[Truncated abstract] One of the standard ways of assessing time since death is from the stages of decomposition of the body. It is well known that the rate of decomposition is affected by environmental factors such as temperature and humidity. Another factor that can affect decompositional rates is the presence of breaches in the protective barrier of the skin, whether arising from antemortem injury or postmortem damage, including that occurring from animal necrophagy. Scavengers have the potential to affect decomposition by breaching the skin allowing access to associated insect material, feeding on the maggot masses, or by consumption of the carcass itself. Each locality will have its own set of features determining the rate of decomposition of the body, and variation may occur within localities based on the seasons. Such variation implies the need for local calibration of time since death against degree of decomposition and to establish the magnitude of interseasonal variation. When the localities are outdoors, the influence of potential scavengers, and the factors affecting their activity need also to be taken into account. This study investigates the interaction of environmental factors and animal scavenging on the rate of decomposition of pig (Sus scrofa) carcasses at four south-west Western Australia sites; Jandakot, Shenton Park, Perup Forest, and Watheroo National Park. Jandakot and Shenton Park are both close to the Perth metropolitan area and the western coast while Perup Forest is southern and inland and Watheroo is northern and inland. ... The most common insectivore feeding in relation to the carcasses was the Willie Wagtail (Rhipidura leucophrys) which was associated with the carcasses in all seasons and all locations except for Perup Forest. The breeding cycle appeared to have a marked influence on the intensity of scavenging by several species. The effect of season on decompositional rates was greatly reduced in carcasses that were exposed to scavenging. It took no additional time for carcasses to achieve skeletonization in winter than in the other seasons in the presence of scavenging. Scavenging had no significant impact on the rate of breakdown of carcasses in summer, when decompositional rates were greatest and scavenging at a minimum. v In Western Australia, it is not uncommon for bodies to remain undiscovered in bush environments for lengthy periods of time due to the low human population density. This study shows conclusively that it is not sufficient simply to consider the accumulated degree day (ADD) when estimating time since death by the degree of decomposition of the body. Attention must also be given to local wildlife assemblages and variations in their activities with the seasons. The implications of this research are in the determination of time of death. If the effects of scavengers accelerate decomposition this must be taken into account when any calculation since time of death is determined. The marked variations between sites in the rates of decomposition of carcasses exposed to natural animal scavenging in this study highlights the need for local calibration of time since death to decompositional stages for all locales. The techniques devised in this study are straight forward and easily conducted yet are informative and essential in determining time since death for bodies which have been exposed to animal scavenging.

1,1,1-trichloro-2,2-bis(4-chlorophenyl)-ethane (DDT) residues (DDTr) are widespread and persistent environmental contaminants, and have been classed as priority pollutants by the United Nations Environment Programme (UNEP). DDTr are potent endocrine disrupting molecules, and have been associated with reproductive abnormalities in juvenile alligators and rats. Microorganisms that metabolise DDTr both aerobically and anaerobically have been isolated and characterised. Bacteria that degrade DDTr aerobically typically utilise a dioxygenase to initiate degradative reactions through ring-hydroxylation, and convert DDTr to 4-chlorobenzoate without further degradation. Terrabacter sp. strain DDE-1 was isolated from DDTr-contaminated soil from Canterbury, New Zealand, and aerobically degrades 1,1-dichloro-2,2-bis-(4-chlorophenyl)-ethylene (DDE) to 4-chlorobenzoate, when grown in the presence of biphenyl (BP). The intermediates of degradation were inferred to be the end products of dioxygenase activity. Sequencing of a large linear plasmid, pBPH-1, from strain DDE-1 identified a cluster of genes with high levels of sequence similarity to BP-degradation genes from Rhodococcus spp. and Pseudomonas spp. This plasmid is lost at high frequency producing the plasmid-cured strain MJ-2, which has lost the ability to degrade BP or DDE. The aim of this study was to confirm that DDE-degradation in strain DDE-1 is encoded by the bph operon located on pBPH-1. No genetic systems to study gene function in either DDE-1 or MJ-2 could be developed using an array of broad-host range vectors. However, heterologous expression of the bph genes in Rhodococcus erythropolis strain TA422 was successful, with the recombinant strain TA425, obtaining the ability to utilise BP and DDE as a sole source of carbon and energy. DDE-1 was shown to convert indole to indigo, but MJ-2 could not, indicating that the biphenyl dioxygenase located on pBPH-1 is responsible for this activity. The bph genes from strain DDE-1 also conferred the ability to produce indigo from indole on strain TA425, confirming successful expression of the functional biphenyl dioxygenase in this strain. Despite several attempts to show quantitative degradation in strain TA425 using gas chromatography, the results were inconclusive Further analysis is needed to provide unequivocal evidence of DDE-degradation by strain TA425. Attempts to express the bph genes in rhizosphere-colonising bacteria, such a Rhizobium spp. or Pseudomonas spp., were unsuccessful, as evidenced by the inability to produce indigo, hence the lack of a functional biphenyl dioxygenase. However, RT-PCR did indeed indicate that P. aeruginosa strain Fin1 produced a bphA1 transcript, indicating that an error is occurring post-transcriptionally in these strains, to prevent production of the functional enzyme. New Zealand has recently been shown to contain hotspots of DDTr-contamination. The second aim of this study was to determine the prevalence of DDTr-degrading bacteria and to gain insight into the types of bacteria that inhabit sites contaminated with DDTr. To investigate this, culture-dependent and culture-independent techniques were employed. Enrichment for DDTr-degrading bacteria yielded species of Rhodococcus and Ralstonia using DDTr-overlayer plate assays. The polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were used to amplify and analyse the 16S rDNA and 16S rRNA for the identification of dominant and active bacteria in soil samples. The results of this analysis identified bacteria such as Williamsia spp. and Gordonia spp. that degrade other types of pollutants. This analysis did not identify a predominance of Rhodococcus or Ralstonia spp., or other bacteria that have been shown to degrade DDTr. To identify ecologically relevant members of the bacterial communities in DDTr-contaminated soils, and potentially important metabolic pathways, identification of ring-hydroxylating dioxygenase (RHD) genes was performed. PCR and restriction fragment length polymorphism (RFLP) analysis were employed together with phylogenetic analyses. The results showed that the RHD genes identified, clustered separately to those genes previously characterised from cultivated bacteria. Among these genes, one phylogenetic group was most closely related to the dioxygenase genes from Ralstonia eutropha H850, which is potent PCB-degrading bacterium that possesses a dioxygenase with a wide substrate range for many types of heavily chlorinated, PCB congeners. The identification of a predominance of genes with similarity to phenyl-propionate dioxygenases has been not been recognised previously in soil studies.

Bibliography: leaves 177-191. / xxi, 191 leaves : ill. (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Soil and Water, 2001

Graduation date: 1998

This study investigated the effect of plant surface area (plant density) on the efficiency of organic carbon removal in a bench-scale constructed wetland. Constructed wetlands are commonly assumed to be biofilm reactors in which organic carbon removal occurs primarily through sedimentation and aerobic degradation by attached microbial biofilms. In conventional biofilm reactors, aerobic degradation of organic carbon is proportional to the amount of surface area for microbial attachment, provided that sufficient oxygen is available. In contrast, current design equations for constructed wetlands assume that the amount of surface area is not an important parameter. A bench-scale simulation of a constructed wetland was conducted, using bulrushes planted at varying plant densities in soil with a free water surface depth of about 0.27 m. The carbon source was diluted ENSUR (TM). Total organic carbon (TOC) removal was measured. Concentration of TOC was correlated with biochemical oxygen demand (BOD). Tests were conducted in conditions of light and dark, and under two different carbon loadings. Performance of bulrushes was compared with that of inert acrylic rods. The rate of carbon removal by mature bulrushes was found to increase with increasing plant density until oxygen became depleted. Higher densities degraded carbon at rates much faster than those predicted by current design equations. Young bulrushes degraded carbon at faster rates than mature bulrushes. Once oxygen was depleted, rates of degradation were reduced to rates anticipated by current models. When plant density was 15% or greater, oxygen became depleted in less than 6 hours. Removal efficiency was greater at higher loadings (70 mg/l BOD) than at lower loadings (25 mg/l BOD). Bulrushes performed significantly better than inert rods, sometimes by a full order of magnitude. The microbial community on the bulrushes appeared to be more complex and robust than that on the rods. Also, the presence of light did not significantly increase degradation rates for the bulrushes but was significant for the rods. The microbial community on the rods contained a larger proportion of epiphytic algae. The presence of light did result is greater overall efficiency of removal for both bulrush and rods. Currently, a major drawback of constructed wetlands in wastewater treatment has been their demand for large areas of land. This study suggests that it would be possible to reduce the land area requirements for constructed wetlands for both carbon removal and nitrification/denitrification provided designs gave more consideration to oxygen supply. Using current designs, a retention time of 4-8 days typically results in 70% BOD removal. This experiment suggests that wetlands with a retention time of about 1 day could provide the same performance if additional oxygen were supplied. / Graduation date: 1995

Carbon isotope analyses of gases extracted from drilling muds while drilling in the Western Canada Sedimentary Basin (WCSB) can be used to create carbon isotopic depth profiles. These profiles provide essentially continuous data through the stratigraphic section, offering a unique opportunity to study the in-situ gases in various rock matrices. Carbon isotope and molecular compositions of Jurassic - Cretaceous mud gases have been examined from ten depth profiles in the undisturbed WCSB. The isotopic profiles are surprisingly complex, showing numerous inflections and deviations towards increasing and decreasing carbon isotope values (13C) and wetness index with depth that suggest a correlation with the stratigraphic framework and can be explained in terms of the origin and alteration of the gases. However, the gas isotope geochemistry must be incorporated and applied in a multidisciplinary approach in order to gain a better understanding of causes of variations. The discernible degree of correlativity of carbon isotope trends between the WCSB wells are likely to be related to the presence of major gas compartments bounded by stratigraphic surfaces, compartmentalization of the gas being strongly influenced by stratigraphic variations. The majority of these boundaries act as effective barriers to gas migration. Mudgas geochemistry is best employed in conjunction with petrophysical analysis and conversion into mineralogy, for defining details of transition zones and reservoir compartments. Combined evidence suggests that isotopic variability of WCSB gases is only partly induced by source maturity at one single location. The main shifts of carbon isotope ratios are likely to be related to the physical properties of the rocks, differences between organic precursors (type II versus type III kerogen), total organic carbon (TOC) content, gas biodegradation and mixing. The present thesis demonstrates that the carbon isotopic mud gas profiles represent a powerful tool that provide information about the compartmentalization of the gas, the effectiveness of low permeability barriers, the origin, alteration and maturity of gases, and the regional gas dynamics. Mudgas geochemistry proves to be one part of the puzzle in the investigation of regional gas dynamics, and should be integrated with geological information, lithostratigraphic-, and sequence stratigraphic information, petrographic information and geophysical data.

Sustainable polymeric materials put emphasis on mastering the whole life-cycle of polymeric materials. This includes the choice of raw materials, selection of synthesis and processing, environmental impact during long-term use followed by detailed knowledge about recycling and waste management.  Within this large efforts are put in the design and development of new biocomposites using renewable fibres instead of inert ones. The thesis deals with surface modifications of agricultural fibres and the design of biocomposites with optimal long-term properties balancing the potential risk for biodegradation.  The first part of this thesis involved surface modifications of oil palm fibres and production of biocomposites with PP as matrix. The chemical surface modifications of oil palm fibres explored propionylation, PPgMA grafting via solution modification and reactive blending and vinyltrimethoxy silanization as methods. All modified fibre/PP biocomposites showed improvements in the mechanical properties followed also by an improvement of water resistance. In comparison with unmodificed fibres/PP matrix the highest water resistance after the surface modifications of oil palm fibres were observed for silanization followed by PPgMA modified,  PPgMA blending and  propionylation. The second part aimed at producing fully biodegradable biocomposites and analysing the resulting properties with respect to potential risk for biodegradation. Sisal fibres were incorporated in PLA and PHBV and the resulting risk for biodegradation using a fungus, Aspergillus niger, monitored. Neat PLA and PHBV were compared with the corresponding biocomposites and already without fibres both polymers were notably biodegraded by Aspergillus niger. The degree of biodegradation of PLA and PHBV matrices was related to the extent of the growth on the material surfaces. Adding sisal fibres gave a substantial increase in the growth on the surfaces of the biocomposites. Correlating the type of surface modification of sisal fibres with degree of biodegradation, it was demonstrated that all chemically modified sisal/PLA biocomposites were less biodegraded than unmodified sisal biocomposites.  Propionylated sisal/PLA demonstrated the best resistance to biodegradation of all biocomposites while sisal/CA/PLA demonstrated high level of biodegradation after severe invasion by Aspergillus niger. In general, the biodegradation correlated strongly with the degree of water absorption and surface modifications that increase the hydrophobicity is a route to improve the resistance to biodegradation. Designing new biocomposites using renewable fibres and non-renewable and renewable matrices involve the balancing of the increase in mechanical properties, after improved adhesion between fibres and the polymer matrix, with the potential risk for biodegradation. / <p>QC 20130325</p>

Protein disulfide isomerases (PDIs) catalyze the oxidation and isomerization of disulfide bonds in proteins passing through the endoplasmic reticulum (ER). Although as many as 20 enzymes are classified as PDI family members, their relative contributions to protein folding have remained an open question. Additionally, Ero1 has been characterized as the ER oxidase that transfers oxidizing equivalents from oxygen to PDI enzymes. However, knockout mice lacking the mammalian Ero1 isoforms, Ero1Lα and Ero1Lβ, are viable, and the role of other potential ER oxidases in maintaining an oxidative ER environment is now an important issue. By systematic depletion of ER PDI family members and potential ER oxidases and assessment of disulfide bond formation of secreted endogenous substrates, I have outlined the functional relationships among some of these enzymes. PDI family member depletion revealed that PDI, although not essential for complete disulfide bond formation in client proteins, is the most significant catalyst of oxidative folding. In comparison, ERp57 acts preferentially on glycosylated substrates, ERp72 functions in a more supplementary capacity, and P5 has no detectable role in formation of disulfide bonds for the substrates assayed. Initially, no impact of depletion of Ero1 was observed under steady state conditions, suggesting that other oxidase systems are working in parallel to support normal disulfide bond formation. Subsequent experiments incorporating a reductive challenge revealed that Ero1 depletion produces the strongest delay in re-oxidation of the ER and oxidation of substrate. Depletion of two other potential ER oxidases, peroxiredoxin 4 (PRDX4) and Vitamin K epoxide reductase (VKOR), showed more modest effects. Upon co-depletion of Ero1 and other oxidases, additive effects were observed, culminating in cell death following combined removal of Ero1, PRDX4, and VKOR activities. These studies affirm the predominant roles of Ero1 in ER oxidation processes and, for the first time, establish VKOR as a significant contributor to disulfide bond formation.

This thesis presents the potential of integrating chemical and biological treatment technologies for the removal of high concentrations of phenol in a bioremediation medium. High concentrations of phenol in wastewater are difficult to remove by purely biological methods. Chemical oxidation is one way to treat high concentrations of phenol but complete oxidation is not always possible or will make the treatment process uneconomical. An experimental design approach, based on central composite rotatable design (CCRD) was used to evaluate the effects of process parameters on phenol oxidation by Fentons reagent and chlorine dioxide. Performance of the chemical oxidation was evaluated by determining the percentage of phenol oxidized at equilibrium. The reaction mechanism for the oxidation of phenol by Fentons reagent was proposed based on identification of the intermediate compounds.<p> The effects of H₂O₂ concentration (2000 to 5000 mg L^-1) and FeSO₄.7H₂O concentration (500 to 2000 mg L^-1) were investigated on phenol oxidation and optimal concentrations of H₂O₂ and FeSO₄.7H₂O for complete oxidation of 2000 mg L^-1 phenol in medium were found to be 4340 mg L^-1 and 1616 mg L^-1, respectively, at 25°C and pH 3. The main oxidation products were identified as catechol, hydroquinone and maleic acid.<p> In the case of phenol oxidation by chlorine dioxide, the effects of chlorine dioxide concentration (500 to 2000 mg L^-1), temperature (10 to 40°C) and pH (3 to 7) on the oxidation of 2000 mg L^-1 of phenol were determined. The optimal concentration of chlorine dioxide to completely oxidize 2000 mg L^-1 of phenol was 2000 mg L^-1. The other parameters did not significantly affect the oxidation over the ranges studied. The main oxidation products were identified as 1,4-benzoquinone and 2-chloro-1,4-benzoquinone.<p> Finally, the biodegradation of 1,4-benzoquinone, the main oxidation product of phenol oxidation by chlorine dioxide, was studied in batch and continuous systems using Pseudomonas putida 17484 in two dose McKinneys medium. The effects of 1,4-benzoquinone concentration and temperature were studied on biodegradation of 1,4-benzoquinone in batch reactors. Under optimal conditions, it was found that 150 mg L^-1 1,4-benzoquinone could be successfully biodegraded at 15°C. In a continuous reactor operating at 15°C the highest removal rate with 500 mg L^-1 of 1,4-benzoquinone was found to be 246 mg L^-1 h^-1. The values of µmax, Ks and yield were also determined as 0.74±0.03 h^-1 and 14.17±3.21 mg L^-1 and 2x10¹³ cell mg^-1, respectively.

Pentaerythritol tetranitrate (PETN), a nitrate ester, is widely used as a powerful explosive and is classified as a munitions constituent of great concern by DoD in U.S.A. It is an environmental concern and poses a threat to ecosystem and human health. Our objective was to examine potential remediation strategies for both PETN-contaminated water and soil. Flow-through iron columns were used to determine the potential for using granular iron to degrade PETN in aqueous phase. PETN transformation in both a 100% iron column and a 30% iron and 70% silica sand column followed pseudo-first-order kinetics, with average half-lives of 0.26 and 1.58 minutes, respectively. Based on the identified intermediates and products, the reaction pathway was proposed to be a sequential denitration process, in which PETN was stepwisely reduced to pentaerythritol with the formation of pentaerythritol trinitrate (PETriN) and pentaerythritol dinitrate (PEDN). Although pentaerythrito mononitrate was not detected, an approximately 100% nitrogen mass recovery indicated that all nitro groups were removed from PETN. Nitrite was released in each denitration step and subsequently reduced to NH4+ by iron. Nitrate was not detected during the experiment, suggesting that hydrolysis was not involved in PETN degradation. Furthermore, batch experiments showed that PETN dissolution was likely a rate-limiting factor for PETN degradation, especially in the case with high amount of iron. Using 50% methanol as a representative co-solvent, PETN solubility was greatly enhanced and thus the removal efficiency was improved. The results demonstrate the use of granular iron to remediate PETN-contaminated water. The biodegradability of aqueous PETN was examined with a mixed microbial culture from a site contaminated with PETN. The mixed culture was enriched and selected using a mineral medium containing acetate and yeast extract as carbon and nutrient sources in the presence of nitrate or sulfate. The final enrichment cultures were used as inocula for studying PETN biodegradation under nitrate-reducing and sulfate-reducing conditions. In addition, PETN degradation was tested using the original microbial culture under the mixed electron acceptor conditions of nitrate and sulfate. The results showed that under all conditions tested, PETN was sequentially reduced, apparently following the same pathway as the abiotic reduction by granular iron. Pentaerythritol mononitrate, a suspected intermediate in the abiotic degradation by iron, was identified in this experiment. The presence of nitrate seemed not to affect the kinetics of PETN degradation, with both PETN and nitrate degrading simultaneously. However, the rate of nitrate reduction was much faster than PETN degradation. With respect to sulfate, its presence did not have an adverse effect on PETN degradation, indicated by the very similar degradation rates of PETN in the presence and absence of sulfate. Under all conditions, PETN appeared to act as a terminal electron acceptor for energy generation during biodegradation. A utilization sequence by bacteria in the order of nitrate, PETN, PETriN, PEDN and sulfate was clearly observed. The study in this phase demonstrated that under anaerobic conditions, with carbon sources provided, PETN can be effectively biodegraded by indigenous bacteria in contaminated soil, most likely by denitrifying bacteria. Based on the successful demonstration of abiotic and biotic degradation of PETN in the aqueous phase, both methods were further tested for remediating PETN-contaminated soil in both laboratory and pilot scale. In the laboratory, a systematic soil microcosm experiment was conducted using soil from a contaminated site and additions of either granular iron or organic materials, with deoxygenated Millipore water. Because of the high concentration in the contaminated soil, solid-phase of PETN was initially present in the microcosms. Two types of DARAMEND products, D6390Fe20 (containing 20% iron + 80% botanical materials) and ADM-298500 (100% botanical materials), were used as sources of carbon and other nutrients. During the 84-day incubation period, more than 98% was removed in all DARAMEND treatments, following pseudo-first-order kinetics with half-lives ranging between 8 and 18 days. The results clearly demonstrated that PETN can be effectively degraded under anaerobic conditions with the addition of carbon and possibly nutrients. As in the aqueous tests, the sequence of microbial utilization was nitrate followed by PETN and sulfate. In contrast to the tests with aqueous PETN, iron was not effective in removing PETN in the contaminated soil, due to iron passiviation caused by the presence of high levels of nitrate in the soil. In addition, a slight enhancement was observed in a combined system of iron and biodegradation over biodegradation only. However, the extent of enhancement is not believed to be significant relative to the extra cost for iron addition. A pilot scale test was conducted at a PETN-contaminated site at Louviers, CO, a waste pond which had received waste water from PETN manufacture for over 20 years. The test involved 10 treatments, one control without amendment, one amended with iron (10%), eight with different types and amounts of organic carbon (1%, 2% and 4% of D6390Fe20; 2% and 4% of ADM-298500 and 1%, 2% and 4% of brewers grain). Each treatment was performed in a plastic tub (45 cm wide × 90 cm long × 25 cm deep), containing approximately 18 cm thick layer of soil and 6-8 cm of standing water. Over 74 days, very little consistent reduction of PETN was found in the iron treatment, which was also due to iron passivation in the presence of nitrate in the soil. In contrast, significant removal of PETN (11,200 to 33,400 mg/kg) was observed in the treatments amended with organic materials, and the extent of removal increased with increasing amounts of organic materials. The pilot test was consistent with the results of the laboratory experiments for iron and biodegradation with carbon addition. For biological treatment, the stoichiometric estimation suggests that the complete remediation in many of the treatments will be ultimately limited by carbon sources. Results of this study showed the great potentials of using granular iron to degrade PETN in solution and using indigenous bacteria present in contaminated soils to biodegrade PETN in both the solution and soil phase. Both iron and biodegradation with carbon addition represent viable approaches for remediation of PETN-contaminated water and soil, though iron may not be appropriate in the presence of high concentration of nitrate.