Cette thèse décrit l’exploration de techniques de catalyse et de flux continu pour faciliter la fermeture de molécules cycliques tendues. En premier lieu, un catalyseur de palladium permet de fermer un hétérocycle aromatique tendu, la structure benzo[a]imidazo[2,1,5-c,d]indolizine.16 La tension de cycle contribue à donner au système  hautement délocalisé de ces molécules des propriétés photophysiques intéressantes, différentes de celles de leurs analogues non tendus.21,33 Il a été démontré que leur longueur d’onde d’émission maximale peut être modulée de manière prévisible en modifiant les groupes fonctionnels conjugués au système aromatique. Le potentiel d’application en biochimie de ces fluorophores à déplacement de Stokes élevé a été exploré en étiquetant deux protéines en milieu biocompatible. En second lieu, une version catalytique de la cycloaddition de Simmons-Smith a été optimisée. Dans cette transformation, une quantité catalytique d’un sel de zinc permet de former un carbénoïde hautement réactif à partir d’un composé aryldiazométhane. Ce carbénoïde peut réagir avec une grande variété d’alcènes pour former les arylcyclopropanes correspondants. Un catalyseur modifié permet même à la réaction d’avoir lieu en présence d’alcools primaires. Enfin, la manipulation des composés aryldiazométhanes utilisés dans la cyclopropanation décrite ci-haut peut s’avérer risquée vu la toxicité et l’instabilité de ces composés. Pour minimiser ces risques, une méthode pour générer et purifier ces réactifs en flux continu a été développée. De cette manière, le composé dangereux est consommé à mesure qu’il est généré, dans un système fermé. Un large éventail d’aryldiazométhanes peut être produit en solution dans un solvant non-coordinant. La compatibilité de ces solutions avec des systèmes catalytiques requérant des réactifs propres et secs a été démontrée. / This thesis describes the exploration of catalysis and continuous flow techniques towards the formation of strained cyclic molecules. First, a palladium catalyst enables the ring closure of a strained aromatic heterocycle, the benzo[a]imidazo[2,1,5-c,d]indolizine.16 Ring strain gives these molecule’s highly delocalized  system interesting photophysical properties that differ from those of unstrained analogs.21,33 Their emissive properties can be predictably modulated by modifying functional groups conjugated to the aromatic core. These high Stokes-shift fluorophores’ application potential in biochemistry was explored by the biocatalyzed labelling of two proteins in biocompatible media. Second, a catalytic version of the Simmons-Smith cycloaddition was optimized. In this transformation, a catalytic amount of zinc salt allows the formation of a highly reactive carbenoid from an aryldiazomethane precursor. This intermediate can then react with a variety of alkenes, forming the corresponding arylcyclopropanes. A modified catalyst even enables the reaction to proceed in the presence of a primary alcohol group. Finally, the handling of the aryldiazomethane precursors used in the above reaction can be hazardous due to these compound’s instability and toxicity. To minimise these risks, a method to synthesise and purify these reagents in continuous flow was developed. This way, the dangerous chemical is consumed as it is generated, in a closed system. A large array of aryldiazomethane solutions in a non-coordinating solvent can be produced. These solutions’ compatibility with sensitive catalytic systems requiring clean and dry reagents was demonstrated.

Les taillis à courte rotation (TCR) permettent de produire de la biomasse ligneuse, alternative aux combustibles fossiles. L'intégration d’espèces d’arbres fixateurs d'azote atmosphérique en mélange avec les essences à croissance rapide peut être un moyen de limiter le risque d'appauvrissement des sols dans les TCR. Le succès d'un tel mélange va dépendre des interactions entre les deux espèces : facilitation, compétition ou complémentarité pour la lumière et les ressources du sol (eau, nutriments). L’objectif de cette étude était d’évaluer l’impact du mélange peuplier / robinier, sur la croissance, la production de biomasse et l'acquisition de l'azote d'une plantation à courte rotation. Un dispositif instrumenté composé de monocultures de peuplier et robinier et le mélange des deux espèces a été étudié pendant quatre ans. La quantification répétée des biomasses aériennes et souterraines associée au suivi des dimensions des arbres a permis de mettre en évidence que la présence des robiniers n'avait pas d'influence sur la croissance, la production et l'allocation de biomasse des peupliers à l'échelle de l'arbre comme à l'échelle du peuplement. En revanche, les robiniers souffraient de la compétition interspécifique : mortalité augmentée, croissance et production de biomasse diminuée. De plus, une approche isotopique (15N) couplée à l'analyse des minéralomasses a montré que les teneurs en azote des robiniers dans le mélange étaient plus faibles que dans la monoculture dues à une fixation de l'azote atmosphérique réduite. Le stock global d'azote dans le milieu était comparable dans les mélanges et les monocultures de chaque espèce. Le mélange n'a pas montré d'intérêt sur la période d'étude en raison notamment des conditions pédoclimatiques inappropriées (en particulier pour le robinier) et d'une incompatibilité entre les deux espèces sur ce site / Biomass from short rotation coppice (SRC) plantations may help reducing fossil fuel consumption. The development of mixed-species plantations, introducing a nitrogen-fixing species could be a solution to reduce the risk of fertility decline in SRC. Nevertheless, the success or failure of the mixture will depend on the competition and complementarity processes, for light and soil resources (water and nutrients), between both species. The objectives of this study were to determine the impact of a mixture of poplar and black locust, on growth, biomass production and nitrogen uptake in the plantation. Instrumented monocultures and mixed plantations of both species have been studied during four years. Repeated above-and belowground biomass estimations associated with tree dimension monitoring have shown that the presence of black locust affected neither growth, nor biomass production and allocation of poplar trees both at tree and plot level. On the other hand, the black locusts trees suffered from interspecific competition: high mortality, decrease in growth and biomass production. Moreover, an isotopic approach (15N) coupled with mineralomass analyses allowed to highlight that nitrogen concentration in black locust trees in the mixture was lower than in the monoculture due to a reduction of the percentage of nitrogen derived from atmospheric fixation. The total nitrogen contents were close in the mixture and in the monocultures of each species. No advantage of the mixture was found during the study period because of inappropriate pedoclimatic conditions (especially for the black locust) and incompatibility between both species on this site

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Les travaux décrits dans ce mémoire ont pour objectif d'imager des cellules par des techniques d'imagerie complémentaires à la spectroscopie de fluorescence : la micro-spectroscopie Raman et l'imagerie NanoSIMS. Le présent manuscrit se divise en quatre chapitres et présente les différents aspects menant à la mise en place de ce projet. Le premier chapitre du manuscrit a pour but de positionner le projet d'un point de vue biologique. Ce chapitre présente l'organite que nous souhaitions marquer, le nucléole, et la façon dont nous avons procédé à sa localisation par l'intermédiaire de sondes moléculaires. Le marquage que nous avons choisi est un immuno-marquage indirect faisant intervenir deux anticorps : un anticorps primaire spécifique à la nucléophosmine, protéine majoritairement présente dans le nucléole et un anticorps secondaire, reconnaissant l'anticorps primaire, marqué par une sonde moléculaire d'intérêt. Ce chapitre a également permis de montrer par une analyse en immunofluorescence l'absence d'interférence des sondes moléculaires dans le cadre de ce marquage. Le second chapitre se focalise sur la synthèse des sondes moléculaires permettant le marquage des anticorps secondaires. Les sondes envisagées pour ce marquage possèdent un groupement ester de succinimide réactif capable de "s'accrocher" de manière covalente aux fonctions amines de l'anticorps secondaire et un ou plusieurs groupements fonctionnels visible par la technique d'imagerie voulue. Trois catégories de sondes ont été préparées et dépendent de la technique d'imagerie employée. Les sondes Raman comportant une triple liaison carbone-carbone visible par cette technique, les sondes NanoSIMS dont l'acquisition d'image sera possible par les halogènes présents dans la structure et les sondes bimodales comportant les deux éléments dans la même structure. Les sondes bimodales sont obtenues par le couplage pallado-catalysé de Sonogashira. Dans la dernière partie du chapitre, une nouvelle série de sonde a été envisagée dans le cadre d'une application future : le marquage de l'ATP-ϒ-SH grâce à une fonction mésylate. Les deux derniers chapitres ont pour but de mettre en application tout ce qui a été présenté dans les chapitres précédents. Les deux techniques employées permettent d'accéder à des types d'informations différentes : la spectroscopie Raman donne accès aux modes de vibrations d'une molécule tandis que l'imagerie NanoSIMS permet d'obtenir des informations élémentaires et isotopiques. Nous présenterons le cheminement suivi pour imager des cellules via leurs constituants par micro-spectroscopie Raman et imagerie NanoSIMS via les sondes moléculaires introduites. / Life sciences imaging are widely used for different applications, they are interested in medical diagnosis as well as basic research. In cells biology, fluorescence microscopy is mainly used for organelles observation at sub-cellular scale. However, techniques based on fluorescence phenomena are limited by some drawbacks like technical resolution, fluorescent dye degradation and the number of channels, which can be visualized. In this context, the exploration and the development of new way for image acquisition are considered as an experimental and technical scientific challenge. Furthermore, it can lead to complementary technique to fluorescence microscopy.This PhD thesis is a life science imaging project development and application allowing image acquisition base on molecular vibrations phenomena and elementary analysis in cells. Two techniques have been chosen in relation to both specificity: micro Raman spectroscopy and NanoSIMS imaging. Micro Raman spectroscopy allows the observation of molecular vibration mode at micron scale and NanoSIMS leads to elementary and isotopic sample information at sub-micronic scale. Combination of both techniques will lead to multi-scale and multi-modal imaging of biological samples. Molecular probes designing and synthesis for both techniques were used to visualize an organelle inside the nucleus: the nucleolus. Nucleolus has a key role in ribosomal RNA transcription and researchers shows some interest in the study of this organelle for his multifunctional role like ribosome biogenesis and nuclear organization. An immuno-labelling method combine with the introduction of molecular probes will allow nucleolus imaging by micro-Raman spectroscopy and NanoSIMS spectrometry. This immuno-labelling is specific to a phosphoprotein mainly localized inside the nucleolus: the nucleophosmin (NPM). In this project, the introduction of molecular probes in an immuno-labelling will act as a Raman Tag or a NanoSIMS tag for NPM's nucleolus observation and studies.This work at the interface between different fields: chemistry, biology and physics shows all the aspect of this project starting from molecular probes synthesis, immuno-labelling methods uses to direct application of both Raman and NanoSIMS techniques.

Thesis (Ph.D. (Criminology)) -- University of Limpopo, 2016 / Community involvement in ex-offenders’ re-integration is an important issue in efforts to reduce recidivism and to control overcrowding in our correctional facilities. Crime is a social problem which requires society to come together to fight against. The Department of Correctional Services (DCS) introduced Community Corrections Forums (CCFs) with the aim of controlling re-offending by ex-offenders. CCFs were established in each region to bring the community, business and stakeholders together to facilitate rehabilitation and re-integration. This study was conducted in the Limpopo Province, in Vhembe District Municipality within four local municipalities, namely Musina, Makhado, Mutale and Thulamela. A total number of 30 participants were interviewed and all were members of Community Corrections Forums. This was necessitated by the fact that Musina is a very small area which compelled the Department of Correctional Services to combine the two (Musina and Makhado) into one social re-integration entity. This is a qualitative research study where participants were selected through the use of purposive sampling. Participants were selected based on the value they would add to this study in order to achieve objectives. The data collection method of this study was the focus group which comprised by 3 groups of 10 participants each. Thulamela and Mutale local municipalities formed a group with (10) participants each whereas Musina (2) and Makhado (8) formed another. Results indicate that the current situation is not conducive for re-integration to be successful. CCF members raised many factors that need serious redress, namely offenders’ discrimination, lack of forgiveness by members of the community which is fuelled by lack of community awareness due to lack of education of communities by the Department of Correctional Services on reduce space of ex-offenders’ re-integration. The relationship between CCF and DCS raises many questions based on the results. Without a good working relationship between these two offices, the study observed that there would be no successful re-integration policy. Theoretical implications of the investigation based on labelling theory are discussed, together with practical applications for ex-offenders. The latter face daunting barriers to successful re-integration. Successful re-entry requires strong community support networks and comprehensive services by DCS, both of which are lacking in Vhembe District.

In this doctoral thesis, the design of algorithms enabling the implementation of a fully automatic system for vertebrae segmentation in 3D computed tomography (CT) image data of possibly incomplete spines, in patients with bone metastases and vertebral compressions is presented. The proposed algorithm consists of several fundamental problems: spine detection and its axis determination, individual vertebra localization and identification (labeling), and finally, precise segmentation of vertebrae. The detection of the spine, specifically identifying its ends, and determining the course of the spinal canal, combines several advanced methods, including deep learning-based approaches. A novel growing circle method has been designed for tracing the spinal cord canal. Further, the innovative spatially variant filtering of brightness profiles along the spine axis leading to intervertebral disc localization has been proposed and implemented. The discs thus obtained are subsequently identified via comparing the tested vertebrae and model of vertebrae provided by a machine-learning process and optimized by dynamic programming. The final vertebrae segmentation is provided by the deformation of the complete-spine intensity model, utilizing a proposed multilevel registration technique. The complete proposed algorithm has been validated on testing databases, including also publicly available datasets. This way, it has been proven that the newly proposed algorithms provide results at least comparable to other author’s algorithms, and in some cases, even better. The main strengths of the algorithms lie in high reliability of the results and in the robustness to even strongly distorted vertebrae of oncological patients and to the occurrence of artifacts in data; moreover, they are capable of identifying the vertebra labels even in incomplete spinal CT scans. The strength is also in the complete automation of the processing and in its relatively low computational complexity enabling implementation on standard PC hardware. The system for fully automatic localization and labeling of distorted vertebrae in possibly incomplete spinal CT data is presented in this doctoral thesis. The design of algorithms enabling the implementation utilizes several novel approaches, which were presented at international conferences and published in the journal Jakubicek et al. (2020). Based on the results of the experimental validation, the proposed algorithms seem to be routinely usable and capable of providing fully acceptable input data (identified and precisely segmented vertebrae) as needed in the subsequent automatic spine bone lesion analysis.

Les composés deutérés sont d’un intérêt grandissant dans des domaines variés. Par exemple, en pharmacologie, l'échange H/D peut améliorer les propriétés pharmacocinétiques de certains médicaments ou réduire leur toxicité. Les composés deuterés peuvent également être utilisés comme étalons internes en spectroscopie de masse. Il est donc important de trouver un moyen simple et sélectif d'échanger l'hydrogène avec le deutérium sur des molécules d’intérêt biologique. Les nanoparticules, de ruthénium en particulier, se sont révélées être des systèmes efficaces pour catalyser cet échange. Cependant, étant très actives, elles conduisent souvent à la réduction de substrats aromatiques. L'objectif principal du doctorat est l’élaboration de nouvelles nanoparticules permettant de contrôler la réactivité en échange isotopique H/D. Nous avons d’abord synthétisé des alliages Ru-Pt afin d’introduire du platine, moins actif en échange H/D, et donc empoisonner la surface du Ru. Nous avons montré qu’en changeant le précurseur de platine, on pouvait changer la distribution atomique de surface, et ainsi moduler la réactivité des nanoparticules. Nous avons finalement synthétisé des nanoparticules de nickel et d'iridium. Ces nanoparticules se sont avérées être des catalyseurs efficaces pour l'échange H/D, sans réduction de fonctions aromatiques. De plus, des sélectivités différentes ont été obtenues en fonction du métal utilisé. / Deuterated compounds are molecules of great interest in various fields. In pharmacology, the H/D exchange can improve the pharmacokinetic properties of some drugs or reduce their toxicity. In addition, deuterium-labelled compounds can be used as internal standards for mass spectroscopy, or as tracers for the understanding of different reaction mechanisms. Therefore, it is important to find a way to exchange hydrogen with deuterium in a simple, selective and efficient way. The main goal of the PhD project is the synthesis of novel nanoparticles for isotopic exchange (H/D). Metal nanoparticles and more particularly ruthenium nanoparticles, has shown their efficiency to catalyze this exchange. However, ruthenium nanoparticles are very active in arene hydrogenation, and often lead to the reduction of aromatic substrates. In a second part of the work, we synthesized Ru-Pt alloys in an attempt to passivate the Ru surface with platinum, which is less-active in H/D exchange. We have shown that by changing the platinum precursor, we can change the atomic distribution of the surface, and thus we were able to modulate the reactivity of nanoparticles. We finally synthesized Ni and Ir nanoparticles. These nanoparticles have proven to be efficient catalysts for H/D exchange, without reducing aromatic functions. In addition, different selectivity was obtained depending on the metal used.

Countless electron transport/transfer (ET) processes occur in living organisms every day. Therefore, their study is a crucial field of modern structural and functional proteomics. In many cases model proteins like azurin from P. aeruginosa are utilised in experiments. This blue copper protein is favoured due to a characteristic absorbance maximum at 630 nm in Cu(II) redox state of the central Cu atom. During its oxidation to Cu(I) state the A630 value decreases allowing UV-Vis detection of ET reaction progress. We have introduced a structural photoinducible analogue of canonical amino acid Met - L-2-amino-5,5-azihexanoic acid (photo-Met) - into azurin structure to study oligomerization in solution via photo-induced cross-linking (PIXL). Using previously optimised protocols for recombinant expression in E. coli B834 we have inserted photo-Met into azurin moieties: wild type azurin and Az2W mutant where two adjacent W residues with confirmed role in electron hopping across protein-protein interface are present. The incorporation percentage of photo-Met in analysed samples was determined after SDS-PAGE and in-gel protease digestion via MALDI-TOF MS. PIXL was employed to study azurin-azurin interaction and oligomerization under different total concentrations of protein (in range of 15-300 µM). The...

The following thesis "Labelling as a part of a pedagogical discourse at a secondary pedagogical school" discusses the labelling process within the pedagogical discourse. The thesis aims to identify discursive practices used by teachers during the labelling process when evaluating their students, as well as to present different kinds of labels and areas that are considered either an asset or are deemed undesirable by teachers. Consequently, the thesis is of a theoretical-empirical nature. The theoretical part focuses on symbolic interactionism, labelling theory, and possible forms of pedagogical discourse. Furthermore, this part covers possible errors in social perception and areas that are most likely to result in a label being assigned to a student. In addition, considerable attention is paid to the typology of teacher personalities, school and class environments, or the impacts of the "hidden" curriculum. The empirical part introduces readers to qualitative research carried out in the form of participant observation at a pedagogical high school. Based on the research analysis the thesis proceeds to describe teachers labelling behaviour and presents a list of possible labels, including their differences. Key words: labelling, social deviation, social perception, education discource, hidden...

Cette thèse porte sur la notion de certification locale, un sujet central en décision distribuée, un domaine du calcul distribué. Le mécanisme de la décision distribuée consiste, pour les nœuds d'un réseau, à décider de manière distribuée si le réseau est dans une configuration correcte ou non, selon un certain prédicat. Cette décision est dite locale, car les nœuds du réseau ne peuvent communiquer qu'avec leurs voisins. Après avoir communiqué, chaque nœud prend une décision, exprimant si le réseau est correct ou non localement, c'est-à-dire correct étant donné l'information partielle récoltée jusque-là. Le réseau est déclaré correct globalement s'il est déclaré correct localement par tous les nœuds.Du fait de la contrainte de localité, peu de prédicats peuvent être vérifiés de cette manière. La certification locale est un moyen de contourner cette difficulté, et permet de décider tous les prédicats. C'est un mécanisme qui consiste à étiqueter les nœuds du réseau avec ce que l'on appelle des certificats, qui peuvent être vérifiés localement par un algorithme distribué. Un schéma de certification locale est correct si seuls les réseaux dans une configuration correcte peuvent être certifiés. L'idée de la certification locale est non seulement séduisante d'un point de vue théorique, comme une forme de non-déterminisme distribué, mais c'est surtout un concept très utile pour l'étude des algorithmes tolérants aux pannes, où une étape-clé consiste à vérifier l'état du réseau en se basant sur des informations stockées par les nœuds.Cette thèse porte sur quatre aspects de la certification locale : la sensibilité aux erreurs, l'uniformité, la redondance et l'interactivité. L'étude de ces quatre sujets est motivée par une question essentielle : comment réduire les ressources nécessaires à la certification et/ou permettre une meilleure tolérance aux pannes? Pour aborder cette question, il est nécessaire de comprendre le mécanisme de certification en profondeur. Dans cette optique, dans cette thèse, nous apportons des réponses aux questions suivantes. À quel point les certificats doivent-ils être redondants, pour assurer une certification correcte? Les schémas de certification classiques sont-ils robustes à un changement de la condition de correction? Le fait d'introduire de l'interactivité dans le processus change-t-il la complexité de la certification? / This dissertation is about local certification, a central topic in distributed decision, a subfield of distributed computing. The distributed decision mechanism consists, for the nodes of a network, in deciding in a distributed manner whether the network is in a proper configuration or not, with respect to some fixed predicate. This decision is said to be local because the nodes of the network can communicate only with their neighbours. After communication, every node outputs a decision, stating whether the network is locally correct, that is, correct given the partial information gathered so far by this node. The network is declared to be globally correct, if and only if, it is declared to be locally correct by every node.Most predicates cannot be verified by this type of computation, due to the locality constraint. Local certification is a mechanism that enables to circumvent this difficulty, and to check any property. It consists in providing the nodes of the network with labels, called certificates, that can be verified locally by a distributed algorithm. A local certification scheme is correct if only the networks that satisfy the predicate can be certified. In addition to its theoretical appeal, as a form of distributed non-determinism, the concept of local certification is especially relevant in the study of fault-tolerant distributed algorithms, where a key step consists in checking the status of the network, based on information stored at the nodes.This dissertation deals with four aspects of local certification: error-sensitivity, uniformity, redundancy, and interactivity. The study of these four topics is motivated by the same essential question: How to reduce the resources needed for certification, and/or ensure a better fault-tolerance? In order to tackle this question we have to understand fundamental properties of certification. In particular, in this dissertation we answer questions such as: How redundant the certificates need to be for a proper certification? Are the classic certification protocols robust to a strengthening of the acceptance condition? and, How does introducing interactivity in the process changes the complexity of certification?