Aroma is one of the most important quality attributes of bread or any food. It will determine whether the product will be tasted and eaten in the first instance and is a major factor in establishing acceptability and preference. The dominant preference by consumers of bread made from refined flour in contrast to whole wheat flour is at least in part due to the strong and different aroma of whole wheat bread. White wheats may have an advantage over red wheat in this regard according to some industry reports, but the science is extremely limited. The goal of this research was to add more science-based knowledge to this topic via the use of machine olfaction technology, specifically electronic (E) nose and gas chromatography combined with mass spectrometry (GC-MS). A state-of-the-art E-nose system (AlphaMOS FOX 3000) with metal oxide sensors (MOS) was used to capture aroma volatiles from crumb, crust and whole slices of breads made from sound Canadian Western Red Spring (CWRS) wheat as well as representative samples of two hard white wheats, viz. Snowbird, a cultivar belonging to the Canada Western Hard White Spring (CWHWS) class of wheat, and Platte, a U.S. Hard White Winter (HWW) wheat. The same CWRS wheat provided the base flour for all the breads. A commercial formula and size format was used to produce breads from four flours for the study, i.e. refined CWRS wheat, and three whole wheat flours comprising blends of 85% CWRS flour and 15% bran from CWRS wheat, Snowbird and Platte. As there was no established protocol in the literature to evaluate bread aroma by E-nose, one was developed. Five temperatures (35, 40, 45, 50 and 60°C) were tested along with two incubation times (5 and 10 min) and four sample sizes (0.05, 0.1, 0.25 and 0.50 g) of ground bread crumbs. Through optimization using E-nose software including principal component analysis, a procedure was adopted using 40 °C, 5 min incubation time and 0.05 g of sample to acquire MOS data from 12 sensors for crust, crumb and whole slices of refined and whole wheat breads. Multivariate analysis methods were used to evaluate the capabilities of the E-nose system to discriminate and correctly classify samples according to bread type. Data for analysis comprised approximately 24 samples each of crust, crumb and whole slices randomly selected from three loaves each of refined and the three whole wheat breads. Results varied according to the nature of the sample, i.e. crust, crumb or whole slices. For crusts, the greatest distinction in aroma was found between refined and whole wheat breads. Refined bread crust was correctly classified 67% of the time. When refined bread crust was misclassified, samples were confused with whole white wheat crust predominantly from Platte bread. For whole wheat bread crusts, the pattern of classification depended mainly on bran colour. Whole wheat bread crust samples had correct classification scores in the range 54-58%. When misclassified, whole wheat CWRS crust was equally confused with the aroma of crust of the white whole wheat breads, Platte and Snowbird. Whole wheat Platte crust tended to be misclassified with the counterpart white whole wheat Snowbird or refined bread crust. In contrast, Snowbird whole wheat crust tended to be misclassified as either its counterpart HW wheat Platte or whole CWRS wheat. Accordingly, Platte bread crust appeared to possess an aroma more in line with refined wheat bread as opposed to whole wheat bread. For bread crumb, the pattern of E-nose differentiation of samples was different. In this case, CWRS whole wheat bread aroma was clearly and perfectly distinguished from the crumb aroma of all the other breads, either whole white wheat or refined CWRS. The latter tended to cluster on its own, as might be expected, and had a correct classification score of 75%, with the balance of samples largely misclassified as Snowbird crumb. Whole wheat Platte and Snowbird bread crumb had identical correct classification scores of 42%, and were similarly confused with the other’s aroma (average 3 4% classified) or the aroma of refined wheat bread (average 21% classified). E-nose results for crumb indicated a clear distinction in aroma between the hard red and white wheats in this study. E-nose analysis of bread samples representing whole slices produced results that provided unsatisfactory discrimination among bread types likely due to the blending of the different aromas of constituent crust and crumb. For whole slices, discrimination between refined and whole wheat breads was substantially lower than that for either crust and crumb samples. Based on this result, analysis of samples that combine both crust and crumb is not recommended for sensory analysis of bread, whether by instruments or human sensory panel. Further understanding of the differences between different types of bread made from refined wheat flour and whole wheat, and how the inclusion of bran from red and white-grained wheats modifies the composition and content of volatile and non-volatile compounds in crust and crumb was determined by gas chromatography-mass spectrometry (GC-MS). In total, 50 compounds were found, the greater majority of which have been previously reported in bread. Major Maillard reaction compounds like furfural, 2-furanmethanol, pyranone, maltol and 5-hydroxymethyl- 2-furancarboxaldehyde were present in highest concentration in whole CWRS bread. Significantly fewer compounds were found in the crust and crumb of CWRS refined wheat bread compared to the other whole wheat breads. In contrast, whole CWRS bread crumb and crust had the highest number of compounds, and in considerably higher total concentration compared to the other two whole white wheat breads, Snowbird and Platte. The higher concentration and number of compounds in whole CWRS bread was attributed to the wheat bran fraction. White whole wheat breads, Snowbird and Platte, had a total number of compounds in crust and crumb approximately intermediate between refined and whole CWRS bread, although Platte whole wheat bread crust was closer to refined bread crust in compound numbers. In terms of total compound concentrations, crust and crumb samples of the whole white breads were clearly more similar to refined CWRS bread, and in the case of whole wheat Platte bread crust, compound concentrations were much lower. On the whole, these aggregate totals of compound numbers and concentrations by GC-MS mirrored the discrimination and classification results obtained by E-nose, and supported the contention that whole wheat bread made with white wheat bran was milder in aroma compared to bread formulated using red wheat bran. While the number of samples of red and white wheats were very few in this study, results support the contention that different wheat genotypes and specifically, the bran tissue of these genotypes, contain differences in compound composition and/or concentration which when processed by breadmaking, manifest volatiles characteristic of those genotypes even between genotypes possessing the same colour of bran. E-nose instrumentation appears to be very capable of accommodating these sorts of complex tasks on fresh bread. It would be highly beneficial in future research to carry out similar studies in parallel with a human sensory panel, and ideally with many more genotypes of red and white grained wheat with an aim to firmly establish the relative superiority of particular genotypes to produce whole wheat bread with aroma profiles more similar to those of white pan bread. The long term goal of such studies would be to foster increased consumption of whole wheat products and constituent bioactive compounds which confer favourable health benefits in the general population.

Limited information exists regarding the effects of light pearling on the properties of physical grain characteristics, composition, and technological and sensory properties of selected varieties of Western Canadian barley especially hulless barley genotypes with modified starch characteristics. Nine barley genotypes with different hull (hulled and hulless) and starch characteristics (normal, waxy, and high amylose (HA)) were pearled to three differing levels. Scanning electron micrographs showed that the pericarp, testa, aleurone, and subaleurone layers were completely removed in heavily pearled barley whereas only a few outer layers were removed in minimally pearled barley. Waxy starch genotype Fibar and HA starch genotypes, SH99250 & SB94893 contained high levels of soluble β-glucan (9-11%). Waxy starch genotypes exhibited higher β-glucan solubility when cooked compared to normal and HA starch genotypes. However, HA starch genotypes had lower in vitro starch digestibility which may provide a lower glycemic response in humans.

The yeast Saccharomyces cerevisiae genome is descendant from a whole genome duplication event approximately 150 million years ago. Following this duplication many genes were lost however, a certain class of genes, termed ohnologs, persist in duplicate. In this thesis we investigate network centrality as it relates to ohnolog re- tention with the goal of determining why only certain genes were retained. With this in mind, we compare physical and genetic interaction networks and genetic and pro- tein sequence data in order to reveal how network characteristics and post-duplication retention are related. We show that there are two subclasses of ohnologs, those that interact with their duplication sister and those that do not and that these two classes have distinct characteristics that provide insight into the evolutionary mechanisms that affected their retention following whole genome duplication. Namely, a very low ratio of non-synonymous mutations per non-synonymous site for ohnologs that retain an interaction with their duplicate. The opposite observation is seen for ohnologs that have lost their interaction with their duplicate. We interpret this in the fol- lowing way: ohnologs that have retained their interaction with their duplicate are functionally constrained to buffer for the other ohnolog. For this reason they are retained; ohnologs that have lost their interaction with their duplicate are retained because they are functionally divergent to the point of being individually essential. Additionally we investigate small scale duplications and show that, generally, the mechanism of duplication (smale scale or whole genomes) does not affect the distri- bution of network characteristics. Nor do these network characteristics correlate to the selective pressure observed by retained paralogous genes, including both ohnologs and small scale duplicates. In contrast, we show that the network characteristics of individual genes, particularly the magnitude of their physical and genetic network centralities, do influence their retention following whole genome duplication. / Graduate / mjrimrie@gmail.com

This thesis examines the use of two specific types of precision agriculture technologies: cost maps and lightbar. Cost maps visually depict spatial differences in production costs. The visual depictions of these costs are represented using ArcGIS in an attempt to aide farmers in further decision making. Results will show that cost maps have great possibilities in their addition to the set of tools that farmers use in decision making. This thesis will expand the understanding of lightbar from a partial budget study to a whole farm model incorporating competition across different enterprises for labor and capital. The results from the study of cost maps indicate that inaccuracy of machinery movement, whether in the application stage or the harvesting stage is very costly. As a result, the suggestion of lightbar as a guidance aide to improve farm profitability is recommended under the conditions analyzed and shows a net farm return increase in just over 6%.

Animal agriculture plays a vital role in the provision of food for the world population; however, in the wake of global warming and greenhouse gas (GHG) emissions, the industry has been under scrutiny as one of the net emitters causing global warming. The same scrutiny applies to beef production in western Canada. The objective of this study is to evaluate the economic impact of GHG mitigation practices (GHGMP) for beef operations, and in the process identify economic and environmental sustainable scenarios. This study was an extension to a study by Beauchemin et al (2011) who studied the mitigation of GHG emissions from beef production in western Canada A beef simulation model was developed to measure the impacts of adopting GHGMPs on the profitability of a mixed farm in Vulcan County, Southern Alberta. Feed for the herd was produced on the farm, and calves were born and finished on the farm. Whole farm gross margin was used as a profitability measure of the farm over a period of 9 years, which is a full beef production cycle. Eleven GHGMPs were examined and compared to the baseline scenario. These scenarios were adopted from Beauchemin et al (2011), and included dietary modifications (change in use of forages, use of canola seed, and corn distillers grains, and improvement in quality of forage), and improvement in animal husbandry (increased weaning rates, and increased longevity of breeding stock). Simulation results showed a discounted whole farm gross margin of $11.38 per acre for the baseline scenario. Feed costs accounted for 47.1 percent of total costs of beef production. The change in whole farm gross margin per acre from implementation of different GHGMPs ranged from an increase of 4 percent to a decrease of 5 percent. Six scenarios were identified as ‘win-win’ scenarios as they improved both environment and economics of the farm. The profit of these scenarios ranged from $238.11 to $30.31 per tonne of GHG reductions expressed in carbon dioxide equivalent). The loss from the other scenarios capable of reducing GHG emissions range from $92.06 to $582.46 per tonne GHG reduced. Based on these results, it was concluded that western Canadian beef producers can adopt sustainable GHGMPs without substantial changing the structure of their operations. Scenarios that improved both the environment and the economics of the farm were: Scenario 7: use of corn distillers dried grain (CDDG) in finishing ration; Scenario 4: use of canola seed in finishing ration; Scenario 8: use of CDDG in breeding stock ration; Scenario 10: increased calve weaning rate (85% to 90%); Scenario 5: use of canola seed in breeding stock ration; and Scenario 9 : improved hay for breeding stock.

Emphasis on using the glycaemic index (GI) in addition to carbohydrate exchange lists has led to a greater variety of foods from which to choose for the diabetic population. Breakfast is regarded as the most important meal of the day and the glycaemic response to lunch can be improved by decreasing the GI of breakfast. However, most conventional breakfast cereals and bread exhibit a high GI. Dried beans have a low GI and various processes such as cooking and canning increase GI values, but still in the low GI range. In recent years, extrusion cooking has become one of the popular new processes developed by the food industry. Extrusion provides a convenient alternative for the ingestion of dry beans in the diet. Muffins are eaten by many South Africans and may be an ideal alternative for breakfast cereals and bread, especially if the GI of the muffins is low. The aim of this study was to determine the GI of a muffin baked with extruded bean flour and compare it to the GI of a muffin baked with whole wheat flour. Subjects and methodology: The study cohort consisted of ten healthy males and ten healthy females. Subjects randomly consumed test meals of glucose (the reference), bean muffins and whole wheat muffins on different days. Each test meal provided 509 available carbohydrate as analysed by the Englyst method. Results: The GI of the muffin baked with extruded bean flour (mean 53.0%, Confidence intervals (CI): 41.7; 64.2) was not significantly different from that of the whole wheat muffin (mean 55.5%, CI: 41.8; 69.2) but still in the low to intermediate GI category. Conclusion: Extrusion of dried beans results in a fine flour with relatively no intact starch which may explain the very low resistant starch content (1.6I100g) of the muffins. The small particle size of the fine flour could further have contributed to the higher than expected GI of the bean muffin because the size of the particle is inversely related to glycaemic response. Muffins baked with extruded dried bean meal are nevertheless regarded as an excellent choice for breakfast and as part of the prudent diet. Beans have additional health benefits and are included in the South African Food Based Dietary Guidelines. / Thesis (M.Sc. (Dietetics))--North-West University, Potchefstroom Campus, 2004.

In this study the exposure of mining vehicle operators, on an opencast goldmine in Tanzania, to certain hazards specific to their occupation was assessed. The aim was to quantify these levels of exposure in order to estimate the risk of health effects but also to report levels of these hazards that exist on mining vehicles. Three different hazards with different physiological effects were assessed and it included exposure to whole-body vibration, A-weighted noise and low frequency noise. In each case correctly calibrated instrumentation was used and internationally accepted methods were followed. It was found that mining vehicles commonly exposed operators to levels of whole-body vibration within and above the ISO Health Guidance Caution Zone (HGCZ) and above the ropean action level, which indicates the need for intervention and control. These levels are a cause for concern and will likely lead to health effects. Noise that damages human hearing (A-weighted noise) was present in high levels on mining vehicles, in each case being higher than the permissible exposure limit of 85 dB(A). Thus operators of mining vehicles are exposed to noise levels that will damage their hearing in time. A potential hazard in the occupational world, low frequency noise, was also included in the assessment. Literature indicates that low frequency noise is capable of causing many human health effects and thus levels on mining vehicles were reported in order to give an indication of what levels may be expected in this department of mining. It was found that much of the sound energy measured on vehicles was located in the low frequency range. In the lowest frequency band measured, Leq levels of more than 100 dB(Z) were commonly found. Controls should be implemented as far as is reasonably practicable to ensure that operators are not exposed above recommended or permissible levels for each hazard. These controls can include good maintenance of vehicles and roads to reduce whole-body vibration, sound proofing of vehicle cabs along with hearing protection devices to protect hearing and further research regarding the exposure and health effects caused by low frequency noise. Following literature indicating the physiological effects of low frequency noise exposure and also the presence thereof in different occupations, it is concluded that A-weighted noise measurements alone can not be used when quantifying the risk involved in a given acoustical environment. / Thesis (M.Sc. (Occupational Hygiene))--North-West University, Potchefstroom Campus, 2009

Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion of multi-gene DNA segments is controversial, as is the question of fractionation bias, namely whether one homeologous chromosome is more vulnerable to gene deletion than the other. As a null hypothesis, we first assume deletion events, on one homeolog only, excise a geometrically distributed number of genes with unknown mean mu, and these events combine to produce deleted runs of length l, distributed approximately as a negative binomial with unknown parameter r; itself a random variable with distribution pi(.). A biologically more realistic model requires deletion events on both homeologs distributed as a truncated geometric. We simulate the distribution of run lengths l in both models, as well as the underlying pi(r), as a function of mu, and show how sampling l allows us to estimate mu. We apply this to data on a total of 15 genomes descended from 6 distinct WGD events and show how to correct the bias towards shorter runs caused by genome rearrangements. Because of the difficulty in deriving pi(.) analytically, we develop a deterministic recurrence to calculate each pi(r) as a function of mu and the proportion of unreduced paralog pairs. This is based on a computing formula containing nested sums. The parameter mu can be estimated based on run lengths of single-copy regions. We then reduce the computing formulae, at least in the one-sided case, to closed form. This virtually eliminates computing time due to highly nested summations. We formulate a continuous version of the fractionation process, deleting line segments of exponentially distributed lengths in analogy to geometric distributed numbers of genes. We derive nested integrals and discover that the number of previously deleted regions to be skipped by a new deletion event is exactly geometrically distributed. We undertook a large simulation experiment to show how to discriminate between the gene-by-gene duplicate deletion model and the deletion of a geometrically distributed number of genes. This revealed the importance of the effects of genome size N, the mean of the geometric distribution, the progress towards completion of the fractionation process, and whether the data are based on runs of deleted genes or undeleted genes.

Aroma is one of the most important quality attributes of bread or any food. It will determine whether the product will be tasted and eaten in the first instance and is a major factor in establishing acceptability and preference. The dominant preference by consumers of bread made from refined flour in contrast to whole wheat flour is at least in part due to the strong and different aroma of whole wheat bread. White wheats may have an advantage over red wheat in this regard according to some industry reports, but the science is extremely limited. The goal of this research was to add more science-based knowledge to this topic via the use of machine olfaction technology, specifically electronic (E) nose and gas chromatography combined with mass spectrometry (GC-MS). A state-of-the-art E-nose system (AlphaMOS FOX 3000) with metal oxide sensors (MOS) was used to capture aroma volatiles from crumb, crust and whole slices of breads made from sound Canadian Western Red Spring (CWRS) wheat as well as representative samples of two hard white wheats, viz. Snowbird, a cultivar belonging to the Canada Western Hard White Spring (CWHWS) class of wheat, and Platte, a U.S. Hard White Winter (HWW) wheat. The same CWRS wheat provided the base flour for all the breads. A commercial formula and size format was used to produce breads from four flours for the study, i.e. refined CWRS wheat, and three whole wheat flours comprising blends of 85% CWRS flour and 15% bran from CWRS wheat, Snowbird and Platte. As there was no established protocol in the literature to evaluate bread aroma by E-nose, one was developed. Five temperatures (35, 40, 45, 50 and 60°C) were tested along with two incubation times (5 and 10 min) and four sample sizes (0.05, 0.1, 0.25 and 0.50 g) of ground bread crumbs. Through optimization using E-nose software including principal component analysis, a procedure was adopted using 40 °C, 5 min incubation time and 0.05 g of sample to acquire MOS data from 12 sensors for crust, crumb and whole slices of refined and whole wheat breads. Multivariate analysis methods were used to evaluate the capabilities of the E-nose system to discriminate and correctly classify samples according to bread type. Data for analysis comprised approximately 24 samples each of crust, crumb and whole slices randomly selected from three loaves each of refined and the three whole wheat breads. Results varied according to the nature of the sample, i.e. crust, crumb or whole slices. For crusts, the greatest distinction in aroma was found between refined and whole wheat breads. Refined bread crust was correctly classified 67% of the time. When refined bread crust was misclassified, samples were confused with whole white wheat crust predominantly from Platte bread. For whole wheat bread crusts, the pattern of classification depended mainly on bran colour. Whole wheat bread crust samples had correct classification scores in the range 54-58%. When misclassified, whole wheat CWRS crust was equally confused with the aroma of crust of the white whole wheat breads, Platte and Snowbird. Whole wheat Platte crust tended to be misclassified with the counterpart white whole wheat Snowbird or refined bread crust. In contrast, Snowbird whole wheat crust tended to be misclassified as either its counterpart HW wheat Platte or whole CWRS wheat. Accordingly, Platte bread crust appeared to possess an aroma more in line with refined wheat bread as opposed to whole wheat bread. For bread crumb, the pattern of E-nose differentiation of samples was different. In this case, CWRS whole wheat bread aroma was clearly and perfectly distinguished from the crumb aroma of all the other breads, either whole white wheat or refined CWRS. The latter tended to cluster on its own, as might be expected, and had a correct classification score of 75%, with the balance of samples largely misclassified as Snowbird crumb. Whole wheat Platte and Snowbird bread crumb had identical correct classification scores of 42%, and were similarly confused with the other’s aroma (average 3 4% classified) or the aroma of refined wheat bread (average 21% classified). E-nose results for crumb indicated a clear distinction in aroma between the hard red and white wheats in this study. E-nose analysis of bread samples representing whole slices produced results that provided unsatisfactory discrimination among bread types likely due to the blending of the different aromas of constituent crust and crumb. For whole slices, discrimination between refined and whole wheat breads was substantially lower than that for either crust and crumb samples. Based on this result, analysis of samples that combine both crust and crumb is not recommended for sensory analysis of bread, whether by instruments or human sensory panel. Further understanding of the differences between different types of bread made from refined wheat flour and whole wheat, and how the inclusion of bran from red and white-grained wheats modifies the composition and content of volatile and non-volatile compounds in crust and crumb was determined by gas chromatography-mass spectrometry (GC-MS). In total, 50 compounds were found, the greater majority of which have been previously reported in bread. Major Maillard reaction compounds like furfural, 2-furanmethanol, pyranone, maltol and 5-hydroxymethyl- 2-furancarboxaldehyde were present in highest concentration in whole CWRS bread. Significantly fewer compounds were found in the crust and crumb of CWRS refined wheat bread compared to the other whole wheat breads. In contrast, whole CWRS bread crumb and crust had the highest number of compounds, and in considerably higher total concentration compared to the other two whole white wheat breads, Snowbird and Platte. The higher concentration and number of compounds in whole CWRS bread was attributed to the wheat bran fraction. White whole wheat breads, Snowbird and Platte, had a total number of compounds in crust and crumb approximately intermediate between refined and whole CWRS bread, although Platte whole wheat bread crust was closer to refined bread crust in compound numbers. In terms of total compound concentrations, crust and crumb samples of the whole white breads were clearly more similar to refined CWRS bread, and in the case of whole wheat Platte bread crust, compound concentrations were much lower. On the whole, these aggregate totals of compound numbers and concentrations by GC-MS mirrored the discrimination and classification results obtained by E-nose, and supported the contention that whole wheat bread made with white wheat bran was milder in aroma compared to bread formulated using red wheat bran. While the number of samples of red and white wheats were very few in this study, results support the contention that different wheat genotypes and specifically, the bran tissue of these genotypes, contain differences in compound composition and/or concentration which when processed by breadmaking, manifest volatiles characteristic of those genotypes even between genotypes possessing the same colour of bran. E-nose instrumentation appears to be very capable of accommodating these sorts of complex tasks on fresh bread. It would be highly beneficial in future research to carry out similar studies in parallel with a human sensory panel, and ideally with many more genotypes of red and white grained wheat with an aim to firmly establish the relative superiority of particular genotypes to produce whole wheat bread with aroma profiles more similar to those of white pan bread. The long term goal of such studies would be to foster increased consumption of whole wheat products and constituent bioactive compounds which confer favourable health benefits in the general population.

Limited information exists regarding the effects of light pearling on the properties of physical grain characteristics, composition, and technological and sensory properties of selected varieties of Western Canadian barley especially hulless barley genotypes with modified starch characteristics. Nine barley genotypes with different hull (hulled and hulless) and starch characteristics (normal, waxy, and high amylose (HA)) were pearled to three differing levels. Scanning electron micrographs showed that the pericarp, testa, aleurone, and subaleurone layers were completely removed in heavily pearled barley whereas only a few outer layers were removed in minimally pearled barley. Waxy starch genotype Fibar and HA starch genotypes, SH99250 & SB94893 contained high levels of soluble β-glucan (9-11%). Waxy starch genotypes exhibited higher β-glucan solubility when cooked compared to normal and HA starch genotypes. However, HA starch genotypes had lower in vitro starch digestibility which may provide a lower glycemic response in humans.