Graduate Theses & Dissertations

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Doing it Right
The cyanidation technique is currently a viable technique for gold recovery that can replace the present amalgamation technique in Guyana. To implement this technique effectively, laboratory scale experiments and at scale runs were conducted to determine the best particle size of the ore, cyanide concentration, and leaching time. In addition, the profitability of cyanidation was compared to the amalgamation technique so as to describe the economic value of cyanidation. Results indicated that up to 94% of gold can be recovered from the ore using an ore particle size of 150 (105 µm), meshes, a cyanide concentration of 0.05% and leaching for 24 h. An economic comparison of this technique with the amalgamation technique indicated that although initial costs are high for the cyanidation technique, profits as high as 83% can be achieved after initializing this method whereas profits would be capped at approximately 25% for the amalgamation technique. Keywords: gold recovery, cyanidation, mercury amalgamation, activated car Author Keywords: activated carbon, cyanidation, gold recovery, mercury amalgamation
Mitogenome characterization of the shortnose sturgeon (Acipenser brevirostrum) for international trade validation of aquaculture-reared caviar
Identifying the population origin of aquaculture-reared caviar is crucial for both conservation and management strategies of farmed fish but could also facilitate international trade of a CITES regulated product. Shortnose sturgeon (Acipenser brevirostrum) is the main source of caviar production in Atlantic Canada, from Breviro Caviar Inc. aquaculture facility. Shortnose sturgeon are also listed as a species-at-risk under the Species At Risk Act. Currently there is no genetic method for delineating wild from aquaculture-reared caviar. By targeting the mitochondrial genome (mitogenome) using novel long-range PCR primers and next-generation sequencing (NGS) methods we have successfully sequenced the full mitogenome of 37 shortnose sturgeon. The purpose of this study was to increase the resolution of diagnostic variation among populations and to validate Canadian aquaculture-reared stock from wild US populations. Results provided a previously unobserved novel control region haplotype in high frequency within both the aquaculture-reared and Saint John River wild sample sets. Similar frequencies were observed with whole mitogenome haplotypes. Diagnostic mitochondrial lineage found in high frequency within the captive Breviro Caviar Inc. population has the potential to allow caviar product from Breviro Caviar Inc. to be distinguished from protected US shortnose sturgeon populations. The application of full mitogenomic characterization provides the potential to further resolve differences between aquaculture and natural Canadian shortnose sturgeon stocks, US/Canadian populations and to contribute to future conservation strategies. Future research identifying signatures of selection on the mitogenome between captive and wild populations and across latitudinal gradients found within the species range. These novel methods have produced a proof-of-concept to provide a "farm-to-fork" validation and ecobrand of Breviro Caviar Inc. product and its aquaculture origin to support importation into US caviar markets. Author Keywords: aquaculture, mitogenome, next-generation sequencing, species-at-risk, sturgeon
Influence of nitrogen and sulfur on cadmium tolerance in Euglena gracilis
Heavy metal pollution threatens human and ecosystem health. E. gracilis was investigated for its potential use in bioremediation due to its tolerance for heavy metals and ability to sequester them from the environment. E. gracilis can remove metals by producing metal binding compounds enriched in sulfur and nitrogen. In this thesis, E. gracilis cultures that were pretreated with elevated levels of sulfur or nitrogen had increased tolerance to CdCl2 compared to non-pretreated cultures. RNA-sequencing revealed that both pretreatments led to transcript level changes and that exposure to CdCl2 led to further transcript level changes. Gene ontology (GO) enrichment analysis reflected changes in nitrogen and sulfur metabolism as well as physiological processes related to metal binding. The data from this thesis revealed important transcription level changes that occur when E. gracilis is challenged with CdCl2 and helps us understand how organisms adapt to heavy metal pollution in the environment. Author Keywords: bioremediation, Cadmium, Euglena gracilis, GO-enrichment, metal-binding, RNA-Sequencing
Characterisation of the Giardia Tata-Binding Protein - Preparation for an in vivo approach
The aim of this work was to identify the DNA sequences recognized by the Giardia TBP (gTBP) in vivo by using a chromatin immunoprecipitation assay (ChIP). Since a specific antibody for the protein of interest is required for this assay, a company was contracted to produce and purify a custom polyclonal antibody from the immunization of rabbits. Recombinant GST-gTBP was produced at a suitable yield and purity and used as the immunogen. The antibody was then tested for reactivity to the native protein in our laboratory. By Western blot analysis, it was possible to observe the enrichment of the gTBP within the nuclear fraction compared to a cytoplasmic fraction extracted from Giardia cells. However, the antibody could not be successfully used in an immunoprecipitation assay - suggesting that the antibody is unable to bind to the native structure of gTBP. Therefore, the focus of this work was changed to analyse gTBP via multiple sequence alignments, homology modelling and BLAST to identify any unique regions that may contribute to its unusual binding characteristics. These techniques were also used to identify specific regions of gTBP that may be used to generate synthetic peptides as immunogens for future antibody production. Author Keywords: ChIP, Giardia intestinalis, Homology modelling, Immunoprecipitation, TATA-binding protein, Western Blotting
Ice age fish in a warming world
In the face of climate change, the persistence of cold-adapted species and populations will depend on their capacity for evolutionary adaptation of physiological traits. As a cold-adapted Ice Age relict species, lake trout (Salvelinus namaycush) are ideal for studying potential effects of climate change on coldwater fishes. I studied the thermal acclimation capacity and aerobic metabolism of age 2+ lake trout from four populations across four acclimation temperatures (8ºC, 11ºC, 15ºC, and 19ºC). One population had marginally significant higher active metabolic rate (AMR) and metabolic scope across all temperatures. There was no interpopulation variation for critical thermal maximum (CTM), standard metabolic rate (SMR), or thermal acclimation capacity. Acclimation resulted in a 3ºC increase in thermal tolerance and 3-fold increase in SMR for all populations. At 19ºC, SMR increased and AMR declined, resulting in sharply reduced metabolic scope for all populations. The limited intraspecific variation in thermal physiology suggests that climate change may threaten lake trout at the species rather than population level. Author Keywords: Climate Change, Lake Trout, Metabolic Rate, Salvelinus namaycush, Temperature, Thermal Acclimation
Do birds of a feather flock together
Populations have long been delineated by physical barriers that appear to limit reproduction, yet increasingly genetic analysis reveal these delineations to be inaccurate. The eastern and mid-continent populations of sandhill cranes are expanding ranges which is leading to convergence and warrants investigation of the genetic structure between the two populations. Obtaining blood or tissue samples for population genetics analysis can be costly, logistically challenging, and may require permits as well as potential risk to the study species. Non-invasively collected genetic samples overcome these challenges, but present challenges in terms of obtaining high quality DNA for analysis. Therefore, methods that optimize the quality of non-invasive samples are necessary. In the following thesis, I examined factors affecting DNA quality and quantity obtained from shed feathers and examined population differentiation between eastern and mid-continent sandhill cranes. I found shed feathers are robust to environmental factors, but feather size should be prioritized to increase DNA quantity and quality. Further, I found little differentiation between eastern and mid-continent populations with evidence of high migration and isolation-by-distance. Thus, the two populations are not genetically discrete. I recommend future population models incorporate migration between populations to enhance our ability to successfully manage and reach conservation objectives. Author Keywords: feathers, genetic differentiation, non-invasive DNA, population genetics, population management, sandhill crane (Antigone canadensis)
Legacy Effects Associated with the World’s Largest Ongoing Liming and Forest Regeneration Program in Sudbury, Ontario, Canada
Soil and tree chemistry were measured across 15 limed sites that were established 14 to 37 years ago within the Sudbury barrens in Ontario, along with two unlimed pre-treatment condition reference sites and an unlimed remnant pine forest. Soil pH and base cation (calcium (Ca), magnesium (Mg), and potassium (K)) concentrations were elevated in surface organic [FH] horizons up to 37-years post limestone treatment. Limestone in the organic horizon was evident by higher Ca/Sr ratios (a good marker of dolomite) in younger sites. Base cation mass budgets were generally unable to account for the mass of added Ca and Mg. Sudbury is characterized by widespread metal contamination. Metal (copper (Cu), nickel (Ni), and lead (Pb)) concentrations were generally greatest within the FH horizon and unrelated to stand age. Copper and Ni concentrations in soil generally decreased with distance from the nearest smelter. Metal partitioning (Kd) in soil was most influenced by soil pH rather than organic matter suggesting that as liming effects fade over time metal availability may increase. Author Keywords: Afforestation, Degraded, Limestone, nutrient, Space-for-time, Sudbury
Speciation of Aluminum and Zinc in Three Streams of a Forested Catchment of the Boreal Zone
This study presents a detailed assessment of the chemical speciation of aluminum and zinc in three streams of a small, acid-sensitive forested catchment on the southern edge of the Precambrian Shield. Speciation analysis was achieved using an in-situ analytical technique known as Diffusive Gradient in Thin film (DGT) which measures labile metals, and a predictive computer algorithm (WHAM VI) which calculates metal species concentrations. Three types of DGT with different metal scavenging capabilities were used and a total of 11 deployments performed across four seasons. WHAM VI predictions showed that the organic fraction of aluminum was the main contributor to the dissolved concentrations in the main inflow stream (PC1) (~ 80 %) and the lake's outflow (PCO) (~ 75%); in the upland stream (PC1-08) the inorganic fraction contributed ~ 75%. For zinc the free ion was the single most important contributor to the dissolved concentration (< 90%) in all three streams. A comparative study of the DGT and WHAM methods showed an agreement between their inorganic concentrations during the spring season. Both methods indicate the greatest environmental impact for Al takes place during snow melt period in PCO and PC1-08 and in the summer for PC1. The greatest environmental impact for Zn predicted with WHAM VI, occurs during the spring in all three streams. Author Keywords: Aluminum, DGT, Metal speciation, WHAM, Zinc
Interseeded Cover Crops in Ontario Grain Corn Systems
Ontario grain corn is highly valuable, accounting for 60% of Canada’s total corn output. Grain producers are increasingly interested in including cover crops (CCs) in their cropping systems, but they have concerns regarding successful CC establishment and potential adverse competitive effects on corn yield and nutrient status. One option to improve the success of CC establishment is the interseeding in corn at the V4 -V6 stages. Interseeding improves the chances of good CC establishment, with potential benefits for soil health, weed control, and plant productivity. This thesis research was conducted to evaluate the short-term effectiveness of interseeding annual ryegrass (AR), red clover (RC), and their mixture (MIX) in grain corn at three locations in central and southwestern Ontario. Cover crop and corn yields, and their nitrogen (N) uptake, residual soil N, soil biological parameters, weed biomass, and residue decomposition rates were measured. CC biomass was highly variable (range: 0 - 1.6 Mg ha-1), influenced by climatic conditions, location, and CC type. Total carbon (C) and N contributions from CCs were similarly influenced by site-year and CC type. Regression analyses showed significant influence of corn biomass on CC establishment. Red clover had a significantly lower C/N ratio (11.8) than AR (18.2) and MIX (15.6). Strikingly, the amount of CC biomass accumulated in early spring reduced weeds by 50%. Moreover, CCs did not reduce corn grain or stover yield, nor N uptake, and soil mineral N in either fall or spring. Soil metabolic activity measured by BIOLOG Ecoplates was significantly greater in plots with AR than RC, MIX or NOCC. Soil biological parameters showed no CC effect. Results of residue decomposition i.e., C and N mineralization showed negligible CC residue effects on corn stover decomposition or N immobilization. The findings from this research suggest the need for assessing a more diverse range of CCs over longer durations to establish more specific CC niches for improving soil health in Ontario corn systems. Author Keywords: CLPP, cover crops, grain corn, nitrogen uptake, residue decomposition, soil health
Abundance and Distribution of Microplastics in Lake Scugog Catchment, Ontario
Plastic pollution is a growing concern, owing to its durability, ubiquity, and potential health impacts. The overall objective of this study was to assess the abundance and distribution of microplastics within Lake Scugog catchment, Ontario. This was fulfilled through two tasks (i) the development of a microplastic particle budget for the lake catchment, and (ii) the determination of the dry deposition of atmospheric microplastics in Port Perry, Ontario. The total input of microplastics into Lake Scugog (atmospheric deposition and stream inflow) was 2491 x106 mp/day, while the output (lake outflow and sedimentation) was 1761 x106 mp/day, suggesting that 29% of inputs were retained in the lake. The dry deposition of microplastics in Port Perry was 1257 mp/m2/day, which was high when compared to bulk deposition (37 mp/m2/day) in the same area. By quantifying the major pathways of microplastics better management techniques can be implemented. Author Keywords: Catchment, Dry Deposition, Microplastics, Ontario, Particle Budget, Plastic pollution
Cytokinin Oxidase/Dehydrogenase (CKX) Gene Family in Soybeans (Glycine max)
Glycine max (soybean) is an economically important plant species that registers a relatively low yield/seed weight compared to other food and oil seed crops due to higher rates of flower and pod abortion. Alleviation of this abortion rate can be achieved by altering the sink strength of the reproductive organs of soybeans. Cytokinin (CK) plays a fundamental role in promoting growth of sink organ (flowers and seeds) by increasing the assimilate demand. Cytokinin oxidase/dehydrogenase (CKX) is an enzyme that catalyses the irreversible breakdown of active CKs and hence reduce the cytokinin content. The current thesis uncovers the members of CKX gene family in soybeans and the natural variations among CKX genes within soybean varieties with different yield characteristics. The identification of null variants of OsCKX2 that resulted in large yield increases by Ashikari et al. (2005) provided a rationale for current thesis. The soybean CKX genes along with the ones from Arabidopsis, Rice and Maize were used to construct a phylogenetic tree. Using comparative phylogeny, protein properties and bioinformatic programs, the potential effect of the identified natural variations on soybean yield was predicted. Five genes among the seventeen soybean CKXs identified, showed polymorphisms. One of the natural variations, A159G, in the gene GmCKX16 occurred close to the active site of the protein and was predicted to affect the activity of enzyme leading to higher accumulation of CKs and hence increased seed weight. Use of such natural variations in marker assisted breeding could lead to the development of higher yielding soybean varieties. Author Keywords: CKX, Cytokinins, Seed weight, Seed Yield, SNPs, Soybeans
Effects of hydrologic seasonality on dissolved organic matter composition, export, and biodegradability in two contrasting streams
Environmental and seasonal processes are important watershed drivers controlling the amount, composition, and fate of dissolved organic matter (DOM) in aquatic ecosystems. We used ten months of water samples and eight months of bioassay incubations from two contrasting catchments (agriculture and natural, forested) to assess the effects of seasonal variability on the composition, export, and biodegradability of DOM. As expected, the DOM composition and exports were more allochthonous-like and autochthonous-like in the forest and agriculture streams, respectively. However, we found no relationship between DOM composition and biodegradability in our study, suggesting that broad environmental factors play a large part in determining bioavailability of DOM. We found that both differences between the catchments and seasonal variability in hydrology and water temperature cause shifts in DOM composition that can affect exports and potentially affect its susceptibility to microbial activity. More research is needed to fully understand the impact of land use and temporal variability on bioavailability and delivery to downstream ecosystems. Author Keywords: Bioavailable dissolved organic carbon, Biodegradability, Dissolved organic matter, Export, Seasonality, Streams

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