Genetic regulatory networks are of great importance in terms of scientific interests and practical medical importance. Since a number of high-throughput measurement devices are available, such as microarrays and sequencing techniques, regulatory networks have been intensively studied over the last decade. Based on these high-throughput data sets, statistical interpretations of these billions of bits are crucial for biologist to extract meaningful results. In this thesis, we compare a variety of existing regression models and apply them to construct regulatory networks which span trancription factors and microRNAs. We also propose an extended algorithm to address the local optimum issue in finding the Maximum A Posterjorj estimator. An E. coli mRNA expression microarray data set with known bona fide interactions is used to evaluate our models and we show that our regression networks with a properly chosen prior can perform comparably to the state-of-the-art regulatory network construction algorithm. Finally, we apply our models on a p53-related data set, NCI-60 data. By further incorporating available prior structural information from sequencing data, we identify several significantly enriched interactions with cell proliferation function. In both of the two data sets, we select specific examples to show that many regulatory interactions can be confirmed by previous studies or functional enrichment analysis. Through comparing statistical models, we conclude from the project that combining different models with over-representation analysis and prior structural information can improve the quality of prediction and facilitate biological interpretation. Keywords: regulatory network, variable selection, penalized maximum likelihood estimation, optimization, functional enrichment analysis. / Science, Faculty of / Graduate

Doctor of Philosophy / Department of Psychological Sciences / Mary E. Cain / Drug addiction is a chronic cyclical disease characterized by periods of drug use and abstinence. Drug craving increases as a function of abstinence period, such that longer periods of abstinence result in greater feelings of craving. Longer periods of abstinence may render cues to become more powerful motivators of drug seeking behavior because of the greater craving response. Neurobiological evidence suggests that changes in glutamatergic transmission in the nucleus accumbens (NAc) plays a pivotal role in the incubation of craving and drug seeking motivation. Specifically, the upregulation of Ca²⁺ permeable AMPA receptors may increase drug seeking following the presentation of a drug cue. Environmental housing manipulations also change the expression of metabotropic glutamate receptors (mGlur) and psychostimulant self-administration. In the current experiments, Sprague-Dawley rats were reared in enriched (EC) or isolated (IC) conditions from PND 21-51. Then rats were implanted with indwelling jugular catheters and allowed to self-administer amphetamine (0.1 mg/kg/infusion) or saline paired with a cue light for 16 days for 1h. Then rats went through a forced abstinence period of 1 day and were then tested in a cue-induced seeking test. Immediately after the seeking test, half the rats were sacrificed and the NAc was dissected and prepared for western blot analyses. The other half of rats rested for 40 days and were tested again in the cue-induced seeking test. Immediately following the seeking test, rats were sacrificed and their NAc was dissected. Factorial ANOVA results indicate that rearing in the IC environment increased drug seeking when compared to EC rats after 1 day of abstinence and after 40 days of abstinence, but drug seeking did not increase after 40 days. Rats in the saline groups showed an increase in seeking after 40 days of abstinence, providing evidence of increased responding. Saline responding was significantly lower when compared to rats that responded for amphetamine. When rats self-administered saline, generally IC rats had more responding than EC rats. Western blot analyses indicated that expression of AMPA subunits GluA1, and GluA2, as well as metabotropic glutamate receptors 1 and 5 (mGlur1, and mGlur5) were not different across the experimental groups, suggesting another mechanism could be implicated in drug seeking after short and long abstinence periods. These results suggest that early life experience can have long lasting effects into adulthood and increase the vulnerability of drug abuse. Our results provide mixed results of incubated seeking. Positive early life experiences reduce drug seeking motivation after short and long abstinence periods, providing evidence for further research to examine how early life experience changes the reward seeking and subsequent structures in the mesocorticolimbic pathway.

>Magister Scientiae - MSc / Lung cancer remains the leading cause of cancer deaths worldwide, with the majority of cases attributed to non-small cell lung carcinomas. At the time of diagnosis, a large percentage of patients present with advanced stage of disease, ultimately resulting in a poor prognosis. The identification circulatory markers, overexpressed by the tumour tissue, could facilitate the discovery of an early, specific, non-invasive diagnostic tool as well as improving prognosis and treatment protocols. The aim was to analyse gene expression data from both microarray and RNA sequencing platforms, using bioinformatics and statistical analysis tools. Enrichment analysis sought to identify genes, which were differentially expressed (p < 0.05, FC > 2) and had the potential to be secreted into the extracellular circulation, by using Gene Ontology terms of the Cellular Component. Results identified 1 657 statically significant genes between normal and early lung cancer tissue, with only 1 gene differentially expressed (DE) between the early and late stage disease. Following statistical analysis, 171 DE genes selected as potential early stage biomarkers. The overall sensitivity of RNAseq, in comparison to arrays enabled the identification of 57 potential serum markers. These genes of interest were all downregulated in the tumour tissue, and while they did not facilitate the discovery of an ideal diagnostic marker based on the set criteria in this study, their roles in disease initiation and progression require further analysis.

Proteases play a crucial role in plant defence mechanisms as well as acclimation to changing metabolic demands and environmental cues. Proteases regulate the development of a plant from germination through to senescence and plant death. In this thesis the role of proteases and their inhibitors in plant response to cold stress and CO2 enrichment were investigated. The activity and inhibition of cysteine proteases (CP), as well as degradation of their potential target proteins was investigated in transgenic tobacco plants expressing the rice cystatin, OC-I. Expression of OC-I caused a longer life span; delayed senescence; significant decrease in in vitro CP activity; a concurrent increase in protein content; and protection from chilling-induced decreases in photosynthesis. An initial proteomics study identified altered abundance of a cyclophilin, a histone, a peptidyl-prolyl cis-trans isomerase and two RuBisCO activase isoforms in OC-I expressing leaves. Immunogold labelling studies revealed that RuBisCO and OC-I is present in RuBisCO vesicular bodies (RVB) that appear to be important in RuBisCO degradation in leaves under optimal and stress conditions. Plants need to respond quickly to changes in the environment that cause changes in the demand for photosynthesis. In this study the effect of CO2 enrichment on photosynthesis-related genes and novel proteases and protease inhibitors regulated by CO2 enrichment and/or development, was investigated. Maize plants grown to maturity with CO2 enrichment showed significant changes in leaf chlorophyll and protein content, increased epidermal cell size, and decreased epidermal cell density. An increased stomatal index in leaves grown at high-CO2 indicates that leaves adjust their stomatal densities through changes in epidermal cell numbers rather than stomatal numbers. Photosynthesis and carbohydrate metabolism were not significantly affected. Developmental stage affected over 3000 transcripts between leaf ranks 3 and 12, while 142 and 90 transcripts were modified by high CO2 in the same leaf ranks respectively. Only 18 transcripts were affected by CO2 enrichment exclusively. Particularly, two novel CO2 -modulated serine protease inhibitors modulated by both sugars and pro-oxidants, were identified. Growth with high CO2 decreased oxidative damage to leaf proteins. / Thesis (PhD)--University of Pretoria, 2009. / Plant Science / unrestricted

Research problem: The restructuring of an organisation can be classified as a transformational intervention (Litwin & Burke, 1992). As such is it has a potential to significantly influence key employee attitudes that are related to employee and organisational performance. Any deterioration in these attitudes could impact negatively on organisational outcomes. As part of the monitoring and review of change interventions, management needs to understand the change in employee attitudes towards their work and management in their business units and towards the broader organisation in order that, if necessary, corrective action can be taken. Research objectives: To address the research problem, research objectives and questions were established. The main objective of the study was to investigate whether there has been a change in attitudes of employees in two business units of a South African National Science Council after the implementation of restructuring in the organisation and the business units. The key attitudes to be measured are job and management satisfaction, perceived organisational support, organisational commitment and a dimension of employee engagement, dedication. Research questions: Four research questions were established and these were; What is the change in employee attitudes post-restructuring? In particular what is the change in employee job satisfaction; management satisfaction, employee engagement, commitment to the organisation and perceived organisational support? What is the relationship between the sub-groups, distinguished by gender, occupational level, race, home language, age, number of years of service and business unit, and employee attitudes pre-restructuring? What is the relationship between the sub-groups distinguished by gender, occupational level, race, home language, age, number of years of service and business unit, and employee attitudes post-restructuring? What is the relationship between the sub-groups distinguished by gender, occupational level, race, home language, age, number of years of service and business unit, and the change in employee attitudes pre and post-restructuring? Research design: The nature of this research is descriptive. In order to solve the research questions the researcher used a pre-test and post-test measurement of employee attitudes. A survey using a structured self-administered questionnaire was used to collect information regarding employee attitudes before and after the restructuring of the organisation and business units. Major findings: The results from the survey showed that there was a change in the levels of organisational commitment, job satisfaction and management satisfaction at the National Science Council after the restructuring had taken place. Also, the impact of the sub-groups in the organisation on affective factors was evident in the level of occupation and employee engagement, race and management satisfaction, the business unit and the levels of perceived organisational support, management satisfaction and employee engagement, home language and employee engagement, the number of years the employee had worked for the organisation and management satisfaction, age and job satisfaction and employee engagement.

Employing a sample of 116 female entrepreneurs, this study investigated how work-family issues, including work-family conflict and enrichment, relate to their intention to grow the business that they own or co-own. Results suggest that family-to-work enrichment directly related to female entrepreneurs’ business growth intentions, and important family members seems highly salient to female entrepreneurs’ business growth decisions.

This study meta-analyzed relationships between proposed antecedents and both directions of work-family enrichment (i.e., work-to-family enrichment and family-to-work enrichment). Proposed antecedents, which were derived from three existing theoretical models on the positive interface between work and family, include contextual and personal characteristics from both work- and family-domains. Primary studies included in the meta-analyses were from both published and unpublished sources between 1990 and 2016. The results suggest that several contextual and personal characteristics are significantly related to work-family enrichment. Gender’s moderating effect on the relationship between contextual characteristics and work-family enrichment received little support. Comparisons between examined antecedents of work-family enrichment and antecedents of work-family conflict supported the notion that work-family enrichment and work-family conflict are distinct constructs; in other words, enrichment is not merely the opposite of conflict. Practical implications and suggestions on future research are discussed.

This study evaluated an experimental program in informal learning, “Light and Illusion,” developed by the Vancouver School Board in cooperation with the Arts and Sciences Centre of Vancouver. A mail questionnaire was developed based upon a review of the literature on informal learning . The questionnaire was distributed to the Vancouver School Board teachers who visited the workshop with their students. The study was conducted over a three month period; 94 of the 150 questionnaires sent out were returned (69% return ) . The questionnaire sought to determine which teachers (grade level and subject area) used the workshop, how teachers used the workshop, what teachers liked and disliked about the workshop, and what suggestions they had for future workshops. The results were reported as percentage responses to the questionnaire items. In addition , a series of observations and recommendations were made. In particular the study showed that 90% of the attending teachers were highly satisfied with the workshop as a learning experience for their students. They commented favorably on the quality of the exhibits , freedom of choice, and the noticeable increase in student interest in science. Elementary teachers rated the workshop more highly than did secondary teachers, although both indicated they benefited by seeing their students work in a novel environment. Teachers thought that further informal learning workshops should be offered to students through the cooperation of the Vancouver School Board and the Arts and Sciences Centre. / Education, Faculty of / Curriculum and Pedagogy (EDCP), Department of / Graduate

Lysine methylation is a post-translational modification that regulates a large array of functionally diverse processes that are vital for cellular function. The role of methylation is best characterized on histone proteins due to their high concentration in the cell, but alongside histone modifications, lower abundance non-histone methylation is emerging as a prevalent and functionally diverse regulator of cellular processes. The direct biological impact of non-histone lysine methylation is less well understood because they are difficult to detect. The dynamic concentration range of the proteome masks their signal during proteomic analysis which impedes the detection of these low abundance methylated proteins. Increasing the concentration of proteins bearing methylation is required for improved discovery. This requires enriching the post-translational modification with a capturing reagent prior to analysis. This thesis details an optimized method for using the supramolecular host p-sulfonatocalix[4]arene as a stationary phase methyllysine enrichment reagent for real-life cell-extracted proteins. Prior to the optimizations described in this thesis, cell-derived peptide extracts were not retained within an early generation upper-rim modified calixarene column. But with the new protocols detailed in this thesis, proteins extracted from both cultured prostate cancer cells and industrially sourced brewer’s yeast were successfully retained by a lower-rim modified calixarene column. Thousands of methylated proteins with diverse functions and cellular localization were discovered using this method. Detection of low abundance methylated proteins will aid our discovery of all cellular methylation marks, which in turn, will help delineate their biological functions. / Graduate / 2020-11-30

Role of N-methylated lysines (K) and arginines (R) was underappreciated for a long time before the turn of the century. With the help of new emerging technologies, their crucial role in chromatin regulation was established and now their mention when discussing gene regulation is almost a given. Despite this, much about how they contribute to the cellular chemistry is still to be discovered. There is a major gap in current knowledge base due to an incomplete list of possible lysine and arginine methylation sites. This is because of their low copy number inside the cell which makes it difficult to detect them. New methylation sites are being added every day. This thesis aims to provide a solution to this problem by establishing methods that can help detect N-methylated lysines and argnines that are present in really low quantity inside the cell. The work is influenced by a previously established fact that p-sulfonatocalix[4]arene binds methylated lysine over unmethylated ones. We have first attempted to improve this native affinity by decorating the calix[4]arene skeleton with different substituents. To this effect, we have developed methods for regioselective functionalization of calix[4]arene scaffold and then studied their effect on its binding profile against a set of test peptides derived from proteins found in vivo. We then demonstrate a proof-of-concept enrichment method using selected molecules from our inventory. We use these calix[4]arene based molecules as a stationary phase modifier in a chromatography setup and then show that it can separate peptides based on presence of N-methylated lysines and arginines. We propose that introduction of such a method would improve the visibility of low level N-methylated peptides by removing the bulk of back ground unmethylated analytes and thus improving their signal strength. Finally, we establish the utility of this method by showing that more N-methylated lysines are detected from a real-world proteomics sample prepared using our enrichment method. This work opens new avenues for use of supramolecular chemistry in proteomics studies. We believe that this thesis is a confident demonstration that host-guest chemistry can help expand the existing knowledge about bimolecular processes found in vivo and must be explored further. / Graduate / 2021-12-23