Stellenbosch University. Faculty of Science. Dept. of Chemistry & Polymer Science.
ENGLISH ABSTRACT: See item for full text
AB diblock copolymers via RAFT-mediated miniemulsion polymerization
(Stellenbosch : Stellenbosch University, 2008-12) Bailly, Nathalie; Sanderson, R. D.; Tonge, M. P.; Stellenbosch University. Faculty of Science. Dept. of Chemistry and Polymer Science.
The Reversible addition fragmentation chain transfer (RAFT) technique is a robust and versatile technique that enables the synthesis of polymers of controlled molecular weight and polydispersity. The application of the RAFT technique in heterogeneous aqueous media has attracted great interest in academics and industry due to it being more environmentally friendly, besides its other advantages. To date, the synthesis of well-defined high molecular weight polymers via the RAFT process under industrially relevant conditions still remains a challenge for polymer chemists. The study addresses the application of the RAFT process in heterogeneous media, namely in miniemulsion polymerization, for the synthesis of AB diblock copolymers of n-butyl methacrylate and styrene. AB diblock copolymers of high molecular weight were successfully prepared via a twostep method. In the first step, a dithiobenzoate monofunctional RAFT agent was used in bulk polymerization with the first monomer, n-butyl methacrylate. After the polymerization, the majority of the polymer chains contained the thiocarbonyl-thio RAFT agent functionality, which makes the chains potentially active for chain extension. The polymeric RAFT agent (also referred to as the starting block) obtained in the first step was chain extended in the second step, in miniemulsion, upon further addition of fresh initiator and the second monomer, styrene. The effects of the initiator/RAFT agent concentration ratio on the miniemulsion systems were investigated. The miniemulsion systems used for the high molecular weight AB diblock copolymers exhibited living features despite the high polydispersity indices. Kinetic results showed an increase in the rate of polymerization throughout the polymerization. Size exclusion chromatography (SEC) results indicated significant broadening in the molecular weight distributions and a steep increase in the polydispersity during the polymerization. It was concluded that the broad molecular weight distributions and steep increase in the polydispersity was not only related to the initiator concentration but possibly due to other factors such as inhomogeneity in the miniemulsion system and a transition in the kinetic behavior during the polymerization. Secondary particle formation emerged from kinetic data and transmission electron microscopy (TEM) results, but this were not supported by the SEC results. The effect of the use of a water-soluble initiator on the miniemulsion system was also investigated. Results indicated a similar behavioral pattern as observed in the AIBNinitiated systems, and not much improvement in terms of the molecular weight distributions and polydispersity was seen. The effect of the molecular weight of the diblock copolymers on the miniemulsion system was investigated. Poly(n-butyl methacrylate)-b-poly(styrene) diblock copolymers of lower molecular weight were synthesized via the two-step process. Kinetic results indicated a similar behavioral trend as to that of the high molecular weight diblock copolymers synthesized, however SEC chromatograms showed narrower molecular weight distributions and low polydispersity indices.
An Ab Initio density functional study of the structure and stability of transition metal ozone complexes
(Stellenbosch : Stellenbosch University, 2002-12) Venter, Gerhard (Gerhard Abraham); Dillen, J. L. M.; Stellenbosch University. Faculty of Science. Dept. of Chemistry & Polymer Science.
ENGLISH ABSTRACT: A thorough search through the literature as well as through the Cambridge Crystallographic Structural Database resulted in no examples of a neutral ozone acting as ligand in a complex with any metal. Ionic compounds containing ozonide as anionic species, however, are well known throughout the literature and not surprisingly the only result for 0₃ and a metal in the CCSD was an ionic rubidium ozonide compound. What follows is a systematic study into the result of placing an ozone ligand within complexing distance of a transition metal (the first transition row from titanium to copper). Due to the novelty of the system, as first approximation four different orientations of the ozone ligand relative to the metal (a metal cation in these calculations) were investigated. It was found that coordination through the terminal oxygens resulted in energy minima for all the metal cations, although not necessarily the absolute energy minimum on the potential energy surface for the specific cation. A further structural study was done by adding carbonyl and hydrogen ligands to the system, according to the 18-electron rule. For these calculations coordination through the terminal oxygens was employed. In both series the dissociation energy was also calculated. The dissociation energies for the M(CO)nHm(0₃) complexes were all positive, indicating that they are theoretically stable structures. The resulting wave functions were then analysed with the help of three techniques: Atoms in Molecules (AIM), Charge Decomposition Analysis (CDA) and Natural Bond Orbital Analysis (NBO). AIM showed that bonds were indeed formed between the ozone ligand and the transition metal and hinted that the bonding model can be interpreted with the Dewar-Chatt-Duncanson (DCD) model of σ-donation and л-back donation. CDA confirmed that this was the case. NBO results proved erroneous due to the largely delocalized electronic structure of the complexes.
The ability of antimicrobial peptides to migrate across the gastrointestinal epithelial and vascular endothelial barriers
(Stellenbosch : Stellenbosch University, 2018-03) Dreyer, Leane; Smith, Carine; Dicks, Leon Milner Theodore; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
ENGLISH ABSTRACT: Antibiotic resistance has become a major threat to humankind, necessitating research and development of alternative antimicrobial compounds. Many bacteria, including lactic acid bacteria, produce small antimicrobial peptides, referred to as bacteriocins. These peptides are generally not toxic, are active at low concentrations and have a narrow spectrum of antimicrobial activity. However, they usually have low in vivo stability due to degradation by proteolytic enzymes. Drug delivery systems are thus required to transport bacteriocins to the site of infection. Probiotic bacteria are an attractive delivery system, since these bacteria normally colonise the gastrointestinal tract and produce bacteriocins. Numerous studies have been done on the probiotic Entiro™ which consists of Lactobacillus plantarum 423 and Enterococcus mundtii ST4SA. The bacteriocins produced by these strains, plantaricin 423 and bacST4SA, respectively, are active against a variety of pathogens and are potential alternatives to antibiotics. However, it is unknown whether these bacteriocins are able to migrate across the gastrointestinal epithelium and vascular endothelium in order to enter the bloodstream. The aim of this study was to evaluate the stability, cytotoxicity and permeability of plantaricin 423 and bacST4SA in vitro and evaluate the potential use of these peptides as an alternative to antibiotics. The well-known lantibiotic, Nisin A, produced by Lactococcus lactis subsp lactis, was used as control and Listeria monocytogenes EGDe as target (sensitive) organism. Migration of the lantibiotic, nisin A and class IIa bacteriocins, plantaricin 423 and bacST4SA across simulated models of the vascular endothelial and gastrointestinal epithelial barriers was studied by growing human umbilical vein endothelial cells (HUVEC)- and human colonic adenocarcinoma (Caco-2) cells on transmigration inserts and adding fluorescently labelled nisin A, plantaricin 423 and bacST4SA to the inserts. All three peptides diffused across HUVECs and Caco2 cells. Only 21% nisin A, 11% plantaricin 423 and 12% bacST4SA remained attached to Caco-2 cells and only 6% nisin A and 3% bacST4SA attached to the HUVECs, and plantaricin 423 did not attach. The viability of both cell types remained unchanged when exposed to 50 μM nisin A, 50 μM plantaricin 423 and 50 μM bacST4SA, respectively. Furthermore, little extracellular lactate dehydrogenase (LDH) activity was recorded when cells were exposed to 100 μM of each peptide, suggesting that the peptides are not cytotoxic. The three peptides retained 60% of their antimicrobial activity when 25 μM of each were exposed to 80% human plasma for 24 h. However, at higher concentrations (50 μM) 68% of the original antimicrobial activity was recorded and at 100 μM the peptides retained 79% of their activity. This is the first report of nisin A, plantaricin 423 and bacST4SA migrating across simulated gastrointestinal- and vascular barriers. In vivo studies are required to confirm these findings and determine the effect these peptides may have in the treatment of systemic infections.
The ability of terrestrial Oligochaeta to survive in ultramafic soils and the assessment of toxicity at different levels of organisation
(Stellenbosch : University of Stellenbosch, 2006-12) Maleri, Rudolf A.; Reinecke, A. J.; Reinecke, S. A.; Mesjasz-Przybylowicz, J.; University of Stellenbosch. Faculty of Science. Dept. of Botany and Zoology.
Metals are natural elements of the earth crust usually present at low concentrations in all soils. Although many metals such as cobalt, copper, iron and zinc are essential to living organisms, at elevated concentrations most metals are toxic to organisms living in and on soils. Elevated concentrations of metals are caused either by anthropogenic deposition following remobilisation from the earth crust or are of natural origin. Ultramafic soils do not only pose unfavourable living conditions such as drought and poor organic content, these soils are also characterized by extremely high concentrations of a range of metals known to be toxic under normal circumstances. Ultramafic soils are of high ecological importance as a high proportion of endemic organisms, especially plants, live on these soils. As it is known that earthworms do occur in ultramafic soils, the aims of the present study were to investigate the abilities of earthworms to survive in these soils and the influences of elevated chromium, cobalt, copper, manganese and nickel levels. For the evaluation of the metal background conditions, soils originating from ultramafic rocks of the Barberton Greenstone Belt, Mpumalanga, South Africa were collected and different fractions representing different levels of bioavailability were analyzed for arsenic, chromium, cobalt, copper, manganese and nickel. To assess the mobile, readily available metal fraction, i.e. Ca2+- exchangeable metal cations, a 0.01 mol/L CaCl2 extraction was performed. To investigate the mobilisable metal fraction, representing the amount of easily remobilisable complexed and carbonated metal ions, a DTPA (di-ethylene-triamine-pentaacetic acid) extraction was conducted. In relation to non-ultramafic or anthropogenic contaminated soils, a far lower proportion of metals were extractable by the above mentioned extraction methods. To investigate the availability and effects of these metals on earthworms, two ecophysiologically different species were employed. Aporrectodea caliginosa and Eisenia fetida were long-term exposed to the ultramafic soils collected at the Barberton region and a control soil from a location at Stellenbosch with a known history of no anthropogenic metal contamination. The responses to the ecological stress originating in the ultramafic soils were measured on different levels of earthworm organisation. As endpoints affecting population development, cocoon production, fecundity and viability were evaluated. On individual level, growth, metal body burden and tissue distribution were investigated. As endpoints on subcellular level, the membrane integrity was assessed by the neutral red retention assay, the mitochondrial activity was measured by the MTT colorimetric assay and as a biomarker for the DNA integrity, the comet assay was performed. Focussing on manganese and nickel, the uptake by E. fetida of these metals was investigated with the exclusion of soil related properties using an artificial aqueous medium to draw comparisons to the uptake of these metals in natural soils. The possible development of resistance towards nickel was tested by exposing pre-exposed (for more than 10 generations) E. fetida specimens to ultramafic soils with concentrations of more than 4000 mg/kg nickel. The results showed that, except on the endpoint survival, which was less sensitive than all other bioassays, significant responses to the ultramafic challenge were observed in all earthworm bioassays and on all levels of organisation. The sensitivity of the responses of the earthworms towards the ultramafic conditions was not predictable by the level of organisation. The two species showed different strategies of metal elimination. In A. caliginosa, metals such as nickel, manganese and chromium were transported to the posterior section and the posterior section was subsequently pushed off by autotomization. In E. fetida, metals such as chromium and nickel were sequestered in storage compartments in the coelomic cells or fluid. Other metals, such as cobalt, were not taken up at elevated concentrations. Although an increased accumulation of nickel was observed in E. fetida specimens pre-exposed to nickel, development of resistance or cross resistance was not observed in this species. In contrast, pre-exposed specimen exposed to elevated concentrations of nickel showed a higher sensitivity in terms of survival, indicating the absence of acclimatisation or even genetic adaptation. A comparison of the two species employed indicated that A. caliginosa was less suited for the assessment of the ultramafic soils due to the high individual variation in metal body burden, the mass loss observed and the slow reproduction rate even in the control soils. This happened despite the fact that A. caliginosa was a soil dwelling species supposed to be better adapted to the soil substrate than the litter dwelling E. fetida. The toxicity of the ultramafic soils was not necessarily related to total or environmentally available amounts of the selected metals. Thus, it can be speculated that either these soils contained unidentified toxicants with resulting interactions between toxicants playing an important role or earthworms were able to remobilize metals occurring in these soils. As the singular application of an ecotoxicological endpoint did not give reliable results, especially seen over the duration of the exposures, it can be concluded that, when studying soils with such a complex composition, the utilisation of endpoints addressing different levels of organisation is necessary for the assessment of toxic stress emerging from these ultramafic soils.
Abrogation of glucocorticoid receptor dimerization correlates with dissociated glucocorticoid behavior of compound A
(HighWire Press, 2010-03) Robertson, Steven; Allie-Reid, Fatima; Vanden Berghe, Wim; Visser, Koch; Binder, Anke; Africander, Donita; Vismer, Michael; De Bosscher, Karolien; Hapgood, Janet; Haegeman, Guy; Louw, Ann; A-7620-2012
Compound A (CpdA), a dissociated glucocorticoid receptor modulator, decreases corticosteroid-binding globulin (CBG), adrenocorticotropic hormone (ACTH), and luteneinizing hormone levels in rats. Whether this is due to transcriptional regulation by CpdA is not known. Using promoter reporter assays we show that CpdA, like dexamethasone (Dex), directly transrepresses these genes. Results using a rat Cbg proximal-promoter reporter construct in BWTG3 and HepG2 cell lines support a glucocorticoid receptor (GR)-dependent transrepression mechanism for CpdA. However, CpdA, unlike Dex, does not result in transactivation via glucocorticoid-responsive elements within a promoter reporter construct even when GR is co-transfected. The inability of CpdA to result in transactivation via glucocorticoid- responsive elements is confirmed on the endogenous tyrosine aminotransferase gene, whereas transrepression ability is confirmed on the endogenous CBG gene. Consistent with a role for CpdA in modulating GR activity, whole cell binding assays revealed that CpdA binds reversibly to the GR, but with lower affinity than Dex, and influences association of [3H]Dex, but has no effect on dissociation. In addition, like Dex, CpdA causes nuclear translocation of the GR, albeit to a lesser degree. Several lines of evidence, including fluorescence resonance energy transfer, co-immunoprecipitation, and nuclear immunofluorescence studies of nuclear localization- deficient GR show that CpdA, unlike Dex, does not elicit ligand-induced GR dimerization. Comparison of the behavior of CpdA in the presence of wild type GR to that of Dex with a dimerization-deficient GR mutant (GRdim) strongly supports the conclusion that loss of dimerization is responsible for the dissociated behavior of CpdA.
The abundance and diversity of Acidobacteria in fynbos soil: a closer look at culturability and function
(Stellenbosch : Stellenbosch University, 2021-04) Conradie, Tersia Andrea; Jacobs, Karin; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
ENGLISH SUMMARY: The Acidobacteria are considered to be one of the most widespread and highly abundant soil bacterial phyla. This phylum was first described in 1997 with only three cultured representatives. Currently, the Acidobacteria is divided into 15 class-level subdivisions, of which only 5 subdivisions contain the 62 successfully cultured and fully described species in the Acidobacteria. The reason for their low representation in culture collections, is partly due to their unculturable, or difficult to culture nature. The application of 16S rRNA gene techniques has revealed that this phylum can represent almost 50% of the soil bacterial community, averaging around 10-20% of the global soil bacteria. Their proliferation in soils suggests that the Acidobacteria play an important role in biogeochemical processes. Microorganisms are an essential part of the terrestrial environment and are important in maintaining ecological functions. These functions are especially important in biomes where nutrient availability is low, and plants depend on their symbiotic relationships with the soil microbiome. One example of such an environment include the fynbos biome in the Cape Floristic Region (CFR) of South Africa. Despite the dominant presence of the Acidobacteria in several habitats, little is still known about their diversity and distribution in the fynbos biome. The aim of this study, therefore, was to explore the Acidobacterial communities in fynbos soils with the use of 16S rRNA gene sequencing, and how they respond to environmental change, as well as agricultural practices. Further, we aimed to isolate as many species as possible from the fynbos biome, and taxonomically characterise novel species. In Chapter 2, we explored the distribution patterns of the Acidobacteria in different fynbos soils from native conservation areas, and in Chapter 3 how the Acidobacteria responds to seasonal changes and the cultivation of Aspalathus linearis (rooibos) and Cyclopia spp. (honeybush), two indigenous plants used in commercial agriculture. A total of 27 soil samples were collected at three nature reserves, namely Jonkershoek, Hottentots Holland, and Kogelberg. In addition, data from two previous studies from our research group, with GenBank accession numbers DRA003953 for Cyclopia spp. (honeybush) and DRA004000 for Aspalathus linearis (rooibos), were included in our analysis. A total of 33 acidobacterial operational taxonomic units (OTUs) were identified in the nature reserve samples, and a total of 32 and 31 OTUs were identified for honeybush and rooibos, respectively. The majority of OTUs in all samples were classified as representatives of subdivisions 1, 2, and 3. Significant differences were observed in the distribution and composition of these OTUs between nature reserves, between seasons for both honeybush and rooibos, as well as between the agricultural practices in some cases. Several OTUs and subdivisions correlated significantly with soil pH, potassium, phosphorus, and in some instances carbon and calcium. In Chapter 4, we successfully isolated two novel species, both within subdivision 1. We proposed the classification of strain HDX4T as the type strain of Edaphobacter sabuleum nom. prov., and strain ADX1T as the type strain of Terriglobus capensi nom. prov. Based on the genome sequences, both strains had the genomic potential for several complete carbohydrate metabolic pathways, organic nitrogen metabolism, as well as several survival mechanisms that contributes to their survival in the soil environment. In short, this study has contributed greatly to our knowledge of the Acidobacteria and their distribution and diversity in the fynbos biome. The successful isolation of two novel species were added to the list of cultivated Acidobacteria from around the globe.

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