We used mouse embryonic stem cells (ESCs) as a model to study the mechanisms that regulate stem cell fate. Using gene expression analysis during a time course of differentiation, we identified 281 candidate regulators of ESC fate. To integrate these candidate regulators into the known ESC transcriptional network, we incorporated promoter occupancy data for OCT4, NANOG and SOX2. We used shRNA knockdown studies followed by a high-content fluorescence imaging assay to test the requirement of our predicted regulators in maintaining self-renewal. We further integrated promoter occupancy data for Polycomb group (PcG) proteins, EED and PHC1 to identify 43 transcriptional networks in which we predict that OCT4 and NANOG co-operate with EED and PHC1 to influence the expression of multiple developmental regulators. Next, we turned our focus to the PcG protein PCL2 which we identified as being bound by both OCT4 and NANOG and down-regulated during differentiation. PcG proteins are conserved epigenetic transcriptional repressors that control numerous developmental gene expression programs. Using multiple biochemical strategies, we demonstrated that PCL2 associates with Polycomb Repressive Complex 2 (PRC2) in mouse ESCs, a complex that exerts its effect on gene expression through H3K27me3. Although PCL2 was not required for global histone methylation, it was required at specific target regions to maintain proper levels of H3K27me3. Knockdown of Pcl2 in ESCs resulted in heightened self-renewal characteristics and defects in differentiation. Integration of global gene expression and promoter occupancy analyses allowed us to identify PCL2 and PRC2 transcriptional targets and draft regulatory networks. We describe the role of PCL2 in both modulating transcription of ESC self-renewal genes in undifferentiated ESCs as well as developmental regulators during early commitment and differentiation.

This study examines how the credentialing process for foreign-trained engineers implemented by the Professional Engineers of Ontario (PEO) affects newcomers from the former Soviet Union and Russia seeking to re-enter the profession. Applying critical sociological theory to its analysis of data generated through qualitative methods, it highlights how the ethnic, racial, and educational background of applicants shapes their encounters with the PEO and the outcome of their applications. It sheds light on the crises of identity and in social and family relations experienced by these individuals, as well as the lack of supporting services to address such crises. This study contributes to existing literature on the subject by taking a new approach to the credentialing of foreign-trained engineers in Ontario, focusing on the perspective of individual applicants rather than structural factors. It concludes with specific recommendations on how the process could be improved and the regulatory body itself reformed.

We used mouse embryonic stem cells (ESCs) as a model to study the mechanisms that regulate stem cell fate. Using gene expression analysis during a time course of differentiation, we identified 281 candidate regulators of ESC fate. To integrate these candidate regulators into the known ESC transcriptional network, we incorporated promoter occupancy data for OCT4, NANOG and SOX2. We used shRNA knockdown studies followed by a high-content fluorescence imaging assay to test the requirement of our predicted regulators in maintaining self-renewal. We further integrated promoter occupancy data for Polycomb group (PcG) proteins, EED and PHC1 to identify 43 transcriptional networks in which we predict that OCT4 and NANOG co-operate with EED and PHC1 to influence the expression of multiple developmental regulators. Next, we turned our focus to the PcG protein PCL2 which we identified as being bound by both OCT4 and NANOG and down-regulated during differentiation. PcG proteins are conserved epigenetic transcriptional repressors that control numerous developmental gene expression programs. Using multiple biochemical strategies, we demonstrated that PCL2 associates with Polycomb Repressive Complex 2 (PRC2) in mouse ESCs, a complex that exerts its effect on gene expression through H3K27me3. Although PCL2 was not required for global histone methylation, it was required at specific target regions to maintain proper levels of H3K27me3. Knockdown of Pcl2 in ESCs resulted in heightened self-renewal characteristics and defects in differentiation. Integration of global gene expression and promoter occupancy analyses allowed us to identify PCL2 and PRC2 transcriptional targets and draft regulatory networks. We describe the role of PCL2 in both modulating transcription of ESC self-renewal genes in undifferentiated ESCs as well as developmental regulators during early commitment and differentiation.

This study examines how the credentialing process for foreign-trained engineers implemented by the Professional Engineers of Ontario (PEO) affects newcomers from the former Soviet Union and Russia seeking to re-enter the profession. Applying critical sociological theory to its analysis of data generated through qualitative methods, it highlights how the ethnic, racial, and educational background of applicants shapes their encounters with the PEO and the outcome of their applications. It sheds light on the crises of identity and in social and family relations experienced by these individuals, as well as the lack of supporting services to address such crises. This study contributes to existing literature on the subject by taking a new approach to the credentialing of foreign-trained engineers in Ontario, focusing on the perspective of individual applicants rather than structural factors. It concludes with specific recommendations on how the process could be improved and the regulatory body itself reformed.

Separate domestication events and strong selective pressures have created diverse phenotypes among existing cattle populations; however, the genetic determinants underlying most phenotypes are currently unknown. Bos taurus taurus (Bos taurus) and Bos taurus indicus (Bos indicus) cattle are subspecies of domesticated cattle that are characterized by unique morphological and metabolic traits. Because of their divergence, they are ideal model systems to understand the genetic basis of phenotypic variation. Here, we developed DNA and structural variant maps of cattle genomes representing the Bos taurus and Bos indicus breeds. Using this data, we identified genes under selection and biological processes enriched with functional coding variants between the two subspecies. Furthermore, we examined genetic variation at functional non-coding regions, which were identified through epigenetic profiling of indicative histone- and DNA-methylation modifications. Copy number variants, which were frequently not imputed by flanking or tagged SNPs, represented the largest source of genetic divergence between the subspecies, with almost half of the variants present at coding regions. We identified a number of divergent genes and biological processes between Bos taurus and Bos indicus cattle; however, the extent of functional coding variation was relatively small compared to that of functional non-coding variation. Collectively, our findings suggest that copy number and functional non-coding variants may play an important role in regulating phenotypic variation among cattle breeds and subspecies.

In the quest to understand cell behavior and cure genetic diseases such as cancer, the fundamental approach being taken is undergoing a gradual change. It is becoming more acceptable to view these diseases as an engineering problem, and systems engineering approaches are being deployed to tackle genetic diseases. In this light, we believe that logic synthesis techniques can play a very important role. Several techniques from the field of logic synthesis can be adapted to assist in the arguably huge effort of modeling cell behavior, inferring biological networks, and controlling genetic diseases. Genes interact with other genes in a Gene Regulatory Network (GRN) and can be modeled as a Boolean Network (BN) or equivalently as a Finite State Machine (FSM). As the expression of genes deter- mine cell behavior, important problems include (i) inferring the GRN from observed gene expression data from biological measurements, and (ii) using the inferred GRN to explain how genetic diseases occur and determine the ”best” therapy towards treatment of disease. We report results on the application of logic synthesis techniques that we have developed to address both these problems. In the first technique, we present Boolean Satisfiability (SAT) based approaches to infer the predictor (logical support) of each gene that regulates melanoma, using gene expression data from patients who are suffering from the disease. From the output of such a tool, biologists can construct targeted experiments to understand the logic functions that regulate a particular target gene. Our second technique builds upon the first, in which we use a logic synthesis technique; implemented using SAT, to determine gene regulating functions for predictors and gene expression data. This technique determines a BN (or family of BNs) to describe the GRN and is validated on a synthetic network and the p53 network. The first two techniques assume binary valued gene expression data. In the third technique, we utilize continuous (analog) expression data, and present an algorithm to infer and rank predictors using modified Zhegalkin polynomials. We demonstrate our method to rank predictors for genes in the mutated mammalian and melanoma networks. The final technique assumes that the GRN is known, and uses weighted partial Max-SAT (WPMS) towards cancer therapy. In this technique, the GRN is assumed to be known. Cancer is modeled using a stuck-at fault model, and ATPG techniques are used to characterize genes leading to cancer and select drugs to treat cancer. To steer the GRN state towards a desirable healthy state, the optimal selection of drugs is formulated using WPMS. Our techniques can be used to find a set of drugs with the least side-effects, and is demonstrated in the context of growth factor pathways for colon cancer.

The purpose of this study was to examine the effectiveness of combining implementation intentions (II) and regulatory fit in the context of two important health goals: increasing leisure time physical activity and decreasing leisure time sedentary behaviour. Implementation intentions specify exactly how, when, and where a behaviour will occur and can be an effective method of increasing goal enactment. Regulatory fit occurs when a goal or strategy used to achieve the goal matches an individual’s regulatory orientation. University students (N = 180) were randomly assigned to a goal (increase activity/decrease screen time) and an experimental condition (II/non-II). Participants formed a goal to increase their physical activity or decrease their screen time over the following four weeks according to their random assignment. Participants’ commitment to their goal was monitored over the course of the study. The II group also formed a detailed plan regarding how they would accomplish their goal. Regulatory fit was determined based on group assignment and score on the regulatory focus questionnaire. Physical activity and screen time were assessed with self-report questionnaires. Follow-up occurred online four weeks after baseline. Data were analyzed separately by goal type using linear regressions to examine the effects of regulatory fit, experimental condition, and goal commitment on the behaviour variables. The regulatory fit manipulation was not successful. Among those with the physical activity goal, no significant effects emerged for the experimental variables. Among those with the screen time goal and in the fit, II group, stronger goal commitment tended to be associated with increased participation in moderate physical activity, β = .17, t(22) = .94, p = .36. Also, participants who set II for the screen time goal and were committed to this goal tended to report less screen time than participants with lower goal commitment (β = -.40, t(69) = -2.05, p = .05). Findings provide preliminary insight into the effectiveness of II and the importance of goal commitment in interventions aiming to reduce sedentary behaviour. / Thesis (Master, Kinesiology & Health Studies) -- Queen's University, 2010-07-02 11:32:18.716

<p>Several lines of cellular and physiological evidence have suggested the presence of a novel class of systemically mobile plant molecules that are recognized by antibodies generated against vertebrate atrial natriuretic peptides (ANPs). Functional characterization of these immunoanalogues, referred to as immunoreactive plant natriuretic peptides (irPNPs) or plant natriuretic peptides (PNPs), has shown that they play important roles in a number of cellular processes crucial for plant growth and maintenance of cellular homeostasis. Although the various biological roles of PNPs in plants are known, their exact mode of action remains elusive. To elucidate the mechanisms of action for these immunoanalogues, we have prepared a biologically active recombinant PNP from Arabidopsis thaliana (AtPNP-A) and the biological activity was demonstrated by showing its ability to induce water uptake into Arabidopsis thaliana protoplasts. In addition, the molecule was shown to downregulate photosynthesis while at the same time up-regulating respiration, transpiration as well as net water uptake and retention capacities in the sage Plectranthus ecklonii. Further analysis of the recombinant AtPNP-A indicated that the peptide can induce systemic response signalling though the phloem. A recombinant Arabidopsis wall associated kinase-like protein (AtWAKL10) that has a domain organization resembling that of vertebrate natriuretic peptide (NP) receptors was also partially characterized as a possible receptor for the recombinant AtPNP-A. Vertebrate NP receptors contain an extracellular ligand-binding domain and an intracellular guanylate cyclase (GC)/kinase domain and signal through the activity of their GC domain that is capable of generating intracellular cGMP from GTP. The structural resemblance of AtWAKL10 to vertebrate NP receptors could suggest a functional homology with receptor molecules and it is conceivable that such a receptor may recognize PNPs as ligands. The characterization of the recombinant AtWAKL10 showed that the molecule functions as both a GC and a kinase in vitro. This strengthened the suggestion that AtWAKL10 could be a possible AtPNP-A receptor especially considering the fact that AtPNP-A applications to plant cells also<br /> trigger cGMP transients. Furthermore, a bioinformatic analysis of the functions of AtPNP-A and AtWAKL10 has inferred both molecules in plant pathogen responses and defense mechanisms, thus indirectly functionally linking the two proteins.</p>

I investigate aspects of fleet dynamics in a mobile gear, groundfish fishery, on the Scotian Shelf; an area subject to a seasonal area closure. Firstly, the direct impacts of the closure on the redistribution of fishing effort and the resultant catch rates of those “fishing the line” (FTL) were examined. Effort was found to concentrate within 30km of the closure boundary. Two areas of potential FTL strategy were identified, which produced variable catch rate trends. East of the closure, areas of highest catch rate corresponded to areas of greatest effort, while to the west, catch rate was often equalized throughout the region, analogous to the ideal free distribution (IFD). Secondly, two effort distributional models were compared: an IFD-based isodar model and a discrete choice model. The isodar was determined to be the preferred model because of both its consistently superior predictive performance and its greater simplicity.

The long-term success of transplantation is limited by the need for immunosuppression; thus, tolerance induction is an important therapeutic goal. A 16-day treatment with rapamycin in mice led to indefinite graft survival of fully mismatched cardiac allografts, whereas untreated hearts were rejected after 8-10 days. Specific tolerance was confirmed through subsequent skin grafts and in vitro lymphocyte assays that showed recipient mice remained immunocompetent towards 3rd party antigens but were impaired in responding to donor antigens. Mechanisms that account for this tolerant state were then investigated. Splenic CD8+CD44+ memory T-cells were reduced in tolerant mice but had increased frequencies of the CD62LLO population. CD4+CD25+Foxp3+ regulatory T-cells were increased in tolerant mice. Through multiplex PCR, 4 regulatory T-cell related genes were found up-regulated and 2 proinflammatory genes were down-regulated in accepted hearts. This expression pattern may serve as a putative biomarker of tolerance in patients undergoing transplantation.