Hybridization refers to mating between species or between genetically differentiated populations of the same species. Although hybrid offspring may exhibit sterility and/or inviability, hybridization can generate novel genotypic and phenotypic diversities, leading to the origin of new traits and new species, the expansion into ecological niches outside of the parental range (e.g., host range), and altered virulence properties in pathogens. However, the relationship between parental genetic divergence and hybrid performance remains largely unknown. The human pathogenic Cryptococcus (HPC) is an ideal model to study the impacts of parental divergence on the genetic and phenotypic consequences of hybridization. HPC consists of a group of divergent lineages with various degrees of interfertility. These yeasts are the etiologic agents of cryptococcosis, a potentially lethal disease in humans and animals. In this thesis, I examined the effects of parental divergence on cryptococcal hybrids from multiple aspects. I conducted genetic crosses between different lineages to evaluate the mating success and the germination of sexual spores (i.e., basidiospores) under various environmental conditions. Then, I investigated the genotypic and phenotypic diversities among the hybrids under different environmental conditions. Furthermore, I examined the genome stability of diploid inter-lineage hybrids through laboratory experimental evolution and the effect of antifungal drug stress on the loss of heterozygosity (LOH) in these hybrids. We found that parental genetic divergence plays an important role in genotypic and phenotypic diversities among hybrid progeny in HPC. However, our results indicate that parental genetic di-vergence alone can’t explain most of the observed variations. Instead, genetic divergence along with specific parental strains, environmental factors, and their interactions all contributed to hybridization success and to hybrid genotypic and phenotypic variations. My findings will broaden the current understanding of the phenotypic and genotypic consequences of hybridization and explore the connection between genetic architecture and hybrid speciation in the human pathogenic Cryptococcus. / Thesis / Doctor of Science (PhD) / The role of hybridization in evolution can vary widely, giving rise to hybrid vigor and hybrid weakness. Hybridization plays an important role in plants and animals, especially crops, with advantages of increased yield and quality of products. However, the emergence of hybrid vigor in pathogens with increased virulence is an increasing threat to plant, animal, and human healths. My PhD thesis aimed at understanding the effects of parental divergence on hybridization and hybrids in the human pathogenic Cryptococcus. Here, I investigated basidiospore germination rate and hybrid progeny genotypes and phenotypes from diverse genetic crosses in this group of pathogens. My findings contribute towards understanding cryptococcal hybrids and establishing treatment plans against infections by these hybrids.

An interspecies hybridization is usually viewed from two sides - either as mistakes in a reproduction resulting in decrease of a hybrids fitness (e. g. loss or decrease of viability and fertility) or as a mechanism helping animals adaptively respond to environmental changes resulting in higher fitness. Fitness is usually represented as a set of correlates. One of the correlates is an organism performance which is represented by a set of maximal values from measured physical activities. This thesis focuses on the evaluation of the endurance and the bite force for gecko species E. macularius and E. angramayniu, their interspecies hybrids and intraspecies hybrids to determine their performance. The results show differences in the bite force among each of the tested groups. E. macularius has the lowest bite force, while the highest bite force was measured in E. angramayniu. The bite force of interspecies hybrids is intermediate in comparison to the parent species. Nevertheless, intraspecies hybrids of large form and white form of E. macularius exceeds their parents in measured bite force. The variability in bite force suggests a positive effect of hybridization on fitness. The bite force differences between the large form and the white form of E. macularius support the hypothesis that there exist more...

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DNA microarrays are a potentially disruptive technology in the medical field, but their use in such settings is limited by poor reliability. Microarrays work on the principle of hybridization and can only be as reliable as this process is robust, yet little is known at the molecular level about how the surface affects the hybridization process. This work uses advanced molecular simulation techniques and an experimentally-parameterized coarse-grain model to determine the mechanism by which hybridization occurs on surfaces and to identify key factors that influence the accuracy of DNA microarrays. Comparing behavior in the bulk and on the surface showed, contrary to previous assumptions, that hybridization on surfaces is more energetically favorable than in the bulk. The results also show that hybridization proceeds through a mechanism where the untethered (target) strand often flips orientation. For evenly-lengthed strands, the surface stabilizes hybridization (compared to the bulk system) by reducing the barriers involved in the flipping event. Additional factors were also investigated, including the effects of stretching or compressing the probe strand as a model system to test the hypothesis that improving surface hybridization will improve microarray performance. The results in this regard indicate that selectivity can be increased by reducing overall sensitivity by a small degree. Another factor that was investigated was the effect of unevenly-lengthed strands. It was found that, when unevenly-lengthed strands were hybridized on a surface, the surface may destabilize hybridization compared to the bulk, but the degree of destabilization is dependent on the location of the matching sequence. Taken as a whole, the results offer an unprecedented view into the hybridization process on surfaces and provide some insights as to the poor reproducibility exhibited by microarrays. Namely, the prediction methods that are currently used to design microarrays based on duplex stability in the bulk do a poor job of estimating the stability of those duplexes in a microarray environment.

Yes / The advent of the Internet of Things has witnessed tremendous success in the application of wireless sensor networks and ubiquitous computing for diverse smart-based applications. The developed systems operate under different technologies using different methods to achieve their targeted goals. In this treatise, we carried out an inclusive survey on key indoor technologies and techniques, with to view to explore their various benefits, limitations, and areas for improvement. The mathematical formulation for simple localization problems is also presented. In addition, an empirical evaluation of the performance of these indoor technologies is carried out using a common generic metric of scalability, accuracy, complexity, robustness, energy-efficiency, cost and reliability. An empirical evaluation of performance of different RF-based technologies establishes the viability of Wi-Fi, RFID, UWB, Wi-Fi, Bluetooth, ZigBee, and Light over other indoor technologies for reliable IoT-based applications. Furthermore, the survey advocates hybridization of technologies as an effective approach to achieve reliable IoT-based indoor systems. The findings of the survey could be useful in the selection of appropriate indoor technologies for the development of reliable real-time indoor applications. The study could also be used as a reliable source for literature referencing on the subject of indoor location identification. / Supported in part by the Tertiary Education Trust Fund of the Federal Government of Nigeria, and in part by the European Union’s Horizon 2020 Research and Innovation Programme under Grant agreement H2020-MSCA-ITN-2016 SECRET-722424

Because of the greatly increased supply of genetic variation which it provides, introgression is of great importance in determining both the rate and the direction of evolution. Hybridization between the genera Cowania and Purshia provides an excellent model for demonstrating the various products which might be expected from introgression. The present study is an attempt to further investigate phylogenetic relationships of Cowania mexicana and Purshia tridentata by use of cytological and biochemical techniques.

In the past twenty years many workers have made contributions to a better understanding of hybridization and introgression through studies of members of the grass family. The present study is an attempt to increase the understanding of the importance and amount of hybridization and introgression in members of the Tribe Hordeae. This study is concerned with a hybrid complex involving Agropyron subsecundum (Link) Hitchc. (bearded wheatgrass), Agropyron trachycaulum (Link) Malte (slender wheatgrass) and Elymus glaucus Buckl. (blue wild rye).

Hybrid vehicles are an important technology for reducing oil use and transportation-related emissions. It is well-known that hybrid and electric vehicles are often designed and tested using standard cycles such as the Highway Fuel Economy Test (HWY), Urban Dynamometer Driving Schedule (UDDS), and the US06 Supplementary Federal Test Procedure (US06). However, this begs the questions: How does real world driving compare to these cycles? Can a vehicle be designed using real world driving data which saves fuel in the real world compared to a vehicle designed using standard cycles? This thesis investigates this issue using a set of 5000km of real world driving data by light-duty pickup trucks, with the goal to optimize the fuel savings of a mild hybrid truck. The challenge with using a model-based design approach on thousands of kilometers of real driving data is the long model run-time required to iterate through plant and control parameters. Thus, this work develops a novel script which reduces optimization time by 78%. The key is to run the full model of the non-hybrid truck one time on the full driving data set, and then use the resulting vehicle speed, engine efficiency, engine torque, and engine speed, as inputs to the faster script. The script is then used to quickly iterate through the driving data set many times to find optimal control and plant parameters. In this work, exhaustive search is used; however, evolutionary optimization algorithms could also be used and would benefit from the fast script iteration on real world driving cycles. Overall, the use of the real world driving set for design of the mild hybrid truck resulted in a 7.10% decrease in fuel consumption compared to the non-hybrid truck, while the use of standard driving cycles for design resulted in a 5.45% fuel consumption decrease compared to the non-hybrid truck. / Thesis / Master of Applied Science (MASc)

Mitochondria are intracellular organelles responsible for oxidative phosphorylation. They contain their own DNA which encodes some components involved in oxidative phosphorylation. Mitochondrial DNA is very susceptible to mutations. Mitochondrial abnormalities have been observed in several disorders of muscle and brain. Alzheimer's disease is a form of dementia characterized by the formation of numerous neuritic plaques and neurofibrillary tangles. There is evidence suggesting a possible role for mitochondrial abnormalities in Alzheimer's disease. The goal of this project was to determine if there were quantitative changes in mitochondrial DNA content in large neurons from Alzheimer's disease patients, compared to age-matched control patients. The relative mitochondrial DNA content per unit area was assessed in brain sections from Alzheimer's disease subjects and age-matched control subjects using in situ hybridization to mitochondrial DNA. The results were not conclusive due to technical concerns with the in situ hybridization technique which are discussed. / Thesis / Master of Science (MS)

Master of Science