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Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Two mathematical models are formulated in this dissertation for the population growth of an Eldana saccharina Walker infestation of sugarcane under the influence of partially sterile released insects. The first model describes the population growth of and interaction between normal and sterile E. saccharina moths in a temporally variable, but spatially homogeneous environment. The model consists of a deterministic system of difference equations subject to strictly positive initial data. The primary objective of this model is to determine suitable parameters in terms of which the above population growth and interaction may be quantified and according to which E. saccharina infestation levels and the associated sugarcane damage may be measured. The second model describes this growth and interaction under the influence of partially sterile insects which are released in a temporally variable and spatially heterogeneous environment. The model consists of a discretized reaction-diffusion system with variable diffusion coefficients, subject to strictly positive initial data and zero-flux Neumann boundary conditions on a bounded spatial domain. The primary objectives in this case are to establish a model which may be used within an area-wide integrated pest management programme for E. saccharina in order to investigate the efficiency of different sterile moth release strategies in various scenarios without having to conduct formal field experiments, and to present guidelines by which release ratios, frequencies and distributions may be estimated that are expected to lead to suppression of the pest. In addition to the mathematical models formulated, two practical applications of the models are described. The first application is the development of a user-friendly simulation tool for simulating E. saccharina infestation under the influence of sterile insect releases over differently shaped spatial domains. This tool provides the reader with a deeper understanding as to what is involved in applying mathematical models, such as the two described in this dissertation, to real-life scenarios. In the second application, an optimal diversification of sugarcane habitats is considered as an option for minimising average E. saccharina infestation levels, and as a further consequence, improving the cost-efficiency of sterile insect releases. Although many special cases of the above model classes have been used to model the sterile insect technique in the past, few of these models describe the technique for Lepidopteran species with more than one life stage and where F1-sterility is relevant. In addition, none of these models consider the technique when fully sterile females and partially sterile males are being released. The models formulated in this dissertation are also the first to describe the technique applied specifically to E. saccharina, and to consider the economic viability of applying the technique to this species. Furthermore, very few examples exist of such models which go beyond a theoretical description and analysis towards practical, real-life applications as illustrated in this dissertation. / AFRIKAANSE OPSOMMING: Twee wiskundige modelle word in hierdie proefskrif vir die populasiegroei van ’n Eldana saccha- rina Walker infestasie van suikerriet onder die invloed van gedeeltelik steriele, vrygelate insekte daargestel. Die eerste model beskryf die populasiegroei van en -interaksie tussen normale en steriele E. saccharina motte in ’n dinamiese, maar ruimtelik-homogene omgewing. Die model is ’n stelsel deterministiese verskilvergelykings onderhewig aan streng positiewe aanvangswaardes. Die primˆere doelstelling met hierdie model is om geskikte parameters te bepaal in terme waarvan die bogenoemde groei en interaksie gekwantifiseer kan word, en waarvolgens E. saccharina infestasievlakke en die gepaardgaande suikerrietskade gemeet kan word. Die tweede model beskryf hierdie groei en interaksie onder die invloed van gedeeltelik steriele insekte wat in ’n dinamiese en ruimtelik-heterogene omgewing vrygelaat word. Die model is ’n gediskretiseerde stelsel reaksie-diffusievergelykings met veranderlike diffusieko¨effisi¨ente onderhewig aan streng positiewe aanvangswaardes en zero-vloei Neumann-randwaardes op ’n begrensde ruimtelike gebied. Die primˆere doelstellings in hierdie geval is om ’n model tot stand te bring wat in ’n area-wye, ge¨ıntegreerde pesbestrydingsprogram vir E. saccharina gebruik kan word om die doeltreffendheid van verskillende steriele motvrylatingstrategie¨e te bepaal sonder om daadwerklik veldeksperimente uit te voer, en om riglyne daar te stel waarvolgens vrylatingsverhoudings, -frekwensies en -verspreidings bepaal kan word wat na verwagting na ’n onderdrukking van die pes sal lei. Bykomend tot die wiskundige modelle in hierdie proefskrif, word twee praktiese toepassings van die modelle ook beskryf. In die eerste toepassing word ’n gebruikersvriendelike simulasie hulpmiddel ontwikkel om E. saccharina infestasie onder die invloed van steriele insekvrylatings in verskillende ruimtelike gebiede te simuleer. Hierdie toepassing fasiliteer ’n dieper begrip van wat ter sprake is in die toepassing van wiskundige modelle, soos die twee modelle in hierdie tesis, tot werklike scenario’s. In die tweede toepassing word ’n optimale diversifisering van suikerriet habitats as ’n opsie vir die vermindering van die gemiddelde E. saccharina infestasie vlakke beskou, en gevolglik word die verbetering van die koste-doeltreffendheid van steriele insekvrylatings afgeskat. Alhoewel verskeie spesiale gevalle van die bogenoemde twee klasse van modelle reeds in die verlede gebruik is om die doeltreffendheid van die steriele-insektegniek te modelleer, beskryf weinig van hierdie modelle die tegniek vir Lepidopteriese spesies met meer as een lewensfase en waar F1-steriliteit ter sprake is. Verder beskryf geen van hierdie modelle die tegniek waar algeheel steriele wyfies en gedeeltelik steriele mannetjies vrygelaat word nie. Die modelle in hierdie tesis is ook die eerste waar die tegniek spesifiek op E.saccharina toegepas word, en waar die ekonomiese lewensvatbaarheid van die tegniek vir hierdie spesie oorweeg word. Verder bestaan daar min voorbeelde van soortgelyke modelle wat verder gaan as ’n teoretiese beskrywing en wiskundige ontleding na praktiese, werklike toepassings, soos in hierdie proefskrif ge¨ıllustreer.

Thesis (PhD (Chemical Engineering))--Cape Peninsula University of Technology, 2019 / The agro-processing industry is currently facing losses due to microbial spoilage of agricultural produce and associated value-added products such as beverages. Decay and undesired fermentation of fruit and beverages by fungal, yeast and bacterial spoilage organisms are among the major contributors of product losses in the food industry. When looking at the different level of food spoilage, it is common to find different spoilage organisms occurring in the same food item; which usually requires food producers to utilise a mixture of synthetic preservatives for spoilage organism control. Some of the synthetic chemical compounds with growth inhibition properties that have been used in food preservation are sulphur dioxide, benzoic, lactic, sorbic and acetic acid. These compounds act against a variety of spoilage microorganisms. In post-harvest control of fungi, triazoles, hydroanilide fenhexamid, dicarboximides and succinate dehydrogenase are also being used. Some spoilage organisms have been found to be resistant to the use of synthetic chemical preservatives which usually favour the use of higher dosage of preservatives in food. The use of synthetic chemicals as preservative and as postharvest control agents has been found to present serious health risks such as cardiovascular diseases, muscles and stomach pains, eyesight and skin damages and impairment of brain functions. The problem posed by the current use of synthetic chemicals in food put pressure on food producers and exporters to seek alternatives that will allow for the eradication of the use of synthetic chemicals as preservative in beverages and as postharvest control agents on fruits. Yeasts have been found to have the ability to grow at a faster rate on cheap media and to colonise dried surfaces rapidly. It has also been found that yeasts produce extracellular compounds of proteinaceous and volatile organic nature with growth inhibition properties against spoilage organisms. The current findings lack some engineering concept that could assist in the design of a production system for high scale production of biopreservation compounds from yeasts. The availability of a cost effective production media, the growth and production kinetics data using a cheaply available nutrient sources as well as the biological thermodynamic data are some of the gaps in biopreservation bioprospecting. Although several yeasts have already been studied to have great inhibition properties against fruit fungal pathogens, it was still unclear what was the minimum inoculum dose to be able to have a fungistatic and fungicidal effect on the growth of fruit spoilage organisms. The concept of combination of biopreservatives and the interaction effect of their biopreservation activity against consortia of spoilage organisms has also been lacking. As an attempt to seek alternatives to the use of synthetic chemicals as preservatives or postharvest control agents, Candida pyralidae Y1117, Pichia kluyveri Y1125 and Pichia kluyveri Y1164 strains were assessed for antimicrobial activity against spoilage yeasts (Dekkera bruxellensis, Dekkera anomala, Zygosaccharomyces bailii) and spoilage fungi (Botrytis cinerea, Colletotrichum acutatum and Rhizopus stolonifer). As alternative to refined media, a cost effective approach was explored whereby the use of agro-waste, i.e. grape pomace extracts (GPE), as production medium for biopreservation compounds, was studied. Production kinetics using modified existing models, subsequent to optimization using response surface methodology (RSM) for biopreservation compounds production was studied for the three biocontrol yeasts using GPE broth as the fermentation medium. The evaluation of the interaction study between mixtures of crude biopreservatives against consortia of common spoilage organisms present in beverages was also conducted by producing the crude biopreservation compounds separately from yeasts and then formulating growth inhibition combinations (GICs); GIC 1 (Candida pyralidae Y1117 and Pichia kluyveri Y1125); GIC 2 (C. pyralidae Y1117 and P. kluyveri Y1164), GIC 3 (P. kluyveri Y1125 and Pichia kluyveri Y1164); GIC 4 (C. pyralidae, P. kluyveri Y1125 and P. kluyveri Y1164). The spoilage organism consortia combinations, i.e. SC1, D. anomala and D. bruxellensis; SC2 (D. anomala and Z. bailii); SC3 (D. bruxellensis and Z. bailii) and SC4 (D. anomala, D. bruxellensis and Z. bailii) were also prepared. This study also investigated the effect of varying inoculum dose (ID) of Candida pyralidae strain Y1117, Pichia kluyveri Y1125 and Pichia kluyveri Y1164 on the biocontrol of Botrytis cinerea by contaminating the headspace of the growth medium with a fungal plug subsequent to biotreatment with different initial inoculum dose of the respective biocontrol yeasts. Finally, grape pomace extracts was used as fermentation medium to study the biological thermodynamics of biopreservation compound production from the three biocontrol yeasts. The results obtained demonstrated some interesting results. The antagonistic properties of C. pyralidae and P. kluyveri were observed on cheap solidified medium (grape pomace extracts) as well as on fruits (grapes and apples). These yeasts produced extracellular volatile organic compounds (VOCs) that could be responsible for yeast and fungal growth inhibition. Twenty-five VOCs in the category of alcohols, organic acids and esters were identified by GC-MS. The results of the kinetic study showed that the highest volumetric zone of inhibition (VZI) was 1.24 L contaminated solidified media (CSM) per mL biopreservation compounds used (BCU) when Candida pyralidae Y1117 was inoculated in a pH 3-diluted GPE broth (150 g L−1) incubated at 25 °C for 24 h. Similar conditions were applied for Pichia kluyveri Y1125 and P. kluyveri Y1164, albeit under slightly elongated fermentation periods (up to 28 h), prior to the attainment of a maximum VZI of only 0.72 and 0.76 L CSM mL−1 ACU, respectively. The potential biopreservation compounds produced were identified to be isoamyl acetate, isoamyl alcohol, 2-phenyl ethylacetate and 2-phenyl ethanol. The growth inhibition interaction study showed a variation in growth inhibition proficiency depending on the spoilage organisms or the consortia of spoilage organisms being deactivated. It was then suggested that, a food environment contaminated with a consortium of spoilage organisms can be controlled by employing either the crude biopreservation compounds from individual yeast or those of the following yeast combinations, GIC1-4, which showed a better growth inhibition proficiency against SC1-3. The fungistatic and fungicidal effects on the fungal pathogen were dose dependent. The fungistatic characteristics against Botrytis cinerea were displayed after 7 days when 102-105 cells mL-1 of Candida pyralidae Y1117, Pichia kluyveri Y1125 and Pichia kluyveri Y1164 were independently used in-vitro and in-vivo. However, 106-108 cells mL-1 inoculum doses displayed fungicidal characteristics. Additionally, the fungicidal property of yeasts studied was also confirmed on table grape (in vivo studies) using closed jar method. The biological thermodynamic study showed that, dried biomass molecular weight of 28.9 g/C-mol, 29.163 g/C-mol, and 27.176 g/C-mol were obtained for Candida pyralidae strain Y1117, Pichia kluyveri Y1125 and Pichia kluyveri Y1164 respectively. The results obtained successfully established useful biological thermodynamic data applicable to the design of adequate biopreservatives production system from yeasts using cheaply available nutrients source.

Pereskia aculeata Miller (Cactaceae) is an environmental weed that is damaging to natural ecosystems in South Africa. The plant is native to Central and South America and was first recorded in South Africa in a botanical garden in 1858. In this thesis, research into the biological control of P. aculeata was conducted with the intention of improving the control of the weed. A pre-release study of the relationship between P. aculeata density and native plant biodiversity indicated that P. aculeata has a negative impact on native biodiversity. The native plant biodiversity associated with different P. aculeata densities was used to determine threshold values and goals for the control of the weed. A threshold value of 50% P. aculeata density was calculated, indicating that P. aculeata density must be maintained below 50% in order to conserve native plant biodiversity. The ultimate goal of the control programme should be to maintain P. aculeata densities below 30%. At these densities there was no significant difference in native plant biodiversity from if the weed were absent from the ecosystem. The biological control agent, Phenrica guérini Bechyne (Chrysomelidae), has been released in South Africa but the potential of the agent to impact P. aculeata is not known and no post release evaluation has been conducted. Impact assessment studies indicate that P. guérini does not impact P. aculeata, even at high densities, but the results of greenhouse experiments should be interpreted with caution because of problems with extrapolation into the field. Although observations in the field suggest that P. guérini has reduced P. aculeata densities at one site, it is clear that new biological control agents are needed to reduce the weed to acceptable levels. Identifying the origin of the South African P. aculeata population was believed to be important to the biological control programme due to the disjunct native distribution and intraspecific variation of the species. Natural enemies associated with plant genotypes in different parts of the native distribution may have developed specialised relationships with certain intraspecific variants of the plant, resulting in differences in agent efficacy on certain host plant genotypes. A molecular study indicated that the closest relatives to the South African weed population found in the native distribution were in Rio de Janeiro Province, Brazil. A bioassay experiment in which fitness related traits of the biological control agent, P. guérini, were measured on various P. aculeata genotypes was conducted to determine the importance of host plant intraspecific variation. There was little variation in fitness traits between genotypes and no evidence of intraspecific host plant specialization. Although intraspecific variation had no effect on agent efficacy in the case of P. guérini, it is possible that other natural enemies may be more specialized. Genotype matching is expected to be more important when natural enemies likely to be specialised to individual genotypes are considered for biological control. Potential biological control agents were prioritized from data collected on surveys in the native distribution. The most promising of these, based on the presence of feeding, incidence, predicted host range, climatic matching, genotype matching and mode of damage, are two species of Curculionidae, the current biological control agent P. guérini and the stem boring moth, Maracayia chiorisalis Walker (Crambidae). The two curculionid species and M. chlorisalis should be considered priorities for host specificity studies. Releases of P. guérini and any new biological control agents should be made at sites where the pre-release study was conducted so that post-release evaluation data can be compared with the pre-release data and the impact of biological control can be evaluated. Retrospective analyses of biological control programmes provide important ways of improving aspects of biological control programmes, such as methods of agent selection. The evaluation of success in biological control programmes is essential for retrospective analyses because factors that have lead to successes or failures can be analysed. Retrospective analyses of biological control programmes, such as this thesis, may improve weed management, thereby contributing to the conservation of natural resources.