Master of Science / Department of Horticulture, Forestry, and Recreation Resources / Jack D. Fry / Dollar spot, caused by Sclerotinia homoeocarpa F.T. Bennett, and silvery-thread moss (Bryum argenteum Hedw.) are pests affecting creeping bentgrass (Agrostis stolonifera L.) that typically require pesticide inputs. New strategies for pest management may reduce chemical inputs. The objectives of these 2009-2010 field studies were to evaluate: 1) creeping bentgrass cultivars for dollar spot susceptibility; 2) alternative chemical controls for silvery-thread moss; and 3) the response of silvery-thread moss to nitrogen (N) sources. During peak dollar spot development, ‘Declaration’, ‘A-4’, and ‘Crenshaw’ had 7.5, 139.4, and 288.9 infection centers m[superscript]-2 under fairway and 2.1, 27.2, and 106.9 infection centers m[superscript]-2 under putting green conditions, respectively. Two spring and two fall spot applications of sodium or potassium bicarbonate (45 g a.i. L[superscript]-1), premixed essential oil, and broadcast applications of carfentrazone-ethyl at 0.09 kg a.i. ha[superscript]-1 suppressed moss 39% to 55% compared to untreated in 2009. Spot sprays of sodium or potassium bicarbonate, and essential oil, were phytotoxic to creeping bentgrass and required up to 8 or 18 days, respectively, to return to acceptable quality. Fertilization with liquid urea (N at 16.3 kg ha[superscript]-1 biweekly, 210 kg ha[superscript]-1 annually) resulted in 147%, 150%, and 155% more moss than fertilization with IBDU, organic N, and granular urea, respectively, and 156% more moss compared to untreated. Fertilization with urea (liquid or granular) resulted in the best creeping bentgrass color. Averaged across the entire season, plots treated with organic N had unacceptable color in 2009. Nitrogen concentrations in moss tissue ranged from 0.4% to 1.0% and were always significantly lower than N concentrations observed in creeping bentgrass (1.1% to 2.1%), regardless of treatment. In 2010, moss treated with liquid urea had higher tissue N concentrations (1.0%) than untreated moss (0.5%) or that fertilized with IBDU (0.4%). In summary, use of dollar spot-resistant creeping bentgrass cultivars could reduce fungicide requirements. Bicarbonate and essential oil products can reduce moss severity at a similar level to carfentrazone-ethyl, but rates and/or application methods need to be optimized to avoid injury to creeping bentgrass. Applications of liquid urea enhanced moss coverage in creeping bentgrass compared to other N sources.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Harvey Morgan Scott / A randomized controlled field trial was designed to evaluate the effects of two treatment strategies on ceftiofur and tetracycline resistances in feedlot cattle. The two strategies consisted of administering ceftiofur crystalline-free acid administration (CCFA) at either one or else all of the steers within a pen, and subsequent feeding/not feeding of therapeutic doses of chlortetracycline. Both strategies were hypothesized to reduce ceftiofur resistance. The effects of treatment strategies were evaluated via metagenome-based and culture-based assays. In this 26-day study, 176 steers were allocated to 16 pens of 11 steers each. The two strategies were randomly assigned to the pens in a two-way full-factorial manner resulting in four treatment groups. The blaCMY-2, blaCTX-M, tet(A), tet(B), and 16S rRNA gene copies/g feces were quantified using qRT-PCR from fecal community DNA. Antimicrobial susceptibility profiles were determined using microbroth dilution technique from the non-type-specific (NTS) E. coli isolates (n=1,050). The NTS E. coli DNA was screened for the presence of blaCMY-2, tet(A), and tet(B) genes. Pens in which all the steers received CCFA treatment showed an increase in blaCMY-2 and blaCTX-M log10 gene copies/g feces and in the proportion of ceftiofur-resistant and blaCMY-2 positive NTS E. coli. This was in contrast to the pens where only one animal received CCFA treatment. There was a significant decrease in quantities of tetracycline genes in community DNA in pens where all animals received CCFA treatment. In contrast to metagenome-based assay results, culture-based assays indicated an increase in the proportion of tetracycline resistant NTS E. coli upon CCFA treatment. Thereafter, chlortetracycline administration led to rapid expansion both of ceftiofur (blaCMY-2, blaCTX-M) and tetracycline [tet(A) and tet(B)] log10 gene copies/g feces. Chlortetracycline treatment delayed the return of the ceftiofur resistance prevalence to baseline among NTS E. coli and thus did not lead to the hypothesized decrease in ceftiofur resistance. Our data suggest that chlortetracycline use is contraindicated when attempting to avoid expansion of resistance to critically important 3rd generation cephalosporins in feedlot cattle. Further studies are required to better establish the animal-level effects of co-housing antimicrobial-treated and non-treated animals together at varying ratios on the levels of antimicrobial resistance.

Several yeast species had previously been isolated from water systems in the North West Province, South Africa. Some of the identified species had, in other studies, been associated with superficial mucosal infections to life threatening diseases. Antifungal drugs are used to treat such yeast infections. However, due to prophylactic usage and continuous exposure some yeast species have developed resistance to some antifungal agents. The aim of this study was to determine the diversity and antifungal susceptibility of yeasts in selected rivers, Mooi River and Harts River in the North West Province, South Africa. Waters samples were collected from the rivers in summer and winter seasons. Physico-chemical parameters such as pH, temperature, total dissolved solids, chemical oxygen demand, nitrates and phosphates were measured to determine the water quality. Yeast colonies were enumerated at room temperature and 37°C using yeast-malt-extract agar (containing 100 ppm chloramphenicol). Pure isolates from 37°C were identified by biochemical tests and 26S rRNA gene sequencing. Yeast sequences of isolated yeasts were sent to Genbank. Phylogenetic tree was conducted to determine phylogenetic relationship between the yeast isolates. Disk diffusion antifungal susceptibility tests were conducted on the yeast species. Physico-chemical parameters of the water were within target water quality range for livestock farming but in most sampling sites out of range for irrigation use. pH, Nitrates, phosphates and chemical oxygen demand levels ranged from 7.40 to 8.64, 0 to 5.4 mg/L, 0 to 7.14 mg/L and 31 to 43 mg/L, respectively. Elevated levels of total dissolved solids were measured in all the sampling sites. Total yeast counts ranged between 320-4200 cfu/L and 27-2573 cfu/L for room temperature and 37˚C. All the yeast colonies isolated were non-pigmented. Diazonium Blue B tests determined the yeasts isolates as ascomycetes. Haemolysin and extracellular enzyme production tests were negative on all the isolates. Yeasts isolates were identified and belonged to the genera Arxiozyma, Candida, Clavispora, Cyberlindnera, Lecythophora, Pichia, Saccharomyces, and Wickerhamomyces. Saccharomyces cerevisiae and Candida glabrata were mostly isolated species. Furthermore, the results indicated that levels of yeast could be correlated to physico-chemical quality of water. A large number of isolates were resistant to azoles, especially fluconazole as well as other antifungal classes. Most of the Candida species were resistant to almost all the antifungals. Several of the isolated yeast species are opportunistic pathogens. They could cause infections in sensitive individuals during occasional direct contact especially immune compromised people. Resistance of these yeast species to antifungal agents is a major health concern. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Several yeast species had previously been isolated from water systems in the North West Province, South Africa. Some of the identified species had, in other studies, been associated with superficial mucosal infections to life threatening diseases. Antifungal drugs are used to treat such yeast infections. However, due to prophylactic usage and continuous exposure some yeast species have developed resistance to some antifungal agents. The aim of this study was to determine the diversity and antifungal susceptibility of yeasts in selected rivers, Mooi River and Harts River in the North West Province, South Africa. Waters samples were collected from the rivers in summer and winter seasons. Physico-chemical parameters such as pH, temperature, total dissolved solids, chemical oxygen demand, nitrates and phosphates were measured to determine the water quality. Yeast colonies were enumerated at room temperature and 37°C using yeast-malt-extract agar (containing 100 ppm chloramphenicol). Pure isolates from 37°C were identified by biochemical tests and 26S rRNA gene sequencing. Yeast sequences of isolated yeasts were sent to Genbank. Phylogenetic tree was conducted to determine phylogenetic relationship between the yeast isolates. Disk diffusion antifungal susceptibility tests were conducted on the yeast species. Physico-chemical parameters of the water were within target water quality range for livestock farming but in most sampling sites out of range for irrigation use. pH, Nitrates, phosphates and chemical oxygen demand levels ranged from 7.40 to 8.64, 0 to 5.4 mg/L, 0 to 7.14 mg/L and 31 to 43 mg/L, respectively. Elevated levels of total dissolved solids were measured in all the sampling sites. Total yeast counts ranged between 320-4200 cfu/L and 27-2573 cfu/L for room temperature and 37˚C. All the yeast colonies isolated were non-pigmented. Diazonium Blue B tests determined the yeasts isolates as ascomycetes. Haemolysin and extracellular enzyme production tests were negative on all the isolates. Yeasts isolates were identified and belonged to the genera Arxiozyma, Candida, Clavispora, Cyberlindnera, Lecythophora, Pichia, Saccharomyces, and Wickerhamomyces. Saccharomyces cerevisiae and Candida glabrata were mostly isolated species. Furthermore, the results indicated that levels of yeast could be correlated to physico-chemical quality of water. A large number of isolates were resistant to azoles, especially fluconazole as well as other antifungal classes. Most of the Candida species were resistant to almost all the antifungals. Several of the isolated yeast species are opportunistic pathogens. They could cause infections in sensitive individuals during occasional direct contact especially immune compromised people. Resistance of these yeast species to antifungal agents is a major health concern. / MSc (Environmental Sciences), North-West University, Potchefstroom Campus, 2015

Laser beam welding has gained a significant interest during the last two decades. The suitability of the process for high volume production has the possibility to give a strong advantage compared to several other welding methods. However, it is important to have the process in full control since various quality issues may otherwise occur. During laser welding of boron steels quality issues such as imperfections, changes in local and global geometry as well as strength reduction can occur. The aspects that need to be considered are strongly depending on alloy content, process parameters etc. These problems that can occur could be fatal for the construction and the lowest level of occurrence is wanted, independent of industry. The focus of this study has been to investigate the properties of laser welded boron steel. The study includes laser welding of boron alloyed steels with strengths of 1500 MPa and a recently introduced 1900 MPa grade. Focus has been to investigate weldability and the occurrence of cracks, porosity and strength reducing microstructure that can occur during laser welding, as well as distortion studies for tolerances in geometry. The results show that both conventional and 1900 MPa boron alloyed steel are suitable for laser welding. Due to the martensitic structure of welds the material tends to behave brittle. Cracking and porosity do not seem to be an issue limiting the use of these steels. For tolerances in geometry for larger structures tests has been done simulating laser welding of A-pillars and B-pillars. Measurements have been done with Vernier caliper as well as a more advanced optical method capturing the movements during the welding sequence. Results from the tests done on Ushaped beams indicates that depending on the geometry of the structure and heat input distortions can be controlled to give distortions from 1 to 8 mm, at a welding length of 700 mm. This means that important geometry points can be distorted several millimeters if the laser welding process not is controlled.

Thesis (MScMedSc (Biomedical Sciences))--University of Stellenbosch, 2010. / Thesis presented in partial fulfillment of the requirements for the degree Master of Science in Medical Biochemistry at the University of Stellenbosch. / Bibliography / ENGLISH ABSTRACT: Tuberculosis (TB) is an infectious disease which has plagued society for thousands of years. Despite public health programs, anti-TB drugs and a vaccine, the absolute numbers of people infected with TB each year continue to rise as populations grow. The high TB-burden areas are also plagued by other debilitating factors including HIV/AIDS infection, poverty and malnutrition. Nutrition has been implicated in TB susceptibility in a number of studies. While most are observational reports made during times of war, famine or natural disaster, multiple studies provide convincing evidence for poor nutritional status increasing the morbidity and mortality of TB. Numerous approaches are currently utilized in TB research, and there has been convincing evidence to support the role of host genetics in TB susceptibility. Based on previous linkage studies and a search of current literature, three genes were selected for this case-control study. Subsequently, variations located in cathepsin Z (CTSZ), melanocortin 3 receptor (MC3R) and melanocortin 4 receptor (MC4R) were genotyped in the South African Coloured (SAC) population to determine the existence of an association with TB disease. CTSZ is a lysosomal cysteine protease expressed in cells of the immune system. Interaction between this 303 amino acid protein and β2 integrin receptors lymphocyte function-associated antigen-1 (LFA-1) and macrophage antigen-1 (MAC-1) leads to altered lymphocyte proliferation. As a result, a single exonic variant in CTSZ, rs34069356, the same identified in a previous linkage study, showed strong evidence for association with TB susceptibility in cases (n = 410) and controls (n = 301) in the SAC population (p< 0.0001). MC3R and MC4R are two of 5 melanocortin receptors. MC3R has been found to be a key regulator in energy expenditure and host metabolism while activation of MC4R leads to a decrease in food intake. Activation of these two receptors is regulated by leptin, a hormone released by adipose tissue. A variant located upstream of the MC3R gene, rs6127698, also showed evidence of disease association with the less frequent allele, T, being under-represented in cases (n = 540) compared to controls (n = 541) (genotypic frequency, p = 0.0039), suggesting a possible resistance phenotype. Functional analysis of this variant revealed an increase in MC3R expression when stimulated with BCG, with individuals homozygous for the T allele exhibiting an even larger upregulation of MC3R expression than individuals homozygous for the G allele, though this difference was not statistically significant. A single haplotype in MC3R was found to be associated with TB susceptibility (p = 0.0008) and this association remained after permutation testing to correct for multiple testing (p = 0.0061) Three variants were selected for genotyping in MC4R and while none of these showed a statistically significant difference between cases (n = 510) and controls (n = 487), this gene should not be ruled out as both MC3R and MC4R have been found to work closely though not redundantly and double knockout experiments result in exacerbated obesity, suggesting that these proteins have a synergistic effect. The results of this study support both a role of host genetics and nutritional status in TB and strongly motivate further research in both of these fields. / AFRIKAANSE OPSOMMING: Tuberkulose (TB) is ‘n aansteeklike siekte wat reeds vir eeue die gesondheid van die publiek bedreig. Ten spyte van publieke gesondheidsprogramme en verskeie anti-TB medikasie middele, groei die aantal van mense wat hiermee ge-infekteer word steeds jaarliks. Dit is veral in areas waar TB steeds groei, waar ook ander neerdrukkende faktore soos HIV/Vigs, armoede en wanvoeding hoogty vier. Na aanleiding van verskeie verslae tydens oorloë, hongersnood en ander natuulike rampe is dit veral duidelik dat swak nutriënt inname morbiditeit en sterftes wat met TB gepaard gaan verhoog. Talle benaderings word tans gebruik in TB-navorsing, Bewyse is oortuigend om die rol van genetika van die gaheer met vatbaarheid vir TB te verbind. Op grond van vorige studies en die huidige literatuur, het ons drie gene gekies vir hierdie pasiënt-kontrole studie. Variante geleë in cathepsin Z (CTSZ), melanocortin 3 receptor (MC3R) en melanocortin 4 receptor (MC4R) is ge-genotipeer in die Suid-Afrikaanse Kleurling bevolking (SAK) (540 gevalle en 540 kontrole) om sodoende die assosiasie met TB te bepaal. CTSZ is ‘n lisosomale sisteïen protease wat uitgedruk word in immuunselle. Interaksie tussen hierdie 303 aminosuur protein en β2 integrin reseptore nl. LFA-1 en MAK-1 bring veranderde limfosiet proliferasie mee. ‘n Enkele eksoniese variant in CTSZ, rs34069356, dieselfde soos ge-identifiseer in ‘n vorige studie, verskaf sterk bewys vir assosiasie met TB vatbaarheid in gevalle (n = 410) en kontrole (n = 301) in die SAK bevolking. MC3R en MC4R is twee van 5 melanokortien reseptore. Daar is gevind dat MC3R 'n sleutelrol speel in die energie regulering van gasheer metabolisme, terwyl die aktivering van MC4R eindelik lei tot 'n afname in voedsel inname. Aktivering van hierdie twee reseptore word gereguleer deur Leptien, 'n hormoon wat vrygestel word deur adipose weefsel, ‘n Variant, stroomop geleë vanaf MC3R, rs6127698, is ook bewys om met TB ge-assosieer te wees, met die T-alleel meer seldsaam in gevalle (n = 540) as in kontroles (n = 541) wat dui op 'n moontlike weerstandsfenotipe. Funksionele analise van hierdie variant onthul 'n toename in MC3R uitdrukking wanneer gestimuleer met BCG, met individue homosigoties vir die T-alleel wat selfs groter opregulation veroorsaak wanneer vergelyk word met individue homosigoties vir die G allele. Hierdie resultaat was egter nie statisties beduidend nie. 'n Enkele haplotiepe in MC3R is ge-assosieer met TB vatbaarheid en die assosiasie is onveranderd nadat ‘n permutasie korreksie aangebring is (p = .0061). Voorts is drie variante gekies vir genotipering in MC4R en ten spyte daarvan dat nie een daarvan 'n statisties beduidende verskil getoon het tussen pasiënte (n = 510) en kontroles (n = 487) nie, behoort hierdie geen nie uitgesluit word nie, Die rede hiervoor is dat beide MC3R en MC4R verskeie kere gevind is om in samewerking ‘n rol te speel om vetsug te voorkom of te vererger. Die resultate van hierdie studie beaam beide 'n rol van gasheer genetika en voedingstatus in TB en motiveer veral verdere navorsing in beide van hierdie vakgebiede.

Thesis (PhD (Civil Engineering))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: In both developing and developed countries, to ensure sustained economic growth the quest for optimal roads performance is an extremely high priority. A global increase in the use of foamed bitumen and bitumen emulsion materials (BSMs) as a solution to roads maintenance, rehabilitation, and upgrading has become evident. This is driven by environmental policies aimed at conserving energy and limiting the exploitation of new borrows pits. It has therefore become imperative that BSMs are used optimally, and, in order to achieve this, practitioners need to understand the mechanisms that influence durability and long-term performance. The changes in the behaviour of materials and the failure mechanisms of BSM mixes are long-term phenomena. This implies that the study of the physicochemical and mechanical properties of the mixes is vital. Therefore, a fundamental understanding of the moisture damage and age-hardening characteristics, which are related to materials’ properties, is required. The main objective of this study is to advance BSM technology by assessing the influence of the selected materials on durability behaviour and long-term performance in all phases of application (i.e. mix design, construction, and in-service condition). This study begins with a comprehensive literature review of research dealing with the interactions of binder and mineral aggregates. The properties of bitumen (foamed bitumen or bitumen emulsion) and mineral aggregates were reviewed. This was followed by review into the colloidal behaviour of foam and emulsion and physicochemical and mechanical interaction with mineral aggregates. Factors influencing the interaction of BSMs were then identified. Finally, the fundamental theories on thermodynamics, hydrodynamics, and electrokinetics were used to describe the step-by-step process by which adhesive bonding and cohesion occur in BSMs. The mixture durability in terms of moisture damage was investigated. To achieve this aim, the physical and mechanical moisture-induced damage process was analysed. The test control parameters were established and a laboratory device to quantify these parameters designed. New moisture conditioning procedures were developed and demonstrated in this study. From the moisture induction simulation test (MIST) procedure, it became evident that pulsing water pressures into compacted and cured BSM mixes simulates the hydrodynamic effect that occurs in the field due to dynamic traffic loading. The different mix matrices typically applicable to the recycling processes – such as Hornfels-RAP and Quartzite crushed stone, stabilised with either foamed bitumen or bitumen emulsion and the addition of active filler (cement or lime) – were investigated. It was found that a new moisture-conditioning procedure using the MIST device and monotonic triaxial testing can distinguish those BSM mixes that are resistant to moisture damage from those that are less resistant. The validation of the MIST and monotonic test results was done using the APT device, which is the MMLS3 wet trafficking test. The results on both tests showed good correlations in evaluating and screening BSMs in terms of moisture susceptibility. Field temperature data was collected and a model to accurately simulate the curing of BSMs was identified and proposed for further investigation and validation. It was found from the field temperature data collected in this study that the temperature gradient on the study site varied according to the depth of the BSMs (that is, 10oC-17oC during winter and 17oC– 47oC during summer). Understanding the influence of the temperature conductivity and rate of evaporation is important for inferring moisture damage and age-hardening behaviour and proper selection of BSMs. The age-hardening behaviour of BSMs is linked to the durability properties and longterm performance of these materials. The fundamental characteristics associated with shortand long-term age hardening were investigated in this study. The short-term dimension involved assessing the age-hardening characteristics of the binder (foamed bitumen colloids and bitumen emulsion droplets) prior to the production of BSMs. The long-term study involved extracting and recovering the binder from the briquettes (made from different mixes) compacted in the laboratory and cores extracted from different field pavement sections which were in service for 8-10 years. The study found that the length of time bitumen is kept in circulation in the laboratory plant at elevated temperature (170oC–180oC) before making BSM-foam contributes to the ageing of the binder, especially after eight hours. The foaming process in itself was found not to alter the bitumen properties. It is recommended that a temperature range between 160oC- 165oC be used for the production of foamed bitumen with softer bitumen. This will not compromise its quality. In addition, the time of circulation of bitumen in laboratory plant should not be longer than three (3) hours. The rheological properties of the bitumen recovered from laboratory briquettes and cores from field pavement show that age hardening on foamed bitumen and bitumen emulsion during in-service life occurred. The ageing also seemed to be dependent on the effect of traffic, with trafficked areas (i.e. on-wheel path and inner-wheel path) experiencing more ageing than untrafficked areas (i.e. between-wheel path). However, the extraction and recovery process was found to be complex, and produce uncertain results. Although the results show that binders in BSMs undergo age hardening, its distinct behaviour in BSM performance was not obvious from the extensive tests carried out in this study. The last part of the study contains its conclusions and recommendations. The study provides an insight into fundamental material durability properties, and this will assist in improving the current procedure for selection, combining and formulation of the mix matrices for BSMs. In addition, the study provides guidelines that will enable practitioners to confidently apply a mix that is durable and long-lasting. The specific durability-related issues addressed in this study are substance for future research. This novel solution to the application of BSMs will benefit all parties involved in the development of pavement recycling technology. / AFRIKAANSE OPSOMMING: Om volgehoue ekonomiese groei te verseker in beide ontwikkelende en ontwikkelde lande, geniet die soeke na die optimale werkverrigting van paaie ’n baie hoë prioriteit. ‘n Wêreldwye toename in die gebruik van skuimbitumen en bitumen-emulsiemateriale (BSMs) as ’n oplossing vir padonderhoud, rehabilitasie en opgradering is merkbaar. Dit word meegebring deur die omgewingsbeleide wat die ontginning van nuwe leengroewe beperk en besparing van energie bevorder. Die korrekte gebruik van hierdie materiale vereis dat die meganismes wat die duursaamheid en langtermyn-werkverrigting daarvan beïnvloed, deeglik verstaan word. Die verandering in materiaalgedrag en falingsmeganismes van BSM materiale is langtermynverskynsels. Dit impliseer dat bestudering van die fisiochemiese en meganiese eienskappe van die mengsels uiters belangrik is. Dis dus voor die hand liggend hoe belangrik vogbeskadiging en verharding met tyd, wat verwant is aan materiaaleienskappe, is. Die hoofdoelwit met hierdie studie is om die vooruitgang van BSM tegnologie te versnel deur dit moontlik te maak om gekose materiale te evalueer op grond van hulle invloed op duursaamheid en langtermyn-werkverrigting in alle toepassingsfases (naamlik mengontwerp, konstruksie en dienstoestand). Hierdie studie begin met ’n uitgebreide literatuuroorsig oor fundamentele begrippe van die karakterisering van interaksie van die bindstof en die minerale-aggregate. Inligting oor bitumen (skuimbitumen en bitumen emulsies) en eienskappe van minerale aggregate is bestudeer. Dit is gevolg deur ’n studie van die fundamentele begrip van die kolloïdale gedrag van skuim en emulsie, asook fisiochemiese en meganiese interaksie met minerale aggregate. Faktore wat die interaksie van BSM-materiale beïnvloed is geïdentifiseer. Die basiese teorie van termodinamika, hidrodinamika en elektrokinetika is daarna gebruik om stap vir stap die proses en formulering van adhesie-binding en kohesie in die BSMs, wat in hierdie studie aangebied word, te beskryf. Die kwantifisering van mengsel-duursaamheid in terme van vogbeskadiging is ontwikkel. Om hierdie doel te bereik, is die fisiese en meganiese proses van beskadiging deur vogindringing geïdentifiseer. Die gekontroleerde parameters is bepaal en ’n laboratoriumapparaat is ontwerp om hierdie parameters te kwantifiseer. Nuwe vogkondisioneringsprosedures is ontwikkel en in hierdie studie gedemonstreer. Van prosedures van voggeïnduseerde sensitiwiteitstoetsing (Engels: moisture induction simulation test (MIST)) was dit duidelik dat pulsering van waterdruk in BSM materiale die hidrodinamiese effek naboots wat in die veld bestaan as gevolg van dinamiese verkeerslaste. Verskillende mengselmatrikse wat tipies is van hergebruik, soos byvoorbeeld hoornfels-hersikleerde asfalt produk (Engels: recycled asphalt product (RAP)) en vergruisde granietklip, met skuimbitumen of bitumenemulsie gestabiliseer en met byvoeging van aktiewe vulmateriaal (sement of kalksteen), is ondersoek. Daar is bevind dat nuwe vogkondisioneringsprosedures (soos bepaal deur MIST apparaat en drie-assige toets) kan onderskei tussen BSM materiale wat weerstandig is teen vogbeskadiging en dié wat minder weerstandig (vatbaar) is. Die geldigheid van die MIST en monotone toetsresultate is bepaal deur gebruik van die APT apparaat wat ’n MMLS3 nat verkeerstoets is. Die resultate van beide toetse toon goeie korrelasie in die keuring van BM materiale in terme van vogvatbaarheid. In hierdie ondersoek is veldtemperatuurdata versamel en die toepaslike model om verouderende BM lae akkuraat te simuleer is geïdentifiseer en voorgelê vir verdere ondersoek en verifikasie. Daar is uit veldtemperatuurdata bevind dat temperatuurgradiënt op die betrokke terrein gewissel het met die dikte van die BSM, naamlik 10oC-17oC gedurende die winter en 17oC-47oC gedurende die somer. Begrip vir die invloed van temperatuuroordragkoëffisiënt en verdampingstempo is belangrik by die afleiding van vogbeskadiging en verharding met ouderdom en die korrekte keuse van BSM materiale.Verouderingsverhardinggedrag van BSMs is verwant aan die duursaamheidseienskappe en langtermynwerkverrigting van hierdie materiale. Die basiese karakteristieke wat met kort- en langtermyn verouderingsverharding geassosieer word, is in hierdie studie ondersoek. Die klem op die kort termyn is geplaas op die verouderingsverhardingsgedrag van die bindstof (skuimbitumen kolloïdes en bitumen-emulsiedruppels) voordat BSMs vervaardig word. In die lang termyn evaluasie het die studie ekstraksie en herwinning van bindstof uit brikette wat in die laboratorium gekompakteer is (van verskillende mengsels) en uit kerns verkry vanaf verskeie plaveiselgedeeltes na 8-10 jaar diens ingesluit. Die ondersoek het bevind dat die tydsverloop waarin bitumen in sirkulasie gehou is by verhoogde temperatuur (170oC-180oC) in die laboratorium-aanleg voordat BSMs vervaardig is, veral indien na 8 uur, bydra tot die veroudering van die bindstof. Die skuimproses op sigself verander nie die bitumeneienskappe nie. Daar word aanbeveel dat temperature tussen die grense 160oC-165oC gehandhaaf word vir produksie van skuimbitumen met sagter bitumen sonder dat die kwaliteit benadeel word en dat die sirkulasietyd nie 2 tot 3 ure behoort te oorskry nie. Die reologiese eienskappe van die herwinde bitumen vanuit laboratoriumbrikette en kerns van plaveisels toon dat ouderdomsverharding van skuimbitumen en bitumen-emulsie tydens die diensleeftyd plaasvind. Die veroudering is skynbaar ook afhanklik van verkeerseffekte, met belaste areas (in wielspoor of binne wielspoor) wat ’n hoër mate van veroudering toon as onbelaste areas (tussen wielspore). Die ekstraksie- en herwinningsproses op sigself was egter bevind as baie kompleks met uiters onseker resultate. Dit het gelei tot onsekere gedrag in terme van ouderdomsverharding van die BSM bindmiddel (skuim of emulsie). Alhoewel resultate toon dat die bindmiddels ouderdomsverharding ondergaan het, is die BSM werkverrigting nie duidelik uit die uitgebreide toetse wat in hierdie studie uitgevoer is nie. Die laaste deel van die studie bevat gevolgtrekkings en aanbevelings. Die studie lewer insig in die fundamentele duursaamheidseienskappe van die materiaal, wat bydra tot verbetering van die huidige prosedure van seleksie, saamstelling en formulering van die mengmatriks vir BSMs. Verder voorsien dit ’n metode wat in die praktyk gebruik kan word om met vertroue duursame mengsels met lang diensbaarheidsleeftye te vervaardig. ’n Nuwe oplossing en vooruitgang in die toepassing van BSMs is daargestel tot voordeel van alle partye betrokke by die ontwikkeling van herwinningstegnologie.

Thesis (PhD (Biomedical Sciences. Molecular Biology and Human Genetics))--University of Stellenbosch, 2009. / Dissertation presented for the degree of Doctor of Philosophy in Medical Biochemistry at Stellenbosch University. / ENGLISH ABSTRACT: The infectious disease tuberculosis (TB) still represents a global threat due to its devastating effect on health and the subsequent high mortality rate. Previous studies have indicated that host genetic factors are implicated in host susceptibility to TB. Since TB is a complex disease, it can be assumed that susceptibility to M. tuberculosis has multiple genetic causative factors (as well as environmental causes). The current study focussed on a number of South African Coloured (SAC) individuals, some of whom were TB cases and others controls. Population substructure was tested in the admixed SAC population as it can be a strong confounding factor for association studies. Our results using the programme STRUCTURE indicated no population substructure in the SAC population. We further investigated the population structure of the SAC group using Affymetrix 500k SNP chip data which showed that the SAC population group has 4 major ancestral components: the Khoesan, European, African and Asian (Indian). A number of candidate polymorphisms in eight genes, previously indicated to play an important role in TB susceptibility, were tested in case-control associations studies. We found statistically significant associations between IFNGR1, IL-8, IL-1Ra and NRAMP1 polymorphisms and TB susceptibility in the SAC population. It has become increasingly evident that gene-gene interactions play a far more important part in an individual’s susceptibility to a complex disease than single polymorphisms would on their own. The importance of epistasis was clearly identifiable in this study with only four associations found between the individual variants and TB susceptibility, but eight instances of statistically significant gene-gene interactions. A combined data set consisting of 106 variants constructed from our database and also used for gene-gene interaction analysis yielded numerous statistically significant interactions. The interaction between the genotype of the human host and the bacterial strain genotype was also investigated and yielded interesting results. Owing to various polymorphisms in several cytokine genes, the protein levels of the main modulators of the immune system, cytokines and chemokines, are changed in several diseases such as infectious diseases and may affect susceptibility or resistance to TB. The functional polymorphisms or haplotype patterns in some of these cytokine genes might be vital for protective immune responses and may serve as biomarkers of protection or susceptibility to TB. The present study investigated 18 cytokines including pro-inflammatory, anti-inflammatory and chemokine factors in healthy (mantoux positive or negative) children using the Linco-plex immunoassay, and investigated potential interactions. The basic research will one day contribute to personalised genetics which may benefit infectious diseases such as TB. If individuals can be identified as potentially more vulnerable, they may require different vaccination strategies, a higher index of suspicion if exposed to TB, and prophylactic treatment. / AFRIKAANSE OPSOMMING: Die infektiewe siekte tuberkulose (TB) is steeds ‘n gevaar wat die hele wêreld bedreig weens die groot impak op gesondheid en die gevolglike hoë mortaliteit. Vorige studies het bevind dat die gasheer se genetiese faktore wel betrokke mag wees by die gasheer se vatbaarheid vir TB. Aangesien TB ‘n komplekse siekte is, kan dit aanvaar word dat vatbaarheid tot M. tuberculosis veelvuldige genetiese oorsaaklike faktore (sowel as omgewingsoorsake) het. Hierdie studie het gefokus op ‘n aantal Suid-Afrikaanse Kleurling (SAC) individue, waarvan sommige TB pasiënte en ander kontroles was. Die gemengde SAC populasie is getoets vir populasie-stratifikasie, aangesien stratifikasie ‘n sterk verwarrende invloed op pasiënt-kontrole studies kan hê. Ons resultate is verkry met behulp van die program STRUCTURE en het aangedui dat daar geen populasie sub-struktuur tussen die pasiënte en kontroles was nie. Ons het ook die populasiesamestelling van die SAC groep ondersoek met data verkrygbaar van die Affymetrix 500k enkel nukleotied polimorfisme mikroskyfie. Hierdie data het getoon dat die SAC populasie uit 4 hoof voorouerlike komponente bestaan naamlik die Khoesan, Europeërs, Afrikane en Asiate (Indiërs). ‘n Aantal kandidaat polimorfismes in agt gene, wat volgens vorige studies ‘n belangrike rol in TB vatbaarheid te speel, was in hierdie pasiënt-kontrole assosiasie studie bestudeer. Ons het statistiese beduidende verwantskappe tussen IFNGR1, IL-8, IL-1Ra en NRAMP1 polimorfismes en TB vatbaarheid in die SAC populasie gevind. Dit het al hoe meer duidelik geword dat geen-geen interaksies ‘n baie belangriker rol in ‘n individu se vatbaarheid vir ‘n komplekse siekte speel as enkel polimorfismes op hul eie. Die belang van epistase kon duidelik in hierdie studie geïdentifiseer word met slegs vier assosiasies wat tussen die individuele variante en TB vatbaarheid gevind is, in vergelyking met agt statisties beduidende geen-geen interaksies. ‘n Gekombineerde datastel wat uit ons databasis saamgestel is en wat 106 variante bevat is ook in ‘n aparte geen-geen interaksie analise gebruik, wat verskeie statisties beduidende interaksies getoon het. Die interaksie tussen die menslike gasheer genotipe en die bakteriese stam genotipe is ook in hierdie studie ondersoek en het interessante resultate opgelewer. Veranderde proteïen uitdrukking van die hoofmoduleerders van die immuunsisteem, sitokine en chemokine, kom voor in verskeie siektes soos infektiewe siektes weens verskillende polimorfismes in verskeie sitokien-gene. Sulke polimorfismes kan ook vatbaarheid vir of weerstandigheid teen TB beïnvloed. Die funksionele polimorfismes of haplotipe patrone in sommige van hierdie sitokien-gene mag noodsaaklik wees vir beskermende immuunresponse en mag ook as biomerkers vir beskerming teen of vatbaarheid vir TB dien. Hierdie studie het 18 sitokiene (insluitend pro-inflammatoriese-, anti-inflammatoriese- en chemokiene faktore), sowel as potensiële interaksies in gesonde (mantoux positiewe of negatiewe) kinders, ondersoek met behulp van die Linco-plex immuno-analise. Hierdie basiese navorsing sal eendag in die toekoms bydrae tot persoonlike genetiese analises wat tot voordeel kan wees vir infektiewe siektes soos TB. Indien individue as potensieël meer vatbaar vir TB geïdentifiseer kan word, kan sulke persone ander vaksineringstrategieë sowel as voorkomende behandeling vereis.

Equine arteritis virus (EAV) is the causal agent of equine viral arteritis, a disease of equids. During natural outbreaks of the disease, EAV can cause abortion in pregnant mares and persistent infection in stallions. Understanding how host cellular proteins interact with viral RNA and viral proteins, as well as their role in viral infection, will enable better characterization of the pathogenesis of EAV and establishment of persistent infection in stallions. Accordingly, we hypothesized that both viral factors and host genetically related factors could influence the outcome of EAV infection in horses. To test this hypothesis, we first combined contemporary molecular biology techniques with dual color flow cytometric analysis to characterize the interactions of viral structural proteins and the equine peripheral blood mononuclear cells in vitro. Results from this study demonstrated that interactions between GP2, GP3, GP4, GP5 and M envelope proteins of EAV play a major role in determining the CD14+ monocyte tropism while the tropism of CD3+ T lymphocytes is determined by GP2, GP4, GP5 and M envelope proteins but not the GP3 protein. Secondly, a genome wide association study using SNP genotyping identified a common haplotype associated with the in vitro CD3+ T lymphocyte/resistance to EAV infection among four breeds of horses. Subsequently, these studies were extended to establish a possible correlation between the in vitro susceptibility of CD3+ T lymphocytes to EAV and establishment of persistent infection in stallions. Interestingly, carrier stallions with susceptible CD3+ T lymphocyte phenotype to EAV may represent those at higher risk of becoming persistently infected. Finally, the precise effect of EAV on the immune system of horses, innate and humoral immunity, was studied. Horses were shown to mount a strong humoral antibody response to nonstructural proteins (nsps) 2, 4, 5 and 12 of EAV, whereas nsps 1, 2 and 11 suppressed the type I interferon production. The data presented in this dissertation suggest new directions for future EAV research using genomic and proteomic approaches to study host cell factors involved in EAV attachment and entry and establishment of persistent infection in the stallions.

<p>The physical properties of the coarse fraction of the till (0.4 to 20 cm) and the surface boulders have been studied at two different sites in Sweden. The research work included: development of a new image analysis software for 3D size and shape measurements of particles; lithological analysis on multiple size fractions in till and magnetic susceptibility survey on coarse till clasts, surface boulders and local bedrock.</p><p>The new 3D image analysis method provides an enormous amount of size and shape data for each particle in the coarse fraction (2 to 20 cm) in till. The method is suitable for field study, cost effective and the software is executable in Matlab. The field imaging method together with the image analysis software give non subjective results of size and shape of coarse particles and makes it feasible and easy to study representative sample size, which is one tonne for testing clasts of size up to 20 cm.</p><p>The lithological analysis of the multiple size fraction of the till clasts has been investigated on six different size fractions of the till (0.4 to 20 cm); the result of the different samples from the two sites shows that this method can potentially be used as a stratigraphic tool in the areas where there is no unique indicator lithologies.</p><p>The magnetic susceptibility has been made on the surface boulders, the 6-20 cm till fraction and on insitu bedrock outcrops near to the study sites. The method has good potential for determining stratigraphic relationships between different till units as well as for determining the provenance ofcoarse clasts and surface boulders.</p>