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<p> Metal contamination from anthropogenic activities is of great concern due to the associated detrimental effects on ecosystem health. An increase in metal concentrations in the dissolved phase creates greater ecosystem impacts. Thus, the relative extent of metal distribution between sediment and dissolved compartments, and an understanding of the factors that control this partitioning is key to assessing metal impacts. In this thesis, metal concentrations were determined for a suite of 12 metals (Cr, Mn, Co, Cu, Sn, Ag, As, Ni, Zn, Cd, Se and Fe) associated with three compartments, dissolved, surficial bed sediment and suspended particulate matter (SPM) in Hamilton Harbour, Ontario. Due to highly dynamic interactions of anthropogenic impacts that may work together to affect metal distributions as well as processes that occur over small or rapid scales, a high-resolution temporal and spatial scale was used to evaluate these metal distributions over a seasonal timeframe. </p> <p> Concentrations of metals amongst sediment fractions indicated that sediment metal uptake was largely controlled by the concentration of the sediment associated amorphous and crystalline oxyhydroxide fractions accounting for up to 90% of total sediment bound metal, even though the oxyhydroxides only accounted for a maximum of 23% of the total sediment mass for both surficial bed sediment and SPM compartments. The formation and dissolution of amorphous oxyhydroxides is commonly a microbially mediated process. Thus, these results underscore the important role of oxyhydroxides and the microbial processes that contribute to their formation and dissolution m controlling metal dynamics, and likely metal impacts in Hamilton Harbour. </p> <p> Metal partitioning was found to be both spatially and temporally variable for all compartments, temporally ranging 0.5 to 4 orders of magnitude for a given element; indicating highly dynamic metal exchanges between sediment and solution compartments and fluctuating distributions over the time and spatial scales examined. </p> <p> The suite of variables that are considered to control metal distribution between dissolved and sediment compartments, and thus impact metal toxicity (i.e., temperature, pH, specific conductivity, oxidation-reduction potential, dissolved organic carbon concentration, SPM concentration (for SPM associated metals only), fraction concentrations i.e. g carbonate /g solid, g amorphous oxyhydroxide I g solid, etc., and dissolved metal concentrations) did not constrain the variability in observed metal distribution behaviour, indicating that other factors in this system, such as hydrodynamic disturbances associated with shipping traffic and channelized water currents, as well as specific point source metal discharges, may play a larger role in determining metal partitioning in Hamilton Harbour, compared to less anthropogenically, impacted systems. Furthermore, no one master variable defming metal partitioning between the dissolved and sediment compartments was found, rather relationships controlling metal distribution behavior were site, compartment, sediment fraction and element specific highlighting the challenges for the development of a Harbour-wide management plan for priority metal contaminants. The results presented in this thesis, show that it is necessary to consider metal, site and compartment specific conditions as well as fully addressing temporal variability in metal behaviour. In addition, the results of this thesis point to the need to address hydrodynamic disturbance and point source influences on metal behaviour in Hamilton Harbour and likely extend to other multi-impacted metal contaminated systems. </p> / Thesis / Master of Science (MSc)

Surface analysis of buna-N-rubber and teflon was performed. Scanning electron microscopy was used to analyze the topography of both materials and x-ray microanalysis identified the elemental chemical composition of the polymers. Teflon was primarily a smooth surface with random irregular spots, while buna-N-rubber had a very rough topography with "caverns" and crevices spread over the surface. The x-ray microanalysis showed that there are no impurities on the surface of teflon; however, calcium, silicone and sulfur were present on the surface of buna-N-rubber. Water contact angle measurements indicated that buna-N-rubber was a more hydrophobic surface than teflon. Qualitative analysis of the attachment of Pseudomonas fragi A TCC 4973, Listeria monocytogenes Scott A and Bacillus cereus ATCC 11778 to buna-N-rubber and teflon was assessed by scanning electron microscopy. These bacteria readily attached to both surfaces. Pseudomonas fragi attached after 2 hours in the presence of this microoorganism and Bacillus cereus and Listeria monocytogenes attached at 12 and 24 hours, respectively. Quantitative analysis of the attachment of Pseudomonas fragi to both surfaces as affected by various milk fat concentrations and temperature, and the availability of nutrients (different dilutions of skim milk, casein, casein and lactose, and whey and lactose) was conducted. Attachment was assessed by impedance microbiology. Milk fat content did not play a significant role in the process of attachment of this organism to either type of surfaces; however, significantly greater numbers attached to buna-N-rubber than to teflon. Overall bacteria attached in higher numbers to both surfaces when grown at 21°C, compared to bacteria grown at 4°C. For buna-N-rubber, bacteria attached in significantly higher numbers when the concentration of nutrients was minimal, while for teflon, the results were, in most cases, opposite to these. / Ph. D.

Variations in ATP content in three ground beef spoilage bacteria, Lactobacillus brevis, Lactobacillus jensenii, and Pseudomonas sp. were investigated using the bioluminescence (luciferin-luciferase) assay. Environmental factors (temperature, atmosphere, pH, aeration, and phase of growth), as well as differences among genera and species, were studied in relation to their effect on cellular ATP. Variations for each of the environmental factors and bacteria were shown statistically to be significantly different at the 0.05 level. The mean ATP/cell for each of the bacteria was 2.71 fg/cell (L. brevis), 2.20 fg/cell (L. jensenii), and 1.36 fg/cell (Pseudomonas sp.). For all three bacteria, ATP/cell was lower and more stable throughout the culture's growth cycle at 3°C or in N₂. In general, ATP/cell increases from a lowest value in lag phase to a highest value in stationary phase. The effect of sonication on ATP/cell was tested for each bacterium at one set of factors. Sonication studies showed that L. brevis cells were clumping, especially in aged cultures. After sonication, ATP/cell remained relatively constant from lag through stationary phase. L. jensenii showed no signs of clumping and ATP/cell increased as the culture aged. Sonication had a lethal effect on the Pseudomonas. Thus the ATP/cell for Pseudomonas increased dramatically as the culture aged. Guidelines concerning temperature, assumed ATP content for major contaminants, and sample handling must be followed in order to use the bioluminescence assay to estimate biomass in foods. / M.S.

Escherichia coli (E. coli) is a gram-negative bacteria found in the intestinal system of humans that can also contaminate food, drinking water, as well as lakes and rivers. While not all strains are pathogenic, some including O157:H7 can cause severe illness. Conventional methods of detecting E. coli contamination in water samples often have limitations for on-site testing applications, which can include their slow detection time or need for expensive laboratory equipment. While several fluorescent biosensors for the detection of E. coli have been developed in the Didar lab, there is increased interest in colourimetric biosensors whose signal can be interpreted with the naked eye. This thesis will describe the development and performance of a hydrogel biosensor, that is made of polyacrylamide chains crosslinked by an E. coli detecting Deoxyribozyme (DNAzyme) and its substrate. In the presence of E. coli, the DNAzyme cleaves its substrate and crosslinking breaks down, resulting in the visible dissolution of the hydrogel. Paired with the use of bacteriophage induced cell lysis to amplify the target protein, detection sensitivity to the order of 10^1 CFU/mL has been achieved using this platform with an incubation time of 18 hours. A convolutional neural network (CNN) trained on optical images of the platform was able to classify samples as contaminated or uncontaminated with a validation accuracy of over 93%. / Thesis / Master of Applied Science (MASc) / Microbial contamination of water sources including surface water, groundwater, and drinking water can pose risks to human health. One bacterial species that can sometimes contaminate these sources is Escherichia coli (E. coli). To determine if E. coli is present in a water sample, it often needs to be sent to a laboratory for testing, which can be time consuming and inconvenient. Therefore, researchers are working to develop new sensors that are able to detect E. coli from water samples, ideally being simple enough to use that testing could be done right away and without sending the sample to another location. In this research project, we have developed a new biosensor that can detect E. coli in water samples. To use the sensor, a water sample is added onto a small red gel in a tube, and this gel breaks apart if E. coli is present in the sample.

A critical first step to improving existing and designing future wide-area networks is an understanding of the load placed on these networks. Efforts to model traffic are often confounded by atypical traffic - traffic particular to the observation site not ubiquitously applicable. The causes and characteristics of atypical traffic are explored in this thesis. Atypical traffic is found to interfere with parsimonious analytic traffic models. A detection and modeling technique is presented and studied for atypical traffic characterized by strongly clustered inliers. This technique is found to be effective using both real-world observations and simulated data. Another form of atypical traffic is shown to result in multimodal distributions of connection statistics. Putative methods for bimodal estimation are reviewed and a novel technique, the midpoint-distance profile, is presented. The performance of these estimation techniques is studied via simulation and the methods are examined in the context of atypical network traffic. The advantages and disadvantages of each method are reported. / Master of Science

No / We have investigated the susceptibility of degraded human hair shaft samples to contamination by exogenous sources of DNA, including blood, saliva, skin cells, and purified DNA. The results indicate that on the whole hair shafts are either largely resistant to penetration by contaminant DNA, or extremely easy to successfully decontaminate. This pertains to samples that are both morphologically and biochemically degraded. We suggest that this resistance to the incorporation of contaminant DNA relates to the hydrophobic and impermeable nature of the keratin structures forming the hair shaft. Therefore, hair samples represent an important and underestimated source of DNA in both forensic and ancient DNA studies.

An alternative on-site wastewater treatment and disposal system (OSWTDS) consisting of a soil infiltrator with low pressure distribution was evaluated in a soil that was unsuitable for a conventional OSWTDS under current Commonwealth of Virginia Sewage Handling and Disposal Regulations, due to a shallow seasonally perched water table and low hydraulic conductivity. The absorption field consisted of two subsystems numbered as 1 and 2 with effluent design loading rates of 5.1 and 10.2 Lpd/m2, respectively (actual loading rates of 2.4 and 4.9 Lpd/m2, respectively). Soil matric potentials compared seasonally for each subsystem and indicated that both provided similar hydraulic performance. Background water quality was generally improved by subsurface movement through the absorption fields. A bacterial tracer was found in shallow (45.7 cm) and deep (213.4 cm) sampling wells within 24 h in the two subsystems (but in low numbers) over both summer and winter sampling periods. A viral tracer was detected within 48 h in both shallow and deep wells, but only in subsystem 2 in the winter. In evaluating denitrification potential, the addition of glucose to soil core samples did increase quantitatively, although not significantly, nitrous oxide production in each subsystem, at each depth, during each season. Overall, the performance of both subsystems was very similar. The soil infiltrator functioned very well, as designed for the site and soil limitations. It appears to be a potential alternative OSWTDS for use in problem soils. / Master of Science

When well water becomes contaminated to the extent that is does not meet EPA drinking water quality standards, it is considered unsafe for consumption. Nitrate and total coliform bacteria are both health contaminants and are both regulated in public water systems. A nitrate concentration of 10 mg/L or higher is considered unsafe, as is the presence of total coliform bacteria. Well degradation, inadequate well construction, and aquifer contamination can all result in contamination of well water. Factors such as well type, well age, well depth, treatment devices, population density, household plumbing pipe materials, and nearby pollution sources may affect household water quality. The specific objective of this study was to determine which factors influence nitrate levels and total coliform presence/absence of household well water. If possible, these influencing factors would be used to develop a relationship that would allow household residents to predict the nitrate level and total coliform presence/absence of their well water. As a result, a means of predicting the contamination risk to a specific well water supply under a given set of conditions, in addition to increasing awareness, could provide the homeowner with a rationale for further investigating the possibility of contamination. Existing data from the Virginia Cooperative Extension Household Water Quality Testing and Information Program were assembled for analyses in this project. The data consisted of 9,697 private household water supplies sampled from 1989-1999 in 65 Virginia counties. Initially, the entire state of Virginia was analyzed, followed by the five physiographic provinces of Virginia: the Blue Ridge, Coastal Plain, Cumberland Plateau, Ridge & Valley, and Piedmont. Ultimately, Louisa County was investigated to evaluate the possibility that better models could be developed using smaller land areas and, consequently, less geological variation. Least squares regression, both parametrically and non-parametrically, was used to determine the influence of various factors on nitrate levels. Similarly, logistic regression was used to determine the influence of the same parameters on nitrate categories, presence/absence of total coliform, and risk categories. Using stepwise model-building techniques, based primarily on statistical significance (p-values) and partial coefficient of determination (partial-R2), first and second-order linear models were evaluated. The best-fitting model only explained 58.5% of the variation in nitrate and none of the models fit well enough to be used for prediction purposes. However, the models did identify which factors were, in a statistical sense, significantly related to nitrate levels and total coliform presence/absence and quantified the strength of these relationships in terms of the percent of variation explained. / Master of Science