This thesis argues that caffeine use offered a survival advantage to our ancestors and that moderate use continues to offer modern humans benefits. Caffeine ingestion, through the blocking of adenosine receptors, elicits broad elements of the mammalian threat response, specifically from the ‘flight or fight’ and ‘tend and befriend’ repertoires of behaviour: in effect, caffeine hijacks elements of the stress response. If the effects of caffeine had been discovered recently, rather than being available to Homo sapiens since Neolithic hunter gatherer times, it is likely that caffeine would be considered a ‘smart’ drug. More caffeine is being ingested today than ever previously recorded. Caffeine use is found across all age groups, all socio-economic strata, most ethnic groups, and is being used increasingly by the medical and pharmaceutical industries and by the armed forces. Yet despite this wide usage and a substantial body of research literature, there is at present no clear pattern or plausible model for the way caffeine achieves its effects. There is much contradiction in the literature and ambiguity as to why caffeine use should improve performance on some tasks, impair it on others and have no effect on other tasks, for some but not all of the time. The present work argues, through an examination of the specificity of caffeine’s operation, that these effects are not arbitrary but elicited by the nature of the tasks, in particular that caffeine ingestion affects those processes and behaviours which improve the probability of survival under perceived threat or stress. This is argued through the perspective of evolutionary psychology and relies theoretically on Polyvagal Theory. The argument generates testable hypotheses and empirical support for the thesis is garnered from nine experiments on card-sorting, verbal and numerical processing, local and global categorization, field dependence-independence, the Stroop task, tests of visuo-spatial ability, and from a correlational study of caffeine use and personality traits. It is concluded that moderate caffeine use in healthy adults promotes behaviours likely to be adaptive under perceived threat or stress. Limitations of both theory and empirical work and are discussed, together with potential practical applications and suggestions for further work.

DNA-binding proteins bind to specific sequences to direct their activity to defined loci in the genome. Regulation of gene expression, for example, is dependent on the recognition of specific DNA sequences by transcription factors (TFs). These TFs receive input from cellular signals to control panels of genes to meet the needs of the cells. Critical to this function is the recognition and binding of TFs to the correct DNA sequence. The main focus of this thesis is to quantitatively determine how proteins, including TFs, distinguish DNA sequences, and to understand how DNA sequence affect their function. Primarily using the Glucocorticoid receptor (GR) as the model TF, I developed novel methods to measure the DNA binding specificity over long binding sites. These methods: 1) Distinguished the sequence specificity of GR and closely related androgen receptor (AR), which helped to both account for differential genomic localization between the two factors, and explained how GR can functionally substitute for AR in castration-resistant prostate cancer (Chapter II); 2) Explored the effect of DNA sequence on GR-regulated transcription through the specification of monomeric versus dimeric binding. Sequence motifs that bias GR binding toward the monomeric state were discovered (Chapter III); 3) Demonstrated a conserved role of intrinsic specificity in directing the degree of GR genomic occupancy in vivo in a fixed chromatin context (Chapter V); 4) Quantitatively modeled and decoupled the DNA binding and cleavage specificities of CRISPR-Cas9 system, providing a rapid pipeline to characterize the genome-editing reagents (Chapter IV). In summary, we showed here that DNA binding specificity is only the initial step in directing the activity of the bound protein. Beyond the affinity-based recruitment, DNA sequences can regulate the protein activity through alternative mechanisms, such as modulating the binding cooperativity, or directly serving as an allosteric ligand for protein function that is independent of DNA binding affinity.

Post-translational modification (PTM) of proteins by enzymes such as methyltransferases, kinases and deacetylases play a crucial role in the regulation of many metabolic pathways. Determining the substrate scope of these enzymes is essential when studying their biological role. However, the combinatorial nature of possible protein substrate sequences makes experimental screening assays intractable. To predict new substrates for proteins, various computational approaches have been developed. Our method relies on crystallographic data and a novel multistate computational protein design algorithm. We previously used our method to successfully predict four new substrates for SMYD2 (Lanouette S & Davey J.A., 2015), doubling the number of known targets for this PTM enzyme that has been difficult to characterize using other methods. This was possible by first extracting a specificity profile of Smyd2 using our algorithm and subsequently screening a peptide library for matching sequences. However, our method did not yield successful results when attempting to reproduce specificity profiles of other proteins (64% accuracy on average). Different protein environments have demonstrated limitations in the methodology and lead us to further develop the algorithm on a more thorough dataset. Using our new optimized method, specificity profile predictions increase by roughly 20% (84% accuracy on average), independent of the structural template used. The algorithm was then used to blindly predict a specificity profile for the methyltransferase Smyd3, an enzyme for which limited data is currently available. A library of 2550 peptides was screened with the predicted profile, yielding 123 matching sequences. We randomly chose 64 for experimental validation (SPOT peptide array) of methylation by Smyd3 and found 45 methylated and 19 non-methylated peptides (70% success rate). Finally, we released to the community a web version of the algorithm, which can be accessed as http://viper.science.uottawa.ca.

In many applications, it is common to have multiple diagnostic tests on each subject. When there are multiple tests available, combining tests to incorporate information from various aspects in subjects may be necessary in order to obtain a better diagnostic. For continuous tests, in the presence of a gold standard, we could combine the tests linearly (Su and Liu, 1993) or sequentially (Thompson, 2003), or using the risk score as studied by McIntosh and Pepe (2002). The gold standard, however, is not always available in practice. This dissertation concentrates on deriving classification methods based on multiple tests in the absence of a gold standard. Motivated by a lab data set consisting of two tests testing for an antibody in 100 blood samples, we first develop a mixture model of four bivariate normal distributions with the mixture probabilities depending on a two-stage latent structure. The proposed two-stage latent structure is based on the biological mechanism of the tests. A Bayesian classification method incorporating the available prior information is derived utilizing Bayesian decision theory. The proposed method is illustrated by the motivating example, and the properties of the estimation and the classification are described via simulation studies. Sensitivity to the choice of the prior distribution is also studied. We also investigate a general problem of combining multiple continuous tests without any gold standard or a reference test. We thoroughly study the existing methods for combining multiple tests and develop optimal classification rules corresponding to the methods accommodating the situation without a gold standard. We justify the proposed methods both theoretically and numerically through exten- sive simulation studies and illustrate the methods with the motivating example. In the end, we conclude the thesis with remarks and some interesting open questions extended from the dissertation.

With aging there is a decrease in a person’s ability to perform activities of daily living (ADL) which may be most effectively addressed using training patterns that are biomechanically similar to ADL. Since aquatic exercise offers the opportunity to provide resistance with a high level of safety, the pool may afford the ideal environment for ADL-specific training in an aging population. Purpose: The purpose of this investigation was to compare a traditional aquatic exercise program (TRAD) to an aquatic program tailored to target ADL (ADLspec). Methods: Eighteen independently living individuals (68.7 + 7.5 years) were randomly assigned to a TRAD or ADLspec aquatic exercise group. The exercise groups attended 1 hr exercise sessions, 2 times per week for 8 weeks. ADL ability was assessed using the short version of the Continuous-Scale Physical Functional Performance Test (PFP-10); while strength and power were assessed using the 30s arm curl and 30 sec. chair stand tests. Results: Mixed design ANOVAs revealed a significant group x time interaction for floor sweep time with the ADLspec group outperforming the TRAD and control (CON) groups (p = .043). Additionally, the ADLspec group improved the pan weight and scarf time components of the PFP-10 (p < .020), while the TRAD group improved pan time and laundry time (p < .046). Both training groups showed similar improvements for jacket time, grocery weight, and 6-min walk, (p < .046). The ADLspec and TRAD groups also made similar improvements in upper and lower body strength, as well as lower body power across time, (p < .043). A student’s t-test revealed the TRAD group spent more time exercising during the hour session than the ADLspec group (p < .05). Conclusion: The results indicate that performing an ADLspec aquatic exercise program can increase performance of ADL that require more complex sequential movements; however, ADL more dependent on fitness may be better addressed using a TRAD intervention. These results can be helpful when designing a periodized aquatic training program to increase independence in older persons.

Cells are complex biological units with advanced signalling systems, a dynamic capacity to adapt to its environment, and the ability to divide and grow. In fact, they are of such high level of complexity that it has deemed extremely difficult or even impossible to completely understand cells as complete units. The search for comprehending the cell has instead been divided into small, relatively isolated research fields, in which simplified models are used to explain cell biology. The result produced through these reductionistic investigations is integral for our current description of biology. However, there comes a time when it is possible to go beyond such simplifications and investigate cell biology at a higher level of complexity. That time is now. This thesis describes the development of mathematical tools to investigate intricate biological systems, with focus on heterogeneous protein interactions. By the use of simulations, real-time measurements and kinetic fits, standard assays for specificity measurements and receptor quantification were scrutinized in order to find optimal experimental settings and reduce labour time as well as reagent cost. A novel analysis platform, called Interaction Map, was characterized and applied on several types of interactions. Interaction Map decomposes a time-resolved binding curve and presents information on the kinetics and magnitude of each interaction that contributed to the curve. This provides a greater understanding of parallel interactions involved in the same biological system, such as a cell. The heterogeneity of the epidermal growth factor receptor (EGFR) system was investigated with Interaction Map applied on data from the instrument LigandTracer, together with complementing manual assays. By further introducing disturbances to the system, such as tyrosine kinase inhibitors and variation in temperature, information was obtained about dimerization, internalization and degradation rates. In the long term, analysis of binding kinetics and combinations of parallel interactions can improve the understanding of complex biomolecular mechanisms in cells and may explain some of the differences observed between cell lines, medical treatments and groups of patients.

Root symbioses with dark septate endophytic fungi (DSE) and arbuscular mycorrhizal fungi (AMF) provide plant tolerance to environmental stresses. This research answers several fundamental questions about the occurrence of these fungi in roots of prairie grasses. Traditional methods and current molecular techniques were combined in order to: 1) define the role and specificity of DSE in plant tolerance to drought; 2) assess the level of host specificity in DSE; 3) document AMF biodiversity and pattern of root colonization at different soil depths; 4) define the influence of soil depth and plant species on the distribution of DSE and AMF in roots and; 5) reveal how DSE and AMF interact in plant roots.<p> Under controlled conditions, DSE isolates showed host preference in colonizing roots and promoting plant growth. They colonized with more intensity the plant species from which they were isolated [Agropyron cristatum L. or Psathyrostachys juncea (Fisch) Nevski subsp. Juncea (Syn: Elymus junceus Fisch)]. Inoculation with five DSE isolates resulted in growth stimulation of the C3 grasses A. cristatum and P. juncea, and growth depression of the C4 grass Bouteloua gracillis (Willd. ex Kunth) Lag. ex Griffiths, under water stress. Plant C concentration suggested that DSE inoculation may have resulted in net C drain from B. gracillis.<p. In the field, soil depth influenced root colonization in A. cristatum, Panicum virgatum L., Nassella viridula Trin and Pascopyrum smithii (Rydb.) A. Löve., while AMF diversity was influenced by the interaction between soil depth and host plant species. Molecular analysis of roots serially sampled during one growing season from the A and B soil horizons, in stands of these grasses, revealed spatial and temporal changes in DSE and AMF community composition, and a significant correlation in DSE and AMF community structure.<p> These results suggest that DSE and AMF are adapted to specific environmental conditions and that root occupation by these fungi is a dynamic phenomenon. It is proposed that temporal variation in root occupation by DSE and AMF impacts plant and ecosystem processes at different times during the growing season.

In the current third wave of internationalization companies from mature markets are investing in emerging markets and increase their foreign activities. For this internationalization process, companies need to enter the market with an appropriate entry mode strategy. Prior research focused mainly on MNC entry modes and also on factors as ownership, location or internalization advantages and not on SMEs and transaction cost theory. This thesis deals with the topic of institutions, transaction costs and entry mode decisions of Swedish SMEs in India. The purpose of this thesis is to understand the managerial perceptions about the influence of institutions on the degree of linkage specificity with which the transaction costs will be explored. This will lead to further knowledge about certain entry mode decisions of Swedish SMEs for the Indian market. This was studied with a qualitative research strategy using a multiple case study method. The empirical data was conducted via secondary data and primary data was collected via interviews with the sales responsible of the four case companies Norden Machinery AB, Slipnaxos AB, Håkansson Sågblad AB and Hedin Lagan AB. Main findings of the research were that institutions are perceived differently by the managers and therefore the institutions dissimilarly influenced the perceptions of the transaction costs. Furthermore, the study revealed that some managers decided their entry mode on the base of the perception of the transaction costs and some managers did not consider transaction costs when entering new markets. All in all it can be stated that transaction costs influence the entry mode of companies. The research is limited by the fact that transaction cost theory in general neglects factors as production costs. Managerial implications are that transactions costs should not be neglected as they help to choose a more successful entry mode and that the assets specificity and the behavioral uncertainties need to be taken into account when deciding upon an entry mode. Theory profits from this thesis as it proved that transaction costs influence entry mode decisions and that the linkage specificity is an important factor to include when combining transaction cost theory with entry mode decisions.

Many of today’s methods for the detection of biomolecules suffer from a high limit ofdetection due to poor signal generation upon recognition of target. By applying andoptimizing proximity ligation assay (PLA) in Western blotting (WB), the limit of detectionhas been lowered down to the picomolar range. In this report I have optimized the differentparameters that affect the signal generation and explored possibilities to increase the ease ofuse, by merging protocol steps and performing signal generating reactions at roomtemperature.

Root symbioses with dark septate endophytic fungi (DSE) and arbuscular mycorrhizal fungi (AMF) provide plant tolerance to environmental stresses. This research answers several fundamental questions about the occurrence of these fungi in roots of prairie grasses. Traditional methods and current molecular techniques were combined in order to: 1) define the role and specificity of DSE in plant tolerance to drought; 2) assess the level of host specificity in DSE; 3) document AMF biodiversity and pattern of root colonization at different soil depths; 4) define the influence of soil depth and plant species on the distribution of DSE and AMF in roots and; 5) reveal how DSE and AMF interact in plant roots.<p> Under controlled conditions, DSE isolates showed host preference in colonizing roots and promoting plant growth. They colonized with more intensity the plant species from which they were isolated [Agropyron cristatum L. or Psathyrostachys juncea (Fisch) Nevski subsp. Juncea (Syn: Elymus junceus Fisch)]. Inoculation with five DSE isolates resulted in growth stimulation of the C3 grasses A. cristatum and P. juncea, and growth depression of the C4 grass Bouteloua gracillis (Willd. ex Kunth) Lag. ex Griffiths, under water stress. Plant C concentration suggested that DSE inoculation may have resulted in net C drain from B. gracillis.<p. In the field, soil depth influenced root colonization in A. cristatum, Panicum virgatum L., Nassella viridula Trin and Pascopyrum smithii (Rydb.) A. Löve., while AMF diversity was influenced by the interaction between soil depth and host plant species. Molecular analysis of roots serially sampled during one growing season from the A and B soil horizons, in stands of these grasses, revealed spatial and temporal changes in DSE and AMF community composition, and a significant correlation in DSE and AMF community structure.<p> These results suggest that DSE and AMF are adapted to specific environmental conditions and that root occupation by these fungi is a dynamic phenomenon. It is proposed that temporal variation in root occupation by DSE and AMF impacts plant and ecosystem processes at different times during the growing season.