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See detailEffets de la fertilisation NP et de l'irrigation à des périodes critiques sur le rendement et la qualité des fruits du figuier de Barbarie (Opuntia ficus-indica (L.) Mill.)
Arba, Mohamed ULiege

Doctoral thesis (2017)

Selon la classification révisée récemment, les cactus appartiennent à la famille des Opuntiaceae Desv. (Synon. Cactaceae Juss.), dont le genre-type Opuntia Mill. est économiquement le plus important car ... [more ▼]

Selon la classification révisée récemment, les cactus appartiennent à la famille des Opuntiaceae Desv. (Synon. Cactaceae Juss.), dont le genre-type Opuntia Mill. est économiquement le plus important car il comprend un ensemble de variétés qui participent à la plupart des systèmes agricoles des régions arides et semi-arides. Récemment, dans le Maghreb, la culture de plusieurs espèces et variétés s'est développée à de fins de production fruitière commercialisable, c’est-à-dire répondant à des critères de qualité de plus en plus sévères et exigeant des technologies culturales précises. La partie expérimentale de notre étude s'est déroulée pendant deux années dans le Sud du Maroc, région d'Agadir, sur trois variétés représentatives. Les essais ont été réalisés à la ferme expérimentale de l'Institut Agronomique et Vétérinaire Hassan II, Complexe Horticole d'Agadir (30°36' Nord, 9°36' Est; altitude: 32 m). Le site est caractérisé par des températures moyennes mensuelles qui varient de 8°C en janvier à 31°C en juillet, la température journalière maximale pouvant atteindre 45°C en juillet-aout. La pluviométrie annuelle varie de 100 à 200 mm. La durée moyenne d'ensoleillement est de 8 heures par jour. Un premier objectif de notre étude a été de préciser les réponses quantitatives (rendement en fruits) et qualitatives à des apports modérés d'eau d'irrigation. Un deuxième objectif consistait à évaluer les effets d'apports limités de fertilisation minérale azotée et phosphatée, ces deux éléments majeurs étant les plus susceptibles de se trouver déficitaires dans le contexte pédoclimatique propre à la région. Un troisième objectif a été de préciser la phénologie des trois variétés - surtout les phases de développement floral et fruitier - afin de mettre en évidence d'éventuels impacts des interventions culturales sur la phénologie et de mieux situer les moments de ces interventions en les reliant de manière plus objective à la physiologie du développement. Dans l'étude sur l'irrigation, les variétés utilisées ont été les inermes 'Aissa' et 'Moussa' d'Opuntia ficus-indica (L.) Mill. et l'épineuse 'Achefri’ d’O. megacantha Salm Dyck. En première année, caractérisée par un printemps pluvieux, les traitements d'irrigation ont été: (T1) 0 mm, (T2) 30 mm à la floraison et 30 mm au grossissement des fruits et (T3) 30 mm seulement au grossissement des fruits; les irrigations ont été appliquées entre la mi-avril et la mi-juin. Les irrigations T2 et T3 ont eu un effet négatif sur le rendement en fruits des variétés inermes 'Aissa' et 'Moussa' (-2,8 kg/plant) et T2 a eu un effet positif hautement significatif (p <0,01) sur la variété épineuse 'Achefri’ (+ 2,7 kg/plant ou +18 %). La qualité des fruits n'a pas été affectée par l'irrigation. En deuxième année, caractérisée par un printemps sec, les traitements d’irrigation ont été: (T1) 0 mm, (T2) 60 mm à la floraison et 60 mm au grossissement des fruits et (T3) 60 mm seulement au grossissement des fruits; les irrigations ont été apportées entre février et mai. Toutes les variétés ont répondu positivement à l'irrigation, les augmentations de rendement très significatives (p <0,01) ont varié entre 30% pour 'Moussa' avec T2 et 63 % pour 'Achefri' avec T3 par rapport au témoin non irrigué. Toutes les irrigations ont augmenté le nombre et la taille des fruits et ont provoqué une légère diminution de la teneur en sucres totaux et de l'acidité titrable. Les irrigations n'ont eu aucun effet significatif sur les autres paramètres physiques, chimiques et organoleptiques participant à la définition de la qualité. L'essai sur la fertilisation minérale azotée-phosphorique sur le cultivar ‘Moussa’, mettait en comparaison cinq traitements: 0N-0P; 0N-80P; 40N-40P; 60N-0P et 60N-80P (en kg N ha-1- kg P2O5 ha-1). En première année, l'application de N et/ou de P n'a eu aucun effet sur le rendement en fruits. En deuxième année, les apports de 60 unités de N ou de 80 unités de P2O5 ont augmenté (p <0,01) le rendement de resp. 3,0 et 6,1 kg par plante (+ 18% et + 36%), par rapport au témoin. L'apport simultané des deux éléments N et P (60N-80P2O5) a conduit à une augmentation très significative (p <0,01) de 14,9 kg/plante (+ 90%) mettant en évidence une interaction positive très significative (p <0,01) entre ces deux éléments. Les apports de N et de P ont eu des effets positifs sur le nombre de fruits et leurs poids moyens mais ils n'ont pas modifié le contenu de la pulpe, la teneur en jus, l'épaisseur de l’écorce, la matière sèche du jus, le pH, l’acidité titrable, les sucres totaux, ni le °Brix. L'étude portant sur la phénologie et le développement a été effectuée simultanément dans un essai spécifique reprenant les trois variétés et dans chacun des essais d'irrigation et de fertilisation. Elle a d'une part permis de préciser la variabilité du déroulement des phénologies comme résultant des conditions de milieu (climat), de la génétique, des techniques culturales (fumure et irrigation), et de certaines de leurs interactions. Notre attention s'est portée prioritairement sur les effets des techniques culturales maîtrisables. En première année, les essais ont montré que l'émission de bourgeons est plus élevée (p<0,05) chez la variété épineuse que chez les inermes (plus de 6 bourgeons émis/cladode contre moins de 4,5 chez les variétés inermes). En 2ème année, l'irrigation a augmenté (p <0,05) l'émission de bourgeons chez les trois variétés (plus de 7 bourgeons émis/cladode pour chacun des traitements T2 et T3 vs pas plus que 5 pour T1). L'irrigation a aussi allongé la durée de la phase de floraison de ces variétés. La fertilisation a montré des effets allant dans le même sens. Cependant, ni l'irrigation, ni la fertilisation minérale n'ont modifié significativement la durée de la réalisation du stade maturité du fruit, ne permettant pas ainsi d'allonger la saison de récolte. [less ▲]

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See detailCaractérisations phénotypiques des populations de pintades (Numida meleagris) locales élevées au Bénin
Houndonougbo, Pascal ULiege

Doctoral thesis (2017)

La pintade (Numida meleagris) est une volaille d’origine africaine. Son élevage est répandu en Afrique subsaharienne dans un système traditionnel où plusieurs variétés sont élevées en liberté. Ces ... [more ▼]

La pintade (Numida meleagris) est une volaille d’origine africaine. Son élevage est répandu en Afrique subsaharienne dans un système traditionnel où plusieurs variétés sont élevées en liberté. Ces variétés qui diffèrent par le coloris de leur plumage sont très peu caractérisées. Au nord Bénin, l’élevage avicole moderne est peu rencontré et la pintade constitue la pondeuse d’œufs de table dans cette région. Mais, la mortalité élevée, la faible productivité de la pintade locale limitent fortement le développement de son élevage. Il est alors nécessaire de caractériser les variétés de pintades élevées pour mieux les valoriser dans un système amélioré. L’objectif de cette thèse est de caractériser phénotypiquement la population de pintade locale élevée au Bénin afin de mieux valoriser l’espèce dans des programmes d’amélioration et de développement du secteur avicole national. Une revue bibliographique (Article de synthèse) a permis de réaliser l’état des lieux de l’élevage de pintade au Bénin et de mieux orienter nos travaux pour une bonne caractérisation des variétés élevées. L’existence de plusieurs variétés dans les élevages a été soulignée dans la revue bibliographique et nous a amené à des enquêtes et un suivi des élevages de pintades en milieu villageois. Ces enquêtes et suivi nous ont permis de caractériser les pintades locales dans leur milieu d’élevage selon les dire des éleveurs. Ils nous ont aussi permis de dégager selon les éleveurs, les objectifs de production, l’importance socio-économique et culturelle des variétés élevées. L’influence de l’alimentation sur les performances technico-économiques des pintades locales a été soulignée dans l’Article de synthèse et l’Article I. Cette influence a été abordée en évaluant l’influence de l’alimentation sur le potentiel de croissance de la pintade locale en station (Article II). Enfin, des travaux ont été réalisés en station pour mieux caractériser les variétés de pintades rencontrées dans les élevages sur le plan morphologique, performances de croissance et de reproduction (Articles III, IV et V). Ces différents travaux nous ont permis de recenser les différentes variétés de pintades locales élevées au Bénin, les objectifs d’élevage des éleveurs ainsi que quelques difficultés liées au développement de cet élevage. Ces travaux nous ont surtout permis de mieux caractériser les variétés rencontrées. Cette caractérisation pourrait être valorisée pour améliorer la productivité des variétés par sélection. [less ▲]

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See detailAnalyse comparée des chaines de valeur du riz dans la plaine de la Ruzizi de la Communauté Economique des pays des Grands Lacs (CEPGL)
Furaha Mirindi, Germaine ULiege

Doctoral thesis (2017)

This thesis aims at carrying out a comparative study of three rice value chains in the Ruzizi plain shared between three countries of the Economic Community of the Great Lakes Countries (CEPGL) namely ... [more ▼]

This thesis aims at carrying out a comparative study of three rice value chains in the Ruzizi plain shared between three countries of the Economic Community of the Great Lakes Countries (CEPGL) namely Burundi, the Democratic Republic of Congo and Rwanda. These include the Burundi rice value chain (Imbo Plain), the Congolese rice value chain (Ruzizi Plain) and the Rwandan rice value chain (Bugarama Plain). The diagnostic analysis was about analyzing the rice-farming environment (ie policies and support services accessed by actors along the value chain), analyzing economic performance of these three value chains and to identify the factors that may foster the development of a value chain with a regional potential. For this purpose, the study adopted the field approach, which allowed carrying out investigations during three years (2013 to 2015). The data collection process involved a sample of 228 actors distributed equitably among the three countries. It combined several techniques, namely, direct stakeholder surveys (producers, processors, collectors, wholesalers and retailers), interviews with various support structures and state services, focus group discussions with producer groups and representatives of their organizations. The analysis of these three value chains driving conditions linked the policies implemented in each country and the access by the actors to certain production factors and services such as land, water, credit and the use of inputs. It also highlighted the issue of wage labor and its different roles in the sector. The analysis shows that land policy in Bugarama plain in Rwanda has reduced the cost of land to more than half compared to land costs in Burundi and the DRC. Moreover, this policy is accused by the producers of Bugarama of limiting their entrepreneurial innovations since they can not enlarge their farms (the cultivated area is 0.23 ha). Despite the high cost of water access and management, all rice plots access irrigation water in Rwanda, while the lack of organization and good water management is one of the factors behind low yields in Burundi and the DRC, where 25% and 40% of the rice plots have difficulties in accessing water. Regarding access to agricultural credit, the results reveal that the value chain of rice in the three countries experiences the lack of funding in spite of improvements observed in Rwanda. The rate of access to credit is 17.5% (in Burundi), 16% (in DRC) and 52.8% (in Rwanda), and among them rice farmers with access to formal credits account for only 8% (in Burundi), 10% (in the DRC) and 37.5% (in Rwanda). Analysis of the wage labour force shows that labor is not as widely available as was thought in the study area. Indeed, the DRC is the zone of deficit in wage labor due to the rural exodus and the diversity of economic activities. In the DRC, 60% of the rice workforce used is foreign, including 46% from Burundi and 14% from Rwanda. This mobility of the workforce leads to technology transfers, the supply of inputs at lower cost, but also to consolidate the social cohesion in a post-conflict context. The economic analysis of these three value chains reveals that production costs in the study area remain very high, varying between 292 and 388USD per ton. The highest costs are observed in the DRC where paradoxically there is a better financial performance in terms of profit and added value. The statistical tests carried out on certain parameters identified by the financial analysis undermines the policies regarding the inputs subsidies, agricultural financing and fixing sales prices. Indeed, there are no significant differences between the means of rice farmers who benefit from these policies and those who do not. Paradoxically, statistical analyzes reveal that rice farmers not affected by the pricing policy (they are not price takers) have a good financial performance in terms of income. The three studied areas are complementary in terms of the development potentials of a regional value chain. Indeed, Rwanda has modern underutilization peeling plants that are capable of responding almost entirely to the needs of the whole plain. In addition, Burundi and the DRC should develop land and water potentials to increase production. Several other regional structures in favor of the regional value chain have to be relaunched or strengthened in logic of rice development in the Ruzizi plain. These include the benefits of economic integration of the CEPGL countries. [less ▲]

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See detailCapturing fine-scale population structure towards molecular reclassification of patients
Chaichoompu, Kridsadakorn ULiege

Doctoral thesis (2017)

During the past decades, population structure analysis has been playing an important role for stratifying populations and tracking back population ancestries. Population structure is mainly due to non ... [more ▼]

During the past decades, population structure analysis has been playing an important role for stratifying populations and tracking back population ancestries. Population structure is mainly due to non-random mating between subgroups in a population because of various reasons, being of social, cultural, or geographical nature. Genetic structure in populations may also arise from known or unknown family relationships. Complex disease analyses, in case-control genetic association studies particularly, can be affected by so-called cryptic relatedness, which refers to unobserved ancestral relationships between study individuals. As population structure may confound results from genetic association studies and studies that aim to detect clinically relevant substructure in patients, its detection is highly relevant. Revealing population structure is really essential. Notably, removing unwanted population structure in molecular-based patient subtypes detection is likely to lead to subtle or fine-scale remaining structure. In this thesis, we developed a novel genetic structure detection tool, hereafter referred to as IPCAPS, which can also be used as, or extended to, a tool for fine-scale reclassification of patients. IPCAPS utilizes a fixation index (FST) to measure the distance between clusters for iterative loop termination. An FST > 0.001 is typically seen as evidence for genetic differentiation between European populations. We also introduced a novel heuristic called EigenFit as one of the stopping criteria. Although our tool has been developed to easily accommodate multiple data types, we have illustrated the conception of IPCAPs and its performance on simulated and real-life data using panels of genome-wide SNP data. SNPs, standing for Single Nucleotide Polymorphisms, are the most common type of genetic variation among people. There are roughly 10 million of them. We evaluated the performance of IPCAPS using a variety of simulation studies and simulation scenarios, including varying sample sizes, varying SNP panel sizes, the absence or presence of outliers, large or very small genetic separation between synthetic populations. The performance of IPCAPS was measured by estimating accuracy and computation time. We observed that our method generally outperformed a selection of other iterative pruning based methods such as ipPCA, iNJclust, and SHIPS. Also in the presence of outliers, IPCAPS' computation time is largely affected by sample size, not by the number of SNPs included in the analysis. We furthermore validated our tools and proposed protocols on a variety of real-life datasets. These datasets differed in complexity and ranged from worldwide sample collections, over regional populations, to geographically confined samples. In particular, we analyzed data from the International HapMap Project, the 1000 Genomes Project, Africa and Thailand. We proposed a suitable protocol to correct for population stratification and to perform patient subgrouping in samples from the International IBD Genetics Consortium (IBD referring to inflammatory bowel disease). All developed analysis protocols involved guidelines for the interpretation of identified strata. In conclusion, IPCAPS is a promising structure detection analysis tool. It was able to identify fine structure in African and HapMap populations, previously unreported. IPCAPS analysis also suggested the presence of at least 3 subtypes of Crohn’s disease and at least 3 subtypes of Ulcerative Colitis patients. More work is needed to evaluate the importance of these findings in clinical practice and for precisions medicine. [less ▲]

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See detailEffect of different crop residue management on soil hydraulic properties - a study in a silt loam soil in Belgium
Parvin, Nargish ULiege

Doctoral thesis (2017)

In recent decades, agriculture is challenged to develop strategies for sustainability which conserve non-renewable natural resources such as soil. Soil improving conservation systems aim at improving soil ... [more ▼]

In recent decades, agriculture is challenged to develop strategies for sustainability which conserve non-renewable natural resources such as soil. Soil improving conservation systems aim at improving soil functions and at the same time ensuring high productivity. Such soil management systems have to be adapted to climate and soil specific conditions, and may include reduced tillage, balanced crop rotation, retention of crop residues, cover crops, and appropriate timing of field operations. Changes in soil functions have huge impacts on environmental flows like hydrology, crop production, solute transfer, and CO2 emission at macroscale. Soil structure is considered as one of the key factors for soil functioning. The effect of different land management on soil structure and consequently on soil hydrodynamics is not fully understood and still under investigation. The main aim of this thesis was to evaluate the effect of crop residue management on soil structure by measuring soil hydraulic properties in pedon and core scale. The agronomic context was different crop residue management in a reduced tillage system. The experimental field is named as Solresidus located in Gembloux, Belgium. Since 2008, the field has been under conservation system. Different residue management includes reduced tillage with incorporation of crop residues (RT-in) and without incorporation (RT-out). A large part of this thesis was methodological development to obtain accurate results from experimentations. Many studies have been made and documented in literature to develop indirect methods to predict soil hydrology from soil water retention curve (SWRC). There is no measuring device available which can determine the SWRC over the entire soil moisture range. Therefore, one of the methodological developments was to obtain complete SWRC by combining three different methods in core scale: X-ray computed microtomography (X-ray CT), HYPROP evaporation and Richards pressure plate method to obtain the entire SWRC. The combination of these methods found well justified to obtain the accurate and complete SWRC. Saturated hydraulic conductivity (Ks), specific connectivity (SC) of soil pores and bulk density of the soil were also measured in core and pore scale. There were soil moisture sensors (capacitance sensors) in the field to observe the soil moisture dynamics in pedon scale. Another important methodological development was to obtain the calibration results with the moisture sensor according to the soil texture and horizons. Calibration results found quite satisfying to get the accurate moisture content of the field; it was also noticed that it could be over estimation of soil moisture without the calibration. Significantly, average higher moisture content was observed by the moisture sensors in RT-in than RT-out during the canopy formation to harvest of winter wheat in 2014. The SWRCs also showed that plant available water content was higher in RT-in than RT-out. SC of soil pores was also significantly higher at the surface soil of RT-in than RT-out. RT-in found to have significant positive effects on soil structure by reducing bulk density, increasing SC, Ks and retention of soil moisture during the observation period of this study. Crop yield was marginally higher and organic matter content was significantly higher in RT-in than RT-out (results from close collaboration). Therefore, reduced tillage with residues incorporation found to have better soil hydraulics together with better crop yield than reduced tillage without incorporation of crop residues. [less ▲]

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See detailValorisation des sous-produits de la graine de Jatropha curcas L. en production de poulets au Sénégal
Nesseim, Thierry ULiege

Doctoral thesis (2017)

This study evaluated the effects of Jatropha curcas kernel meal incorporated in poultry feed in Senegal. All experimentations were conducted in the experimental station of the National Superior School of ... [more ▼]

This study evaluated the effects of Jatropha curcas kernel meal incorporated in poultry feed in Senegal. All experimentations were conducted in the experimental station of the National Superior School of Agriculture (ENSA) of Thies University (Senegal). In the same way, all chemical analyses were performed in the feed science laboratory of the Department of Animal Production of ENSA. The first part of this study was a description of toxic and anti-nutritional compounds present in J. curcas seed meal, which most important are phorbol esters, characteristics of Euphorbiaceae, known for its inflammatory effects, and curcin, a toxalbumin which manifested by an irritant action. Other compounds, also present, interfere more or less with digestive process in animals. Different treatments were applied, with different levels of success, to reduce or eliminate these toxic and anti-nutritional compounds for the valuation of this meal in animal feed. A particular emphasis was placed on the biological treatment, not only for a significant reduction of these compounds but also to improve the nutritional quality of the meal. The second part of this work has focused on the study of the effect of the J. curcas kernel meal obtained by chemical de-oiling, incorporated in corn at 4, 8, and 12% and distributed to broiler chickens at the end their growth phase to assess their feed intake, their daily weight gain and diet digestibility. For all diets, feed intake was inversely influenced by the incorporation on the jatropha kernel meal, leading a weight gain decrease in animals that received the largest amounts of jatropha despite the absence of toxicity signs and mortality. Similarly, the apparent digestibility of each nutrient has been affected by the incorporation of jatropha kernel meal as well as the differential digestibility thereof. The low digestibility, especially protein was explained by the low availability of meal proteins incorporated corn, but also the presence of anti-nutritional and toxic factors still present in the diets used. The third part of this work has presented results of two experimentations conducted successively. The first one studied the effect of jatropha kernel meal obtained by a chemical de-oiling, incorporated in diets at 4 and 8%, on broiler chickens performance during growing/finishing. The second experimentation studied the effect of the same cake that was heat treated before incorporated in diets at 8%, on day-old broiler chicks’ performance. In one as the other experimentation, feed intake and daily weight gain were affected by the incorporation of jatropha kernel meal. It was the same for the total mortality rates recorded despite the absence of visible signs of toxicity. These experimentations confirmed other experimentations have shown that the de-oiling of jatropha kernel meal followed by heat treatment, even if it caused a significant reduction of anti-nutritional compounds, did not remove all the toxic factors that may even interfere with feed intake and weight gain of animals. These observations were not confirmed in the fourth part, which studied the effects of jatropha kernel meal obtained by chemical de-oiling, subject to heat treatment then biological treatment with Aspergillus niger and incorporated in diets at 8%, on day-old broiler chicks performance. Indeed, the feed intake, the weight gain as well as the viability of animals were not affected by the incorporation of jatropha. These successive studies were among the first which interested the same animal species at different levels of development based on a product whose nutritional quality is proven, but has toxic and anti-nutritional factors could not be completely eliminated despite different treatments applied. The application of heat treatment may have helped to reduce some anti-nutritional compounds (curcin and trypsin inhibitor) but without improve feed intake and weight gain. Considering the reaction of animals subjected to diet, biological and heat treatments may have reduced the toxicity of jatropha kernel meal, which has afected the feed intake of animals and thus the weight gain. This study showed that, despite its nutritional level, J. curcas kernel meal presented limitations in its use as a raw material that can integrate a ration for broilers in Senegal but hopes remain with biological treatments. [less ▲]

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See detailContraintes et stratégies d’amélioration de la filière maïs au Rwanda
Musabanganji, Edouard ULiege

Doctoral thesis (2017)

For more than a decade, Rwanda has adopted a series of policies and strategies aimed at economic development and the improvement of the living conditions of its predominantly agricultural population. In ... [more ▼]

For more than a decade, Rwanda has adopted a series of policies and strategies aimed at economic development and the improvement of the living conditions of its predominantly agricultural population. In agriculture, implementation of these strategies and related programs has been accompanied by a series of advances in the adoption of farming technologies and increasing agricultural production. However, the country's economy is still characterized by subsistence agriculture, and for the maize sector in particular, the country is continuously depending on imports to meet domestic demand, and maize processing plants always operate below their productive capacity. This research aims to examine the level of competitiveness of this sector in the current production and marketing conditions in order to identify existing constraints and formulate the strategies that can improve the level of economic performance of maize production and maize marketing system. The data used to study the economic performance of maize production come from close monitoring of maize production activities on a sample of 50 producers from five maize producers’ cooperatives selected in the districts of Huye, Rusizi, Gasabo, Burera and Bugesera during two growing seasons. They were supplemented by direct observation, interviews with targeted resource persons, and focus group discussions. The analysis was done using group analysis and appropriate statistical methods. The study of the maize marketing system used the 'Structure-Conduct-Performance' model with data collected from a sample of 150 producers and 17 assemblers selected in the districts of Burera, Bugesera and Huye, and 15 transporters, 5 wholesalers and 15 retailers selected at the national market of Kigali. The results revealed that for many producers, the yield is very low compared to theoretical expected yields, production costs are higher and exceed sales prices, gross margin and family labor income are negative, and the gross added value created by maize producers is not high even though it is positive. The analysis showed that the increase in the selling price positively influences the gross margin, added value and family labor income, and that the rational use of improved seeds, chemical fertilizers and soil conditioners improves the yield. This clearly shows that improving the selling price and rational use of inputs can significantly contribute to making maize production a more profitable and income-generating activity. The study also identified challenges that hamper the production process. These include non-availability of, and low access to inputs, inadequate technical support, limited financial resources and low access to formal agricultural credit, high marshlands rental fee, method of fixing the maize floor price and lack of mechanisms ensuring its use by potential buyers, the lack of storage infrastructure, and the unsustainability of inputs subsidies granted by the government. At the marketing level, the results revealed that several actors are involved in the marketing of maize. The study also revealed that maize imported from Uganda is sold on domestic market at lower prices than locally produced maize, which attests the increase in the cost of maize production in Rwanda compared to Uganda and the low level of competitiveness of the local maize compared to Ugandan maize. The improved status of feeder roads and the high level of access to price information by actors were highlighted among the technological innovations that helped improve the marketing system of foodstuffs in general and maize in particular, which was also evidenced by the level of integration observed between districts maize markets and the national market of Kigali. However, the lack of enough capital and low access to formal credit were noted as major constraints by most of the chain actors. In the light of all these results, it is clear that the production and marketing of maize are not done in good conditions at all levels. This in turn undermines the sector's ability to respond adequately to domestic demand, generate income for actors and integrate itself into both domestic and regional markets. Therefore, strategies aiming at scaling-up the maize production and marketing, and improving working conditions of the sector operators were recommended. These strategies include the implementation of actions to improve access to finance by farmers and other actors; making inputs avail and accessible; reorganizing the marketing system especially in terms of fixing and using the floor price; making available storage facilities where necessary; improving the monitoring, training and sensitization of maize producers on farming techniques and the use of improved technologies; and harmonizing the marshland rental fee at national level. [less ▲]

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See detailDéfinition d’un outil d’aide à la décision spatiotemporel structurant et articulant les potentialités de développement agricole : cas du Niger
Andres, Ludovic ULiege

Doctoral thesis (2017)

The concern about food insecurity in rural populations needs to be rethought and adapted to the overall living conditions of households by shifting to a concentrated spatial scale and a long-term analysis ... [more ▼]

The concern about food insecurity in rural populations needs to be rethought and adapted to the overall living conditions of households by shifting to a concentrated spatial scale and a long-term analysis. This change will allow identifying territories on a finer scale than the national level in order to allocate development objectives and to link them to areas with high development potential. The finer level of analysis will also allow regrouping the actions carried out on a smaller scale in order to structure all the activities carried out on the targeted area and population. The general comment that the development and emergency aid has been focused in circumscribed areas and that the level of analysis is based on two scales, one "macro" (national, regional, departmental) and the other "micro" (village, community, household, individual and community) reinforces the need to create an intermediate level of analysis. The latter will serve to improve the structure other actions carried out at different levels and the articulation of the activities to be carried out and the targeted population. From a state of the art analysis of subject such as development, targeting, territory, food security, resilience, etc; different finding have led to the definition of a major question and an objective which form the core structure of the present dissertation. The research question is defined as "how to structure the targeting and identification of areas with high potential to articulate all the emergency and development actions carried out on several scales of analysis?”. At the end of these observations, the objective of this research is "the establishment of a tool to support spatial and temporal decision making in structuring the emergency and development actions and targeting of populations subjected to food insecurity ". Three considerations emerge from this objective and research question: spatiotemporal analysis and targeting, development potentials, rural production systems. The various productions are also studied over a long series in order to consider the yield variations over time. Finally, these two analyzes, spatial (systems) and temporal (yields) are crossed in order to demonstrate the contribution of this decision-supporting tool in the articulation and structuring of the other two levels of targeting populations to food insecurity. The decision-supporting tool has been tested on the case study of the Nigerian population. The main outcomes are: the characterization of the opportunities and constraints of the Nigerian rural production systems; the identification of the products to be developed by production system; the identification of the most promising pathways by means of the distribution of the yields by systems. Finally, an essential point must be made about the increase of conservation methods and transformations for increasing the added value obtained by Nigerian households. At the end of this dissertation, the tool demonstrated its importance in structuring and articulating the targeting of food insecurity in the field of emergency aid and development: The territorial zones in the production systems identify the problems to which one or several solutions must be found. Production systems allow a concentration of actions according to the definition of the general and specific objectives of the agricultural development assistance programs. Potential outputs to be developed in production systems allow diversification of agriculture and structuring of development from a national point of view. The actions defined by the Technical and Financial Partners at the level of a village, a community and / or a commune can be more easily integrated into this scale of analysis and can be structured later in national development policies Agricultural policy. The increase in productivity in Niger depends on the development of products within the most favorable zones and not on the whole territory. However, this tool is complementary to the other targeting tools already in place. It should also be complemented by the same type of analysis at the level of West Africa and an analysis of the flows and prices condition to favor the flow of production. [less ▲]

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See detailPhenotyping hygienic behavior and studying diversity in honey bees (Apis mellifera L.): methodological issues and solutions
Leclercq, Gil ULiege

Doctoral thesis (2017)

Honey bees (Apis mellifera L.) are a crucial resource for world agriculture. The global stock of honey bees has increased over the last five decades. In contrast, honey bees have been declining in several ... [more ▼]

Honey bees (Apis mellifera L.) are a crucial resource for world agriculture. The global stock of honey bees has increased over the last five decades. In contrast, honey bees have been declining in several regions, especially in the northern hemisphere. Among the factors responsible for these regional declines, the parasitic mite Varroa destructor plays a central role and is considered as one of the main threats for apiculture. A sustainable solution to the problems caused by V. destructor is to breed Varroa-resistant honey bees. In this context, in Belgium, a research project was developed with the aim of studying the diversity of honey bees in Wallonia, and selecting, within this “local” diversity, Varroa-resistant honey bees. This project required methods to accurately phenotype Varroa-resistance traits, and methods to study the diversity of honey bee populations. In this thesis, we decided to work on these methods, which are a prerequisite for such research project. Two independent objectives were developed: (1) solving the controversy and methodological issues regarding the quantification of hygienic behavior in honey bee colonies, and (2) designing a new method to study the diversity of honey bee admixed populations covering a large-scale area, using pool-based sequencing data. The hygienic behavior of worker bees contributes to the social immunity of honey bee colonies. The manifestation of this behavior consists in detecting and removing unhealthy or dead brood. In this thesis, we reviewed the drawbacks, the benefits, and the methods to test for hygienic behavior, in honey bee colonies. We concluded that, while hygienic behavior was efficient against some brood diseases, it was difficult to draw any definitive conclusion on the efficiency of this behavior against V. destructor. Hygienic behavior likely contributes to Varroa-resistance, but the controversy is fueled by the use of inappropriate bioassays to quantify the hygienic removal of Varroa-infested brood. In our experiments, we showed that a commonly used bioassay, the freeze-killed brood removal bioassay, was unreliable to approximate the benefits arising from the hygienic removal of Varroa-infested brood. As an introduction to the second part of the thesis, we reviewed how human has contributed to reshape the diversity of honey bee populations worldwide, except in Africa. Human management was shown to increase the proportion of admixed populations, sometimes to the detriment of subspecies populations (such as in Belgium). Then, we presented a new approach to study the admixture of hybrid honey bee populations. It was based on a reduced representation of the genome (through genotyping-by-sequencing). In this approach, we enabled the use of pool-based sequencing data by simulating an individual genotype for each pool, sampled from a hybrid colony. Finally, some conclusions and discussion were brought on a few perspectives and research avenues about (1) the phenotyping of hygienic behavior towards Varroa-infested brood, and (2) the study of admixture in honey bee populations. [less ▲]

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See detailLipin-1 regulates cancer cell phenotype and is a potential target to amplify the effect of metabolic inhibitors
Brohée, Laura ULiege

Doctoral thesis (2017)

An increased lipogenesis was reported in various cancers and its inhibition represses proliferation and induces apoptosis of cancer cells while barely affecting most normal cells. The family of lipins ... [more ▼]

An increased lipogenesis was reported in various cancers and its inhibition represses proliferation and induces apoptosis of cancer cells while barely affecting most normal cells. The family of lipins encompasses three members: lipin-1, -2 and -3. All exhibit dual functions as enzymes, catalyzing the de-phosphorylation of phosphatidic acid to diacylglycerol, and as co-transcriptional regulators. Thus, they are able to regulate lipid homeostasis at several nodal points. However, no studies addressed the involvement of these proteins in cancer progression neither in vitro nor in vivo. During this PhD work, we first investigated the importance of lipin-1 on prostate cancer cell phenotype. We showed that lipin-1 expression is increased in various cancer cell types both in vitro and in vivo in human prostate tumor samples. The specific inhibition of lipin-1 in prostate and breast cancer cells demonstrated its critical importance for cell proliferation and migration through deregulation of several intracellular signaling pathways. This study demonstrated for the first time that the targeting of lipin-1 is a potential new anti-cancer strategy that could be used alone or in combination with drugs like rapamycin. During the course of these investigations, we also observed a compensatory regulation between lipin-1 and lipin-2 preventing the complete inhibition of lipins enzymatic activity when using a siRNA approach. Therefore, we focused our interest on inhibiting all lipins through treatment with a pharmacological inhibitor, propranolol. This drug also induced a blockade of the late phases of autophagy, likely because the inhibition of all lipins decreases diacylglycerol synthesis, which is required for the maturation of autolysosomes. Autophagy is a pro-survival mechanism induced by several stresses or by anticancer agents. In the case of the glycolysis inhibitor 2DG, the induction of autophagy limits its anticancer effects in monotherapy. In the light of their individual specific effects on cancer cells, we hypothesized that the combination of propranolol and 2DG might exert a more than additive toxic effect on cancer cells. In this second study, we report that combined treatment is effective on preventing prostate cancer cell proliferation, inducing cell apoptosis, altering the function of several organelles as mitochondria, endoplasmic reticulum and Golgi apparatus in vitro but also in suppressing tumor growth in vivo. Altogether, our data suggest that lipins are key players involved in cancer progression. Targeting lipins, alone or in combination with other treatments, could open new avenues in anticancer therapy. [less ▲]

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See detailEnvironmental sustainability of the Walloon cereal sector using Life Cycle Assessment (LCA) fed with local data - Current situation and potential evolution scenarios
Van Stappen, Florence ULiege

Doctoral thesis (2017)

In a world facing a growing population and diminishing resources, agriculture has a major role to play in terms of sustainable provision of food and feed, job creation in rural areas, preservation of ... [more ▼]

In a world facing a growing population and diminishing resources, agriculture has a major role to play in terms of sustainable provision of food and feed, job creation in rural areas, preservation of natural resources and climate change mitigation. As a very intensive agricultural region, Wallonia (southern Belgium) dedicates more than half of its arable land to cereal crops. Thanks to a long history of research and development, rich soils and favorable climate conditions, yields of cereals such as wheat or barley cropped in Wallonia are amongst the highest in the world. As a major sector in the Walloon agricultural landscape, the cereal sector therefore calls for production and processing opportunities that meet the requirements for sustainable agriculture. In this context, the objectives of the present thesis were to evaluate the environmental sustainability of current and potential evolution scenarios for the Walloon cereal sector using the Life Cycle Assessment (LCA) methodology fed with local data. On the basis of current uses of cereals grown in Wallonia, this research aimed first at describing various scenarios for the future of the Walloon cereal sector. Based on contrasting hypotheses, four scenarios for the uses of Walloon cereals by 2030 were defined with the support of stakeholders involved in all parts of the sector. Issues such as competition between food uses (both direct and indirect) and non-food uses or Walloon dependency on cereal imports were addressed in these scenarios, which illustrate contrasting future situations, from food self-sufficiency to drastic globalization, through the development of new outlets combining changes in crop-growing practices and consumption habits and new technologies. Using the widely used, yet continuously improved, methodology of LCA, the second part of this work evaluated the environmental impacts of cereal production in Wallonia. It identified the production steps with the greatest contribution to environmental impacts. The leading contributor was mineral fertilizer production, for which this work used up-to-date data from best available technologies and demonstrated the importance of using such recent data. The second greatest contributor to environmental impacts was emissions from mineral and organic fertilizer use on field, before and during plant growth until harvest. As well as being very important, these emissions are also extremely variable, depending on agricultural practices, soil and weather conditions, and thus particularly difficult to assess. This is particularly true of nitrogen- and carbon-related emissions, whose dynamics are very problematic to evaluate. This work demonstrated the limits of commonly used emission models, which use generic emission factors and therefore weaken LCA results. As a result, the use of more specific models, based on field trials and adapted to local conditions, was placed at the top of the list for future research in this area. From a methodological point of view, this part of the work also confirmed the influence of the functional unit used to express LCA results. It showed the strong link between yield and environmental impacts, and identified cereal crops demonstrating efficient input management, with lower impacts per kilogram of product, per hectare and per euro. Other methodological choices, such as the choice of allocation factor between grain and straw, also showed their relevance. In short, this part of the work demonstrated the pertinence of using local data to feed LCAs of agricultural productions and identified the most sensitive parameters to be adjusted in priority to achieve good quality LCAs. Thirdly, on the basis of an original methodology comparing equivalent balanced animal diets, a case study on cereal processing in a biogas plant assessed the consequences of diverting feedstock from the animal feed industry into the bioenergy sector. Despite the environmental benefits brought by fossil fuel displacement and digestate use as organic fertilizer, the replacement of raw materials previously used as animal feed induces additional impacts potentially more important than the benefits of this technology. The key message from this finding is that it is urgent to stop using potentially edible raw material for bioenergy production. The only countervailing consideration here is that current trends towards decreasing meat consumption would in the longer term make lands and raw material available for purposes other than animal feed. The strength of all the LCA results in this work was tested using a wide range of sensitivity and uncertainty analyses. These good practices, often neglected due to time constraints, proved to be essential to be able to draw robust conclusions. Through the application of LCA to the Walloon cereal sector, this work had some practical implications for enhancing the quality of LCAs of agricultural productions. It showed the sensitivity of the method to the use of local data and demonstrated the strengths and limitations of the method. It has produced specific LCA references for cereal production in Wallonia, which are useful for feeding environmental impact assessments of cereal-based products sourced with Walloon cereal crops. Further improvements could include the use of specific models to assess on-field emissions from fertilizer use and the consideration of additional impact indicators regarding soil organic stock changes, biodiversity impacts and water consumption. Additionally, assessing impacts at the rotation scale would reflect more accurately the way farmers optimize their crops and allow for the evaluation of more diverse cropping systems. [less ▲]

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See detailOf trees and men: new insights into man-environment relationships in the moist forests of central Africa during the late Holocene
Morin, Julie ULiege

Doctoral thesis (2017)

In central Africa, vegetation history has been documented by paleoenvironmental studies (especially palynology), which mainly concerned the way climate has shaped the forest landscapes. Human impacts in ... [more ▼]

In central Africa, vegetation history has been documented by paleoenvironmental studies (especially palynology), which mainly concerned the way climate has shaped the forest landscapes. Human impacts in this region have hardly been studied so far, especially at local scale. The main objective of this PhD is to propose an approach based on archaeology and the use of charred botanical remains found in soils, either wood charcoal or seeds, in order to document the Holocene anthropogenic impacts on the forest structure and composition. When coupled with the diachronic analysis of human activities, these land-use biomarkers can allow a better understanding of the relationship between man and his environment in central Africa during this period. Thereby, the first part of this PhD introduces the conceptual framework and the materials and methods used during the research. Then, the second part constitutes the core of the work, and presents the chronology of human activities in the northern Congo Basin, the use of biomarkers to discrimate between these activities, either domestic or agricultural, and the effect of the recent anthropogenic activities in the dynamic of several light-demanding tree populations. Finally, the third part draws the main recommendations of the work, and formulates potential for additional research. [less ▲]

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See detailPush-Pull strategy to control aphids in Belgium and China
Xu, Qingxuan ULiege

Doctoral thesis (2017)

Wheat (Triticum aestivum L.) is one of the most cultivated crops in temperate climates. As its pests are mainly controlled with insecticides which are harmful to the environment and human health ... [more ▼]

Wheat (Triticum aestivum L.) is one of the most cultivated crops in temperate climates. As its pests are mainly controlled with insecticides which are harmful to the environment and human health, alternative practices such as intercropping have been studied for their potential to promote biological control. Fifty original research papers were obtained from a systematic search of the peer-reviewed literature. Results from a vote-counting analysis indicated that, in the majority of studies, pest abundance was significantly reduced in intercropping systems compared with pure stands. However, the occurrence of their natural enemies as well as predation and parasitism rates were not significantly increased. Nevertheless, other practices could be combined with intercropping to favour natural enemies and enhance pest control. Dispersal of viruses is intimately tied to their vectors. Aphids are known to invest in costly antipredator behavior when perceiving cues of predators. Before presenting the results and the answers to the previous questions, a brief research was conducted in order to have an overview of the intercropping on the spread of aphids, to assess the potential impact of intercropping systems attracting natural enemies on the virus transmission. We studied aphid antipredator behavior in intercropping with wheat-broad bean (Vicia faba L.) as a model. The bird cherry-oat aphid, Rhopalosiphum padi Linnaeus, is an important vector of the barley yellow dwarf virus. The effects of two natural aphid enemies, adult and larvae of the seven-spot ladybeetle, Coccinella septempunctata Linneaus, on R. padi dispersion was studied under laboratory conditions. Results show that in receptor lines (other lines than the source one), two hours after the experiment started, aphids were more abundant in monoculture than intercropping in the presence of ladybeetle adults and larvae and after 24 hours, it was still the case in the presence of predatory larvae. These results might be explained by the non-host plant chemical cues and the physical barrier that was broad-bean plants confusing R. padi when searching for their host plants after being dropped from wheat by predators. After make sure that the intercropping can reduce the dispersal of aphids in the presence of predators, in fine potentially limiting virus dispersal, especially shortly after aphids colonize plants. Then we try to solve how to increase the number of natural enemies of intercropping in Belgium and China. Semiochemical substances have been tested to enhance biological control, with inconsistent results. Combining semiochemical and intercropping can be an interesting way to maximize pest control. In Belgium, a two-year setup involving wheat–pea strip intercropping combined with the release of E-β-farnesene (EBF) or methyl salicylate (MeSA) was tested as a push–pull strategy to simultaneously repell aphids and attract beneficials. Two types of slow-release formulation (i.e., oil and alginate beads) containing EBF or MeSA were deployed with intercropping. The abundance of aphids was significantly decreased, hoverfly larvae and mummified aphids increased on both pea plants and wheat tillers by the release of oil-formulated EBF and MeSA. The proportion parasitism of aphids-parasitism rate was also increased by treating both crops in both years. Releasing EBF through oil rather than alginate beads proved significantly better for attracting natural enemies and reducing aphids. Aphids were negatively correlated with the density of hoverflies (both adults and larvae) and numbers of mummies. We also tested the combining in China and the experiments were set-up: wheat-pea strip intercropping solely, intercropping combined with the release of EBF, and intercropping combined with the release of MeSA, each treatment repeated three times. The total number of aphids throughout the growing season was significantly decreased in treatments with releases of semiochemicals compared to intercropping solely. The effect was stronger with MeSA than with EBF on the control of R. padi, and hoverflies and lacewings were twice more numerous in MeSA. All the results showed that combining intercropping with the release of EBF or MeSA formulated in oil can significantly reduce aphid density and attract their natural enemies. Therefore, the combination of both strategies could help farmers reduce the use of insecticides Dispersal of viruses is intimately tied to their vectors. Aphids are known to invest in costly antipredator behavior when perceiving cues of predators. Before presenting the results and the answers to the previous questions, a brief research was conducted in order to have an overview of the intercropping on the spread of aphids, to assess the potential impact of intercropping systems attracting natural enemies on the virus transmission. We studied aphid antipredator behavior in intercropping with wheat-broad bean (Vicia faba L.) as a model. The bird cherry-oat aphid, Rhopalosiphum padi Linnaeus, is an important vector of the barley yellow dwarf virus. The effects of two natural aphid enemies, adult and larvae of the seven-spot ladybeetle, Coccinella septempunctata Linneaus, on R. padi dispersion was studied under laboratory conditions. Results show that the total number of aphids was higher in intercropping than monoculture in treatments without ladybeetles, while the contrary was observed in the presence of ladybeetle larvae. These results might be explained by the non-host plant chemical cues and the physical barrier that was broad-bean plants confusing R. padi when searching for their host plants after being dropped from wheat by predators (i.e. associational resistance). After make sure that the intercropping can reduce the dispersal of aphids in the presence of predators, in fine potentially limiting virus dispersal, especially shortly after aphids colonize plants. Next step will be to solve how to increase the number of natural enemies of intercropping in Belgium and China. Semiochemical substances have been tested to enhance biological control, with inconsistent results. Combining semiochemical and intercropping can be an interesting way to maximize pest control. In Belgium, a two-year setup involving wheat–pea strip intercropping combined with the release of E-β-farnesene (EBF) or methyl salicylate (MeSA) was tested as a push–pull strategy to simultaneously repell aphids and attract beneficials. Two types of slow-release formulation (i.e., oil and alginate beads) containing EBF or MeSA were deployed with intercropping. The abundance of aphids was significantly decreased, hoverfly larvae and mummified aphids increased on both pea plants and wheat tillers by the release of oil-formulated EBF and MeSA. The proportion parasitism of aphids-parasitism rate was also increased by treating both crops in both years. Releasing EBF through oil rather than alginate beads proved significantly better for attracting natural enemies and reducing aphids. Aphids were negatively correlated with the density of hoverflies (both adults and larvae) and numbers of mummies. We also tested the combining in China and the experiments were set-up: wheat-pea strip intercropping solely, intercropping combined with the release of EBF, and intercropping combined with the release of MeSA, each treatment repeated three times. The total number of aphids throughout the growing season was significantly decreased in treatments with releases of semiochemicals compared to intercropping solely. The effect was stronger with MeSA than with EBF on the control of R. padi, and hoverflies and lacewings were twice more numerous in MeSA. All these results showed that combining intercropping with the release of EBF or MeSA formulated in oil can significantly reduce aphid density and attract their natural enemies. Therefore, the combination of both strategies could help farmers reduce the use of insecticides. [less ▲]

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See detailIdentification et analyse fonctionnelle de nouveaux variants d’épissage du CD46 des bovidés, le (co)-récepteur du virus BVD/MD
Alzamel, Nidal ULiege

Doctoral thesis (2017)

The pestivirus bovine viral diarrhea virus (BVDV) is known to bind to the CD46 molecule, which subsequently promotes entry of the virus. Mapping of the BVD-virion-binding site has shown that two peptides ... [more ▼]

The pestivirus bovine viral diarrhea virus (BVDV) is known to bind to the CD46 molecule, which subsequently promotes entry of the virus. Mapping of the BVD-virion-binding site has shown that two peptides, 66EQIV69 and 82GQVLAL87, located on antiparallel beta sheets in the most distal complement control protein module (CCP1), provide the attachment platform. In the present study, we reveal new CD46-encoding transcripts that are predicted to encode CCP1-containing soluble forms. Further, we show that the serum of most adult cattle contains soluble CD46 (sCD46) and that a recombinant soluble isoform neutralizes BVDV infectivity in an in vitro assay. We have then established an ELISA for determination of plasma sCD46 in a large cohort of animals. Overall, serum sCD46 amounts to 8 ± 18 ng/mL (mean ± SD, n = 543), with a IC [95-105] ranging from 6,4 to 9,8 ng/mL and extreme values between 0 and 178 ng/mL. We found that sCD46 is not detectable in fetal and neonatal sera and that its plasma concentration increases progressively up to adulthood. We also detected high- and low-sCD46 performers and show that this phenotype does not depend of environment. As modern rearing techniques make it possible to disseminate genetically-determined phenotypes very quickly in a population, a large-scale study examining whether high-sCD46 animals provide epidemiological protection against BVDV infection and transmission should be undertaken [less ▲]

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See detailAdaptive capacity assessment of damselfishes (Pomacentridae)
Gajdzik, Laura ULiege

Doctoral thesis (2017)

Assessing the multiple facets of adaptive capacity is a core issue as it reflects species' ability to cope with variations in environmental conditions. Within the threatened coral reefs, the Pomacentridae ... [more ▼]

Assessing the multiple facets of adaptive capacity is a core issue as it reflects species' ability to cope with variations in environmental conditions. Within the threatened coral reefs, the Pomacentridae (damselfishes) represent a very suitable model to undertake such issue. Damselfishes are one of the most ecologically dominant reef fish families whose lineages repeatedly radiated across convergent trophic strategies. These strategies comprise (1) pelagic feeders (mainly picking zooplankton in the water column), (2) benthic feeders (essentially feeding on algae and vagile invertebrates on the benthos) and (3) an intermediate group (foraging in the entire bentho–pelagic compartment). To date, most studies compared the degree of vulnerability between specialists and generalists because the first ones are thought to have a higher risk of extinction. The tripartite trophic guild system in Pomacentridae provides the opportunity to step out of the binary "specialist–generalist" classification and to robustly grasp the adaptive capacity by focusing on fundamental units in assemblages. In the present thesis, I estimated the ecology of damselfishes by quantifying their eco–functional diversity (including trophic, habitat and behavioural diversity and also the ecosystem functions they performed) and by gauging their abiotic (i.e. species–environment relationship) and biotic (i.e species–species relationship) interactions. Ecological results revealed (a) the systematic presence of the three main trophic guilds in each assemblage, and (b) a consistent pattern of species eco–functional niches that are highly differentiated and evenly distributed in eco–functional spaces of similar size, but they provided (c) limited support for any degree of trophic plasticity (i.e. little evidence for any geographic variation in the diet of widespread species). The trophic guilds were also functionally dissimilar and displayed different levels of functional diversity. The intermediate group was the least functionally diverse guild with the lowest functional redundancy, while opposite findings were found for the pelagic–feeding guild. Then, I quantified the genetic diversity, which varied among trophic guilds and was associated with variation in their trophic ecology and habitat–behavioural traits (e.g. pelagic feeders have the lowest genetic and ecological diversity). Using a phylogenetic framework, I found that functional traits were evolutionarily labile and accumulated at a similar rate within the three trophic guilds. Transition rates among guilds were also biased, suggesting differences in the evolvability. The evaluation of all of these components indicated that some processes occurring at an "ecological" timescale and others at an "evolutionary" timescale had concordant effects (e.g. the coupling between levels of genetic and ecological diversity supported by the evolvability result for the intermediate group), although sometimes one type of process had more important effects (e.g. the principle of competitive exclusion probably shaped the high functional diversity of pelagic feeders). Overall, I demonstrated that the adaptive capacity of Pomacentridae is bounded and that trophic guilds are not equal in the face of environmental changes. The case of pelagic feeders illustrates a scenario wherein evolution and the right environmental conditions led to the success of a given group, but their persistence may be jeopardized by a low genetic diversity. The two other guilds possess more intrinsic assets (e.g. less restricted habitat and dietary requirements) to adapt. Given the uncertainty regarding the pace at which evolutionary processes will occur and the potential imperilment of evolvability to act as a source of future diversity, the ability to diversify along many niche axes associated with broad intrinsic characteristics (i.e. higher genetic diversity) may help organisms to sustain themselves in a long–term perspective and to maintain more ecosystem functions. [less ▲]

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See detailThe Cyanobacterial Biota of Polar Regions: a Molecular Approach
Stelmach Pessi, Igor ULiege

Doctoral thesis (2017)

Cyanobacteria are major components of Polar ecosystems. They comprise a considerable amount of the total biomass, are the main primary producers, and play important roles in the initial development of ... [more ▼]

Cyanobacteria are major components of Polar ecosystems. They comprise a considerable amount of the total biomass, are the main primary producers, and play important roles in the initial development of terrestrial and aquatic habitats. Although the cyanobacterial diversity in the Polar Regions has been well studied, research has been mostly limited to traditional methods such as microscopy, culturing, and Sanger-based molecular ecology approaches. High-troughput sequencing (HTS) has revolutionized our knowledge of microbial diversity and distribution, but a thorough investigation of polar cyanobacterial communities using HTS has not yet been performed. As a result, knowledge of the distributional patterns of polar cyanobacterial communities and the mechanisms underlying their structure is fragmentary. In this thesis, we applied the HTS approach to investigate the diversity and distributional patterns of cyanobacteria in a range of polar habitats. The main goals were: 1. To evaluate the use of HTS as a tool for assessing the cyanobacterial diversity in polar environments, including an assessment of different bioinformatics pipelines and the improvement represented by HTS in comparison to traditional methods; 2. To assess the spatial patterns of cyanobacterial communities across polar environments and the environmental factors shaping cyanobacterial community composition; 3. Tho study the successional dynamics of cyanobacterial communities following the colonization of recently deglaciated habitats. Due to its higher analytical depth, HTS was proven a valuable tool for the study of the cyanobacterial biota of Polar Regions. Nevertheless, the analysis of artificial communities highlighted the importance of strict bioinformatics control of HTS reads, as PCR and sequencing errors might bias the observed structure of the communities. Given the strict bioinformatics workflow applied, our results suggest a previously undetected polar cyanobacterial rare biosphere. On one side, the HTS approach revealed that microbial mat and biological soil crust (BSCs) across different Antarctic and Svalbard (High Arctic) regions are somewhat homogeneous, being dominated by filamentous cyanobacteria from the orders Pseudanabaenales and Oscillatoriales. At the phylotype level (97.5% similarity threshold), on the other hand, cyanobacterial communities were highly variable along environmental gradients within and between habitats. A study of benthic mat communities in Antarctic lakes revealed cyanobacterial communities highly structured by lake conductivity, and comparable compositions in lakes from distant Antarctic regions. In a study of BSC communities in four nunataks and mountain ridges in the Sør Rondane Mountains (Dronning Maud Land), highly dissimilar communities were observed between locations. Finally, two studies of BSC communities in Petunia Bay (Svalbard) revealed a marked, linear cyanobacterial community turnover along gradients of soil development. Altogether, the results obtained in the present thesis show that HTS is a powerful yet underused tool for the study of cyanobacterial diversity, not only in Polar Regions, but also on a global scale. This can be attributed to the very high sequencing depth achieved by HTS, which provides more robust assessments of community turnover and with a stronger statistical support than Sanger- based molecular ecology approaches. [less ▲]

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See detailétude fonctionnelle des facteurs d’épissage SR (Ser/Arg-rich) au cours du développement embryonnaire de Danio rerio.
Joris, Marine ULiege

Doctoral thesis (2017)

Ser/Arg-rich (SR) proteins constitute a phylogenetically conserved family of RNA binding proteins characterized by one or two RNA-recognition motifs (RRMs) at the N-terminus and a C-terminal domain ... [more ▼]

Ser/Arg-rich (SR) proteins constitute a phylogenetically conserved family of RNA binding proteins characterized by one or two RNA-recognition motifs (RRMs) at the N-terminus and a C-terminal domain enriched in Ser/Arg dipeptides. They are important regulators of constitutive and alternative splicing. Moreover, SR proteins are involved in many other aspects of RNA metabolism, including transcription, non-sense mediated decay, mRNA export, translational control as well as maintenance of genome stability. While the roles of SR splicing factors have been widely studied at a molecular level, their functions during animal cell differentiation and development are still largely undetermined. In this study, we decided to take advantage of the vertebrate model organism Danio rerio (zebrafish) to investigate SR protein functions by using molecular and genetic approaches. Fifteen zebrafish SR genes were identified belonging to the three subfamilies of SR proteins [SRSF1 (1RRM and 1 pseudo-RRM), SRSF2 (1RRM) and SRSF7 (1RRM +1ZnK)] initially described in humans. The current PhD thesis aimed to study of four of them, Srsfs5a, Srsf9, Srsfs7 and Srsf2b. We first determined the expression pattern of all SR genes by in situ hybridization at 24, 48 and 72 hours post-fertilization. This analysis revealed an ubiquitous expression pattern for SR genes, however pointing a higher expression in the brain and in the eyes. We next performed “knock-down” experiments using morpholinos (MOs) microinjection to determine SR gene functions. One splicing MO, designed to target srsf5a (sMOsrsf5a) showed an interesting phenotype that coincides with the expression pattern of the gene in the eyes. As none of the four other MOs used to target srsf5a could confirm the phenotype, we generated stable knockout mutant lines using TALEN and CRISPR/Cas9. Interestingly, the corresponding homozygous mutants did not display any phenotypic traits. These inconsistencies were attributed to a possible genetic compensation mechanism in mutants, but also to an underestimated large number of inadvertent morpholino RNA targets. Indeed, we uncovered that only 11 consecutive bases complementary to the 25 MO bases are sufficient for binding and subsequent blocking of splice sites, suggesting that the sMOsrsf5a induced phenotype was not due to the inactivation of this unique, specific gene. In addition, we observed that sMOsrsf5a secondary targets can be slightly reduced by increasing embryos growth temperature after microinjection. Our study contributes to the debate concerning MO specificity, efficacy and the number of unknown targeted sequences.   [less ▲]

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See detailFunctional diversity and mowing regime of flower strips as tools to support pollinators and to suppress weeds
Uyttenbroeck, Roel ULiege

Doctoral thesis (2017)

Intensification of agriculture during past decades is one of the causes of biodiversity declines. Ecological intensification has been proposed as a more sustainable alternative of intensive agriculture ... [more ▼]

Intensification of agriculture during past decades is one of the causes of biodiversity declines. Ecological intensification has been proposed as a more sustainable alternative of intensive agriculture that should be able to fulfill worldwide demands of food, by optimizing ecosystem functions and services and reducing environmental impacts. One way to restore ecosystem functions and services in arable fields is creating flower strips in field margins. These flower strips enable wild plant communities to thrive and provide food and shelter to associated fauna. It is often suggested that increasing plant functional diversity could be a tool to optimize ecosystem functioning and ecosystem service delivery, and it could thus be a goal for the creation and management of flower strips. An example of ecosystem functioning studied in this manuscript, is the mutualistic interaction between plants and pollinators. To convince European farmers to implement flower strips, they are included in the subsidized Agri-Environment Schemes. However, there exists no clear appraisal of the pros and cons of flower strips for farmers. By systematically reviewing the literature for pros and cons, we found that most studies concerned agronomical and ecological processes related to flower strips, but few or no studies were dedicated to the social and economic aspects. Furthermore, pollination appears to be an important pro, and weed infestation a possible con, depending on flower strip creation and management. We focused on these two examples in the further study. We investigated (1) whether the increase of plant functional diversity can be used as tool to optimize flower strips for pollinators, (2) whether forb competition and adapting timing and frequency of mowing can be used as tools to limit weeds in flower strips, and (3) whether flower strips perform equally in supporting pollinators as the natural habitat for which they are thought to be a surrogate. To use functional diversity as a tool to optimize flower strips for pollinators, we first tested whether it is possible to create a flower strip with a desired functional diversity level. We sew experimental flower strips with increasing functional diversity, based on visual, morphological and phenological flower traits and surveyed the vegetation composition the first year after sowing. The sown gradient of functional diversity was present, but with lower absolute values due to unequal cover of sown species and due to the presence of spontaneous species. To test the effect on pollinator support, we monitored the plant-pollinator networks in the experimental strips during two years. In contrast to our expectations, pollinator species richness and evenness were not influenced by functional diversity, and increasing functional diversity even resulted in lower flower visitation rates. To investigate the effect of forb competition and timing and frequency of mowing on weed infestation, we created experimental flower strips either with grass and forb species in the seed mixture, either with only grass species. Three different mowing regimes were applied: summer mowing, autumn mowing and mowing both in summer and autumn. The cover of important weed, Cirsium arvense, was limited by adding forbs to the seed mixture and by mowing in summer or in summer and autumn. At last, by surveying plant-pollinator networks in perennial flower strips and natural hay meadows in the same landscape context, we observed that both the plant and the pollinator communities differed between the flower strips and the meadows. Perennial flower strips can thus be considered as a complementary habitat in the landscape and not a hay meadow surrogate. This study suggests that it is possible to manipulate the vegetation as well as infestation by certain weeds in flower strips by adapting the seed mixture and the mowing regime. However, to promote pollinators in flower strips, increasing plant functional diversity appears not to be the key, and the abundance of certain attractive plant species can be more important. Moreover our results suggest that pollinators perceived a lower redundancy of functional plant trait values when functional diversity was higher, as they had more separate feeding niches (less visited flower species in common). Our results also suggest that there could be a trade-off between the increase of functional trait diversity and the floral resource abundance per niche or functional trait combination. With the results of the tested flower strip creation and management methods and their effect on pollinator support and weed infestation, farmers and administrations can try to create and manage flower strips with the desired balance between pros and cons, and researchers can try to refine these methods and test the effects on other pros and cons. [less ▲]

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See detailAnalyse de l’effet de la température et du préférendum thermique sur les mécanismes du déterminisme sexuel et de la différenciation gonadique chez le poisson-chat Africain, Clarias gariepinus
Santi, Saïdou ULiege

Doctoral thesis (2017)

Les poissons constituent le groupe de vertébré le plus diversifié présentant des systèmes de déterminisme et de différenciation sexuels aussi divers que variés. Ces systèmes sont caractérisés par une ... [more ▼]

Les poissons constituent le groupe de vertébré le plus diversifié présentant des systèmes de déterminisme et de différenciation sexuels aussi divers que variés. Ces systèmes sont caractérisés par une grande labilité et sont influencés par des facteurs génétiques, physiologiques et environnementaux, ces derniers pouvant influencer à la fois, le déterminisme du sexe et la différenciation des gonades. Le poisson chat africain Clarias gariepinus, une espèce présentant un déterminisme sexuel à homogamétie femelle (XX/XY), n’a fait l’objet que de peu d’études sur le rôle des facteurs environnementaux sur la détermination et différenciation sexuelle. Nous avons choisi d’étudier le rôle de la température dans ces mécanismes par trois approches complémentaires. Une approche histologique nous a permis de mettre en évidence qu’une haute température (36°C) influence la différenciation gonadique très précocement, de 6 à 8 jours post-l’éclosion (jpe), en entrainant fréquemment une déviation significative du sexe-ratio vers les mâles. La précocité de la thermosensibilité, avant le premier signe de différenciation histologique des gonades, suggère que la haute température pourrait agir sur d’autres cibles que les gonades elles-mêmes, telles que les cellules germinales primordiales, ou le cerveau, pour induire une masculinisation de la progéniture. Nous avons de plus mis en évidence que la distribution du sexe-ratio dans les différentes populations était très variable, suggérant le rôle de déterminants génétiques mineurs dans le processus de déterminisme du sexe chez le poisson-chat africain. Globalement, nous ces résultats sont caractéristiques de la présence d’une inversion du sexe température-induite (TISR) ainsi que des traits d’un déterminisme génétique polyfactoriel du sexe chez le poisson-chat africain. Une approche physiologique et génétique nous a permis de mettre en évidence que globalement, la haute température n’influence ni les profils des concentrations des trois principaux stéroïdes sexuels (17β-œstradiol, 11-cétotestostérone et testostérone), ni les expressions des gènes cyp19a1b et dmrt1 généralement impliqués dans ces mécanismes. Toutefois, les progénitures très thermosensibles présentent des expressions plus faibles du gène cyp19a1b six jours après l’exposition à la haute température. De même, les plus fortes expressions du gène de dmrt1 ont été observées chez les individus contrôles. Ces résultats renforcent notre hypothèse de sexualisation précoce du cerveau dans le processus de masculinisation température-induite. Des études supplémentaires sur l’action de la haute température sur la prolifération de cellules germinales primordiales, ainsi que d’autres processus comme l’activité ou la méthylation des gènes de la différenciation sexuelle doivent être envisagées. Une approche comportementale nous a finalement permis de mettre en évidence que les juvéniles indifférenciés présentent un comportement migratoire vers les hautes températures lorsqu’ils sont placés dans un continuum thermique (28,0 – 32,0 – 36,0°C), associés à une masculinisation de 50,0 à 82,5%, soulevant la question suivante : le déplacement à hautes températures confère-t-il des avantages particuliers aux individus ou à la population en milieu naturel ? Cette thermosensibilité contribuerait à augmenter la proportion de femelles dans la population, lorsque les pseudomales (XX) vont se reproduire avec des femelles XX. L’augmentation de la capacité reproductive de la population, résultante, pourrait permettre un accroissement de l’effectifs des larves et juvéniles, pour rétablir l’équilibre du sexe-ratio lors du retour à des conditions environnementales normales. Globalement nous pouvons conclure que Clarias gariepinus présente un TISR avec une implication des déterminants génétiques mineurs dans la différenciation du sexe. La thermolabilité pourrait conférer un avantage adaptatif à l’espèce, mais l’adaptabilité d’un tel processus d’établissement du sexe reste une question très ouverte. [less ▲]

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See detailQuality evaluation of peach chips and anticancer activity of pectin extracted from chips dehydrated by explosion puffing drying
Lyu, Jian ULiege

Doctoral thesis (2017)

The objectives of this research are to discriminate the overall quality level of peach and nectarine chips prepared by explosion puffing drying (EPD), determine the changes of texture and water soluble ... [more ▼]

The objectives of this research are to discriminate the overall quality level of peach and nectarine chips prepared by explosion puffing drying (EPD), determine the changes of texture and water soluble pectin (WSP) during EPD processing and study the anticancer activity of WSP on malignant mesothelioma (MM). Principle component analysis (PCA), Analytic hierarchy process (AHP), K-mean cluster and Discriminant analysis (DA) are used to distinguish the overall quality level of peach and nectarine chips and get the characteristic evaluation indicators, which of them (e. g. rehydration ratio and expansion ratio) are corresponding to texture properties of dehydrated products. Additionally, biochemical changes of the cell wall (e. g. pectin) are also related to texture changes. The investigate on the changes of texture and WSP at different stages of EPD processing in which osmotic dehydration (OD) was used as the pretreatment, show that OD with the appropriated concentration can improve the texture quality of dried products. The drying processing causes the degradation and structure modification of WSP, which can induce apoptosis in MM cells. EPD technology can be carried out as a potential pathway on modification of pectin, which may contribute to the development of a potential therapy against MM. [less ▲]

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See detailStatistical analysis of areal quantities in the brain through permutation tests
Winkler, Anderson ULiege

Doctoral thesis (2017)

In this thesis we demonstrate that direct measurement and comparison across subjects of the surface area of the cerebral cortex at a fine scale is possible using mass conservative interpolation methods ... [more ▼]

In this thesis we demonstrate that direct measurement and comparison across subjects of the surface area of the cerebral cortex at a fine scale is possible using mass conservative interpolation methods. We present a framework for analyses of the cortical surface area, as well as for any other measurement distributed across the cortex that is areal by nature, including cortical gray matter volume. The method consists of the construction of a mesh representation of the cortex, registration to a common coordinate system and, crucially, interpolation using a pycnophylactic method. Statistical analysis of surface area is done with power-transformed data to address lognormality, and inference is done with permutation methods, which can provide exact control of false positives, making only weak assumptions about the data. We further report on results on approximate permutation methods that are more flexible with respect to the experimental design and nuisance variables, conducting detailed simulations to identify the best method for settings that are typical for imaging scenarios. We present a generic framework for permutation inference for complex general linear models (GLMs) when the errors are exchangeable and/or have a symmetric distribution, and show that, even in the presence of nuisance effects, these permutation inferences are powerful. We also demonstrate how the inference on GLM parameters, originally intended for independent data, can be used in certain special but useful cases in which independence is violated. Finally, we show how permutation methods can be applied to combination analyses such as those that include multiple imaging modalities, multiple data acquisitions of the same modality, or simply multiple hypotheses on the same data. For this, we use synchronised permutations, allowing flexibility to integrate imaging data with different spatial resolutions, surface and/or volume-based representations of the brain, including non-imaging data. For the problem of joint inference, we propose a modification of the Non-Parametric Combination (NPC) methodology, such that instead of a two-phase algorithm and large data storage requirements, the inference can be performed in a single phase, with more reasonable computational demands. We also evaluate various combining methods and identify those that provide the best control over error rate and power across. We show that one of these, the method of Tippett, provides a link between correction for the multiplicity of tests and their combination. [less ▲]

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See detailLes pathologies intestinales chirurgicales chez le cheval: activation neutrophilique, pronostic et complications postopératoires
Salciccia, Alexandra ULiege

Doctoral thesis (2017)

Postoperative complications after colic surgery in horses remain of major concern as they are associated with non-negligible mortality rates. Many of these postoperative complications have an important ... [more ▼]

Postoperative complications after colic surgery in horses remain of major concern as they are associated with non-negligible mortality rates. Many of these postoperative complications have an important inflammatory component involving leukocytes, and particularly neutrophils, which represent the majority of granulocytes. Activated neutrophils produce reactive oxygen species and release inflammatory mediators and oxidative and proteolytic enzymes such as myeloperoxidase and elastase, which in turn will exacerbate pre-existing tissue lesions. This cascade of events will lead to the systemic inflammatory response syndrome. In an effort to improve the understanding of the systemic inflammatory reaction that follows colic surgery in horses, we described the time-trends of blood leukocytes and granulocytes counts and plasma myeloperoxidase and elastase concentrations during the perioperative period. Globally, survivor horses presented curves of blood leukocytes and granulocytes counts evolution lower and curve of evolution of plasma myeloperoxidase concentrations higher than those of non-survivor horses. These findings confirm the major influence of the inflammatory reaction on patient survival and allowed us to determine a prognostic value of blood leukocytes counts, a parameter easily available and routinely used in the aftercare of horses undergoing a colic surgery. We showed that in our population, non-survivor horses were more likely to have at least one blood leukocyte count inferior or equal to 3.9×10³/mm³ between 28 and 60 hours after surgery than survivor horses. Our following research, based on clinical studies, were directly or indirectly related to 2 common postoperative complications: incisional complications and ileus. In a study evaluating more than 600 exploratory laparotomies for colic, we showed that short laparotomy incisions, partially closed with interrupted vertical mattress sutures on the linea alba, and protected and supported by an abdominal bandage applied before the recovery from anaesthesia were associated with relatively low incisional complication and infection rates. These rates were respectively 9,52% and 5,31% after a single laparotomy and respectively 33,33% and 26,67% after repeat laparotomy. Bandage related complications occurred rarely. Risk factors of an incisional complication or infection in our population were prolonged anaesthesia duration, performing an enterotomy and postoperative intravenous lidocaine administration. The knowledge of these elements will certainly contribute to reduce the incidence of these complications in the future. Transabdominal ultrasonography of the small intestine is frequently used to diagnose and monitor a postoperative ileus. In order to improve the interpretation of ultrasonographic images after surgery, we determined the influence of general anaesthesia on these images. Using a protocol including horses anaesthetised for non-abdominal surgeries, we showed that although anaesthesia induces a physiologic ileus of short duration, expressed by a decreased of borborygmi without abdominal discomfort, its effects on the ultrasonographic images of the small intestine consisted mainly of a temporary increase (less than 12 hours) of the jejunal visualisation and diameter (with most of the observations remaining in the normal range) without thickening of the intestinal wall. Therefore the effects of general anaesthesia on ultrasonographic images of the small intestine can be distinguished from those of a pathological process. Our last study, including sound horses revealed that lidocaine, a molecule frequently used for treatment of postoperative ileus, may have a mild hypotensive effect on the arterial blood pressure and a mild prokinetic effect on the duodenum. Nevertheless, these results, original about the hypotensive effect, and controverted about the prokinetic effect, need to be confirmed in longer and larger studies. Our work has allowed us to bring some new elements leading to the improvement of our understanding of inflammatory processes related to the neutrophilic activation during the perioperative period of colic horses. Despite the improvement of methods of prevention, detection and treatment of postoperative complications, prognoses after this type of surgery still need to be enhanced. It seems that a huge work remains to be done to precisely determine the effects of various treatments, such as lidocaine. Numerous perspectives appear in the search of new molecules aiming to reduce the inflammatory reaction and to prevent or treat postoperative complications of horses undergoing colic surgery. [less ▲]

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See detailCharacterizing Thiamine Status and Mechanisms of Thiamine Supplementation on Subacute Ruminal Acidosis Attenuation in Dairy Cows
Pan, Xiaohua ULiege

Doctoral thesis (2017)

Dairy cows are often fed high grain diets to maximize milk production in today’s intensive management farms. However, overfeeding high grain diets increases the risk of subacute ruminal acidosis (SARA ... [more ▼]

Dairy cows are often fed high grain diets to maximize milk production in today’s intensive management farms. However, overfeeding high grain diets increases the risk of subacute ruminal acidosis (SARA), which is characterized by prolonged decrease in rumen pH and high levels of lipopolysaccharide (LPS). SARA challenge has been confirmed to severely impair animal health, production performance and farm profitability, and more and more attentions have been paid to prevent the occurrence of SARA in dairy industry worldwide. Our teams’ previous research found that thiamine supplementation relieved SARA in dairy cows, but the modes of action of thiamine in SARA attenuation are still unclear. In this context, this thesis was conducted to increase our understanding of relationships between SARA induction and thiamine, and to explore the mechanisms of thiamine supplementation on SARA attenuation by determining its effects on rumen fermentation, microbiome composition and anti-inflammatory response. Firstly, the first experiment in Chapter III demonstrated that thiamine status in rumen and blood were altered by SARA induction and thiamine deficiency occurred during SARA challenge. Regression analysis proved the ruminal thiamine content was positively related to pH and the concentrations of acetate in the rumen, and negatively correlated to the lactate contents, indicating the altered rumen fermentation would affect thiamine status. Secondly, the mRNA expression of thiamine transporters in ruminal epithelium (Chapter IV) and ruminal bacteria compositions (Chapter V) in SARA and control cows were detected. We found that thiamine concentration was positively correlated with Bacteroides, Ruminococcus 1, Ruminobacter, Pyramidobacter and Fibrobacter, and the decrease in these genera implied SARA challenge altered ruminal thiamine status by inhibiting the growth of thiamine synthesis related bacteria. The positive correlation between ruminal and blood thiamine, and the down-regulation of thiamine transporters’ expression in rumen epithelium indicated the reduced ruminal thiamine synthesis and thiamine absorption by SARA challenge resulted in low blood thiamine content of SARA cows. Thirdly, the effects of thiamine on rumen fermentation (Chapter III), anti-inflammatory response (Chapter IV) and microbiome composition (Chapter V) were evaluated to reveal its mechanisms on SARA attenuation. We found that thiamine supplementation promoted acetate-producing bacteria including Ruminococcus 1, Pyramidobacter, Succinivibrio and Bacteroides, and decreased bacteria positively related to ruminal lactate (Succiniclasticum and Ruminococcaceae NK4A214). Consequently, rumen fermentation was improved by reducing the accumulation of lactate and increasing ruminal pH. In addition, thiamine supplementation alleviated inflammatory response in rumen epithelium by reducing the release of LPS and phosphorylation of NFκB protein, which is conducive to SARA attenuation. In summary, this thesis had increased our understanding of thiamine nutrition in dairy cows, and provided a new control strategy for subacute ruminal acidosis in dairy cows. However, further investigations are needed to deeply understand the relationship between thiamine and SARA induction, such as the isolation and validation of thiamine synthesis bacteria affected by SARA challenge, as well as to figure out metabolic pathways through which SARA induction affects thiamine synthesis in the rumen. Moreover, the impacts of overfeeding high grain diets on intestinal thiamine absorption are still unclear and need to be illuminated in dairy cows. [less ▲]

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See detailOmics insights into rumen ureolytic bacterial community and urea metabolism in dairy cows
Jin, Di ULiege

Doctoral thesis (2017)

Urea has been used in the diets of ruminants as a non-protein nitrogen source. Ureolytic bacteria are key organisms in the rumen producing urease enzymes to catalyze the breakdown of urea to ammonia (NH3 ... [more ▼]

Urea has been used in the diets of ruminants as a non-protein nitrogen source. Ureolytic bacteria are key organisms in the rumen producing urease enzymes to catalyze the breakdown of urea to ammonia (NH3), and the NH3 is used as nitrogen for microbial protein synthesis. In the rumen, hydrolysis of urea to NH3 occurs at a greater rate than NH3 can be utilized by rumen bacteria, and excess ammonia absorbed into blood may be harmful to the animals. Nowadays, little is known about the information of ureolytic microorganisms in the rumen, and the changes that occur in the rumen microbial and host metabolites induced by urea nitrogen have not been fully characterized. ‘Omics’ approaches, such as metagenomics and metabolomics have been applied to analyzing rumen microbial community and nutrients metabolism in dairy cows. The objective of this study is to investigate the rumen predominant ureolytic bacteria community and the mechanisms of urea utilization in ruminants using sequencing and metabolomics approaches. Firstly, an in vitro experiment trying to explore the ruminal ureolytic bacterial community was performed. Urea or acetohydroxamic acid were supplemented into the rumen simulation systems as the stimulator and inhibitor for ureolytic bacteria, respectively. The bacterial 16S rRNA genes were analyzed by Miseq sequencing and used to reveal the ureolytic bacteria by comparing different treatments. We found that urea supplementation significantly increased the proportion of ureC genes. The rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus and unclassified Succinivibrionaceae. Secondly, an in vivo experiment was taken to investigate differences in ureolytic bacterial composition between the rumen digesta and rumen wall based on ureC gene classification. Six dairy cows with rumen fistula were assigned to a two-period cross-over trial. One group was fed a total mixed ration without urea and the treatment group was fed rations plus 180 g urea per cow per day. Rumen bacterial samples from rumen content and rumen wall fractions were collected for ureC gene amplification and sequencing using Miseq. More than 55% of the ureC sequences did not affiliate with any known taxonomically assigned urease genes. The wall-adherent bacteria had a distinct ureolytic bacterial profile compared to the bacteria in the rumen content. The most abundant ureC genes were affiliated with Methylococcaceae, Clostridiaceae, Paenibacillaceae, Helicobacteraceae and Methylophilaceae families. Relative abundance of the operational taxonomic units (OTUs) affiliated with Methylophilus and Marinobacter genera were significantly higher in the bacteria on the rumen wall than that in the rumen content. Thirdly, based on the in vivo experiment, rumen fluid and blood samples were collected and analyzed using nuclear magnetic resonance spectroscopy and multivariate analysis of variance. Concentrations of valine, aspartate, glutamate, and uracil in the rumen, and urea and pyroglutamate in the plasma were increased after urea supplementation. Metabolic pathways include pantothenate and CoA biosynthesis, beta-alanine metabolism, valine, leucine, and isoleucine metabolism in the rumen, and urea and glutathione metabolism in the plasma were significantly increased by urea nitrogen. In conclusion, this study identified significant populations of ureolytic bacterial community that have not been recognized or studied previously in the rumen and provides a basis for obtaining regulatory targets to moderate urea hydrolysis in the rumen. The findings also provided novel information to aid understanding of the metabolic pathways affected by urea nitrogen in dairy cows, and could potentially help to guide efforts directed at improving the efficiency of urea utilization in the rumen. [less ▲]

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See detailHistoire évolutive du complexe Afzelia Smith (Leguminosae - Caesalpinioideae) dans les écosystèmes forestiers et savanicoles en Afrique tropicale
Donkpegan, Segbedji ULiege

Doctoral thesis (2017)

The genus Afzelia Smith (Fabaceae, Caesalpinioideae) is known to have seven African tree species two of which are found in the Zambezian region, one is distributed in the Sudanian region and the four ... [more ▼]

The genus Afzelia Smith (Fabaceae, Caesalpinioideae) is known to have seven African tree species two of which are found in the Zambezian region, one is distributed in the Sudanian region and the four other are endemic to the Guineo-Congolian region. These taxa, of high commercial value, are difficult to identify. They are therefore marketed under the same "doussié" name. These difficulties of distinction can prove detrimental to the sustainable management of populations. The aim of this doctoral thesis is to characterize the evolutionary history of the Afzelia genus. More specifically, this study aims to: (i) evaluate the level of morphological divergences within the Afzelia genus and describe the phylogenetic relationships in order to quantify the reproductive isolation between taxa by highlighting the role of past climate change and / or ecological gradients in the speciation of the genus; (ii) proceed to an analysis of the spatial genetic diversity and structure of Afzelia spp.; (iii) identify and describe ecological, biotic and abiotic factors that may influence population-level gene flows of an Afzelia species (A. bipindensis). A morpho-genetic analysis of Afzelia species was carried out and confirmed the strong botanical resemblance between the taxa. The savannah species are diploid and have half the size of the genome of forest species that are tetraploid. The phylogenies of genes (nuclear and chloroplastic) differ from one another and do not allow the separation of tetraploid taxa from one another. Such differences can be generated as a result of episodes of ancestral hybridization between species. These hybridizations would probably be old and would have occurred between lineages of the forest species and A quanzensis (a species of the Zambezian savannahs) lineages. Polyploidy would have occurred between 7 and 9.4 million years in the evolutionary history of the genus. In addition, Bayesian assignment and reproductive isolation analyzes suggested interspecific crosses, but only in forest species distributed sympatrically. At a more limited spatial scale, we observed two well differentiated genetic groups in sympatry in A. bipindensis. These show a morphological differentiation and a phenological shift of flowering which can contribute to their reproductive isolation. This study highlighted some important points: the discovery of a polyploid complex within the Afzelia genus, the confirmation of the delimitation of the diploid savannah species and the need to revise the delimitation of forest tetraploid species. [less ▲]

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See detailSoil Acidification in Southern China: Spatio-temporal Evolution and Effects on Phosphorus Availability
Zhou, Xiaoyang ULiege

Doctoral thesis (2017)

Rapid industrial development and intensive agriculture induced serious soil degradation in recent decades worldwide and specifically in China. In cropland, soil acidification and nutrient deficiency are ... [more ▼]

Rapid industrial development and intensive agriculture induced serious soil degradation in recent decades worldwide and specifically in China. In cropland, soil acidification and nutrient deficiency are often associated with increased use of nitrogen (N) fertilizers. Soil acidification can lead to reduction of phosphorus (P) availability, even though with high inputs of P fertilizer. The studies presented in the thesis deal with spatio-temporal evolution of soil pH in different soil types and land uses in southern China and effects of soil acidification on soil P availability. Evolution of inorganic P fractions in Red Soil was characterized upon fertilization trials, as a response to long-term fertilization and soil acidity changes. The first focus of the thesis deals with spatio-temporal evolution and main factors of soil acidification in different soil types, parent materials and land uses of Southern China. Firstly, data from 20 monitoring sites under 25-year fertilization on Paddy Soil were investigated to research changes of pH. Paddy Soil pH significantly declined from 1988-1998, then stabilized from 1998-2013 with conventional fertilization. Chemical N fertilization, manure application, soil available N and total N increases were significantly correlated with soil pH. Secondly, changes of pH in Red Soil and Paddy Soil were assessed in 32 monitoring sites of Hunan Province (Southern China) under 10-year fertilization in order to analyze soil acidification in different soil types and agro-systems. Soil pH decline was observed in Paddy Soils under rice-vegetable rotation but not observed in Paddy Soil under continuous cropping with rice. Soil pH significantly declined in Red Soil with high initial soil pH. Thirdly, spatio-temporal characteristics of soil pH were investigated by comparison of soil pH between 1982 and 2014 in Qiyang County (Hunan Province). Average topsoil pH declined of 0.58 units between the two surveys. Soil pH in the south was lower than in the north both in 1982 and 2014. Land use and parent materials are the main drivers of differences in the soil pH changes in Qiyang County. Soil pH declined significantly in forest and upland crop over non-alkaline parent materials during 1982-2014 period. Chemical N fertilizer application can have generated 12-42 kmol H+ ha-1yr-1, which is much higher than removal by crop harvest. Reduction of chemical N fertilization and return of straws to field should be conducted to reduce H+ production and supplement base cations in Qiyang County. The second approach studied evolution of inorganic P fractions in Red Soil under 25-year fertilization, and available P and inorganic P fractions responses to various soil acidity levels. Inorganic P fractions increased under P fertilization from 1990-2015, especially Ca2-P, Ca8-P and Al-P, but inorganic P fractions significantly decreased without P fertilization. Contributions of soil properties (SOC, C:P ratio and N:P ratio) and cumulative P apparent balance (CPAB) to inorganic P fractions were ≥ 95%, while interaction of CPAB and soil properties made greater contributions than did any single factor. Soil dissolved inorganic P (DIP) decreased with rising pH value, and a minimum DIP was observed between pH 5.5 and 6.5. Olsen-P, Ca-P and Al-P increased significantly with pH between 3.4 and 5.0. Soil with pH <5.0 P availability was much lower than soil with pH ≥5.0. Managing soil acidity is a key issue regarding availability of P in Red Soil of China and our results suggest that at least a pH of 5.0 should be targeted. [less ▲]

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See detailPlant traits variability within and among populations in the context of calcareous grassland restoration
Harzé, Mélanie ULiege

Doctoral thesis (2017)

In Western Europe, abandonment of traditional forms of agriculture has caused the fragmentation of semi-natural grasslands, affecting ecosystems functioning as well as population survival. Habitat ... [more ▼]

In Western Europe, abandonment of traditional forms of agriculture has caused the fragmentation of semi-natural grasslands, affecting ecosystems functioning as well as population survival. Habitat restoration has become a crucial aspect of grasslands conservation, and one of the main issues is evaluating restoration success and setting appropriate criteria to do so. Indicators used to judge whether a restoration has been successful may concern a wide range of organisms. They may be defined at different geographical scales and may concern various levels of biodiversity organization. Among them, population parameters are less represented despite their usefulness. To consider restoration as a success, restored populations of targeted species should demonstrably possess characteristics allowing their dispersal, reproduction, growth and adaptation to the environment. In this thesis, the use of plant population parameters for evaluating grassland restoration was assessed based on a literature review. Then, the success of calcareous grassland restoration was determined regarding colonization of restored grasslands by five calcareous grasslands species; Helianthemum nummularium, Hippocrepis comosa, Potentilla tabernaemontani, Sanguisorba minor and Scabiosa columbaria. Population establishment and intra-specific functional trait variability in response to the environment were observed and compared among restored and reference populations of those species, through field inventories and in-situ traits measurements in calcareous grasslands of south Belgium. Moreover, a glasshouse experiment was set-up with the aim to evaluate the intra-specific variability in response to drought stress in reference populations of P. tabernaemontani. The results indicated that population parameters were less well studied for evaluating grassland restoration success compared to indicators related to ecosystems and communities. The population parameters used to assess the success of calcareous grassland restoration showed that the study species colonized restored sites and established new populations. The fitness of the restored populations was very high. High intra-specific trait variability was highlighted at a very local scale in the reference habitat. Individuals exhibited high leaf dry matter content (LDMC), low specific leaf area (SLA) and low vegetative height in relation to low soil depth and high potential incident radiation (PDIR). These environmental variables are possibly linked to the availability of soil moisture. Further, the relationship between traits and environmental variables was not always consistent in restored sites. However, the intra-specific variability of plant traits was similar in the reference and restored grasslands. Finally, the findings from the glasshouse experiment suggested that individuals originating from drier parts of calcareous grasslands better survive drought stress.   The overall conclusion of this thesis is rather optimistic concerning restored populations of the five specialist plant species studied, specifically regarding their colonization, persistence and response to the environment or to potential climate change. The conclusions must, however, be modified depending on the reference ecosystem used as a model. This approach has to be integrated into a multi-scales and a multi-species approach to fully evaluate restoration outputs. Yet, this thesis has contributed to the understanding of population responsiveness to habitat restoration, as well as to the evaluation of restoration success of calcareous grasslands in Belgium. [less ▲]

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See detailQUALITY IMPROVEMENT OF POTATO STEAMED BREAD USING FOOD HYDROCOLLOIDS
Liu, Xingli ULiege

Doctoral thesis (2017)

Nowadays, there is an increasing interest for composite or gluten-free products due to some economic, nutritional reasons or the number of the celiac patient. The estimated prevalence of Celiac disease is ... [more ▼]

Nowadays, there is an increasing interest for composite or gluten-free products due to some economic, nutritional reasons or the number of the celiac patient. The estimated prevalence of Celiac disease is about 1% of the general population, and it affects persons of any age, race, and ethnic group. Steamed bread is a traditional staple food of China, and has been consumed for at least 2000 years, taking up almost 40% of wheat consumption, and the popularity is increasing around the world. However, most traditional wheat steamed bread lack essential nutrients, including lysine, dietary fiber, vitamins, and minerals, etc. Therefore, the use of composite flour for steamed bread making has attracted great attention. Potato (Solanum tuberosum) is one of the most widely planted vegetables worldwide and is the only tuber used as a major food crop. Potato has a balanced amino acid composition, high total vitamin and mineral levels, and also contains phytochemicals such as polyphenols, polyamines, and carotenoids. However, the replacement of wheat flour is a major challenge for food technologist to produce the steamed bread with desirable quality and technological properties because that gluten is important to retain gas to obtain the desired volume and texture in a dough system. It is essential to form a strong protein network required for the desired viscoelasticity, and the easiest way to ensure the viscoelasticity properties is via the use of food hydrocolloids. Therefore, the aim of this work was to study the quality improvement of potato steamed bread using food hydrocolloids. Firstly, the influence of potato flour on dough rheological properties and quality of steamed bread showed that the dough stability and specific volume of steamed bread were significantly decreased with the potato flour proportions increasing. Then we carried out the comparative study of the nutritional quality of steamed and baked breads from four potato cultivars because that the steamed and baked breads were two type of staple food in eastern and western countries, respectively. The results showed that potato flour addition increased the contents of dietary fiber, potassium, vitamin C, and total polyphenol contents and antioxidant activity. Hongmei was the optimum choose of the studied four cultivars, followed by Blue Congo, Shepody, and Atlantic, in terms of nutritional value. For the same cultivar, the nutritional value of steamed bread was higher than that of baked bread. Secondly, the effect of different food hydrocolloids on the dough rheology and steamed bread quality parameters in composite and gluten-free formulations based on potato flour was studied. Compared to control, the food hydrocolloids addition significantly increased tightly bound water population, water absorption, starch gelatinization temperature, dough viscoelasticity, recovery percentage and development height. Little adhesion and aggregation of starch were observed and the density of potato protein bands was decreased when food hydrocolloids were added, suggesting that some aggregation formed between starch-hydrocolloids or proteins-hydrocolloids. Moreover, steamed breads with food hydrocolloids presented higher specific volume, lower hardness, and lower estimated glycemic index. In conclusion, food hydrocolloids showed the potential as a gluten replacement in composite or gluten-free potato steamed bread, particularly HPMC. Thirdly, we optimized the formulations of gluten-free potato steamed bread. The optimal gluten-free steamed bread could be produced by adding 4.84 g/100g pregelatinized potato flour (PGPF), 1.68 g/100g hydroxypropylmethylcellulose (HPMC), 5.87 g/100g egg white protein (EWP) and 69.69 g/100g water based on potato flour, and this optimal bread was compatible with regular wheat bread in key sensory properties. Moreover, the optimized solid phase microextraction parameters (sample weight 2.42 g, extraction time 60 min, and extraction temperature 50°C) were adopted to determine the volatile compounds of gluten-free potato steamed bread. 72 volatile compounds were detected in the dough and crumb. The contents of alcohols, acids and esters increased significantly with the fermentation time increasing, which would improve the aroma of steamed bread. However, further investigations are needed to elucidate the underlying mechanisms of action and the interactions with dough components and making additives. The other studies should be focused on technological approaches to improve steamed bread quality, which involved different flour particles, high pressure technology and application of sourdough. [less ▲]

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See detailRôle des lymphocytes T TCR γδ dans la progression des lésions associées à l'infection par les papillomavirus humains
Van Hede, Dorien ULiege

Doctoral thesis (2017)

Cervical cancer was the fourth most frequent cancer in women in 2012, with the majority of cases occurring in less developed countries. Although this cancer is induced by Human Papillomavirus (HPV ... [more ▼]

Cervical cancer was the fourth most frequent cancer in women in 2012, with the majority of cases occurring in less developed countries. Although this cancer is induced by Human Papillomavirus (HPV) infections that have a high prevalence, only a very few percentage of infected women will developed this disease. Host immune defenses are essential to clear infection and to kill virus-infected transformed cells. Indeed, majority of infected women clear the virus within two years while immunocompromised patients are more likely to develop cervical preneoplastic lesions and cancers. γδ T cells have been shown to protect against the formation of squamous cell carcinoma (SCC) in several models. Nowadays, the contribution of γδ T cells in HPV associated uterine cervical SCC is unknown. Here we investigated the impact of γδ T cells in a transgenic mouse model of carcinogenesis induced by HPV16-oncoproteins. Surprisingly, γδ T cells promoted the development of HPV16-oncoprotein-induced lesions. These oncoproteins induced a decrease in epidermal Skint-1 expression and modification of the associated anti-tumor Vγ5+ γδ T cells (or DETC), which were joined by other γδ T cell subsets actively producing IL-17. Consistent with a proangiogenic role, γδ T cells promoted the formation of blood vessels in the dermis underlying the HPV-induced lesions. In human cervical, IL-17+ γδ T cells could be only observed at the cancer stage (SCC) (but not in less advanced cervical lesions), where HPV oncoproteins are highly expressed, supporting the clinical relevance of our observations in mice. Overall, our results suggest that HPV16-oncoproteins induce a reorganization of the local epithelial-associated γδ T cell Subpopulations thereby promoting angiogenesis and cancer development. [less ▲]

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See detailSpatial diversification of agroecosystems towards biological control of insect pests: A focus on intercropping and wildflower strips
Hatt, Séverin ULiege

Doctoral thesis (2017)

Facing the limits of input-intensive agriculture, agroecology aims at thinking ways to design a sustainable agriculture that is economically viable and socially relevant. It notably invites to mobilize ... [more ▼]

Facing the limits of input-intensive agriculture, agroecology aims at thinking ways to design a sustainable agriculture that is economically viable and socially relevant. It notably invites to mobilize ecological processes within agroecosystems in order to enhance the delivery of ecosystem services towards reducing the use of external inputs – among others insecticides. For enhancing biological control of insect pests, a strategy is to spatially diversify agroecosystems at the field scale. Whereas increasing plant diversity could directly negatively affect pest development on the one hand (i.e. bottom-up effect), providing flowering features could allow the enhancement of natural enemies and their direct effect on pest populations on the other hand (i.e. top-down effect). The present thesis focused on intercropping (i.e. the cultivation of at least two crop species simultaneously in a same field) as a way to diversify crop habitat, and the sowing of wildflower strips as a non-crop feature. A systematic analysis of the literature revealed that, in most of studies, wheat (Triticum aestivum L.)-based intercropping allows a reduction of insect pests on crops, without necessarily favouring their natural enemies, compared to pure-stands. Besides, the provision of flowering resources, by for instance sowing wildflower strips, can attract and support flower visiting predators and parasitoids. Hence, in a first set of field experiments, combining the two tactics of increasing crop diversity and providing flowering resources was tested. First in China, wheat crop was associated with oilseed rape (Brassica napus L.), but it neither allowed reducing aphid (Hemiptera: Aphididae) abundance nor enhancing their natural enemies compared to pure stands. Instead, aphid density – independently from the treatments – affected natural enemy abundance, and interspecific relations between aphids and their natural enemies were observed. Second in Belgium, wildflower strips were sown within a wheat field, which led to a reduction of aphid density in wheat plots in between flowering features and an increase of aphidophagous hoverflies (Diptera: Syrphidae) compared to pure-stand wheat. Nevertheless, the presence of flowering strips did not affect the other natural enemies, i.e. lacewings (Neuroptera: Chrysopidae), ladybeetles (Coleoptera: Coccinellidae) and parasitoid wasps (Hymenoptera: Braconidae). Therefore, a second set of field experiments focussed on ways to compose mixtures of wild flowers attractive to a diversity of natural enemies. Flower functional traits were considered due to their effect on insect behaviour. First, the hypothesis that mixtures with high functional diversity attract and support a high abundance and diversity of aphid flower visiting predators was tested. This hypothesis was not verified. Instead, the high density in the plots of some flower species (especially the Asteraceae Leucanthemum vulgare Lam.) known to be attractive to flower visitors was supposed to have overwhelmed the effect of functional diversity. Second, a methodology was developed to identify which flower traits significantly affect natural enemy abundance – in this experiment parasitoids of oilseed rape beetle pests (i.e. Meligethes spp. [Coleoptera: Nitidulidae] and Ceutorhynchus spp. [Coleoptera: Curculionidae]) – in flower mixtures. Among seven traits, visual traits (i.e. colour, ultra-violet reflectance) and the one related to food availability (i.e. corolla morphology) were found to significantly affect parasitoid abundance. These results highlight that (i) increasing plant diversity at the field scale can – but not systematically – favour a reduction of insect pests, (ii) including flowering features can enhance some – but not all – of their natural enemies, and (iii) in order to compose flower mixes attractive to natural enemies, specific flower traits – rather than functional diversity at the mixture level – can be considered. These results are discussed in a broader perspective. Indeed, strategies to spatially diversify crop and non-crop habitats in agroecosystems are various, as well as the ways to compose, manage and design such habitats. Also, processes at larger scales than the field may be determinant. Moreover, insects are not the only pests, and pests are not the only biotic or abiotic elements that need to be regulated in agroecosystems. Controlling multiple pests simultaneously but also enhancing the provision of multiple regulating services represent challenges for future research in agriculture. [less ▲]

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See detailThe behavior of pesticide during beer brewing and the toxicity of pesticide using state-of-the-art omic tools
Kong, Zhiqiang ULiege

Doctoral thesis (2017)

Beer is an extremely popular beverage worldwide, representing the third-most popular drink after water and tea. And barley is the major raw material used for beer production. However, various combinations ... [more ▼]

Beer is an extremely popular beverage worldwide, representing the third-most popular drink after water and tea. And barley is the major raw material used for beer production. However, various combinations of pesticides are widely used at several stages of barley culti¬vation and during post-harvest storage to control pest and fungal disease. Hence, traces of these pesticides might remain in the beer produced from the treated ingredients. Hence, monitoring trace levels of pesticide residues during beer brewing and investigated the effects of pesticide residue on the quality of beer is essential. First, the behavior and fate of 3 pesticides (triadimefon, malathion, and dichlorvos) and the main metabolites (triadimenol and malaoxon) during barley storage or beer processing were assessed using a pilot-plant equipment. The residues of all products were determined using liquid chromatography coupled with tandem mass spectrometry. Field investigation of the dissipation rate kinetics for triadimefon and malathion during storage indicated that their half-life was twice as high when 5 times the recommended dosage was used. Milling had little effect on removing dichlorvos and malathion residues, whereas they were substantially removed when the spent grains were mashed. The calculated processing factors after processing were all <1, indicating that the residual ratios of dichlorvos and malathion were reduced during the entire process. In conclusion, storage and processing extensively reduced pesticide residue levels in barley and beer; however, greater focus needs to be paid to the toxicity of their metabolites in commercial by-products. Then we selected the triadimefon as the target fungicide to further study its behavior, the dissipation kinetics of TF during fermentation mediated by two different yeast strains, Saccharomyces cerevisiae IAPPST 1401 (Y1) and CICC 1202 (Y2), and found that Y2 promoted the degradation of TF. Response surface methodology was used to optimize fermentation process variables, in order to achieve the maximum removal rate of TF and the minimum production of its corresponding metabolite, triadimenol (TN). Triadimefon is also a widely used triazole fungicide with one chiral carbon center, Stereoselective degradation of triadimefon was found during barley storage, the half-life of S-(+)-triadimefon was 36.5d, 31.5d and 30.1d, while R-(-)-traidmefon was 69.3d, 53.3d and 33d under 4°C, 25°C and 40°C, respectively. During brewing process, both enantiomers of triadimefon were easily degraded. After fermentation, little triadimefon detected in the beer, while RS-(+) and SS-(-)-triadimenol were detectable. This research provides accurate information for evaluating the risk of food safety. Furthermore, we investigated the effect of triadimefon affect the quality and flavor of the fermented beer, The effect of triadimefon on yeast growth and the sensory quality of beer were studied. There were significant differences in sensory quality between beer samples fermented with and without triadimefon based on data obtained with an electronic tongue and nose. Such an effect was most likely underlain by changes in yeast fermentation activity, including decreased utilization of maltotriose and most amino acids, reduced production of isobutyl and isoamyl alcohols, and increased ethyl acetate content in the fungicide treated samples. Furthermore, yeast metabolic profiling by phenotype microarray and UPLC/TOF-MS showed that triadimefon caused significant changes in the metabolism of glutathione, phenylalanine and sphingolipids, and in sterol biosynthesis. Thus, triadimefon negatively affects beer sensory qualities by influencing the metabolic activity of S. cerevisiae during fermentation, emphasizing the necessity of stricter control over fungicide residues in brewing by the food industry. [less ▲]

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See detailCrop water productivity of winter wheat at multi-scale and its improvements over the Huang-Huai-Hai Plain, China
Liu, Qin ULiege

Doctoral thesis (2017)

Droughts and water shortage are generally accepted to be one of the most critical problems faced by worldwide agriculture, and it is so especially in China where agricultural production and prosperity are ... [more ▼]

Droughts and water shortage are generally accepted to be one of the most critical problems faced by worldwide agriculture, and it is so especially in China where agricultural production and prosperity are largely dependent on the timely, adequate and proper distribution of rainfall. The analysis of water productivity is becoming very critical in light of population growth, food security and increasing pressure on water resources. However, there is limited understanding of the spatio-temporal variation of crop water productivity (CWP) from the rotation system and its key influencing factors in Huang-Huai-Hai Plain (3H Plain) in which there is an over-exploitation of groundwater region and where future warmer and drought conditions will intensify crop water demand. As the largest water user, agricultural sector is facing a challenge to produce more crops with less water. Consequently, 3H Plain faced the double threat of both making contributions of high and stable yield to government and improving CWP of winter wheat through reducing water consumption. The overall ambition of this thesis was to investigate to what extent the grain yield and crop water productivity for winter wheat can respond to climate change and drought across the 3H Plain. In our study, a combined dataset composed of a historical 54-year time series and the RCP 8.5 scenario from 40 meteorological stations was provided by the China Meteorological Administration. Among these 40 stations we selected 12 stations with more detailed information available. The minimal data sets required for model operation include daily climatic variables, soil information and management information collected from the China Soil Scientific Database. Finally, we also used satellite data to estimate water productivity mainly involved in MODIS products including MOD11A1 (land surface temperature/surface emissivity), MOD13A2 (NDVI) and MCD43B3 (surface albedo). We used SPEI-PM method, DSSAT-CERES-Wheat model and SEBAL model to explore the characteristics in grain yield and crop water productivity for winter wheat in response to climate change and drought associated with their improvements across the 3H Plain. Our work demonstrated the investigation that an increase of ET0 was predicted leading to subsequent drought rise in frequency, duration, severity and intensity under the RCP 8.5 scenario. The cumulative probability of the simulated yield reduction was detected to be higher during jointing to heading stage in northern than southern region due to water stress and changes in the management inputs. The lower CWP was mainly situated in the low plain-hydropenia irrigable land and dry land (zone2) and the hill-wet hot paddy field (zone6), which suggests that it is an important issue and opportunity for improving agricultural water management in the water-scarce 3H Plain. The spatial increase of yield principally controlled increase of water productivity in north agricultural sub-regions and the spatial increase of water productivity was more governed by increment of yield than the reduction of ETa in other agricultural sub-regions. It will be adopted to develop feasible straw mulching, regulated deficit irrigation, and soil water storage and preservation to reduce pressure on groundwater over-exploitation, especially for winter wheat in the 3H Plain. In our work, major agronomic consequences have been drawn regarding the reform of the common agricultural policy in Huang-Huai-Hai Plain, China. Researchers are encouraged to further investigations into how to implement these practices with emphasis of improving the sustainability of these agro-ecosystems. [less ▲]

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See detailGENETIC DIVERSITY AND FACULTATIVE SYMBIONTS INFECTION PATTERNS OF TWO RHOPALOSIPHUM APHIDS
Guo, Jianqing ULiege

Doctoral thesis (2017)

Aphids, during the long-term evolution, kept their genetic traits for continuation of the species while some variations caused by selection, migration, mutation, and genetic drift occurred meanwhile to ... [more ▼]

Aphids, during the long-term evolution, kept their genetic traits for continuation of the species while some variations caused by selection, migration, mutation, and genetic drift occurred meanwhile to adapt to novel environments. The differentiation takes place not only among species but could also be observed within species that finally contributes to the population genetic diversity. However, the migrant behavior of aphid can enhances the gene flow among populations, as a result, decreasing the genetic variation. Additionally, insect such as aphids usually hold the mutualistic relationships with endosymbionts which may affect the adaptive characteristics of the host aphid. Both Corn leaf aphid Rhopalosiphum maidis (F.) (Hemiptera: Aphididae) and Bird cherry-oat aphid Rhopalosiphum padi (L.) (Hemiptera: Aphididae) are worldwidely severe pests that attack cereal crops such as maize, barley, wheat, sorghum and oats. They suck the phloem and can transmit viruses including Maize dwarf mosaic virus (MDMV) and Barley yellow dwarf virus (BYDV), the main virus of maize and barley, which may result in serious damage for the yield and quality of the host plant. Moreover, one aphid species usually exerts genetic differentiation among populations which is related to factors such as geographic conditions, host plants and life history. Hence, it is necessary to have a clear understanding of the genetic structure and variation among geographic populations to further explore the historical expanding routes and occurrence of these pests and design efficient control strategies. Targeting the genetic divergence among populations of two Rhopalosiphum aphids, 32 populations of R. padi and 38 populations of R. maidis were collected on maize from most regions of China as well as some countries in Europe. The sequencing results of two mitochondrial (COI and COII) and one nuclear (EF-1α) genes indicated that a high level of gene flow existed among the populations of R. maidis in terms of geographic locations, proving the migratory capacity of this aphid. With regard to R. padi, high genetic diversity were found between the populations from China and Europe based on combined COI-COII, however, the genetic diversification among Chinese populations and European populations were low, which illustrated that the length of geographic distance may play an important role in genetic diversity. The infection patterns of seven facultative symbionts (Serratia symbiotica, Hamiltonella defensa, Regiella insecticola, Rickettsia, Spiroplasma, Wolbachia and Arsenophonus) in R. padi and R. maidis were investigated as well. Both aphids were found to have wide symbiotic associations with variant symbionts. Unlike Acyrthosiphum pisim (H.) which is frequently infected with S. symbiotica, R. insecticola, Rickettsia and Spiroplasma were dominant facultative symbionts in these two Rhopalosiphum aphids. The results also indicated that the geographic conditions such as latitude of collecting locations may have an effect on the distribution of facultative symbionts, implying the adaptive function of the facultative symbionts to various environmental conditions on their host aphids. Considering the population diversity within species, we also tested the survival and reproduction rates of two R. maidis populations (i.e. Beijing and Mangshi) on barley and maize of small (10 cm) and high (50 cm) size. Direct observation method was used and none of the populations could survive on maize of small size whereas they were capable to develop on maize of high size, but with much lower growing speeds compared with barley on which both populations showed the best performances. In addition, Beijing population was found to perform significantly better than Mangshi population which may be related to the infection of facultative symbionts. We hypothesize that the lethality on small maize may result from the secondary metabolites synthesized to be more abundant in young maize seedlings. [less ▲]

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See detailDevelopment and applications of CRISPR-Cas9 and RNAi for rice and wheat agronomic traits improvement
Sun, Yongwei ULiege

Doctoral thesis (2017)

Genome editing technologies enable precise modifications of DNA sequences in vivo and offer a great promise for harnessing plant genes in crop improvement. The precise manipulation of plant genomes relies ... [more ▼]

Genome editing technologies enable precise modifications of DNA sequences in vivo and offer a great promise for harnessing plant genes in crop improvement. The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks (DSBs) by sequence-specific nucleases (SSNs) to initiate DNA repair reactions that are based on either non-homologous end joining (NHEJ) or homology-directed repair (HDR). NHEJ can result in frame-shift mutations that often create genetic knockouts. These knockout lines are useful for functional and reverse genetic studies but also have applications in agriculture. HDR has a variety of applications as it can be used for gene replacement, gene stacking, and for creating various fusion proteins. An overview of development and applications of precise GT in plants using SSNs systems is presented in Chapter I. Cereals high in amylose content (AC) and resistant starch (RS) offer potential health benefits. Starch branching enzyme (SBE) plays a major role in determining the fine structure and physical properties of starch. Here, we use CRISPR/Cas9 technology to generate targeted mutagenesis in SBEI and SBEIIb in rice. The frequencies of obtained homozygous or bi-allelic mutant lines with indels in SBEI and SBEIIb in T0 generation were from 26.7 to 40%. SbeII mutants showed higher proportion of long chains presented in debranched amylopectin, significantly increased AC and RS content to as higher as 25.0% and 9.8%, respectively. The details of results are presented in Chapter IV Complete knockouts and loss-of-function mutations are very valuable in defining gene functions, their applications in crop improvement are somewhat limited because many agriculturally important traits are conferred by point mutations or a change of gene expression levels. Development of a technology that enables gene replacement rather than gene inactivation will greatly facilitate plant breading. In this study, we report an efficient method to introduce multiple discrete point mutations in the rice ALS gene using CRISPR/Cas9-mediated homologous recombination. We not only generated homozygous herbicide resistance rice plants in one generation, but also demonstrated that the presented strategy is feasible and effective in precise gene replacement by using CRISPR/Cas9 system to facilitate crop genetic improvement. The details of results are presented in Chapter V Aphids are major agricultural pests which cause significant yield losses of wheat each year in China. Present attempts to improve the aphid resistance of wheat through conventional breeding in China are being confronted by slow progress due to lack of aphid resistant wheat germplasm, the complexity of plant-aphid interactions and the rapid development of resistant pest biotypes. An overview of the engineering of plants for aphid resistance is presented in chapter II. We identify a gene (23028) related to aphid ingestion and digestion from the aphid, S. avenae. Aphids fed on plant material expressing double-stranded RNA (dsRNA) specific to 23028 and C002 show a decline in growth, reproduction and survival rates. The details of results presented in the chapter VI. [less ▲]

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See detailStrategies of host defense and viral counter defense: analysis of Fusarium graminearium responses to FgHV1 infection
Wang, Shuangchao ULiege

Doctoral thesis (2017)

Viruses that selectively infect fungi are named fungal viruses or mycoviruses. Fungal viruses exist in all major groups of fungi and are important in both fundamental research and biological control of ... [more ▼]

Viruses that selectively infect fungi are named fungal viruses or mycoviruses. Fungal viruses exist in all major groups of fungi and are important in both fundamental research and biological control of plant pathogens. Fusarium graminearum hypovirus 1 (FgHV1) was the first virus isolated from F. graminearum belonging to the hypoviridae family. FgHV1 was supposed to encode two open reading frames, which had high sequence identities with Cryphonectria hypovirus 1 and 2 (CHV1 and CHV2). F. graminearum strain infected with FgHV1 showed lower growth rate and reduced conidia production, but with no pathogenicity change. To elucidate the host defense and viral counter defense mechanism, we analyzed the F. graminearum stress responses to FgHV1 infection from several aspects. In the first part, we preliminarily elucidated the RNA silencing mechanism of the F. graminearum/hypovirus system from a small RNA (sRNA) perspective. The length distributions of F. graminearum sRNA were altered by FgHV1 infection, especially 24-nt sRNA. Extensive FgHV1-derived sRNAs were detected, yielding the first high resolution map of sRNA from mycoviruses. In particular, the RNA silencing-related genes FgDicer1 and FgRdRp5 were predicted targets of FgHV1- and FgHV2-derived siRNAs, possibly revealing a novel anti-RNA silencing strategy employed by mycoviruses. In the second part, we performed genome-wide expression analysis to reveal stress-related genes with expression changes in response to FgHV1 infection. A total of 248 differentially expressed genes were identified. Cellular redox regulation related genes were the most affected categories in F. graminearum challenged with FgHV1. Then we verified that FgHV1 encoded protein 20 (p20) could induce the H2O2 accumulation and hypersensitive response in Nicotiana benthamiana leaves. In the last part, our experiments confirmed that p20 functioned as a RNA silencing suppressor (RSS) with the agroinfiltration-mediated technique, making p20 the third RSS identified in mycoviruses. By incorporating single strand sRNA, p20 could suppress host RNA silencing. Globally, the defense responses of F. graminearum to FgHV1 infection were studied all-around and in-depth. On the other hand, FgHV1 developed counter defense strategies to protect from invasion resistance. [less ▲]

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See detailDisease detection and management at the wildlife-livestock-human interface
Chaber, Anne-Lise ULiege

Doctoral thesis (2017)

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See detailImprovement of the ChIP-seq technique for histone posttranslational modifications through enhanced laboratory protocols and data processing methods
Laczik, Miklos ULiege

Doctoral thesis (2017)

Massively parallel sequencing has rapidly become the dominant technique in various omics studies as it provides an unequalled amount of high quality quantitative data for a reasonable cost that is ... [more ▼]

Massively parallel sequencing has rapidly become the dominant technique in various omics studies as it provides an unequalled amount of high quality quantitative data for a reasonable cost that is decreasing ever since the first next generation sequencers appeared. Subsequently, chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq) is the prevailing method of choice for investigating protein–DNA interactions in a genome-wide manner. Bioinformatics tools are also evolving quickly to meet the increasing demands of processing huge amounts of ChIP-seq data and to open the way for novel techniques and insights. However areas still exist that could benefit from improved wet-lab and dry-lab methods. One such area is data visualisation and interpretation; another is the ChIP-seq study of histone posttranslational modifications, especially the research of inactive histone marks which tend to produce diffuse broad enrichments instead of point-source peaks. Achieving proper enrichment and unbiased analysis in such histone mark studies proves to be a great challenge. In this doctoral thesis we show how we addressed these issues on both the level of bioinformatics and the level of sample processing methods. We present our innovative analysis tools we developed to this end, among others a highly customisable, feature rich viewer for next generation sequencing data visualisation, and an analysis pipeline specifically aimed to handle broad enrichments from ChIP-seq studies of (inactive) histone marks. We propose specific software and specific peak calling settings to detect a range of histone modifications accurately, and we describe the way to determine the optimal settings. Along the pipeline we also present a protocol designed to enhance enrichments and facilitate peak detection in broad peak studies typical of inactive histone marks. We demonstrate how this method affects various enrichment types and propose potential applications that could benefit from it. Furthermore we show diverse achievements with the analysis pipeline, including the interpretation of the aforementioned wet-lab method, and the development of an automated ChIP-seq protocol optimised for low cell numbers. [less ▲]

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See detailField border flowering strips as a source of valuable compounds
Paul, Aman ULiege

Doctoral thesis (2017)

Intensification of agricultural practices has caused irreversible damage to environment during the last few years. Several consumers are now deviating towards healthier diets produced from eco-friendly ... [more ▼]

Intensification of agricultural practices has caused irreversible damage to environment during the last few years. Several consumers are now deviating towards healthier diets produced from eco-friendly and sustainable agricultural systems. In this regard, the possibilities of utilizing edible biomass originating from sustainable agricultural practices have gained recent attention. The underutilized edible plants, especially their seeds could be one of the interesting alternates, as some of these seeds are not only nutritious, but could also be produced using sustainable practices. Similarly, edible insects represent another category of biomass which are rich in nutrients and could be produced sustainably. The seeds from underutilized edible plants and the edible insects could be simultaneously harvested using a sustainable agricultural system involving field border flowering strips. Field border flowering strip is a part of agricultural landscape that is reserved for herbaceous vegetation. These strips are popularly grown throughout the world to enhance biodiversity. The main objective of this thesis is to utilize seeds from some of the plants grown as field border flowering strips and insects that find refuge in these plants for the provision of food and health promoting substances. From the literature reviewed in chapter two, it was observed that: (1). Most plants that are grown in field border flowering strips are edible, and their aerial parts have been extensively analyzed for chemical composition. However, there is a scarcity of literature evaluating chemical composition/food utilization of the seeds from plants that are grown as field border flowering strips. So, the primary objective of this thesis is to investigate the nutritional and health promoting potential of the seeds from some plants that are grown in these strips. (2). A number of grasshopper species find refuge in field border flowering strips. Several grasshopper species are considered edible throughout the world and they are interesting source of nutrients. So the secondary objective of this thesis is to screen some edible grasshopper species that are present in field border flowering strips, analyze their nutritional value, and investigate possibilities to establish their commercial rearing for ensuring year-long availability of edible biomass. The research strategy adopted to achieve the objectives of this thesis is mentioned in chapter three. This chapter includes details about the selection of raw materials (both plant seeds and insects), and subsequent analysis. Chapter four contains the detail about the materials and methods used for analysis during this study. Chapter five includes details about the investigations on edible insects. Chorthippus parallelus Zetterstedt species grasshoppers were shortlisted for detailed investigation due to their high densities in field border flowering strips. This insect species was analyzed for proximate composition, amino acid profile, fatty acid profile and mineral profile. Moreover the toxicity of these insects was also evaluated using two different models. Results indicated that these insects could be consumed as an alternate source of proteins (69%) and omega-3 fatty acid rich lipids (10%). Rearing trials done during this study indicates that commercial rearing could be developed to produce sufficient and safe biomass for human consumption. The selection of seeds from three plant species (Achillea millefolium L., Anthriscus sylvestris (L). Hoffm. and Prunella vulgaris L.), for detailed analysis on the basis of lipid content and fatty acid profile has been mentioned in chapter six. Chapter seven, eight and nine include the details about the composition and anti-oxidant activity of A. millefolium, A. sylvestris and P. vulgaris seeds, respectively. Proximate composition, lipid profile, amino acid profile, mineral profile, lignocellulosic profile, phenolic profile and phytate content of the three plant seeds were investigated during this study. Two new phenolic acids were discovered originating from P. vulgaris seeds. These compounds were named amolsamic acid A and amolsamic acid B. Discovery of these compounds was the true highlight of this thesis. All the three plant seeds were found to contain substantial level of total phenolics (0.8-2.6%) and interesting phenolic profiles (dominated by chlorogenic acid, rosmarinic acids and related compounds). Keeping this in mind, the detailed anti-oxidant activity (including anti-radical scavenging, horseradish peroxidase response modulation, cellular anti-oxidant, myeloperoxidase response modulation and anti-lipid peroxidation activity) of their respective seed extracts was also analyzed. Results obtained during this study indicate that A. millefolium, A. sylvestris and P. vulgaris seeds not only contain interesting level of nutrients, but their extracts also exhibit significant anti-radical scavenging, horseradish peroxidase response modulation, cellular anti-oxidant (IC50 values order: P. vulgaris>A. sylvestris>A. millefolium) and myeloperoxidase response modulation activity (IC50 values order: A. sylvestris>A. millefolium>P. vulgaris for both direct and SIEFED assay). The main conclusions (chapter ten) of this PhD dissertation are: (1). C. parallelus insects could be viewed as an alternative source of nutrients to diversify human diets. The preliminary rearing studies done during this study indicate that commercial rearing could be developed for generation of substantial (and safe) biomass to support human consumption. (2). A. millefolium, A. sylvestris and P. vulgaris seeds could be included in food formulations (or consumed as whole) as a source of proteins, lipids, minerals and phenolics. P. vulgaris seeds could also be used for the extraction of two new phenolic constituents (amolsamic acid A and amolsamic acid B). The first investigations involving A. millefolium, A. sylvestris and P. vulgaris seeds realized during this study, indicate that seed extract (or whole seeds) from all three plants could possibly be consumed for the prevention of neutrophil and myeloperoxidase mediated damage in human body. [less ▲]

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See detailImpact of spatio-temporal sahde on crop growth and productivity, perspectives for temperate agroforestry
Artru, Sidonie ULiege

Doctoral thesis (2017)

Currently, silvoarable agroforestry is receiving renewed interest in Europe, as a land use system that allows for combining the production of commodities with a range of non-commodity outputs, such as ... [more ▼]

Currently, silvoarable agroforestry is receiving renewed interest in Europe, as a land use system that allows for combining the production of commodities with a range of non-commodity outputs, such as environmental protection. Despite the potential of this practice, it remains rarely implemented in Northwestern Europe. One of the obstacles in the adoption of silvoarable agroforestry systems is the lack of quantitative knowledge on the long term performance of different crops when they are competing for resources with trees. In the face of a wide range of possibilities, it remains difficult to obtain a clear overview of overall system functioning. In this thesis, we simplify this complexity by focusing our research questions on the resource of light, based on the assumption that in Belgian climatic conditions light is likely to be the predominant constraint for understorey crops in a silvoarable agroforestry system. With regard to this resource, we develop our research in order to gain insights into the growth mechanisms and final yield of shaded winter wheat and sugar beet crops. We address these questions using an artificial shade system, which has been developed to reproduce the effect of the heterogeneous spatio-temporal pattern of light observed under late-flushing trees in an agroforestry system, isolated from the competition effects for water and nutrients. The shade structures recreate two shade environments: continuous and periodic. The continuous shade treatment leads to shade throughout the entire day, while the periodic shade treatment induces an intermittent shade period, which varies during the day and according to structure orientation. Winter wheat responded to the late application of both shade treatments with a significant decrease in grain yield, which was partly compensated for by an increase in grain protein content. When shaded, sugar beet compensated through morphological adaptations of the aboveground part of the plant, and by a decrease in the final root dry matter and sugar yield. Overall, for both crops, the magnitude of the final yield repercussion varied with the level and period of shade application. Additionally, an arable plot bordered by a row of poplar trees was selected to evaluate the effect of real trees on the winter wheat. The reduction in the final grain yield follows a gradient, from underneath the trees to the centre of the field. Notwithstanding that interactions other than light competition may have occurred, the maximum yield reduction observed under the trees never reaches the level of decrease which is observed under the continuous shade treatment simulated by the artificial shade arrangement. This experimental approach with winter wheat was complemented by a modelling study, in which we evaluate the ability of the STICS crop model to simulate crops growing under dynamic shade. The results highlight the limits of the STICS model when it is used to simulate crop growth under contrasted shade conditions. Finally, we propose agroecology as a conceptual framework for developing sustainable and profitable agroforestry systems in Europe, and reflect on agricultural practices, food systems, and research methodologies. [less ▲]

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See detailEtude de la gestion des ressources génétiques ovines et caractérisation de leurs marchés en région périurbaine de Ouagadougou, Burkina Faso
Tindano, Kisito ULiege

Doctoral thesis (2017)

Sheep production in Burkina Faso supplies internal consumption and exportation markets, in countries of West Africa (Côte d’Ivoire, Ghana, Nigeria, and Benin). In this region, sheep have both economic and ... [more ▼]

Sheep production in Burkina Faso supplies internal consumption and exportation markets, in countries of West Africa (Côte d’Ivoire, Ghana, Nigeria, and Benin). In this region, sheep have both economic and socio-cultural importance. While production is mainly located in the rural area, it is nevertheless noted that suburban livestock is developing, in particular around the capital city of Ouagadougou. Suburban production differs from rural livestock production, in particular by the actors involved, the economic orientation of production as well as by the availability of resources and production factors (services, inputs, land and capital). This context leads to the search for genetic resources favourable to this environment production, allowing for an optimisation of the activity. This implies a specific management of these resources. However, there is no information on how farmers in the suburban area manage their sheep genetic resources and on the sustainability of this management. Aiming to fill this information gap, this work focuses on (i) the characteristics of sheep farms in Ouagadougou suburbs and in neighbouring rural areas, (ii) the sheep traits, that have an impact on the their price, and finally (iii) the relative importance of some traits in the choice of breeding ram by breeders. In order to characterise sheep farming in the suburban area of Ouagadougou in terms of socio-economic motivations, breeding practices, including genetic resources management, and in order to better understand the dynamics of the sector, a survey was conducted among 80 breeders in the area. The results showed that the sector essentially comprises two categories of livestock, with almost half (42.5%) of the breeders who can be described as traditional livestock keepers. The latter breeders are illiterate at 94.1% and have no non-agricultural economic activities (88.2%). They don’t have sheltered enclosures (70.6) and their sheep don’t receive systematic deworming (61.8%). They keep Mossi sheep (88.2%) and their main selection objective is rusticity (64.7%). The other category includes 50% of the livestock keepers. These tend to intensify production through the use of better infrastructures (enclosures, shelters), better feeding and systematic de-worming of animals (87.5%). They report keeping animals for generation of additional income and they practice crossbreeding. Their main selection objective is to improve the young growth and adult weight. Reproduction is generally characterised by a lack of mating control, especially during the dry season when the animals are allowed to graze freely. This phenomenon, in the context of the practice of crossbreeding by some breeders, creates negative externalities for breeders preferring the purity of their herd for rusticity motives. This also undermines the sustainability of the systems by an uncontrolled increase in the share of Fulani genetics in herds and the loss of sources of Mossi pure breed. To investigate the possibility for the rural area to constitute a source for purebred Mossi sheep for the suburban area, another survey was conducted among 63 livestock keepers in the region of the Central Plateau of Burkina Faso. This study showed that sheep in this area are kept in sedentary systems and the Mossi sheep is the most encountered. A selective breeding strategy can be found for all breeders through the choice of males. The most cited selection objectives were the improvement of the adult weight (84.1%), the young growth (79.4%) and the maintenance of the rusticity (73%). In agreement with their goal of improving the weight and growth of animals, Mossi sheep females are often crossed with Fulani ram. These males are eliminated from the herd after the birth of the first crossbred lambs, while the latter are subsequently used for breeding. By removing the Fulani males after a short period of use, management appears to be better mastered and more sustainable compared to the suburban area, but leads to reconsider the notion of "purebred" in the region, as the management of breeders includes the mixed use of available breeds. However, with regard to the use of this area as a source of replacement females, if farmers appear to be willing to sell females to other farmers, the size of their herds doesn’t allow the sale of large numbers because of their own replacement needs. Added to this is the tendency expressed by some farmers to only sell to farmers they know, in hopes of reciprocity, hence for social rather than commercial motives. Consumer market demand for different phenotypic traits was investigated through a monitoring of market transactions (revealed preference surveys) and surveys among sheep exporters and butchers. A total of 338 transactions were monitored over three different periods (the Muslim Eid al-Adha feast period, Christmas and New Year period and a neutral period). The interviews involved 25 exporters and 15 butchers, who were asked about the characteristics of the animals quested for and their purchase localities. Survey results showed that exporters have preferences for large-framed and good body conditions animals while local butchers mark their preferences for small-framed and low-fitness animals. Markets are categorised into collection, assembly and terminal markets through which animals pass before reaching the final consumer. The revealed preferences have shown that phenotypic traits such as coat colour, weight and height at the withers have a highly significant (p<0.001) influence on prices. The weight has shown a non-linear, increasing influence on prices with increasing marginal income per kg of live weight. The purchase period, which is embedded with the purchase motive, also showed a highly significant (p<0.001) influence on prices, showing a superiority of the prices during the Eid al-Adha, but no difference between prices during the Christmas and New Year period and the neutral periods. Finally, the purchase period and coat colour showed highly significant interactions with the weight, the white-coloured animals and the Eid al-Adha period having better valorised the increase in weight. This study sheds light on the links between markets and demands for a certain orientation of sheep genetic resources. It is suggested, for example, that an improvement on the basis of higher weight and white colour criteria, which are more valued on the market, would rather favour a niche market linked to feasts periods and exports, and some breeders benefiting improved livestock resources. On the contrary, an improvement towards rusticity for small-framed animals would supply a more ordinary market, contributing to food security of households and an income generation for a wider range of sheep producers. In this market context, a final study aimed at highlighting the trade-off that breeders are willing to make for the improvement of the different traits, whether "productive" or "adaptive". A stated choice experience, taking into account the traits such as weight, colour, susceptibility to diseases and the feed requirement, was carried out with 137 breeders. These farmers mainly use natural grazing (82.5% of the farmers involved). Crossbreeding is observed in 23.4% of farmers. The highest willingness to pay (WTP) was observed for resistance to diseases with 261€. However, among the farmer practicing crossbreeding, there was an apparent preference for susceptibility to disease with a WTP of 45€. A significant WTP was also revealed for the white coat colour (21€) then preferred to the bicoloured. The preference for large-framed animals compared to medium-framed ones was significant but relatively lower than preferences for white coat colour and resistance to diseases. On the other hand, farmers showed indifference for the transition from the medium body size to the small body size. For all traits, farmers practicing crossbreeding showed a preference for extreme levels compared to intermediate levels. Two trends emerged from this study: on the one hand, farmers willing to take the risk of reducing resistance to diseases in order to increase productivity; on the other hand, those with greater risk aversion, strongly willing to spend to gain resistance to diseases. The case of crossbreeding farmers suggests an interesting double preference, demonstrating a WTP for opposed traits being considered as typical of one breed or the other, then depreciating the intermediate traits indicating the possibility of a crossbred. All the studies indicate that the management of sheep genetic resources in Ouagadougou's suburban area, although it does not really present threats to the different breeds in its present state, nevertheless shows signs, particularly from the market, that could hamper the sustained use of small-framed and environmentally adapted sheep. It is therefore necessary to find a strategy to better organise this management to make it sustainable. The establishment of a terminal crossbreeding scheme involving suburban and rural livestock farmers is a possible strategy. This nevertheless requires truly commercial livestock at the end of the scheme and means to overcome certain constraints raised in this thesis. [less ▲]

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See detailRégulation de voies de signalisation par deux acteurs de la voie Nonsense-mediated Decay, Dhx34 et Nbas: la cas particulier de l'adénohypophyse.
Windhausen, Thomas ULiege

Doctoral thesis (2017)

In eukaryotes, biosynthesis of functional mRNAs is the core process of genetic expression and is monitored by highly conserved pathways that prevent appearance of aberrant mRNAs. Amongst them the Nonsense ... [more ▼]

In eukaryotes, biosynthesis of functional mRNAs is the core process of genetic expression and is monitored by highly conserved pathways that prevent appearance of aberrant mRNAs. Amongst them the Nonsense-Mediated Decay (NMD) pathway is the surveillance mechanism that detects and degrades mRNAs containing premature termination codons (PTCs). The translation of transcripts containing such nonsense codon within the coding sequence would leads to the production of C-terminally truncated proteins that could exhibit dominant negative or gain-of-function activities. The NMD is thus a key determinant of the phenotypic outcome of numerous diseases involving PTCs such as the β-thalassemia, the Duchenne muscular dystrophy or even some cancers. In addition to its quality control function degrading aberrant mRNA, the NMD is also involved in the abundance regulation of several physiological transcripts. For example the NMD is involved in the regulation of the concentration of splicing factors in a process called AS-NMD (Alternative splicing- Nonsense-mediated Decay), establish a threshold for some stress responses such as the UPR pathway (Unfolded Protein Response) and constitute a defence mechanism against ARN(+) viruses. Despite tremendous studies, the study of the developmental and physiological impact of the NMD pathway is restrained due to the early lethality of the mammals embryos that underwent knock-out of one of the NMD actor. As an alternative model we propose Danio rerio which as a vertebrate with external development and a large panel of genetic inactivation methods is a wonderful model for developmental studies and represent a excellent tool to study the NMD pathway. Initial studies in zebrafish conducted by morpholino knock-down, showed that depletion of upf1, upf2, smg5, smg6, dhx34 or nbas leads to the NMD blockage and induce similar developmental defects mainly in brain, eyes and somites. Moreover, it’s has been showed that as in mammals the NMD in fish also implicated in the regulation of natural transcripts. We present here a functional study of two key actors of the NMD, Dhx34 and Nbas, in the interesting case of the pituitary gland development. In the present study, we shed light on the NMD pathway importance for the developmental process of the pituitary gland. Using in situ hybridization confirmed by RT-qPCR quantification, we observed that the NMD inactivation thought inhibition of two crucial actors of this surveillance pathway, Dhx34 and Nbas, lead to a hypertrophy of the gland coupled with a promotion of the anterior cell fates and a repression of the posterior fates at 2 dpf. We proved that this endocrine deregulation is due to a late general increase of the Sonic Hedgehog and Delta-Notch signalling during AH formation. In addition to previous works, our results show that the NMD pathway is required to control the activity diverse signalling pathways involved in the developmental process. As confirmation, we could observe serious abnormalities in a variety of tissues such as underdeveloped eyes, intestine, liver and skeleton, defects in brain, somites and vascular patterning. [less ▲]

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See detailInnate signaling by mycolate esters of the cell wall of Mycobacterium tuberculosis and relevance for the development of adjuvants for subunit vaccines
Tima, Giresse ULiege

Doctoral thesis (2017)

Tuberculosis remains among the most deadly health threats to humankind. This povertyrelated disease, caused by bacteria of the Mycobacterium tuberculosis complex, kills each year more than 1.5 million ... [more ▼]

Tuberculosis remains among the most deadly health threats to humankind. This povertyrelated disease, caused by bacteria of the Mycobacterium tuberculosis complex, kills each year more than 1.5 million people. It is estimated that a further 2 billion individuals are latently infected with M. tuberculosis. Most of them will never develop any clinical symptoms, although 5 to 10% of these latently infected individuals are at risk to develop TB in their lifetime. During the last decades the situation worsened because of deteriorating socioeconomic conditions, the increased incidence of drug-resistant M.tuberculosis strains and the co-infection with HIV (a major risk factor for development of TB). Currently only one vaccine is available against TB, the Bacille of Calmette and Guérin (BCG). However, its efficacy is extremely variable against the contagious form of TB - pulmonary TB - in adults and adolescents (ranging from 0 to 80%). Therefore, to control and eliminate TB, a better vaccine, efficient drug treatments and more rapid and cheaper diagnostic techniques are needed. In this PhD thesis we have attempted to provide additional information to reach this goal. Indeed, we investigated the inflammatory and adjuvant potential of mycolate esters homologous of those found in the cell wall of M. tuberculosis. These mycolate esters vary in terms of sugar (trehalose, glucose and arabinose) and lipid (alpha-, methoxy-, keto-, wax-ester MAs) moieties. TDM, TMM, GMM and AraMM were found to be potent activators of BMDCs in vitro. This activation was shown to be dependent on the Mincle pathway. Our results demonstrated that the classes of MAs bound to sugar do not consistently impact the level of pro-inflammatory and adjuvant responses induced. Rather, the nature of the sugar and the number of acyl chains bound to it seem to dictate the affinity of the glycolipid for Mincle receptor in vitro. In vivo, we observed that TDM, TMM and GMM induce similar immune responses characterized by a production of antigen-specific IFN-γ and IL-17A. The immune responses induced by AraMM are dependent on the type of formulation. Indeed, AraMM in emulsion does not induce substantial level of Th1 while AraMM in DDA liposome induces Th1 immune response. This study increases our knowledge on host-pathogen interactions during M. tuberculosis infection by identifying the receptor involved in the recognition of several PAMPs. Furthermore, we showed that the activation of this receptor by these mycolate esters triggers the induction of protective Th1 and Th17 immune responses [less ▲]

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See detailEtude descriptive et relationnelle des facteurs de risque d’infécondité et d’infertilité des vaches laitières au sud Viet Nam
Nguyen, Kien Cuong ULiege

Doctoral thesis (2017)

Increasing milk production is a key issue for Vietnam. Improving milk production involves controlling direct or indirect factors responsible for this. These factors are genetics, feed, environment, and ... [more ▼]

Increasing milk production is a key issue for Vietnam. Improving milk production involves controlling direct or indirect factors responsible for this. These factors are genetics, feed, environment, and reproductive performance. The identification and control of individual or collective factors responsible for reproductive performance is therefore an important step in improving milk production. The general objective of our study is to describe the milk and reproductive performances of dairy smallholding in Vietnam and to analyze the effects of risk factors on reproductive performance. The specific objectives are:(1) to describe the physiological and pathological characteristics of genital tract of culled dairy cows in dairy smallholding; (2) to specify the fecundity and fertility of heifers and dairy cows of small dairy farms; (3) to identify the postpartum (PP) reproductive disorders of cows in dairy smallholders (4) to analyze the effects of individual and environmental risk factors on the reproductive performance of heifers and cows; and (5) to analyze the risk factors for the postpartum (PP) reproductive disorders of cows. The first work of our study was conducted from February to August 2012 on 507 culled crossbred Holstein Friesian (HF) x Lai Sind (LS) dairy cows at two slaughterhouses in HCMC. Age and body condition score (BCS) of cows were determined prior to slaughter. A visual examination of vulva region was also performed to identify the presence of eventual discharges. Then, vaginoscopic examination was performed to determine the presence of discharges and pneumovagina or even urovagina. After slaughter, the uterus was incised to examine the contents. Oviducts were observed to identify abnormalities. The ovaries were collected to evaluate eventual structures (number and diameter of follicles, corpus luteum - CL and cysts) using an ultrasound (KX5200, 6.5 MHz linear probe). The results of this study revealed some important pathological characteristics of examined cows. Nearly half (44.4%) of examined cows had a BCS lower than 2.5. The prevalence of pneumovagina and urovagina was 33.1% and 14.7%, respectively; age and BCS have had a significant effect on the prevalence of these pathologies. The frequencies of vaginal discharges and abnormal uterine contents were 12.1% and 5.4%, respectively. 226 out of 507 examined cows (44.6%) were in anœstrus. The frequencies of functional pathological anœstrus, cystic, pyometral and gestation were 37.3%, 2.0%, 0.4% and 4.9%, respectively. Type 0 and I anœstrus have been more often observed in cows with low BCS and in cows aged less than 6 years. The results of the first work reinforced us in the need to set up specific monitoring of small dairy farms at HCMC. The total of 232 heifers and 244 cows (261 lactations) of 35 small farms in Cu Chi district, HCMC were observed during the years 2013 and 2014. The animals are kept permanently indoors. Their diet consists of fodder (Pennisetum purpureum or natural grass and rice straw), concentrates and by-products (spent grain and cassava waste). Each farm was monitored monthly for reproduction of heifers and cows by transrectal palpation, ultrasound (KX5200, 6.5 MHz linear probe) and vaginoscopy. Reproductive data (dates and type of calving, calf sex, complications, results of clinical examinations, date of heat, date of insemination), milk production (daily average milk yield per cow), BCS and weight of heifers were updated at each visit. The reproductive performance was assessed by fecundity and fertility parameters. The fecundity of heifers and cows was calculated by (1) birth to conception interval (heifers) (or age at conception – AC) or calving to conception interval (cows) (or days open - DO), (2) birth to first service (heifers) (or age at first service – AFS) or calving to first service (cows) (or waiting period - WP) and (3) days between first and last service (DFLS). The fertility of heifers and cows was determined by (1) number of services per conception (NSC), (2) conception rate at first service (CRFS) and (3) overall conception rate (CR). The prevalence of PP disorders (dystocia, retained placenta or RP, clinical endometritis, urovagina, cysts and anœstrus) was also determined. The monthly temperature and humidity index (THI) for the years 2013 - 2014 has been calculated. The body weight and average daily gain of heifer at 6, 12 and 16 months of age were 159, 280 and 351 kg and 690, 646 and 705 g/day respectively. The average daily milk yield per cow was 11.6 (± 0.5) kg. The average duration of lactation was 368 (± 100) days. The overall mean of AFS, DFLS and AC of heifers was 479 (± 80), 38 (± 80) and 517 (± 114) days, respectively. The NSC, CR and CRFS was 1.8 (± 1.4), 55% and 58%, respectively. A significant decrease in AFS and AC according to the year of birth and a significant increase in AFS with a heavier weight (> 320 kg) at first AI were observed. CRFS of heifers inseminated in 2013 was higher than that of heifers inseminated in 2014 (64% vs 50%, P <0.05). The monthly CR in heifers was negatively correlated with the monthly THI during observed period (P = 0.003). The overall mean of WP, DFLS, DO of cows was 109 (±52), 133 (±114) and 242 (±129), respectively. The mean for NSC, CR and CRFS was 4.3 (±2.7), 23 % and 14 %. A significant decrease in WP, DFLS, DO and NSC with an increase according to the year of calving was observed in this study. Calving occurring during rainy season was accompanied by a significant increase in WP. The presence of PP disorders was accompanied by an increase in WP (108 vs 98 days), DO (249 vs 216 days) and NSC (4.7 vs 3.9). A decrease in BCS between calving and day 60th (C60) and between day 60th and 120th PP resulted in a significant increase in WP and DO. The decrease in BCS between C60 also leaded to a significant reduction in CRFS (8 vs 18%, P <0.05). The year and season of insemination, and the BCS at insemination had a significant effect on the NSC and CR of cows. There was a negative correlation between monthly CR in cows and THI (r = -0645, P = 0.02). A total of 353 calvings and PP periods of 302 cows were observed. The prevalence of dystocia, RP, clinical endometritis, urovagin, PP anestrus and ovarian cysts was 24.4%, 16.4%, 19.2%, 5.6%, 49.9% and 6.3%, respectively. The primiparous cows had 1.7 times more risk of dystocia than the multiparous cows (29.9% vs 20.4%, P <0.05). Cows that calved in 2014 or in rainy season had 6 or 2.1 times more than risk of dystocia than cows that calved in 2013 (P <0.001) or in dry season (P <0.01), respectively. The frequency of RP was higher in 2014 than in 2013 (21.8% vs. 11.7%, P <0.01). Cows that calved in 2014 or in rainy season showed more frequently clinical endometritis than cows that calved in 2013 (OR = 3.03, P = 0.001) or in dry season (OR = 3.78, P <0.001). Dystocia (OR = 2.8; P = 0.003) and RP (OR = 4.7, P = 0.001) were the major risk factors of clinical endometritis. The difficult calving, clinical endometritis and insufficient BCS at calving (< 3) or day 30th in PP were accompanied by an increase in risk of type I anestrus. In conclusion, the reproductive performance was satisfactory for heifers, but poor for cows. The infertility and PP anestrus are the major factors responsible for this situation. Heat stress and under-nutrition are the major causes of infertility and PP anestrus. Moreover, the frequency of reproductive disorders (dystocia, RP, clinical endometritis and PP anestrus) is also important in this study. Dystocia and RP are the risk factors for clinical endometritis and this disorder also had a negative effect on fertility and resumption of ovarian activity in cows. [less ▲]

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See detailCaractérisation des amidons de sorgho et de mil perlé cultivés dans le Sahara algérien
Boudries, Nadia ULiege

Doctoral thesis (2017)

Starches of sorghum (Sorghum bicolor (L.) Moench) and pearl millet (Pennisetum glaucum (L.)) cultivated in Tidikelt (In Salah) and Ahaggar (Tamanrasset), were the subject of a characterization study. The ... [more ▼]

Starches of sorghum (Sorghum bicolor (L.) Moench) and pearl millet (Pennisetum glaucum (L.)) cultivated in Tidikelt (In Salah) and Ahaggar (Tamanrasset), were the subject of a characterization study. The approach consists of the isolation of starches, the determination of physico-chemical and functional properties and the study of enzymatic hydrolysis modification. The starches with a rate ranging from 63.1 to 66.8 % were isolated according to the alkaline method. The purity of the obtained starches is satisfactory (91.4-96.7 %).However the extraction yield remains average (59.1-61.2 %). The physical properties (color, shape and size of the granules), chemical composition (moisture, starch and amylose) and rheological properties (solubility, swelling power and viscosity) of the isolated starches were determined. Important results were obtained highlighting interesting functional properties of these starches. Indeed, the average diameter of native starches granules had reached 18 and 10µm for sorghum and pearl millet respectively. These values are lower than those of others regions cultivars and close to those of corn and cassava. The amylose content (23.0 and 27.1 %) revealed that the analyzed cereals are normal varieties. The analysis of viscosity showed a very high peak viscosity that is reached rapidly. The DSC analysis has revealed higher gelatinization temperatures, attributed to high maturity temperatures. The X-rays diffraction patterns show the type A characteristic of cereals and allowed deducing the relative degrees of cristallinity. The kinetic studies of hydrolysis showed that the sorghum and pearl millet starches present susceptibility for hydrolysis in presence of fungal, bacterial and human amylases. However, this susceptibility varies according to the treatment used with the integral grinding (flour) and to enzyme source. The experimental conditions allowing to enzymatic hydrolysis reactions of isolated starches to follow the Michaelis-Menten model were determined and kinetic constants (KM and Vmax) were calculated. The HPAEC-PAD profiles of oligosaccharides in sorghum starches hydrolysates were determinated for highlight the amylases activities. The study demonstrated the potential of sorghum and pearl millet starches and considers their applications and bioprocessing. [less ▲]

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See detailCaractérisation et élaboration d'un outil de surveillance des cuvettes oasiennes et de leurs alentours par télédétection et système d'information
Karimou Barké, Mahamadou Salifou ULiege

Doctoral thesis (2017)

Situées en zone semi-aride, les cuvettes oasiennes du centre-est du Niger sont des agro-écosystèmes à hautes potentialités. C’est seulement à l’intérieur de ces dernières que l’agriculture est possible ... [more ▼]

Situées en zone semi-aride, les cuvettes oasiennes du centre-est du Niger sont des agro-écosystèmes à hautes potentialités. C’est seulement à l’intérieur de ces dernières que l’agriculture est possible durant toute l’année. Ces cuvettes oasiennes ont connu de nombreux investissements de la part de plusieurs ONGs et projets au cours des dernières années. Cependant, elles sont souvent peu connues par ces acteurs du développement du fait de leur grand nombre et de leur extrême diversité. Cette thèse cherche à réduire cette méconnaissance à travers les activités suivantes: • évaluer les performances de trois méthodes de classification d’images appliquées à la détection de ces cuvettes oasiennes dans le Département de Gouré. Ces méthodes sont l’analyse pixellaire, l’analyse texturale et l’analyse par objet. Elles sont appliquées à des images SPOT 5-THX de 2.5 m de résolution ; • caractériser la forme des cuvettes oasiennes avec deux indices morphologiques (l’indice de compacité de Gravelius et l’indice fractale de leurs contours) ainsi que leurs orientations en utilisant les secteurs de la rose de vent comme repères ; • évaluer les contraintes et potentialités liées aux unités de paysage des cuvettes et de leurs alentours pour l’ensemble des cuvettes oasiennes à partir des extensions de ces unités de paysage, élaborer des indicateurs spatiaux de caractérisation des cuvettes ; • analyser la dynamique de l’occupation des sols de cuvettes oasiennes et de leurs alentours en utilisant les images Landsat 5-TM de 1984, les images SPOT 3 de 1996 et les images SPOT 5-THX de 2013. • proposer un outil de monitoring et une esquisse de système expert orienté à partir des données récoltées par ce biais sur l’ensemble des cuvettes de la zone d’étude. L’évaluation des résultats montre que l’approche par objet (précision globale égale à 97.12%, coefficient Kappa égal à 0.97) est plus performante que celles utilisant la texture (précision globale égale à 89.61%, coefficient Kappa égal à 0,90) et l’analyse par pixel (précision globale égale à 80.58 %, coefficient Kappa égal à 0.80). Une première information originale, à savoir le nombre, la position et la surface de l’ensemble des cuvettes sur la zone d’étude est fournie. Le nombre total de cuvettes oasiennes dans le Département de Gouré est ainsi estimé à 10717. Cet inventaire de ces lieux stocks de ressources est une première étape obligatoire pour leur caractérisation morphologique et pour l’évaluation de leurs potentialités agricoles. L’indice de forme de Gravelius met en évidence une certaine diversité de leurs contours : des cuvettes circulaires (9%), ovales (47%), amiboïdes (11%), étirées (18%) et très étirées ou étirées-amiboïdes (16%). La dimension fractale permet de distinguer trois classes de cuvette selon le degré de lissage de ces contours : très lissées (39%), lissées (50%) et moyennement lissées (10%). Le lissage est interprété ici comme un indicateur d’éolisation des pourtours des cuvettes. Enfin la détermination de l’orientation des grands axes des cuvettes a permis d’identifier quatre secteurs majeurs : E-W (23%), N-S (21%), NE-SW (22%) et SE-NW (34%). Ces analyses morphologiques et d’orientation appliquées pour la première fois à l’ensemble des cuvettes oasiennes du Département de Gouré offrent des éléments permettant de comprendre les processus d’ensablement des cuvettes oasiennes dans cette zone. L’analyse des indicateurs des potentialités naturelles à la mise en valeur agricole montre que les cuvettes oasiennes sont des espaces multi-usages, avec des aptitudes en arboriculture, maraîchage, en natron et en foresterie selon les unités géomorphologiques. Le pourcentage des surfaces cultivables est faible pour 45.8% des cuvettes et fort à très fort pour seulement 3.9 %. Celui des surfaces boisées est très fort sur 61.6 % des cuvettes soit 51.4 % en superficie. Les cuvettes possédant un sol nu à natron et/ou une nappe d’eau affleurante représentent 17.6 % des cuvettes. Quant aux indicateurs de risque de dégradation, ils montrent que 3.3 % et 0.5 % des cuvettes ont respectivement une menace d’ensablement fort et très fort à moyen terme. Alors qu’à terme immédiat, c’est respectivement 3% et 0.8 % des cuvettes dont la menace d’ensablement est fort et très fort. Concernant l’évolution récente de ces milieux, les superficies des cuvettes oasiennes ont régressé de 46783 ha en 1984, à 40831 ha en 1996 et 34553 ha en 2013. Inversement, leur nombre a augmenté de 1984 (8911) à 2013 (10717). Ceci s’explique certes pour partie par les résolutions différentes des images satellitaires utilisées, mais surtout par la fragmentation de certaines cuvettes du fait de leur dégradation et la création de nouvelles cuvettes par l’érosion éolienne. Cette dynamique est accentuée par celle de l’occupation humaine des paysages. Les abords des cuvettes et des vallées sèches constitués souvent d’édifices dunaires sont de plus en plus occupés par les cultures pluviales qui les exposent davantage à l’érosion. En 1984, les édifices dunaires et vallées sèches à culture pluviale représentent 295697 ha alors, qu’en 1996 et 2013, elles occupent respectivement 368153 ha et 423876 ha. Les systèmes d’information à référence spatiale esquissés permettent d’observer et de suivre la totalité des cuvettes oasiennes. Ce système, conçu en utilisant le langage UML, a permis non seulement d’établir des relations entre les indicateurs de potentiel valorisable et de dégradation mais aussi des informations supplémentaires récoltées sur le terrain (village, marché, zone de fixation biologique et mécanique des dunes). Ils offrent un accès aisé à ces indicateurs grâce à une interface informatique. À travers des requêtes sur cette base de données, les cuvettes à menace très forte nécessitant une intervention urgente pour leur conservation ont été mises en évidence ainsi que les variables explicatives du niveau d’exploitation des cuvettes. [less ▲]

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See detailClimate change and insect pests: Impact on carbon dioxide increase on aphid behavior and semiochemistry
Boullis, Antoine ULiege

Doctoral thesis (2017)

There is no longer any doubt on the incidence of rising carbon dioxide (CO2) concentration on global change. Climate modifications are responsible of perturbations in interactions between living organisms ... [more ▼]

There is no longer any doubt on the incidence of rising carbon dioxide (CO2) concentration on global change. Climate modifications are responsible of perturbations in interactions between living organisms. This research topic is in the light of scientists since several decades and is considered to be of major interest in the understanding of future ecosystems’ functioning. In this prospect, interactions between insect herbivores and their natural enemies have received little attention under a climate change scope, while they are of paramount importance in the proper equilibrium of agro-ecosystems. As the efficacy of natural enemies is governed largely by behavioral mechanisms, changes in the predators’ behaviors but also in those related to prey defenses can change the dynamics of insect populations. As aphids are considered as one of the main crop pests in temperate regions, relative literature on impact of increases in atmospheric CO2 concentrations on aphid population dynamic now exists. However, few publications about their chemical ecology are reported. Aphids are using many chemical signals to communicate with each other or in their interactions with higher trophic levels. Here, I tempted to identify the impact of an increase in atmospheric CO2 concentration on the interactions between aphids and their natural enemies mediated by semiochemicals. Aspects of phytovirus transmission by aphids were also covered. After being involved in three literature reviews, I was interested in the aphid alarm signaling which strongly supports aphid-predators interactions. In the pea aphid Acyrthosiphon pisum (Harris), this signaling is mediated by a pheromone, namely the (E)-β-farnesene. For my experiments, I took into consideration the importance of all the steps that this molecule has to pass by, from its production into the emitter individual to the induced behavioral response of the receivers. The results obtained during these experiments highlighted an imbalance in aphid chemical communication for populations grown under elevated CO2 conditions, by modifications in several steps of the signal (decrease in pheromone production, emission and associated behavior). The results obtained here were supported by previous studies indicating that increases in CO2 concentration reduce the aphid escape behavior, which makes them potentially more susceptible to predation. We know that many plant pathogens are dependent on aphid dispersal to spread, so it is of major importance to predict how these insect vectors could be affected by forecasted climate. I thus carried my interest on the ability of aphids to transmit phytoviruses under changing atmosphere. Using another aphid model, the green peach aphid Myzus persicae (Sulzer), we have not observed any modifications in terms of virus and aphid spread in laboratory trials when tested under either actual or forecasted CO2 concentration. However, the viral transmission efficiency via aphids is increased under CO2-enriched atmosphere. Finally, the host searching behavior of an aphid predator was studied. The efficiency of natural enemies of insect pests is mainly driven by their ability to find food sources or oviposition sites in their environment. The conducted study highlighted the preference of the hoverfly Episyrphus balteatus De Geer towards aphid colonies grown under actual CO2 levels, suggesting modifications in chemical cues guiding hoverflies to a suitable oviposition site, due to increase of CO2. The results and knowledge obtained during these studies will add novel information on how a major component of climate change may impact tritrophic interactions and thus the efficiency of natural enemies of insect herbivores in biological control scope. [less ▲]

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See detailUtilisation du D-galactose et du D-tagatose chez Bacillus sp.: Etude des protéines GalM et PBP4a de B. subtilis et B. amyloliquefaciens et Etude de la voie catabolique PTS-dépendante du D-tagatose chez B. licheniformis.
Van der Heiden, Edwige ULiege

Doctoral thesis (2017)

Cette thèse s’intéresse à la métabolisation de deux sources de carbones, le galactose et le tagatose, dans des souches du genre Bacillus. La première partie de la thèse vise à montrer le rôle de GalM, une ... [more ▼]

Cette thèse s’intéresse à la métabolisation de deux sources de carbones, le galactose et le tagatose, dans des souches du genre Bacillus. La première partie de la thèse vise à montrer le rôle de GalM, une galactose mutarotase, dans la métabolisation du galactose chez B. subtilis ATCC 21332 et B. amyloliquefaciens FZB42. Le gène galM est organisé en opéron avec le gène dacC qui code pour un PBP de faible poids moléculaire, le PBP4a. Des mutants ponctuels et de délétion ont été générés dans le but d’étudier l’implication des produits de cet opéron dans la formation de biofilms in vitro, dans le remodelage de la paroi bactérienne et dans la colonisation de racines de plantes (plants de tomate et Arabidopsis thaliana). Une différence significative de colonisation a été mise en évidence entre la souche sauvage de B. amyloliquefaciens FZB42 et son double mutant uniquement sur les racines de plants de tomate. Toutefois, il pourrait s’agir d’un effet indirect lié à la méthode. Après analyse des muropeptides composant le peptidoglycane isolé en phase végétative, aucun rôle in vivo n’a pu être attribué au PBP4a. Cependant, l’attachement de cette protéine à la membrane de la bactérie a pu être mis en évidence. Une couronne de charges positives en surface du domaine II du PBP4a est responsable de cette localisation. La seconde partie de la thèse présente la voie de métabolisation du tagatose découverte chez B. licheniformis. Cette source de carbone est transportée et phosphorylée par les composants du système phosphotransférase (PTS) : EIIAT AG (TagM) et EIIBCT AG (TagL). La fonctionnalité du cluster de gènes identifié dans le génome de la bactérie a été démontrée par des expériences de supplémentation dans deux souches initialement incapables de métaboliser cette source de carbone : B. subtilis et E. coli. Le tagatose est phosphorylé durant son transport au niveau du carbone C1. Le tagatose-1-phosphate, présent principalement sous la forme -pyranose, est ensuite phosphorylé par l’enzyme TagK, une tagatose-1-phosphate kinase. Les paramètres cinétiques de l’enzyme ont été déterminés et la spécificité en faveur du tagatose-1-phosphate a été démontrée. Le tagatose 1,6-bisphosphate généré par TagK est hydrolysé en DHAP et G3P par GatY, une tagatose 1,6-bisphosphate aldolase de classe II. [less ▲]

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See detailCattle grazing dynamics under contrasted pasture characteristics at temporal and spatial scales
Andriamandroso, Andriamasinoro ULiege

Doctoral thesis (2017)

Grassland constitutes an important and a low-cost food source for grazing livestock. Optimal management should consider both forage resource productivity and animal needs. For cattle, grazing is a normal ... [more ▼]

Grassland constitutes an important and a low-cost food source for grazing livestock. Optimal management should consider both forage resource productivity and animal needs. For cattle, grazing is a normal behavior displayed in an attempt to eat the amount of forage to fulfill their nutritive requirements for maintenance and production. It is the most time-consumed activity of cows reared in pasture-based systems. With the increase of herd size, on one hand, farmers have been constrained to integrate innovative tools and techniques, such as milking robot, to improve the production system in particular to reduce the labor cost. On the other hand, such change might reduce time allocated for grazing on pasture. However pasture-based systems constitute a real pillar for sustainability as they are socially acceptable and environmentally profitable as they play an important role on ecosystem services and biodiversity provision. Studying grazing processes at individual level, which finally is the key point of animal-plant interactions, is a valuable research domain to enhance the knowledge about this mechanism and to feed decision support tools. This thesis aimed to link the changes in pasture characteristics to the grazing behavior of cattle in order to better understand the grazing strategy under different pasture characteristics and forage allowances. To allow an individual monitoring, sensor technology has integrated within farms and livestock researches to monitor many physical variables, inducing the emergence of precision livestock farming approach. Different types of sensors were designed, and already commercialized for some, primarily for physiological status detections such as heat, parturition or diseases. Grazing behaviors could be monitored using pressure, electromyography, acoustic or accelerometric sensors by classifying posture and movements of the animal into unitary behaviors (grazing, ruminating, resting, walking, etc.) and finer behavior such as chews and bites through jaw movements’ detection. When compared to real observation, detection accuracies of these behaviors were variable according to the type of sensor, its position on the animal during data acquisition on pasture, the data recording frequency, the time-window and the method dedicated to the post-recording data analysis. State-of-the-art analysis demonstrated a great performance of accelerometers for unitary behaviors and bites detection. An inertial measurement unit, integrating accelerometer, gyroscope and location sensors, was used for recording cattle movements during grazing at high sampling rate (100Hz). It allows a correct detection of grass intake and rumination behaviors with an average accuracy of 91% using 1-second time-window when calibrating and validating the detection algorithm. Deeper analysis of accelerometric signal allowed us to detect bites and chews performed during grazing and ruminating. Effects of pasture heights on grazing bites characteristics were differentiated by a higher frequency when pasture is at a lower height. Finally when combined to geographical information, a similar pattern was observed for cattle grazing on the same spot confirming their herd movement during grazing in terms of bites location. Differences were visible under different pasture heights but not significant. Such bites location, combined with continuous monitoring of cattle behaviors, through use of sensors, should be furtherly linked with more pasture characteristics, if possible with the same accuracy, and monitored on longer period in order to obtain a complete coverage of cattle grazing strategy and the effect of contrasted environment in order to purpose valuable tool for a better grazing management. [less ▲]

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See detailImprovement of genetic evaluation systems for maternally influenced traits and multi-breed livestock populations
Vanderick, Sylvie ULiege

Doctoral thesis (2017)

Animal breeding programs are designed to genetically improve livestock populations over many generations to enhance farm sustainability and competitiveness. Genetic improvement is achieved by selecting ... [more ▼]

Animal breeding programs are designed to genetically improve livestock populations over many generations to enhance farm sustainability and competitiveness. Genetic improvement is achieved by selecting genetically superior animals, based on estimated breeding values, to be the parents of the next generation. These estimated breeding values are calculated by solving mixed model equations characterizing appropriate statistical genetic evaluation models. To guarantee effective genetic selection, genetic evaluation models must be tailored to the specific characteristics of the traits and population under evaluation. This PhD thesis focused on the development of genetic evaluation models suitable for categorical maternally influenced traits and for multi-breed populations. Appropriate genetic animal models were developed and assessed: (1) for two categorical maternally influenced traits based on calving ease scores from Walloon Holstein dairy cattle and on lamb survival data from a New Zealand sheep population; (2) for two multi-breed populations based on milk yield records of New Zealand purebred and crossbred dairy cattle, and on purebred and crossbred calving ease scores from Walloon Belgian Blue and Holstein cattle. Results showed that (1) fitting maternal effects was required to avoid biasing the estimated breeding values, and there was no clear advantage in using non-linear mixed models instead of linear mixed models for the genetic analysis of the two categorical maternal traits studied; (2) breed-dependent breeding values could be estimated using the proposed multi-breed models, and that combining purebred and crossbred data had a positive influence on the accuracy of the breeding values of purebred animals. Finally, part of the research presented in this thesis contributed to the development of the genetic evaluation systems currently used in Walloon Region of Belgium and in New Zealand. [less ▲]

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See detailContribution à la mise en place d’une plateforme de transgénèse chez la volaille domestique: culture, cryopréservation et ingénierie génétique de cellules germinales primordiales.
Tonus, Céline ULiege

Doctoral thesis (2017)

Primordial germ cells (PGCs) are the intermediate of choice for domestic fowl transgenesis and genome editing. These can support large transgenes insertions and, as precursors of the germline, can ... [more ▼]

Primordial germ cells (PGCs) are the intermediate of choice for domestic fowl transgenesis and genome editing. These can support large transgenes insertions and, as precursors of the germline, can transmit a genetic modification to the next generation. Moreover, given the difficulties for cryopreserving avian gametes (spermatozoa and, above all, oocytes), PGCs represent the material of choice for germplasm preservation in these species. Despite the obvious advantages of PGCs use, recently described related technologies appear generally as more difficult to pursue, and as less effective than expected. In this context, we have developed and optimized some of them which appear as essential for carrying complex chicken genome engineering projects. We first focused on improving the effectiveness of culture and cryopreservation of PGCs. By developing a culture method in inserts, ending up with an efficiency close to 40 %, we were able to isolate and long-term cultivate chickens PGCs from 3 commercial breeds and 2 Belgian endangered local breeds. The cells showed all the characteristics of the PGCs in terms of morphology, markers' expression and gonadal migration. We also applied a cryopreservative vitrification method, which showed results superior to those obtained by conventional slow freezing. During the last part of this work, we genetically engineered PGCs to obtain stable transfectants expressing GFP. These transfectants allowed us to examine long-term gonadal colonization and germline transgene transmission. We also tested a Cre recombinase-mediated site-specific cassette exchange method. As a final result, we have developed the methods and know-how mandatory to allow efficient harvesting, expansion, genetic engineering, reimplantation and cryopreservation of chicken PGCs, and we have shown the possibility of germline transmission of a long term cultured and genetically modified PGCs line. [less ▲]

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See detailDiscrimination of mercury contamination sources and pathways using Hg stable isotopes in the European seabass, Dicentrarchus labrax
Cransveld, Alice ULiege

Doctoral thesis (2017)

Mercury (Hg) is a persistent toxic compound whose amount in the global biosphere has at least tripled since industrialization. The biogeochemical cycle of mercury is particularly complex because elemental ... [more ▼]

Mercury (Hg) is a persistent toxic compound whose amount in the global biosphere has at least tripled since industrialization. The biogeochemical cycle of mercury is particularly complex because elemental mercury is very volatile, has a long residence time in the atmosphere and thus can potentially reach locations that are very distant from the initial emission source. Since the 70’s, many international organisations (OECD, EU, UNEP) have implemented different policies to reduce Hg pollution. However, for these policies to be efficient, the polluters/Hg sources have to be fully assessed and identified. So, there is a crucial need to trace Hg sources and to assess the quantitative impact of local versus global Hg sources on ecosystems. Recently, the study of the seven Hg stable isotopes has emerged as a new promising technique affording to explore the Hg cycle both in situ and in laboratory. Mercury stable isotopes display both mass dependent fractionation (MDF, reported as δ202Hg) and mass independent fractionation (MIF, reported as Δ199Hg and Δ201Hg). The combination of both values should allow to trace back sources and pathways of Hg and methylmercury (MeHg). But, so far, few studies have considered Hg isotopes in marine vertebrates. Thus, the general objective of this thesis was to study a marine predator, the European seabass, Dicentrarchus labrax, to explore the possibility of using mercury stable isotopes to investigate Hg sources and pathways in European coastal waters. Our specific objectives were to characterize the Hg profile (THg, MeHg and isotopy) of wild populations of seabass, to assess whether Hg isotopes differed between populations and could give indications on Hg sources, with special attention paid to differentiate local versus global Hg sources. We also wanted to explore internal variation of Hg profiles by comparing several tissues. And, we wanted to validate our interpretations of in situ results by experimentally evaluating the potential fractionation between muscle and liver tissues of D. labrax, and between the diet and fish tissues. To fulfill our objectives, we split the thesis in 3 axes. First, juvenile seabass were collected in seven geographically distinct locations: the Agiasma lagoon in the northern Aegean Sea (AeS), the North Sea (NS) along Belgian and English coasts, the Seine estuary (SE), the Turkish coast of the Black Sea (BS), the Marano and Grado lagoons in the northern Adriatic Sea (NAS), the Portuguese lagoon, Ria de Aveiro, at two distinct sites: a very contaminated one (RAC) and a least contaminated one (RAR). v Our results showed seabass displayed extremely variable THg (Total mercury) concentrations amongst locations. Environmental contamination of the fish habitats seemed to be the main driving factor of THg concentrations in their tissues. Then, we showed that the populations also had distinct Hg isotopic niches (using SIBER on Hg stable isotopes, a premiere!), and that Hg isotopes (Δ199Hg and δ202Hg) could be used as a discriminating tool. We showed that Hg isotopes also told more about the origin of THg contaminating juvenile seabass: Δ199Hg values indicated a rather coastal MeHg source while δ202Hg could be linked with the global versus local Hg origin. Some populations like AeS were thought to be affected mainly by background, global Hg source, while other sites such as RAC (and SE and NAS) that were more heavily contaminated, would undergo a strong influence of local contamination. The previous observations were made in muscle tissue. Since different tissues often have distinct turnover times and different affinity for pollutants, the second axis of this thesis aimed at comparing liver and muscle results. So, we investigated the liver tissue of the very same individuals than in axis 1. The THg RATIO (THgliver/THgmuscle) was very variable amongst populations. We found that Hg organotropism (affinity for different organs) was influenced by the overall contamination level and maybe also by the food regime (via the %MeHg in diet). The Hg isotope composition also differed between muscle and liver of wild seabass. Hg speciation was most probably not the only cause of such a difference, and there was certainly an internal fractionating process (MDF). We even found serious indication of mercury demethylation happening in seabass, although demethylation in fish had yet to be proven. This is what our 3rd axis addressed. We exposed captive juvenile seabass to environmentally relevant THg concentrations through the diet. Observations confirmed in situ results: Hg organotropism depends on the %MeHg in diet, and THg RATIOs < 1 are to be related to the extremely small proportion of inorganic Hg in the seabass diet. Most of all, we found strong and concordant indications of demethylation process occurring in seabass that would be responsible for the systematically distinct δ202Hg values observed between muscle and liver. In conclusion, our findings constitute the first large scale Hg stable isotope study, on a single fish species, from European coastal waters. They demonstrate the interest and relevance of using Hg stable isotopes to investigate the Hg cycle and sources on both small and large scales and show the possibility to differentiate between global and local Hg sources. This takes a crucial sense in the current context where tracing Hg contamination sources is necessary to implement efficient environmental policies. [less ▲]

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See detailGénération d’une librairie de mutants de Bacillus licheniformis 749/I par l’insertion aléatoire d’un transposon pour identifier les gènes impliqués dans l’induction de la β-lactamase BlaP
Lebrun, Sarah ULiege

Doctoral thesis (2017)

La production de la b-lactamase BlaP chez Bacillus licheniformis 749/I est induite par la présence d’un antibiotique à noyau b-lactame (b-lactamine) dans le milieu extérieur. Le récepteur membranaire ... [more ▼]

La production de la b-lactamase BlaP chez Bacillus licheniformis 749/I est induite par la présence d’un antibiotique à noyau b-lactame (b-lactamine) dans le milieu extérieur. Le récepteur membranaire BlaR1 détecte la présence de la b-lactamine et transmet un signal vers le cytoplasme. La protéine BlaR1 est composée de deux domaines : le domaine C-terminal (BlaR-CTD) exposé à l’extérieur de la cellule qui détecte la présence de l’antibiotique et le domaine N-terminal membranaire (BlaR-NTD) agissant comme un transducteur et un amplificateur du signal perçu par le domaine senseur. En présence de b-lactamine, l’acylation de BlaR-CTD par l’antibiotique entraîne un changement conformationnel des segments transmembranaires menant à l’activation de la boucle L3 de BlaR-NTD. Le répresseur BlaI, qui réprime la transcription du gène blaP, est inactivé par liaison d’un coactivateur, le dipeptide D-Glu--mA2pm issu de la dégradation du peptidoglycane à l’extérieur de la cellule. La voie d’entrée de ce dipeptide n’est pas connue ainsi que le locus blaR2 impliqué dans l’induction de la b-lactamase. L’objectif principal de ce travail est l’identification du locus blaR2 par la construction d’une banque aléatoire de mutants par transposition. La première étape du travail était la mise au point de la transformation de Bacillus licheniformis 749/I par un plasmide possédant une origine thermosensible et porteur d’un transposon modifié. Un clone recombinant a été obtenu par la méthode de transformation de protoplastes avec de l’ADN sous forme concatémère. Une banque d’environ 11.300 clones a été générée et validée. Une méthode de criblage sur boite via un test iodométrique a mis en évidence cinq mutants sur l’entièreté de la banque présentant une différence d’induction par rapport à la souche sauvage. L’identification des insertions chromosomique du transposon a été réalisée par PCR inverse et par AP-PCR et a permis d’identifier trois clones insérés dans le gène blaR1 et deux dans le gène blaP. Ces mutants sont tous différents entre eux. Une seconde stratégie a été envisagée en vue d’identifier le locus blaR2 par complémentation du mutant chimique blaR2- par l’ADN génomique isssus des mutants de la souche sauvage générés à partir du transposon. La souche blaR2- a été transformée cependant, aucun événement de recombinaison n’a pu être observé. Sur base de ces expériences, la question de l’identification du locus blaR2 reste en suspens. Néanmoins, au cours de l’isolement des clones contenant le transposon, nous avons mis en évidence des clones présentant des colonies possédant un phénotype « luisant » par rapport à l’aspect mat de la souche sauvage. Un gène codant pour une estérase (Bl-EstA) a été ainsi identifié et le produit du gène étudié. Bl-EstA appartient à la famille des lipases « hormone-sensitive lipase like_1 » (Famille IV de la classification d’Arpigny et Jaeger (1999)) et possède toutes les caractéristiques des a/b hydrolases. Bl-EstA est sous la forme dimérique en solution et peut adopter différents comportements cinétiques en fonction des substrats qu’elle hydrolyse : une cinétique Michaélienne classique, allostérique ainsi qu’une inhibition par le substrat. Ces comportements impliquent, au moins, la présence d’un site régulateur. Enfin, l’inactivation de Bl-EstA par les alcools n’est pas favorable à son utilisation pour des réactions de transestérifications et dès lors pour des applications industrielles. [less ▲]

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See detailModélisation spatiale de la production fourragère en zone pastorale nigérienne
Garba, Issa ULiege

Doctoral thesis (2017)

This work was carried out on the pastoral zone of Niger, the main objective was to contribute to the improvement of the methods of forage yields predicting mainly in the Sahel and especially in Niger ... [more ▼]

This work was carried out on the pastoral zone of Niger, the main objective was to contribute to the improvement of the methods of forage yields predicting mainly in the Sahel and especially in Niger. This is specifically to validate the model BIOMASAH of ARC; test the MEIA model; to establish a reference model by multiple linear regression; test the similarity method and finally compare the methods. The work was carried out on the one hand with the data measured on the ground by the MEIA from 2001 to 2012, reel rainfall of Niger observations network, meteorological parameters from ECMWF and also with satellite images as SPOT NDVI VEGETATION and MODIS, RFE2 of FEWS NET. Validation of BIOMASAH model was made by t and Wilcoxon tests to compare reel biomass and outputs of the model. Pearson, Kendall and Spearman correlation testing was also made. The MEIA model performance was tested by confronting the results between and within SPOT VEGETATION and MODIS sensors, by comparing R² and RMSE from the integral and maximum NDVI as a predictor of forage yield. Average comparisons by parametric and nonparametric tests were also made to compare the results. The reference model (RM) was produced by multiple linear regression with stepwise method. The selection of variables was based on adjusted R² and RMSE and the LOOCV leave one out cross validation to calculate R² for validation, we made also systematic diagnosis of residues for better characterization of the model. The similarity method was performed using the R², MAD and RMSE as a criterion, the profile of the vegetation growth period of each pixel was plotted for all years. Then we compare the profile of the target year with those of other years to identify the similar year. One hand the results of similarity were compared with actual data with the Pearson correlation test, Spearman and Kendall and secondly using t and Wilcoxon tests to compare means. Comparison of models was made on the basis of R², Adjusted R² and RMSE. Model BIOMASAH result on significant difference between average (p <0.001). Pearson correlations, Kendall and Spearman are low. Regarding the MEIA model, globally R² (0.56) is best, there’s no difference to use MODIS NDVI or SPOT vegetation, the RMSE is 367 kg.ha-1. R² and RMSE vary greatly from one year to another. On a global scale the multiple linear model gave a good R² adjusted (0.69) and RMSE (282 kg / ha) the difference between the calculated and the RMSE of validation is 2.72 kg. Comparing averages of the similarity to the real ones showed that there are no significant differences (p <0.001) for R² with the differences are significant against the same threshold for the MAD and RMSE. The Comparison of the models shows that the multiple linear regression one (reference model) is the best. Research should continue with index like LAI, FARAR and EVI. [less ▲]

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See detailGovernance of plant health and management of crop diversity - the case of common bean health management among members of the association Croqueurs de Carottes
Klaedtke, Stephanie ULiege

Doctoral thesis (2017)

All over the globe, networks of seed growers are cultivating crop diversity in fields and gardens. Their contribution to the maintenance of this diversity has been studied, but research has widely left ... [more ▼]

All over the globe, networks of seed growers are cultivating crop diversity in fields and gardens. Their contribution to the maintenance of this diversity has been studied, but research has widely left aside their management of plant health. The governance of bean health practiced by an association of artisanal seed companies, Croqueurs de Carottes, is approached as a case study in the objective of specifying how management of crop diversity and governance of plant health are articulated. Their concern for the governance of bean health is elucidated from an agroecological perspective, taking an interdisciplinary and transformative approach. Actor-network theory constitutes the backbone of the thesis, situated between agronomy and sociology and drawing upon a threefold research device: on-farm experiments, semi-directive interviews and participant observation. The Croqueurs' approach to bean health is described as in situ approach, in which plant populations are considered healthy if they are able to live with potential plant pathogens and adapt to their growing environments. Relying on ecological interactions, competences of plant health management are distributed throughout the production system. Both for plant health and crop diversity management, a seed lot is determined by a complex system of interactions. A clear boundary distinguishing plant populations from their growing environment cannot be drawn. This implies (i) that plant health must be judged upon in situ in the plants' growing environment and (ii) that the governance of plant health must be considered at the collective scale. [less ▲]

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See detailMonitoring Lions (Panthera leo) using Digital 3D Models of their Tracks
Marchal, Antoine ULiege

Doctoral thesis (2017)

As the Earth may be entering a new human-influenced geological time, the Anthropocene, the pressure on biodiversity due to increasing human populations and activities is unprecedented. Monitoring animal ... [more ▼]

As the Earth may be entering a new human-influenced geological time, the Anthropocene, the pressure on biodiversity due to increasing human populations and activities is unprecedented. Monitoring animal populations is essential to gain demographic data and assess their viability. Because of the difficulties linked to invasive methods that involve direct observation or handling, many researchers have explored alternative approaches such as using tracks. Tracks are the material by-product of the interaction between terrestrial animals and their physical environment due to gravity. The interpretation of tracks exists since the dawn of mankind and is a crucial factor for human evolution. As an integral part of hunting, the art of tracking involves cognitive thinking that may well be part of the origin of science. However, monitoring species through their tracks is controversial due to several reasons: unreliable recording techniques limited to two-dimensions, manipulator bias, substrate variation, misidentification of the foot from which each track originates, and subjective identification of the age, sex and/or individual. The aim of this thesis was to evaluate the possibility of monitoring lions Panthera leo through digital three-dimensional (3D) models of their tracks. The first step was to assess close-range digital photogrammetry as a low-cost, rapid, practical and reliable field technique for the digital 3D modelling of lion paws, tracks and trails. A trail, that is a continuous sequence of tracks made by the same individual, reflects the morphology and kinematics of that individual. The use of traditional morphometrics enabled the extraction of variables such as distances, angles and areas from the digital 3D trails originating from individuals of known age, sex and/or identity. When comparing adult lions walking at the same gait (i.e. same kinematics), the trail variables provided sufficient information to identify the sex and individual. The digital solution permitted the extraction of more variables than the usual pace, stride and straddle. These additional variables enabled a better discrimination between the sexes and individuals. As for the paw and track morphology, traditional morphometrics conveys limited information about the geometric structure, and fails to quantify the shape variations along curves and surfaces. To overcome these drawbacks, geometric morphometrics allowed the extraction of the form (i.e. size and shape) by means of superimposed fixed landmarks, and curve- and surface-slider semi-landmarks. Using fixed landmarks, the paws and tracks presented enough shape variation to identify their position along the anteroposterior (front or hind) and mediolateral (right or left) axes. We used fixed landmarks, with and without curve- and surface-sliders, on paws and tracks from lions of known age, sex and/or identity. The identification of the age and sex from the paws, and the age, sex and individual from the tracks achieved higher accuracies when using size and shape variables together rather than independently. The information from curves and surfaces offered an advantage for the identification from the tracks but not from the paws. Due to the variation in anatomy, paw morphology and individuality in walking, tracks and trails contain information about the individual lion that created them. Recent advances in digital close-range photogrammetry and geometric morphometrics allow the recording and extraction of that information, which can then provide data to help monitor lion populations using a non-invasive approach. [less ▲]

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See detailAssessing microbial diversity changes associated with different tillage and crop residue managements: study case in a loamy soil
Degrune, Florine ULiege

Doctoral thesis (2017)

The major challenge of modern agriculture is to produce enough food for the growing population, and at the same time, minimize environmental harm. To meet this challenge, Agroecology aims to replace non ... [more ▼]

The major challenge of modern agriculture is to produce enough food for the growing population, and at the same time, minimize environmental harm. To meet this challenge, Agroecology aims to replace non-renewable external inputs with ecological processes to diversify the ecosystem services and attenuate the dis-services of agriculture. In this light, the ability to manage the soil microbiota, that has great effects on soil quality, is receiving attention. Plowing, the most widely used tillage practice in intensive agriculture has proven its efficiency in maximizing crop productivity, but its long term detrimental effects on soil quality, such as soil erosion and organic matter loss, have called for alternative tillage practices. However, the success of the implementation of these practices in Europe is still debated. In the upper part of Wallonia (Belgium), the soil is highly fertile and 80% of land is occupied mostly by intensive cropping systems. To date in Walloon cropping systems, few studies have explored the soil microbiota in association with different soil managements. Here, we used a meta-barcoding approach to explore differences in soil microbial community structure under two contrasting tillage regimes, conventional (CT) and reduced tillage (RT), either with or without crop residue retention. The effects of these soil treatments were explored at different depths and during the growing season of two crops. Our work demonstrated clear differences in microbial diversity between tillage regimes, but no clear differences between residue management practices. The observed differences appeared to be associated with differences in physical (e.g. structure and moisture) and chemical (nutrients) soil properties. Notably, the nutrient concentrations and moisture were higher under CT than under RT. Overall, soil under CT had higher or similar microbial diversity than under RT. Analysis of β-diversity revealed differences in the taxonomic structure of microbial communities. Certain microbial groups were more abundant under CT than under RT and vice versa. For example, mycorrhizal fungi, economically and ecologically important in agroecosystems, were more abundant under RT. Finally, the magnitude of tillage effects on the microbial diversity varied strongly with the sampling depth, whereas it varied moderately with the growing season. This work highlighted CT was not necessarily unfavourable in maintaining microbial diversity when compared to RT. However, the study raises new questions regarding the impacts of microbial diversity changes on soil functioning. We encourage researchers to undertake further investigations into the functional role of microbiota in order to improve our understanding of agroecosystem functioning and its sustainability. [less ▲]

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See detailTrees and shrubs influence the behaviour of grazing cattle and rumen fermentation
Vandermeulen, Sophie ULiege

Doctoral thesis (2017)

Hedgerows and woody strips have been used to enclose fields but declined due to the loss of a direct economic value, abandonment of traditional management techniques and agricultural intensification ... [more ▼]

Hedgerows and woody strips have been used to enclose fields but declined due to the loss of a direct economic value, abandonment of traditional management techniques and agricultural intensification. Nowadays, shrubs and trees on pastures are promoted again through environment-friendly policies and the interest in using them as forage for ruminant increases in both temperate and tropical ecosystems. Woody plants on farmland could yield a wide range of ecosystem services and provide benefits for farmers and their animals such as forage supply to livestock, animal protection against severe weather and reduced parasitic infestation. Moreover, shifts in digestive physiology can be observed that will in turn affect the welfare and the performances of the animal and the production system as a whole. Therefore, in order to contribute to the development of sustainable systems using shrubs and trees as a feed component in its full right, the aim of this work was to investigate the influence of trees and shrubs on the behaviour of grazing cattle and their selectivity towards woody species, and to determine the changes induced by temperate and tropical shrub and tree species on rumen fermentation. Firstly, the behaviour of grazing dairy heifers was recorded during the whole grazing season as well as their selectivity towards temperate woody species in a hedge. It was concluded that having access to a hedge influenced the behaviour of grazing cattle, as the animals ingested woody plants in each season but mostly when the available pasture biomass was lower. The most selected species were Carpinus betulus, Corylus avellana, Cornus sanguinea and Crataegus monogyna. Secondly, the chemical composition, in vitro rumen fermentation profile and protein precipitation capacity (PPC) of the temperate shrub and tree species were measured. The analyses showed that Fraxinus excelsior presented the most interesting profile in terms of chemical composition and in vitro fermentation production. Among the preferred species, C. monogyna and C. avellana produced lower CH4 and the latest had the highest PPC. Thirdly, three newly-developed cultivars of the tropical Desmanthus genus were studied for their effects on in vitro rumen fermentation including potential to reduce CH4. Desmanthus leptophyllus and D. bicornutus had the highest anti-methanogenic potential, and D. bicornutus was more digestible. In conclusion, both temperate and tropical shrub and tree fodder are promising to supplement cattle with good quality forage. Cattle can browse woody species voluntarily, however, further investigations are needed to provide relevant practical recommendations on how to manage this resource adequately in order to balance intake by the animal and regrowth capacity of the plant. The impact of management strategies relying on cutting and preservation should also be assessed. Moreover, benefits of shrubs and trees on pastures beyond the animal feeding and nutrition are still poorly characterized while, in an agroecological perspective, they can contribute to a significant improvement of the sustainability of ruminant production systems. [less ▲]

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See detailComment le changement climatique influence-t-il la croissance du hêtre (Fagus sylvatica L.) le long du gradient bioclimatique de la Belgique ? Une approche dendroécologique.
Latte, Nicolas ULiege

Doctoral thesis (2017)

Health anomalies (e.g., worsening crown conditions) on beech (Fagus sylvatica L.) observed throughout Europe since the 1990s have raised growing concerns among foresters, particularly about the future ... [more ▼]

Health anomalies (e.g., worsening crown conditions) on beech (Fagus sylvatica L.) observed throughout Europe since the 1990s have raised growing concerns among foresters, particularly about the future behavior of the species in the face of climate change. This PhD research examined the relationship between beech and its environment in the context of global changes using dendroecology, combination of dendrochronology and forest ecology. The radial growth was used to evaluate the effects of global changes, particularly climate change, on beech development and vitality over time along a bioclimatic gradient in Belgium. Various analyses were carried out using dendrochronological tools (pointer years, mean sensitivity, growth-climate correlation, etc.) and modeling approaches (linear and non-linear mixed models, partial least squares regression, etc.) considering several scales: tree, stand and region. Results show that climate predominantly influenced beech growth since the mid-20th century and did so rather uniformly across Belgium. Beech mean sensitivity increased mainly in response to the higher frequency and intensity of summer heat waves and spring droughts. Isolated but pronounced annual growth reductions induced a gradual diminution of mean growth. The increasing influence of climate progressively concealed the effect of local site growing conditions inducing strong between-sites synchronization along the bioclimatic gradient. Increasing mean sensitivity and decreasing mean growth were more pronounced in lowlands than in uplands, and for a given site, older trees are more affected than younger ones. Although mean sensitivity increases and mean growth decreases naturally with age, the climate change effect was much more important than the age effect. Furthermore, within a tree, along the main stem, climate sensitivity slightly decreased from breast height to crown base and strongly increased from crown base to tree top. These results were interpreted based on ecophysiological knowledge of beech. The influences of silviculture, soil compaction and nitrogen deposition (as part of atmospheric pollution) as well as the consequences of the past and future climate change on beech were discussed. Comparisons with other studies in Europe highlighted that beech is affected on a large part of its natural distribution range (except in high altitude and high latitude). Contrary to what one might think, beech is not only affected in the southern limit (Mediterranean). Although growing conditions are more favorable in Belgium, beech has also more to lose. Beech has coped with global change up to now. Although its climate sensitivity increased and its mean growth decreased, diebacks observed these last years in Belgium were scarce and generally scattered. However, considering the upcoming climate change, the phytosanitary risk will undeniable increased. Forest policy should now integrate that risk and prepare managers to anticipate and prevent it. [less ▲]

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See detailTHE IMPACT OF SURFACTANTS ON VEGETBLE WHIPPED CREAM PROPERTIES IN RELATION WITH THE EMPLOYED FAT
Petrut, Raul Flaviu ULiege

Doctoral thesis (2017)

Vegetable whipped creams are nowadays a popular alternative to the traditional dairy whipped creams. The emulsions standing at the base of vegetable whipped creams are classified as O/W emulsions. During ... [more ▼]

Vegetable whipped creams are nowadays a popular alternative to the traditional dairy whipped creams. The emulsions standing at the base of vegetable whipped creams are classified as O/W emulsions. During whipping air is incorporated and entrapped by a fat crystallize network. This is achieved by the fat droplets interaction through the partial coalescence mechanism. Hence the presence of a crystalline fat phase is imperative within the formulation of the whipped cream. In order to control the partial coalescence and stabilize both the emulsion and the whipped cream, emulsifiers are required. Therefore in such systems, proteins and LMW surfactants coexists and dictate the degree and rate of partial coalesce. This allows the tailoring of the sensorial attributes and physico-chemical properties of the whipped cream (e.g. stability, overrun, texture). Nevertheless the impact of the components on the whipped cream properties has to be understood as a whole and not as individual effects of fats, proteins and LMW surfactants. [less ▲]

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See detailDépolution des sédiments d’une mangrove de l’estuaire du Wouri : évaluation du potentiel de microflores.
Semboung Lang, Firmin ULiege

Doctoral thesis (2017)

L’importance des écosystèmes de mangroves n’est plus à démontrer dans l’équilibre naturel des côtes des régions tropicales. Elles constituent un écosystème particulier et jouent un rôle important dans la ... [more ▼]

L’importance des écosystèmes de mangroves n’est plus à démontrer dans l’équilibre naturel des côtes des régions tropicales. Elles constituent un écosystème particulier et jouent un rôle important dans la production de la biomasse. Mais l’exploitation excessive du bois des palétuviers, les pollutions diverses suite à l’exploitation pétrolière et gazière, sont autant de facteurs qui contribuent à la dégradation des forêts de mangroves. Ainsi, entre 1980 et 2000, environ 35% de la superficie mondiale des mangroves a disparu. La pollution a entraîné une dégradation considérable des mangroves. Une quantité grandissante de déchets résultant des activités urbaines, industrielles et agricoles et de l’exploitation en mer du pétrole et du gaz est rejetée sans aucun traitement dans la mer et se retrouve au niveau des mangroves. Les déversements accidentels d’hydrocarbures en mer entraînent une grave pollution des mangroves et la pollution marine provenant des navires est une menace qui va sans doute s’accroître avec le développement de l’exploitation pétrolière. L’objectif de cette thèse était de mettre au point une méthode de dépollution par voie biologique des sédiments de mangroves pollués par les hydrocarbures. Il s’agissait plus précisément d’évaluer les capacités intrinsèques de dégradation de la microflore spécifique endogène, de comparer le potentiel de dégradation de cette microflore avec d’autres souches pures connues pour leur capacité à dégrader les hydrocarbures et enfin d’évaluer les différentes techniques de biodégradation adaptées pour l’élimination des hydrocarbures dans les sédiments de mangroves. Des procédés biologiques adaptés ont été mis en œuvre au cours de ce travail pour restaurer les écosystèmes de mangroves. Différentes techniques de traitements biologiques impliquant la microflore spécifique endogène ont été mises en œuvre. L’évaluation du potentiel de dégradation de cette microflore a été réalisée par rapport à trois souches pures exogènes. Les résultats obtenus ont montré que le potentiel de dégradation de la microflore spécifique est comparable à celui de Rhodococcus erythropolis lorsqu’on augmente sa concentration dans les sédiments (107 CFU.g-1 de matière sèche). La croissance de cette microflore est accélérée avec la présence des nutriments tels l’azote et le phosphore. Ce qui relève davantage le taux de dégradation des hydrocarbures. Le taux de dégradation obtenu en combinant les traitements par bioaugmentation de la microflore spécifique endogène et biostimulation (86%) nous ont amené à proposer cette méthode pour dépolluer les sédiments de mangroves. L’utilisation de la microflore spécifique endogène évite de travailler avec des souches exogènes qui nous exposent aux problèmes écologiques et éthiques liés à leur utilisation. [less ▲]

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See detailDevelopment of molecular tools for rapid detection and quantification of indoor airborne molds to assess their impact on public health
Libert, Xavier ULiege

Doctoral thesis (2017)

Currently, contamination of the indoor environment by fungi is suggested to be a public health problem, although scientific evidence on the causal link is still limited. The monitoring of indoor airborne ... [more ▼]

Currently, contamination of the indoor environment by fungi is suggested to be a public health problem, although scientific evidence on the causal link is still limited. The monitoring of indoor airborne fungal contamination is a common tool to help understanding the link between fungi in houses and respiratory problems. Classical monitoring methods, based on cultivation and microscopic identification, have some limitations. For example, uncultivable or dead fungi (“unknown” fraction) cannot be identified, although they could have an impact on human health. In this context, molecular tools seem to be a valuable alternative. In this PhD work, different molecular tools were developed, from simplex to multiplex, to detect and identify indoor airborne fungi. The goal was to improve the detection of fungal contaminants, including the “unknown” fraction, as compared to the currently used classical monitoring methods. The necessary air sampling and DNA extraction protocols, adapted to the downstream molecular monitoring methods have also been developed. Through the application of the developed tools to specific case studies, we aimed to improve the current knowledge on fungal contamination. At first, we developed a specific ITS-based SYBR®green real-time PCR (qPCR) assay for Aspergillus versicolor, a species frequently observed in indoor air and known to be allergenic. Additionally, an ITS-based qPCR assay was developed for the specific detection of Exophiala jeanselmei, a pathogenic yeast suspected to be a part of the “unknown fraction”. The performance of these qPCR methods was assessed. This comparison demonstrated that SYBR®green qPCR assays can be used as a molecular alternative for monitoring of contaminated samples while eliminating the need for culturing and thereby considerably decreasing the required analysis time. However, qPCR has some limitations especially concerning the discrimination of genetically close species and multiplexing. The first issue was addressed through the use of post-qPCR high resolution melting (HRM) analysis, providing a proof-of-concept for this approach, using 3 closely related Aspergillus, i.e., A. versicolor, Aspergillus creber and Aspergillus sydowii. This HRM tool will allow a more accurate monitoring of these closely related indoor air contaminants, thereby contributing to an improved insight in the causal link between the specific presence of these species and health issues. The multiplexing issue was overcome through a Luminex xMAP® assay, developed for the simultaneous detection of the 10 most frequently in indoor air found fungi. All the species identified with the classical method were also detected with the xMAP® assay, however in a shorter time frame, and using less sample material. This assay will improve the communication with the involved medical team and the patient. To provide scientific evidence for the causal link between indoor airborne fungi and health problems, the full diversity needs however to be identified. This cannot be achieved by using a targeted assay. Therefore, next generation sequencing (NGS) could offer a valuable alternative as an open approach multiplex monitoring method. An NGS-based metagenomics approach was used to investigate the “unknown” agents in air samples of offices in contact with air-conditioning reservoirs and showed the first detection of E. jeanselmei in indoor air. Finally, a metagenomics analysis was performed to investigate the indoor airborne fungal diversity in contaminated residences in Brussels where people with health problems were living. This demonstrated that NGS could contribute to improved data concerning the indoor airborne fungal diversity, as compared to the currently used classical methods. The methods developed in this PhD work and the insights obtained are a first step for a better understanding of the causal link between indoor airborne fungi and public health. [less ▲]

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See detailÉtude du cytosquelette de microtubules et implication de la vimentine dans le développement postnatal de la cochlée chez les rongeurs
Renauld, Justine ULiege

Doctoral thesis (2017)

According to the World Health Organization, nearly 5% of the population suffers from hearing impairments. These can lead to social isolation, depression, or a reduction in professional abilities. There ... [more ▼]

According to the World Health Organization, nearly 5% of the population suffers from hearing impairments. These can lead to social isolation, depression, or a reduction in professional abilities. There are two types of hearing impairments : conductive hearing impairment and sensorineural hearing impairment. The first results from a defect in sound conduction at the level of the outer or middle ear, the latter results from defects in the cochlea or auditory nerve. In recent years, most studies on the organ of hearing have focused on sensory cells, which are actual receptors of auditory information, whereas supporting cells have been little explored. However, the latter, surrounding the sensory cells, contain a highly developed cytoskeleton, essential to the architecture of the mature organ of Corti. During this thesis work, we first observed the setting up of microtubules within the supporting cells of the organ of Corti. Our morphological data revealed important changes in microtubular cytoskeleton of these cells during the first week of life. We identified an arrangement of microtubules into two distinct bundles. We then demonstrated a modification in the morphology of these microtubules, revealing an increase in the diameter and the number of protofilaments of these cells. We finally demonstrated that tubulin βV has a more specific spatiotemporal distribution than the other tubulins. This characteristic suggests that tubulin βV plays an important role in the maturation of the Corti organ. In the second part of this thesis, we analyzed the involvement of vimentin in cochlear development, and more particularly in the opening of the intercellular spaces and in the myelination of the spiral ganglion, which is the first relay of the auditory pathway. In order to study the role of vimentin in the development of the inner ear, we examined the cochlear morphology and auditory capacities of vimentin deficient mice. Our results indicated that the absence of vimentin does not seem to affect the architecture of the organ of Corti. We then showed a slight morphological difference in the nerve fibers between wildtype and vimentin-knockout mice. We finally checked the hearing physiology of these mice and concluded that vimentin does not play a major role in hearing. [less ▲]

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See detailLandscape ecological consequences of the (sub)urbanization process in an African city: Lubumbashi (Democratic Republic of Congo)
Andre, Marie ULiege

Doctoral thesis (2017)

If anthropogenic effect is a general term accounting for the influence of human activities on environment, it may also designate specific influences that may be inter- and intralinked. Thus, urbanization ... [more ▼]

If anthropogenic effect is a general term accounting for the influence of human activities on environment, it may also designate specific influences that may be inter- and intralinked. Thus, urbanization and suburbanization are anthropogenic processes contributing to the broad anthropogenic effect. They hide in turn other subprocesses of land transformation that will be called here the secondary spatial impacts. However, although the growing influence of the latter processes, they are still not defined consensually nor exist a comprehensive and applied-oriented methodology to delimit them. The general objective of this thesis is to develop a spatially explicit methodology to evaluate the landscape ecological consequences of the urbanization and suburbanization processes, taking a representative city of Sub-Saharan Africa as a case study: Lubumbashi (Democratic Republic of Congo), and the last decade as the period of study. That general objective is addressed through two themes, to which correspond specific objectives. The first theme concerns the evaluation of the anthropogenic land use and land cover dynamics and the second one proposes a methodology to evaluate the expansion of urban and suburban areas, in relation with consistent definitions of the areas in the urban-rural gradient. For both themes, the propositions are based on remote sensing techniques and landscape ecology metrics. Results show that the region of Lubumbashi underwent a global anthropisation increase mostly constituted of minor rises of anthropisation levels but impacting mainly the most natural landscape classes. Urban and suburban areas were located through the use of the proportion of built-up metric, the secondary spatial impact area through the use of adjacencies of the less natural landscape patches. The growth shape of the urban and suburban areas is concentric, except in the south-western part of the city where an affluent of the river Kafubu and its adjacent wetlands slow the urban expansion. The secondary spatial impact area dynamics seems determined, in the north-west, by the relief and, in the north-east, by a transportation axis. It is the latter dynamics that is dominant for the period. It corresponds to the so-called savanisation process, probably due to wood fuel and charcoal production. The methodologies developed here could be improved by taking connectedness into account, by using an additional configuration metric for the definition of urban areas or by taking advantage of spatially explicit socio-economic data. They could also be tested on mining sites, other cities and/or using images of different spatial resolution. [less ▲]

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See detailContribution à l'étude de la diversité des abeilles sociales (Apini et Meliponini) et leurs parasites au Gabon
Fabre Anguilet, Edgard ULiege

Doctoral thesis (2017)

Les abeilles sociales Meliponini et Apini (Apidae: Apinae) contribuent à la pollinisation des plantes à fleurs et à l'amélioration des rendements agricoles. Elles font soit l’objet d’un élevage soit d’un ... [more ▼]

Les abeilles sociales Meliponini et Apini (Apidae: Apinae) contribuent à la pollinisation des plantes à fleurs et à l'amélioration des rendements agricoles. Elles font soit l’objet d’un élevage soit d’un pillage pour utiliser les produits de la ruche. La diversité, la répartition et l'abondance de ces abeilles dépendent de l'écosystème dans lequel elles évoluent. Les aspects liés à la diversité des espèces, à la distribution, à la biologie, à l'écologie et à l'abondance des nids de même que la situation des parasites majeurs est peu documentée dans de nombreuses régions en Afrique, dont la région d’Afrique centrale. Au vu des nombreuses activités humaines menées dans cette région et du fait que la perte d’habitat et la prédation des nids par l’homme constituent des menaces pour ces abeilles, il convient d’apporter un éclairage sur ces insectes en Afrique centrale. C’est dans ce but que le présent travail a été réalisé afin de contribuer à une meilleure connaissance des relations entre diversité spécifique, abondance des abeilles sociales (Apini et Meliponini) et le niveau de perturbation de l’habitat au Gabon. De même, une attention particulière a été portée sur la situation des parasites majeurs dans ce pays. Les résultats obtenus ont contribué dans un premier temps à clarifier la taxonomie des abeilles sociales étudiées en Afrique et ont mis également en avant l’effet négatif de la perte d’habitat forestier sur la diversité spécifique et la composition d’espèces. Aussi, les espèces qui semblent être fortement impactées par la perte d’habitat forestier ont été identifiées. L’exploitation forestière sélective n’a pas eu d’effet sur la communauté d’espèces. L’étude sur la densité des nids a montré principalement que la distance au cours d’eau avait un effet significatif sur la présence d’un nid et que la méthode d’inventaire par comptage des nids présente une faible capacité de détection de ceux-ci. Concernant les parasites, l’étude a mis en évidence la présence de deux espèces au Gabon : le Varroa destructor Anderson & Trueman et Aethina tumida Murray. Toutefois, les taux d’infestation restent faibles dans les colonies sauvages étudiées. Concernant la domestication de Meliponula bocandei Spinola, le parasite A. tumida est à l’origine du taux élevé d’échec. L’ensemble des résultats de cette étude constituent une base dans la mise en place d’une stratégie de préservation des communautés d’espèces d’abeilles Apini et Meliponini au Gabon, mais aussi dans le cadre d’une domestication de celles-ci. [less ▲]

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See detailDEVELOPMENT OF ANALYTICAL TOOLS FOR THE DETERMINATION OF MARKERS OF LIPID ALTERATION IN FOOD
Douny, Caroline ULiege

Doctoral thesis (2017)

It is now well-known that n-3 polyunsaturated fatty acids (omega-3 PUFA) have beneficial effects on health but are also rapidly oxidized in potentially toxic compounds, which means that healthy food ... [more ▼]

It is now well-known that n-3 polyunsaturated fatty acids (omega-3 PUFA) have beneficial effects on health but are also rapidly oxidized in potentially toxic compounds, which means that healthy food products, rich in n-3 PUFA, can become toxic for the consumer if not stored or processed appropriately. The main objective of this work was to develop new analytical tools to study markers of lipids alteration in food, in order to allow an adequate monitoring of possible toxic compounds in n-3 PUFA rich food products. The first chapter of this PhD thesis is a literature review about fatty acids, their oxidation and the different oxidation products generated. The different analytical techniques used to study the oxidative stability of polyunsaturated fatty acids and their degradation products in food are also described. Chapter 2 describes the development of a gas chromatography coupled to mass spectrometry (GC-MS) method to analyze the fatty acids in food. The method was applied to eggs and pork (both standard and n-3 enriched) submitted to various cooking processes and storage conditions. This study confirmed that the fat of standard eggs or pork from the Belgian market cannot be considered as a source ofn-3 PUFA.. Indeed, in this work, we measured no n-3 PUFA in meat or only around 2 % for eggs, while the fat of both enriched eggs and pork contained about 10 % of n-3 fatty acids. After storage or cooking without culinary fat no change of the fatty acid profile was observed, in standard eggs or pork. We made the same observation for n-3 enriched products, except for some cooking processes (pan-frying and oven cooking), which induced a slight but significant loss of n-3 fatty acids in n-3 enriched eggs or pork. The fairly stable behavior of the fatty acids after various cooking and storage experiments indicates that the fatty acid profile is not a good marker of lipid alteration. As a consequence, this work was oriented to the development of analytical tools to evaluate the presence of toxic aldehydes in food and feed as secondary oxidation products coming from polyunsaturated fatty acids. Chapter 3 is dedicated to the study of the oxidative stability of linseed oil, an oil rich in n-3 fatty acids. Section 3.1 describes the development of a liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) method to evaluate the aldehyde content in linseed oil. After optimisation of the extraction, derivation, detection and quantification steps, the method was validated according to guidelines from the European legislation as well as the recommendations of the AFNOR protocol NF V 03-110 (AFNOR, 2010). The evaluated parameters included specificity/selectivity, recovery, precision, accuracy, uncertainty, limits of detection and quantification, determined using the concept of accuracy profiles. When the method was applied to first pressure linseed oil stored for several days at 60 °C according to the Schaal oven test, it was shown that 4-hydroxy-2E-hexenal (4-HHE) was the most produced aldehyde. In Section 3.2, the different patterns of oxidation of linseed oil in real-time and accelerated aging assays were investigated, in order to verify the hypothesis commonly accepted for vegetal oil that one day aging at 60 °C is equivalent to one month real time aging at room temperature. Oxidation was evaluated with the peroxide value and para-anisidine value, as well as the content in conjugated dienes and aldehydes. All four indicators of oxidation showed very different kinetic behaviours at 20 and 60 °C, showing that the hypothesis (1 day at 60 °C = 1 month at 20 °C) is not valid for linseed oil. Chapter 4 describes the adaptation and the validation of a LC-MS/MS method to determine aldehydes in animal feed samples. Indeed, as animal feed is often enriched with linseed to increase the human intake of n-3 fatty acids through the consumption of food from animal origin, the study of the oxidative stability of n-3 enriched animal feed is also of interest. To achieve that goal, the LC-MS/MS method previously developed for linseed oil was adapted to include more aldehydes and was validated using the same guidelines as in section 3.1. Finally, chapter 5 presents the discussion and conclusions about the developed methods and the results obtained as well as their comparison with literature. Future prospects to improve the evaluation of and the exposure to the markers of lipid alteration in food are proposed. [less ▲]

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See detailEQUINE OSTEOCHONDROSIS: IMPACT OF THE ENVIRONMENT ON THE EVOLUTION OF THE DISEASE AND PREDICTIVE BIOMARKERS THROUGH METABOLIC AND TRANSCRIPTOMIC PROFILES
Mendoza García, Luis ULiege

Doctoral thesis (2017)

Developmental orthopaedic diseases and specially osteochondrosis (OC), are one of the main causes of subsequent joint disease. The principal aims of this study are to determine the current prevalence of ... [more ▼]

Developmental orthopaedic diseases and specially osteochondrosis (OC), are one of the main causes of subsequent joint disease. The principal aims of this study are to determine the current prevalence of OC in Belgium, to investigate the impact of the environment in OC evolution and the research of possible biomarkers for OC diagnosis and prediction through transcriptomic and metabolic profiles. 38.37% of the Belgian Sport yearlings presented OC lesions. The most commonly affected joint was the fetlock followed by the hock and stifle. Palmar/plantar fragmentations in the margin of the proximal phalanx were not included in the final evaluation of OC prevalence. Concerning the effect of the environment in the evolution of OC, foals fed with concentrates show a higher probability of the development of OC lesions (p=0.06), while foals not receiving concentrates, show a higher probability of healing from existing lesions (p=0.001). The effect of housing conditions was not statistically significant. As environment is able to modify the evolution of the disease, diagnostic and predictive biomarkers where researched with two main procedures transcriptomic analysis and ELISA technique. This later technique showed that sclerostin concentrations (a glycoprotein related to the bone formation) where higher in OC affected foals of 6 month of age, but not in 18 month ones. That test showed that there was not relation between sclerostin concentrations and the type of environment. In the transcriptomic analysis OC affected foals showed a different expression of several genes when compared to a control group and this expression was influenced by age and affected joint. Differential expression of genes according to the joint was also studied and based on the profiles of expression of some genes, the localization of the disease can be determined. Besides, transcriptomics allowed to study the transcript profile of foals in order to predict the presence of the disease. The Odds ratio showed a relationship between the OC status assessed by a radiographic protocol at 18 months of age and the OC status given by transcriptomic tools at 6 months of age. In conclusion, this research may open the door to an OC predictive tool since OC prevalence is still quite high. [less ▲]

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See detailApplication des techniques de photogrammétrie par drone à la caractérisation des ressources forestières
Lisein, Jonathan ULiege

Doctoral thesis (2016)

Une gestion raisonnée et multifonctionnelle des forêts n’est possible qu’avec une description à jour de l’état de la ressource naturelle. Les inventaires forestiers traditionnels, réalisés sur le terrain ... [more ▼]

Une gestion raisonnée et multifonctionnelle des forêts n’est possible qu’avec une description à jour de l’état de la ressource naturelle. Les inventaires forestiers traditionnels, réalisés sur le terrain, sont couteux et ne couvrent qu’un échantillonnage de la surface boisée. L’essor des drones civils pour la cartographie a initié une révolution dans le domaine de la télédétection environnementale. La polyvalence et la diversité des systèmes drones sont une aubaine pour la foresterie de précision. Ceux-ci sont utilisés pour la réalisation de cartographie très fine des habitats naturels avec une résolution temporelle et spatiale sans précédent. Nous explorons les possibilités d’utilisation de mini-drones pour la caractérisation quantitative et qualitative de la ressource forestière. Nous nous intéressons en particulier à l’estimation de la hauteur des arbres et à la caractérisation de la composition spécifique au sein de peuplements forestiers. La hauteur de la canopée est une variable dendrométrique de première importance : elle est un bon indicateur du stade de développement des peuplements et intervient notamment dans les estimations de biomasse ou de niveau de productivité. La composition spécifique est une information essentielle en regard des principales fonctions que remplit la forêt (conservation, production, récréation, etc). Nous avons comparé l’estimation de la hauteur des peuplements à partir de mesures LiDAR et celle obtenue par photogrammétrie. Bien que permettant une mesure de hauteur individuelle avec une incertitude de l’ordre de 1.04 m (RMSE) en feuillus, la photogrammétrie par drone sur des zones forestières est systématiquement moins précise que les mesures par LiDAR (RMSE de 0.83 m). Ces résultats sont cependant prometteurs, étant donné que la mesure sur terrain de la hauteur totale des arbres est également sujette à une importante imprécision. De plus, la grande flexibilité que confère les petits drones permet d’acquérir, au moment propice du stade de végétation, et l’information de relief de la canopée, et l’information spectrale. La période de fin de feuillaison, au début du mois de juin, s’est avérée le moment le plus propice à une discrimination automatique de cinq groupes d’essences feuillues (le chênes pédonculé, les bouleaux, l’érable sycomore, le frêne commun et les peupliers). Une erreur globale de classification des houppiers de 16% est obtenue avec des acquisitions monotemporelles, alors que l’utilisation d’images acquises à différentes dates permet encore d’améliorer cette classification (erreur globale de classification de 9% pour la meilleure combinaison de 3 dates). Les contraintes de la législation régissant l’utilisation des aéronefs sans pilote à bord restreignent le champs d’action des drones civils. Ainsi, afin d’assurer une sécurité pour tous les usagers de l’espace aérien, les opérations avec un drone sont limitées sous un seuil d’altitude et à une distance maximale du télépilote, ce qui ne permet pas une utilisation optimale de cette technologie pour la couverture de grands domaines forestiers (plusieurs milliers d’hectares). De plus, d’autres outils de télédétection utilisés en foresterie, tels que le LiDAR et l’imagerie satellite et aéroportée, sont plus compétitifs que les drones dès qu’il s’agit de couvrir de grandes surfaces (plusieurs milliers d’hectacre). C’est pourquoi nous pensons que les drones resterons un outils d’analyse de petites surfaces (dizaines voire centaines d’hectares), plus utiles à des fins de recherches scientifiques qu’à une utilisation en gestion forestière. [less ▲]

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See detailValorisation des variétés de dattes secondaires tunisiennes par l’application de traitement hydrothermique
Mrabet, Abdessalem ULiege

Doctoral thesis (2016)

The fruit of the date palm (Phoenix dactylifera L.) is one of the most abundant fruits in the world. Nearly 2,000 cultivars of date palm are known, but only some of them are evaluated for their ... [more ▼]

The fruit of the date palm (Phoenix dactylifera L.) is one of the most abundant fruits in the world. Nearly 2,000 cultivars of date palm are known, but only some of them are evaluated for their performance and their fruit quality. This work is a contribution to give value addition to date palm fruit (flesh and seed), from Tunisian secondary varieties, by studying physico-chemical and techno-functional properties of their heir solid fraction rich in fiber and their fraction liquid and rich in phenol and sugar, obtained after pretreatment. Date fleshes contained essentially 60 % total carbohydrates, 23-27 % lignin and 5-4 % dietary fibers. The rest of the components were lower than 4%, with remarkably low amounts of fat (0.3-0.5%) and phenols (0.04-0.07%). In contrast, the percentage of fat (13-17%) and phenols (1-5%) present in date seeds were of great interest. Due to these amounts of phenols, the antiradical activity of seeds was much higher (131-400 mmol TE/Kg dry weight) than that of the flesh (32-47 mmol TE/Kg dry weight). A pretreatment was tested for the total utilization of these dates. After applying several steam treatments condition, valuable dietary fiber concentrates have been obtained. Their recoveries were very similar for the different assays. Only its granulometry showed differences, increasing the fraction with size lower than 4 mm in more intense treatments. DFC had also a good nutritional quality, with high phenol (4-8%), cellulose (12-20%), hemicellulose (5-22%), protein (9-14%), fat (5-11%) and lignin (44-71%). Treatment conditions had higher influence than date variety in the chemical composition. Study of functional properties of these DFC revealed good water and oil retention capacities (5,37-8.50 g water/g DFC and 7,03-8.74 g oil/g DFC, respectively). Furthermore, DFC had also very high antiradical activity (230-580 mmols Trolox/ Kg FC). Thus, these DFC could be considered as a valuable source of antioxidant dietary fiber. The study of physicochemical characteristics showed that DFC had the highest potential to be used as a food ingredient. As an application, the DFC were incorporated in muffin formulations at levels of 2,5 and 5 %. The addition of DFC slightly influenced the technological characteristics of dough and increased their antioxidant properties compared to control. Study of sensory characteristics revealed that there are no significant differences between control and the muffin with DFC. The only concern about the use of this DFC is that its ratio between insoluble and soluble fiber (IF/SF) is very high, around 19, but the best physiological effects are obtained with ratios 1-2.3. For this reason an enzymatic digestion has been assayed in order to decrease this ratio. The different results have shown that, the amount of SF increased from 1.8% to 6.3%, and the ratio IF/SF changed from 19 to 2-3. Moreover, in addition to an increase in the antiradical activity the SF, gluco-, manno-, and xylo-oligosaccharides were identified, oligosaccharides which has been postulated as prebiotics. The study of the liquid phase, rich in soluble antioxidant (phenols), and sugars, was also necessary for the total utilization of the thermally treated dates. The obtained liquid fractions were characterized and their antioxidant capacity determined. The concentration of total phenols increased, by treatments up to 5311 mg/kg of fresh dates, and their antioxidant activity up to 62.5 mmol Trolox/kg of fresh date. Different phenolic extracts have been obtained from the liquid phase in order to used as a antioxidant in food or nutraceutical formulation. The date phenolic extract were fractionated chromatographically using adsorbent or ionic resins to determine the most active fractions. The phenolic profiles were determined for each fraction, yielding fractions with interesting antioxidant activities with EC50 values of up to 0.08 mg/L or values of TEAC of 0.67 mmol Trolox®/g of extract. In addition, the antioxidant properties on lipophilic matrix of the organic extracts of date were also determined, using vegetable and fish oils, as well as the antimicrobial activity. The result showed a remarkable protection against lipid oxidation in oils, increasing the stability of sunflower oil by Rancimat method by four-fold. In addition, some extracts with interesting antimicrobial effects. [less ▲]

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See detailApproche expérimentale de la collision entre les plis vocaux en phonation et du phonotraumatisme : Études in vivo et sur larynx humains excisés
Lagier, Aude ULiege

Doctoral thesis (2016)

The collision between the vocal folds during phonation is a physiological phenomenon with a powerful role in the synchronization of their vibration. This collision is also a component of the phonotrauma ... [more ▼]

The collision between the vocal folds during phonation is a physiological phenomenon with a powerful role in the synchronization of their vibration. This collision is also a component of the phonotrauma. The role of phonotrauma in the pathophysiology of dysphonia is commonly accepted but its nature still unclear and its quantification remains difficult. This work proposes, an in vivo study in healthy subjects, and ex vivo ones on excised human larynges. The purpose of this work was to study the laryngeal behavior when the larynx is subjected to extremely high subglottic pressure. In vivo, the shouted voice was recorded with constant measure of subglottic pressure. Ex vivo, the subglottic pressure was directly manipulated independently from other parameters. The ex vivo study required a methodological development to modernize the experimental bench used for animal larynges studies and to adapt it to the human larynx. The results showed, in healthy speakers the existence of a "plateau" in the vocal intensity and in the electroglottographic signal for very high levels of subglottic pressure. The studies on excised larynges measured the collision force between the vocal folds and its changes depending on subglottic pressure. They also highlighted the existence of a "plateau" in the collision force when subglottic pressure was very high. The observations presented in this work are, to our knowledge, unprecedented. They have important clinical interest for understanding the concept of phonotrauma. Their interpretation in physical terms remains very incomplete. [less ▲]

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See detailL'Afrique centrale: entre traditions et transitions. La mutation des socio-écosystèmes en Afrique centrale
Gillet, Pauline ULiege

Doctoral thesis (2016)

The forests of the Congo Basin are among the best preserved areas on Earth. Nevertheless, the factors causing deforestation around the world are also present in this subregion. The forest transition ... [more ▼]

The forests of the Congo Basin are among the best preserved areas on Earth. Nevertheless, the factors causing deforestation around the world are also present in this subregion. The forest transition theory describes how the trend of forest areas decline at national level may precede an increase in these areas. If the effects of the forest transition are well known in terms of forest cover degradation, little is known about the effects of forest transition on socio-ecosystems (SES) (understood as a group of actors with impacts on a group of resources and subject to specific institutions). The general objective of this thesis is to characterize the mutation of socio-ecosystems in the Congo Basin in order to identify dynamic of change of Congo Basin forested SES and their possible futures. The collection of socioeconomic data, focusing on the description of the population, the description of the different activities and incomes, the description of food intake and the access to land and resources, were conducted in three SES with a forest cover gradient, located in Cameroon and Gabon. The results show that the cost price of meals is globally increasing with the loss of forest cover. The share of food intake related to the exploitation of natural resources such as hunting, fishing and gathering decreases in favor of proteins from livestock and agricultural products. This leads to the translocation of demand but also to pressures on other anthropogenic ecosystems. The effects of deforestation are then visible at the local level but also on neighboring areas. The diversity of the game and prey decreases moving towards smaller species with the progression of the forest transition. Consequently, there is a reduction in the proportion of these products in both the food intake and household incomes. This analysis shows a decline in the importance of NTFPs in the production and villagers livelihoods. Slash and burn agriculture is practiced in three SES. If the ratio between fallow period and cultivation period decreases with the forest transition, there is an increase in crop diversification leading to a diversification of the diet. Access to forest resources, agricultural land, markets and an external source of employment condition the village activities. The land potential is made to report levels of ownership and co-management of customary space (Le Roy et al., 1996). During the progression of the forest transition curve, the land potential evolves from relatively loose to privatization and the ability to alienate resources. These important modifications of traditional control systems of the relations between man and resources lead to a more adequate management of some commercial resources value (such as agricultural products or mining resources). But, this process is incompatible with the maintenance of certain ecosystem services like large populations of wildlife preservation. If these results fit rather well with the forest transition curve, this is not the case of all SES in Central Africa. Therefore, we propose to combine some results to reflect significant changes of the qualities of a socio-ecosystem, regardless of forest cover rate. The priority would be to establish a standardized data collection protocol to test sites with different forest cover and located on different trajectories. The use of a socio-economic index would make it possible to predict the evolution of SES under different scenarios, whether linked to global or regional pressures (such as the emergence plans enacted by the Central African States) or in contexts of economic crisis or the introduction of new legislation. [less ▲]

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See detailEvaluation des impacts des projets de développement sur les exploitations agricoles familiales et les ménages de l’ATACORA (Nord-Ouest du Benin)
Tohinlo, Yecy ULiege

Doctoral thesis (2016)

This doctoral research aims to contribute to a better understanding of the effects of development projects on the improvement of living conditions and livelihoods of rural households in Benin. It begins ... [more ▼]

This doctoral research aims to contribute to a better understanding of the effects of development projects on the improvement of living conditions and livelihoods of rural households in Benin. It begins with the analysis of development trends in Atacora known about the last three decades. It is focused on matching between the dynamics promoted by intervention devices and those endogenous or emerging to lead a part in the consideration of the productive trajectories and performance of family farms and also in the analysis of effects of development projects on food security, living standards and poverty of rural households. The post-development theories and the various conceptions of poverty have served as a guideline for research work. The intervention mechanisms conducted in Atacora (north-western Benin) by the various cooperations (bilateral and multilateral) between 1990 and 2010 constituted the research object of this thesis. The empirical phase took place in the communes of Cobly (West) and Péhunco (East). These communes were selected from their contrasting agro-ecological and socio-economic situations and socio-economic indicators on the one hand and on the other on a typology of the concentration of development projects and the perception of their effects by local people. A stratified sample of 344 households (respectively 214 in Cobly and 130 in Péunco) was formed for the characterization survey. Later, a thorough investigation on living conditions and livelihood of households followed and involved 208 households (129 Cobly; 79 Péhunco). Finally 16 case studies (8 per commune) were conducted on the trajectories of evolution and accumulation of property and wealth of households and farms. Due to the empirical research, special attention was given to primary data collection which lasted more than three (3) years. Qualitative and quantitative tools (including PSM) were combined for the analysis of collected data through individual and group interviews. Results show that the development interventions do not always promote the endogenous dynamics but they generate and maintain, in rural areas, pathways that allow the integration and participation of producers in the world market for agricultural products. And to benefit from various promotional activities, producers adopt supported crops, this have some positive and negative consequences. The integration and participation of rural producers of Atacora to international trade, promote the increase of production and crop yields while further increasing their dependence on the world prices of agricultural products. So while the income of producers is increasing their vulnerability to food insecurity is also increasing because many of the food crops, already insufficient (because of the share of the cotton planted and the cotton production quotas established by the government) to cover food needs, are substracted from consumption to be sold on the market to meet urgent liquidity needs. Thereby, Atacora's rural households, despite the increase of their food production, suffered a rupture of food stocks resulting to annual food crises of at least 4 months (16 weeks) which strikes indiscriminately both recipient households than non-project beneficiaries. However with the increase of sources and income level of recipient households (36% of households of the study sites), those beneficiaries improve their homes and food consumption and invest more in the education of their children. This marks a significant difference between beneficiaries and non-beneficiaries of development projects. Indeed, installed with the same resources, we counted, in 2014, twice more prosperous households and fewer poor among beneficiaries than non-beneficiaries. Furthermore farms and households beneficiaries of assistance have accumulated and hold more productive assets (land, farm equipment, livestock rearing), economic assets and holdines (transportation measures, housing, plots and houses to rent, etc.) than non-beneficiaries with a highly significant difference at 1%. However the level of improvements and living conditions induced by development interventions are still inadequate and insecure, as reduced to the equivalent adult,income as well as capital show no significant difference between beneficiaries and non-beneficiaries. Thus, households (even beneficiaries) remain vulnerable to crises so that any natural disaster (flood, drought, pest invasion, etc.), illness, injury and death of a member of the household, provokes the rapid degradation of living standards and the fall into poverty. This is compounded by the fact that farms owners’ don’t invest really in the restoration and enhancement of the capital '' land fertility ''; mainly in Cobly where the soil fertility level experienced a drastic decline with a consequent increasing use of chemical fertilizers that degrade the soil structure furthermore. It follows that any action aimed at poverty reduction should allow a sustainable improvement in conditions and livelihoods of rural producers by the preservation and restoration of soil fertility on the one hand and the increased resilience to crises on the other hand. Actions to identify specific needs with measures and solutions adapted to each category of producers and households with mainly particular mechanisms of management and restoration of the fertility of agricultural land shall be considered and implemented. [less ▲]

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See detailApplication des biotechnologies post-récolte pour la valorisation des produits de terroirs marocains par des microorganismes sélectionnés impliqués dans la fermentation de fruits : cas du vinaigre
Mounir, Majid ULiege

Doctoral thesis (2016)

Dans cette étude, de nouvelles souches microbiennes (levures et bactéries acétiques) ont été isolées, sélectionnées, identifiées et caractérisées pour évaluer leur usage comme starters pour la production ... [more ▼]

Dans cette étude, de nouvelles souches microbiennes (levures et bactéries acétiques) ont été isolées, sélectionnées, identifiées et caractérisées pour évaluer leur usage comme starters pour la production industrielle de vinaigre de fruits. Dans un premier temps, la levure Saccharomyces cerevisiae YS-DN1 a été isolée à partir de dattes locales et étudiée pour ces pouvoirs de fermentation des sucres et de résistance aux différents facteurs de stress (éthanolique, thermique et osmotique). Cette souche s’est distinguée comme étant la plus performante dans la production d’éthanol en comparaison à deux autres souches industrielles de référence. En effet, YS-DN1 était la seule souche capable de se développer à une température entre 35 et 40°C en présence d’un taux alcoolique élevé (>8% éthanol) et une pression osmotique agressive (>18 °Brix). Dans un deuxième temps, deux souches de bactéries acétiques CV01 et AF01, identifiées par des techniques moléculaires comme étant affiliées à l’espèce Acetobacter pasteurianus, ont été isolées respectivement de cactus et de pommes. A l’issue des caractérisations physiologiques et des cinétiques de fermentation réalisées en erlens et en bioréacteurs (6 L, 20 L et 500 L), ces deux souches ont montré des pouvoirs de thermotolérance et d’acétification notables. L’étude enzymatique réalisée sur les enzymes membranaires ADH et ALDH formant le complexe enzymatique impliqué dans le processus d’oxydation de l’éthanol a révélé que, contrairement aux souches de référence, ces enzymes maintiennent une activité normale à haute température (38°C). L’étude cinétique en bioréacteur 20 L a montré que la souche CV01 était moins sensible à la variation de la composition du milieu de fermentation et a pu produire plus d’acide acétique (10 g/L) que la souche AF01. Durant le même cycle de fermentation, la souche CV01 était notablement la seule souche capable d’orienter son mécanisme métabolique pour la production de l’acide gluconique simultanément avec l’acide acétique. Par ailleurs, la méthode des surfaces de réponse (RSM) a été utilisée pour l’optimisation de la production en biomasse de la souche CV01. Les valeurs optimales des facteurs influents, à savoir l’éthanol, l’acide acétique, le glucose et le pH, permettant d’obtenir le maximum de biomasse cellulaire (2.21 g/L) étaient de 28.18 g/L, 10.12 g/L, 15.15 g/L et 5.33, respectivement. Dans une troisième partie, la souche A. pasteurianus CV01 a été évaluée pour sa capacité à résister aux conditions de stress thermique en bioréacteur. Les résultats obtenus montrent une habilité de cette souche à contrecarrer l’augmentation excessive de température (>35°C) au cours d’un cycle de fermentation sans refroidissement. En outre, un protocole de démarrage de fermentation en mode semi-continu a été proposé et adopté pour la production de vinaigre de fruits en bioréacteur 500 L. La caractérisation aromatique du vinaigre de pomme produit à l’échelle pilote moyennant la technique de l’espace de tête – microextraction en phase solide (HS-SPME) – a permis d’identifier dans la composition de son arôme des molécules associées à des descripteurs généralement appréciés . Ces souches, caractérisées pour leur thermotolérance notable, pourront être utilisées comme starters pour la production à grande échelle de vinaigre de fruits. [less ▲]

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See detailEtude de la régulation de l'expression de l'opéron ftsW-psr-pbp5 chez Enterococcus hirae
Maréchal, Maxime ULiege

Doctoral thesis (2016)

Les entérocoques sont des microorganismes commensaux du tractus digestif de la plupart des animaux mais sont également des pathogènes opportunistes. Lorsque les entérocoques sont associés à une infection ... [more ▼]

Les entérocoques sont des microorganismes commensaux du tractus digestif de la plupart des animaux mais sont également des pathogènes opportunistes. Lorsque les entérocoques sont associés à une infection, la sélection d’un traitement antibiotique adéquat peut s’avérer difficile. Cela est dû à la résistance, intrinsèque ou acquise, des entérocoques à de nombreux antibiotiques. Dans ce travail, nous nous sommes intéressés à leur résistance intrinsèque aux β-lactamines. Un des mécanismes de résistance envers ces antibiotiques est la production d’un PBP de faible affinité. Cependant, le facteur responsable de la surproduction de cette protéine chez les souches présentant un niveau de résistance plus élevé n’est pas encore connu. Ce travail avait pour objectif principal de contribuer à une meilleure compréhension du mécanisme moléculaire responsable de la résistance aux β-lactamines et d’établir le rôle de l’opéron ftsWpsr-pbp5 chez Enterococcus hirae. La première partie de ce travail a été focalisée sur les protéines codées par les gènes ftsW, psr et pbp5. La publication du premier génome d’E. hirae ATCC9790 nous a permis d’identifier et situer dans le génome d’autres gènes codant pour des protéines de la même famille (SEDS pour FtsW, LCP pour Psr, et les autres PBPs pour PBP5). Nous avons produit et purifié ces différentes protéines avec pour visée principale la possibilité d’obtenir des anticorps spécifiques pouvant servir à localiser les protéines au sein de la cellule d’E. hirae. Nous avons établi que la protéine Psr lie le peptidoglycane, se localise avec PBP5 au niveau du site de division et possède des caractéristiques en accord avec une fonction similaire à celle proposée pour d’autres protéines LCP. La seconde partie du travail était axée sur la sélection et l’étude de nouveaux mutants hyperrésistants aux β-lactamines. L’analyse de leur physiologie, de l’expression du PBP5 et de l’environnement génétique du gène pbp5 chez chacun d’eux a été réalisée. Le séquençage du génome de deux mutants a été effectué afin de pouvoir identifier les mutations présentes permettant leur résistance. Des analyses de la force promotrice des séquences en amont de chaque gène de l’opéron ftsW-psr-pbp5 d’E. hirae ont été menées en utilisant le gène rapporteur de la luciférase de luciole. Ces expériences et les mutations observées chez les mutants, nous ont permis d’identifier des éléments régulateurs qui ont une influence sur l’expression de l’opéron ftsW-psr-pbp5. [less ▲]

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See detailContribution to the study of the effect of drying on the nutritive value of corn grain (Zea mays L.) for poultry and pigs feeding
Odjo, Djosse Psijus Sylvanus ULiege

Doctoral thesis (2016)

Corn grain (Zea mays L.) is widely produced all over the world and is intensively used in poultry and pigs feeding. Drying with hot air is usually utilized to preserve corn after harvest by decreasing the ... [more ▼]

Corn grain (Zea mays L.) is widely produced all over the world and is intensively used in poultry and pigs feeding. Drying with hot air is usually utilized to preserve corn after harvest by decreasing the water content. During high temperature drying, major components (starch and proteins) of corn grain undergo some structural changes with possible nutritional implication. This thesis aimed at increasing knowledge regarding the effect of the drying process on the feeding value of the corn grain for broilers and pigs feeding. After the general introduction and a review which attempts to summarize the major findings of previous studies carried out on the effects of drying on the nutritive value of corn for broilers feeding, the first in vitro experiment performed aimed to assess the effect of fluidized-bed drying on the digestibility of dry matter, starch and protein using a sequential pepsin-pancreatin protocol. It appeared that when corn grains harvested at similar moisture content are dried at different temperatures, the digestibility of starch and that of crude proteins are not affected in a similar way. Higher drying temperatures increased the final digestibility of starch while the digestibility of crude proteins decreased mainly during the pepsin step of digestion. Differences in the kinetics of starch digestion according to the corn grain temperature were attributed to the structural modifications induced within starch granules and proteins in response to the drying conditions. As the digestion of starch involves the breakdown of glycosidic bonds and results in the production of various oligosaccharides, a second experiment was performed in order to get more insight into the nature of saccharides released after the in vitro digestion of corn grains. Three methods were thus compared in their ability to provide relevant information about sugar saccharides released during an in vitro digestion procedure that mimics the pig digestive model. High Performance Anion Exchange Chromatography coupled with a Pulsed Amperometric Detector was revealed to give the most effective qualitative and quantitative information regarding the digestion of starch. Five major saccharides were found as the result of in vitro pepsin-pancreatin digestion of corn grain: glucose, isomaltose, maltose, maltotriose and glucosyl-maltotriose. The relative concentration of these saccharides varied according to the temperature applied during the corn drying, suggesting that structural changes occurring within starch granules (partial gelatinization) would lead to different digestion profiles in the small intestine and may therefore affect the nutritional physiology in pig intestinal tract. Protein is also affected by the high drying temperature. Among corn protein subgroups, salt-soluble proteins are the most sensitive to heat and their solubility decreases when the drying temperature increases. In a third experiment, the denaturation of salt-soluble proteins during corn drying and hydrothermal treatment was monitored and modelled. The impairment of corn protein solubility in saline buffer was revealed to depend mainly on temperature, time of processing and moisture content of materials treated. The evolution of extractible salt-soluble proteins content of corn kernels during drying at high temperature was more correctly described using the second order kinetic reaction than with the first order kinetic reaction when classical kinetic models were compared. In a forth study the relationship between the in vitro digestibility of dry matter and the salt-soluble protein index was assessed. It was found that the use of salt-soluble protein index as an indicator of the may lead to doubtful conclusion due to confounding factors (temperature and moisture content). Although this study has achieved some progress in understanding the possible link between corn drying parameters and their effects on the performance of poultry and pigs feeding using corn-based diets, as well as on methodologies that may be used to assess the nutritive value of dried corn grains, complementary studies aiming to determine the effectiveness of these effects on livestock and pigs have to be done. [less ▲]

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See detailStudying the genetics of Mendelian and complex traits with high-throughput genotyping and sequencing in cattle
Li, Wanbo ULiege

Doctoral thesis (2016)

Background For decades, identifying genes and mutations underlying inherited diseases and economically import traits has been at the core of genetic studies in domestic animals. The initial arduous task ... [more ▼]

Background For decades, identifying genes and mutations underlying inherited diseases and economically import traits has been at the core of genetic studies in domestic animals. The initial arduous task of gene mapping with microsatellites or low-density SNP panels was then followed by a often fruitless and tedious attempt to isolate the causative mutations for both monogenic and polygenic traits. The availability of high-density SNP arrays considerably accelerated the gene mapping process. More recently, advances in second-generation high-throughput sequencing (HTS) including whole genome, exome, and RNA sequencing have brought tremendous efficiency into dissecting the genetic underpinnings of phenotypes of interest. In this thesis, we describe the use of these new technologies to decipher the genetic basis of several monogenic and polygenic traits, in both forward and reverse genetic settings. Results We first describe the use of medium-density SNP arrays to dissect genetic basis of a monogenic disease (Crooked Tail Syndrome, CTS), as well as of complex phenotypes related to meiotic recombination in cattle. With regards to CTS, we first demonstrate that a common 2bp-deletion in the MRC2 gene causes the condition in Belgian Blue cattle (BBC), and that the frequency of the condition is due to a pleiotropic effect of the mutation on muscle mass. We discover a second loss-of-function mutation in the same gene MRC2, supporting the hypothesis of pleiotropy and balancing selection. With regards to recombination, we report that genetic variants in REC8 and RNF212 affect the genome-wide recombination rate in cattle. The RNF212 gene has also been shown to be associated with genome-wide recombination rate in humans, however REC8 is not supported as a candidate gene by newer data. We also demonstrated that several variants in the zinc-finger domain of a gonosomal PRDM9 paralogue influence hotspot usage in cattle, reminiscent of previous findings in human and mice. The subsequent application of HTS technology in forward genetic analyses, allowed us to identify: i) an intronic mutation in the PIGH gene that causes the skipping of exon 2, and is the cause of arthrogryposis in BBC, ii) a 3.3 kb deletion removing exons 25-27 of the FANCI gene, that causes brachyspina in Holstein-Friesian cattle. We finally used a reverse genetic approach to identify embryonic lethal (EL) mutations compromising fertility in beef (BBC) and dairy cattle (Holstein-Friesian and Jersey). We mined whole genome and exome sequence data from more than 500 animals for candidate embryonic lethal variants corresponding to loss-of-function (stop gain, frameshift and splice site variants) and disruptive missense variants. By doing so we demonstrate that against expectations domestic Bos taurus cattle are genetically more variable than humans including Africans, however, that their burden of disruptive variants is similar, amounting to ∼100 such variants per individual. We interpret this as resulting from more effective purifying selection in recent times as a result of increased inbreeding. We have genotyped thousands of animals for thousands of EL candidates, and estimate – from the observed depletion in homozygotes - that no more ∼15% of those are developmentally essential. We do not find evidence for synthetic epistasis between candidate EL mutations. By evaluating the departure from Mendelian expectations in matings between carrier sires and dams, we unambiguously demonstrate the embryonic lethal nature of nine relatively common candidate EL variants. All of them affect genes that are involved in basic cellular processes. We demonstrate that only one of these would have been detected using the haplotype-based approach that were applied thus far. The established list of loss-of-function variants is being mined for putative non-lethal, yet major phenotypic effects of medical relevance. Among these, we uncovered a 10-bp deletion in the MLPH gene, which results a premature stop codon, that causes diluted color – ‘cool gray’ – in BBC. Conclusions and Perspectives Due to the intensive use of some elite sires by means of artificial insemination in cattle, several outbursts of genetic defects have been observed in recent years. We herein demonstrate that uncovering the genetic basis of such Mendelian disorders can be very effective when integrating high-throughput genotyping and sequencing technology. Fertility in cattle and other domestic animals has declined over the last decades. Our discovery of a number of embryonic lethal variants segregating in cattle provide a complementary explanation for the decline in fertility, in addition to the theory of negative energy balance of high producing cows. The reverse genetic approach we developed for screening EL variants has at least two advantages. First, our approach also works in small sized populations. Second, our approach has higher sensitivity than the haplotype-based approach. It has been suspected for some time that most of the variants underlying complex traits map to noncoding regions. Deciphering the functional consequence of these regulatory variants has proven challenging. The ENCODE projects in human and mice provide good examples of how high-throughput functional assays based on NGS technology may enhance our knowledge of the non-coding regions of the genome. It is reasonable to anticipate that the release of ENCODE-like data in the animal research field will assist in the discovery of the genetic basis of complex traits at an unprecedented pace. [less ▲]

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See detailEtude des intermattes des herbiers à Posidonia oceanica
Abadie, Arnaud ULiege

Doctoral thesis (2016)

Among Mediterranean marine ecosystems, Posidonia oceanica (L.) Delile seagrass meadows form a habitat playing an important ecological and economical role. They form heterogeneous seascapes influenced by ... [more ▼]

Among Mediterranean marine ecosystems, Posidonia oceanica (L.) Delile seagrass meadows form a habitat playing an important ecological and economical role. They form heterogeneous seascapes influenced by the impact of natural and anthropogenic phenomenon (of which the anchoring of leisure ships). These impacts lead to the formation of sand and bare mat patches called ‘intermattes’. By describing and using intermatte characteristics observed in Calvi Bay and more widely around Corsica, these PhD works precisely described intermatte and P. oceanica seascape dynamics in order to develop new methods of analysis. On the one hand, natural sandy intermattes formed by bottom currents show two types of border. Each has its own characteristics at the level of the sediments biogeochemistry. On the other hand, anthropogenic intermattes generated by anchoring (bare mat) present different sizes and shapes resulting from specific dynamics. They are not recolonized when the anchoring pressure remains high. A depletion of the substrate chemical quality occurs after the mechanical destruction. A new cartographic seascape index, the Patchiness Source Index, was created using the size and the nature of intermattes at large spatial scale. After a comparison of methods used for the study of intermattes, two new indices (Map Anchoring Index and Anchoring Index) for managers of coastal areas were developed to evaluate the impact of anchoring within P. oceanica meadows. [less ▲]

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See detailProcessus écologiques et évolutifs impliqués dans le succès de l’introduction de Quercus rubra L. en Europe
Merceron, Nastasia ULiege

Doctoral thesis (2016)

Le chêne rouge d’Amérique (Quercus rubra L.) est un arbre originaire d’Amérique du Nord et introduit en Europe à partir de la fin du XVIIème siècle pour l’ornementation et le commerce du bois. Le but de ... [more ▼]

Le chêne rouge d’Amérique (Quercus rubra L.) est un arbre originaire d’Amérique du Nord et introduit en Europe à partir de la fin du XVIIème siècle pour l’ornementation et le commerce du bois. Le but de cette thèse est de comprendre les mécanismes écologiques et évolutifs qui contribuent à la dynamique et au succès de l’introduction de Q. rubra en Europe. Nous avons montré que cette espèce naturalisée et plantée dans certains pays européens parvient aisément à se développer de façon naturelle dans les forêts de feuillus et de conifères. La dispersion de ses glands est notamment rendue possible par des animaux fouisseurs-disperseurs, tels que les écureuils et les mulots, qui cependant préfèrent les glands du chêne natif Q. robur. Lors de l’introduction d’une espèce dans un nouvel environnement, des processus évolutifs sont susceptibles de se produire et d’engendrer des modifications phénotypiques et génétiques au sein des populations introduites. Une analyse comparative de la structure et de la diversité génétique des populations natives et introduites de Q. rubra a démontré que seulement deux des trois groupes génétiques de l’aire américaine sont actuellement présents en Europe. Aucun goulot d’étranglement fort n’a été détecté lors de l’introduction des populations en Europe laissant supposer que des introductions multiples ont pu maintenir la diversité génétique dans les populations introduites. Une analyse comparative des traits phénotypiques a permis de montrer que les populations introduites de Q. rubra présentent une croissance supérieure par rapport aux populations natives. Une différenciation génétique au sein des populations introduites est en cours pour le trait de débourrement foliaire suggérant une possible évolution adaptative rapide depuis l’introduction. [less ▲]

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See detailAssessment of fodder biomass in Senegalese rangelands using earth observation and field data
Diouf, Abdoul Aziz ULiege

Doctoral thesis (2016)

Senegalese livestock size has largely increased during the last three decades in relation to the population growth. The fodder biomass stock available at the end of the growing season, therefore, becomes ... [more ▼]

Senegalese livestock size has largely increased during the last three decades in relation to the population growth. The fodder biomass stock available at the end of the growing season, therefore, becomes increasingly limited to meet feeding needs of pastoral livestock which provides third of the national agricultural wealth. With the reduction of natural grazing lands mostly generated by the expansion of croplands, and the reduction of fodder biomass production due to drought effects, the increase of the livestock size leads to the rangelands overload whose persistence can lead in turn to their degradation. A technique based on a simple linear relationship between the temporal integration of the Normalized Difference Vegetation Index (NDVI) and the ground biomass data, developed in the 1980s, has been operationally applied by the Centre de Suivi Ecologique (CSE) of Dakar (Senegal) to assess the fodder biomass available in rangelands at the end of the growing season. The derived map of total biomass production enables to help pastoral livestock managers as well as national stakeholders against food insecurity and natural resources degradation. Carried out annually, this approach comprises unfortunately some uncertainties as: (1) the saturation drawback of NDVI in areas with high biomass productivity, (2) the temporal scale which is restricted to biomass data of the ongoing year not being used again in the following year, (3) the low predictive ability due to the large time gap between data collection and published results, and (4) the high costs for annual data collection. In addition, although the earth observation (EO) data have largely progressed during the last three decades, this technique has not changed over this period and consequently is not state-of-the-art. To tackle these limitations and advance the traditional method, new statistical models that include new earth observations datasets and historical in situ plant biomass data were developed for estimating and / or predicting the forage availability at the end of the growing season in Senegalese semi-arid rangelands. A backward analysis of the linear regression approach currently applied in Senegal provided evidence that nonlinear regression functions such as Exponential and Power are more suited to estimate the end-of-season total biomass in this region using annual data solely. A completely new methodology using multiple-linear models which include various phenological metrics from the time series of the Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) and 14 years of in situ total biomass samples was developed. The proposed approach provided more reliable and accurate estimates as compared to the current CSE biomass product. Multiple-linear models developed with specific metrics adapted to ecosystem properties increased the overall accuracy of the fodder biomass estimates and mitigated the saturation of FAPAR obtained with models run across the whole study area. With this new approach, timely information about possible deficits/surplus of total fodder biomass can be provided to stakeholders using phenological metrics that are available relatively early in the growing season. Another new approach based on a machine learning algorithm (i.e., Cubist) was developed, as never done before, to assess herbaceous biomass in Senegalese Sahel. Three Cubist models using FAPAR seasonal metrics and/or agrometeorological variables (i.e., soil water status indicators) were established and compared. The Cubist model including both FAPAR and agrometeorological variables provided the best estimation performance. This model enabled to mitigate the saturation affecting optical remotely sensed vegetation data in areas of high plant productivity as well as the discrepancy between herbaceous biomass and greenness, and corrected therefore for herbaceous biomass underestimations observed with the sole FAPAR based model, particularly in sparsely vegetated areas. In contrast to the date of the growing season onset retrieved from FAPAR seasonal dynamics, the rainy season onset was significantly related to the herbaceous biomass and its inclusion in models could constitute a significant improvement in forecasting risks of fodder biomass deficit. The methods developed in this research provide tools to assess Senegalese forage resources at two levels: herbaceous and total fodder biomass (Herbaceous + woody leaf biomass). They require limited data and free available software and therefore can be easily replicated in other countries of the West African Sahel. [less ▲]

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See detailPlace de l'élevage bovin dans l'économie rurale des Peuls du Nord Bénin
Chabi Toko, Roukayath ULiege

Doctoral thesis (2016)

Fulani belong to a socio-cultural group mainly encountered in West Africa and usually raises cattle. In Benin, Fulani are predominantly met in the two eastern departments of the North where they lead an ... [more ▼]

Fulani belong to a socio-cultural group mainly encountered in West Africa and usually raises cattle. In Benin, Fulani are predominantly met in the two eastern departments of the North where they lead an agro-pastoral way of life. In addition to livestock farming, they cultivate food and cash crops such as cotton. However, they hold majority of the country’s cattle population. The present study was initiated to understand to what extend cattle contributes to their rural economy. A stratified random sample of 150 heads of Fulani households, cattle farmers have been identified in Malanville, Banikoara and Kalalé districts in Borgou and Alibori departments. The criteria considered were: the agro-ecological zone, cattle population and the importance of Fulani population. The first series of surveys enable to characterize Fulani’s cattle farming system and their family farms. Among the 50 heads of households of Kalalé district (which has the more important Fulani community), 16 were selected and it is within their households that the study continued. The households selected were that with a better milk production. Surveys were then carried out during two years, both in dry season and rainy season to describe the Fulani’s household’s economy. The cattle stock composition showed a gender imbalance, with a preponderance of female stock (76%). Cattle herds which average size were 66 animals are made of 86% of Borgou breed. The herds have low breeding performance characterized by a high rate of calf mortality (10%) and low reproductive parameters: calving and fertility rates were 64%. The purchase of fodder in dry season, which concerns 17% of farmers, is a practice encountered in agroecological zones that register light rainfall. Fulani’s large households enable them to have enough family labor to carry out both livestock and agriculture activities. The land is mostly inherited and the average size for a household is about 10.5 ha. All Fulani households are crops producers of which majority (80%) is consumed. A significant part (45%) of them grow an average of 3.3 ha of cotton. In Fulani family farms, cattle represent 52% of the household livestock size; there is also small ruminants and poultry. This cattle permit to majority (76%) of Fulani households to have milk for sale. But milk is managed to favor household consumption and ensure the herd's reproduction. The organization around milk involves male and female. The profits from milk and cheese are distributed among the women of the household at various levels. Although the low (7%) cattle market rate, it contributes significantly (68%) to the household’s monetary income in rainy season and represents the second source (27%) of revenue in dry season. The 20% of food products are mainly sold in dry season and thus contribute to the majority (64%) of income sources. However, when rains started late and the delayed payment of cotton fees, the majority of Fulani households’ cash income in the rainy season, came from cotton (64%) and food products (23%). The growing involvement of Fulani cattle herders of northern Benin on the foodstuffs market and in cotton will lead to two types of farms with opposed production targets (those that will favor livestock and others agriculture). Fulani are a target population that should receive a little more support from authorities because enable them to value their resources would ensure availability and accessibility of food and pastoral products and contribute to the improvement of country’s agricultural production. [less ▲]

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See detailEvaluation de l'impact socio-économique en aval des aménagements hydroélectriques : exemple du barrage hydroélectrique de Nam Mang 3 au Laos
Kouangpalath, Phimthong ULiege

Doctoral thesis (2016)

Since two decades, hydropower projects are multiplying in Laos. These projects are often criticized in the media and civil society organizations for their negative social and environmental impacts, which ... [more ▼]

Since two decades, hydropower projects are multiplying in Laos. These projects are often criticized in the media and civil society organizations for their negative social and environmental impacts, which can also generate regional geopolitical tensions in Southeast Asia. In this sensitive context, our interest has focused on rural populations downstream of hydropower dams; these populations are often ignored by compensation programs reserved for displaced populations from upstream. The objective of the research is to identify and assess the socio-economic effects in the Nam Nyam Valley (Vientiane Province, Lao PDR), downstream of the Nam Mang 3 hydropower dam. A current diagnostic-analysis of the agrarian system of the valley, together with a characterization of the recent evolution was conducted by household surveys in different villages. The diachronic study of agrarian dynamics and understanding the links of causality enabled us to model a counterfactual scenario to isolate, by difference with the current situation (scenario "with project"), the specific effects of the dam. In parallel, a similar approach was employed downstream of the Nam Lik 1-2 hydropower dam in the Meuang Feuang basin (Vientiane province, Lao PDR) in order to compare with the results of the Nam Nyam Valley, to better characterize the specific effects of hydropower infrastructure developments. As a result, the evolution of agrarian systems in the valleys downstream depends on the combination, variable over time, of several political, economic, demographic, environmental, technical, social, etc. factors. A hydropower dam, like the one of Nam Mang 3 is part of complex and continuous dynamics of transformation; its impact is not only the sole cause of changes affecting the communities. The socio-economic effects influence over time a much larger population downstream than upstream, even if the media attract the attention on punctual displacement of villages (and their compensation) to fill the reservoir. The hydropower dam project effects differ according to phases (construction, reservoir filling, operation) and social categories, depending on the investment capacities, adaptation and networks of each category. The socio-economic impact downstream is not assumed to be correlated with the size of hydropower dam, but its design and mode of water management are the key criteria of the importance of negative externalities. The massive investments in these projects have also positive effects for the local population, such as the development of local infrastructure, which open up villages and provide access to public services and markets. However, these positive externalities mainly concern well-off villagers disposing of capital and networks to benefit of new opportunities, while poor families are more vulnerable to changes in the political, environmental, technical and socio-economic context. Thus, hydropower dams contribute to increased socio-economic differentiation in villages downstream, with the poor left out of the profits from the energy export. [less ▲]

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See detailCaractérisation multi-échelle des bandes riveraines des cours d’eau wallons par télédétection active et passive
Michez, Adrien ULiege

Doctoral thesis (2016)

Les bandes riveraines des cours d’eau constituent des milieux d’une richesse exceptionnelle aux multiples facettes, comportant les habitats parmi les plus variés, dynamiques et complexes de la surface ... [more ▼]

Les bandes riveraines des cours d’eau constituent des milieux d’une richesse exceptionnelle aux multiples facettes, comportant les habitats parmi les plus variés, dynamiques et complexes de la surface terrestre. Elles sont au cœur des stratégies des politiques de préservation et de restauration de l’environnement qui impliquent la mise en place de suivis multi-échelles devant être répétés dans le temps. La télédétection peut fournir des informations fines tant sur la végétation qui compose les bandes riveraines que sur la structure et les paramètres physiques de celles-ci. Le présent projet de doctorat est articulé autour de l’évaluation de la télédétection en tant qu’outil pour la gestion des cours d’eau ; tant au niveau local (<20 km de cours d’eau, usage de drone) qu’au niveau de l’ensemble du réseau hydrographique wallon (> 12 000 km de cours d’eau). Au niveau local, les drones civils tendent à émerger comme outils de caractérisation environnementale depuis le début des années 2000. Leurs principales caractéristiques sont relatives à leur résolution spatiale et temporelle, permettant d’obtenir des données très fines (résolution au sol ≤ 10cm) au sein d’une fenêtre temporelle très restreinte. Leur usage a été évalué avec succès afin de localiser les plantes invasives des bandes riveraines et de caractériser la composition spécifique et l’état sanitaire de l’aulne glutineux (Alnus glutinosa) en Ardenne. Des résultats satisfaisants ont été atteints dans le cas de l’étude de la détection des trois principales espèces végétales invasives des bandes riveraines wallonnes : balsamine de l'Himalaya (I. glandulifera), berce du Caucase (H. mantegazzianum) et renouée du Japon (F. sachalinensis et F. japonica et hybrides). Les meilleures précisions globales obtenues sont de 97% pour la berce du Caucase. A l’échelle régionale, l’approche développée est basée sur l’usage de données 3D (LiDAR et photogrammétriques) afin de caractériser les bandes riveraines associées à l’ensemble du réseau hydrographique wallon (> 12 000 km) à partir de 6 paramètres. Ces paramètres sont descriptifs de composantes physiques de l’hydromorphologie mais également de la structure des forêts riveraines. Une évaluation des patrons spatiaux de ces paramètres en lien avec différentes informations (occupation du sol, régions naturelles) a été réalisée. S’appuyant sur différentes techniques d’agrégation permettant des visualisations à l’échelle régionale, les résultats obtenus reflètent la connaissance a priori des cordons rivulaires, notamment le constat négatif relatif à la fonctionnalité des bandes riveraines en région limoneuse. Les principales perspectives d’application au domaine de la gestion des cours d’eau sont relatives au développement d’outils d’aide à la décision pour les gestionnaires. A l’échelle locale, une adaptation des solutions développées pour l’usage des drones est nécessaire tant en matière de plateforme (couverture d’un linéaire plus important) qu’en tant qu’outil d’analyse (simplification des chaînes de traitement). A l’échelle régionale, la construction d’indicateurs de gestion nécessitera un travail spécifique quant à la comparaison de la valeur observée à une valeur référence. [less ▲]

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See detailIsolement et caractérisation de mutants affectés dans le transport d'électrons photosynthétique en anoxie chez la microalgue verte Chlamydomonas reinhardtii. Photoproduction d'hydrogène et Voie de biosynthèse de la phylloquinone.
Emonds-Alt, Barbara ULiege

Doctoral thesis (2016)

La microalgue verte Chlamydomonas reinhardtii, qui a contribué de façon remarquable à la compréhension de nombreux mécanismes biologiques tels que la photosynthèse, intéresse aujourd’hui plus ... [more ▼]

La microalgue verte Chlamydomonas reinhardtii, qui a contribué de façon remarquable à la compréhension de nombreux mécanismes biologiques tels que la photosynthèse, intéresse aujourd’hui plus particulièrement le secteur des énergies renouvelables pour sa capacité à produire de l’hydrogène moléculaire (H2) à la lumière. Cette photoproduction d’H2 est liée à la présence en anoxie d’hydrogénases qui sont connectées via la ferrédoxine à la chaîne de transport d’électrons photosynthétique. On distingue deux voies de transfert d’électrons: la première dépendant de la photolyse de l’eau par le PSII (voie PSII-dépendante), la seconde de l’action d’une NAD(P)H déshydrogénase de type II (NDA2, voie PSII-indépendante). En raison de la sensibilité des hydrogénases à l’oxygène, cette production n’est que transitoire. Bien que ce processus puisse potentiellement réduire notre dépendance aux énergies fossiles, il est à l’heure actuelle économiquement inexploitable compte tenu de sa faible productivité. L’amélioration génétique des microalgues pourrait partiellement remédier à ce problème mais cette stratégie nécessite toutefois de posséder une connaissance fondamentale de toutes les voies métaboliques impliquées dans ce processus spécifique de l’anoxie. Afin d’identifier de nouvelles enzymes clés contrôlant la photoproduction d’H2 et de manière plus générale le métabolisme anaérobique, chez l’algue modèle Chlamydomonas reinhardtii, nous avons cherché dans un premier temps à comprendre la fonction de la protéine NDA3, une NAD(P)H déshydrogénase de type II chloroplastique. A l’instar de NDA2, celle-ci pourrait potentiellement participer à la réduction non-photochimique du pool de plastoquinones. Dans un deuxième temps, nous avons contribué au développement d’une nouvelle technique de criblage «haut débit» basée sur l’enregistrement de la cinétique d’induction de fluorescence des algues lors d’une transition de l’obscurité à la lumière en anoxie. Grâce à l’efficacité et à la rapidité de cette méthode nous avons pu identifier au sein d’une large collection de mutants insertionnels (~ 23 000) quatre mutants déficients pour le facteur d’assemblage HYDG (essentiel à la maturation des hydrogénases) et quatre autres mutants déficients pour la voie de biosynthèse de la phylloquinone. La caractérisation subséquente de ces mutants par des méthodes génétiques, moléculaires, biochimiques et biophysiques, nous a ainsi permis de comprendre in fine l’impact négatif de la perte du facteur HYDG ou de la phylloquinone sur le transfert d’électrons photosynthétique en anoxie. [less ▲]

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