Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Accounting for respiration motion during imaging helps improve targeting precision in radiation therapy. Respiratory motion can be a major source of error in determining the position of thoracic and upper abdominal tumor targets during radiotherapy. Thus, extracting respiratory motion is a key task in radiation therapy planning. Respiration-correlated or four-dimensional CT (4DCT) imaging techniques have been recently integrated into imaging systems for verifying tumor position during treatment and managing respiration-induced tissue motion. The quality of the 4D reconstructed volumes is highly affected by the respiratory signal extracted and the phase sorting method used. This thesis is divided into two parts. In the first part, two image-based respiratory signal extraction methods are proposed and evaluated. Those methods are able to extract the respiratory signals from CBCT images without using external sources, implanted markers or even dependence on any structure in the images such as the diaphragm. The first method, called Local Intensity Feature Tracking (LIFT), extracts the respiratory signal depending on feature points extracted and tracked through the sequence of projections. The second method, called Intensity Flow Dimensionality Reduction (IFDR), detects the respiration signal by computing the optical flow motion of every pixel in each pair of adjacent projections. Then, the motion variance in the optical flow dataset is extracted using linear and non-linear dimensionality reduction techniques to represent a respiratory signal. Experiments conducted on clinical datasets showed that the respiratory signal was successfully extracted using both proposed methods and it correlates well with standard respiratory signals such as diaphragm position and the internal markers’ signal. In the second part of this thesis, 4D-CBCT reconstruction based on different phase sorting techniques is studied. The quality of the 4D reconstructed images is evaluated and compared for different phase sorting methods such as internal markers, external markers and image-based methods (LIFT and IFDR). Also, a method for generating additional projections to be used in 4D-CBCT reconstruction is proposed to reduce the artifacts that result when reconstructing from an insufficient number of projections. Experimental results showed that the feasibility of the proposed method in recovering the edges and reducing the streak artifacts.

L'objectif principal de cette thèse est de comprendre l'impact de la diversité des racines fines sur les composantes du stockage de carbone à différents niveaux d'organisation. Nous avons fait l'hypothèse que les traits des racines fines, mesurés au niveau de l'espèce ou de la communauté, influencent trois processus majeurs liés aux entrées et sorties de C dans le sol : la production, la respiration et la décomposition racinaires et ont ainsi des conséquences sur les stocks de C du sol. Nos résultats montrent que les traits fonctionnels racinaires sont de bons proxys des processus de décomposition et de respiration au niveau de l'espèce. Un compromis de gestion de la ressource carbonée a été mis en évidence entre des espèces caractérisées par de fortes densités racinaires et de forts ratio C/N ou lignine/N qui ont de faible vitesse de respiration et de décomposition et celles caractérisées par de fortes longueurs spécifiques racinaires et teneurs en azote, qui ont un métabolisme rapide. Au niveau de la communauté, ce schéma n'est pas vérifié. La décomposition d'un mélange racinaire ne peut pas être prédite à partir de la décomposition des espèces qui le composent ou des traits du mélange. Les variations de stocks de carbone dans le sol sont expliqués par la quantité et la productivité des racines mais pas par leur qualité ou le turnover. Ces travaux ont révélé la difficulté d'extrapoler les résultats trouvés au niveau de l'espèce, au niveau de communautés in situ pour prédire le fonctionnement de l'écosystème. / The main objective of this thesis is to understand the impact of fine root functional diversity on carbon storage components at different levels of organization. We hypothesized that fine root traits, measured at the species and community levels, influence three major processes of carbon inputs and outputs : root production, respiration and decomposition and thus have consequences on soil carbon stocks. Ours results show that root functional traits are good proxies of processes of decomposition and respiration at the species level. A carbon resource trade-off exist between species characterized by high root tissue density, C/N and lignin/N ratio with a low rate of respiration and decomposition and those characterized by high specific root length and nitrogen content with a rapid metabolism. At the community level, this scheme is not confirmed. Root mixture decomposition is not predicted by decomposition of species composing it or by root traits. Variations of soil carbon stocks are explained by root quantity and productivity but not by their quality or turnover. Those studies revealed the difficulty to scale up results found at the species level to the community level to predict ecosystem functioning.

La respiration est un processus fondamental qui doit être optimisé en réponse aux besoins cellulaires et aux conditions environnementales. Il a été démontré que la localisation subcellulaire dynamique du complexe nitrate réductase (NR) chez la bactérie E. coli est un moyen efficace de contrôler le flux d’électrons au cours la respiration nitrate.Pendant ma thèse, deux questions ont été posées : (i) Quels sont les facteurs moléculaires impliqués dans le mécanisme de localisation de la nitrate réductase ? (ii) Comment rendre compte de l’augmentation du flux d’électron dans la chaîne respiratoire lorsque le complexe est localisé aux pôles de la cellule ?Dans un premier temps, j’ai développé un crible génétique visant à identifier le ou les facteurs impliqués dans l’organisation spatiale de la nitrate réductase. En parallèle, j’ai mis en place une approche d’immunoprécipitation visant à identifier des protéines en interaction avec la NR lorsque celle-ci est localisée aux pôles. Cette approche associée à des expériences de microscopie à fluorescence nous ont permis de démontrer le regroupement de la formiate déshydrogénase FdnGHI avec la NR en condition de respiration nitrate expliquant l’importance de l’organisation spatiale de la NR pour l’efficacité de la chaîne respiratoire. Dans cet interactome, nous avons également identifié des acteurs impliqués dans l’homéostasie du NO qui est une molécule toxique dont la production est associée à l’optimisation de la respiration nitrate. Ainsi, le regroupement d’acteurs impliqués dans la chaîne de transfert d’électrons et dans l’homéostasie du NO semble être la clef du maintien de l’équilibre efficacité et toxicité. / Respiration is a fundamental process that must be optimized in response to metabolic demand and environmental changes. It has recently been demonstrated that dynamic subcellular localization of the respiratory complex nitrate reductase in E. coli is an efficient mean to control the electron flux during nitrate respiration, known to be crucial for gut colonization by enterobacteria when inflammation occurs.During my PhD, I focused on two key questions: (i) What are the molecular factors involved in the localization mechanism of nitrate reductase? (ii) How to account for the increase of the electron flux in the respiratory chain when the complex is localized at the cell poles? First, I designed a genetic screen aiming at identifying the underlying factor(s) involved in the spatial organization of nitrate reductase. Concomitantly, I implemented an immunoprecipitation approach to identify protein interacting with nitrate reductase when localized at the poles. Using this approach and fluorescence microscopy, we demonstrated the clustering of formate dehydrogenase FdnGHI and nitrate reductase at the poles under nitrate respiring condition. These data provide a mechanistic explanation on the importance of subcellular organization towards nitrate respiration efficiency. In this specific interactome of nitrate respiring condition, we also identified factors involved in NO homeostasis, a toxic compound resulting from the maximization of nitrate respiration. Hence, the clustering of actors involved in electron transfer and NO homeostasis seems to be the key to maintain the balance between maximizing electron flux and the resulting toxicity.

This study investigated whether or not a relationship exists between ventilation and oxygen uptake at 40% and 85% of V02 peak intensity in 30 upper body fit and 30 unfit 18- 35-year-old women. The correlations between ventilation and oxygen uptake at 40% of peak intensity for the fit group (r = -.51) and the unfit group (r = -.48) were modestly negative. At 85% intensity the relationship between ventilation and oxygen uptake in the two groups was -.44 and -.66, respectively. The lower correlations between ventilation and oxygen uptake observed at the 85% level of peak intensity among the unfit group could be due to a lower ventilatory threshold (66% = fit; 49% = unfit), lesser local muscle changes, along with reduced lactate and C02 management; all of which would be improved with training.

Projected climate change may alter soil carbon dioxide (CO2) efflux from terrestrial ecosystems; yet disentangling effect of plant species from climate drivers remains a key challenge. We explored the effects of the dominant plant species, warming, and precipitation distribution on soil CO2 efflux, its underlying components, and mycorrhizal abundance in southern post oak savannah. Post oak savannah in the south-central US are dominated by three contrasting plant functional types: Schizachyrium scoparium (Michx.) Nash. (little bluestem) a C4 grass, Quercus stellata Wangenh.(post oak)a C3 deciduous tree, and Juniperus virginiana L. (eastern redcedar) a C3 evergreen tree. Monocultures and tree-grass plots were warmed using infrared heaters and precipitation events were manipulated to intensify summer drought and augment cool season precipitation. Soil CO2 efflux, the root, bacterial and hyphal components of CO2 efflux, and mycorrhizal abundance were measured. Soil CO2 efflux varied with seasonal changes in soil VWC and temperature, with higher soil CO2 efflux rates in the spring and lower rates in both the cooler winter season and at the end of the dry summer period. There was no relationship between root length density or root mass density and soil CO2 efflux during the short term precipitation distribution campaigns. Partitioning of root, fungal, and bacterial component contribution to soil CO2 efflux indicated a substantial contribution of bacterial respiration to soil CO2 efflux within this system. There was no relationship between microbial biomass [microbial dissolved organic carbon (DOC)] and soil CO2 efflux, or root length (or mass) density and microbial biomass. This suggests that species and climatic effects on root and microbial activity drive soil CO2 efflux. As plant species within this system differed in their association with mycorrhizal fungi and had a strong effect on the individual components of soil CO2 efflux, we conclude that shifts in vegetation cover and growth and the response of vegetation to long term warming and potential future extreme precipitation events (e.g., large preciptation events, prolonged drought) will be major drivers of changes in soil carbon (C) dynamics and associated soil CO2 efflux.

第22回名古屋大学年代測定総合研究センターシンポジウム平成21(2009)年度報告

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Cox11 (cytochrome c oxidase 11) is an ancient and conserved protein family present in most respiring organisms. Studies of several family members, mainly in yeast and bacteria, have revealed that these proteins are in charge of Cu+ delivery to the respiratory complex IV (COX). Absence of Cox11 leads to a non-functional COX complex and a complete respiratory deficiency. Although it is assumed that homologues in other species perform the same function, experimental data supporting this notion are lacking. The aim of this work was to characterize the putative Arabidopsis homologue AtCox11 (encoded by locus At1g02410) and to determine its functions. Comparison of AtCox11 with the well-studied ScCox11 in yeast revealed that the two proteins share high similarity in their sequences (32% amino acid identity) and in the predicted secondary structures. Surprisingly, despite this high similarity AtCox11 proved not to be able to functionally replace the yeast protein in ΔSccox11 yeast deletion strains. As presumed, AtCox11 is localized to mitochondria, probably tethered to the inner mitochondrial membrane with its C-terminus facing the intermembrane space. The subsequent experimental work addressed the functions of AtCox11. To this end AtCOX11 knock-down (KD) and overexpression lines (OE) were generated and their impact on plant phenotype was investigated. KD lines that were obtained by artificial micro RNA technology, possess approximately 30% of the WT AtCOX11 mRNA levels. Overexpression resulting in 4-6 fold higher AtCOX11 mRNA levels, was achieved by placing AtCOX11 under the control of the 35S promoter. Remarkably, both KD and OE plants had reduced levels of COX complex activity (~45% and ~80%, respectively) indicating that AtCox11 is, as expected, involved in COX complex assembly. The KD and OE plants exhibited reduced root lengths and pollen germination rates (compared to WT). As both processes are dependent on respiratory energy, these phenotypic changes seemingly result from the reduced COX activity. Interestingly, the short-root phenotype in OE plants was rescued by a surplus of copper in the media, whereas copper deficiency intensified the phenotype. By contrast, KD plants did not respond to changes of the copper concentration. This difference in the copper response between KD and OE plants hints at a different cause for the reduced COX activity. It is proposed that the concentration of AtCox11 in KD plants limits the efficient insertion of Cu+ into COX, independent of the available copper concentration. In OE plants, binding of the limited copper by the high AtCox11 level may lead to a copper deficiency for the copper chaperone AtHcc1 that is required to load copper to subunit AtCoxII. Indeed, addition of copper to the media was able to rescue the phenotype. In line with these data, the analysis of the expression pattern of AtCOX11 revealed that it is expressed in tissues which require substantial mitochondrial and COX biogenesis to sustain their high metabolic and/or cell division rates. Furthermore AtCOX11 was shown to be up-regulated as part of the plant’s response to increased oxidative stress induced by the addition to the plant media of peroxides or inhibitors of respiratory complexes. The up-regulation of AtCOX11 in response to oxidative stress was corroborated with publicly available RNA microarray data and analysis of the AtCOX11 promoter, which revealed the presence of a number of potential oxidative stress responsive elements. Taken together, the experimental results presented in this thesis support the conclusion that AtCox11 is a member of the conserved Cox11 protein family. Most probably, this mitochondrial protein participates in the assembly of the COX complex by inserting Cu+ into the CuB center of the AtCoxI subunit. In addition to this expected role, the data indicate that AtCox11 might participate in cellular oxidative stress response and defense via a yet unknown mechanism.

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