The aims of this work were to investigate the signal transduction pathways controlling the yeast-hyphal morphological transition of Candida albicans, and to gain a clearer understanding of the importance of hyphal formation of the virulence of this organism. The work can be divided into two areas. Firstly, the recently discovered species Candida dubliniensis, the only species in addition to C. albicans capable of forming true non-constricted hyphae, was examined in comparison to C. albicans to compare their virulence capability in vitro and in vivo. The two species were compared with respect to hypha formation, adherence, possession of SAP genes and virulence in the mouse model of systemic candidosis. C. dubliniensis possessed at least a homologue to each of the nine known C. albicans SAP genes, adhered to human cells to a greater degree on exposure in glucose, formed hyphae slightly less efficiently than C. albicans and was less virulent in mice. C. dubliniensis has been isolated particularly from the mouths of HIV positive and AIDS patients. The results of the virulence assessment could be interpreted as reflecting its epidemiological occurrence, - increased adherence on exposure to glucose may be a response to dietary sugar and the reduced virulence would explain in part its association with immunocompromised hosts. Secondly, the role of phosphoinositide signalling in control of the yeast-hyphal transition was investigated by the cloning and characterisation of two putative phosphatidylinositol 4-kinase genes from C. albicans, named CaPIK1 and CaPIK2. Both genes were cloned through their homology to the S. cerevisiae PIK1 gene. Disruption of the CaPIK1 gene in C. albicans indicated that it had no obvious role in the control of hypha formation.

Aim The aim was to determine the epidemiology of invasive fungal infections at Chris Hani Baragwanath Hospital. The specific objectives were to determine the 1) risk factors, 2) clinical presentation, 3) laboratory abnormalities, 4) organisms and their susceptibilities and 6) outcome in neonates with positive blood or CSF fungal cultures at Chris Hani Baragwanath Hospital. Methods This was a retrospective record review of patients who had positive blood or CSF cultures. Patients were identified by a computerized microbiological surveillance database. The data was collected over a three-year period from January 2002 to December 2004. Patient hospital files were reviewed for clinical signs, full blood count (FBC), C-reactive protein (CRP) and outcomes. Fungal culture results were reviewed for susceptibilities. To identify risk factors a convenient cohort was compared to the patients with fungal sepsis. The data was analysed using a Statistica software package. Results There were 150 patients with fungal sepsis among admissions over this 3 yearperiod giving an incidence of 1.3 per 100 admissions. Thirty-nine records were not found thus 111 patient records were reviewed. The median birthweight was 1280g and the gestational age 30 weeks. The median age of onset was 16 days and 6.3% had early onset fungal sepsis. There were 61 males. Twenty-eight percent of patients were born to HIV positive mothers. Candida parapsilosis was the commonest (56%) organism isolated followed by C. albicans (43%). All the C. albicans isolates and 93% of the C. parapsilosis isolates were susceptible to amphotericin B. Fluconazole susceptibilities were reported as, 96% for C. albicans, and 60% of the C. parapsilosis as being susceptible. Central venous catheters (CVCs) (p=<0.001), the use of TPN (p=<0.001) and third generation cephalosporins were identified as risk factors associated with fungal sepsis. The all-cause mortality and Candida–related mortality were 30% and 23% respectively. The non-survivors had lower platelet counts (p=0.007) than the survivors. Patients with Gram-negative sepsis had lower platelet counts than the fungal group (p=<0.001) on the repeat laboratory parameters. Conclusion The incidence is 1.3 per 100 admissions. Risk factors associated with fungal sepsis are very low birthweight and gestational age, the use of TPN, CVCs and third generation cephalosporins. Candida parapsilosis is the common organism causing fungal sepsis in neonates. Candida albicans was associated with a higher mortality. Thrombocytopenia is not organism specific to fungal sepsis.

Thesis (MScIng)--University of Stellenbosch, 2006. / Bibliography. Also available via the Internet.

No description available.

Comparisons were made between the sensitivities of unique ‘wild’ isolates and domestic isolates of the dry rot fungus, <i>Serpula lacrymans</i>, to temperature, water potential and pH. Comparisons were also made between their capacities of timber decay. The ‘wild’ Himalayan isolates displayed slightly less marked sensitivities to high and low temperature and lowered water potential, yet the isolates were equally tolerant of pH. In general, the linear growth rates of the domestic isolates proved to be twice those of the ‘wild’ Himalayan set, whereas little variation occurred between their rates of timber decay. This study also resulted in the first isolation and reliable identification of ‘wild-growing’ <i>S. lacrymans</i> collected in Europe. The main part of the project involved the construction of novel chambers in order to examine the effects of lowered humidity and moving air flow on the activity of <i>S. lacrymans</i>. In the smallest and simplest of these, its growth and timberdecaying activities could be stopped by incubation at 86% relative humidity or by the application of a pumped air flow rate of 2.5 litres per minute; however, <i>S. lacrymans</i> was not inactivated until more-stressful conditions were applied. In addition, an intermediate rate of air flow provoked marked directional growth away from the stress. Furthermore, the introduction of stone, brick and plaster into these models encouraged the capacities of timber decay and mycelial growth. The use of a larger and more representative model incorporating simulated flooring and plaster walling within glass tanks revealed differences in the appearances and patterns of colonisation by <i>S. lacrymans</i> depending upon whether aged or new materials were used. Treatments involving air drying by fans caused both a shrivelling and a loss of viability of the fungus only when there was no ‘reservoir’ of water available; when there was water present, latent activity remained. An elaboration of this experimental design tested the effects of a combined biological and environmental treatment. Subsequently, the application of <i>Trichoderma harzianum</i>, a known antagonist of <i>S. lacrymans</i>, proved not to be an effective remedial treatment on its own, but appeared to impart a mildly protective effect when combined with a drying regime. Importantly, in the latter situation <i>T. harzianum</i> caused a severe degradation of the part of the colony responsible for the uptake of water in <i>S. lacrymans</i>. Another workshop-scale model simulating more authentically a damp sub-floor space and a cavity behind aged plaster walling was developed. When respective treatments by fan drying and passive ventilation were compared, the former were more effective, but its efficacy could be augmented by incorporating low-level passive ventilation via discreet vents. In this manner, a successful remedial treatment of <i>S. lacrymans</i> could be effected, though the prevalence of mould could prove to be undesirable in practice. However, some samples of this displayed antagonistic effects against <i>S. lacrymans</i>. A further experiment was designed to test the effects of air drying on the production of the stress-protective carbohydrate trehalose and of some associated solutes by <i>S. lacrymans</i>. In contrast to reports of some other organisms, no definite stockpiling of any of the compounds occurred. A final series of experiments revealed that <i>S. lacrymans</i> removed calcium, silicon and iron from sandstone and calcium, sulphur and iron from aged plaster; these elements were sequestered on its hyphae, especially in the form of calcium oxalate. Degradation of the sandstone was implicit but not obvious microscopically. Furthermore, <i>S. lacrymans</i> transported iron from these building materials through its mycelial system. An attempt to determine the effects of separate minerals in sandstone and plaster on timber decay revealed few variations.

No description available.

Cacao (<i>Theobroma cacao </i>L.) is an ancestrally cultivated crop that has been the source of one of the most beloved commodities, chocolate. Its worldwide demand has shaped the history of its cultivation. In Chapter 1, the center of origin of cacao, its center of domestication, the most outstanding movements of germplasm from the Pre-Columbian to the Republican era, the appearance and discovery of major diseases, among other important economic, agricultural and social aspects regarding cacao cultivation are reviewed. The following chapters focus on one of the major pathogens of cacao in the Americas, <i>Moniliophthora roreri</i> causing frosty pod rot disease. Chapter 2 presents evidence that the center of origin of <i>M. roreri </i>is not limited to the Magdalena Valley in Colombia, as other studies have suggested, but extends to Ecuador and the Peruvian Upper Amazon. Chapter 3 focuses on the <i>A </i>and <i>B </i>mating type loci diversity of <i>M. roreri </i>and reports a new <i>A </i>mating allele in Colombia and new mating types in Colombia, Ecuador and infers the presence of even more mating types in Ecuador and the Peruvian Upper Amazon. Additionally, Chapter 3 introduces rapid approaches to collect <i>M. roreri </i> and to diagnose mating types. Finally, Chapter 4 touches the genomic aspect of <i>M. roreri </i>and its close relatives within the Marasmiineae suborder. It presents the most complete genome of a <i>Moniliophthora </i>species generated so far and describes the evolution of predicted effectors and other proteins that might be involved in pathogenicity in this suborder. It also releases a custom program called SyLOCAL that evaluates synteny of a cluster of genes between two genomes.

Endophytic fungi live within tissues of plant hosts without causing symptoms of disease. These fungi are broadly split into the taxonomically and ecologically cohesive Clavicipitaceous endophytes, which infect grasses, and the taxonomically diverse non-Clavicipitaceous endophytes, which are found in nearly all plants and have diverse ecological strategies. My dissertation has two sections: Section A investigates the intersection of Clavicipitaceous endophyte ecology with other ecological theory, including invasion ecology (Chapter II) and community ecology and climate change (Chapter III); Section B investigates the ecology of one group of non-Clavicipitaceous endophytes, the Xylariaceae, using a culture-based study in Ecuador (Chapter IV) and a next-generation sequencing based endophyte survey in Taiwan (Chapter V). Section B is centered on testing the Foraging Ascomycete (FA) hypothesis—the idea that some decomposer fungi may adapt an endophytic lifestyle to escape limitations in primary substrate in both time and space. In Chapter II, I utilized a host-specific Epichloë endophyte present ubiquitously in the European native range of the Pacific Northwest (PNW) invasive grass Brachypodium sylvaticum to test theories of invasion. In Chapter III, I examined the grass Agrostis capillaris in the context of a climate manipulation experiment in prairies in the PNW to elucidate patterns of interaction between multiple symbionts (Epichloë endophytes, dark septate root endophytes, and arbuscular mycorrhizal fungi) within single hosts across climatic variation. In Chapter IV, I began to test the FA hypothesis by examining spatial relationships of Xylaria endophytic fungi in the forest canopy with Xylaria decomposer fungi on the forest floor in a remote Ecuadorian cloud forest. In Chapter V, I build on the results from the previous study, using a novel technique to examine spatial ecology of the Xylariaceae, pairing traditional mycological collection with the preparation of a next-generation sequencing metabarcode library of endophytes over a much greater area. This dissertation includes previously published and unpublished coauthored material.

The goal of my dissertation research is to elucidate the population structure of two understudied but increasingly important fungal pathogens of humans. Coccidioides immitis and C. posadasii cause the disease coccidioidomycosis (Valley fever). These fungi occur in the soil of the desert regions of North and South America. Although studied for over 100 years, the primary host, ecological niche, and sexual cycle of Coccidioides spp. still remain unknown. Understanding the population structure of these fungi will permit identification of fundamental aspects of their ecology and allow researchers to identify potential hosts. Assessing genotypic diversity of pathogens is one step to understanding the population structure and evolutionary potential of organisms, and is the focus of this dissertation. The first appendix focuses on developing and evaluating methods to obtain environmental samples, and comparison of genotypes found in soil vs. human patients. Direct inoculation of mice proved to be the most reliable method of obtaining environmental strains. Environmental isolates from Tucson group with Arizona patient isolates. Comparing genotypes of human, environmental and non-human host strains of Coccidioides may help to determine if gene flow occurs over long distances and provide some indication of the population structure of C. posadasii in the environment, and is the focus of the second appendix. Finally, whole-genome sequencing and resequencing has been completed for 20 strains of C. immitis and C. posadasii. The resulting data provide greater insight into variation between and within species. In particular, the final appendix provides evidence for hybridization and gene flow between species. Data show that a region of C. posadasii origin is found at a higher frequency among the C. immitis southern California and Mexico patient isolates, and is found rarely among patient isolates from the San Joaquin Valley. Of particular interest is the fact that there is a conserved border region for all instances of introgression, and the gene immediately adjacent to this border is a metalloproteinase gene. Together these studies provide insight into the population biology of two human pathogenic fungi: gene flow is limited between species and populations, but genetic exchange occurs at all levels.

The objective of this thesis was to assess the diversity and community structure of fungi in a forest plot in Ontario using a variety of field sampling and analytical methods. Three broad questions were addressed: 1) How do different measures affect the resulting view of fungal diversity? 2) Do fruiting bodies and soil rDNA sampling detect the same phylogenetic and ecological groups of Agaricomycotina? 3) Will additional rDNA sampling resolve the phylogenetic position of unclassified fungal sequences recovered from environmental sampling? Generally, richness, abundance, and phylogenetic diversity (PD) correspond and identify the same dominant fungal groups in the study site, although in different proportions. Clades with longer branch lengths tend to comprise a larger proportion of diversity when assessed using PD. Three phylogenetic-based comparisons were found to be variable in their ability to detect significant differences. Generally, the Unifrac significance measure (Lozupone et al., 2006) is the most conservative, followed by the P-test (Martin, 2002), and Libshuff library comparison (Singleton et al., 2001) with our dataset. Fruiting body collections and rDNA sampling recover largely different assemblages of fungi at the species level; however, both methods identify the same taxonomic groups at the genus-order level as well as ectomycorrhizal fungi as the dominant functional type of Agaricomycotina. This work also shows that the Soil Clone Group I (SCGI) clade is widespread in soils of diverse origins and represents a novel subphylum of Ascomycota.