La fibrillation auriculaire (FA) est l'arythmie cardiaque la plus répandue dans le monde et est associée à une hausse de morbidité et une mortalité importante. Des progrès substantiels dans notre compréhension de l'étiologie de la maladie ont été réalisés au cours des deux dernières décennies, conduisant à une amélioration du traitement et de la gestion de la maladie. Cependant, le fardeau de la FA continue d'augmenter. De plus, les mécanismes moléculaires et cellulaires sous-jacents à l’initiation et à la progression de la FA restent incomplètement compris. Dans cette thèse, mon objectif était de caractériser de nouveaux déterminants moléculaires et cellulaires de la FA en utilisant une approche multiomique. J'ai d'abord utilisé le séquençage de l'ARN (RNAseq) pour l'ARN total et les micro-ARN (miRNA) afin de dévaluer l'effet de la FA sur l’expression génique dans deux modèles canins de FA. Ces résultats ont impliqué le locus orthologue humain 14q32 et son lien potentiel avec la signalisation du glutamate. Dans le chapitre trois, j'ai démontré les lacunes actuelles des modèles statistiques utilisés pour prédire l'effet régulateur des régions de chromatine ouvertes sur l'expression des gènes dans des essais multiomiques à noyau unique et suggéré des alternatives montrant un meilleur pouvoir prédictif. Dans le chapitre quatre, j'ai utilisé des analyses par locus quantitatifs d'expression (eQTL) pour caractériser les variants génétiques communs associés à la FA. Grâce à des analyses de colocalisation, une cartographie fine et un multiome à noyau unique, j'ai justifié mécaniquement l’effet de variants non-codants et fait la priorisation de gènes candidats, notamment GNB4, MAPT et LINC01629. Enfin, dans le chapitre cinq, j'ai fourni une caractérisation approfondie des gènes persistants de FA différentiellement exprimés au niveau cellulaire et identifié les facteurs de transcription potentiels impliqués dans leur régulation. En résumé, l’utilisation d’une approche multiomique a permis de découvrir de nombreuses nouvelles voies cellulaires et génétiques modifiées au cours de la FA ainsi que des gènes candidats impliqués dans le risque génétique de la FA. Ces résultats fournissent des informations et ressources importantes pour concevoir de nouvelles stratégies thérapeutiques, impliquant à la fois des cibles génétiques et nouvelles voies cellulaires pour lutter contre cette maladie cardiaque commune. / Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia worldwide and is associated with important morbidity and mortality. Substantial advancement in our understanding of the disease etiology have been made in the past two decades leading to improved treatment and management of the disease, however, AF burden continues to increase. Moreover, the molecular and cellular mechanisms underlying AF initiation and progression remain incompletely understood. In this thesis I aimed to characterise novel molecular and cellular determinants of AF using a multiomic approache. In chapter two, I used RNA sequencing (RNAseq) for total RNA and micro-RNAs (miRNA) to decipher the effect of AF in two canine models, which implicated the orthologue human locus 14q32 and its potential role in glutamate signaling regulation. In chapter three, I demonstrated current shortcomings of statistical models used to predict the regulatory effect of open chromatin regions on gene expression in single nuclei multiomic assays and suggested alternatives showing better predictive power. In chapter four, I used expression quantitative loci (eQTL) to characterize AF associated common genetic variants. Through co-localization analyses, fine-mapping and single nuclei multiome, I mechanistically substantiated non-coding variants and prioritized strong candidate genes including GNB4, MAPT and LINC01629. Finally, in chapter five, I provided a deep characterization of persistent AF differentially expressed genes (DEGs) at the cellular level and identified potential transcription factors involved in their regulation. In summary, using a multiomic approach unraveled numerous new cellular and gene pathways altered during AF and candidate genes implicated in AF genetic risk. These findings provide important insights and data resources to design novel therapeutic strategies, targeting both genetically derived candidate genes and cellular pathways to address this pervasive cardiac disease.

Doctor of Philosophy / Department of Chemistry / Christopher T. Culbertson / Analytical separations form the bulk of experiments in both research and industry. The choice of separation technique is governed by the characteristics of the analyte and purpose of separation. Miniaturization of chromatographic techniques enables the separation and purification of small volume samples that are often in limited supply. Capillary electrophoresis and immunoaffinity chromatography are examples of techniques that can be easily miniaturized with minimum loss in separation efficiency. These techniques were used in the experiments presented in this dissertation. Chapter 1 discusses the underlying principles of capillary electrophoresis and immunoaffinity chromatography. In the second chapter, the results from immunoaffinity chromatography experiments that utilized antibody-coated magnetic beads to purify serine proteases and serine protease inhibitors (serpins) from A. gambiae hemolymph are presented and discussed. Serine proteases and serpins play a key role in the insect innate immunity system. Serpins regulate the activity of serine proteases by forming irreversible complexes with the proteases. To identify the proteases that couple to these serpins, protein A magnetic beads were coated with SRPN2 antibody and then incubated with A. gambiae hemolymph. The antibody isolated both the free SRPN2 and the SRPN2-protease complex. The purified proteases were identified by ESI-MS from as few as 25 insects. In Chapter 3, an integrated glass/PDMS hybrid microfluidic device was utilized for the transportation and lysis of cells at a high throughput. Jurkat cells were labeled with 6-CFDA (an internal standard) and DAF-FM (a NO specific fluorophore). Laser-induced fluorescence (LIF) detection was utilized to detect nitric oxide (NO) from single Jurkat cells. The resulting electropherograms were used to study the variation in NO production following stimulation with lipopolysaccharide (LPS). 3 h LPS-stimulation resulted in a two fold increase in NO production in both bulk and single cell analysis. A comparison of bulk and single cell NO measurements were performed and the average NO production in single cells compared well to the increase measured at the bulk cell level. Chapter 4 discusses the preliminary experiments with a T-shaped microfluidic device that exploit the property of poly(dimethylsiloxane) (PDMS) as an electroactive polymer (EAP), to enhance fluid mixing. EAPs deform when placed in an electric field. A thin layer of PDMS was sandwiched between chrome electrodes, positioned on the horizontal arms of the T design, and the electrolyte-filled fluidic channel. A potential difference across the PDMS layer caused it to shrink and stretch, thereby increasing the channel volume. The electrodes were actuated at 180[degrees] out of phase and this caused the fluid stream in the vertical channel to fold and stretch resulting in enhanced contact surface area and shorter diffusion distances of the fluid, thereby improving mixing efficiency. All the experiments presented in this dissertation demonstrate the application of miniaturized chromatographic techniques for the efficient analysis of small volume biological samples.

No description available.

During the last decade high throughput DNA sequencing of single cells has evolved from an idea to one of the most high profile fields of research. Much of this development has been possible due to the dramatic reduction in costs for massively parallel sequencing. The four papers included in this thesis describe or evaluate technological advancements for high throughput DNA sequencing of single cells and single molecules. As the sequencing technologies improve, more samples are analyzed in parallel. In paper 1, an automated procedure for preparation of samples prior to massively parallel sequencing is presented. The method has been applied to several projects and further development by others has enabled even higher sample throughputs. Amplification of single cell genomes is a prerequisite for sequence analysis. Paper 2 evaluates four commercially available kits for whole genome amplification of single cells. The results show that coverage of the genome differs significantly among the protocols and as expected this has impact on the downstream analysis. In Paper 3, single cell genotyping by exome sequencing is used to confirm the presence of fat cells derived from donated bone marrow within the recipients’ fat tissue. Close to hundred single cells were exome sequenced and a subset was validated by whole genome sequencing. In the last paper, a new method for phasing (i.e. determining the physical connection of variant alleles) is presented. The method barcodes amplicons from single molecules in emulsion droplets. The barcodes can then be used to determine which variants were present on the same original DNA molecule. The method is applied to two variable regions in the bacterial 16S gene in a metagenomic sample. Thus, two of the papers (1 and 4) present development of new methods for increasing the throughput and information content of data from massively parallel sequencing. Paper 2 evaluates and compares currently available methods and in paper 3, a biological question is answered using some of these tools. / <p>QC 20160127</p>

Deal or no deal? Hold ‘em or fold ‘em? Buy, hold or sell? When faced with uncertainty, a wise decision-maker evaluates each option and chooses the one they deem most valuable. Scientists studying decision making processes have spent much theoretical and experimental effort formalizing a framework that captures how decision makers can maximize the amount of subjective value they accrue from such decisions. This thesis tested two hypotheses. The first was that subjective value guides our simplest and most common of motor actions similar to how it guides more deliberative economic decisions. The second was that subjective value is allocated across pre-motor regions of the brain to make our actions more efficient. To accomplish these goals, I adapted a paradigm used by behavioural economists for use in neurophysiological experiments in non-human primates. In our task, monkeys repeatedly make quick, orienting eye movements, known as saccades, to targets, which they learned through experience, had different values. In support of the hypothesis that subjective value influences simple motor actions, the speed with which monkeys responded, known as saccadic reaction time (SRT), and their saccadic choices to valued targets were highly correlated and therefore both acted as a behavioural measures of subjective value. Two complimentary results support the hypothesis that subjective value influences activity in the intermediate layers of the superior colliculus (SCi) – a well-studied brain region important to the planning and execution of saccades - to produce efficient actions. First, when saccades were elicited with microstimulation, we found that the timing and spatial allocation of pre-saccadic activity in the SC was shaped by subjective value. Second, the baseline preparatory activity and transient visual activity of SCi neurons prior to saccade generation was also influenced by subjective value. Our results can be incorporated into existing models of SC functioning that use dynamic neural field theory. I suggest that saccades of higher subjective value will result in higher activation of their associated neural field such that they will be more likely and more quickly selected. In summary, this thesis demonstrates that subjective value influences neural mechanisms, not only for deliberative decision making, but also for the efficient selection of simple motor actions. / Thesis (Ph.D, Neuroscience Studies) -- Queen's University, 2013-06-25 17:18:25.393

<p>Olfactory sensory neurons (OSNs), which detect a myriad of odorants, are known to express one allele of one olfactory receptor (OR) gene (Olfr) from the largest gene family in the mammalian genome. The OSNs expressing the same OR project their axons to the main olfactory bulb where they converge to form glomeruli. This “One neuron-one receptor rule” makes the olfactory epithelium (OE), which consists of a vast number of OSNs expressing unique ORs, one of the most heterogeneous cell populations. However, the mechanism of how the single OR allele is chosen remains unclear along with the question of whether one OSN only expresses a single OR gene, a hypothesis that has not been rigorously verified while we performed the experiments. Moreover, failure of axonal targeting to single glomerulus was observed in MeCP2 deficient OSNs where delayed development was proposed as an explanation for the phenotype. How Mecp2 mutation caused this aberrant targeting is not entirely understood.</p><p>In this dissertation, we explored the transcriptomes of single and mature OSNs by single-cell RNA-Seq to reveal their heterogeneity and further studied the OR gene expression from these isolated OSNs. The singularity of sequenced OSNs was ensured by the observation of monoallelic expression of X-linked genes from the hybrid samples from crosses between mice of different strains where strain-specific polymorphisms could be used to track the allelic origins of SNP-containing reads. The clustering of expression profiles from triplicates that originated from the same cell assured that the transcriptomic identities of OSNs were maintained through the experimental process. The average gene expression profiles of sequenced OSNs correlated well to the conventional transcriptome data of FACS-sorted Omp-positive cells, and the top-ranked expression of OR was conceded in the single-OSN transcriptomes. While exploring cellular diversity, in addition to OR genes, we revealed nearly 200 differentially expressed genes among the sequenced OSNs in this study. Among the 36 sequenced OSNs, eight cells (22.2%) showed multiple OR gene expression and the presences of additional ORs were not restricted to the neighbor loci that shared the transcriptional effect of the primary OR expression, suggesting that the “One neuron-one receptor rule” might not be strictly true at the transcription level. All of the inferable ORs, including additional co-expressed ORs, were shown to be monoallelic. Our sequencing of 21 Mecp2308 mutant OSNs, of which 62% expressed more than one OR genes, and the expression levels of the additional ORs were significantly higher than those in the wild-type, suggested that MeCP2 plays a role in the regulation of singular OR gene expression. Dual label in situ hybridization along with the sequence data revealed that dorsal and ventral ORs were co-expressed in the same Mecp2 mutant OSN, further implying that MeCP2 might be involved in regulation of OR territories in the OE. Our results suggested a new role of MeCP2 in OR gene choice and ratified that this multiple-OR expression caused by Mecp2 mutation did not accompany delayed OSN development that has been observed in the previous studies on the Mecp2 mutants.</p> / Dissertation

Doctor of Philosophy / Department of Chemistry / Christopher T. Culbertson / Recent approaches in analytical separations are being advanced towards the “lab-on-a-chip” concept in which multiple lab functions are integrated into micro/nano fluidic platforms. Among the variety of separation techniques that can be implemented on microfluidic devices, capillary electrophoresis is the most popular as it provides high efficiency, simple, fast and low cost separations. In addition, integrating miniaturized fluid manipulation tools into microfluidic devices with separations is essential for a variety of biological applications. Chapter 1 discusses the fundamentals of capillary electrophoresis and miniaturized fluid manipulation tools and provides an over view of single cell analysis in microfluidics. In chapter 2, the integration of miniaturized peristaltic pumps into multilayer microfluidic platforms is discussed. In addition, device characterization, precise fluid control and high throughput single cell analysis are discussed. As a proof of principle, T-lymphocytes were loaded with two fluorescent probes Carboxyfluorescein diacetate (CFDA) and Oregon green (OG). Thousands of single cells were automatically transported, lysed on these devices and analytes from the lysate were electrophoretically separated. 1120 cells were analyzed over the course of 80 min (14 cells/min) and separation characteristics of analytes released from individual cells were investigated. In the third chapter, the development of microfluidic platforms for the electrochemical detection of nitric oxide (NO) and other reactive nitrogen species (RNS) at the single cell level is discussed. A microfluidic system was developed to perform rapid cell lysis followed by electrochemical detection. Miniaturized microband electrodes were designed and integrated with a microfluidic separation channel. Three alignment techniques (in-channel, end-channel and off-channel configurations) were used to detect the electrochemical response of the analyte of interest. Furthermore, a model analyte (CFDA) was used to demonstrate the potential of performing the simultaneous dual detection with electrochemical and laser induced fluorescence detection. In addition, the same microfluidic platform was adapted to detect intracellular superoxide using laser induced fluorescence. In the fourth chapter, the off-chip integration of optical fiber bridges with multilayer microfluidic chips is discussed. A multimode optical fiber (~10cm long) was integrated between the single cell lysing spot and a spot downstream of the separation channel in order to detect both intact cells and the analyte in the lysate. This technique was used to create two detection spots on the microfluidic platform with the use of a single excitation source and single detector. Fluorescently labeled T-lymphocytes were automatically transported and lysed in a manner similar to that described in chapter 2. Hundreds of single cells were analyzed and the absolute migration time was determined for the analytes in the lysate. In addition, the separation characteristics of fluorescently labeled protein kinase B peptide substrates were investigated. Furthermore, this technique was used to measure cell size and the velocity of intact cells (discussed in 5th chapter) by making use of a light tunneling concept available in multimode optical fibers. All the experiments presented in this dissertation exploit the use of multilayer microfluidic platforms to investigate intracellular components in single cells in a high throughput manner that has several advantages over current conventional techniques.

Doctor of Philosophy / Department of Grain Science and Industry / Praveen V. Vadlani / Microbial lipids derived from oleaginous yeasts are a promising alternative source of edible oils due to the following advantages: no requirement of broad lands; availability of year-round production; and no food versus fuels controversy. Oleaginous yeast has an inherent ability to accumulate lipids inside cells and their lipids are preferable as starting materials in oleo-chemical industries because of their distinct fatty acid composition. Lignocellulosic biomass is a promising substrate to supply carbon sources for oleaginous yeast to produce lipids due to the high content of polysaccharides and their abundancy. Lignocellulosic-based sugar streams, which can be generated via pretreatment and enzymatic hydrolysis, contained diverse monosaccharides and inhibitors. The major objectives of this study were: 1) to develop a novel purification method to generate clean sugar stream using sorghum stalks after acid pretreatment; 2) to optimize fermentation conditions for Trichosporon oleaginosus to achieve high yields and productivity of microbial lipids using lignocellulosic hydrolysates; 3) to investigate the potentials of sorghum stalks and switchgrass as feedstocks for microbial lipid production using oleaginous yeast strains, such as T. oleaginosus, Lipomyces starkeyi, and Cryptococcus albidus; 4) to develop an integrated process of corn bran based-microbial lipids production using T. oleaginosus; and 5) to develop bioconversion process for high yields of lipids from switchgrass using engineered Escherichia coli. In our investigation, major inhibitory compounds of lignocellulosic hydrolysates induced by pretreatment were acetic acid, formic acid, hydroxymethyl furfural (HMF) and furfural. The activated charcoal was effective in removing hydrophobic compounds from sorghum stalk hydrolysates. Resin mixtures containing cationic exchangers and anionic exchangers in 7:3 ratio at pH 2.7 completely removed HMF, acetic acid, and formic acid from sorghum stalk hydrolysates. T. oleaginosus was a robust yeast strain for lipid production. In the nitrogen-limited synthetic media, total 22 g/L of lipid titers were achieved by T. oleaginosus with a lipid content of 76% (w/w). In addition, T. oleaginosus efficiently produced microbial lipids from lignocellulosic biomass hydrolysates. The highest lipid titers of 13 g/L lipids were achieved by T. oleaginosus using sorghum stalk hydrolysates with a lipid content of 60% (w/w). L. starkeyi and C. albidus also successfully produced microbial lipids using lignocellulosic hydrolysate with a lipid content of 40% (w/w). Furthermore, corn bran was a promising feedstock for microbial lipid production. The highest sugar yields of 0.53 g/g were achieved from corn bran at the pretreatment condition of 1% acid and 5% solid loading. Microbial lipids were successfully produced from corn bran hydrolysates by T. oleaginosus with lipid yields of 216 mg/g. Engineered E. coli also effectively produced lipids using switchgrass as feedstocks. E. coli ML103 pXZ18Z produced a total of 3.3 g/L free fatty acids with a yield of 0.23 g/g. The overall yield of free fatty acids was 0.12 g/g of raw switchgrass and it was 51 % of the maximum theoretical yield. This study provided useful strategies for the development of sustainable bioconversion processes for microbial lipids from renewable biomass and demonstrated the economic viability of a lignocellulosic based-biorefinery.

<p>Cancer comprises a collection of diseases, all of which begin with abnormal tissue growth from various stimuli, including (but not limited to): heredity, genetic mutation, exposure to harmful substances, radiation as well as poor dieting and lack of exercise. The early detection of cancer is vital to providing life-saving, therapeutic intervention. However, current methods for detection (e.g., tissue biopsy, endoscopy and medical imaging) often suffer from low patient compliance and an elevated risk of complications in elderly patients. As such, many are looking to “liquid biopsies” for clues into presence and status of cancer due to its minimal invasiveness and ability to provide rich information about the native tumor. In such liquid biopsies, peripheral blood is drawn from patients and is screened for key biomarkers, chiefly circulating tumor cells (CTCs). Capturing, enumerating and analyzing the genetic and metabolomic characteristics of these CTCs may hold the key for guiding doctors to better understand the source of cancer at an earlier stage for more efficacious disease management.</p><p> The isolation of CTCs from whole blood, however, remains a significant challenge due to their (i) low abundance, (ii) lack of a universal surface marker and (iii) epithelial-mesenchymal transition that down-regulates common surface markers (e.g., EpCAM), reducing their likelihood of detection via positive selection assays. These factors potentiate the need for an improved cell isolation strategy that can collect CTCs via both positive and negative selection modalities as to avoid the reliance on a single marker, or set of markers, for more accurate enumeration and diagnosis.</p><p> The technologies proposed herein offer a unique set of strategies to focus, sort and template cells in three independent microfluidic modules. The first module exploits ultrasonic standing waves and a class of elastomeric particles for the rapid and discriminate sequestration of cells. This type of cell handling holds promise not only in sorting, but also in the isolation of soluble markers from biofluids. The second module contains components to focus (i.e., arrange) cells via forces from acoustic standing waves and separate cells in a high throughput fashion via free-flow magnetophoresis. The third module uses a printed array of micromagnets to capture magnetically labeled cells into well-defined compartments, enabling on-chip staining and single cell analysis. These technologies can operate in standalone formats, or can be adapted to operate with established analytical technologies, such as flow cytometry. A key advantage of these innovations is their ability to process erythrocyte-lysed blood in a rapid (and thus high throughput) fashion. They can process fluids at a variety of concentrations and flow rates, target cells with various immunophenotypes and sort cells via positive (and potentially negative) selection. These technologies are chip-based, fabricated using standard clean room equipment, towards a disposable clinical tool. With further optimization in design and performance, these technologies might aid in the early detection, and potentially treatment, of cancer and various other physical ailments.</p> / Dissertation

No description available.