Doctoral Degrees (Genetics)
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Browsing Doctoral Degrees (Genetics) by Author "Grobler, J. P."
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Item Open Access Chemical profiling of the street cocktail drug ‘nyaope’ in South Africa using gas chromatography-mass spectrometry (GC-MS)(University of the Free State, 2020) Mthembi, Pabalala Meshack; Mwenesongole, E. M.; Cole, M. D.; Grobler, J. P.𝑬𝒏𝒈𝒍𝒊𝒔𝒉 The street cocktail drug nyaope, commonly found in South Africa, is a mixture of low-grade heroin, cannabis products, antiretroviral drugs and other materials added as bulking agents. This research led to the development of an analytical method for the identification and profiling of the street cocktail drug nyaope, using gas chromatography – mass spectrometry. This study determined for the first time the most suitable organic solvent in which the common components of nyaope, namely Δ9-tetrahydrocannabinol, heroin, caffeine, dextromethorphan, phenacetin and the antiretrovirals efavirenz and nevirapine, which have different chemical characteristics, are stable prior to an analysis of nyaope samples. The main nyaope components, when extracted into tertiary butyl alcohol, exhibited the greatest autosampler stability of up to 72 hours of storage. From these results it can be determined that tertiary butyl alcohol is a suitable solvent for the identification, comparison and profiling of nyaope samples. With regard to analytical method validation, the method gave acceptable repeatability with the %RSD less than 10% for the 10.0 and 1000.0 mg/L concentration levels for the majority of the components. The linear concentration ranges managed linearity with r2 ≥ 0.997. The detection limits varied between 9.90–39.0 pg on column and the limit of quantitation between 30.0–120 pg on column. The method exhibited acceptable recoveries and ruggedness. The method developed is fit for the purpose of quantitative profiling of the major components of nyaope using gas chromatography-mass spectrometry. The majority of the components in the street cocktail drug nyaope were shown to be stable up to at least 24 hours when stored in a refrigerator. For profiling purposes, samples need to be extracted within 24 hours of seizure in a solvent in which they are stable, such as tertiary butyl alcohol and analysed within 72 hours. At all times the samples need to be protected from light to prevent the photo-decomposition of Δ9-tetrahydrocannabinol and from moisture to prevent the hydrolysis of diamorphine. The chemical components of simulated nyaope samples as well as actual seized street nyaope samples were successfully identified and quantitatively determined using gas chromatography – mass spectrometry. The simulated and actual seized street samples were successfully discriminated into original batches using the identified nyaope components and two unsupervised chemometric methods, namely principal component analysis and hierarchical clustering, as well as chromatographic profiles. Thus, for the first time, a validated analytical method has been developed for the identification, quantitation and profiling of nyaope using gas chromatography – mass spectrometry. The method will assist law enforcement agencies in the identification and comparison of nyaope samples and facilitate the prosecution of illicit drug trafficking offences. ___________________________________________________________________Item Open Access Genetic control of wood properties of Pinus patula in southern Africa(University of the Free State, 2013) Nel, André; Fossey, A.; Grobler, J. P.; Kanzler, A.English: Pinus patula is the most widely planted softwood species in Southern Africa and is utilised for various solid wood and pulp and paper products. Tree improvement programmes for forestry species started in Southern Africa during the 1950’s, with an initial focus on volume improvements. The focus for many advanced tree improvement programmes has moved to the improvement of wood properties. This quantitative genetics study utilized half-rotation age P. patula progeny material from a 5 × 5 full diallel mating design and additional factorial crosses. A radial wood sample at 1.3 m above ground level from each of 300 trees was used to study a range of wood density, tracheid cross-sectional and -dimension characteristics. A large range of family variation was found for all wood properties. The combining ability analysis indicated that general combining ability was the most predominant effect and that specific combining ability effects were absent for nearly all the investigated wood density and tracheid traits. Reciprocal, maternal and non-maternal effects were also not significant for all but a few traits. Some of the wood properties were influenced by the specific site where trees were grown. Heritability estimates for many of the important wood density and tracheid traits were moderate to high, indicating strong additive genetic control of these properties. Wood density traits were under strong genetic control, with a pith-to-bark increase in wood density traits. Latewood proportion and earlywood density had a strong effect on weighted mean wood density. There were also strong positive correlations for density traits between growth rings, indicating that early selection would be possible. Tracheid cross-sectional properties were also strongly inherited, and strong correlations were found between the cross-sectional traits and calculated pulp and paper traits. Tracheid dimension traits such as tracheid length, width and cellwall thickness had lower heritability estimates than those found for wood density and tracheid cross-sectional traits. These were, however, of higher magnitude than growth trait heritabilities. Several strong positive and negative correlations were found between growth, wood density and tracheid property traits. These negative correlations would make multi-trait selections very problematic. Predicted gains for some of the studied wood properties were substantial, but correlated responses between primary and secondary selection traits were often negative. The structuring of genetic material into wood property specific sub-populations would ensure the improvement of selected important wood properties. These different properties can then be combined by means of controlled pollinations, and be deployed via vegetative propagation. This study has provided novel information on the genetic inheritance of physical wood properties of P. patula grown in Southern Africa, and will allow tree breeders to include some of these properties in breeding programmes.Item Open Access Linking geographic origin and mitogenomes of the ground pangolin in southern Africa(University of the Free State, 2021-11) Du Toit, Zelda; Grobler, J. P.; Kotze, A.; Dalton, D. L.; Jansen, R.The order Pholidota includes the most trafficked mammal species globally. The family Maninae with recognized species are categorized as Endangered and Critically Endangered on the IUCN Red List of Threatened Species. Due to the sharp decline in Asian pangolin numbers, the shift was towards the African pangolin species, to meet the demand in Asia and in Africa. Subsequently, the status of Smutsiinae has been revised by the IUCN and varies between Vulnerable and Endangered. This study contributes to clarify the genetic status of the four African pangolin species using molecular technologies. The first part of the study aimed to assemble mitogenomes of the four African pangolin species using NGS technologies. Whole mitogenomes were assembled and compared with published mitogenomes available in online databases. Mitogenomes were only available for six of the eight pangolin species. Our results showed different genome lengths for the four species: Temminck’s pangolin (16 558 bp), giant pangolin (16 540 bp), white-bellied pangolin (16 565 bp) and black-bellied pangolin (16 649 bp). Three distinctive clusters were observed supporting three genera. The first cluster consisted of the Asian pangolins (Manis), the second cluster was the African tree pangolins (Phataginus) and the third cluster represented the African ground pangolins (Smutsia). There were also two insertions found in the control region of the black-bellied pangolin which could indicate a recent mutation or selection event. The second part of the study focused on the development of species-specific STRs for Temminck’s pangolin and in combination with previous developed mtDNA markers the aim was to assess the population structure across the distribution range in southern Africa. Three mtDNA loci were analysed (Co1, Cytb, control region) with 30 STRs. A total of 62 individuals from six countries were included in the study. The results showed little to no geographical differentiation across the identified sampling locations. This indicates high levels of gene flow between the populations. Three distinctive clusters were observed within the different sampling areas. This could indicate inherited ancestral traits in juveniles with dispersal into new home ranges following a stepping stone model. Temminck’s pangolin has been reported to cover vast distances in search of new home ranges or territories. This study provides the first account of a combination of mtDNA and STR markers to investigate possible geo-referencing of Temminck’s pangolin in southern Africa. It is evident that the mtDNA and STRs markers used in this study, are not robust enough to discriminate between different sampling locations or populations. Further in-depth investigations, including whole genome analysis and SNPs are recommended. A more comprehensive sampling strategy is required to include all areas within the distribution range as well as more individuals for an in-depth genome analyses.