Search

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment and Sc, Science, Environment, Engineering and Technology, The Great Artesian Basin (GAB) is a vast subterranean thermal aquifer system underlying over 20% of the Australian continent. Substantial reserves of oil, gas and minerals exist within the GAB and combined with industrial activities can often contaminate the groundwaters. The current study investigated the bacterial ecology of bore waters that were in or close to oil deposits. Three sites were selected, two in the Quilpie/Eromanga region of Queensland (Naretha bore registered number 4022 and Adavale bore registered number 305), and the other in the Moomba oil field of South Australia (Moomba bore 9). A wide diversity of bacteria was detected across all of the samples collectively, including members of 32 bacterial phyla. There was greater diversity in the water samples from bores 4022 and 305 compared with Moomba 9, which was likely due to its closer association with oil. The most dominant bacterial taxa were similar in bores 4022 and 305, families Rhodobacteraceae, and Xanthomonadaceae and the order Bacillales. In contrast, the dominant taxa from Moomba 9 were the family Oxalobacteriaceae and the genus Agrococcus. Three different water samples were tested from bore 4022, from the source, 100 m and 250 m downstream in the runoff channel water. The bacterial diversity increased the further away the water flowed from the bore, due to the cooler water and contamination from the surrounding environment. A comprehensive anaerobic thermophilic enrichment program revealed that bacteria grew on a wide variety of organic substrates and a range of heavy metals as terminal electron acceptors. Isolation yielded 164 bacteria capable of using substrates from sugars and extracts through to polycyclic aromatic hydrocarbons (PAH) and reducing the metals iron(III), vanadium(V), cobalt(III) and manganese(IV). Seven pure iron(III) reducing polycyclic aromatic hydrocarbon (PAH) degrading bacteria, designated strains RN40AT, RN40BT, RN40CT, RN40DT, RN305AT, RN305BT and MBA9BT, were selec

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Environment and Sc, Science, Environment, Engineering and Technology, Nucleic acids are key macromolecules of living organisms transferring genetic inheritance from one generation to the next. From how a living individual is created to how it interacts with external factors, all and all, can be found in the nucleic acid sequences inside every single cell of every organism. Therefore, the analysis of nucleic acids sequences is a critical capability for cancer and pathogen diagnoses, genotyping, and disease monitoring. To date, numerous methods have been used to detect both characterised and uncharacterised mutations and sequence variations. However, the detection of low amounts of mutant genes in the presence of high levels of wildtype sequences is still a challenge, and existing technologies has room for improvement. The classical approaches for nucleic acid detection and analyses mainly include DNA sequencing and the polymerase chain reaction (PCR). Although these methods with high analytical performance and reliability have facilitated the interrogation of the nucleic acids, some key obstacles such as the need of labelling, high costs for routine clinical use, slow turnaround time for giving results, the complexity of operation, and the inability to dually detect the genetic mutation in one step have limited their applications. To avoid drawbacks of the traditional approaches, a number of chip-based methods leverage electrochemical readouts or microfluidics to identify nucleic acids. However, there is still an unmet need for a less complex, rapid, low-cost, sensitive and accurate method to enable nucleic acid analysis even in resource-poor settings. The overall objective of this PhD thesis is to develop simple, inexpensive and accurate platforms for nucleic acid evaluation. To achieve the aforementioned goal, the first attempt was to develop a lab-on-a-chip platform for cancer diagnosis by detection of circulating tumor nucleic acids (ctNAs) in plasma samples of cancer patients. ctNAs are fragmented DNA released from cancerous cells

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), Griffith School of Engineering, Science, Environment, Engineering and Technology, Maturation ponds are used for the treatment of wastewater and often form part of a municipal water treatment system. The primary purpose of a maturation pond is to disinfect pathogenic organisms present in the wastewater. Current knowledge of the disinfection mechanisms attributes ultraviolet radiation from sunlight as the most significant factor affecting die-off in maturation ponds. However, these artificial ponds are shallow ( 1m) and open to the atmosphere. This presents complex dynamics arising from climatic interactions at the water surface, in-water spatial effects from attenuation of sunlight, spatial distributions of pathogenic organisms, and the coupling effects of thermal gradients to turbulent dispersion. These interactions form a typical diurnal cyclic pattern, and as such have been segregated in previous studies. There exists a gap in the literature in understanding the effects and implications of the coupling between disinfection and hydrodynamics when transient and spatially applied sunlight is present. Experimental and modelling methods were used to evaluate the diurnal patterns of Escherichia coli die-off, natural mixing and their effects. Experimentally, an operational maturation pond was studied in the South East Queensland region of Australia. Extensive data for the pond was recorded. To investigate the coupling dynamics and implications of assumptions, the system was modelled by completely stirred tank reactor (CSTR) zero-dimensional, one-dimensional, and two-dimensional computational fluid dynamics (CFD) approaches. In modelling the maturation pond, the transport equations for E. coli featured a source term with disinfection kinetics included as a function of local ultraviolet radiation intensity. Within the literature, several sunlight disinfection terms were identified and tested in the models against our set of experimental data. The maturation pond was found to stratify and completely destratify in a diurnal cycle. E. coli concentrations w

Seventy four SNP genotypes and 54 E. coli genomes from kangaroo, Tasmanian devil, reptile, cattle, dog, horse, duck, bird, fish, rodent, human and environmental water sources were screened for the presence of the CRISPR 2.1 loci flanked by cas2 and iap genes. CRISPR 2.1 regions were found in 49% of the strains analysed. The majority of human E. coli isolates lacked the CRISPR 2.1 locus. We described 76 CRISPR 2.1 positive isolates originating from Australian animals and humans, which contained a total of 764 spacer sequences. CRISPR arrays demonstrated a long history of phage attacks especially in isolates from birds (up to 40 spacers). The most prevalent spacer (1.6%) was an ancient spacer found mainly in human, horse, duck, rodent, reptile and environmental water sources. The sequence of this spacer matched the intestinal P7 phage and the pO111 plasmid of E. coli.

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Biomolecular and Physical Sciences, Science, Environment, Engineering and Technology, The research presented in this thesis was initiated and supported by Gold Coast Water (Queensland Australia) in response to severe taste and odour issues experienced during a prolonged dry period that impacted on its drinking water service. The intent of this research project was to gain a better understanding of the presence, source and perseverance of geosmin and MIB within the Hinze Dam and the treated water distribution system and to explore potential environmental and physiological triggers for the microbial production of geosmin and MIB. Both field-based and laboratory-based research was undertaken to achieve this goal. The outcomes of this research have contributed to the knowledge of factors influencing taste and odour events and have provided further guidance, management options and research to understand and manage taste and odour events. A 13-month sampling program of the Hinze Dam was undertaken, during which time a significant taste and odour event occurred. High concentrations of geosmin were detected in the surface water of Gold Coast Water’s raw water source, Hinze Dam, during the Summer months and were strongly correlated with an increase in numbers of the cyanobacterium Anabaena sp. The increase in these cyanobacterial cells occurred immediately after a significant rainfall event and an accompanying pulse in nutrients during a time of warmer water temperatures. However, high rainfall and a pulse of nutrients did not render the same effect during colder months. Thus it was concluded that temperature and nutrient concentrations are important parameters involved in the microbial production of geosmin and MIB. This study also revealed that geosmin is present throughout the depth of the dam at most times throughout the year, albeit at concentrations not likely to cause aesthetic concerns for Gold Coast Water. This study did not find evidence to support the supposition that the taste and odour compounds, geosmin and MIB, were being produced by biofilm-at

Full Text, Thesis (PhD Doctorate), Doctor of Philosophy (PhD), School of Biomolecular and Physical Sciences, Science, Environment, Engineering and Technology, Giardia duodenalis is a protozoal, intestinal parasite that is a common aetiological agent of infectious diarrhoea in humans worldwide. Chemotherapeutic intervention presently offers a limited range of drugs and these are usually only employed after clinical diagnosis. Moreover, these drugs are ineffective against the infectious cysts, can produce unpleasant side effects, and are expensive with limited availability in developing countries. Frequent reports of drug toxicity, treatment failure and parasite drug resistance have, in some instances, also resulted in the increasing reluctance to over-prescribe synthetic anti-microbials. Alternatively, there is now mounting evidence to suggest that some of the naturally derived, mediumchain, saturated fatty acids (MCSFAs) possess anti-microbial and antiparasitic properties. I have therefore examined the effects of four different fatty acids on G. duodenalis trophozoites in vitro. Cytotoxicity was determined using fluorescence, scanning and transmission electron microscopic techniques and standard cytotoxicity assays. My studies have confirmed that the MCSFA, dodecanoic acid (C:12; common name lauric acid; DA), is anti-giardial with an LD50 concentration comparable to that of metronidazole, the drug of choice in the treatment of giardiasis. DA appears to induce trophozoite death by accumulating within the parasite cytoplasm resulting in rupture of the cell membrane. In vivo trials in mice using DA and coconut oil (which consists of 45-55% DA) as dietary supplements have also appeared promising against G. duodenalis infection, however the water soluble derivative, monolaurin (C:15; dodecanoic acid, 2,3-dihydroxypropyl ester) did not. These studies have opened fresh avenues for development of natural drug therapy in which food supplementation may augment, or even replace, some of the standard chemotherapeutic agents presently employed in the treatment of giardiasis and possibly other infectious intestinal diseases. In order t