Thesis (M.Sc. (Biochemistry))--North-West University, Potchefstroom Campus, 2007.

Surface water reservoirs in rural areas of the Canadian prairies often have poor water quality due to contamination by dissolved organic carbon (DOC). DOC can activate growth of microorganisms in water distribution systems and form disinfection by-products (DBPs) in water treatment. The presence of microbiological contaminants and DBPs are potentially harmful to human health. Therefore, rapid and simple methods for DOC characterization are needed to evaluate potential water sources and to assist in understanding how best to remove DOC. The first objective of this project was to develop a sample preparation and analysis procedure utilizing Fourier Transform Infrared Spectroscopy (FTIR) to characterize the DOC content of water samples. The second objective was to compare FTIR analysis results for fractionated and un-fractionated water samples to more convention DOC characterization methods (such as UV, SUVA and specific THMFP). The third objective was to demonstrate the application of the procedure to source water assessment and water treatment process evaluation by characterizing the DOC content of several typical treated and un-treated prairie water samples at several locations in Saskatchewan.<p> In the first phase of the study prepared samples of known DOC concentration were separated into six fractions (hydrophobic acid (HPOA), hydrophobic neutral (HPON) and hydrophobic base (HPOB); and hydrophilic acid (HPIA), hydrophilic neutral (HPIN) and hydrophilic base (HPIB)) using resin fractionation techniques. FTIR and conventional UV spectroscopic measurements, DOC concentration, and trihalomethane formation potential (THMFP) measurements were taken on the un-fractionated samples and their fractions. A water matrix interference problem in the FTIR measurements was overcome by depositing a residue of dry solids from the aqueous solution containing the DOC on a flat, organic compound free and non-infrared absorptive gold plated slide before analysis. This simple evaporation procedure developed for concentrating water samples successfully deposited a solid residue for FTIR scanning. Scanning of the solid residue of each sample at multiple locations successfully produced a spectrum of average results suitable for interpretation.<p> Each organic fraction separated from the prepared samples of known DOC was then assessed using FTIR analysis. Comparison of the spectra from the resin adsorption fractions gave an indication of the relationship between functional groups and the hydrophobic/hydrophilic nature of the DOC. The results suggest that the hydrophobic fractions contain more aromatic functional groups. This demonstrates that the FTIR spectra can provide information regarding the hydrophobic/hydrophilic nature of the DOC as an alternative to the resin separation procedure. The sample preparation and FTIR analysis procedure was then used to characterize the DOC content of source and treated waters at several locations within Saskatchewan. The results of these initial investigations indicate the method can effectively identify the major organic functional groups present in source waters and the changes in the major functional groups that occur as the water is subjected to water treatment unit operations and processes. Further, the presence of several key functional groups is related to an increase in THMFP.

<p>The legally binding international declaration of the Convention on Biological Diversity (signed by over 180 countries) recently acknowledged the importance of conserving genetic diversity within livestock species. This study aimed to help Canada assess molecular diversity in its horse and pony (<i>Equus ferus caballus</i>) genetic resources. Here, 24 populations were examined, with special focus on the native Canadian, Mountain and Moorland, and Nordic pony populations, using two well accepted molecular tools. Additional horse breeds and feral populations were also included in this project as some may have influenced the development of the three equine groups of interest. Altogether, 821 individuals were genotyped at 38 microsatellite loci, and 280 individuals were sequenced using a 421 base pair portion of the mitochondrial displacement Hypervariable Region I.</p> <p>Results from the microsatellite analyses indicated that 13.33% of genetic diversity arose from breed differences, whereas 84.60% and 2.07% of diversity arose from within and among individuals respectively. The New Forest and Welsh breeds were found to be the most diverse while having the highest average effective number of alleles and allelic richness (4.31 and 6.01; 4.33 and 5.87 respectively). The Eriskay and Lac La Croix breeds were found to have the lowest average effective number of alleles and allelic richness (2.51 and 3.98; 2.83 and 4.01 respectively). Expected heterozygosities were lowest in the Lac La Croix (0.61) and highest in the Welsh and New Forest (0.74) breeds, whereas observed heterozygosities were highest in the Kerry Bog (0.77) and lowest in the Exmoor (0.57) breeds. The genetic structure and admixture analyses suggested that the most probable number of unique genetic clusters was 21 as opposed to the 24 predefined populations.</p> <p>Results from the mitochondrial sequence data revealed that there were 36 informative sites producing 62 haplotypes, 20 of which were previously unreported. The Connemara was found to have the highest haplotype diversity of the pony breeds (0.89); however, the Highland pony was found to have the highest nucleotide diversity and pairwise difference (0.16 and 6.73 respectively). In contrast, the Fell pony had the lowest haplotype diversity (0.22), and the feral Sable Island population had the lowest nucleotide diversity and pairwise difference (0.01 and 0.29 respectively). Multiple phylogenetic trees were reconstructed and produced similar topologies. In general, the Mountain and Moorland and Nordic breeds were spread among the clades, whereas native Canadian populations were most frequent in the D and E clades. Interestingly, a large portion of ponies were found within the rare E clade as opposed to horses.</p> <p>Information gathered from this project can be incorporated with other available data into pre-existing conservation/breeding programs currently managed by the various breed societies to ensure that the most optimal and sustainable strategies are in place.</p>

Electronic commerce servers have a significant presence in today's Internet. Corporations want to maintain high availability, sufficient capacity, and satisfactory performance for their E-commerce Web systems, and want to provide satisfactory services to customers. Workload characterization and the analysis of customers' interactions with Web sites are the bases upon which to analyze server performance, plan system capacity, manage system resources, and personalize services at the Web site. To date, little empirical evidence has been discovered that identifies the characteristics for Web workloads of E-commerce systems and the behaviours of customers. This thesis analyzes the Web access logs at public Web sites for three organizations: a car rental company, an IT company, and the Computer Science department of the University of Saskatchewan. In these case studies, the characteristics of Web workloads are explored at the request level, functionlevel, resource level, and session level; customers' interactions with Web sites are analyzed by identifying and characterizing session groups. The main E-commerce Web workload characteristics and performance implications are: i) The requests for dynamic Web objects are an important part of the workload. These requests should be characterized separately since the system processes them differently; ii) Some popular image files, which are embedded in the same Web page, are always requested together. If these files are requested and sent in a bundle, a system will greatly reduce the overheads in processing requests for these files; iii) The percentage of requests for each Web page category tends to be stable in the workload when the time scale is large enough. This observation is helpful in forecasting workload composition; iv) the Secure Socket Layer protocol (SSL) is heavily used and most Web objects are either requested primarily through SSL or primarily not through SSL; and v) Session groups of different characteristics are identified for all logs. The analysis of session groups may be helpful in improving system performance, maximizing revenue throughput of the system, providing better services to customers, and managing and planning system resources. A hybrid clustering algorithm, which is a combination of the minimum spanning tree method and k-means clustering algorithm, is proposed to identify session clusters. Session clusters obtained using the three session representations Pages Requested, Navigation Pattern, and Resource Usage are similar enough so that it is possible to use different session representations interchangeably to produce similar groupings. The grouping based on one session representation is believed to be sufficient to answer questions in server performance, resource management, capacity planning and Web site personalization, which previously would have required multiple different groupings. Grouping by Pages Requested is recommended since it is the simplest and data on Web pages requested is relatively easy to obtain in HTTP logs.

Stratosphere-troposphere exchange processes are responsible for controlling the distribution of chemically and radiatively important trace gases in the upper troposphere and lower stratosphere. Extensive characterization of exchange processes is critical to the development of our understanding and prediction of the climate system. This study examines the occurrence and dynamical and chemical characteristics related to two primary stratosphere-troposphere exchange processes: Rossby wavebreaking and moist convection. Intrusions of air from the tropical upper troposphere into the extratropical stratosphere above the subtropical jet via Rossby wavebreaking potentially have a significant impact on the composition of the lowermost stratosphere (the stratospheric part of the "middleworld"). We first present an analysis of tropospheric intrusion events observed in aircraft observations using kinematic and chemical diagnostics. The transport processes operating during each event are discussed using high-resolution model analyses and backward trajectory calculations. In situ chemical observations of the tropospheric intrusions are used to estimate the mixing timescales of the observed intrusions through use of a simple box model and trace species with different photo-chemical lifetimes. We estimate that the timescale for an intrusion to mix with the background stratospheric air is 5 to 6 days. Detailed analysis of small-scale features with tropospheric characteristics observed in the stratosphere suggests frequent irreversible transport associated with tropospheric intrusions. We also present a 30-year climatology (1981-2010) of anticyclonically and cyclonically sheared Rossby wave-breaking events along the boundary of the tropics in the 350-500 K potential temperature range from ECMWF ERA-Interim reanalyses. Lagrangian transport analyses show poleward transport at altitudes below and above the 370-390 K layer. Poleward transport at lower levels is in disagreement with previous studies and is shown to be largely dependent on the choice of tropical boundary. In addition, transport analyses reveal three modes of transport for anticyclonic wavebreaking events near the tropical tropopause (380 K): poleward, equatorward, and bidirectional. These transport modes are associated with distinct characteristics in the geometry of the mean flow. Stratospheric intrusions (tropopause folds) are known to be major contributors to stratosphere-troposphere exchange. The specific mixing processes that lead to irreversible exchange between stratospheric intrusions and the surrounding troposphere, however, are not entirely understood. This study presents direct observations of moist convection penetrating into stratospheric intrusions. The characteristics of convective injection are shown by using in situ aircraft measurements, radar reflectivities, and model analyses. Convective injection is observed at altitudes up to 5 km above the bottom of a stratospheric intrusion. Aircraft measurements show that convective injection in stratospheric intrusions can be uniquely identified by coincident observations of water vapor greater than about 100 ppmv and ozone greater than about 125 ppbv. Trajectory analyses show that convective injection can impact transport in both directions: from troposphere to stratosphere and from stratosphere to troposphere. We present a conceptual model of the synoptic meteorological conditions conducive to convective injection in stratospheric intrusions. In particular, convective injection is found to be associated with a "split front" where the upper-level frontal boundary outruns the surface cold front.

The basidiomycete cereal pathogens Ustilago hordei and U. maydis are closely related and possess genomes with a high degree of homology and synteny. I report on the disparity of the RNAi phenomenon between U. hordei and U. maydis. Using an RNAi expression vector I targeted both a GUS transgene and an endogenous mating-type gene and confirmed the presence of double-stranded (ds)RNA in transgenic cells of both species. However, down-regulation of the GUS gene and production of siRNAs were seen only in U. hordei. The biological effect was a reduction in GUS protein and activity, and reduced mating only in U. hordei. In support of this experimental evidence, homologs to Dicer and Argonaute were found in the U. hordei genome but not in the published U. maydis genome. Interestingly, preliminary U. hordei sequences reveal conservation and synteny in U. maydis in the regions spanning these loci, with the only noticeable difference being the lack of Dicer and Argonaute genes in U. maydis. U. maydis also appears to differ from U. hordei with respect to genes presumed to be involved in transcriptional gene silencing and also has far fewer transposons in its genome. Efforts to clone the avirulent gene UhAvr1 led to a locus containing a large number of small proteins predicted to be secreted. This locus appears to be heterochromatic and is orthologous to the largest cluster of secreted proteins in U. maydis. Other laboratories have reported that deletion of this cluster in U. maydis results in a dramatic reduction in virulence. Genetic evidence for an avirulence gene at this locus in U. hordei suggests that the locus may also be important for U. hordei. Differences between these two smut fungi at this locus and at others identified in this study point to key differences in gene regulation and genome evolution.

Rayleigh matroids are a class of matroids with sets of bases that satisfy a strong negative correlation property. Interesting characteristics include the existence of an efficient algorithm for sampling the bases of a Rayleigh matroid [7]. It has been conjectured that the class of Rayleigh matroids satisfies Mason’s conjecture [14]. Though many elementary properties of Rayleigh matroids have been established, it is not known if this class has a finite set of minimal excluded minors. At this time, it seems unlikely that this is the case. It has been shown that there is a single minimal excluded minor for the smaller class of binary Rayleigh matroids [5]. The aim of this thesis is to detail our search for the set of minimal excluded minors for ternary Rayleigh matroids. We have found several minimal excluded minors for the above class of matroids. However, our search is incomplete. It is unclear whether the set of excluded minors for this set of matroids is finite or not, and, if finite, what the complete set of minimal excluded minors is. For our method to answer this question definitively will require a new computer program. This program would automate a step in our process that we have done by hand: writing polynomials in at least ten indeterminates as a sum with many terms, squared.

Carbon nanotubes (CNTs) are advanced materials that have numerous novel and useful properties. Controlling the synthesis and properties of CNTs is the major challenge toward their future applications. This thesis addresses this challenge with several contributions. This thesis begins with the brief introduction of CNTs, including the history of their discovery, their geometric structure, unique properties and potential applications. Then focus is laid on the subsequent three sections: characterization, synthesis, and manipulation of CNTs. Chapter 2 describes three characterization tools: AFM, SEM and Raman, which are commonly used to analyze CNTs and other nanomaterials. They offer both qualitative and quantitative information on many physical properties including size, morphology, surface texture and roughness. Also, they can be used to determine the structure of CNTS. Chapter 3 addresses the synthesis of CNTS, because synthesis is an important and indispensible process to study CNTs experimentally. Specifically, two controllable synthesis techniques are realized, which are capable to produce iron catalyst nanoparticles for single-walled carbon nanotube (SWNT) growth. Iron nanoparicles of different sizes obtained from both wet chemistry and electrodeposition can be used for diameter-controlled synthesis of SWNTs. Following synthesis, two manipulation methods of CNTs are discussed in Chapter 4. Firstly, effort of electrical breakdown of CNTs is introduced. Both SWNTs and MWNTs (Multi-walled carbon nanotubes) are cut using this method. Moreover, SWNT kink is shown using AFM tip manipulation. These two manipulation methods provide us a possibility to fabricate large cavity from a MWNT for our purposes. In the end of this thesis, conclusions on my master work in research field of CNTs are drawn and future research directions are proposed.

<p>The legally binding international declaration of the Convention on Biological Diversity (signed by over 180 countries) recently acknowledged the importance of conserving genetic diversity within livestock species. This study aimed to help Canada assess molecular diversity in its horse and pony (<i>Equus ferus caballus</i>) genetic resources. Here, 24 populations were examined, with special focus on the native Canadian, Mountain and Moorland, and Nordic pony populations, using two well accepted molecular tools. Additional horse breeds and feral populations were also included in this project as some may have influenced the development of the three equine groups of interest. Altogether, 821 individuals were genotyped at 38 microsatellite loci, and 280 individuals were sequenced using a 421 base pair portion of the mitochondrial displacement Hypervariable Region I.</p> <p>Results from the microsatellite analyses indicated that 13.33% of genetic diversity arose from breed differences, whereas 84.60% and 2.07% of diversity arose from within and among individuals respectively. The New Forest and Welsh breeds were found to be the most diverse while having the highest average effective number of alleles and allelic richness (4.31 and 6.01; 4.33 and 5.87 respectively). The Eriskay and Lac La Croix breeds were found to have the lowest average effective number of alleles and allelic richness (2.51 and 3.98; 2.83 and 4.01 respectively). Expected heterozygosities were lowest in the Lac La Croix (0.61) and highest in the Welsh and New Forest (0.74) breeds, whereas observed heterozygosities were highest in the Kerry Bog (0.77) and lowest in the Exmoor (0.57) breeds. The genetic structure and admixture analyses suggested that the most probable number of unique genetic clusters was 21 as opposed to the 24 predefined populations.</p> <p>Results from the mitochondrial sequence data revealed that there were 36 informative sites producing 62 haplotypes, 20 of which were previously unreported. The Connemara was found to have the highest haplotype diversity of the pony breeds (0.89); however, the Highland pony was found to have the highest nucleotide diversity and pairwise difference (0.16 and 6.73 respectively). In contrast, the Fell pony had the lowest haplotype diversity (0.22), and the feral Sable Island population had the lowest nucleotide diversity and pairwise difference (0.01 and 0.29 respectively). Multiple phylogenetic trees were reconstructed and produced similar topologies. In general, the Mountain and Moorland and Nordic breeds were spread among the clades, whereas native Canadian populations were most frequent in the D and E clades. Interestingly, a large portion of ponies were found within the rare E clade as opposed to horses.</p> <p>Information gathered from this project can be incorporated with other available data into pre-existing conservation/breeding programs currently managed by the various breed societies to ensure that the most optimal and sustainable strategies are in place.</p>

Rayleigh matroids are a class of matroids with sets of bases that satisfy a strong negative correlation property. Interesting characteristics include the existence of an efficient algorithm for sampling the bases of a Rayleigh matroid [7]. It has been conjectured that the class of Rayleigh matroids satisfies Mason’s conjecture [14]. Though many elementary properties of Rayleigh matroids have been established, it is not known if this class has a finite set of minimal excluded minors. At this time, it seems unlikely that this is the case. It has been shown that there is a single minimal excluded minor for the smaller class of binary Rayleigh matroids [5]. The aim of this thesis is to detail our search for the set of minimal excluded minors for ternary Rayleigh matroids. We have found several minimal excluded minors for the above class of matroids. However, our search is incomplete. It is unclear whether the set of excluded minors for this set of matroids is finite or not, and, if finite, what the complete set of minimal excluded minors is. For our method to answer this question definitively will require a new computer program. This program would automate a step in our process that we have done by hand: writing polynomials in at least ten indeterminates as a sum with many terms, squared.