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Identifying Potential Neuroplasticity Changes In The Brains Of Young Chinook Salmon During Salt Water Entry, Brennen Coristine
Identifying Potential Neuroplasticity Changes In The Brains Of Young Chinook Salmon During Salt Water Entry, Brennen Coristine
Electronic Theses and Dissertations
As organisms encounter different environments, their ability to process new and changing information directly impacts survival. In vertebrates, this ability often occurs through the development of cognitive processes, which is facilitated by neuroplasticity. Chinook salmon ( Oncorhynchus tshawytscha ) smolts experience a large environmental change as they migrate from their freshwater natal streams into the ocean, and must be able to learn, react to, and remember new stimuli. I used RNA sequencing techniques to investigate transcription differences between brains of Chinook salmon who had been exposed to salt water for 24h and a freshwater control group. I also investigated differences …
Sparse Machine Learning Models In Bioinformatics, Yifeng Li
Sparse Machine Learning Models In Bioinformatics, Yifeng Li
Electronic Theses and Dissertations
The meaning of parsimony is twofold in machine learning: either the structure or (and) the parameter of a model can be sparse. Sparse models have many strengths. First, sparsity is an important regularization principle to reduce model complexity and therefore avoid overfitting. Second, in many fields, for example bioinformatics, many high-dimensional data may be generated by a very few number of hidden factors, thus it is more reasonable to use a proper sparse model than a dense model. Third, a sparse model is often easy to interpret. In this dissertation, we investigate the sparse machine learning models and their applications …
Algorithmic Aspects Of Some Problems In Computational Biology, Md. Shafiul Alam
Algorithmic Aspects Of Some Problems In Computational Biology, Md. Shafiul Alam
Electronic Theses and Dissertations
Given a sequence of pairs of numbers ( a i , l i ), i = 1, 2, ..., n , with l i > 0, and another pair of numbers L and U , the length-constrained maximum density segment problem is to find a subsequence [ a i , a j ]whose density is the maximum under the constraint L ≤ [Special characters omitted.] Sjs=i l s ≤ U . It has application to DNA sequence analysis in Computational Biology, particularly in the determination of the percentage of CG contents in a DNA sequence. A linear time geometric …
Developing Molecular Tools To Assess The Biogeochemical/Microbial Community Structure Of Oil Sand Processed Waste Material, Sabari Prakasan Mullapulli Raveendran
Developing Molecular Tools To Assess The Biogeochemical/Microbial Community Structure Of Oil Sand Processed Waste Material, Sabari Prakasan Mullapulli Raveendran
Electronic Theses and Dissertations
Microbial communities can dominate Fluid Fine Tailings (FFT) in the presence of electron acceptors (e.g. Sulfate). Sulfate reduction can produce hydrogen sulfide, one of several chemical constituents responsible for sediment oxygen demand (SOD). The preservation of RNA is a crucial step to study active microbial populations and their activity in FFT and hence understand the biological factors contributing to SOD. In our study different RNA preservation methods were tested to preserve microbial RNA in FFT sample. The results confirmed that LifeGuard(TM) Soil Preservation Solution (MO BIO Laboratories, Inc, California) is the best preservative method for RNA preservation. Through T-RFLP analysis …
Serotonergic Modulation Of Odour-Evoked Neural Activity In The Olfactory Bulb Of The Sea Lamprey (Petromyzon Marinus), Karl C. Boyes
Serotonergic Modulation Of Odour-Evoked Neural Activity In The Olfactory Bulb Of The Sea Lamprey (Petromyzon Marinus), Karl C. Boyes
Electronic Theses and Dissertations
Serotonergic (5-hydroxytryptamine, 5-HT) fibers are distributed throughout the olfactory nerve and olfactory bulb of the sea lamprey. This study tested for 5-HT modulation of olfactory sensory responses to pheromone, amino acid and bile acid odours in the dorsal and lateral regions of the olfactory bulb by recording local field potentials. The peak amplitude of dorsal and lateral olfactory bulb responses to amino acid odours declined during 5-HT bath-application. The peak amplitude of responses to all odours increased during pharmacological blockade of the 5-HT1a receptor, but was not affected when 5-HT was added to the 5-HT1a antagonist, spiperone. The 5-HT1a antagonist, …
Novel Pattern Recognition Approaches For Transcriptomics Data Analysis, Iman Rezaeian
Novel Pattern Recognition Approaches For Transcriptomics Data Analysis, Iman Rezaeian
Electronic Theses and Dissertations
We proposed a family of methods for transcriptomics and genomics data analysis based on multi-level thresholding approach, such as OMTG for sub-grid and spot detection in DNA microarrays, and OMT for detecting significant regions based on next generation sequencing data. Extensive experiments on real-life datasets and a comparison to other methods show that the proposed methods perform these tasks fully automatically and with a very high degree of accuracy. Moreover, unlike previous methods, the proposed approaches can be used in various types of transcriptome analysis problems such as microarray image gridding with different resolutions and spot sizes as well as …
The Polo-Like Kinases As Recipients And Enablers Of Epigenetic Modifications In Tumourigenesis, Rosa Alejandra Ward
The Polo-Like Kinases As Recipients And Enablers Of Epigenetic Modifications In Tumourigenesis, Rosa Alejandra Ward
Electronic Theses and Dissertations
Many highly conserved proteins have evolved specific niches in the cell cycle. For the Polo-like kinases (PLKs), these roles include centrosome duplication and maturation, the interaction with key DNA damage response proteins, cytokinesis, and chromosome separation. The PLKs deliver their effects via phosphorylation of their substrates at serine and threonine residues. Due to their importance in the cell cycle, expression of the PLKs is strictly governed. PLK deregulation is ubiquitously associated with malignancy. Elucidating how these proteins are regulated is key to understanding how their proper function can be restored in tumourigenesis. In recent years, the study of epigenetics as …
Prediction Of Protein-Protein Interaction Types Using Machine Learning Approaches, Mina Maleki
Prediction Of Protein-Protein Interaction Types Using Machine Learning Approaches, Mina Maleki
Electronic Theses and Dissertations
Prediction and analysis of protein-protein interactions (PPIs) is an important problem in life science research because of the fundamental roles of PPIs in many biological processes in living cells. One of the important problems surrounding PPIs is the identification and prediction of different types of complexes, which are characterized by properties such as type and numbers of proteins that interact, stability of the proteins, and also duration of the interactions. This thesis focuses on studying the temporal and stability aspects of the PPIs mostly using structural data. We have addressed the problem of predicting obligate and non-obligate protein complexes, as …
Behrens-Fisher Analogs For Discrete And Survival Data, S.M. Khurshid Alam
Behrens-Fisher Analogs For Discrete And Survival Data, S.M. Khurshid Alam
Electronic Theses and Dissertations
Discrete data often exhibit variation greater or smaller than predicted by a simple model. Negative binomial distribution and beta-binomial distribution are popular and widely used to accommodate the extra-Poisson and extra-binomial variations respectively in analyzing discrete data. Weibull distribution is one of the most popular distributions in survival data analysis. Often both discrete and survival data appear in groups and it may be of interest to compare certain characteristics of two groups of such data. The purpose of this dissertation is to deal with Behrens-Fisher analogs for data that follow negative binomial, beta-binomial and Weibull distributions. We first develop six …
Acoustic Communication In Thicket Habitats: Vocal Behaviour And Vocal Divergence In Mesoamerican Melozone Ground-Sparrows, Luis Andres Sandoval Vargas
Acoustic Communication In Thicket Habitats: Vocal Behaviour And Vocal Divergence In Mesoamerican Melozone Ground-Sparrows, Luis Andres Sandoval Vargas
Electronic Theses and Dissertations
Acoustic communication is a critical component of social interactions in birds. There are relatively few quantitative studies of the vocal behaviour of tropical bird species, in spite of the rich avian biodiversity in the tropics and the extensive variety of vocalizations they produce. This lack of information inhibits our ability to understand the behaviour and ecology of tropical birds, and impairs our ability to perform comparative analyses from an evolutionary perspective. In this dissertation, I study the vocalizations of three species of tropical ground-sparrow: Melozone biarcuata (Prevost's Ground-sparrow), Melozone kieneri (Rusty-crowned Ground-sparrow), and Melozone leucotis (White-eared Ground-sparrow). I provide the …
Determinants Of Rapid Response Success For Alien Invasive Species In Aquatic Ecosystems, Boris Beric
Determinants Of Rapid Response Success For Alien Invasive Species In Aquatic Ecosystems, Boris Beric
Electronic Theses and Dissertations
Alien invasive species (AIS) have received much attention for their harmful effects on health, ecology and the economy. Although the best approach is prevention of introductions, it is imperative that rapid response (RR) countermeasures be available, should prevention fail. I analyzed 127 cases involving RR to AIS in aquatic systems. Results indicated the rate of eradication success was greater, and slightly higher, for plant versus animal AIS, and when chemical versus mechanical methods were used, respectively, but was unaffected by habitat size. Suppression of AIS was most successful in small habitats and with chemical versus mechanical methods, but was unaffected …
Exploring The Developmental Roles Of Plk4, Candace Rapchak
Exploring The Developmental Roles Of Plk4, Candace Rapchak
Electronic Theses and Dissertations
Plk4 is a member of the Polo-like kinase family of cell cycle regulators that has well established roles in the regulation of centrosome duplication, cytokinesis and the DNA damage response in adult cells. Mice with homozygous Plk4 null mutations are embryonic lethal at E7.5 and do not develop somites, notochord nor a proper neural tube. In this study, plk4 was cloned and characterized for expression and function during the embryonic development of Xenopus laevis. Xenopus plk4 is expressed in a diverse number of tissues including the somites, lens and retina. Translational knockdown of plk4 via morpholinos causes perturbations to somitogenesis …
The Effect Of Sodium Salicylate On The Level Of Gabab Receptor Subunits In The Rat's Central Auditory System, Sehrish Butt
The Effect Of Sodium Salicylate On The Level Of Gabab Receptor Subunits In The Rat's Central Auditory System, Sehrish Butt
Electronic Theses and Dissertations
Tinnitus is a phantom sensation of sound in the absence of acoustic stimulus and can be induced by ototoxic drugs such as sodium salicylate (SS). Tinnitus is likely related to hyperactivity in central auditory structures. In the central nervous system, activity is dependent on excitatory/inhibitory neurotransmission. Gamma-aminobutyric acid (GABA) is a major inhibitory neurotransmitter. It can activate the type-B GABAergic receptor (GABA B receptor), which can control the level of excitation/inhibition through regulating the release of neurotransmitters and lowering the cell membrane potential. I hypothesized that SS affects hearing by changing the level and distribution of the GABA B receptor …
Environmental Sustainability Of Sporting Events In Local Communities: Assessing The Ecological Footprint Of The 2013 International Children's Games, Andrew Bakos
Electronic Theses and Dissertations
Sport management literature regarding the environmental sustainability (ES) of sport events has been predominately focused on the environmental consequences of staging major events. As a result, there is little research concerned with the environmental impacts of small-scale events on host communities. The primary objective of this study was to calculate the Ecological Footprint (EF) of the 2013 International Children's Games (ICG). Developed in the early 1990s by Wackernagel and Rees, the EF is an analysis tool that measures the resource consumption of a human population within a geographical boundary. The EF of the 2013 ICG was estimated through the creation …
Polo-Like Kinase 4 At The Nexus Of Epigenetic Modifications And The Dna Damage Signaling Network, Gayathri Sivakumar
Polo-Like Kinase 4 At The Nexus Of Epigenetic Modifications And The Dna Damage Signaling Network, Gayathri Sivakumar
Electronic Theses and Dissertations
The evolutionarily conserved polo-like kinases (PLKs) are pivotal cellular proteins that govern mitotic progression, DNA damage, centrosome replication, and neuronal processes. Appropriate expression of these serine/threonine kinases is essential for cellular homeostasis as perturbations to PLK expression often results in oncogenic transformation and tumor development. In addition to loss of heterozygosity, the PLKs are also susceptible to aberrant epigenetic modifications in tumorigenic states. My studies describe the deregulation of the PLKs in the context of hematological malignancies and provide support that the methylation-dependent dysregulation may possess diagnostic and prognostic value. Moreover, I have characterized novel interacting substrates (PRMT5 and GADD45a) …
Investigating The Effects Of Food Chain On Sympatric Speciation Using Ecosim, Sara Bandehbahman
Investigating The Effects Of Food Chain On Sympatric Speciation Using Ecosim, Sara Bandehbahman
Electronic Theses and Dissertations
The study of sympatric speciation in evolutionary biology is facing the obstacle of unifying empirical studies with existing theoretical investigations. Disruptive selection due to preferential food resource usage is considered as the main hypothesis to explain the sympatric speciation occurrence in empirical studies. We extend an individual based evolving predator-prey ecosystem platform called "EcoSim" [Gras et al. 2009a] to model a dual resource system. We investigated whether and in which conditions the selective pressures acting on foraging behaviors drove sympatric speciation. We observed clear results showing some behavioral modifications occurring as a consequence of preferential resource usage. We also observed …
Can Tropical Macrophytes Establish In The Lower Laurentian Great Lakes?, Amanda P. Eyraud
Can Tropical Macrophytes Establish In The Lower Laurentian Great Lakes?, Amanda P. Eyraud
Electronic Theses and Dissertations
Many macrophyte species sold in stores across Canada are perceived as unlikely to invade owing to climate mismatches. This does not account for climate change, which may make the Great Lakes more suitable to invaders. This study aimed to assess the invasion potential of two macrophytes ( Pistia stratiotes and Eichhornia crassipes ) that were recently discovered in the Great Lakes, and determine the mechanisms responsible for their persistence. I surveyed the Canadian shoreline of the Great Lakes to determine their current range, and tested three hypotheses that may account for their continued presence. Surveys conducted in 2010, 2011 and …
Female Round Goby (Neogobius Melanostomus) Movement Responses To Pheromones: An Investigation Of Current Methods And Future Needs, Jennifer Lee Smith
Female Round Goby (Neogobius Melanostomus) Movement Responses To Pheromones: An Investigation Of Current Methods And Future Needs, Jennifer Lee Smith
Electronic Theses and Dissertations
The round goby ( Neogobius melanostomus ) is an invasive benthic fish species to the Laurentian Great Lakes. Earlier studies have suggested that reproductive male urine containing conjugated 3α-hydroxy-5β-androstane-11,17-dione (11-O-ETIO), including 11-O-ETiO-3-S (a potent odorant to gobies), attracts reproductive females. However attraction to isolated or synthetic 11-O-ETIO-3-S has not been tested. This thesis investigates chemical attraction in the laboratory environment by examining the effect of (1) providing the female with shelter, (2) fractionated conditioned water containing 0.1 nM 11-O-ETIO derivatives on females without a shelter and (3) 1 uM synthetic 11-O-ETIO derivatives in arenas with a shelter. It was found …
Vocal Behaviour, Geographic Variation, And The Evolution Of Song In Troglodytes Wrens, Jose Roberto Sosa Lopez
Vocal Behaviour, Geographic Variation, And The Evolution Of Song In Troglodytes Wrens, Jose Roberto Sosa Lopez
Electronic Theses and Dissertations
Animal acoustic signals are important for mate attraction, resource defense, and species recognition. When vocalizations diverge between closely related groups they can play a key role in speciation. Therefore it is important for biologists to describe the vocalizations of wild animals, to document geographic differences in acoustic signals, and to evaluate the relationship between acoustic variation, genetic variation, and ecological variation. In this dissertation, I study the songs of New World wrens in the genus Troglodytes , small territorial songbirds distributed throughout the Americas, including several oceanic islands, that are well known for their loud, complex songs. I conducted observational …
Quantification Of Molecular Changes In The Brown Bullhead ( Ameiurus Nebulosus) Exposed To Environmental Toxins, Rebecca A. Williams
Quantification Of Molecular Changes In The Brown Bullhead ( Ameiurus Nebulosus) Exposed To Environmental Toxins, Rebecca A. Williams
Electronic Theses and Dissertations
Areas of the Great Lakes are classified as polluted and are inclusive of PAHs and PCBs, both of which are agonists of the aryl hydrocarbon receptor. To determine whether resident brown bullhead ( Ameiurus nebulosus ) populations have developed resistance to the genotoxic effects of these compounds, we measured population level differences in CYP1A and p53 expression in in fish from clean and contaminated sites. At the resting level, fish from polluted sites had lower CYP1A expression and high p53 expression. When fed 50mg/kg x3 doses of Benzo[a]pyrene treated food, p53 expression decreased in contaminated fish and increased in clean …
Cooperative Functions Of Duetting Behaviour In Tropical Wrens, Kristin Ashley Kovach
Cooperative Functions Of Duetting Behaviour In Tropical Wrens, Kristin Ashley Kovach
Electronic Theses and Dissertations
Vocal duets occur when two breeding partners coordinate their songs into a joint display. Duetting serves functions both within and between pairs, and functionality is often context dependent. I explore the function of temporal coordination of male and female songs into duets, testing the hypothesis that coordinated duets are more threatening territorial signals than poorly coordinated duets or solos in three closely related species of wren. Results indicate that birds respond with similar levels of physical aggression to all three levels of coordination; however, they sing more duets in response to both categories of duets. I also explore duets and …
Theory Of A Hybrid Plasmonic - Waveguide Biosensor For The Detection Of Turbid Analytes, Daniel-Anthony Travo
Theory Of A Hybrid Plasmonic - Waveguide Biosensor For The Detection Of Turbid Analytes, Daniel-Anthony Travo
Electronic Theses and Dissertations
The characterization of turbid media, such as colloidal suspensions such as milk, is a challenging task due to the attenuation of incident fields within the medium. In this work, the potential performance of a novel sensing technology is assessed for the characterization of such media. The device is a hybrid plasmonicwaveguide biosensor and consists of an array of gold nanoparticles deposited atop a waveguide multilayer structure. The performance of the device is modelled using a Green function approach and is benchmarked to a surface plasmon resonance (SPR) sensor. The results of the analysis show the hybrid sensor to be several …
Finding Differential Splice Junctions In Rna-Seq Data As Transcriptional Biomarkers For Prostate Cancer, Ahmad Tavakoli
Finding Differential Splice Junctions In Rna-Seq Data As Transcriptional Biomarkers For Prostate Cancer, Ahmad Tavakoli
Electronic Theses and Dissertations
Alternative RNA splicing is a naturally occurring phenomenon that has been associated with different types of cancer. Detecting splice junctions in the genome of an organism is the key to the study of alternative splicing. RNA-Seq as a high-throughput sequencing technology has recently opened new horizons on the studying of various fields of transcriptomics, such as gene expression, chimeric events and alternative splicing. In this research, we study prostate cancer from the viewpoint of splicing events as the second most common cancer in North America. We have proposed a method for differentially detecting splice junctions, and in a broader sense …
Fac-Pin: An Efficient And Fast Agglomerative Clustering Algorithm For Protein Interaction Networks To Predict Protein Complexes And Functional Modules, Mohammad Shamsur Rahman
Fac-Pin: An Efficient And Fast Agglomerative Clustering Algorithm For Protein Interaction Networks To Predict Protein Complexes And Functional Modules, Mohammad Shamsur Rahman
Electronic Theses and Dissertations
Proteins are known to interact with each other to perform specific living organism functions by forming functional modules or protein complexes. Many community detection methods have been devised for the discovery of functional modules or protein complexes in protein interaction networks. One common problem in current agglomerative community detection approaches is that vertices with just one neighbor are often classified as separated clusters, which does not make sense for module or complex identification. In this thesis, we propose a new agglomerative algorithm, FAC-PIN, based on a local premetric of relative vertex-to-vertex clustering value. Our proposed FAC-PIN method is applied to …
The Evolution Of Iridescent Plumage In The Galliformes: Proximate Mechanisms And Ultimate Functions, Kevyn K. Gammie
The Evolution Of Iridescent Plumage In The Galliformes: Proximate Mechanisms And Ultimate Functions, Kevyn K. Gammie
Electronic Theses and Dissertations
Iridescence is a specialized type of structural colouration that produces some of the most spectacular visual displays found in animals. However, the proximate mechanisms and ultimate functions that shape the evolution of iridescent colouration remain poorly studied. The Galliformes comprise a diverse order of birds with multiple sexually dimorphic traits thought to have evolved by sexual selection. Using a phylogenetic approach, I model the evolution of iridescent plumage and its corresponding barbule nanostructures in Galliformes. I show that nanostructural innovations have allowed iridescent colouration to evolve multiple times in Galliformes, allowing them to produce a much broader range of colours. …
Regulation Of The Anaphase Promoting Complex/Cyclosome In Drosophila Female Meiosis, Osamah Batiha
Regulation Of The Anaphase Promoting Complex/Cyclosome In Drosophila Female Meiosis, Osamah Batiha
Electronic Theses and Dissertations
Meiosis is an important biological process that results in the formation of 4 haploid gametes. It is a modified cell division that involves two rounds of chromosome segregation without intervening DNA replication. Meiosis stages are driven by cell cycle regulators that, to a large degree, are shared with mitosis. We studied the role and the regulation of the cell cycle regulator, the Anaphase Promoting Complex/Cyclosome (APC/C) in Drosophila female meiosis. We first investigated the role of the Spindle Assembly Checkpoint (SAC), a known inhibitor of APC/C activity in mitosis, in controlling APC/C activity during meiosis. We find that the loss …
Avian Species-Area Relationships And Environmental Covariates In Natural And Constructed Wetlands Of Northeastern Alberta, Sheeva Nakhaie
Avian Species-Area Relationships And Environmental Covariates In Natural And Constructed Wetlands Of Northeastern Alberta, Sheeva Nakhaie
Electronic Theses and Dissertations
I examined the patterns of species distribution and richness as they relate to area in boreal wetlands of northeastern Alberta. I conducted point counts of bird species in natural and constructed wetlands of various sizes. Plant species richness, habitat attributes, and habitat heterogeneity were also estimated to determine whether these factors influenced the strength of the avian species-area relationship. The species-area relationship was statistically significant in natural but not in constructed wetlands. Plant richness varied independently of area for both wetland classes. Area and anthropogenic disturbance were significant predictors of avian species richness in natural wetlands, but richness was uncorrelated …
Adaptive Responses To Aquatic Pollution: Dispersal, Physiological Acclimation, Genetic Adaptation In The Brown Bullhead (Ameiurus Nebulosus), Linda Söderberg
Adaptive Responses To Aquatic Pollution: Dispersal, Physiological Acclimation, Genetic Adaptation In The Brown Bullhead (Ameiurus Nebulosus), Linda Söderberg
Electronic Theses and Dissertations
Organisms are likely to display adaptive responses to their local environment, it may be local adaptation or physiological acclimation, and both improve performance (increase fitness) in stressful habitats. In this dissertation, I explore adaptive responses to pollution stress in the brown bullhead ( Ameiurus nebulosus ) from the Detroit River, as a model for integration of evolutionary and ecotoxicologial analyses. I develop a systematic hierarchical scheme to investigate the role of adaptive processes in response to stressful environments. My literature-based review suggests initial investigation of dispersal as confounding adaptive response to degraded local environment. If there is low dispersal I …
The Influence Of Weather And Ambient Light On The Dawn Chorus Start Times Of North Temperate Birds, Adrianna Bruni
The Influence Of Weather And Ambient Light On The Dawn Chorus Start Times Of North Temperate Birds, Adrianna Bruni
Electronic Theses and Dissertations
The dawn chorus is a bout of increased song output performed by birds prior to sunrise during the breeding season. Although nearly ubiquitous among avian species, the dawn chorus is poorly understood compared to daytime song. Little is known about how extrinsic variables influence dawn chorus performance. In this thesis, I measured relationships between dawn chorus start times and moon brightness, cloud cover, precipitation, ambient temperature, and artificial light exposure in a community of north temperate birds. I found that birds begin their dawn choruses significantly earlier with increasing moon brightness and ambient temperature, and significantly later with presence of …
Rats' (Rattus Norvegicus) Encoding And Retrieval Of Spatial And Non-Spatial Environmental Features In A Foraging Task, Corrine Nicole Keshen
Rats' (Rattus Norvegicus) Encoding And Retrieval Of Spatial And Non-Spatial Environmental Features In A Foraging Task, Corrine Nicole Keshen
Electronic Theses and Dissertations
Animals use various spatial and non-spatial cues when navigating the environment. They can use spatial cues such as a landmark's local position, global position and orientation, or they can use a landmark's non-spatial featural information. The objectives of this thesis were: 1) to determine the conditions under which rats process information separately or simultaneously; 2) to determine how rats process stimuli when previously fixed information becomes more variable; 3) to determine whether animals can use spatial information when a previously encoded non-spatial cue is occasionally eliminated. The results obtained from this research suggest that rats use two different types of …