Development and validation of novel methods for microbial source tracking based on Escherichia coli as an indicator of water quality

Microbial pollution in water periodically affects human health in Australia, particularly in times of drought and flood. There is an increasing need for the control of waterborn microbial pathogens. Methods, allowing the determination of the origin of faecal contamination in water, are generally referred to as Microbial Source Tracking (MST). Various approaches have been evaluated as indicatorsof microbial pathogens in water samples, including detection of different microorganisms and various host-specific markers. However, until today there have been no universal MST methods that could reliably determine the source (human or animal) of faecal contamination. Therefore, the use of multiple approaches is frequently advised. MST is currently recognised as a research tool, rather than something to be included in routine practices. The main focus of this research was to develop novel and universally applicable methods to meet the demands for MST methods in routine testing of water samples. Escherichia coli was chosen initially as the object organism for our studies as, historically and globally, it is the standard indicator of microbial contamination in water. In this thesis, three approaches are described: single nucleotide polymorphism (SNP) genotyping, clustered regularly interspaced short palindromic repeats (CRISPR) screening using high resolution melt analysis (HRMA) methods and phage detection development based on CRISPR types. The advantage of the combination SNP genotyping and CRISPR genes has been discussed in this study. For the first time, a highly discriminatory single nucleotide polymorphism interrogation of E. coli population was applied to identify the host-specific cluster. Six human and one animal-specific SNP profile were revealed. SNP genotyping was successfully applied in the field investigations of the Coomera watershed, South-East Queensland, Australia. Four human profiles [11], [29], [32] and [45] and animal specific SNP profile [7] were detected in water. Two human-specific profiles [29] and [11] were found to be prevalent in the samples over a time period of years. The rainfall (24 and 72 hours), tide height and time, general land use (rural, suburban), seasons, distance from the river mouth and salinity show a lack of relashionship with the diversity of SNP profiles present in the Coomera watershed (p values > 0.05). Nevertheless, SNP genotyping method is able to identify and distinquish between human- and non-human specific E. coli isolates in water sources within one day. In some samples, only mixed profiles were detected. To further investigate host-specificity in these mixed profiles CRISPR screening protocol was developed, to be used on the set of E. coli, previously analysed for SNP profiles. CRISPR loci, which are the pattern of previous DNA coliphages attacks, were considered to be a promising tool for detecting host-specific markers in E. coli. Spacers in CRISPR loci could also reveal the dynamics of virulence in E. coli as well in other pathogens in water. Despite the fact that host-specificity was not observed in the set of E. coli analysed, CRISPR alleles were shown to be useful in detection of the geographical site of sources. HRMA allows determination of ‘different’ and ‘same’ CRISPR alleles and can be introduced in water monitoring as a cost-effective and rapid method. Overall, we show that the identified human specific SNP profiles [11], [29], [32] and [45] can be useful as marker genotypes globally for identification of human faecal contamination in water. Developed in the current study, the SNP typing approach can be used in water monitoring laboratories as an inexpensive, high-throughput and easy adapted protocol. The unique approach based on E. coli spacers for the search for unknown phage was developed to examine the host-specifity in phage sequences. Preliminary experiments on the recombinant plasmids showed the possibility of using this method for recovering phage sequences. Future studies will determine the host-specificity of DNA phage genotyping as soon as first reliable sequences can be acquired. No doubt, only implication of multiple approaches in MST will allow identification of the character of microbial contamination with higher confidence and readability.

A geographical analysis of the role of water supply and sanitation in the risk of helminth infections of children in West Africa

Background We investigated the geographical variation of water supply and sanitation indicators (WS&S) and their role to the risk of schistosomiasis and hookworm infection in school age children in West Africa. The aim was to predict large-scale geographical variation in WS&S, quantify the attributable risk of S. haematobium, S. mansoni and hookworm infections due to WS&S and identify communities where sustainable transmission control could be targeted across the region. Methods National cross-sectional household-based demographic health surveys were conducted in 24,542 households in Burkina Faso, Ghana and Mali, in 2003–2006. We generated spatially-explicit predictions of areas without piped water, toilet facilities and finished floors in West Africa, adjusting for household covariates. Using recently published helminth prevalence data we developed Bayesian geostatistical models (MGB) of S. haematobium, S. mansoni and hookworm infection in West Africa including environmental and the mapped outputs for WS&S. Using these models we estimated the effect of WS&S on parasite risk, quantified their attributable fraction of infection, and mapped the risk of infection in West Africa. Findings Our maps show that most areas in West Africa are very poorly served by water supply except in major urban centers. There is a better geographical coverage for toilet availability and improved household flooring. We estimated smaller attributable risks for water supply in S. mansoni (47%) compared to S. haematobium (71%), and 5% of hookworm cases could be averted by improving sanitation. Greater levels of inadequate sanitation increased the risk of schistosomiasis, and increased levels of unsafe water supply increased the risk of hookworm. The role of floor type for S. haematobium infection (21%) was comparable to that of S. mansoni (16%), but was significantly higher for hookworm infection (86%). S. haematobium and hookworm maps accounting for WS&S show small clusters of maximal prevalence areas in areas bordering Burkina Faso and Mali smaller. The map of S. mansoni shows that this parasite is much more wide spread across the north of the Niger River basin than previously predicted. Interpretation Our maps identify areas where the Millennium Development Goal for water and sanitation is lagging behind. Our results show that WS&S are important contributors to the burden of major helminth infections of children in West Africa. Including information about WS&S as well as the “traditional” environmental risk factors in spatial models of helminth risk yielded a substantial gain both in model fit and at explaining the proportion of spatial variance in helminth risk. Mapping the distribution of infection risk adjusted for WS&S allowed the identification of communities in West Africa where integrative preventive chemotherapy and engineering interventions will yield the greatest public health benefits.

The Law and Governance of Water Resources : The Challenge of Sustainability

To achieve the sustainable use and development of water resources is a daunting challenge for both the global and local communities. It requires commitments by all groups within the international, national and local communities from their own particular, possibly conflicting, perspectives. Without a set of coherent legal arrangements designed to ensure effective governance of water resources, their sustainable use and development are unlikely to be achieved. This study looks at how the legal arrangements for managing water resources have evolved across the continents over hundreds of years; their relevance for contemporary society; how the norms of current international and national legal regimes are responding; and, most importantly, how legal rights and duties should be structured so as to achieve sustainability in the future.

Drawing the line : the legal status and treatment of the 17-year-old accused in Queensland

Seventeen year olds who come into contact with the police in Queensland are classified as adults and are not afforded the protections available under the Youth Justice Act 1992 (Qld) (YJA). As with any other adult, their offences are dealt with under a raft of legislative provisions including the Criminal Code 1889 (Qld) (the Code), the Police Powers and Responsibilities Act 2000 (Qld) (PPRA) and the Penalties and Sentences Act 1992 (Qld) (PSA). This article argues that this situation is unfair and contravenes international human rights agreements which Australia has ratified, in particular the United Nations Convention on the Rights of the Child (CROC). Article 1 of that Convention defines a child as a person under the age of 18. The youth offences legislation in Queensland only applies to those who have not yet turned 17. This article examines the effects of this anomaly in Queensland, focusing in particular on the pre-adjudication treatment of ‘17 year old adults’.

Applications of medical image processing in the diagnosis and treatment of spinal deformity

In Chapter 10, Adam and Dougherty describe the application of medical image processing to the assessment and treatment of spinal deformity, with a focus on the surgical treatment of idiopathic scoliosis. The natural history of spinal deformity and current approaches to surgical and non-surgical treatment are briefly described, followed by an overview of current clinically used imaging modalities. The key metrics currently used to assess the severity and progression of spinal deformities from medical images are presented, followed by a discussion of the errors and uncertainties involved in manual measurements. This provides the context for an analysis of automated and semi-automated image processing approaches to measure spinal curve shape and severity in two and three dimensions.

Optimal allocation of water in village irrigation systems of Sri Lanka

This PhD study examines whether water allocation becomes more productive when it is re-allocated from 'low' to 'high' efficient alternative uses in village irrigation systems (VISs) in Sri Lanka. Reservoir-based agriculture is a collective farming economic activity, which inter-sectoral allocation of water is assumed to be inefficient due to market imperfections and weak user rights. Furthermore, the available literature shows that a „head-tail syndrome. is the most common issue for intra-sectoral water management in „irrigation. agriculture. This research analyses the issue of water allocation by using primary data collected from two surveys of 460 rice farmers and 325 fish farming groups in two administrative districts in Sri Lanka. Technical efficiency estimates are undertaken for both rice farming and culture-based fisheries (CBF) production. The equi-marginal principle is applied for inter and intra-sectoral allocation of water. Welfare benefits of water re-allocation are measured through consumer surplus estimation. Based on these analyses, the overall findings of the thesis can be summarised as follows. The estimated mean technical efficiency (MTE) for rice farming is 73%. For CBF production, the estimated MTE is 33%. The technical efficiency distribution is skewed to the left for rice farming, while it skewed to the right for CBF production. The results show that technical efficiency of rice farming can be improved by formalising transferability of land ownership and, therefore, water user rights by enhancing the institutional capacity of Farmer Organisations (FOs). Other effective tools for improving technical efficiency of CBF production are strengthening group stability of CBF farmers, improving the accessibility of official consultation, and attracting independent investments. Inter-sectoral optimal allocation shows that the estimated inefficient volume of water in rice farming, which can be re-allocated for CBF production, is 32%. With the application of successive policy instruments (e.g., a community transferable quota system and promoting CBF activities), there is potential for a threefold increase in marginal value product (MVP) of total reservoir water in VISs. The existing intra-sectoral inefficient volume of water use in tail-end fields and head-end fields can potentially be removed by reducing water use by 10% and 23% respectively and re-allocating this to middle fields. This re-allocation may enable a twofold increase in MVP of water used in rice farming without reducing the existing rice output, but will require developing irrigation practices to facilitate this re-allocation. Finally, the total productivity of reservoir water can be increased by responsible village level institutions and primary level stakeholders (i.e., co-management) sharing responsibility of water management, while allowing market forces to guide the efficient re-allocation decisions. This PhD has demonstrated that instead of farmers allocating water between uses haphazardly, they can now base their decisions on efficient water use with a view to increasing water productivity. Such an approach, no doubt will enhance farmer incomes and community welfare.

Core-shell microspheres with surface grafted poly(vinyl alcohol) as drug carriers for the treatment of hepatocellular carcinoma

Core(polyvinyl neodecanoate-ethylene glycol dimethacrylate)-shell(polyvinyl alcohol) (core (P(VND-EGDMA))-shell(PVA)) microspheres were developed by seeded polymerization with the use of conventional free radical and RAFT/MADIX mediated polymerization. Poly(vinyl pivalate) PVPi was grafted onto microspheres prepared via suspension polymerization of vinylneodecanoate and ethylene glycol dimethacrylate. The amount of grafted polymer was found to be independent from the technique used with conventional free radical polymerization and MADIX polymerization resulting into similar shell thicknesses. Both systems—grafting via free radical polymerization or the MADIX process—were found to follow slightly different kinetics. While the free radical polymerization resulted in a weight gain linear with the monomer consumption in solution the growth in the MADIX controlled system experienced a delay. The core-shell microspheres were obtained by hydrolysis of the poly(vinyl pivalate) surface grafted brushes to form poly(vinyl alcohol). During hydrolysis the microspheres lost a significant amount of weight, consistent with the hydrolysis of 40–70% of all VPi units. Drug loading was found to be independent of the shell layer thickness, suggesting that the drug loading is governed by the amount of bulk material. The shell layer does not appear to represent an obstacle to the drug ingress. Cell testing using colorectal cancer cell lines HT 29 confirm the biocompatibility of the empty microspheres whereas the clofazimine loaded particles lead to 50% cell death, confirming the release of the drug.

The philosophy and practice of water sensitive urban design : is it consistent with a whole system approach

This paper provides a critique of the Water Sensitive Urban Design (WSUD) paradigm by discussing its congruence with an established sustainable design principle called 'whole system design'. It was found that WSUD is congruent with the whole system design approach as a philosophy, but not in practice. Future improvement of WSUD practice may depend on the adoption of a front-loaded, teamwork-based design and planning process that is embedded in the principle of whole system design.

Three-dimensional geological modelling and multivariate statistical analysis of water chemistry data to analyse and visualise aquifer structure and groundwater composition in the Wairau Plain, Marlborough District, New Zealand

Concerns regarding groundwater contamination with nitrate and the long-term sustainability of groundwater resources have prompted the development of a multi-layered three dimensional (3D) geological model to characterise the aquifer geometry of the Wairau Plain, Marlborough District, New Zealand. The 3D geological model which consists of eight litho-stratigraphic units has been subsequently used to synthesise hydrogeological and hydrogeochemical data for different aquifers in an approach that aims to demonstrate how integration of water chemistry data within the physical framework of a 3D geological model can help to better understand and conceptualise groundwater systems in complex geological settings. Multivariate statistical techniques(e.g. Principal Component Analysis and Hierarchical Cluster Analysis) were applied to groundwater chemistry data to identify hydrochemical facies which are characteristic of distinct evolutionary pathways and a common hydrologic history of groundwaters. Principal Component Analysis on hydrochemical data demonstrated that natural water-rock interactions, redox potential and human agricultural impact are the key controls of groundwater quality in the Wairau Plain. Hierarchical Cluster Analysis revealed distinct hydrochemical water quality groups in the Wairau Plain groundwater system. Visualisation of the results of the multivariate statistical analyses and distribution of groundwater nitrate concentrations in the context of aquifer lithology highlighted the link between groundwater chemistry and the lithology of host aquifers. The methodology followed in this study can be applied in a variety of hydrogeological settings to synthesise geological, hydrogeological and hydrochemical data and present them in a format readily understood by a wide range of stakeholders. This enables a more efficient communication of the results of scientific studies to the wider community.

Feasibility study for thermal treatment of solid tire wastes in Bangladesh by using pyrolysis technology

In this study on the basis of lab data and available resources in Bangladesh, feasibility study has been carried out for pyrolysis process converting solid tire wastes into pyrolysis oils, solid char and gases. The process considered for detailed analysis was fixed-bed fire-tube heating pyrolysis reactor system. The comparative techno-economic assessment was carried out in US$ for three different sizes plants: medium commercial scale (144 tons/day), small commercial scale (36 tons/day), pilot scale (3.6 tons/day). The assessment showed that medium commercial scale plant was economically feasible, with the lowest unit production cost than small commercial and pilot scale plants for the production of crude pyrolysis oil that could be used as boiler fuel oil and for the production of upgraded liquid-products.

Vertical Inhibition of the PI3K/Akt/mTOR Pathway for the Treatment of Osteoarthritis

Osteoarthritis is characterized by degenerative alterations of articular cartilage including both the degradation of extracellular matrix and the death of chondrocytes. The PI3K/Akt pathway has been demonstrated to involve in both processes. Inhibition of its downstream target NF-kB reduces the degradation of extracellular matrix via decreased production of matrix metalloproteinases while inhibition of mTOR increased autophagy to reduce chondrocyte death. However, mTOR feedback inhibits the activity of the PI3K/Akt pathway and inhibition of mTOR could result in increased activity of the PI3K/Akt/NF-kB pathway. We proposed that the use of dual inhibitors of PI3K and mTOR could be a promising approach to more efficiently inhibit the PI3K/Akt pathway than rapamycin or PI3K inhibitor alone and produce better treatment outcome.