Plasmodium falciparum is a protozoan parasite that causes a severe form of malaria, a mosquito-borne infectious disease in humans. P. falciparum encodes a number of proteins to facilitate its life-cycle, including a type II heat shock protein 40 (Hsp40), Pfj2. Pfj2 shows a degree of homology to human ERdj5, a resident protein of the endoplasmic reticulum (ER) that promotes protein quality control by facilitating the degradation of misfolded proteins. The overall aim of this study was to further understand the function of Pfj2 in the P. falciparum cell by characterising it biochemically. A bioinformatic analysis of Pfj2 was carried out to enable the identification of a potential ER signal sequence and cleavage site. Furthermore, an analysis of Pfj2 protein sequence was performed to compare domain similarities and identities with typical type II Hsp40s namely, human ERdj5, S. cerevisiae Sis1, human Hsj1a and human DnaJB4. The method used included the insertion of the codon-optimised coding sequence for the processed ER form of Pfj2 into the prokaryotic expression vector, pQE30, to enable overproduction of a histidine-tagged protein. A 62 kDa His₆-Pfj2 was successfully expressed in Escherichia coli and purified using denaturing nickel affinity chromatography. ATPase assays were performed to determine the ability of His₆- Pfj2 to stimulate the chaperone activity of the ER Hsp70, also called immunoglobulin binding protein (BiP). Initial studies were conducted on readily available mammalian His₆-BiP as a control, which was shown to have an intrinsic activity of 12.07±3.92 nmolPi/min/mg. His₆- Pfj2 did not stimulate the ATPase activity of mammalian His₆-BiP, suggesting that it either could not act as a co-chaperone of mammalian His₆-BiP (specificity), or it required a misfolded substrate in the system. Therefore, ongoing studies are addressing the interaction of Pfj2 and misfolded substrates with P. falciparum BiP. The results of these studies will further our understanding of a poorly-studied parasite chaperone that represents a potential drug target for development of novel strategies for the control of a serious human disease

Magister Curationis - MCur / Background: Health care workers, more specifically, nursing students are at increased risk of occupational injury and exposure to blood borne pathogens. Compliance with universal precautions (UP) will minimise risk or transmission of HIV and HBV (Hepatitis B virus) according to the Department of Health of South Africa. Aim: The aim of this study was to investigate the knowledge and practice of universal precautions amongst nursing students and their fear of occupational exposure to blood borne pathogens. Rationale: The rationale for the study was to investigate what the studentss knowledge and practice of UP were, to see if this could be a possible contributing factor to occupational exposure. Research design: The study was a quantitative, cross sectional survey using a questionnaire that included one open ended question. Participants: The participants for the study were the undergraduate nursing students in year levels two to four (n = 253) who and were selected by means of stratified random sampling. Procedures: A questionnaire was administered to the participants by the researcher. Analysis of the data collected was done through statistical package for social sciences (SPSS 16.0) and content analysis. Results: The researcher established that there is indeed a lack of knowledge regarding UP and that the students’ self reported practice of UP is poor. No statistically significant correlation between knowledge and practice of UP were found. There is underreporting of occupational exposures to staff at the School of Nursing. The majority of students reported a moderate to severe fear for occupational exposures and contributing factors raised by them are reality in the clinical facilities. / South Africa

Chagas disease is caused by the parasite Trypanosoma cruzi and transmitted by multiple triatomine vectors across the Americas. In Central America, the predominant vector is Triatoma dimidiata, a highly adaptable and genetically diverse Hemiptera. In this research, we used a novel reduced-representation DNA sequencing approach to discover community dynamics among multiple biotic factors associated with Chagas disease in Central America, and assess the infestation patterns of T. dimidiata after seasonal and chemical disturbances in Jutiapa, Guatemala. For our first study, we used a hierarchical sampling design to obtain multi-species DNA data found in the abdomens of 32 T. dimidiata specimens from Central America. We aimed to understand (1) the prevalence of T. cruzi infection, (2) the population genetics of the vector and parasite, (3) the blood meal history of the vector, and (4) gut microbial diversity. Our results indicated the presence of nine infected vectors harboring two distinct DTUs: TcI and possibly TcIV. We found significant clusters among T. dimidiata populations in countrywide and within-country levels associated with sylvatic ecotopes and diverse domestic genotypes. There was significantly higher bacteria species richness in infected T. dimidiata abdomens than those that were not infected, with further analysis suggesting that gut bacteria diversity relates to both T. cruzi infection and the local environment. We identified vertebrate blood meals from five T. dimidiata abdomens including chicken, dog, duck and human; however, additional detection methods are necessary to confidently identify blood meal sources. In our second study, we analyzed the GBS genotypes of 440 T. dimidiata specimens collected in two towns of Jutiapa, Guatemala. Our aim was to assess (1) the domestic population patterns that aid the recovery of T. dimidiata after an insecticide treatment in El Carrizal and (2) the seasonal changes that regulate the dispersal of the vector in the untreated communities of El Chaperno. Results showed that the insecticide application was effective at reducing the population abundance immediately after the application in El Carrizal; nevertheless, 18-month post-treatment the town-wide infestation and genetic diversity were recovering. Within-house relatedness among specimens recovered 18 months post-treatment, suggesting that the insecticide treatment failed to fully eliminate domiciliated colonies. In contrast, lack of change in abundance or genetic diversity in El Chaperno implied absence of dispersers from sources beyond the town periphery, while evidence of a decrease of relatedness among individuals implied dispersal among houses. After the insecticide treatment in El Carrizal, population reduction led to lack of genetic spatial autocorrelation; nevertheless, rapid dispersal into neighboring houses lead to autocorrelation 18 months after the insecticide treatment. This pattern was also observed in El Chaperno, where an increase in spatial autocorrelation during seasonal dispersal suggests spillover to close-by households. The creation of a novel genomics pipeline allowed us to understand community and dispersal patterns of T. dimidiata and other biotic factors important for the prevalence and transmission of Chagas disease at local and regional levels. Future studies should include complementary approaches for taxa verification (e.g. bacteria 16S barcoding, PCR-base detection), as well as expand the scope of local population analyses to peridomestic and sylvatic genotypes that could suggest a broader range of vector sources and region-wide patterns of temporal and spatial dispersion.

This study attempted to characterise 5 field stocks of B. canis, collected from various geographic areas of southern Africa in terms of pathogenicity, immune response, cross resistance and antigenic composition. This was done by means of artificial infection of two to four year old Beagle dogs. Serological tests included indirect fluorescent antibody tests, polyacrylamide gel electrophoresis , Western blotting of B. canis antigen and immune serum transfers. The ZIM1, GHT1 , QTN1 and DBN1 stocks were found to be virulent and the JHB1 stock, which might be a cardiac form of babesiosis, was found to be highly virulent. Immune responses of dogs to primary challenges were poor. A second challenge or relapse was important in the development of a resistant immunity. Heterologous challenges showed that dogs which were immune to the ZIM1, QTN1 and DBN1 stocks were partially immune to the JHB1 stock. The dog that was immune to the GHT1 stock was the only one that was totally resistant to the JHB1 stock. Western blots revealed interstock antigenic variation between the JHB1 and the other four stocks. These differences were, however, not great enough to separate the stocks taxonomically.

Kumba Iron Ore, Ltd. is the world‘s fourth largest supplier of sea-borne iron ore and currently operates two mines in South Africa namely: the Sishen mine in the Northern Cape and Thabazimbi mine in Limpopo. The Sishen mine, located at the northern end of the Maremane anticline where the bulk of the hematite ore is buried beneath younger cover lithologies, was our focus area. Here the iron resources are made up by laminated and massive ore bodies that belong to the Asbestos Hills Subgroup. These ore bodies are overlain by conglomerates, shales, flagstone and quartzite. The alkalis, potassium and phosphorous, are common constituents of iron ore, which is known to have a deleterious effect on the manufacturing of iron and steel. Therefore steel making companies charge penalties when purchasing iron ore concentrates with alkali concentrations above predetermined levels. To ensure that the export batches at the Sishen mine stay within set limits, the ores from different batches (with alkali concentration greater and below set limits) are mixed to produce a batch which meet requirements. However this solution will soon become ineffective as the low alkali ore is progressively depleted. Conventional methods used to treat high alkali ores include pyro-and hydrometallurgical methods. These approaches have several limitations such as poor product recovery, involvement of high process and energy cost and an increase in pollution load of water resources. Therefore necessitating research and development of alternative cheap and environment friendly procedures, which could supplement or replace conventional methods to ensure that mining stays economically feasible at the Sishen Iron Ore mine. The application of microorganisms to mining practices is collectively referred to as biohydrometallurgy and includes bioleaching and biooxidation processes. The phrase bioleaching refers to the conversion of an insoluble metal (typically a metal sulfide) into a soluble form (typically a metal sulfate), via microbial activity. When metals are extracted into solution, the process is referred to as bioleaching, whereas if the metal remains in the mineral, it is referred to as biooxidation. The latter term biobeneficiation refers to the selective dissolution of undesired minerals from the ores by direct or indirect action of microbes, thereby enriching the desirable mineral content. Therefore the objective of this study was to determine whether bacteria (naturally occurring on the ore or introduced species) could be used to selectively remove the alkalis from the iron ore mined at Sishen. The species evaluated were able to change the solution pH and/or form biofilms, which is assumed to have affected mineral mobilization. Data obtained during this study suggests that the composition of the ore plays a significant role in its susceptibility to bioleaching. Furthermore we also found that the indigenous cultures were more effective than the introduced species to mobilize the alkalis, which could possibly be ascribed to an adaptation of the microbes present. These preliminary results suggest that bioleaching is an effective alternative cost effective approach to treat iron ore and could possibly be implemented in future into the mining schedule at Sishen. / Dissertation (MSc)--University of Pretoria, 2011. / Microbiology and Plant Pathology / unrestricted

L’émergence des formes d'onde numériques en radar et l’engouement de la communauté scientifique pour leur versatilité éprouvée en télécom, soulèvent naturellement chez les ingénieurs radaristes la question de l’amélioration effective des performances opérationnelles par ces nouvelles formes d’onde, notamment en matière de haute-résolution. Les travaux publiés sur le sujet sont prometteurs, à ceci près qu’ils sont le plus souvent basés sur des modèles théoriques un peu éloignés de la réalité opérationnelle ou sur des scénarios simplistes relativement à la capacité haute résolution envisagée (par exemple le faible nombre de sources pris en compte). En effet la prise en compte d’un modèle d’observation réaliste (large bande, à fréquence d’échantillonnage élevée) et de scénario à grand nombre de contributeurs conduit à des estimateurs dont la complexité d’implémentation n’est pas compatible des puissances de calcul actuelles. Une approche alternative, et compatible des puissances de calcul actuelles, pour la qualification des performances haute résolution est l’utilisation des bornes inférieures d’estimation, principalement la borne de Cramèr-Rao déterministe. L’examen de la littérature courante (notamment les monographies de référence) sur la borne de Cramèr-Rao déterministe a fait apparaître des lacunes relatives à sa formulation dans le contexte radar qui nous intéresse, à savoir MIMO large bande, multisources, multiparamètres à observations multiples. En effet dans la littérature courante, les observations multiples sont définies comme des réalisations multiples indépendantes d’un même modèle d’observation, alors qu’en radar il s’agit en général de la combinaison de modèles d’observation différents (variation de la forme d’onde). Ce constat a motivé l’essentiel de ce travail, à savoir l’établissement d’une expression analytique générale de la borne de Cramèr-Rao déterministe MIMO large bande, multisources, multiparamètres à modèles d’observations multiples pour la qualification (asymptotique) des performances en estimation d’un radar actif. Ce travail fournit un outil de comparaison des performances haute-résolution des différentes formes d’onde, dont les nouvelles formes d’onde numériques. De façon générale, l’expression analytique générale de la borne de Cramèr-Rao obtenue fournit la base théorique pour le développement des futurs radars à haute résolution. / The emergence of digital waveforms in radar and the enthusiasm of the scientific community for their versatility proven in telecom raise the question for radar engineers about improving operational performance by using these new waveforms, particularly in high-resolution scenarios. The results on the subject in open literature are promising, except that they are often based on theoretical models which are a little away from the operational reality or used in simplistic scenarios (e.g. the low number of sources taken into account). Indeed, taking into account a realistic observation model (wideband, high sampling frequency and multisource scenario) leads to estimators whose implementation complexity is not compatible with the computation power available nowadays. An alternative approach is the use of lower bounds on the mean square error of estimators, mainly the deterministic Cram´er-Rao bound. The review of the open literature (including reference books) on the deterministic Cramér-Rao bound reveals lacks in its formulation in the context of radar that interests us, namely MIMO wideband, multisource, multiparameter and multiple observations. Indeed, in the current literature, multiple observations are defined as multiple independent realizations of the same observation model, whereas in radar it is usually a combination of different observation models (waveforms change). This has motivated much of our work, namely the derivation of a general analytical expression for the Cram´er-Rao bound for deterministic MIMO wideband active radar. This work provides a tool for comparing the performance of different highresolution waveforms, including new digital waveforms. In general, the analytical expression of the general Cramér-Rao bound obtained provides the theoretical basis for the development of future high-resolution radar.

The control of ticks, and to some extent tick-borne diseases, over much of South Africa is currently dependent on acaricides and will probably remain so for the foreseeable future. Resistance to these chemicals by ticks thus poses a major threat to the livestock industry especially as these chemicals constitute an ever-diminishing resource with fewer being discovered and the cost of their development becoming prohibitive. In order to determine the extent of acaricide resistance in the eastern region of the Eastern Cape Province one-, two- and three-host ticks were collected from cattle at 58 dip-tanks over a period of 2 years. The one-host tick selected was Rhipicephalus (Boophilus) microplus, the two-host tick Rhipicephalus evertsi evertsi and the three-host tick Rhipicephalus appendiculatus. The ticks were tested for resistance to three compounds, namely amitraz, cypermethrin and chlorfenvinphos. The Shaw Larval Immersion Test detected emerging resistance to amitraz in the one-host tick R. (Boophilus) microplus at two dip-tanks and resistance at a third. It also revealed resistance in this tick to cypermethrin at one dip-tank, and emerging resistance to chlorfenvinphos at eight dip-tanks and resistance at two. The two-host tick R. evertsi evertsi was susceptible to amitraz and cypermethrin at all dip-tanks, but showed emerging resistance to chlorfenvinphos at seven dip-tanks and resistance at four. The three-host tick R. appendiculatus was susceptible to amitraz and chlorfenvinphos at all dip-tanks and demonstrated emerging resistance to cypermethrin at one. With the exception of R. (Boophilus) microplus, in which emerging resistance to amitraz was detected at one dip-tank by the Reproductive Estimate Test, all three tick species at all dip-tanks at which sufficient numbers of ticks had been collected, were susceptible to the three acaracides in both the Egg Laying Test and the Reproductive Estimate Test. Thus despite its fairly long and widespread use in the eastern region of the Eastern Cape Province very little or no resistance to amitraz was detected in three tick species regularly encountered on cattle in this region, namely R. (Boophilus) microplus, R. evertsi evertsi and R. appendiculatus. On the other hand resistance to chlorfenvinphos was detected in both R. (Boophilus) microplus and R. evertsi evertsi at a number of dip-tanks even though it, or other organophosphorous-based compounds, had probably not been used for tick control in the region for a number of years. The localities at which ticks were collected had already been mapped and the localities at which acaricide resistant ticks were encountered were mapped during this study. The three tick species that were targeted for acaricide resistance testing were widespread throughout the study region, but no pattern of geographic distribution for the acaricide resistant strains of these species that were detected, emerged. The rapidity of selection for acaricide resistance appeared to be closely related to the life cycles of the three ticks and the number of days that they theoretically would spend annually on their preferred host animals. Thus a greater number of acaricide resistant strains were encountered amongst the one-host tickR. (Boophilus) microplus and the two-host tick R. evertsi evertsi than the three-host tick R. appendiculatus. The fist two ticks both complete more than one life cycle a year and hence spend a longer time on their cattle hosts than the three-host tick R. appendiculatus, which completes only one life cycle a year and in addition is a rapid feeder in all its stages of development. To counter selection for acaricide resistance it is proposed that regular testing for resistance should be carried out, and that as soon as emerging resistance is detected in ticks on cattle at a particular dip-tank, that the acaricide in use at that dip-tank should be changed to a compound belonging to a completely different group of chemicals. Copyright / Dissertation (MSc)--University of Pretoria, 2009. / Veterinary Tropical Diseases / unrestricted

Thesis (M.Sc. (Agriculture)) --University of Limpopo, 2017 / Root-knot nematodes (Meloidogyne species) are the major soil-borne pests of tomato (Solanum lycorpesicum) plants. Due to the global withdrawal of effective chemical nematicides from the agrochemical markets, nematodes are difficult to control under the production systems. Currently, botanicals are being researched and developed as alternative to chemical nematicides with promising results, although they have challenge of phytotoxicity. The objective of this study was to determine the Mean Concentration Stimulation Point (MCSP) of Tickberry (Lantana camara) extracts for tomato plant-infected with M. javanica. Treatments consisted of six levels of L. camara extracts, namely, 0, 2, 4, 6, 8 and 10% per pot, which were arranged in a randomised complete block design, with ten replicates. Tomato seedlings were inoculated with 2500 second-stage juveniles (J2S) of M. javanica at five days after transplanting, with treatments applied at seven days after inoculation. At 56 days after inoculation, L. camara extracts had positive effects on plant height, stem diameter, number of leaves, number of fruits and fruit mass, contributing 65, 74, 61, 25 and 61% in total treatment variation (TTV), respectively, under greenhouse conditions. Under microplot conditions, treatments contributed 55, 85, 61, 36 and 85% in TTV of the respective plant variables. Under greenhouse it contributed 60, 35 and 77% and 29, 79 and 70% under microplot on dry shoot mass, dry root mass and galling index respectively. Treatments did not have any effects on soil pH and electrical conductivity (EC). Under greenhouse conditions, treatments contributed 88, 94 and 92% in TTV of nematode in roots, soil and final population, respectively, whereas under microplot conditions 94, 97 and 95% in xvii TTV of the respective nematode stages. The derived mean concentration of L. camara extracts for tomato was 5.76 and 5.31% under microplot and greenhouse conditions, respectively. The overall sensitivity of tomato plants to L. camara extracts under microplot and greenhouse were 3 and 0, respectively. In conclusion Meloidogyne species can be managed using L. camara extracts 5.31 and 5.76% under glasshouse production and field production system respectively.

Listeria monocytogenes is the etiological agent of listeriosis in humans and ruminants causing bacteremia, central nervous system (CNS) infections, abortion, and gastroenteritis among other clinical outcomes. Recent studies have integrated whole genome sequence (WGS), epidemiology data, and host susceptibility to provide evidence for variation in virulence among strains, as a small number of hypervirulent clones have been found linked to a high proportion of human and ruminant invasive listeriosis cases, however, still little is known about variation in virulence across different L. monocytogenes subgroups. To assess and compare the genetic diversity of clinical listeriosis isolates from ruminants in the Upper Great Plains states, we used multilocus sequence typing (MLST) and found that the variation in virulence potential varies among clonal complex (CC), which is reflected in the epidemiology of L. monocytogenes. Based on these results, we evaluated the strains’ virulence potential in Galleria mellonella through larvae survival, LD50, and cytotoxicity, and monitored health index scores and bacterial concentrations post-infection as quantifiable indicators of virulence and immunogenicity. Our findings suggest that strains belonging to CC14, as well as isolates from MN infections are hypervirulent in G. mellonella, as they need a lower bacterial concentration to cause disease and produce a low-level infection that could help in evading the host immune response. We also identify genomic elements associated with strains causing three different clinical outcomes: bacteremia, central nervous system infections, and maternal-neonatal infections. By analyzing 232 whole genome sequences from invasive listeriosis cases, we identified orthologous genes of phage phiX174, transfer RNAs and type I restrictionmodification (RM) system genes along with SNPs in loci associated with environmental adaptation such as rpoB and the phosphotransferase system (PTS) associated with one or more clinical outcomes. Novel genetic variants may be associated with a particular virulence phenotype, as it is likely that strains causing the same clinical outcome share unique genetic elements. Variation in virulence among L. monocytogenes subgroups may confer an increased ability to cross host barriers or higher adaptability to food processing environments, thus the investigation of strainspecific genetic features can impact the design of prevention and management plans for listeriosis.

This observational study of 100 dogs naturally infected with Babesia rossi determined whether severity of parasitaemia was associated with outcome of infection and documented the relative distribution of parasitised red blood cells (pRBC) in capillary and venous circulation. The association between increased parasitaemias and outcome with a clinically compromised circulation was also investigated. Outcome was defined as either hospitalisation with death, or hospitalisation with eventual recovery or treatment as an outpatient. Dogs were enrolled if large babesias were found on stained thin capillary blood smears made from an ear prick. Thin venous smears were prepared from jugular or cephalic blood. Parasitaemias were manually counted and expressed as the percent pRBC. Ten dogs died, 50 recovered after hospitalisation and 40 were treated as outpatients. Venous sampling site did not affect venous parasitaemia (P = 0.6). Both capillary and venous parasitaemias of dogs that died were significantly higher than those of dogs that recovered after hospitalisation (P = 0.002) and dogs that were treated as outpatients (P < 0.0001). When assessing the whole group, capillary parasitaemia (median 0.61%, range <0.05-71.6%, interquartile range (IQR) 0.22-3.75%) was significantly higher than venous parasitaemia (median 0.14%, range 0-30.6%, IQR 0.046–0.52%) with P < 0.0001. The 21 dogs with a clinically compromised circulation were more likely to die (P <0.0001) and had significantly higher capillary (median 5.98%, range 0.09-71.6%, IQR 2.44-19.41%) and venous (median 2.81%, range <0.05-30.6%, IQR 0.17-9.03%) parasitaemias than the 79 dogs with a clinically normal circulation (capillary median parasitaemia 0.38%, range <0.05-12.87%, IQR 0.16-1.42%; venous median parasitaemia 0.096%, range 0-6.13%, IQR <0.05-0.33%; P < 0.0001). This study shows that high parasitaemia is significantly associated with death in B rossi infected dogs. Unfortunately, there was a wide overlap in the parasitaemias of the three outcome groups with the result that neither capillary nor venous parasitaemias appear prognostically useful. The previous clinical suspicion that capillary parasitaemias are usually higher than venous parasitaemias is confirmed. Thus capillary samples are the most appropriate diagnostic samples. Prior observations that a clinically compromised circulation is associated with death are confirmed. This association provides a rapid means of identifying patients in need of intensive monitoring and treatment. Despite the highly significant association between compromised circulation and higher parasitaemia, it is thought unlikely that parasite burden is the sole trigger for circulatory collapse. Copyright 2006, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Bohm, M 2006, The comparative assessment of capillary and venous Babesia rossi parasitaemias on thin blood smears and their association with disease manifestation, MMedVet dissertation, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-05042007-154527 / > / Dissertation (Master of Veterinary Medicine (Small Animal Medicine))--University of Pretoria, 2006. / Companion Animal Clinical Studies / unrestricted