1834 research outputs found
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Development of GC-MS methods for the analysis of tyre pyrolysis oils
No full textGas chromatography coupled to mass spectrometry (GC-MS) and comprehensive two-dimensional gas chromatography (GC×GC) methods were developed for the analysis of tyre derived oils (TDOs). Using GC-MS with either solvent back extraction or liquid dilution for sample preparation, 33 volatile compounds were identified using standards, while an additional 71 compounds were tentatively identified in TDOs. The most abundant TDO constituents were found to be dl-limonene, p-cymene, benzothiazole, ethylbenzene, toluene, p-xylene, 3-ethyltoluene and α-terpinolene. For quantification of the volatile organic compounds which are known to have market value, both internal standard and standard addition methods were used. The quantitative data obtained from these two methods were comparable differing within ±1-5%. To accommodate some of the compounds occurring in trace amounts in some TDO samples, a selected ion monitoring (SIM) method was also developed for better sensitivity. The developed GC-MS method was validated and demonstrated to be suitable for the quantitative analysis of target compounds in a range of TDOs.
Since 1-dimensional (1-D) GC failed to provide complete separation of the complex TDO samples, GC×GC was explored for their in-depth qualitative analysis. As proof of principle, a GC×GC-FID equipped with a novel single-stage thermal modulator was used to demonstrate the benefits of improved separation offered by GC×GC for TDO analysis. For detailed identification, a commercially available instrument fitted with a dual stage cryogenic modulator and hyphenated to time-of-flight mass spectrometer (TOFMS) was used. Analysis of the data obtained on this instrument allowed tentative identification of some 137 compounds using mass spectral and retention index data. The analytical methods reported in this thesis show promise both in terms of the routine quantification of market-value constituents of TDOs, and for the more detailed chemical analysis of these samples.National Research Foundatio
Evaluating the involvement of mtDNA variants in patients diagnosed with myalgic encephalomyelitis
No full textIn mitochondrial research, many investigators have examined the association between mitochondrial DNA (mtDNA) variants in rare as well as common complex diseases. Previous studies at the CHM (NWU) detected three known pathogenic mtDNA variants (m.7497G>A, m.9185T>C and m.10197G>A) at low allele frequencies in a number of patients diagnosed with myalgic encephalomyelitis (ME). Since no diagnostic examinations or conclusive treatments currently exist for ME, an association between ME and known pathogenic variants, or a cumulative effect of rare non-synonymous variants (pathogenicity score) on ME, could provide valuable insights into understanding the causes of ME. Literature shows contradicting data regarding the role of mitochondrial dysfunction in ME, and while uncommon mtDNA deletions have been reported, the three known pathogenic mtDNA variants introduced here have not previously been observed in ME patients (but were later identified as sequencing artefacts in the duration of this study), nor has the combined effect of numerous rare non-synonymous variants on the mitochondrial bioenergetics of ME patients been assessed. To do this, cytoplasmic hybrid (cybrid) cells were developed by fusing ρ0 (mtDNA-depleted) cells with healthy control and ME patient‟s blood platelets (containing solely mtDNA). These cybrid cells were used for mitochondrial bioenergetic analyses, using a Seahorse XFe96 analyser, and for determination of the relative mtDNA copy number (RMCN), using real-time PCR. In addition, conditions for analysing selected cell lines (including the cybrids) using the Seahorse XFe96 analyser were optimized. While no apparent bioenergetic irregularities were observed in ME patient cybrids compared to healthy controls, an increased pathogenicity score appeared to be associated with a decrease in ATP production and a decreased electron transport system (ETS) capacity in ME patients. This new approach for investigating mtDNA variants and a common complex disease may provide new insights into the diagnostic and causative factors of ME.National Research Foundatio
Choosing your PhD supervisor
No full textPresentations SA PhD Project Conference: Free State 25-26 February 201
The doctorate in SA: trends, challenges and constraints
No full textPresentations SA PhD Project Conference: Free State 25-26 February 201
Current situation on standards for knowledge management
No full textStudy meeting of the South African information and knowledge management practitioners, held at the National Research Foundation, 8 July 2016
Comparison of genetic and immunological responses to tick infestation between three breeds of sheep in South Africa
No full textThe study investigated genetic parameters and immunological responses to tick infestation in three South African sheep breeds (Namaqua Afrikaner [NA], Dorper and SA Mutton Merino [SAMM]). The study aimed to estimate genetic and crossbreeding parameters for tick count (TC) and weaning weight (WW), to examine the histology of tick attachment and control sites, to select reference genes for normalizing gene expression data in this study, to compare cytokines gene expression at tick attachment and control sites and finally to compare cutaneous hypersensitivity reactions to unfed larvae extracts (ULE) of Rhipicephalus evertsi evertsi between NA, Dorper and SAMM sheep.
Genetic parameters for WW and TC were estimated using data of lambs maintained on the Nortier Research Farm from 2010 to 2015. Firstly, data of purebred commercial Dorper and SAMM lambs were combined with data of their reciprocal crosses to assess breed effects and the possible effect of non-additive genetic variation on WW and TC. In the second analysis, data of purebred commercial Dorper lambs were combined with data of the unimproved, indigenous NA and the NA x Dorper cross. In Analysis 1 the coefficient of variations (CV) were 24%, 95% and 50% for WW, untransformed total TC and square root transformed total TC, respectively. Genotype affected WW but not TC. A heterosis estimate of approximately 4% was derived for WW. A single-trait h² estimate for TC was 0.11±0.09. A model analysing across-genotype h² yielded a slightly lower h² estimate of 0.08 ± 0.07. In Analysis 2 the CV were 27% and 55% for WW and square root transformed total TC, respectively. WW and TC were affected by genotype. WW exhibited heterosis amounting to 8.5% while the corresponding value for TC amounted to -23%. The single-trait h² estimate for TC was 0.06±0.05. A model analysing across-genotype h² yielded a substantially higher h² estimate of 0.27±0.07. These results suggest that genetic variation in TC was primarily associated with differences among genetic groups while differences between individual animals within genetic groups were not as important. Heterosis estimates for WW were variable between two analyses, but within ranges reported in the literature. This study established significant variation in TC between sheep genotypes when the indigenous NA breed formed part of the analysis. The NA x Dorper cross resembled the improved Dorper breed for WW but the unimproved, resistant NA for TC and exhibited worthwhile levels of heterosis for both traits. Indigenous ovine genetic resources may be instrumental in providing genetic material for adaptive traits in environments susceptible to high levels of tick infestation. Further research is required to elucidate the role that adapted indigenous ovine genetic resources may play in an integrated tick management strategy under conditions characterised by high levels of tick challenge.
A histological study was conducted to assess histological features at tick attachment and control sites in pure breeds. Skin biopsies were examined using routine histological techniques for immunological cell infiltration and skin reactions. Marked variation in immunological responses to tick attachment within and between sheep breeds was observed. There were differences between the attachment and control sites in most of the skin changes (defects) except for four skin defects in the NA. However, all breeds had similar frequencies of skin defects at tick attachment sites. Tick attachment sites were more likely to be infiltrated by cells within as well as across breeds. The NA and SAMM breeds tended to demonstrate greater cellular infiltrations of specific leukocytes at tick attachment sites compared to Dorpers. Basophils, mast cells and eosinophils were increasingly recruited at tick attachment site in NA ewes compared to the Dorper and, occasionally, the SAMM breeds. These results suggest the importance of these cells in sheep resistance to tick infestation. Tick genera influenced the recruitment of neutrophils to tick attachment sites. Tick gender, sampling site as well as tick engorgement level did not affect the number of immunological cells. Further studies should be done with one tick species at a time to better comprehend the species-specific impact of tick attachment to animals belonging to divergent sheep breeds.
Five genes (18S, GAPDH, YWHAZ, B2M and SDHA) were tested for their stability. SDHA, YWHAZ and B2M were the most suitable reference genes recommended by geNorm analysis for normalizing gene expression data in sheep skin. These findings will assist in normalizing data in gene expression studies at tick attachment and control sites of the NA, Dorper and SAMM breeds. This study suggested that no reference gene is stably expressed in different experimental conditions.
The expression of IL-1β, IL-8, CCL2 and CCL26 was quantified in real-time qPCR. IL-1β and IL-8 were more highly expressed at tick attachment than at control sites. NA ewes expressed IL-1β more at tick attachment sites than Dorpers. The NA breed was also more likely to upregulate the expression of the CCL2, CCL26 and IL-8 genes at tick attachment sites compared to control sites than the other breeds. This indicates that IL-1 β, CCL26 and IL-8 may play a part in resistance or susceptibility of sheep to tick infestation. The differences in expression of the two chemokines between the resistant NA and more susceptible SAMM and Dorper imply that the NA breed could be able to overcome the anti-chemokine activity of tick saliva.
ULE of R. evertsi evertsi induced hypersensitivity reactions in all the breeds. The indigenous NA displayed stronger reactions, immediate and delayed, than the commercial breeds. The results suggest that cell-mediated immune responses are invoked to fight against tick infestation in the NA. The hypersensitivity reaction may be used as a phenotypic marker to select animals or breeds that are more resistant to tick infestation. It is well-known that challenge-based research for promoting resistance to pathogens is under scrutiny from an ethical and welfare perspective. The methods employed here could be refined to enable routine evaluation of valuable animals without resorting to more invasive strategies, such as allowing adequate natural challenge to accrue over time in selection candidates. Overall, the component studies reported in the thesis increased the present understanding of ovine tick-host interactions and factors contibuting to breed differences in tick loads.National Research Foundatio
An experimental approach to assess the role of nest predation in the population dynamics of the sociable weaver (Philetairus socius)
No full textPredation is a widespread population process that has been shown to affect the distribution,
abundance and dynamics of populations in ecosystems. This is the first study that used an
experimental approach to assess the effect of nest predation on the population dynamics of
the sociable weaver (Philetairus socius), a keystone species in the semi-arid savannas of the
Kalahari and Namib regions. Snakes were excluded from five colonies for five breeding
seasons and two colonies for three breeding seasons, with another eight colonies acting as the
controls. Reproductive output, colony size, dispersal events and several environmental
variables were measured between 2010 and 2015. This was done to determine (1) what effect
nest predator exclusion had on reproductive output; (2) how this related to colony and
population size trends by using a matrix-projection metapopulation model; (3) how protected
colonies influence movement patterns; and (4) if nest predation had a compensatory or
positive effect by reducing the intraspecific competition of a colony. The fourth aim was
investigated by tracking the foraging paths of eight colonies of varying sizes, with foraging
distance acting as a proxy for intraspecific competition. Colonies that were protected from
snake predation produced, on average, more than double the number of fledglings per female
per breeding season that were produced in unprotected colonies. However, the magnitude of
this effect decreased with increasing colony size of protected colonies, most likely due to the
negative effects that large colony sizes have on reproductive output. Increasing aridity was
found to have a negative effect on reproductive output and warmer winter minimum
temperatures were found to have a positive effect. My results suggested that protecting a
subset of colonies in the metapopulation may be sufficient in preventing population declines
under climate change conditions. The protected colonies played an important role in
structuring and connecting the movement network of the metapopulation, whilst colony size
explained the migration rates of colonies. However, predation was not found to have a
compensatory effect in reducing the intraspecific competition (measured as foraging distance)
of a colony. Instead, foraging distance was probably determined by the ability to
thermoregulate under hot and humid conditions. To fully understand the effects of nest
predation on sociable weaver population dynamics, future studies need to investigate the
response of snake predators to sociable weaver behaviour and environmental conditions.National Research Foundatio
South African PhD project : creating diversity for the future
No full textPresentations SA PhD Project Conference: KwaZulu-Natal Province 17 August 2016
Deceptive publishing and the impact on the scholarly publishing community
No full textPresentations SA PhD Project Conference: KwaZulu-Natal Province 17 August 2016
Quantification and analysis of biogenic amines using a liquid chromatography tandem mass spectrometric method
No full textIntroduction: Biogenic amines are a group of endogenous compounds which play an important role in maintaining homeostasis. These compounds are produced from amino acid precursors and exert strong physiological effects despite being at low concentrations (low pg/ml). There are a wide variety of affects and effects controlled by biogenic amines. Different conditions can be brought on by changes in the concentrations of these biogenic amines that can alter the levels or be brought about by incorrect levels. Thus biogenic amine concentrations may prove to be valuable biomarkers if the extremely low levels can be accurately and rapidly quantitated. The aim of this study was to develop and validate a method which is able to quantitate multiple biogenic amines in a single run from low sample volumes. Methods and Materials: Quantification of the blood levels of biogenic amines was performed following extraction using derivatisation and an appropriate liquid chromatography tandem mass spectrometric method. The derivatisation was performed at mild conditions for an hour and extracted using ethyl acetate. The LC-MS/MS system used was an Agilent 1100 series HPLC and an ABSciex 4000 QTrap. The system was operated in positive ESI mode and appropriate MRM precursor-product pairs were selected. In order to validate the method a series of 8 dilutions from 0.05 2.5 ng/ml were prepared in solvent and plasma. These were then processed according to the developed method and analysed using Analyst software. Results and discussion: The validation of the biogenic amines was performed according to the ICH guidelines. The calibration curves were fitted using linear regression (1/x weighting) over the linear range of the calibration curve. Metanephrine and melatonin were validated in plasma between 0.1 2.5 ng/ml. Serotonin, histamine and normetanephrine were validated in solvent between 0.25 2.5 ng/ml. Adrenaline, dopamine, noradrenaline and 5-hydroxy-3-indoleacetic acid were validated in solvent between 5 50 ng/ml. Metanephrine exhibited the highest sensitivity and showed linearity between 0.05 2.5 ng/ml in solvent. The catecholamines and 5-HIAA were the least sensitive of the analytes and had estimated LLOQs between 0.5 2.5 ng/ml. Stability tests show the derivatised analytes to be stable at -20°C for 5 days and recovery testing shows recoveries of over 70% for metanephrine and melatonin. Conclusion: Sensitivity still remains an issue when working with biogenic amines. The extremely low physiological concentrations are further exacerbated by the low sample volumes used in this study. Despite the challenges the compounds were all validated according to ICH guidelines and an LC-MS/MS method was developed that was able to analyse 9 biogenic amines of different classes in a single run using only 250 ?l of human plasma, after multistep sample preparation whilst achieving high sensitivity.National Research Foundatio