Les procédés membranaires hybrides (PMH) allient la filtration membranaire basse pression à l’usage du charbon actif en poudre (CAP). Afin de diminuer les coûts opérationnels du procédé, il a été proposé de laisser vieillir le CAP dans le PMH et donc de minimiser le dosage de CAP frais. Peu d’information est disponible quant à la capacité résiduelle d’adsorption de suspensions de CAP âgées. L’importance relative de l’adsorption et de la biodégradation dans les réacteurs à CAP âgés sur le traitement des composés dissous est inconnue, ce qui empêche notamment l’optimisation du procédé. <p><p>Le principal objectif de ce projet de recherche est de décrire la performance du contacteur à CAP du PMH pour l’enlèvement de l’azote ammoniacal, du carbone organique dissous (COD), du COD biodégradable (CODB) et des micropolluants. Dans ce projet, l’emphase est placée sur l’opération du PMH avec de hauts temps de rétention de CAP. <p><p>La première phase de ce projet a consisté en une série de développements méthodologiques, base nécessaire à l’étude du CAP âgé. Des méthodes permettant la quantification de la biomasse hétérotrophe et nitrifiante colonisant le CAP âgé ont mis en évidence des densités de biomasse similaires à celle du charbon actif en grain en surface de filtre biologiques. L’irradiation aux rayons gamma a été démontrée comme une méthode adéquate pour produire des témoins abiotiques à partir de CAP de 10 et de 60 jours.<p><p>La seconde partie de cette étude s’est concentrée sur la démonstration de l’efficacité du PMH pour l’enlèvement de l’azote ammoniacal, du COD, ainsi que d’un mélange de micropolluants. Les cinétiques d’enlèvements ayant lieu au sein de des contacteurs à CAP ont été simulées en laboratoire sous diverses conditions (température, concentration en CAP, âge de CAP, matrice d’eau variable, temps de contact). Deux modèles cinétiques prédisant l’enlèvement de l’azote ammoniacal et du COD dans le PMH ont été développés sur base des simulations en laboratoire suivies sur CAP neuf, colonisé et abiotique. <p><p>De manière générale, les travaux réalisés au cours de ce doctorat ont mis en évidence le rôle majeur de l’adsorption résiduelle sur l’enlèvement de la contamination dissoute. Alors que l’enlèvement d’azote ammoniacal a majoritairement eu lieu par nitrification, le COD et les micropollutants sont principalement adsorbés sur le CAP colonisé. Il a aussi été montré que la capacité d’adsorption résiduelle des suspensions de CAP âgées peut agir en tampon, permettant de faire face à une augmentation soudaine de la concentration en azote ammoniacal, en COD ou en micropolluants. Le suivi des cinétiques d’enlèvement a permis de démontrer que la concentration, l’âge de CAP et le temps de rétention hydraulique (TRH) sont trois paramètres clefs pour l’optimisation du procédé. D’un point de vue économique, un TRH inférieur à 15 min est néanmoins désiré pour limiter les coûts du procédé. Par ailleurs, l’intérêt économique associé à l’augmentation de l’âge du CAP peut-être atténué par le besoin d’augmenter la concentration en CAP si l’adsorption est le mécanisme visé. De façon générale, ce projet démontre qu’une optimisation à l’échelle pilote du procédé est nécessaire car les objectifs de traitement, la qualité de l’eau à traiter et le fait que les 3 paramètres d’opération soient inter-reliés complexifient l’optimisation du PMH. Étant donné l’impact du TRH sur le coût du PMH, de futures recherches devraient viser à l’optimisation du mélange. <p>Hybrid membrane processes (HMPs) couple membrane filtration with powdered activated carbon (PAC). In HMPs, low-pressure membranes ensure an efficient particle removal, including protozoan parasites such as Cryptosporidium, while the PAC contactor is devoted to the removal of dissolved compounds. Such processes are emerging as a promising alternative to conventional treatment chains, which no longer allow the drinking water facilities to comply with increasingly stringent regulations on the treated water quality. To decrease the operating costs associated with virgin PAC consumption, it was suggested to let the PAC age in the PAC contactor of the process. Until now, the potential of using aged PAC in HMPs has been demonstrated for ammonia and DOC removal, but the potential to remove micropollutants remains unknown. It is suggested that the biological activity in aged PAC contactors contributes significantly to the removal of the dissolved compounds. Yet, neither the extent of the biomass on the aged PAC, nor the residual adsorption capacity, was quantified. No study focused on discriminating the mechanisms responsible for the treatment when using aged PAC suspensions. Most of the data published on HMPs using aged PAC were gathered at pilot scale under warm water conditions, yet the efficiency of the process is most likely sensitive to temperature changes. There is currently little information available on the efficiency of HMPs under cold water conditions. This lack of information hinders the optimization of the HMP, leading to sub-optimal usage of aged PAC.<p><p>The main objective of this research project is to describe the performance of the PAC contactor of HMPs in removing ammonia, dissolved organic carbon (DOC), biodegradable DOC (BDOC) and micropollutants. In particular, emphasis was placed on the operation of the HMP under high PAC residence times. On a more detailed level, the objectives of this project were (1) to develop and compare methods to quantify the biomass developed on aged PAC, (2) to develop a method to produce an abiotic control for aged PAC, (3) to characterize the removal kinetics of ammonia, DOC, BDOC and micropollutants occurring in the carbon contactor of an HMP, (4) to evaluate the impact of water temperature on the performance of the carbon contactor of an HMP, (5) to discriminate the relative importance of adsorption versus biological oxidation as mechanisms responsible for ammonia, DOC and micropollutants removal in the PAC contactor of an HMP, and finally (6) to differentiate the relative importance of the hydraulic retention time (HRT), the PAC age and the PAC concentration as key operating parameters on the optimization of the performance of the PAC contactor of an HMP.<p><p><p>To set the basis on the study of aged PACs, the first part of this research project consisted in methodological developments i) to quantify the heterotrophic and nitrifying biomass colonizing aged PAC, and ii) to create a reliable abiotic control of the colonized PAC, which is required for discriminating the mechanisms occurring on aged PAC. Heterotrophic and nitrifying biomass quantifying methods developed for colonized granular activated carbon (GAC) were successfully adapted to the aged PAC. The preferred methods were the potential 14C-glucose respiration (PGR) rate and the potential nitrifying activity (PNA), as they quantify the active heterotrophic and nitrifying biomass, which is most likely responsible for the depletion of BDOC and ammonia. An alternative method to the PGR, the potential acetate uptake (PAU) rate, was developed to alleviate the logistical and budgetary issues associated with the utilization of radio-labeled glucose. The densities (per gram of dry PAC) of both active heterotrophic and nitrifying biomasses were found comparable to that of the GAC sampled from the surface of a biological GAC filter. The gamma-irradiation was demonstrated as a reliable method to produce abiotic samples from soils, and was therefore chosen to produce abiotic colonized PAC samples in this project. In order to determine the optimized dosage of gamma-rays, increased doses were applied on PAC samples. Heterotrophic plate counts and methylene blue adsorption kinetics were used to determine respectively the lowest gamma ray dose required to inhibit the bacterial activity, and the highest dose that could be applied without affecting the aged PAC adsorption capacity and kinetics. Refractory DOC (RDOC) adsorption kinetics confirmed the accuracy of the dose chosen as the adsorptive behavior of the aged PAC was not affected. PGR rates were decreased 83% at the optimized dose. The gamma-irradiation method was therefore proven efficient and used in the following work phases of this research.<p><p>The second part of this study focused on the removal of ammonia, DOC and a mixture of micropollutants. Firstly, the PAC contactor of an HMP was simulated at lab-scale to monitor ammonia removal kinetics. Three PAC concentrations (approximately 1-5-10 g/L) of three PAC ages (0-10-60 days) were tested at two temperatures (7-22°C), in settled water with ambient influent condition (100 µg N–NH4/L) as well as under a simulated peak pollution scenario (1000 µg N–NH4/L). The kinetics evidenced that ammonia flux at pilot scale limited biomass growth (HRT = 67 min). In contrast, PAC colonization was not limited by the available surface and thus, PAC concentration was not a key operating parameter under the colonizing conditions tested (5-10 g/L). Ammonia adsorption was significant onto virgin PAC but the ammonia nitrification was crucial to reach complete ammonia removal at 22°C. When using colonized PAC, the 60-d PAC offered a better resilience to temperature decreases (78% at 7°C) as well as lower operating costs than the 10-d PAC (<10% at 7°C). Significant ammonia adsorption was also evidenced on 60-d PAC suspension, most probably due to PAC and the presence of suspended solids, but not on 10-d PAC. Adsorption and nitrifying activity were superior on 60-d PAC than on 10-d PAC at 7°C. In case of peak pollution, the process was most probably phosphate-limited but a mixed adsorption/nitrification still allowed 50% ammonia removal on 10-d and 60-d PAC at 22°C. A kinetics based model was developed to predict ammonia removals and to determine the relative importance of the adsorption and nitrification on colonized PAC under the conditions tested. <p><p>DOC, BDOC and RDOC removals occurring in the PAC contactor of an HMP were also simulated at lab-scale. Similar conditions to that of the ammonia removal kinetics were tested. The initial ammonia concentration remained untouched in the water matrices (settled water and raw water) but the BDOC-to-DOC ratio was altered by pre-ozonation (0 to 1.5 g O3/g C). The 10-d and 60-d abiotic controls were used to discriminate DOC adsorption from biodegradation. DOC biodegradation contributed marginally to DOC removal in the investigated conditions and DOC adsorption was increased at higher temperature. An original model integrating the PAC age distribution was developed to predict DOC removal in aged PAC contactors operated at steady-state. At a mean PAC residence time of 60-d, the younger PAC fraction (25-d and less) was primarily responsible for DOC adsorption (> 80%). This fraction represents 34% of the mass of PAC in the contactor. When using a water matrix with a higher initial DOC concentration (raw water) or a lower affinity for PAC (pre-ozonated settled water), the residual adsorption capacity of that older fraction was proven useful. <p><p>Lastly, a mixture of micropollutants (atrazine, deethylatrazine (DEA), linuron, microcystin, caffeine, carbamazepine, sulfamethoxazole, diclofenac, progesterone and medroxyprogesterone) was spiked at environmentally relevant concentrations (from 130 ng/L to 33 µg/L) in settled water (0 and 0.85 gO3/gC). The micropollutants concentration depletion was monitored over a period of 7h to 48 h on 1 g/L of 0-d, 10-d, 60-d PAC and gamma-irradiated 60-d PAC. Even in presence of NOM, the spiked micropollutants were rapidly adsorbed on aged PAC. No biodegradation was observed. Removals superior to 95% were reached within 5 minutes, and direct competition with NOM did not impact the efficiency of the process when micropollutants were spiked at environmentally relevant concentrations. Therefore, HMPs operated to remove DOC and ammonia can control transient micropollutant pollution and comply with the World health Organization recommendations for atrazine (2 µg/L) and microcystin (1 µg/L). However, the stricter European regulations for atrazine and DEA (0.1 µg/L) could not be met with 10-d and 60-d PAC under the operating conditions tested. Reaching such strict treatment objective would require a specific optimization of the process. <p><p>In general, this PhD research evidenced the role of the residual adsorption of aged PAC suspensions for the treatment of dissolved compounds. From the results obtained in this project, the potential of HMPs using aged PAC to remove micropollutants was evidenced. Additional research is however required to validate this potential under varied operating conditions. The modeling work improved the understanding of aged PACs. Finally, this research work provides original information on the optimization of HMPs. The optimization of the operating parameters will vary with the water quality targeted and the quality of the influent water. The PAC concentration, PAC age and HRT are inter-related. Therefore, it is recommended to optimize the operation of HMPs at pilot scale. Seasonal variations should be accounted for. An HRT of at least 15 min is required when the biological activity is mandatory to reach the water quality objectives. Lower HRT might be applied if adsorption is favored. Finally, as the HRT has a strong impact on the total cost of the process (capital and operational expenditure), PAC contactors’ hydraulic should be the point of focus of future research.& / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

La cécidomyie orange du blé, Sitodiplosis mosellana (Géhin), est un ravageur commun du froment. Présente sur les trois continents de l’hémisphère Nord, cette espèce est connue depuis deux siècles mais son contrôle reste difficile tant par sa présence discrète que par ses effectifs hautement variables. En Wallonie, les niveaux d’infestations sont globalement faibles mais atteignent localement des seuils inquiétants.<p>Au début des années 2000, la phéromone sexuelle de S. mosellana a été identifiée au Canada. Cette découverte a permis la fabrication de pièges qui ont considérablement amélioré la détection et la mesure des vols de cet insecte minuscule. De 2007 à 2010, les captures de S. mosellana ont été mesurées quotidiennement dans plusieurs dizaines de champs de Wallonie, aux historiques et aux couverts variés.<p>Les volumes de captures au piège à phéromone sexuelle ont été très importants. Il a fallu en étudier la signification, notamment en termes de mesure du risque. En effet, si les mâles sont efficacement capturés, seules les femelles constituent un risque de dégâts. L’interprétation correcte des captures à l’aide de ce type de piège, a été rendue possible par l’observation de différences fondamentales concernant la mobilité et la distribution spatiale des mâles et des femelles de S. mosellana. Même s’ils ne mesurent pas directement l’émergence proprement dite, les pièges à phéromone ont permis, grâce à leur très grande sensibilité, de préciser les connaissances sur l’émergence des adultes et de révéler que plusieurs vagues d’émergence pouvaient se succéder au cours d’une même année.<p>La prévision des émergences de la cécidomyie orange du blé, constitue la clé de voûte de la lutte contre ce ravageur dont un contrôle efficace par des insecticides ne se justifie éventuellement que lorsque la courte saison des pontes coïncide avec l’épiaison des froments. Les patrons d’émergence obtenus par les pièges ont été confrontés aux prévisions de différents modèles conçus en Europe ou en Amérique du Nord, et appliqués aux conditions météorologiques observées de 2007 à 2010. Aucun de ces modèles n’a prévu correctement les émergences sur l’ensemble des quatre années.<p>Les données d’émergence obtenues à l’aide des pièges à phéromone (effectifs élevés et relevés quotidiens) ont fait apparaître une relation de cause à effet entre, d’une part les vagues d’émergences et, d’autre part les épisodes pluvieux observés trois à six semaines plus tôt. L’écart entre une &61618;pluie inductrice&61618; et la vague d’émergence induite correspondante s’est avéré constant en termes d’accumulation de température :il équivaut à 160 degrés-jours en base 7°C. Partant de ce constat et des acquis des modèles antérieurs, un modèle prévisionnel original des émergences a été développé et validé sur le terrain. Allié à une meilleure connaissance de la biologie du ravageur, il constitue un outil majeur de la lutte intégrée.<p>Par ailleurs, les travaux menés ont également révélé l’existence d’un biais fréquent dans les essais d’évaluation des variétés, entraîné par la concentration des pontes de cécidomyie orange sur les premières parcelles atteignant le stade épiaison. Dans le système d’évaluation en vigueur, notamment pour l’inscription dans les catalogues nationaux, ce biais conduit à une sous-estimation du potentiel de rendement des variétés de blé les plus précoces.<p>Enfin, la découverte du rôle inducteur des pluies sur l’émergence des adultes a été exploitée en conditions contrôlées pour planifier des émergences échelonnées, et pour disposer, pendant une longue période, de jeunes adultes prêts à pondre. Cette application permet dès à présent de mesurer en serre le niveau de résistance des variétés exposées de façon homogène à l’insecte, quel que soit leur degré de précocité.<p>De diverses façons, cette étude contribue à une meilleure connaissance de la cécidomyie orange du blé et offre de nouveaux outils pour la lutte intégrée contre ce ravageur.<p><p>--------------------------------------------------<p><p>The orange wheat blossom midge, Sitodiplosis mosellana (Géhin), a common pest of wheat throughout the northern hemisphere, is known for two centuries but remains difficult to control due to its discrete behavior and its highly variable population level.<p>In general, the infestation levels in Wallonia (Belgium) are low, although levels could locally exceed worrying thresholds. <p>In the early 2000s, the sexual pheromone of S. mosellana has been identified in Canada. This discovery has led to the manufacturing of traps which have greatly improved the detection of this tiny insect. From 2007 to 2010 in Wallonia, S. mosellana captures have been daily registered in about 20 fields with different cropping histories and grown with different crops.<p>Insect captures by pheromone traps were numerous. Relation between amount of captures and risk measurement has been studied. As expected, only the males are attracted by the pheromone and the risk of ears infestation is mainly related to the presence of females. The correct interpretation of captures in pheromone traps has been established by the observation of fundamental differences between males and females concerning their mobility and their spatial distribution. <p>Despite the fact that pheromone traps are not real emergence traps, they have led to new information on adult emergence indicating that several emergence waves can be consecutive during the same year. <p>Forecasting the emergence of the adult orange wheat blossom midge is a key element on pest management. Insecticides treatments are sometimes justified when the egg laying period of the insect coincides with ear emergence of wheat. Emergence patterns established from captures of pheromone traps have been compared with the forecast of several models built in Europe or North America. These forecasting models were used with the meteorological data observed from 2007 until 2010. None of the six tested models provided a reliable forecast across the four years of our study. <p>Emergence data from catches in pheromone traps were very accurate because the number of catches were high and were taken each day. This emergence data showed a relation between emergence waves and rainfalls occurring during the preceding 3 to 6 weeks. The lag between inductive rain and emergence wave is constant in terms of temperature accumulation: it is equivalent to 160 degree–days above 7°C. This discovery, combined with experience from previous models, was incorporated into a new forecasting model.<p>In addition, the present work has also revealed the existence of a common bias in variety evaluation trials leading sometime to the concentration of the eggs in the earliest earing variety. In the current evaluation system, this bias leads to a sub-evaluation of the yield for the most precocious varieties. <p>Finally, the discovery of the inductive rain for adult emergence has been used in the screening for resistant varieties to S. mosellana by providing adults during the complete duration of the test. This application of the model allows to measure, under controlled conditions, the level of resistance of all varieties (early and late heading varieties) which are exposed homogeneously to the insect.<p>In total, this study has contributed to a better understanding of the orange wheat blossom midge and provides some new tools in the management of this pest.<p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Dans la première partie de cette thèse effectuée en collaboration avec le groupe expérimental de C. Chazaud (Clermont Université), nous avons étudié théoriquement un processus de différenciation cellulaire intervenant avant l’implantation de l’embryon dans l’utérus. Il s’agit de la spécification des cellules de la masse cellulaire interne (MCI) en épiblaste (EPI) et en endoderme primitif (EPr), processus dans lequel les facteurs de transcription Nanog et Gata6 jouent un rôle essentiel. En effet, en absence de Nanog, les cellules de la MCI acquièrent toutes une identité EPr, tandis qu’en absence de Gata6, elles se différencient toutes en EPI. De plus, la voie de signalisation Fgf/Erk active l’expression de Gata6 et inhibe celle de Nanog. Enfin, Nanog active la sécrétion dans le milieu extracellulaire de Fgf4, une molécule qui active la voie de signalisation Fgf/Erk en se liant au FgfR2. Nous avons développé un modèle mathématique pour ce réseau de régulations, fondé sur des équations différentielles ordinaires décrivant l’évolution temporelle des niveaux de protéines Nanog, Gata6, Fgf4 et Fgfr2 et de l’activité de la voie Fgf-Erk. Nous avons validé ce modèle en montrant qu’il récapitule les résultats expérimentaux obtenus in vivo, dans les embryons wild-type et dans les mutants Nanog-/- et Gata6-/-. De plus, l’analyse des résultats du modèle permet de proposer un nouveau mécanisme pour l’émergence d’une population mixte de cellules EPI et EPr au sein de la MCI. Ce mécanisme repose sur le fait que le système décrit par notre modèle peut présenter trois états stationnaires stables, dont les niveaux d’expression de Nanog et Gata6 correspondent à l’EPI, l’EPr et la MCI non-différenciée, respectivement. De plus, le modèle a été utilisé afin d’interpréter des résultats expérimentaux récents et contre-intuitifs, concernant les embryons hétérozygotes Gata6+/-. Enfin, nous avons établi des prédictions théoriques, dont certaines ont été ultérieurement vérifiées en laboratoire. <p>Dans la seconde partie de la thèse, effectuée dans le laboratoire d’O. Pourquié (Université de Strasbourg), nous avons étudié un processus de différenciation in vitro, par une approche expérimentale. Il s’agit de la différenciation des cellules souches embryonnaires (ES) en cellules de mésoderme paraxial, un tissu dont dérivent –au cours du développement embryonnaire– les cellules formant notamment les vertèbres, les côtes, la peau et les muscles squelettiques du dos.<p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Le virus de l’influenza aviaire hautement pathogène (IAHP) de type H5N1 apparu en Chine en 1996 constitue une menace pour la santé humaine en raison de sa circulation endémique dans les volailles domestiques et de son potentiel zoonotique. La sévérité de l'infection liée à l'IAHP H5N1 est variable selon les espèces d'oiseaux: certains anatidés sont porteurs sains et asymptomatiques du virus tandis que dans les élevages de poulets, l'IAHP est fortement contagieux et caractérisé par des taux de mortalité supérieurs à 90%. Chez les humains, l'impact de l'IAHP H5N1 reste à ce jour modéré (630 cas humains dont 375 morts, World Health Organization Juin, 2013) en raison de la faible transmission du virus des volailles aux humains et d'humain à humain. Cependant, étant donné les taux de létalité élevés (>50%), un changement des modalités de transmission pourrait mener à un impact beaucoup plus élevé.<p>Depuis son émergence, l'IAHP H5N1 a eu un impact économique important dans de nombreux pays d’Asie du Sud-Est. La Thaïlande, pays qui fait partie des principaux exportateurs mondiaux de viande de volaille, a été sévèrement touchée par les multiples vagues épidémiques entre 2003 et 2005. Ces épisodes ont eu un impact sur les revenus des petits et moyens producteurs, mais également causé des pertes économiques importantes dans le secteur de la production intensive de volailles en raison de l'embargo imposé par les principaux marchés d'exportation. <p>L'objectif de ce travail est d’étudier quantitativement l'association entre la production intensive de la volaille et la distribution spatio-temporelle de l'IAHP H5N1 en Thaïlande. Deux approches ont été développées pour aborder cette étude: le développement d’une part de modèles statistiques visant à identifier les déterminants du risque d'IAHP H5N1, et d'autre part, de modèles mécanistiques visant à simuler des trajectoires épidémiques sur base de la connaissance des mécanismes de transmission de l'IAHP H5N1, de la structure du secteur de la production de volaille et des mesures d'intervention mises en place. <p>A l’aide de facteurs environnementaux et anthropogéniques, nous montrons que: (i) la distribution des canards domestiques en Asie peut être prédite en utilisant des modèles de régression non-linéaire, et (ii) la production de volailles peut être désagrégée entre production extensive et intensive sur base du nombre de volailles par éleveur. Enfin (iii), nous montrons en utilisant des arbres de régression boostés ("Boosted Regression Trees", BRT) que les principaux déterminants de la distribution du risque d'IAHP H5N1 sont les canards élevés en systèmes intensifs, le nombre de cycles de culture de riz et la proportion d'eau présente dans le paysage. Finalement, nous illustrons les potentialités des modèles mécanistiques pour évaluer l'efficacité des mesures d'intervention implémentées, tester des scénarios alternatifs d'intervention et identifier des stratégies optimales de prévention et d'intervention contre de futures épidémies<p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

In tropical forests, ants are numerous, diversified and ecologically important, being present from forest floor to upper canopy and exploiting a wide variety of diets. Nearly half of the ant species are directly in contact with the ground stratum, including the leaf-litter and the underlying soil, for nesting or foraging. The main factors known to influence ant distribution and abundance can be environmental (e.g. heterogeneous distribution of microhabitat size, nutrient availability, microclimate, soil properties) or biotic (e.g. inter- and intraspecific competition, prey availability). Some of these factors, such as leaf-litter volume or prey availability, may also vary seasonally. Also, the Ecuadorian Andes are known as being a hotspot of biodiversity for a large array of organisms, but it was not documented until now if this is also the case for ants.<p><p>The general aim of the PhD project was to identify, by both descriptive and experimental approaches, the factors determining the structure of a ground-dwelling ant assemblage at a small-spatial scale and its temporal variation in an evergreen premontane tropical forest of the Ecuadorian Andes.<p><p>In the descriptive part of the project, we studied both horizontal (along a transect) and vertical (across ground layers) species diversity and distribution of ground-dwelling ants. To attempt to explain the observed patterns, we measured a series of environmental factors varying at small spatial scale and/or seasonally: canopy openness, leaf-litter quantity, slope, and a series of soil physico-chemical properties (e.g. texture). The ant assemblage richness appeared to be at least as high as in the Amazonian Basin, with up to 33 species per m². The heterogeneity of species spatial distribution at small spatial scale was high, with distinct species composition (average Jaccard index = 0.2 ± 0.08 SD) and abundance (up to 40 fold) in contiguous plots. We observed a strong seasonal effect on the ant assemblage structure. The higher ant diversity and abundance found at the surface and in the mineral soil during the dry season suggested a seasonal peak of activity on the ground surface and the seasonal migration of drought-sensitive species downwards in the soil. Ant diversity was related to distinct environmental factors according to the ground layer considered. We found strong correlations between litter amount and dominant ant distribution in the leaf-litter layer, while we found no correlation with any factor in the soil layer. The low amount of negative association between dominant species suggested a low interspecific competition.<p><p>In the experimental part of the project, our aim was to identify experimentally the relative importance of habitat size vs. prey availability in structuring the leaf-litter ant assemblage. We studied the response of various ant trophic groups to an increased nutrient availability which boosted the decomposition of their leaf-litter habitat and enhanced the abundance of their prey. Bottom-up effect on the ant fauna (and other predaceous arthropods) regarding species composition and dominance was also studied. Stable isotope analysis was used to distinguish trophic groups among ants and mesofauna. Ants responded differentially according to their trophic group: despite increased prey availability, predatory species were negatively affected by nutrient supply, while other ant trophic group densities did not change. Our results showed that predatory ants are limited by habitat size rather than by prey availability, and that these ants are more affected by habitat loss than their prey, other ant trophic groups and other macrofauna taxa. Furthermore, a taxonomic shift occurred within each ant trophic group, leading to the replacement of dominant genera in fertilized plots.<p><p>As a conclusion, our results emphasize the importance of distinguishing layers among the ground matrix, since both ant faunas and their response to environmental factors vary vertically and seasonally. The distribution of ground-dwelling ants was only weakly explained by both the environmental factors measured and by biotic interactions, at a small spatial scale. Also, our results emphasize the importance of distinguishing trophic groups among the ant assemblage, since the response of these groups under changing conditions was different. In this regard, stable isotope analysis was a useful tool for investigating the trophic ecology of various leaf-litter taxa, and it was successfully used for the first time to assess the diet of leaf-litter ants and their position in the Brown Food Web relative to other taxa. Also, the isotopic approach allowed us to increase the knowledge about the biology of a rare and cryptic ant species, by revealing its top-predatory position. The outstanding local species richness that we observed confirms that the Ecuadorian Andes are also a biodiversity hotspot for ants. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

This study focuses on the vegetation of the African city of Bujumbura, Burundi. Urban flora is detailed according to the origin of the species (native or introduced), their life form, the use of these species by the local population and their behaviour (invasive or not). <p>The correlation between different natural and anthropogenic environmental factors and the composition of plant communities has been demonstrated through the analysis of vegetation plots. Three types of green areas were studied: spontaneous vegetation on terra firma, wetlands <p>and domestic gardens.<p><p>The main ecological factor correlated to the composition of the spontaneous vegetation of terra firma is the degree of urbanization. From the suburb to the city centre, savannah species typical for the region are replaced by alien invasive species, mostly ruderals. The latter generally have a large distribution, often on several continents. The physiognomy of the vegetation also changes, with hemicryptophytes and phanerophytes in the outskirts and the dominance of therophytes and chamaephytes in the city centre.<p><p>In most of wetlands, a large proportion of the plant species are natives, but some wetlands are almost totally invaded by alien species. Soil type is the main environmental factor correlated with <p>the variability of the vegetation.<p><p>The flora of domestic gardens is mainly composed of introduced species used as ornamental, food or medicinal plants. The socio-economical status of the neighbourhood is the main factor correlated with the variability of the garden flora. In high standing neighbourhoods, most species are onamental, with many trees and shrubs. In popular neighbourhoods, the flora is mainly utilitarian (vegetables and fruits), with a significant proportion of native species, and composed mainly of annual species. <p>A small proportion of the alien species cultivated in gardens has become invasive in the semi-natural vegetation of the city and its surroundings. Many other species cultivated in the gardens could become invasive, based on their ecology and their invasive behaviour in other regions with a climate similar to that of Bujumbura.<p><p>Overall, the city of Bujumbura has a diverse flora, with many useful species (vegetables and fruits, traditional medicine, construction of fences and roofs, material for mats and art objects.). The vegetation also hosts wildlife: birds, fishes, hippos, crocodiles etc… <p><p>In conclusion, the vegetation of Bujumbura contributes to biodiversity conservation and provides services to the urban population, but the expansion of alien invasive species and the consequent homogenization of the vegetation is a challenge for the future.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

Breast cancer is a global public health problem since it is the most frequently diagnosed cancer in women in Western countries. Clinical guidelines for breast cancer prognosis/diagnosis are currently based on tumour size, histological type and grade, lymph node status as well as the expression of various cellular receptors. Yet, current predictions remain unsatisfactory to identify the best treatment for the individual patient. The search for identifying new predictive and prognostic factors is ongoing. Furthermore, compelling evidences have solidified the notion that the evolving epithelial cells, founders of the breast disease, are helped in their malignant course by the tumour microenvironment. Better characterizing the dual effect of the immune regulation but also the epithelial-stromal cross-talk on both tumour-promotion and -suppression is essential for understanding patient uniqueness and their implication in disease outcome. Because of its potential to probe tissues and cells at the molecular level without requirement for extrinsic contrast agents, infrared spectroscopy was seen as an attractive tool for clinical and diagnostic analysis in order to complement the existing methods. <p>In a first step, recording and processing methodology had to be defined in order to optimally compare IR spectra. The methodology developed and the analysis tools tested on carcinoma cell lines, demonstrated that spectra could be distinguished based on the cell line phenotypic nature. <p>The potential of IR imaging for breast tissular structure differentiation was highlighted in this thesis, demonstrating that spectral signature can be correlated with the major histological cell types observed in breast disease tissues. In order to develop a robust algorithm translating spectral data into helpful histopathological information, a spectral database of histologically well-defined breast tissues was built and used for the development of a cell type classifier. This latter one was extensively validated on independent clinical cases. Firstly, the IR-based histopathological classifier correctly assigned spectra acquired on eleven breast disease samples based on their histological nature. Secondly, lymphocyte and Collagen & Fibroblasts spectral signatures were demonstrated to be independent from tissue type and organ since, although trained on reference spectra recorded into breast disease samples, the cell type classifier correctly assigned spectra acquired on lymph nodes/tonsils and scar tissues respectively. Thirdly, we concluded that spectroscopically, breast carcinoma cell lines in culture are well-suited tumour models since spectra acquired on these carcinoma cell lines were correctly recognized as epithelium by the IR-based histological classifier. <p>By spectral characterizing lymphocytes from lymph nodes and tonsils, we demonstrated that the spectra acquired contained enough information to statistically discriminate them according to their lymphocyte activation states. Although considered as activated, the breast disease lymphoid infiltrates were found to present distinct spectral signature from lymphocytes acquired on activated lymph nodes and tonsils. Furthermore, tumour microenvironment, characterized by IR-imaging was demonstrated to exhibit a distinct spectral signature from wound healing tissues. These studies proved the uniqueness of the signature of both lymphoid infiltrate and tumour microenvironment in breast disease context. Correlating these specific spectral signatures to patient outcome and therapeutics response could help better consider the uniqueness of the patient. In a last step, considering the epithelial signature of carcinomas of both low and high grades, we demonstrated that the biochemical information reflected in the IR micro-spectra was clinically relevant for grading purpose.<p><p> <p><p>Le cancer du sein est le cancer le plus fréquemment diagnostiqué chez les femmes dans les pays occidentaux. Jusqu’à peu, les cellules épithéliales tumorales étaient vues comme les seuls acteurs de la carcinogenèse ;processus se déroulant dans un milieu extracellulaire considéré au pire comme passif ou permissif à l’évolution tumorale des cellules épithéliales adjacentes. Cependant, de nombreuses études ont montré que ce microenvironnement tumoral pouvait soit promouvoir le processus de carcinogenèse soit le combattre empêchant par la même, l’occurrence de la maladie. <p>Ce projet de thèse s’inscrit dans une problématique actuelle, à savoir une meilleure compréhension de la maladie mais également une prise en charge plus individualisée des patientes. Nous abordons ici une voie de recherche novatrice basée sur la signature globale des molécules cellulaires via leur spectre infrarouge. La technologie utilisée, à savoir la spectroscopie infrarouge, nous fournit une observation quantitative et qualitative de milliers de vibrations moléculaires. L’adaptation de réseaux de plusieurs milliers de détecteurs indépendants aux microscopes infrarouges permet, grâce aux méthodes statistiques multivariées, d’investiguer l’architecture macromoléculaire des cellules au sein d’une coupe tissulaire et de corréler les informations spectrales ainsi obtenues à l’histopathologie des tissus. Par cette technologie, nous visons à mettre au point un outil diagnostique et pronostique pour le cancer du sein basé sur l’imagerie IR. <p>Durant ce projet, nous avons montré que les différents types cellulaires observés dans les carcinomes mammaires pouvaient être distingués par le biais de leur spectre IR, qu’un modèle de reconnaissance histologique pouvait être construit, validé et surtout automatisé et que ce modèle pouvait être transposé à l’étude d’autres tissus (ganglions, amygdales et cicatrices) et d’autres types d’échantillons (cellules épithéliales en culture). Nous avons également montré que les spectres de cellules épithéliales pouvaient être corrélés au grade histopathologique de la tumeur. Les spectres acquis de ganglions/amygdales ont montré que les profils spectraux pouvaient être corrélés à l’état d’activation lymphocytaire. De plus, l’étude de l’état d’activation lymphocytaire et fibroblastique a permis de mettre en avant un profil spectral propre et bien distinct des infiltrats lymphocytaires d’une part et de la matrice extracellulaire aux abords des tumeurs invasives d’autre part. <p> / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Cupriavidus metallidurans CH34 is a Gram-negative & / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Spatially-explicit information is essential for planning and implementing interventions against vector-borne diseases. This is also true for African trypanosomoses, a group of diseases of both humans and animals caused by protozoa of the Genus Trypanosoma, and transmitted by tsetse flies (Genus Glossina).<p>In this thesis the knowledge gaps and the requirements for an evidence-based decision making in the field of tsetse and trypanosomoses are identified, with a focus on georeferenced data and Geographic Information Systems (GIS). Datasets, tools and analyses are presented that aim to fill some of the identified knowledge gaps.<p>For the human form of the disease, also known as sleeping sickness, case detection and treatment are the mainstay of control, so that accurate knowledge of the geographic distribution of infections is paramount. In this study, an Atlas was developed that provides village-level information on the reported occurrence of sleeping sickness. The geodatabase underpinning the Atlas also includes the results of active screening activities, even when no cases were detected. The Atlas enables epidemiological maps to be generated at a range of scales, from local to global, thus providing evidence for strategic and technical decision making.<p>In the field of animal trypanosomosis control, also known as nagana, much emphasis has recently been placed on the vector. Accurate delineation of tsetse habitat appears as an essential component of ongoing and upcoming interventions against tsetse. The present study focused on land cover datasets and tsetse habitat. The suitability for tsetse of standardized land cover classes was explored at continental, regional and national level, using a combination of inductive and deductive approaches. The land cover classes most suitable for tsetse were identified and described, and tailored datasets were derived.<p>The suite of datasets, methodologies and tools presented in this thesis provides evidence for informed planning and implementation of interventions against African trypanosomoses at a range of spatial scales. / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished

Au début des années 2000, les hêtraies ardennaises belges et des régions limitrophes ont connu un déclin soudain et intense. Des nécroses sont apparues sur les troncs, accompagnées d’attaques de scolytes xylomycophages et du développement de champignons secondaires. Des phénomènes similaires ont été signalés dans les années 1930s et 1940s en Belgique et en Allemagne. <p><p><p>Des coups de gel pourraient être à l’origine de ces épisodes de déclin. Pour tester cette hypothèse, plusieurs démarches complémentaires ont été utilisées.<p><p>•\ / Doctorat en Sciences agronomiques et ingénierie biologique / info:eu-repo/semantics/nonPublished