Success of hybrid poplar plantations will rely on the efficient management of nutrients and weeds. Relatively little is known about the root uptake characteristics of hybrid poplar and weeds, their belowground interactions and particularly, the quantitative understanding of nutrient uptake using mechanistic models under weed-competing conditions. Therefore, the objectives of this study were to investigate the effects of dandelion and quackgrass on the growth of hybrid poplar, to establish their root uptake characteristics and to quantify their nutrient uptake using the soil supply and nutrient demand (SSAND) model. In a pot study, hybrid poplar stem height, root collar diameter, shoot and root biomass, root length, and N, P and K uptake significantly decreased in the presence of dandelion and quackgrass weeds. Similar weed competition effects on growth of hybrid poplar were also observed in the field at the Pasture and Alfalfa sites where hybrid poplar was grown with and without weeds for 50, 79 and 100 days. In a hydroponic experiment, Imax values for NH4-N, NO3-N, P and K varied significantly among hybrid poplar seedlings and dandelion and quackgrass weed species and was greatest for dandelion followed by hybrid poplar and then quackgrass. The Km values were lowest for quackgrass compared to the other plant species for all of the nutrients. Simulation results from the SSAND model for the pot study showed that N uptake was underpredicted in hybrid poplar by 58 to 73%, depending upon soil type and weed treatment. Incorporation of N mineralization as a model input improve the hybrid poplar N uptake predictions by 24 and 67% in the Pasture and Alfalfa soil, respectively, when grown without weeds. SSAND model underestimated P uptake by 84-89% and overestimated K uptake by 28 to 59% for hybrid poplar depending upon the soil type and weed treatment. In the field, N uptake by hybrid poplar was in close agreement to measured N uptake in the control treatment. N uptake was greatly underestimated for both hybrid poplar and weeds in the weed treatment. Including changing water content greatly improves the N uptake by hybrid poplar and weeds in weed treatments. Results from this study suggest weed control is an essential practice to establish successful hybrid poplar plantations. Also, SSAND model can be an effective tool for predicting the nutrient uptake under two plant species competing environment if all the processes of nutrient supply are adequately described in the model.

Success of hybrid poplar plantations will rely on the efficient management of nutrients and weeds. Relatively little is known about the root uptake characteristics of hybrid poplar and weeds, their belowground interactions and particularly, the quantitative understanding of nutrient uptake using mechanistic models under weed-competing conditions. Therefore, the objectives of this study were to investigate the effects of dandelion and quackgrass on the growth of hybrid poplar, to establish their root uptake characteristics and to quantify their nutrient uptake using the soil supply and nutrient demand (SSAND) model. In a pot study, hybrid poplar stem height, root collar diameter, shoot and root biomass, root length, and N, P and K uptake significantly decreased in the presence of dandelion and quackgrass weeds. Similar weed competition effects on growth of hybrid poplar were also observed in the field at the Pasture and Alfalfa sites where hybrid poplar was grown with and without weeds for 50, 79 and 100 days. In a hydroponic experiment, Imax values for NH4-N, NO3-N, P and K varied significantly among hybrid poplar seedlings and dandelion and quackgrass weed species and was greatest for dandelion followed by hybrid poplar and then quackgrass. The Km values were lowest for quackgrass compared to the other plant species for all of the nutrients. Simulation results from the SSAND model for the pot study showed that N uptake was underpredicted in hybrid poplar by 58 to 73%, depending upon soil type and weed treatment. Incorporation of N mineralization as a model input improve the hybrid poplar N uptake predictions by 24 and 67% in the Pasture and Alfalfa soil, respectively, when grown without weeds. SSAND model underestimated P uptake by 84-89% and overestimated K uptake by 28 to 59% for hybrid poplar depending upon the soil type and weed treatment. In the field, N uptake by hybrid poplar was in close agreement to measured N uptake in the control treatment. N uptake was greatly underestimated for both hybrid poplar and weeds in the weed treatment. Including changing water content greatly improves the N uptake by hybrid poplar and weeds in weed treatments. Results from this study suggest weed control is an essential practice to establish successful hybrid poplar plantations. Also, SSAND model can be an effective tool for predicting the nutrient uptake under two plant species competing environment if all the processes of nutrient supply are adequately described in the model.

Relative to other metals, little is known about lead toxicity in fish. The use of predictive models such as the biotic ligand model (BLM) has been limited, a situation that is at least partially due to the lack of understanding of lead's acute toxic mechanism and characterization of key binding sites involved in this toxicity. Using the rainbow trout as a model species, the acute toxic mechanism for lead was found to be ionoregulatory disruption. While having no apparent respiratory or acid/base effects, Pb exposure resulted in significant ionoregulatory impacts that affected Ca2+ homeostasis, as well as Na+ and Cl- balance. Active Ca2+ uptake by the gills obeyed typical Michaelis-Menten kinetics, and Pb interacted in a competitive fashion with the uptake process. Exposure to increasing waterborne Pb concentrations resulted in significant increases in Km value while Jmax showed little or no change. A slower, non-competitive interaction occurred after prolonged Pb-exposure, evidenced by a significant reduction of high-affinity Ca2+ -ATPase activity that correlated well with branchial Pb accumulation. Conversely, calcium had a protective effect against branchial Pb accumulation, this relationship being predominately competitive in nature. Voltage-independent calcium channel blockers La3+, Cd, and Zn significantly reduced gill Pb burden while the voltage-dependent, L-type calcium channel blockers, nifedipine and verapamil, did not, suggesting Pb enters fish by a similar mechanism to that of Ca2+. Stimulated stanniocalcin release by CaCl2 injection also significantly reduced branchial Pb accumulation. Based on the evidence presented in this thesis, it is apparent that acute Pb toxicity occurs by ionoregulatory disruption. It is likely that Pb shares a similar uptake pathway as that for Ca2+ and that resulting accumulation results in disruption of Ca2+ influx as well as Na+ and Cl- balance. This study has provided data essential to the characterization of key binding sites involved in Pb toxicity, and ultimately, validates the development and application of predictive models such as the BLM. / Thesis / Master of Science (MSc)

The flavonols are a varied and abundant sub-class of flavonoids that are associated with a number of essential physiological functions in plants and pharmacological activities in animals. The 2-oxoglutarate-dependant dioxygenases(2-ODDs), flavonol synthase (FLS) and flavanone 3-hydroxylase (F3H), are essential for flavonol synthesis. The primary goal of this study has been to gain a deeper understanding of the biochemistry of these enzymes in Arabidopsis. To accomplish this goal, an activity assay employing recombinant protein expression and HPLC as a detection system was developed for F3H and adapted for use with FLS. The assay was employed to establish the biochemical parameters of F3H from Arabidopsis, and to further characterize the F3H mutant allele, <i>tt6</i>(87). Enzymatic activity was demonstrated for F3H enzymes from <i>Ipomoea alba</i> (moonflower), <i>Ipomoea purpurea</i> (common morning glory), <i>Citrus sinensis</i> (sweet orange), and <i>Malus X domestica</i> (newton apple), each of which had previously been identified solely based on sequence homology. Arabidopsis contains six genes with high similarity to <i>FLS</i> from other plant species; however, all other central flavonoid pathway enzymes in Arabidopsis are encoded by single genes. The hypothesis that differential expression of FLS isozymes with varying substrate specificities is responsible for observed tissue-specific differences in flavonol accumulation was tested. Sequence analysis revealed that <i>AtFLS2, 4</i> and <i>6</i> contain premature stop codons that eliminate residues essential for enzyme activity. AtFLS1 was found to have a strong preference for dihydrokaempferol as a substrate. However, no enzyme activity was observed for AtFLS3 or AtFLS5 with a number of different substrates under a variety of reaction conditions. To identify structural elements that may contribute to the observed differences in biochemical activity, homology models for each of the isoforms were generated utilizing Arabidopsis anthocyanin synthase (ANS) as a template. A domain at the N-terminus of AtFLS1 that is missing in the other isozymes was insufficient to convey activity to an AtFLS1/5 chimera. These findings suggest a single catalytically-active form of FLS exists in Arabidopsis. The possibility that the apparently expressed but non-catalytic proteins, AtFLS2, 3, and 5, serve noncatalytic roles in flavonol production were explored by yeast 2-hybrid analysis. / Ph. D.

This thesis summarizes the results of studies on two aspects of nucleic acids. Chemically modified antisense oligonucleotides (AONs) have been evaluated with regards to their suitability for mRNA targeting in an antisense approach (Paper I – III). The chemically modified nucleotidic units 2'-O-Me-T, 2'-O-MOE-T, oxetane-T, LNA-T, azetidine-T, aza-ENA-T, carbocyclic-ENA-T and carbocyclic-LNA-T were incorporated into 15-mer AONs and targeted against a 15-mer RNA chosen from the coding region of SV-40 large T antigen. The comparative study showed that a single modified nucleotide in the AON with North-East locked sugar (oxetane-T and azetidine-T) lowered the affinity for the complementary RNA whereas North locked sugars (LNA-T, aza-ENA-T, carbocyclic-ENA-T, and carbocyclic-LNA-T) significantly improved the affinity. A comparative RNase H digestion study showed that modifications of the same type (North-East type or North type) in different sequences gave rise to similar cleavage patterns. Determination of the Michaelis-Menten parameters by kinetic experiments showed that the modified AONs recruit RNase H resulting in enhanced turnover numbers (kcat) although with weaker enzyme-substrate binding (1/Km) compared to the unmodified AON. The modified AONs were also evaluated with regards to resistance towards snake venom phosphodiesterase and human serum to estimate their stability toward exonucleases. The aza-ENA-T and carbocyclic-ENA-T modified AONs showed improved stability compared to all other modified AONs. In general, the modified AONs with North type nucleotides (except LNA-T) were found to be superior to the North-East type as they showed improved target affinity, comparable RNase H recruitment capability and improved exonuclease stability. The second aspect studied in this thesis is based on physicochemical studies of short RNA molecules utilizing NMR based pH titration and alkaline hydrolysis reactions (Paper IV – V). The NMR based (1H and 31P) pH titration studies revealed the effect of guaninyl ion formation, propagated electrostatically through a single stranded chain in a sequence dependent manner. The non-identical electronic character of the internucleotidic phosphodiesters was further verified by alkaline hydrolysis experiments. The internucleotidic phosphodiesters, which were influenced by guaninyl ion formation, were hydrolyzed at a faster rate than those sequences where such guaninyl ion formation was prevented by replacing G with N1-Me-G.

In 2019, Adams, Ehlting, and Edwards developed a four-variable system of ordinary differential equations modelling phenylalanine metabolism in plants according to Michaelis-Menten kinetics. Analysis of the model suggested that when a series of reactions known as the Shikimate Ester Loop (SEL) is included, phenylalanine flux into primary metabolic pathways is prioritized over flux into secondary metabolic pathways when the availability of shikimate, a phenylalanine precursor, is low. Adams et al. called this mechanism of metabolic regulation the Precursor Shutoff Valve (PSV). Here, we attempt to simplify Adams and colleagues’ model by reducing the system to three variables and replacing the Michaelis-Menten terms with piecewise-defined approximations we call ramp functions. We examine equilibria and stability in this simplified model, and show that PSV-type regulation is still present in the version with the SEL. Then, we define a class of systems structurally similar to the simplified Adams model called biochemical ramp systems. We study the properties of the Jacobian matrices of these systems and then explore equilibria and stability in systems of n ≥ 2 variables. Finally, we make several suggestions regarding future work on biochemical ramp systems. / Graduate

Cette thèse est consacrée à la modélisation mathématique de l'hématopoïèse et des maladies sanguines. Plusieurs modèles traitant d'aspects différents et complémentaires de l'hématopoïèse y sont étudiés.Tout d'abord, un modèle multi-échelle de l'érythropoïèse est analysé, dans lequel sont décrits à la fois le réseau intracellulaire, qui détermine le comportement individuel des cellules, et la dynamique des populations de cellules. En utilisant des données expérimentales sur les souris, nous évaluons les rôles des divers mécanismes de retro-contrôle en réponse aux situations de stress.Ensuite, nous tenons compte de la distribution spatiale des cellules dans la moelle osseuse, question qui n'avait pas été étudiée auparavant. Nous décrivons l'hématopoïèse normale à l'aide d'un système d'équations de réaction-diffusion-convection et nous démontrons l'existence d'une distribution stationnaire des cellules. Puis, nous introduisons dans le modèle les cellules malignes. Pour certaines valeurs des paramètres, la solution "disease-free" devient instable et une autre solution, qui correspond à la leucémie, apparaît. Cela mène à la formation d'une tumeur qui se propage dans la moelle osseuse comme une onde progressive. La vitesse de cette propagation est étudiée analytiquement et numériquement. Les cellules de la moelle osseuse échangent des signaux qui régulent le comportement cellulaire. Nous étudions ensuite une équation integro-différentielle qui décrit la communication cellulaire et nous prouvons l'existence d'une solution du type onde progressive en utilisant la théorie du degré topologique et la méthode de Leray et Schauder. L'approche multi-agent est utilisée afin d'étudier la distribution des différents types de cellules dans la moelle osseuse.Finalement, nous étudions un modèle de type "Physiologically Based Pharmacokinetics-Pharmacodynamics" du traitement de la leucémie par l'AraC. L'AraC agit comme chimiothérapie et induit l'apoptose de toutes les cellules proliférantes, saines et malignes. La pharmacocinétique donne accès à la concentration intracellulaire d'AraC. Cette dernière, à son tour, détermine la dynamique des populations cellulaires et, par conséquent, l'efficacité de différents protocoles de traitement. / This PhD thesis is devoted to mathematical modelling of haematopoiesis and blood diseases. We investigate several models, which deal with different and complementary aspects of haematopoiesis.The first part of the thesis concerns a multi-scale model of erythropoiesis where intracellular regulatory networks, which determine cell choice between self-renewal, differentiation and apoptosis, are coupled with dynamics of cell populations. Using experimental data on anemia in mice, we evaluate the roles of different feedback mechanisms in response to stress situations. At the next stage of modelling, spatial cell distribution in the bone marrow is taken into account, the question which has not been studied before. We describe normal haematopoiesis with a system of reaction-diffusion-convection equations and prove existence of a stationary cell distribution. We then introduce malignant cells into the model. For some parameter values the disease free solution becomes unstable and another one, which corresponds to leukaemia, appears. This leads to the formation of tumour which spreads in the bone marrow as a travelling wave. The speed of its propagation is studied analytically and numerically. Bone marrow cells exchange different signals that regulate cell behaviour. We study, next, an integro-differential equation which describes cell communication and prove the existence of travelling wave solutions using topological degree and the Leray-Schauder method. Individual based approach is used to study distribution of different cell types in the bone marrow. Finally, we investigate a Physiologically Based Pharmacokinetics-Pharmacodynamics model of leukaemia treatment with AraC drug. AraC acts as chemotherapy, inducing apoptosis of all proliferating cells, normal and malignant. Pharmacokinetics provides the evolution of intracellular AraC. This, in turn, determines cell population dynamics and, consequently, efficacy of treatment with different protocols.