Genetic engineering of superior wood properties and exploiting natural genetic variation found within commercially important trees, such as Eucalyptus spp., promise to increase cellulose biomass production. It is therefore essential to understand the molecular genetics of wood formation. Digital Gene Expression (DGE) profiling is adept in not only assessing the expression level of genes transcriptome-wide, but also in characterising alternative splice forms of transcripts and identifying novel transcripts. Tension wood is a specialised type of wood which functions in the response to mechanical stress in trees and is formed on the upper side of a branch or a bent stem. The characteristics of tension wood differ from normal wood by increased cellulose and xyloglucan content and decreased lignin and xylan content. During tension wood formation, transcriptome-wide changes in the expression of genes involved in secondary cell wall formation underlie changes in cell wall composition. Most notably is an increase in fasciclin-like arabinogalactan protein (FLA) and xyloglucan endotransglucosylase (XTH) and a decrease in lignin biosynthesis gene expression. Differential expression patterns are shown by cellulose synthase (CesA) genes, which have been found to be either up- or down-regulated during tension wood formation. No previous study has profiled gene expression during early as well as late tension wood formation. The aim of this M.Sc study was to identify genes that are differentially expressed during early tension wood induction and late tension wood formation in the immature xylem tissues of Eucalyptus grandis x Eucalyptus urophylla hybrid trees. DGE profiling is a transcriptome-wide expression profiling technique based on ultra-high throughput second generation DNA sequencing technology. The processing, analysis and interpretation of DGE data has not yet been standardised. To address this problem, a case study was performed of DGE data mapping to seven well characterised Eucalyptus grandis CesA (EgCesA) genes. The DGE data processing guidelines developed based on this case study produced EgCesA expression profiles in normal wood that were comparable to the profiles of these genes determined with other technologies. A possible alternative splice variant occurring during tension wood formation was identified for the secondary cell wall gene EgCesA3. However future work is needed for the validation of this observation. Early tension wood induction and late tension wood formation was investigated by sampling differentiating xylem from ramets of a Eucalyptus grandis x Eucalyptus urophylla clone induced to form tension wood for 6 hours, 24 hours, 1 week, 2 weeks and 6 months. Up to 2,654 transcripts were found to be significantly differentially expressed during tension wood formation. FLA transcripts were the highest expressed transcripts and were, along with XTH genes, highly up-regulated in early and late tension wood formation. Genes differentially regulated during early tension wood formation reflected a general stress response and hormone signalling pathways. Late tension wood formation was marked by the differential regulation of secondary cell wall biosynthetic genes, which reflected the chemical composition of tension wood. Two secondary cell wall CesA genes were significantly up-regulated, while genes involved in lignin and xylan biosynthesis were significantly down-regulated. Observations suggest that the eucalypt trees used in this study formed tension wood to stabilise the bent stem, while apical dominance was transferred to new side branches which showed signs of extra secondary growth. / Dissertation (MSc)--University of Pretoria, 2011. / Genetics / unrestricted

Microbial community in the gut of pigs provides a vast and complex microbial network of community diversity important for its health and development. Pathogenic Escherichia coli are responsible for acute profuse diarrhoea with resultant high morbidity and mortality. Antibiotics are used as growth promoters and for therapeutic purposes in pigs. Misuse, abuse and overuse of these antibiotics have led to development of resistant bacterial strains. This study reports the effect of antimicrobial usage on frequency in which growing pigs habour ETEC and VTEC virulence genes and compared phenotypic and genotypic antibiotic resistance pattern of E. coli and metagenomics analysis of fecal samples collected from; (i) pigs receiving normal farm treatment without antibiotics usage, over a 70 day period, and (ii) pigs allowed treatment with antibiotics and monitored over a 70 day period. Our hypothesis was that the use of antibiotics in commercial pig farms affect gut microbial population. A total of 241 E.coli strains were isolated and antibiotics resistance testing through disk diffusion and PCR was conducted. Sequencing was also done using the Miseq Illumina platform. Virulence genes were detected in [24.8% (Cl95%: 18.2-32.7)] of the antibiotic group isolates and [43.5% (Cl95%: 34.5-52.9)] of the non antibiotic group with a significant difference (P=0.002). Phenotypic resistance to oxytetracycline was most common and were significant (P = 0.03) in samples of days 10 (P = 0.02) and 21 (P = 0.01). Furthermore, [63.9% (Cl95%: 57.6, 69.7)] possesed one or more of the four tested tetracycline resistance genes. Significant statistical difference exists in bacterial structure and composition in the gut of growing pigs P<0.05. Firmicutes, Bacteriotedes and Proteobacteria were the three most abundant phyla and composition was statistically significant during the growing period. The study showed that antibiotics usage increases gut bacterial population in growing pigs. Disease causing virulence genes and antibiotics resistance genes may occur even without antibiotics usage in growing pigs and other factors may be involved. / Dissertation (MSc)--University of Pretoria, 2018. / Veterinary Tropical Diseases / MSc

Mining activities greatly contribute to economic growth and development in South Africa. However, post-mining soils have limited land-use potential due to low fertility, deficiency in organic matter content and poor physical, chemical, and microbiological properties. Mechanical methods to improve soil conditions, such as ripping, are expensive and provide temporary improvements. Alternatively, exploring biological methods could aid in creating arable land from degraded soils, where the placed soil is sufficiently deep. Dung beetles could potentially improve several aspects of soil degradation, complementing current rehabilitation efforts. Studies in relatively undisturbed soils of agro-ecosystems have found that dung burial introduces essential nutrients to the plant root zone. This study aimed to determine whether these benefits could be maintained in soils on reclaimed mined land, where very high rates of compaction may inhibit tunnelling by dung beetles. Two experiments were conducted. The first experiment investigated the effects of tunnelling dung beetle activity on plots simulating reclaimed mine soil, while the second experiment examined the effects of dung beetle activity on reclaimed mined land near Emalahleni, Mpumalanga. Treatments consisting of dung and dung beetles (D+B), dung only (D) and no dung or dung beetles (X - control) were applied to both the plot and field experiments, with an added treatment of naturally-occurring dung beetles and dung (N) being included for the field-based experiment on reclaimed mined land. In both experiments, soil and plant measurements were taken one month after beetle and dung applications and repeated six months later to determine the longevity of effects. Soil and plant measurements included water infiltration rate, herbaceous plant biomass, plant protein content, soil penetration resistance, and various soil properties and elements. Results obtained from both experiments were similar in most respects. The D+B treatments significantly increased water infiltration rates and magnesium content in the soil. Water infiltration rates for D+B treatments increased by an average of 60% compared to D and X treatments on simulated plots and increased by an average of 38% for reclaimed mined land. Soil strength (penetration resistance) was significantly reduced on the simulated plots and the reclaimed mined land where dung beetles were active. Soil pH was increased by dung beetle activity for both experiments but was variable between sampling intervals. Although plant protein content was not significantly altered for any treatment, it was consistently higher for D+B treatments. Based on these results, the activity of applied dung beetles greatly improved reclaimed mined land soil and in some instances the effects persisted for at least six months with no further dung beetle or dung applications. Where effects were not sustained for six months, it is possible that the random sampling method may have missed effects of dung beetle activity that were concentrated beneath dung pats. A high degree of variability in plant biomass and soil strength was observed on the reclaimed mined land, reflecting the more complex environmental conditions and interactions in the field. Naturally-occurring dung beetles were not as effective as applied dung beetles, because their abundance was much lower and consisted of small-bodied rollers. In conclusion, dung beetle application to reclaimed post-mining soil may alleviate degraded soil conditions but may require frequent applications to augment naturally-occurring populations. / Dissertation (MSc)--University of Pretoria, 2018. / Zoology and Entomology / MSc

The Refugees Act 130 of 1998 enabled South Africa to treat asylum seekers in a humanitarian and dignified manner. However, more than 20 years into democracy, the refugee status determination system, which is the responsibility of the Department of Home Affairs (DHA) is overburdened with asylum applications. The core criticism against the DHA is its failure to finalize asylum application within 180 days. The key attraction of South Africa’s asylum regime is its non-encampment policy, which bestows on an asylum seeker the right to work or study pending the outcome of the asylum application. This mini-dissertation will not focus on challenges that asylum seekers and refugees may encounter when asserting a specific entitlement. The aim is instead to highlight red flags which will assist any interested party to have a basic understanding of what refugee status determination in South Africa entails. Although refugee status determination is an administrative process, South African courts have laid down jurisprudence confirming the following: (i) At the moment a foreigner expresses an intention to apply for asylum, he or she must be afforded the opportunity to do so; (ii) Illegal entry into the state do not bar application for asylum; (iii) Equality before the law affords asylum seekers suspected of being illegal the right to appear before a competent court within 48 hours of arrest; and (iv) Asylum seekers must apply for immigration permits from abroad. Differently put, an asylum seeker may not apply for a change in status, pending adjudication of an asylum claim in South Africa. To deter illegal migration to South Africa, the DHA has done the following: (a) It unilaterally closed the Cape Town and Port Elizabeth Refugee Reception Offices (RRO’s); (b) It established a Border Management Agency to dispense with adjudication of asylum applications at a border post or point of entry; (c) It granted special dispensation work permits to asylum seekers from Southern African Development Community (SADC) countries. Refugee status determination and dissecting a persecution claim may be perceived as two different enquiries. The latter enquiry is often the subject matter of statutory tribunals and courts during judicial review proceedings. This study explains the key functions of roleplayers, their different processes and inherent functions under the umbrella of refugee status determination. It is recommended that attorneys and non-governmental organisations be allowed to actively participate, from the inception stage, in South Africa’s refugee status determination process. This will minimise the life-cycle of an asylum claim which often ends in judicial review proceedings. This forces the DHA to be accountable, transparent and to reflect on its commitment to treat asylum seekers, refugees and foreigners in good faith and dignity. / Mini Dissertation (LLM)--University of Pretoria, 2018. / Centre for Human Rights / LLM / Unrestricted

Plasmodium falciparum is the causative agent of the most commonly fatal form of malaria in Africa with annual deaths of more than 300 000. The rapid development and spread of antimalarial drug resistance by the parasite have stimulated research into the development of new drug classes. Target-based drug discovery have been used as a prominent and efficient tool to identify lead drugs. Reports suggest that selectively inhibiting the parasite mitochondrial electron transport could be a potential treatment effective at multi-stages of the parasite life cycle. Inhibitors of cytochrome bc1 (Cyt bc1), an essential inner mitochondrial membrane protein that drives ATP synthesis in the mitochondria are claimed to be lethal to apicomplexan species including Plasmodium. The emergence of resistance to atovaquone, a Cyt bc1 complex Qo site inhibitor, casts doubt over the long-term efficacy of new drugs targeting these mitochondrial proteins. Many aspects of potential drugs must be investigated to assess the suitability of new emerging drugs targeting the mitochondrion. In silico target-based drug design methods using Autodock vina were used to design compounds that would theoretically bind to and inhibit the Qi site of Cyt bc1 of the P. falciparum. The potential candidate compounds were selected from compounds defined by Gamo et al., (2010) and tested using in silico docking experiments. Homology models were developed and modified to improve their drug-likeness according to the Lipinski rule, QED parameters and synthesised by Wuxi App Tec. This study assessed the antiproliferative activity of six candidate compounds on P. falciparum parasites in vitro following in silico compound docking and drug likeness assessment. Initial in vitro screening data was obtained for the test compounds at 1 and 5 ?M over 96 h and full dose-response curves was performed for compounds showing >70% proliferation inhibition at 1 ?M against the 3D7 strain. Four of the test compounds, EE1, EE3, EE5 and EE7 gave IC50 values of 89 nM, 664 nM, 64 nM and 249 nM, respectively. The candidate compounds had a marginal >2-fold selectivity towards malaria parasites but did not show cross resistance, with resistance indices of >120. In conclusion, in silico docking using software programs could be utilised as a potential tool for rapidly identifying feasible target-based antimalarial compounds while avoiding high throughput screening. Other possible target sites on the mitochondrion can be used to design new chemotypes. All the designed compounds showed significant antimalarial activity against the asexual stages tested on 3D7 strain with a significant resistance index. However, these compounds showed minimal activity on the gametocyte stage. Finally, compound EE5 showed to be the most potent, more selective and with higher resistance index, hence this can be further optimised for preclinical studies. / Dissertation (MSc)--University of Pretoria, 2018. / Pharmacology / MSc

This study examines oversight and accountability in relation to good governance in Ekurhuleni Metropolitan Municipality. It also explores the implementation of the separation of powers governance model since its inception in August 2011. The study accentuated the significance of legislative mechanisms to foster greater oversight and separation of powers within the municipality’s governance structures. It demonstrates that the relevance of the available mechanisms in current legislation can lead to the practical separation of executive and legislative powers as well as sound oversight within the municipality. The study acknowledges the conflation of executive and legislative functions in the municipal council as stipulated in the Constitution of the Republic of South Africa, 1996 section 151(2) that resulted in a lack of clarity of the roles of office bearers causing an oversight deficit. The literature review acknowledged that the concept of good governance is conducted through a policy approach that highlights the roles of the political, organisational and economic standards of lawfulness and efficacy in the daily operations of the public sector. The study illustrates the significance of the section 79 committees as an oversight mechanism established in respect of Section 43 of the Local Government: Municipal Structures Act, 1998 (Act 117 of 1998) of the municipal council in relation to the separation of powers governance model. The study applied qualitative research methods, which included open-ended questionnaires and secondary sources to comprehend the separation of powers governance model in local government. Triangulation of data was fundamental to ensure that the case study provided the correct interpretation of the participants’ perceptions. The case study concludes with recommendations as informed by the research to improve the functionality of the separation of powers governance model in the Ekurhuleni Metropolitan Municipality. The commendations could assist policy makers to institute municipal systems of governance separating the executive functions from the legislative functions to create meaningful oversight to stimulate good governance. The implementation of separation of powers governance model provides an opportunity within local government to contribute towards the attainment of good governance. Ultimately, this study contributes to the knowledge and modernisation in local government within metropolitan municipalities in South Africa. / Dissertation (MAdmin)--University of Pretoria, 2018. / School of Public Management and Administration (SPMA) / MAdmin / Unrestricted

The prevalence of Hypoactive delirium and delirium in Intensive Care Units (ICU) can be as high as 80% and is characterized by decreased cognitive function, inattentive thinking, and fluctuation of consciousness, disorientation and confusion which could result in an increase of 6 months mortality and cognitive impairment. If no screening tool for detection for hypoactive delirium and delirium is utilized, it will be undetected and the outcome will be worse if no non-pharmacological interventions are in place. The aim and objective of the study was to assess the effect of non-pharmacological interventions on the severity and duration of hypoactive delirium and delirium in ICU patients following cardio-thoracic surgery. The Quasi experimental non-equivalent control group design was used. The setting was a private hospital of 138 beds with 18 ICU beds based in Gauteng. The population was chosen by convenient sampling and consisted of post-operative Cardio-thoracic surgery participants who met the inclusion criteria and gave informed consent pre-operatively. The control group of 30 participants enrolled firstly. If the participants screened positive for hypoactive delirium or delirium on day 1 at 8:00 with screening utilizing the Intensive care delirium screen checklist (ICDSC), they were enrolled into the study and received standard nursing care. They were screened again at 16:00 with the ICDSC to assess the prevalence and duration of delirium or hypoactive delirium if no intervention was implemented. The intervention group was enrolled in the same manner and screened with the ICDSC at 8:00 and 16:00. They received non-pharmacological interventions instead together with standard nursing care. The difference in the ICDSC checklist scores was utilized for data analysis. The results showed that the duration in hours from hypoactive delirium and delirium to no delirium in the intervention group (62,4 hours to no delirium) was significantly shorter than in the control group (72,3 hours to no delirium) thus therefore supported the hypothesis. Limitations to this study were that only one ICU unit in a private hospital was used with a small sample size consisting out of cardio-thoracic patients. / Dissertation (MCur)--University of Pretoria, 2017. / Nursing Science / MCur / Unrestricted

Information and Communications Technologies (ICTs) are acknowledged as a vital ingredient for the transformation of any society. Since the late 1990’s the Department of Education implemented several curriculum-based interventions aimed at improving the quality of education in South African schools. During this time there was also a gradual introduction of ICT in some schools, mainly because there seemed to be a belief that the integration of ICT in schools can transform education, reduce challenges, and lead to enhanced education in South Africa. The data for this study originated from the TIMSS 2011 and TIMSS 2015 assessments conducted by the International Association for the Evaluation of Educational Achievement (IEA). This study investigated the relationship between the investment in ICT in South African schools and the mathematics achievement of the Grade 9 participants. The aim of the study was to identify trends in the use of ICT in schools, as well as the relationship between the use of ICT and mathematics achievement. The findings from the study indicated a decrease in the availability of ICT for teaching and learning from 2011 to 2015. The study found that even where ICT was available, it was rarely used. At the same time Grade 9 participants reported an increase in the use of ICT for schoolwork outside of their school environment. While there was an increase in educator professional development focusing on the integration of ICT in education, the number of educators that used ICT for mathematics teaching and learning, decreased between 2011 and 2015. The research results suggested that educators seemed to battle to optimally use and implement new technologies. A new model for improved integration of ICT in schools is therefore proposed. The proposed IIIA-Model for the integration of ICT in Schools (IIIA-Model) is based on an adaptation of the Dynamic Model of Educational Effectiveness (Creemers & Kyriakides, 2010) and the TIMSS curriculum model (Mullis & Martin, 2013). The IIIA-Model aims to direct the implementation and integration of ICT in schools by identifying different zones of impact, role-players involved, as well as curriculum expectations during the process of ICT integration. / Science, Mathematics and Technology Education / PhD / Unrestricted

South Africa has made a recent transformation from Property Loan Stock companies and Property Unit Trusts to the internationally recognised Real Estate Investment Trust structures. The locally listed companies that decided to adopt this structure should experience increased global interaction. This study focused primarily on the international direct or indirect real estate investments made from a South African Real Estate Investment Trust perspective. When conducting this investment, the respective companies must obtain financing for the investments, which will have an impact on capital and shareholder structure. The capital structure acts as an umbrella term that includes the shareholder’s equity and debt of a company. The study mainly focused on long-term debt. The shareholder structure focuses on the equity of South African Real Estate Investment Trusts in depth and determines if international activity had taken place. Global investments usually have a structure through which money is transferred to foreign countries to execute an investment. This is predominantly referred to as the company structure. The top 13 Real Estate Investment Trusts, by market capitalisation, were examined to first determine whether international investment took place and secondly whether their company structure experienced change after foreign property investments had been made. Emphasis was placed on the risks involved during the international investment process, the reason for company structure changes, as well as the benefits associated with these decisions. The various direct and indirect impacts that the previous themes have on the bottom line of a specific South African Real Estate Investment Trust were also explored, should these investors choose to capitalise on a global scale. / Dissertation (MSc (Real Estate))--University of Pretoria, 2017. / Construction Economics / MSc (Real Estate) / Unrestricted

Space cooling energy demand is projected to increase due to climate changes. For example, the South African climate change model projected warming to reach around 3 to 4°C along the coast, and 6 to 7°C in the interior. Such temperature increases will significantly increase the energy demand by building cooling applications. Thus, there is an urgent need to improve the energy efficiency in buildings and to reduce the peak cooling loads. Various studies for building free cooling using phase change materials have shown to reduce or avoid the need for mechanical space cooling. Very few of these studies covered Southern African climatic conditions and no research was found reporting a comparison of free cooling thermal performance of different PCM types for an individual climate scenario. The purpose of this study was to experimentally evaluate and compare the cooling performance of three PCM materials in plate-air heat exchanger modules subjected to Southern African climatic conditions and to use the data to deduce empirical correlations that can be used by thermal designers to determine the number of modules required to maintain an objective cooling load within the range of operating conditions. In this experimental investigation the cooling (discharging) performance of plate encapsulated Phase Change Materials (PCMs) for passive cooling applications were evaluated as measured by its average effectiveness, cooling power, energy absorption and phase transformation duration. A test facility that mimics a PCM-air heat exchanger module installed in a ventilation duct was used to consider the impact of varying air flow rate and inlet air temperature. PCM plate encapsulations with a thickness of 10 mm orientated vertically and spaced at a pitch of 15 mm were investigated. The thermal storage characteristics of three commercial PCMs were considered. Two paraffin type PCMs with melting temperature ranges of 25 °C to 28 °C and 22 °C to 26 °C and one type salt hydrate with a phase change temperature range 24 °C to 25 °C were used in air flows ranging in temperature from 30 °C to 35 °C and duct air velocities ranging from 0.4 m/s to 0.9 m/s. The results indicated that average effectiveness of the PCM modules decreased with increasing convective air mass flow rate. Increasing air mass flow rate (at constant inlet air temperature) or increasing the inlet air temperature (at constant air mass flow rate) increased the average cooling power. The phase transformation durations of the PCMs decreased as both the air flow rate and inlet air temperature increased. The salt hydrate (SP24E) module had the highest energy absorption capacity for all experimental conditions. The rate of energy absorption increased with inlet air temperature. From a design standpoint the desirable thermal performance of PCM is to have a high instantaneous heat absorption capacity and also extended over a longer period. Paraffinic PCMs met the first condition of high instantaneous heat absorption but did not meet the second condition of extended heat absorption duration. SP24E met the condition for extended heat absorption duration but had a lower instantaneous heat absorption capacity than the paraffin. Empirically-based correlations for determining the number of modules to maintain an objective cooling load were developed using a multiple regression analysis technique. From this, air conditioning system designers can determine the number of modules (installed in parallel) required to maintain an objective cooling load within the range of operating conditions tested. / Dissertation (MSc)--University of Pretoria, 2017. / Mechanical and Aeronautical Engineering / MSc / Unrestricted