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Méthodologie et essai de constitution de terroirs géochimiques : application aux céramiques communes d'ateliers du Nord de la Gaule
No full textLe sujet de cette thèse évalue la possibilité de délimiter des terroirs géochimiques sur le territoire de l’actuelle Belgique, à partir de l’étude géochimique des formations argileuses. Ce questionnement trouve son origine dans la problématique de la détermination de provenance des céramiques communes gallo-romaines. La comparaison des compositions géochimiques d’argiles sensu lato et de céramiques communes provenant de sites de consommation mettrait en évidence les plus fortes ressemblances, ce qui désignerait la région d’origine : un des terroirs géochimiques. Pour démêler la possibilité de délimiter des terroirs géochimiques, les trois autres problématiques suivantes ont dû être résolues. D’une part, distinguer les différentes formations argileuses à potentiel céramique (utilisation au tour) entre elles sur base de leur composition géochimique. Ceci a pu être démontré par l’analyse des compositions géochimiques pour sept formations argileuses dont le potentiel céramiques avait été évalué auparavant sur un ensemble de quinze formations échantillonnées ; Ensuite, identifier la matière première de groupes de référence céramique de sites de production, ce qui n’avait, jusqu’à ce jour, pu être fait. Trois ateliers de potiers de la Cité des Tongres (Amay, Liberchies et Tirlemont), fabriquant de la céramique commune et situés dans des contextes géologiques différents, ont été choisis pour faire l’objet d’une caractérisation archéométrique poussée de leur production. Les résultats montrent que dans chaque officine il y a eu mélange de deux types d’argile pour la fabrication des pâtes : une des argiles utilisées est à chaque fois une argile de type smectitique, plutôt riche en fer (Fe2O3≥ 3 %) et l’autre argile est une argile de type kaolinitique, assez pauvre en fer (Fe2O3≤ 3 %). Enfin, distinguer les productions d'ateliers exploitant des formations argileuses différentes. Ceci a pu être démontré sur la base de l’étude des productions des trois officines étudiées. Les résultats montrent que les pressions socio-économiques semblent imprimer leur dictat sur la production des potiers mais ces derniers y intègrent la notion de coût bien sûr et font les choix technologiques qui s’imposent, en fonction des ressources locales et des possibilités de ressources extra-locales. Les résultats montrent également que l’idée de délimiter des terroirs géochimiques sur la base des formations argileuses doit être repoussée. En lieu et place de terroirs géochimiques, il pourrait être possible de délimiter des terroirs géo-archéologiques ; en effet, les ateliers peuvent être discriminés et cette discrimination tient dans l’utilisation de ressources distinctes pour chaque atelier ET de « recettes » différentes. C’est donc la rencontre des ressources géologiques et des hommes qui crée le terroir. Un terroir archéo-géologique rassemble des ateliers produisant des céramiques à partir de ressources identiques (locales et extra-locales) ET de « recettes » identiques.(DOCSC04) -- FUNDP, 201
Density functional theory simulation and interpretation of inelastic electron tunneling spectra of molecular junctions: from model to complex systems.
No full textUsing molecules to mimic the behavior and the functions of electronic components offers a broad potential towards the miniaturization of the electronic devices. The integration of such molecular components into nanoelectronic devices requires however a careful design to combine with their synthesis, preparation, and characterization. Understanding the physical phenomena at the nanoscale is another challenge to meet, where numerical simulations are very useful. The Inelastic Electron Tunneling (IET) spectroscopy is one of these nanoscale-oriented techniques. It can probe the structure of single molecules sandwiched between metallic electrodes by detecting the inelastic interactions between the tunneling electrons and the vibrational modes of the molecule. This thesis deals with the simulation of IET spectra of these molecular junctions by relying on a Green’s function approach combined with quantum chemistry calculations performed at the density functional theory level of approximation and with the analysis of the vibrational signatures in order to unravel their structural and electronic characteristics. In particular, this thesis considers systems of increasing complexity, starting from model dithiol-terminated compounds and going towards molecular switches, π-conjugated oligomers, and fullerene derivatives.(DOCSC02) -- UNamur, 201
Chemistry and Physics of Plasma Polymerization probed by Mass Spectrometry
No full textNowadays, deposition of thin films is one way to completely refashion our well-known glasses, metals and semiconductors. Among deposition techniques, the ones using plasma – the fourth state of matter or the ionized gas – have many advantages. The deposited coating is tightly adherent to its substrate, covers it completely and can have a large diversity of tunable properties. Plasma polymerization is one of them, allowing the thin film production of plastic, or polymeric, material. The present work investigated the low-pressure plasma polymerization in a radio-frequency reactor with planar inductive power coupling. The monomers studied were styrene (C8H8), benzene (C6H6), ethylene (C2H4) and acetylene (C2H2), which are pure hydrocarbons, but also methyl methacrylate (C5H8O2 - MMA) which contains oxygen. The neutral by-products of their plasmas were investigated by mass spectrometry (MS) downstream of the discharge. In the case of styrene and MMA, the elemental composition of the plasma-deposited polymers was measured by X-Ray Photoeletron Spectroscopy (XPS) and the deposition rate by contact profilometry. The main results of the thesis are the following. • A systematic approach based on low electron impact energy and Threshold Ionization Mass Spectrometry (TIMS) allowed an extensive species identification of the by-products. To explain the many new species detected, light-weighted carbon containing radicals with low hydrogen content are proposed as intermediates of reaction. In the case of MMA, the dominating species suggested that oxygen containing radicals are not likely to participate to recombination reactions. • In addition, the partial pressures of the dominant species were quantified by MS in the discharges of styrene, benzene, ethylene and acetylene. Varying the plasma power revealed a systematic and large content of hydrogen and acetylene in the discharge. Effects due to hydrogen were proposed to explain the lower depletion of ethylene compared to the three other monomers. • Surface characterization of the plasma deposited styrene film revealed an abrupt increase of the deposition rate. The simultaneous occurrence of two phenomena is discussed with the specific planar inductive geometry: a non-linear increase of the coupling efficiency (E-to-H transition) and a sudden pressure drop. • Finally, the study of the MMA discharge pressure has led to the discovery of a method to quantify for the first time the partial flows of plasma pumped by a nitrogen trap. The result is important, giving access to the production rates of the plasma effluents. In summary, the present work has developed a complete methodology to detect and quantify the neutral by-products of plasma polymerization. Its application allowed a deeper insight into the plasma chemistry of hydrocarbons and oxygen containing monomers. It opens the way to correlate this chemistry with the thin plasma polymer films.(DOCSC01) -- UNamur, 201
Analyse d'une méthode originale de repliement de protéines associant le sodium dodécyle sulfate et le 2-méthyle-2,4-pentanediol
No full textCurrently, the investigation of protein refolding processes involves several time-consuming steps that require large amout of protein. In that context, it has been reported that 2-methyl-2,4-pentanediol (MPD) is able to modulate the denaturing properties of sodium dodecyl sulfate (SDS) and to induce the refolding of proteins. Nonethless and even though this cosolvent effect was previously observed on the refolding of several proteins (including the lysozyme, the carbonic anhydrase, and PagP), little is known about the mechanism by which the MPD can turn the unfolding properties of SDS. The general objective of this thesis was therefore to go deeper in the understanding of the related mechanisms. In that context, a 4-steps strategy was developed: (i) the protcol was extended to the trimeric membrane protein Omp2a in order to demonstrate the transferability of the method to a multimeric protein and determine the optimal detergent/cosolvant ratio. (ii) The combination of experimental (biophysic spectroscopies) and theoretical (molecular dynamics) outputs gives us the opportunity to describe the SDS-induced unfolding states of model peptides. (iii) Then, the key role of MPD to induce the SDS micelle dissociation was unveiled by dynamic light scattering and molecular dynamics simulations. (iv) Finally, the refolding of model peptides was investigated in the presence of the detergent and the cosolvent.La compréhension du phénomène de repliement constitue un défi majeur en biochimie structurale et en biophysique des protéines: la connaissance des mécanismes par lesquels les protéines adoptent une structure 3D particulière peut aider à comprendre et/ou prédire les fonctions des protéines. Il n'existe actuellement aucune méthode générale permettant de replier et caractériser une protéine. En effet, bien que de nombreux protocoles soient référencées dans la littérature, l'étude d'une nouvelle protéine fait, presque toujours, intervenir de nombreuses étapes préliminaires afin d'identifier les conditions permettant son repliement. Dans ce contexte, une méthode originale a récemment été mise en évidence, associant un détergent, le sodium dodécyle sulfate (SDS; connu pour ses propriétés dénaturantes), à un cosolvant, le 2-méthyle-2,4-pentanediol (MPD). Bien que cette combinaison ait préalablement été appliquée avec succès afin d'induire la renaturation de différentes protéines (lysozyme, anhydrase carbonique et PagP), les mécanismes associés sont encore peu connus. L'objectif général de cette thèse est donc d'améliorer les connaissances générales afin de pouvoir optimiser la méthode. Pour cela, une stratégie en quatre temps a été suivie: (i) L'utilisation de l'Omp2a comme modèle de protéine membranaire multimérique a permis d'identifier le rapport de concentrations entre le détergent et le cosolvant menant à un repliement optimal de la protéine. (ii) En combinant des études expérimentales (mesures biophysiques) et théoriques (dynamique moléculaire), il a été possible de caractériser le processus de dénaturation de peptides modèles dans le SDS. (iii) La dissociation de micelles de SDS par le MPD a ensuite été mise en évidence par des mesures en diffusion lumineuse dynamique et des simulations en dynamiques moléculaires. (iv) Finalement, le repliement des peptides solubles en présence du couple SDS/MPD a permis de mettre en évidence le rôle clé du MPD pour protéger les peptides de l'effet dénaturant du SDS et permettre ainsi leur repliement.(DOCSC02) -- FUNDP, 201
Protection of Wistar-Furth rats from post-ischemic acute renal injury: a role for Nitric Oxide and Thromboxane?
No full textWistar-Furth (WF) rats are a strain of rats usually employed in models of full major histocompatibility complex-mismatched kidney transplantation. These were demonstrated to be resistant to several models of chronic kidney disease. In our study, we investigated their potential resistance to a renal ischemia-reperfusion (I/R) injury in comparison to another strain, Wistar-Hanover (WH) rats. Anesthetized male WH and WF rats were submitted to I/R by occlusion of the left renal artery, followed by contralateral nephrectomy. Urine, blood and tissue samples were collected at different time-points post-I/R to evaluate renal function, inflammation and tubular injury along with the determination of the NO synthase expression. In post-ischemic WF rats, the renal function was better preserved than in the post-ischemic WH rats. In addition, the post-ischemic WF rats presented less inflammation than the WH rats. These observations were associated with the maintenance of the nNOS expression along with a lower induction level of iNOS expression in WF rats than in WH rats. Moreover, WF rats excreted also a significant smaller amount of TxB2. In conclusion, our results showed that WF rats were more resistant to an I/R injury than WH rats. This could be explain to the differential regulation of intrarenal NOSs expression as well as the TxA2 production.En guise d’introduction de ce projet de recherches, rappelons que de nos jours, l’insuffisance rénale aiguë (IRA) reste un problème de santé publique majeur corrélé avec des taux de morbidité et de mortalité élevés. En particulier, la nécrose tubulaire aiguë (NTA) consécutive à l’ischémie/reperfusion (I/R) du rein constitue l’une des causes majeures du développement de l’IRA. L’insuffisance rénale aiguë post-ischémique détermine une entité clinique complexe, associant de nombreux médiateurs et processus différents. Ce type de pathologie est à l’origine d’altérations du tissu rénal qui compromettent les mécanismes de régulation homéostasiques. Parmi les multiples intervenants potentiels impliqués dans les diverses étapes qui conditionnent le devenir du rein post-ischémique, on peut citer notamment le monoxyde d’azote (NO) et les métabolites de l’acide arachidonique. Dans ce contexte, l’objectif de ce projet était d’explorer les rôles de certains médiateurs, comme le NO ou le thromboxane, dans le développement de l’IRA post-ischémique. 1°) Dans un premier volet expérimental mis en œuvre afin de rencontrer les objectifs de cette étude, la méthodologie a consisté à induire une insuffisance rénale ischémique chez deux souches de rat, à savoir le rat Wistar Hanovre (WH), communément utilisé en expérimentation animale et le rat Wistar Furth (WF). Notre choix s’est porté sur cette dernière souche car elle se caractérise par la particularité de présenter une résistance naturelle à différents modèles d’insuffisance rénale chronique (IRC) (Sciotti et Galant, 1987 ; Fitzgibbon et al. 1999 ; Erdely et al., 2003, 2004, 2006), notamment associée à un maintien de la production du NO. Les résultats obtenus au cours de cette approche expérimentale indiquent que la concentration plasmatique de la créatinine et l’excrétion urinaire de NGAL, deux biomarqueurs de l’insuffisance rénale, sont moins perturbés en conditions post-ischémiques chez le rat WF que chez le rat WH, ce qui suggère que le rat WF démontre une meilleure capacité à préserver sa fonction rénale dans ce contexte physiopathologique. La comparaison de l’infiltration leucocytaire ainsi que des résultats du dosage du MCP-1, un chémoattractant des macrophages, indique également que l’inflammation est significativement moins sévère chez le rat WF que chez le rat WH. L’évaluation de la fonction tubulaire par la mesure de l’excrétion fractionnelle de sodium (FENa) indique en outre que les rats WF conservent une meilleure capacité à réabsorber le sodium. En revanche, si ce n’est que la protéinurie soit significativement moins élevée chez le rat WF que chez le rat WH, aucune analyse histologique des lésions tissulaires (tubules nécrotiques, kystiques, NAG, NEP) n’a permis de mettre en évidence une protection des atteintes tubulaires chez le rat WF. De même, le dosage du malondialdéhyde, un marqueur de la peroxydation lipidique, n’a pas révélé de différence entre les deux souches. Par ailleurs, chez les rats WF, l’expression de la NO synthase neuronale (nNOS) est maintenue, ce qui n’est pas le cas chez les rats WH, tandis que l’induction de l’expression de la NO synthase inductible (iNOS) est moins sévère que celle observée chez les rats WH après un épisode d’I/R. Enfin, en ce qui concerne le métabolisme de l’acide arachidonique, nos résultats ont montré que, comparativement aux rats WH, les rats WF excrètent une quantité significativement plus faible de thromboxaneB2. En conclusion, nous avons donc démontré une meilleure capacité du rat WF à résister à l’IRA post-ischémique. Cette résistance à l’ischémie des rats WF pourrait s’expliquer, tout au moins en partie, par une régulation différente de l’expression intrarénale des NOS et de la production du thromboxane A2. 2°) La seconde partie du projet a été abordée par une approche interventionnelle dont l’objectif visait à évaluer les effets du naftidrofuryl (Nafronyl oxalate salt, Sigma) dans l’IRA post-ischémique. En effet, l’évaluation des effets potentiels de cet outil pharmacologique nous a semblé pertinente, étant donné que le naftidrofuryl exerce un effet antagoniste sur les récepteurs sérotoninergiques 5-HT2 et le récepteur TP, tout en ayant démontré, dans le cadre d’études in vitro, sa capacité à préserver le métabolisme énergétique de cellules endothéliales soumises à une atteinte hypoxique et de limiter leur activation. Pour évaluer les effets du naftidrofuryl, la méthodologie expérimentale à consisté à prétraiter des rats WH pendant deux jours avec du naftidrofuryl administré dans l’eau de boisson à raison de 30 mg/kg/24h, avant d’effectuer la procédure d’ischémie-reperfusion. Le même traitement a été poursuivi jusqu’au terme du protocole. Les résultats obtenus démontrent que les rats traités au naftidrofuryl présentent un maintien de la créatininémie. De plus, l’évaluation des lésions grâce à un scoring histologique et une mesure de la protéinurie révèle une différence significative entre les deux groupes d’animaux. En effet, le naftidrofuryl semble présenter des effets protecteurs sur l’intégrité du tissu rénal. Par contre, l’infiltration leucocytaire ainsi que la production de MCP-1 restent sensiblement similaires à celles observées chez les animaux non-traités. En conclusion, le traitement au naftidrofuryl permet un maintien de la fonction rénale et une protection des atteintes tubulaires en conditions post-ischémiques.(DOCMED02) -- FUNDP, 201
Le journalisme à l'épreuve des réseaux : étude de l'utilisation des blogs au sein des pratiques journalistiques
No full textThe present thesis analyses the use of blogs by professional journalists in francophone Belgium. It exposes the reasons and logics of the incorporation and legitimization of blogs as professional tools inside the journalism sector. The central question of this sociological research is the following : does journalistic blogging constitute a mere transposition of the journalistic work to an additional medium, or does it lead specific types of practices inside the field of journalism ? In this thesis, it appears that the main values of blogging (autonomy, transparency and participation) are also defended by journalists-bloggers. The thesis shows how these journalists-bloggers intend to combine the ideology of professional journalism with the values of the "network society".(DOCSESG02) -- UNamur, 201
RNA Polymerase II Carboxy-Terminal Domain Serine 2 phosphorylation: a role in Nucleosome Depleted Regions establishment on specific genes.
No full textThe RNA Polymerase II is a macromolecular complex composed of 12 subunits. Its biggest subunit, Rpb1, exhibits a peculiar domain on its carboxy-terminal region named CTD. It is composed of the highly conserved repeat of the heptapeptid Y1S2P3T4S5P6S7 repeated 26, 29 and 52 times in S. cerevisiae, S. pombe and mammals respectively. The CTD follows a pattern of phosphorylation-dephosphorylation in the course of gene transcription. The serine in position 5 (of every heptapeptid repetition) is phosphorylated (S5P) close to the promoter region while the serine in position 2 is phosphorylated (S2P) next to the 3’ of transcribed regions. This phosphorylation combination both reinforces and restricts the recruitment of proteins required for mRNA maturation. Indeed, under certain states of phosphorylation, the CTD serves as a docking platform for capping and splicing enzymes or poly-adenylation factors. It was also later shown that the phosphorylated CTD recruits chromatin modifiers. Transcription occurs through nucleosomes, the base unit of chromatin. One nucleosome is formed of a heterodimer of histones H2A and H2B and a tetramer of histones H3 and H4 surrounded by 147 base pairs of DNA. The histones can be moved, replaced, evicted or modified in a covalent way. Many enzymes are involved in such active processes. The nucleosome occupancy is not homogeneous across the genome. Some regions are depleted in nucleosomes and hence called Nucleosome Depleted Region (NDR). Their formation is an ATP-consuming active process and requires chromatin remodelers. Those NDRs are often located in genes promoter regions and make the DNA sequence accessible to initiate transcription. Their presence/absence is thus an important layer of transcriptional regulation. Surprisingly, in S. pombe, a subset of genes shows an unexpected pattern of CTD phosphorylation: S2P reaches high level in 5' regions where it is usually low. Strikingly, the complete absence of S2P has only a minor impact on genome expression. However, S2P is critical for sexual differentiation in fission yeast. Indeed, in a S2A mutant (where every serine in position 2 of the CTD are replaced by alanine) or in a S2 kinase mutant, the ste11 expression (master regulator of sexual differentiation) is severely impaired making those strains sterile. This lowered expression correlates with a severe drop in Pol II occupancy along the ste11 locus. Here we show by a genome-wide nucleosome mapping study that S2P is required in S. pombe for the proper establishment of NDR in promoter region in a subset of genes with early S2P. We investigated the mechanical of this process through two model genes in S. pombe: ste11 and inv1 (model gene for sugar metabolism). We also broadened the scope of this work with another model gene in a different model organism: IME1 (key regulator of meiosis) in S. cerevisiae. We propose the following model of a new kind of transcriptional regulation: S2P prevents the binding of histone deacetylases in the promoter region of genes with early S2P by interfering with S5P. It results in hyperacetylated histones in the promoter region allowing the recruitment of histone remodeling complexes promoting NDR formation whence potentiating chromatin for gene expression.(DOCSC03) -- UNamur, 201
Synthèse et évaluation biologique de glycoclusters contre la virulence bactérienne
No full textBecause of the appearance of more and more bacteria resistant to antibiotics, it is an urgent need to find new antibacterials. Several approaches have developed in the last few years such as antivirulence. This strategy is based on the weakening of the bacteria rather than killing it. Therefore, we interested in this principle and we developed new antibacterials to combat the bacterial virulence. We based our approach on multivalent scaffolds, as the multivalency is well know to improve the inhibition and/or activation of biological processes. We synthesized new multimeric compounds such as glycofullerenes, glycopillararenes and glycorotaxanes. We showed that these molecules are good inhibitors of glycosyltransferases and lectins, multivalent effects were observed in several cases.(DOCSC02) -- FUNDP, 201
Model Checking for the Masses
No full textThe model-checking problem for software product lines is harder than for single systems. Indeed, one has to verify all the software variants of a product line, whose number grows exponentially in the number of their differences. Techniques intended for single systems are inefficient in this case, for these can only be applied to all products separately. Variability-aware modelling formalisms and algorithms were designed as a more appropriate answer to that problem. Their strength lies in their ability to check a behaviour common to several products only once, which leads to substantial performance gains. Although they constitute a major step toward the efficient verification of product lines, these techniques are not yet mature enough to truly achieve this objective. They still lack optimisations to verify large models, the expressiveness to represent complex forms of variable behaviour, as well as usable languages and tools required for industrial transfer. This thesis aims at improving product-line model checking in order to provide formalisms, algorithms, and tools that together hold the potential to verify real-world software product lines. We first study the state-of-the-art model-checking approaches for software product lines. We compare them in terms of available formalisms and algorithms, and we determine that the approach based on Featured Transition Systems (FTS) is the most suitable to act as a basis for the design of novel techniques. We then extend its theory along two axes: efficiency and expressiveness. For the former, we propose abstraction methods that can reduce the size of the model to check while maintaining correctness and completeness; they consist of extensions of single-system abstraction techniques applied to FTS, and of new techniques that abstract away from their variability. As for expressiveness, on the one hand we propose featured timed automata as a combination of FTS and real-time behaviour. On the other hand, we analyse how to support in FTS complex forms of variability such as numeric features and multi-features. We implemented our theoretical results into a new model-checking tool named ProVeLines. As all our extensions are based on FTS, they share many commonalities. ProVeLines was therefore designed as a product line whose each variant implements a distinct combination of verification formalisms and algorithms. Finally, we show that the principles we designed for product-line model checking can also be applied to other formal methods, namely the verification of adaptive systems and the synthesis of controllers for product lines.(DOCSC06) -- UNamur, 201
Convergences et divergences en droits intellectuels sur la question de la contrefaçon
No full textThis thesis concentrates on infringing (non-slavish) similarity in three main domains of intellectual property law, namely trademarks, designs and models, and copyright. Traditionally, the infringing similarity between two objects – as far as the form is concerned - is treated differently depending on the specific right involved. The respective regimes differ on a number of essential points: theoretical criteria for assessing the infringement (likelihood of confusion, similar overall impression, taking over of original elements); relevant public; functions of the right; consideration for the particular products or services at stake. Moreover, the apparent divergences at the level of the scope of protection seem to be closely related to essential differences at the level of the access to the protection. The substantive conditions to benefit from the protection are generally considered to be unlike: distinctive character, novelty and individual character, and originality. At the basis of this study, there is the idea that the distance between the respective IP-regimes might not as important as it is usually said. The thesis examines the feasibility of a convergence in two steps, mainly in the light of the jurisprudence of the Court of justice of the European Union. The first part of the thesis is dedicated to the conditions of the protection. It is suggested that the notion of originality in a broad sense plays a relevant role under the three regimes. The second part of the study is dedicated to the scope of protection. It is argued that the criterion of similar overall impression constitutes a relevant test in the three domains. Moreover, the thesis takes the view that the assessment of the similarity between the conflicting objects should focus in the first place on the objects as such rather than on the specific rules that are allegedly applicable to the case. Various examples are developed to illustrate that the final outcome of the assessment should not be that different, if different at all, under the three regimes. As a result, it is advocated that the judges should design a solution in function of the concrete circumstances of the case rather than on the basis of the official vocabulary generally used the specific IP-regime at stake.(DOCJURI00) -- UNamur, 201