References of "Dissertations and theses"
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See detailTransfer of greenhouse gases in the soil – vadose zone – groundwater – river – atmosphere system
Nikolenko, Olha ULiege

Doctoral thesis (2020)

One of the major global challenges of this century is to find the balance between the intensive agricultural production and the environmental damage that it causes by contributing to climate change and ... [more ▼]

One of the major global challenges of this century is to find the balance between the intensive agricultural production and the environmental damage that it causes by contributing to climate change and deterioration of water resources and soils. Agriculture accounts for up to one third of anthropogenic emissions of greenhouse gases (GHGs) which exacerbate the climate change (increase in nitrous oxide (N2O), methane (CH4), and carbon dioxide (CO2)) and lead to the depletion of stratospheric ozone layer (N2O). Recent studies have suggested that in agricultural areas groundwater systems might be the significant sources of GHGs emissions, especially N2O, to the atmosphere due to intensive application of nitrogen containing inorganic and organic fertilizers used to increase soil fertility. However, the dynamics of N2O, CH4 and CO2 in aquifers is still poorly characterized due to the insufficient insight into kinetics and controls of processes regulating their production, transport and consumption. That is why, it is important to obtain more information regarding functional zones controlling fate of GHGs in subsurface. This knowledge is important for constraining the GHGs budgets, understanding the mechanisms behind climate change and developing mitigation measures to stop the rise of concentrations of N2O, CH4 and CO2. In this context this study focuses on evaluating the potential role of aquifers affected by the agricultural activities as a source of GHGs emission to the atmosphere and improving the understanding of the impact of the spatial heterogeneity of subsurface media on the dynamics of N2O production and consumption processes. In this project advanced techniques and methods from hydrogeological, isotope and microbiological fields were used for investigation of the actual subsurface conditions and analysis of their impact on production and consumption of N2O in groundwater. The study was divided into two stages: 1) regional investigations and 2) local-scale explorations. The main aim of the regional survey was to examine the distribution and accumulation of GHGs in different parts of the studied aquifer across its lateral and vertical dimensions and to obtain better information regarding the hydrogeochemical conditions of the subsurface. Meanwhile, the local scale investigations were focused on the occurrence of biochemical stratification in the same aquifer and analysis of its impact on N2O dynamics. It aimed to identify and quantify the rates of N2O production/consumption processes using data obtained from ambient groundwater and laboratory designed experiments. Since N2O production and consumption processes can proceed through abiotic and biotic pathways, the measurements of the activity of the microorganisms that accomplish biotic N transformations were conducted to obtain more information about N2O dynamics. [less ▲]

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See detailInteractions trophiques Hémiptères – plantes-hôtes : Etude des stratégies de contournement des défenses végétales induites
Serteyn, Laurent ULiege

Doctoral thesis (2020)

Along this thesis, we investigate phytophagous insects of the piercing-sucking guild, belonging to the Hemiptera Order. In the state of the art, we identify two key-elements of their strategies to ... [more ▼]

Along this thesis, we investigate phytophagous insects of the piercing-sucking guild, belonging to the Hemiptera Order. In the state of the art, we identify two key-elements of their strategies to counteract plant defenses, at the plant-insect interface: feeding behavior and salivary proteins. In such context, we notice several gaps in the knowledge of Pentatomidae, and more largely of Heteroptera: variable feeding behavior, lack of studies on salivary compounds and unclear plant-insect interactions. Moreover, many studies pointed out the influence of microbial agents on plant-insect interactions, which complexify greatly the conclusions. The aim is to enlighten the roles of feeding behavior and salivary proteins in the counteraction of induced plant defenses, taking into account four trophic levels: the rhizobacteria Bacillus velezensis FZB42 as an inducer of plant defense priming, the plant Vicia faba L., the Hemipteran insects, the brown marmorated stink bug (BMSB) Halyomorpha halys (Stål) and the pea aphid Acyrthosiphon pisum (Harris), and the endosymbiont Hamiltonella defensa. As preliminaries, we detail the feeding behavior of the stink bug H. halys by electropenetrography (EPG), providing a first EPG waveforms library for this invasive pest. We also set up a protocol to extract its salivary proteins, preceding a sensitive analysis of salivary proteome by mass spectrometry. We then applied these methods to evaluate the perturbation of feeding behavior and salivary proteins following the exposure to insect-induced plant defenses. First, the feeding behavior is perturbed when insects feed on these elicited plants. Second, proteomics on stink bug’s saliva highlight an up-regulation of proteins potentially involved in plant-insect interactions, including the detoxification of plant defense metabolites, following a short exposure to elicited plants. In the next chapter, we focus on BMSB salivary proteome, as a key-strategy to counteract plant defenses. We aim to identify the qualitative and quantitative changes in salivary proteins of insects exposed to the priming of plant defenses provoked by a third agent, the rhizobacterium B. velezensis FZB42. And indeed, BMSB saliva includes, once more, up-regulated proteins potentially involved in plant defense deactivation, following a short exposure to inoculated plants. In the last experimental chapter, we work on two genotypes of the pea aphid A. pisum, differing by the presence of the symbiont H. defensa. We analyse the defense pathways induced by B. velezensis FZB42 and we quantify the development and the feeding behavior of aphids exposed to the defenses. As a matter of fact, bacteria associated with the aphid add a greater complexity to the interpretation of observed phenomena. Such quadripartite interactions deserve more studies in order to better understand the actual role played by endosymbionts and/or the genotype in the counteraction of induced plant defenses. [less ▲]

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See detailVers une meilleure gestion de l’eau agricole à partir des plateformes libres de télédétection et de communication au Burkina Faso
Pale, Sié ULiege

Doctoral thesis (2020)

Water is an important resource for agriculture in Sahelian region countries like Burkina Faso. Therefore, several agricultural development projects seek to address challenges related to water management ... [more ▼]

Water is an important resource for agriculture in Sahelian region countries like Burkina Faso. Therefore, several agricultural development projects seek to address challenges related to water management. To this day, uptake of available opportunities and solutions by local administrations remains limited, as exemplified by The Upper-Comoé river basin in southwest Burkina Faso. Without improved water management, there is limited possibility of increasing productivity in a region where agriculture remains the main economic engine. The research for thesis aimed to contribute to enhanced management of surface water for agriculture in the Upper-Comoé basin. Focusing on open source satellite remote sensing tools and communication platforms (instant open messaging apps), the study examined their potential for improving water management. Having ascertained that challenges in communication and information access, a WhatsApp based information system was tested in the river basin. The system was enhanced by a Google Earth Engine based vegetable irrigated plots evaluation method established along Comoé river, and a water delivered adequacy metric, that allowed us to compare water discharges delivered to different user groups with their water needs, thereby enabling an identifying of water wasters. The suite of methods and measures constitute a hydro-agricultural monitoring tool, which was provided to the Local Water Committee for purposes of improving equity and transparency in water management. The information system was developed based on findings from a baseline study of water users’ needs. Two others data collection and analysis activities carried out during the fieldwork. Areas of small irrigated vegetable holdings were estimated by way of a Classification and Regression Tree (CART) algorithm, a satellite images classifier. This method simultaneously combines Sentinel-1 and Sentinel-2 images and spectral indices (NDVI, NBR2, MNDWI) for classification. It is based on a Javascript script elaborated from Google Earth Engine platform. Before developing the research design, a reconnaissance survey was conducted to assess the potential for utilisation of the water management tools proposed by research to gain a basic understanding of the water management system and issues in the region. Results showed that the level of utilisation of the water management tools in question is low. It likewise suggested that the perfect institutionalisation of such tool may improve their utilisation by workers. It revealed that main challenges related to water management were, lack of accurate information that would enable users to plan allocation, low efficiency of water usage, expansion of planted areas despite productivity remaining low, and the gap between water demand and supply. Finally, we found that communication among stakeholders is a weak link in water management. While the Local Water Committee provided a vehicle for disseminating information about water resources, such information often did not go beyond it technical sub-committee charged with elaborating water allocation plans. This thesis demonstrated that open source tools could serve as a simple, low cost, user-friendly mechanism to address water challenges in Burkina Faso. It also suggested ways of bridging scientific knowledge with practical applications. [less ▲]

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See detailOptimization of phenolic compounds extraction from Tetrapleura tetraptera and Aframomum citratum and biological assessments
Eyenga, Manga ULiege

Doctoral thesis (2020)

This thesis explores the optimization of phenolic compounds extraction and the biological activities of two non woody forest products (Tetrapleura tetraptera and Aframomum citratum fruit extracts) spread ... [more ▼]

This thesis explores the optimization of phenolic compounds extraction and the biological activities of two non woody forest products (Tetrapleura tetraptera and Aframomum citratum fruit extracts) spread in three agro-ecologic zones in Cameroon in a home food consumption context. The fruits are used for seasoning traditional recipes and in the traditional pharmacopeae. The general objective of this study was to contribute to a development of a therapeutic and preventive dietary supplement rich in dietary antioxidant to fight against oxidative stress on diabetic patents. As they are geographically harvested in many agro-ecologic areas, the various specific objectives were to investigate on their chemical and biological variabilities; on the impact of heat treatment (roasting) on their properties; to define the optimum conditions for total polyphenol recovery of a mix of the spices; and to administer a beverage obtained under optimum extraction conditions to diabetic rats in other to study their antidiabetic capabilities. The first trials results showed that for T. tetraptera, samples from the bimodal forest zone (BFZ) possess more sugars, calories, minerals and phenolic compounds. Gallic acid, chlorogenic acid, benzoic acid, 2-OH cinnamic acid, salycilic acid, flavone, gallocatechin, epigallocatechin gallate, naringin, phlorizin were among the predominant phenolic compounds identified in aqueous extract. Concerning A. citratum, samples from the BFZ contain more protein, fiber, phenolic and minerals (especially samples from the East region). A total of six dominant phenolic acids (Gallic, chlorogenic, protocatechuic, 2-OH cinnamic, caffeic, p-coumaric) and five flavonoids (epigallocatechin gallate, resveratrol, phlorizin, rutin, epicatechin, luteolin) were observed on the extracts. All the aqueous extracts biological activities (antioxidant, anti-inflammatory) of spices from the BFZ are dose dependent and more effective. Heat treatment significantly reduces fat, raw proteins and total sugars but improves raw fibre, phenolic contents and the biological activities of all the spices. For the total polyphenols recovery, the optimal conditions were: roasting temperature of 150°C, roasting time of 12.6 min, a brewing time of 11.9 min. After in vivo test on rats, the effect of the beverage alone is significantly the same as the conjoined administration of the beverage and the antidiabetic drug (Glibenclamide) reference and the administration the α-glucosidase inhibitor (Acarbose) after 4hrs when assessing the anti-hyperglycemic test on diabetic rats. The Glibenclamide effect is significantly improved by the beverage administration on hypoglycaemic assay and this synergy reduces diabetes complications on diabetic rats. As conclusion, the best areas to harvest are in the BFZ and the heat treatment applied has to be controlled. The beverage obtained with 95/5 Tetrapleura tetraptera/Aframomum citratum formulation possesses antoxidant, anti-nflammatory and hypoglycaemic activities. However there is a need for additional in vivo tests in order to confirm the different in vitro biological activities observed and to determine the human relevance of the beverage at the dose used. [less ▲]

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See detailApple microbiome-based improvement of biocontrol agents for postharvest pathogens management
Sare, Abdoul Razack ULiege

Doctoral thesis (2020)

Biocontrol using biocontrol agents (BCA) is a sustainable way to manage postharvest diseases. Nevertheless, their reliability (stability of efficacy) must still be improved to reach efficacy of synthetic ... [more ▼]

Biocontrol using biocontrol agents (BCA) is a sustainable way to manage postharvest diseases. Nevertheless, their reliability (stability of efficacy) must still be improved to reach efficacy of synthetic chemical pesticides. Indeed, when BCA are applied on the plant surface, they meet contrasted microbial community in which ecological relationships take place, thus potentially interfering with their efficacy and stability. Understanding better the role of fruit microbiota composition in the disease development and in the efficacy of BCA is an emerging research area. This could allow the isolation of more beneficial strains or the identification of molecules that modulate host microbiota to favour BCA and to limit disease development. In this thesis, apple microbiota was deeply characterized and used in situ to improve the efficacy and stability of Pichia anomala strain K, a BCA against Botrytis cinerea rot. At first, several protocols to harvest the epiphytic microbiota were tested and compared. Results showed that a first wash harvested one third of culturable microorganisms, and that three successive washes harvested around 80% of them. There were significant differences between protocols, thus inducing potential bias among studies using different protocols to study the epiphytic microbiota. However, this bias was offset by pooling the successive washes, that besides increased overall microbial richness. Then, the metagenome of apple fruit microbiota was studied by shotgun highthroughput sequencing (HTS) on three symptomless samples of apple fruit Pinova variety. Results showed a very high fungal (79.0 %) and bacterial (13.8 %) diversity. The prevalent phyla were Ascomycota for fungi and Bacteroides for bacteria. Genera of known apple postharvest pathogens and known BCA were identified. The functional analysis showed important genes potentially involved in biocontrol activity. On the other hand, the incompleteness of current databases and the complexity of the analysis limited the complete exploitation of the results and are blockages of using such technic currently. Finally, contrasted apple microbiomes were harvested and studied to identify beneficial strains and molecules to control Botrytis cinerea. Eighteen apple microbial communities (representing fifteen cultivars and four management practices) were harvested and characterized by HTS of 16s rRNA gene and Internal Transcript Spacer (ITS) amplicons. The biocontrol efficacy against B. cinerea of these microbiotas applied alone or with a BCA was also evaluated and the metabolisation of 190 carbon sources was studied. Results showed that apple microbiota is diversified and contrasted at taxonomic level, biocontrol efficacy and carbon source metabolisation. Certain microbiota significantly raised the strain K efficacy up to 100%. The alpha diversity of the apple microbiota was not correlated to the biocontrol efficacy. Coclustering of Spearman correlations were used to drive the isolation of promising beneficial strains (BCA candidates or helper strains supporting BCA efficacy) and molecules allowing better control of the pathogen. Biocontrol efficacy of the new strains and molecules was further confirmed in vivo. Results of this work can contribute to increase the reliability of BCA in real condition. [less ▲]

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See detailFrom "Coal to Gas" to "Coal to Biomass": Sustainable Development Path for Coupling Rural Energy Improvement and Straw Utilization in China
Wang, Qiang ULiege

Doctoral thesis (2020)

Currently, the Chinese government is promoting the diversification of energy sources in rural areas to reduce the consumption of coal. The development of biomass resources in agricultural areas is an ... [more ▼]

Currently, the Chinese government is promoting the diversification of energy sources in rural areas to reduce the consumption of coal. The development of biomass resources in agricultural areas is an alternative means of energy supply. This thesis assesses the potential offered by the centralized biogas production and straw briquetting fuel. Firstly, the environmental and economic performances of these two methods are assessed through an emergy analysis for two cases. The results show that, while the two projects studied have a high reproducibility and a low environmental load, the indicators of long-term sustainability are not favorable, in particular, in the event of a marked deficit in demand on the biogas or briquetting fuel. However, since the indicators of sustainability and economic profitability improve when the load tends towards the maximum capacity of the productions, the two models studied exist optimization margins. In the second step, the positioning of consumers relatively one of the two aforementioned markets, namely that of biogas, was explored by the method of contingent valuation method (CVM). This made it possible to estimate the rural residents’ willingness to use (WTU) and the willingness to buy (WTB) for this renewable energy source and to identify the determinants factors of these willingnesses. The results show that, although most of the respondents support the product, there is a significant gap between the amount of WTB and the costs of producing biogas. The propensity of potential consumers to use biogas and the amount of WTB depend not only on their personal and family characteristics but also on some non-economic factors, such as their level of knowledge on environmental issues, their attitudes, and practices regarding energy consumption. Consequently, it is recommended to reinforce awareness campaigns in order to improve the level of knowledge, influence the attitude of rural residents with regard to environmental issues, guide their practices in terms of the use of clean energy. Understanding the factors that influence demand has also made it possible to offer a suitable financial support mechanism capable of supporting market development. The third part of this thesis deals with the question of financing such projects. The public–private partnership (PPP) model is seen as a response that can mobilize social capital to finance investments in these new modes of production and energy supply in rural areas. Based on an analysis of the strengths, weaknesses, opportunities, and threats (SWOT) of the two projects considered above, an analytic hierarchy process (AHP) was carried out with the assistance of experts in order to clarify the strategic choices which are more suitable for investors. The strategic decision model identifies that a pioneering strategy based on opportunities is promising for the straw briquetting fuel project, while an aggressive type strategy in struggling strategy is essential for the centralized biogas production project. In order to encourage investors to adopt a positive and optimistic attitude towards the two projects, the public authorities have a role of guidance to ensure the mobilization of the social capital necessary for the construction of the projects. Finally, the results of the research recommend the implementation of a safeguarding strategy to promote the two modes. The first is to strengthen the capacity to design adequate guidance and support policies. Second, efforts must be made to innovate and promote technologies and business models in order to quickly remove barriers to their adoption. Third, improvements must be made in terms of financial incentives to increase the effectiveness of support funds. Fourth, stakeholder participation in the service structure must be established in order to clarify the responsibility of each role. [less ▲]

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See detailThe complex impact of temperature and carbon dioxide concentration on a multitrophic interaction involving aphids
Blanchard, Solène ULiege

Doctoral thesis (2020)

Global warming is now widely recognized in the scientific community. These changes are mainly caused by the increase of greenhouse gases, among which the carbon dioxide (CO2) is considered as a major gas ... [more ▼]

Global warming is now widely recognized in the scientific community. These changes are mainly caused by the increase of greenhouse gases, among which the carbon dioxide (CO2) is considered as a major gas. Recent studies showed that abiotic changes will impact the entire ecosystem, and more particularly multitrophic interactions, which are strongly dependent on their environment. In this study, we hypothezise that an increase of atmospheric CO2 concentration and mean temperature will impact the interactions between a plant, a pest aphid, the mutualistic ant of this aphid and its natural enemy, the hoverfly. Since organic volatile compounds are involved in these interactions, we first studied the impact of the two abiotic factors on their emission by two plants, Vicia faba and Triticum aestivum and evaluated the capacity of the plant to attract their pests, respectively Aphis fabae and Sitobion avenae. An elevation of temperature, whether or not coupled with CO2 impacted the volatile profiles of these two plant species as well as the concentration of particular compounds of the terpene and alcohol family. These modifications did not impact the foraging behavior of aphids, which indiscriminately located and selected plants grown under ambient or elevated conditions. During infestation, these volatile profiles evolved in the same way under the different climatic conditions. Secondly, we evaluated the impact of temperature on the mutualistic interaction between the aphid A. fabae and the ant Lasius niger. The mean temperature of 23°C estimated for the end of the 21th century reinforces this interaction, by an increase of ants flows and their collection of honeydew. These positive effects are more attenuated, and the balance of this interaction seems to weakened when one considers one of the most pessimistic climatic models with a 6°C increase (26°C). Aphid honeydew has a preponderant role in multitrophic interactions. The combination of temperature and CO2 concentration increases the honeydew production as well as its concentration in sucrose and melezitose, which are attractive to ants. On another hand, a high concentration of CO2 had an impact on the volatile profile of the honeydew, but these changes did not affect the oviposition behavior of the hoverfly Episyrphus balteatus, known to use honeydew volatiles, as well as the aphid alarm pheromone, to locate the most suitable sites for oviposition. Taken together, these results demonstrated that the predicted increase of temperature and CO2 concentration will have a significant influence on multitrophic interactions, but its understanding remains complex and challenging. [less ▲]

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See detailGenetic engineering of Yarrowia lipolytica for the production of thiol compounds from organic by-products
Do Thi Hoang, Diem ULiege

Doctoral thesis (2020)

Tripeptide glutathione (GSH), the most abundant non-protein thiol compounds in cells, plays an important role in many cellular mechanisms. GSH is also a biotechnology-oriented molecule with applications ... [more ▼]

Tripeptide glutathione (GSH), the most abundant non-protein thiol compounds in cells, plays an important role in many cellular mechanisms. GSH is also a biotechnology-oriented molecule with applications in medicine, food, and cosmetics. The GSH precursor, namely gamma-glutamylcysteine (γ-GC), has also shown its therapeutic potential. Y. lipolytica is a non-conventional yeast and is of interest as a cell factory for pharmaceuticals, food- and feed-related applications. In this thesis, we firstly improve the glutathione production in Y. lipolytica by overexpression of the endogenous biosynthetic genes GSH1 and GSH2, encoding γ-glutamylcysteine ligase (GCL) and glutathione synthetase (GS) enzymes, respectively. The strain was further engineered for the ability to metabolize carbon sources from organic wastes including glycerol, lactose, starch, and inulin. The glutathione overproducing strain with inulin-adapted metabolism showed the highest GSH productivity. During bioreactor culture, maximal productivity and yield from inulin were 510 μmol/gDCW and 626 mg/L, respectively. One of the main bottlenecks in glutathione overproduction is the feedback inhibition of the GCL enzyme by glutathione. Unfortunately, multicopy integration of the GSH1 gene did not overcome this bottleneck. As a second strategy to increase thiol accumulation, we focused on glutathione precursor γ-GC, a dipeptide that can substitute for GSH in some cell mechanisms. We firstly disrupted the GSH2 gene before overexpressing GSH1 in multicopy. The constructed strains showed an increase in intracellular thiol production as demonstrated by means of NMR and LC-QTOF/MS as well as thiol measurement in the cell extract. [less ▲]

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See detailCaractérisation de la diversité des stratégies conçues par les producteurs laitiers wallons : déterminants socio-économiques et dynamique d’adaptations face aux enjeux passés, présents et futurs
Dalcq, Anne-Catherine ULiege

Doctoral thesis (2020)

Agricultural producers are necessary for reasons of food security but they are subject to great economic, social and environmental issues, jeopardizing their continuity. More particularly, the European ... [more ▼]

Agricultural producers are necessary for reasons of food security but they are subject to great economic, social and environmental issues, jeopardizing their continuity. More particularly, the European dairy producers have recently experienced a big change of their economic and political context following the end of the dairy quota system. For the sustainability of the sector and what this implies for our society and our environment, it is interesting to know the development paths implemented, planned and considered by the producers facing these changes. This thesis studied these development paths from the point of view of the producers, who are the first to be impacted by these changes of context and the first actors of solutions needed to adapt and maintain a profitable activity. The actions and the opinions of the Walloon producers were studied using the technicoeconomic database of Elevéo as well as surveys conducted in 2014-2015 and 2020. The objectives of the thesis were (1) to study the strategies of the producers and the evolution of these strategies in a recent past, their planning from 2020 onwards and their consideration for an ideal future, (2) to study the link between these strategies and other information, reflecting the causes of these choices, the environmental considerations, the wishes for training and the quality of life of the producers, providing an insight of the determining factors and the sustainability of these strategies, (3) to study the relevance to adapt the management depending on the adopted strategy(ies). First, the level of intensification was measured in this thesis thanks to an index created on the basis of several variables related to feeding, coming from the technicoeconomic database. This index aims to provide a more complete and exact measure tool of intensification. Its evolution between 2007 and 2017 was measured per individual to highlight the evolution patterns. We observed that 27% of producers were having a constant evolution, 8% a linear positive tendency, 24% a quadratic evolution with a maximum in 2012, which was a year of dairy crisis. Secondly, just before the end of the dairy quota system (2014-2015), 3 strategies of production in the short term in post quota era were studied and concerned: the increase of the milk quantity produced, the alternative valorization of milk production and the diversification of the activities. We found out that, according to the survey, more than half of the producers (55%) have chosen the status quo in quantity of milk produced, nearly 40% the increase of the production, 10% the alternative valorization and 10% the diversification of the activities. This shows that alternative activities were seldom considered by the producers on the eve of an important change of the production framework, in contrast to the increase of the dairy production activity. Thirdly, the characteristics of the ideal farm of the future were studied throughout 7 strategies : intensive vs. extensive, specialized vs. diversified, weakly vs. strongly based on new technologies, management by an independent producer vs. by an association of producers, familial vs. salarial workforce, production of milk with a standard vs. differentiated quality, for the global vs. local market. From the multivariate analysis of the answers of the producers collected in the 2014-2015 survey, clusters between some characteristics were observed, leading to highlight two models of ideal future farm : the “Local-based extensive”(LBE) model and the “Global-based intensive” (GBI) model supported, respectively, by 26% and 46% of producers respondents. The producers were positioning themselves more or less strongly regarding these two extremes. Hence, a gradient of ideal future farm (IFF) between the model LBE and GBI was defined to express the tendency of a producer to consider a model or the other as ideal. Significant relationships were then observed between the IFF gradient and the variables related to the reasons of the choice of this model, the environmental considerations and the training. Thus, the producers tending to GBI or LBE model do not have the same environmental considerations and represent two different guests in terms of training paths and areas. Fourth, the producers with different production systems were selected to answer a survey concerning their quality of life. No significant relationship was observed between the variables linked to quality of life and their production profile, except for the mixed producers (i.e., having several activities on the farm, i.e., 3rd group that standed out of the variability of the surveyed producers) who showed some lower quality of life results and for the extensive producers who were better supporting the society perception of the agriculture. Thus, the farm model does not seem to impact the quality of life of the producers, except if they have several activities. Fifth, we studied the relevance to vary a management parameter in particular, the calving interval (CI), as a function of the feeding systems. Significantly different gross margins per cow were observed between the herds having different percentages of cows with short or long CI, inside the different feeding systems. This chapter allowed to understand the effects of feeding on the herd and the importance to take them into account to define the herd management that maximizes the economic results. Finally, all these results allowed to establish a temporal evolution of the strategies of dairy producers, to provide an overview of the sustainability of the two models of farm supported for the future and to draw a scenario of the causes leading to this choice. The survey of 2020, conducted in Wallonia, allowed to bring additional information regarding the points raised in this thesis, 5 years after the end of the dairy quota system. The results of this survey validate or record the evolution of the tendencies observed previously and show a change of strategy concerning the ideal future farm. Indeed, the current occurrence is that 49% of the producers are in favour of LBE model vs. 33% of GBI model. In conclusion, the strategies of dairy producers are multiple and have evolved these last years, in relation to the available resources, the mentality of the producers and the changing framework, whose major event was the end of the dairy quota system. The occurrence of the producers between LBE and GBI is important to know given their economic, social and environmental sustainability. Thus, in order to build a suitable framework for the dairy activity for the next years and generations, this information must be taken into account by all the actors on the ground. [less ▲]

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See detailHow to finance agricultural activities in mountainous areas of Viet Nam? A case study in Lao Cai province
Bui Thi Lam, ULiege

Doctoral thesis (2020)

In the Northern Midlands and Mountains (NMM) region, the agricultural sector plays an essential role in the local economy because it is the main livelihood of the majority of the rural population. Among ... [more ▼]

In the Northern Midlands and Mountains (NMM) region, the agricultural sector plays an essential role in the local economy because it is the main livelihood of the majority of the rural population. Among the factors influencing agricultural development, capital/financing has been becoming increasingly important because it affects the inputs used, investment in fixed assets, and the application of advanced technology. Unfortunately, the NMM region is the poorest area of the country, therefore, almost farmers here lack of capital to finance their agricultural production. This explains the reason why they still remain to be stuck in the cycle of chronic poverty: low investment, low productivity, low income. Moreover, several recent empirical studies reveal that agribusiness and other agriculture-based actors in Viet Nam also face with financial shortages. This study, therefore, examines financial demands of farmers and other farming actors in Lao Cai province as well as their constraints to access affordable credit to finance agricultural activities, and then, suggests feasible recommendations to increase funds to agriculture in the research site. In this study, we approach the agricultural financial markets in Lao Cai province based on financial supply-side and demand-side analysis. On the supply side, 24 in-depth interviews with financial providers about their agricultural credit provision were conducted. On the agricultural finance demand side, we study two subclasses: (i) agricultural production by local farmers and (ii) the Seng Cu (SC) rice value chain, including production, processing, and consumption activities. At the general level, agricultural production, the study surveyed 193 farm households to determine their financial needs and their actual access to credit for agricultural investments. At the agricultural value chain financing analysis, we conducted 160 SC rice producers and 31 chain actors (small collectors, large collectors, and retailers). In addition, two econometric models are applied to determine the factors affecting the results of banking credit application of households; and, the influence of internal and external financing on SC rice production. Our findings show that the financial sources for agricultural activities are diverse: formal sector (two state-owned banks: VBARD and VBSP); semi-formal sources (Farmers’ Union, Women's Union); informal actors (moneylenders, friends, relatives), and direct Government’s subsidies (Program 135, 30A and World Bank’s Project). Compared to other financial providers, VBARD and VBSP have many advantages related to loanable funds, transaction points, and low-interest credit. However, credit provision of banks likely creates credit constraints to local farmers. Specifically, VBARD just devoted a small proportion (18.3%) of credit volume to farmers. In addition, VBARD’s and VBSP’s decision-making on disbursement strongly depends on assessments of local authorities, it is sometimes distorted by nepotism. In addition, credit services in terms of duration and repayment methods are not much improper, compared to clients’ demands. The survey of 193 farm households shows that a large proportion (84%) of the households have high credit demand because their own capital is not enough to finance their agricultural activities. Among farmers applied a loan at banks, 48% of them received nothing or smaller loans than their desires. They are mainly small and medium farmer households. Using the Multinomial Logistic Model (MLM), the study points out determinants of credit access of households: (i) lack of collateral; (ii) lack of good relationships with local authorities involved in application screening, (iii) low human capital (education/ethnicity). Difficulties in formal credit access, these farmers often fall into the following three actions: 1) reduce investment in agriculture; 2) using a large proportion of self-produced and low-quality inputs; and/or, 3) borrow money from informal lenders at very high interest rates. All these actions make agricultural production inefficient and undermine farmers’ income. Arguably, although they are the beneficiaries of the preferential credit policy, they are often excluded from the formal credit market, which leads them still to be stuck in a vicious cycle of chronic poverty. Likewise, the majority of actors participating in the SC rice value chain had high specific financial needs. SC rice growers received high-quality inputs and technical assistance from the input supplier (JVC) and the purchasing enterprise (TPC), which help them to reduce diseases, price, and market risks. Besides the advantage of SC rice's selling retail price, the linkages between chain actors contributed to the great potential of this value chain. However, banks still maintained the strict risk-avoidance strategy, which strongly depends on collateral of individual chain actors, not the entire chain. As a result, almost chain actors received lower-than-expected loans from banks, especially SC rice growers in uplands and TPC. From the above research results, we can conclude that improving banks’ efficiency in credit provision and banks’ participation in the chain are the first steps to improving the agricultural finance system in the research site. In addition, farmers and other chain members need to improve their production capacity and financial management in order to be assessed creditworthy by the bank. In addition, it is necessary to enact new legal regulations from the Government to encourage value chain financing models nationwide and to support the infrastructure system in mountainous areas. The coordination among four key players: producers, businesses, banks, and the public sector is a comprehensive solution for agricultural finance in the research site. [less ▲]

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See detailStudy of the pathogenesis of Usutu virus infection in ovo and in vivo
Benzarti, Emna ULiege

Doctoral thesis (2020)

Usutu virus (USUV) is a mosquito-borne flavivirus, closely related to the West Nile virus (WNV). Similar to WNV, USUV may cause infections in humans, with occasional, but sometimes severe, neurological ... [more ▼]

Usutu virus (USUV) is a mosquito-borne flavivirus, closely related to the West Nile virus (WNV). Similar to WNV, USUV may cause infections in humans, with occasional, but sometimes severe, neurological complications. Further, USUV can be highly pathogenic in wild and captive birds and its circulation in Europe has given rise to substantial avian death. Adequate study models of this virus are still lacking but are critically needed to understand its pathogenesis and virulence spectrum. In this thesis, we used natural infection cases and experimentally infected animals (chicken embryos, canaries and immunocompetent mice) to fill some gaps in our knowledge regarding the pathogenesis and epidemiology of USUV in Belgium. [less ▲]

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See detailInsight into the role of Dual Specificity Phosphatase 3 in non-alcoholic fatty liver disease and insulin resistance
Jacques, Sophie ULiege

Doctoral thesis (2020)

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in Western countries. It encompasses a broad spectrum of liver conditions ranging from simple steatosis to the more ... [more ▼]

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in Western countries. It encompasses a broad spectrum of liver conditions ranging from simple steatosis to the more severe and progressive disease, non-alcoholic steatohepatitis (NASH) that can lead to hepatocellular carcinoma (HCC). Obesity and related metabolic syndrome and insulin resistance are important risk factors for the development of NAFLD, NASH and HCC. We investigated the impact of DUSP3 deficiency in metabolic syndrome manifestations and in HCC using a knockout (KO) mouse model. While aging, DUSP3-KO mice became obese and exhibited insulin resistance. These phenotypes were exacerbated under HFD and were accompanied by NAFLD and associated liver damages. In addition, DEN administration combined to HFD led to a rapid HCC development compared to WT mice. DUSP3-KO mice had more serum triglycerides, cholesterol, AST and ALT than control WT mice under both regular chow diet (CD) and HFD. The level of fasting insulin was higher compared to WT mice, though, fasting glucose as well as glucose tolerance were similar to those of control mice. At the molecular levels, HFD led to a decrease of DUSP3 expression at both protein and RNA levels. Under CD, DUSP3 deletion was associated with increased phosphorylation of the insulin receptor (IR) and subsequently, with higher activation of the downstream signaling pathway. The difference of IR phosphorylation was maintained between mutant and WT mice under HFD. However, IR downstream signaling pathway was equally activated in both groups of mice. Liver RNA sequencing and differential expression genes analysis demonstrated the effect of the diet on the expression of several genes, including genes from lipid metabolism. Gene set enrichment analysis highlighted pathways specifically regulated in DUSP3-KO mice, such as fatty acid metabolism and DNA repair pathways. Collectively, our results support a new role for DUSP3 in obesity, insulin resistance, NAFLD and liver damage. [less ▲]

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Picavet, Pierre ULiege

Master of advanced studies dissertation (2020)

Disposer de matériaux de greffe afin de combler les déficits osseux d'origine traumatique ou néoplasique a toujours été une préoccupation dans le domaine de la chirurgie orthopédique vétérinaire et ... [more ▼]

Disposer de matériaux de greffe afin de combler les déficits osseux d'origine traumatique ou néoplasique a toujours été une préoccupation dans le domaine de la chirurgie orthopédique vétérinaire et humaine. Les xénogreffes sont couramment utilisées en raison de leur grande disponibilité, même si les greffes osseuses autologues sont toujours considérées comme la référence en pratique clinique malgré de nombreuses limitations. Des recherches approfondies sont actuellement en cours au sujet de matériaux synthétiques et biomatériaux dont les performances in vivo sont étudiées avec des modèles chez les animaux pour combler un déficit osseux de taille critique. Le bois de cerf est une structure osseuse primaire facile à collecter et qui pourrait servir de xénogreffe. Cette étude examine le comportement de cylindres d’os spongieux de bois de cerf élaphe comblant un déficit osseux spongieux de taille critique chez le lapin et évalue l’effet de protocoles de décellularisation. Onze lapins de Nouvelle-Zélande blancs en bonne santé âgés de 6 à 7 mois avec un poids moyen de 4,2 kg ont été utilisés. Des cylindres (10x4,8mm) en os spongieux en bois de cerf avec une porosité de 42,1% ± 0 ,9 ont été implantés dans des conditions aseptiques dans l'épiphyse fémorale distale bilatéralement. Pour évaluer le rôle des protéines et des lipides, deux régimes de préparation (A et B) de la xénogreffe ont été utilisés. Les radiographies ont été prises immédiatement après la chirurgie et juste après l'euthanasie 12 semaines après l'implantation. L'évaluation histologique a été réalisée sur des coupes non décalcifiées de 10 microns avec un protocole de coloration picro-fuchsine van Gieson. Une région d'intérêt a été définie pour chaque coupe histologique, évaluant la réaction inflammatoire, le processus de fibrose et l’ostéogenèse. Chaque section histologique a finalement été microradiographiée pour évaluer le contact osseux, la présence de synostose, les processus de remodelage et d'ossification. Tous les cylindres de bois ont été implantés avec succès et tous les lapins se sont bien remis de la chirurgie sans signes d’ostéomyélite. L'analyse radiographique finale a démontré l'ostéointégration de la plupart des implants à différents stades. Une réaction inflammatoire légère à modérée autour des greffons fut notée à l’histologie, avec un seul cas montrant une encapsulation complète. Un degré d'intimité variable entre l'implant et l'os hôte a été mis en évidence à la microradiographie, avec un remodelage osseux et une nouvelle ostéogenèse d'intensité variée présents dans tous les sites implantés. De façon surprenante, la présence ou l'absence de lipides et de protéines dans les greffons ne semble pas avoir d'importance. Les protocoles de décellularisation et de stérilisation pourraient être incriminés. Bien que présentant plusieurs limites, cette étude montre des résultats prometteurs justifiant des investigations supplémentaires. [less ▲]

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See detailCharacterization of Vietnamese microalgae strains for aquaculture wastewater treatment and biomass valorization
Luu Thao Nguyen, ULiege

Doctoral thesis (2020)

The study aims to isolate microalgal strains from shrimp – farm wastewater and select some of them suitable for production of biomass, biodiesel and other valuable products. We have isolated 4 isolates ... [more ▼]

The study aims to isolate microalgal strains from shrimp – farm wastewater and select some of them suitable for production of biomass, biodiesel and other valuable products. We have isolated 4 isolates, namely NL3, NL4, NL6 and NL12. The four isolates were preliminarily identified using molecular techniques based on partial sequence of 18S rRNA gene and classified into four different genera belonging to two phyla, Desmodesmus, Chlorella, Nannochloris (Chlorophyta) and Nannochloropsis (Eustigmatophyta). They were subjected to characterization in terms of growth, protein content, pigment and fatty acid content and profiles. As a result, isolates NL3 and NL6 were chosen for the project. The two strains were further identified based on the whole sequence of 18S rDNA – ITS1-5.8S-ITS2. Isolate NL3 was identified as Desmodesmus sp. NL3, which is proposed to be a new species with two group I introns (S516 and S1046) while isolate nl6 was 100% identical to Nannochloropsis salina (D12, accession number JX185299.1) from Shandong in China, so named Nannochloropsis salina NL6. Those two strains were further characterized in terms of growth, protein, pigment, fatty acid profiles and salinity tolerance (10‰, 20‰, 30‰ and 35‰). The two strains are tolerant to the different salinities studied. Nannochloropsis salina NL6 was characterized by a high percentage of fatty acids (40% DW at the end of exponential phase) and a fatty acid profile suitable for biodiesel production. Desmodesmus sp. NL3 was characterized by high protein (40% DW), biomass (1.54 g/L), and lutein (7 mg/g DW) contents at the end of the exponential phase. Notably, Nannochloropsis salina NL6 (N. salina NL6) was able to produce eicosapentaenoic acid (EPA) and astaxanthin. Their performance on the production of these compounds did not change much across the four salinities. The two strains, therefore, fit the project goals. [less ▲]

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See detailTemperature-induced sex reversal in Nile tilapia (Oreochromis niloticus): consequences on the brain, behavior and sound production
Dussenne, Mélanie ULiege

Doctoral thesis (2020)

As opposed to the fixed mechanism of sex determination of endotherms, the sex determination system of poikilotherms is variable and can depend (partially or totally) on environmental parameters, mainly ... [more ▼]

As opposed to the fixed mechanism of sex determination of endotherms, the sex determination system of poikilotherms is variable and can depend (partially or totally) on environmental parameters, mainly temperature. In fish, high temperature generally drives masculinization of the progenies independently from their genotype, creating individuals presenting a mismatch between their genotype and phenotype. Nile tilapia (Oreochromis niloticus) is a cichlid species presenting a male heterogamety (XY/XX). If temperature is superior to 32°C during the period of sex differentiation, genetic XX progenies are masculinized into XX “neomales”. In adulthood, these neomales sire 100% female progenies that can in turn be masculinized if temperature allows so. This process is naturally relevant, as neomales have been described in the wild. Indeed, climate change could increase the frequency of sex reversals, eventually leading to the decline of a population. As Nile tilapia is a species of high value in aquaculture, sex reversal has been investigated mainly through hormonal treatments. Consequently, few data are available on temperature-induced sex reversed individuals and the consequences in adulthood are unknown. This thesis aimed at determining the consequences of temperature-induced sex reversal via two main axes of research whose goals were to: 1. Investigate the influence of sex reversal on testis maturation and physiology, and on two neuronal populations: the gonadotropin-releasing hormone (GnRH) neuron population and the arginine-vasotocin (AVT) neurons populations (each divided into three subpopulations). These were specifically chosen because they are sexually different and are implicated in the regulation of socio- sexual behaviors. We found that neomales present a reduced number of GnRH1 neurons compared to both XY males and females. Surprisingly though, neomales present the same characteristics regarding testis maturation and hormone secretion (testosterone, 11-ketotestosterone, 17β-estradiol) as XY males. As GnRH1 neurons stand at the apex of the hypothalamo-pituitary-gonadal (HPG) axis, we formulated several hypotheses regarding a potential compensation mechanism that could take place at the three functional levels of this HPG axis. Neomales also presented differences in the number and area of AVT neurons compared to XY males and females, which we hypothesized to be linked with an increased risk to adopt a subordinate behavior, probably reflected in high cortisol circulating concentrations. 2. Investigate the consequences of sex reversal on behavior. The hypothesis regarding neomales subordination could be directly tested. We compared the behavior of neomales and XY males in agonistic interactions, as well as other parameters (size of the nest, hormone concentration, sound production). During dyadic confrontations, neomales present a higher aggression level compared to iii XY males, but almost always end up being subordinate. In this context, sound production seemed unnecessary. We also investigated if neomales were as attractive as XY males for gravid females. These females do not prefer any type of male, even though neomales are once again extremely aggressive. When next to a female, both male types emitted sounds that differed in duration and number of pulses. Surprisingly, no difference could be detected regarding hormone circulating concentrations (testosterone, 11-ketotestosterone, cortisol) in both contexts between the two male types. Interestingly, neomales were found to build smaller nests than XY males only when housed with a XY male. Overall, our results suggest that the sex chromosomes and/or the sex reversal procedure impacted the brain of neomales in a long-lasting manner. Neomales, presenting different brain characteristics than XY males in a region implicated in the integration and treatment of various internal/external informations, would react differently than XY males to the same stimuli. [less ▲]

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See detailSocial sustainability assessment in the biobased economy
Rafiaani, Parisa ULiege

Doctoral thesis (2020)

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See detailInvestigating the effects of plants and their root exudates on PAHs bioaccessibility to soil microorganisms and their impact on aged-contaminated brownfields remediation.
Davin, Marie ULiege

Doctoral thesis (2020)

In Wallonia, there are 6,000 estimated brownfields (rising to over 3.5 million in Europe) that require remediation. Polycyclic aromatic hydrocarbons (PAHs) are persistent organic compounds of major ... [more ▼]

In Wallonia, there are 6,000 estimated brownfields (rising to over 3.5 million in Europe) that require remediation. Polycyclic aromatic hydrocarbons (PAHs) are persistent organic compounds of major concern that tend to accumulate in the environment, threatening ecosystems and health. They represent 17% of all encountered pollutants. The thesis, articulated around several axes, focused on improving less aggressive PAHs remediation techniques in brownfields, such as bioremediation and phytoremediation, as alternatives to environmentally aggressive, expensive and often disruptive current soil remediation strategies. More specifically, it was built on several authors' observation that PAHs soil contents decrease in the presence of plants. The hypothesis was made that this could be related to the production of plant root exudates. A bioaccessibility measurement protocol was adapted to two brownfield soils using Tenax® beads in order to compare PAHs bioaccessibility in soil samples. In both experimental soils, PAHs desorption kinetics were established, described by site distribution models, and common extraction times were calculated (respectively 48 h and 24 h for both experimental soils). The potential of saponin (a natural surfactant) as extracting agent and as a bioremediation enhancer on an aged-contaminated soil was investigated. In a first experiment, soil samples were extracted with saponin solutions (0; 1; 2; 4 and 8 g L-1). In a second experiment conducted in microcosms (28°C), soil samples were incubated for 14 or 28 days in presence of saponin (0; 2.5 and 5 mg g-1 DW). CO2 emissions were monitored throughout the experiment. After the incubation, dehydrogenase activity was measured as an indicator of microbiological activity, and the bioaccessible and residual PAHs contents were determined. The 4 g L-1 saponin solution globally extracted significantly more PAHs than water. Neither PAHs dissipation nor bioaccessibility were enhanced in presence of saponin compared to control samples after 28 days. However, CO2 emissions and dehydrogenase activities were significantly more important in presence of saponin, suggesting no toxic effect of this surfactant towards soil microbiota. The role of two Fabaceae (Medicago sativa L. or Trifolium pratense L.) root exudates in enhancing PAHs bioaccessibility and dissipation in an aged-contaminated soil was investigated during an incubation experiment (28°C). The CO2 emissions were significantly higher in presence of T. pratense exudates; the dehydrogenase activities (measured after 14 and 28 days) showed improvements of the soil microbial activity in presence of both types of root exudates compared to untreated soil samples; the PAHs residual contents decreased more in untreated samples than in the presence of T. pratense exudates; and M. sativa exudates lowered PAHs bioaccessibility but not residual contents. The effects of Medicago sativa L. and Trifolium pratense L. on the PAHs’ bioaccessibility and dissipation in an aged-contaminated soil throughout a rhizoremediation trial were investigated. The bioaccessible and residual PAH contents were quantified after three, six and twelve months of culture. The rhizoremediation results show that M. sativa developed better than T. pratense on the contaminated soil. When plants were absent (control) or small (T. pratense), the global PAHs’ residual contents dissipated from the rhizosphere to 8% and 10% of the total initial content, respectively; in the presence of M. sativa, dissipation after 12 months was only 50% of the total initial content; and the PAHs bioaccessible content increased more significantly in the absence of plants. Finally, a review of three scientific trends that lead PAHs contaminated soils/sediments remediation studies and management was conducted. (i) The choice of PAHs compounds that are being studied and targeted in scientific literature were discussed, and it was suggested that the classical 16 PAHs from the American Environmental Protection Agency’s (US-EPA) watch list might no longer be sufficient to meet actual environmental challenges. (ii) The choice of experimental material in remediation studies was discussed. Bibliometric measures were used to show the lack of PAHs remediation trials based on co-contaminated or aged-contaminated material. (iii) The systematic use of the recently validated bioaccessibility measurement protocol (ISO/TS 16751:2018) in remediation trials was discussed, and it was suggested that such measurement should be implemented as a tool to improve remediation processes and management strategies. [less ▲]

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See detailWorking mechanisms of inulin concerning intestinal mucosal immunity and microbiota in chickens infected with Salmonella Enteritidis
Song, Jiao ULiege

Doctoral thesis (2020)

Salmonella, one of the most common foodborne pathogens, is a concern for human health, contaminates poultry and egg products, and causes huge economic losses to the poultry industry. The gut of chicken ... [more ▼]

Salmonella, one of the most common foodborne pathogens, is a concern for human health, contaminates poultry and egg products, and causes huge economic losses to the poultry industry. The gut of chicken contains mechanical, immune, chemical, and microbial barriers, and is an important digestive, immune, and endocrine organ. Salmonella Enteritidis (SE) damages the intestinal epithelial cells structure, mucosal immunity, and microbial composition. Because of the emergence of antibiotic resistance, the development of dietary alternative strategies to reduce the susceptibility of SE colonization should be a priority. It has been previously concluded that prebiotics, such as inulin, can improve the overall health by providing an intestinal environment that is unfavourable for foodborne pathogens such as Salmonella. The aims of the research described in this thesis are to (1) select an optimal inulin supplementation dosage that optimizes the intestinal mucosal morphology and immune status of specific pathogen-free (SPF) chickens; (2) investigate whether optimal inulin supplementation dosage improve the mechanical, immune, and chemical barriers in JAK–STAT signalling in intestinal mucosal tissue at 1 and 3 days post-infection (dpi) in SE-infected SPF chickens; and (3) investigate whether inulin alter the microbial composition and function of SE-infected SPF chickens. In the first trial, we determined the optimum level of inulin supplementation for effectiveness in the gut. The mucosal morphology and immune indexes of SPF chickens that fed a basal diet supplemented with 0, 0.25, 0.5, 1.0, or 2.0% inulin were analyzed on days 7, 14, and 21, respectively. The results showed that the SCFA concentrations in the cecum and serum were increased by dietary inulin supplementation at 21 d. The mucosal morphology was improved in the duodenum and ileum of SPF chickens fed inulin. Also, inulin at a low concentration (0.25% or 0.5%) significantly decreased the gene expression of NF-κB and LITAF at 7, 14, and 21 d, and of IL-6 and iNOS at 7 and 14 d; and increased that of MUC2 and claudin-1 in the ileum of SPF chickens at 7, 14, and 21 d. The results indicated that the effects of inulin on mucosal immune function occurred in a dose-dependent manner. A low inulin concentration (0.25% or 0.5%) may be beneficial in promoting intestinal immune function. In the second trial, we investigated whether and how inulin administration influenced the intestinal barrier function and mucosal immunity with SE infection. A control group (CON) chicken fed a basal diet and three SE-infected groups fed a basal diet supplemented with inulin 0% (SE), 0.5% (0.5% InSE), and 1% (1% InSE), respectively. Until 28 d of addition, chickens in the four groups were orally infected with SE or vehicle (phosphate-buffered saline). The SE challenge significantly increased the mucosal gene expression of proinflammatory cytokines and serum concentrations of antibodies, but significantly decreased the gene expression of MUC2 and claudin-1 compared with the CON group. However, Inulin supplementation reversed these gene expression and relieved the injury of duodenum, jejunum, and ileum at 1 and 3 dpi within the SE-challenged groups. The SE challenge significantly increased ileal protein expression of p-STAT3 and JAK1 at 3 dpi compared with the CON group, while inulin supplementation suppressed p-STAT3 and JAK1 protein expression at 3 dpi compared with the SE group. The results showed that inulin alleviated SE-induced gut injury by decreasing the pro-inflammatory response and enhancing mucosal immunity in chickens. In the third trial, the impact of inulin on SCFAs, microbial composition, and microbiome functions of SPF chickens infected with SE were investigated. The SE infection led to significantly decreased cecal butyrate concentrations compared with the CON group, and inulin supplementation reversed these changes. SE infection significantly decreased the alpha diversity, while inulin supplementation significantly increased the alpha diversity and richness. At the phylum level, Inulin addition at 1% increased abundance of Firmicutes and decreased abundance of Bacteroidetes compared with the SE group according to the Student’s t-test. The correlations of the microbiota genera with metabolite SCFA contents showed that SCFA-producing bacteria had positive correlations with acetate and butyrate contents. Analysis of the functional capacity in cecal microbiome at pathway level 2 showed that inulin supplementation at 0.5% and 1% reversed the abundance of KEGG pathways and KOs in SE infected chickens. In short, SE infection decreased the alpha diversity of cecum microbiota and SCFA contents, and accordingly increased the abundance of KEGG pathways and KOs related to nutritional and energy metabolism, whereas inulin addition reversed these changes and had inhibitory effects on SE infection. The results of the above three experiments indicate that SE caused the rapid induction of pro-inflammatory cytokines and changes in gut morphology, gut microbiome, microbial functional activities, and SCFA production, which resulted in activation and normalization of the immune system in the bird’s early life. However, the intestinal parameters and SCFA concentration were altered by inulin in a dose-dependent manner. The 0.5% inulin relieved the intestinal inflammatory environment and injury induced by SE infection through the JAK–STAT signaling pathway and the changes of SCFA-producing bacteria composition and function. As a whole, these observations may lead to the development of novel prevention and control strategies of Gram-positive bacterial infections with prebiotic administration in chickens and may even be applicable to other animal species. Moreover, determining the role played by inulin in gut microbiota-driven pathways using metagenomics approaches further elucidated how prebiotics contribute to the gut microbiota combating pathogen infection. [less ▲]

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See detailSimulation du rendement en maïs grain à Lubumbashi, République Démocratique du Congo
Banza Mukalay, John ULiege

Master of advanced studies dissertation (2020)

Face à l’insécurité alimentaire et la démographie galopante, la production agricole doit augmenter de manière significative pour combler les besoins alimentaires des populations. Le recours aux modèles de ... [more ▼]

Face à l’insécurité alimentaire et la démographie galopante, la production agricole doit augmenter de manière significative pour combler les besoins alimentaires des populations. Le recours aux modèles de prédiction de rendement agricole à l’échelle locale ou nationale constitue actuellement une stratégie et garantie pour la sécurité alimentaire. Dans cette étude, le modèle AquaCrop de la FAO a été utilisé pour simuler le rendement en maïs grain dans le contexte agroécologique de Lubumbashi, République Démocratique du Congo. Il s’agit d’un modèle basé sur la productivité eau-sol-plante nécessitant des données météorologiques, culturales et de sol. L’étude a été menée à la ferme Ubuntu pour la campagne agricole 2016-2017. Les données climatiques de la base des données satellitaires de la NASA, les fonctions de pédotransfert (FPT) pour les données manquantes du sol et les données de trois variétés de maïs réparties dans 7 blocs ont été utilisées dans le modèle. L’indice de végétation NDVI a été effectué pour apprécier la couverture végétale des blocs. Les résultats montrent, sur la description climatique du site pour les années 2016 et 2017, des valeurs qui sont restées dans la gamme enregistrée dans la région de Lubumbashi pour toutes les variables observées. L’évaporation de référence montre une moyenne de 6,35 mm/jour au cours des années 2016 et 2017 avec un maximum de 8,73 mm/jour et un minimum de 1,29 mm/jour. Néanmoins, aucun stress hydrique n’a été observé sur les plantes au cours de la culture. Les rendements en maïs grains dans le site ont varié entre 4,1 et 9,73 t/ha. Le bloc F avec la variété SC719 a donné le rendement le plus élevé et le bloc I avec la variété PAN 53 le plus faible. Ces rendements augmentent relativement avec la teneur en matière organique du sol. Les résultats de FPT révèlent une densité apparente des sols variant entre 1,42 et 1,58 g/cm3 et la réserve en eau utile entre 1,06 à 1,57 mm/cm dans les blocs. L’analyse de NDVI a révélé la couverture végétale de chaque bloc au cours de la culture. La fonction logarithmique de stress de fertilité développée en fonction de la matière organique montre, un coefficient de corrélation faible ce qui implique une étude expérimentale ultérieure qui permettrait mieux de clarifier cette observation. Les résultats des simulations des rendements en maïs grain avec AquaCrop montrent des valeurs très proches entre les rendements mesurés et simulés (R2 = 0,94 et l’erreur moyenne de prédiction Pe = 14%). Les rendements potentiels varient entre 13,17 et 14,6 t/ha. Le stress de fertilité de sol est à la base des faibles rendements obtenus. Cette étude constitue une approche robuste pour accroître le rendement et pour optimiser les stratégies des gestions des champs à l'échelle locale ou nationale. [less ▲]

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See detailLa fluorescence chlorophyllienne associée aux composés phénoliques des feuilles pour évaluer le statut azoté de la biomasse de la pomme de terre
Ben Abdallah, Feriel ULiege

Doctoral thesis (2020)

Interroger la plante pour en déterminer son statut azoté est la stratégie utilisée en cours de saison pour le raisonnement de la fertilisation azotée des cultures de plein champ. L’établissement d’une ... [more ▼]

Interroger la plante pour en déterminer son statut azoté est la stratégie utilisée en cours de saison pour le raisonnement de la fertilisation azotée des cultures de plein champ. L’établissement d’une méthode de référence permettant l’évaluation du statut azoté en culture de pommes de terre a nécessité d’établir, en première étape, la courbe critique de dilution de l’azote (N) en Belgique pour la variété Bintje et d’en déduire l’indice de nutrition azotée (INN). L’INN est l’indicateur de référence reconnu pour l’évaluation du statut azoté d’une culture en cours de saison. L’INN a permis de définir l’optimum azoté de la culture pour assurer la production et le maintien d’un couvert végétal optimal nécessaire à l’obtention du rendement maximum en tubercules. Cependant, cette méthode de référence est basée sur un échantillonnage intrusif et donc laborieux et consommateur de temps qui rend son application à l’échelle du champ difficile à mettre en œuvre. Dans ce cadre, des méthodes optiques rapides sont souvent utilisées en cours de saison culturale pour l’évaluation du statut azoté en culture de pommes de terre de plein champ. Afin de remédier aux limitations des méthodes optiques usuellement utilisées en plein champ et qui reposent sur l’estimation de la teneur en chlorophylle des feuilles (limitations liées à la saturation des mesures, au retard ou au défaut de détection par rapport à l’entrée réelle en carence azotée et au manque de spécificité des mesures vis-à-vis de l’N), une nouvelle approche a été étudiée pour l’évaluation du statut azoté en culture de pommes de terre. Cette approche est basée sur la signature de la fluorescence chlorophyllienne (ChlF) pour l’estimation de la teneur en composés phénoliques des feuilles, plus spécifiquement les flavonoïdes. Les potentialités des mesures de la ChlF des feuilles ont été évaluées par comparaison avec des mesures optiques sur le feuillage en cours de saison durant trois années (2012, 2013 et 2014) pour deux variétés de pommes de terre cultivées en Belgique (Bintje et Charlotte) et recevant des doses croissantes de fumure azotée. Les résultats indiquent que les mesures de ChlF basées sur l’estimation des flavonoïdes comme indicateurs foliaires du statut azoté de la culture, et combinés à la teneur en chlorophylle des feuilles, sont les plus pertinentes pour l’évaluation du statut azoté comparativement aux mesures de transmittance ou de réflectance. Les potentialités des mesures de la ChlF mises en évidence pour l’évaluation du statut azoté en culture de pommes de terre sont i) la sensibilité de réponse tout particulièrement en couplant les indicateurs flavonoïdes aux indicateurs chlorophylle, ii) la précocité de détection de la déficience en N (liée à l’accumulation des flavonoïdes suite à une déficience en N), et iii) l’exactitude (justesse et répétabilité) des mesures des indicateurs combinés pour l’évaluation de teneur en N au niveau de la plante. La principale limitation pointée au niveau de ce travail de recherche est la faible spécificité des indicateurs foliaires qui ne sont pas exclusivement reliés à la fourniture en N. Les indicateurs foliaires testés sont en effet sensibles à d’autres facteurs externes tels que la variété, l’année d’expérimentation et la date de mesure. En travaillant avec les valeurs relatives des mesures par la prise en compte d’une fenêtre de référence (soit une fenêtre sans apport d’N, soit une fenêtre surfertilisée), la limitation liée à la spécificité des mesures est atténuée comparativement aux valeurs absolues. Les mesures analytiques des feuilles de pommes de terre récoltées ont confirmé que la déficience en N induit l'accumulation des composés flavonoïdes foliaires et plus précisément de la sous-classe des flavonols. La teneur totale en flavonols mesurée pour Bintje, identifiée comme composée de la rutine, de la quercétine et du kaempférol-3-rutinoside, a été corrélée aux mesures de ChlF en relation avec le statut azoté de la culture. Cependant, l'identification et la quantification d'autres composés spécifiques de la sous-classe des flavonols dont l’accumulation est liée au statut azoté de la culture n’ont pas été possibles au niveau de ce travail de thèse, en particulier pour la variété Charlotte. En conclusion, les mesures de ChlF liées à l’estimation de la teneur en flavonoïdes (en particulier la sous-classe des flavonols) combinés à la teneur en chlorophylle sont prometteuses pour l’évaluation en cours de saison du statut azoté de la culture de pommes de terre. En raison de la faible spécificité tant de la chlorophylle que des flavonoïdes pour l’évaluation du statut azoté, il est préconisé pour la mise en œuvre de ces indicateurs de travailler avec les valeurs relatives des mesures plutôt qu’avec leurs valeurs absolues. [less ▲]

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See detailCregNET: Meta-Analysis of Chlamydomonas reinhardtii Gene Regulatory Network
Pham, Cam Ngoc ULiege

Doctoral thesis (2020)

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See detailBehavioral flexibility and ecological impact of opportunist northern pigtailed macaques (Macaca leonina) in a degraded environment of Thailand: Ranging pattern, foraging strategies and seed dispersal
Gazagne, Eva ULiege

Doctoral thesis (2020)

Southeast Asia experiences exceptionally high anthropogenic pressure, due to rapid human population growth. The resulting primary tropical forest loss and conversion to agricultural lands, plantations ... [more ▼]

Southeast Asia experiences exceptionally high anthropogenic pressure, due to rapid human population growth. The resulting primary tropical forest loss and conversion to agricultural lands, plantations, and infrastructures, are the driving forces leading to a massive tropical biodiversity crisis. The last remaining old-growth forests have been converted into archipelagos of forest fragments, rapidly becoming degraded. Animal and plant populations are directly threatened by degradation of forest structure, as well as distribution, quality and availability of forest resources, which ultimately modify overall ecosystem functionalities. One key feature is the extirpation of many large-bodied frugivores, the first affected by habitat degradation with a reduced fruit availability and an increased hunting pressure. Primates are particularly vulnerable to these threats, and nearly 84% of all Southeast Asian primate species are currently threatened with extinction. Only a few flexible and generalist species, such as macaques, are able to survive in human-modified landscapes. However, the way they respond to habitat degradation is not well understood yet, especially when it comes to skittish species. Since they are among the major seed-dispersal agents and play crucial roles in forest regeneration and maintenance, primates’ disappearance could result in detrimental long-term effect on tropical forest biodiversity. The omnivorous and opportunist northern pigtailed macaque (Macaca leonina) is an effective large-seed disperser, contributing to the tropical rainforest succession. However, very little is known about its ecology and behavioral response to habitat degradation. In order to understand how macaques adapt their movement ecology, ranging patterns, sleeping site selection, diet and foraging strategies under conditions of degradation, we studied the species in a degraded forest fragment within the old-growth Acacia and Eucalyptus plantations of the Sakaerat Biosphere Reserve (Sakaerat, hereafter), Northeastern Thailand. We concomitantly studied macaques’ generated seed shadow (i.e. the seed deposition pattern of a plant population) and their role as seed dispersers for potential forest regeneration. To do so, we followed a large wild-feeding troop of northern pigtailed macaques inhabiting Sakaerat for a 20-month period and collected eco-ethological data in regards to resource availability. We first habituated the troop of macaques to the observer’s presence and analyzed the habituation process over time. Based on the number of encounters, contact duration with the studied troop, and behavioral responses to the observer, we brought statistical evidences of the habituation progress over five stages: early, minimal, partial, advanced, and full. The complete habituation process took nearly thirteen months. Reduced native fruit availability in this degraded forest fragment, macaques’ limited experience of human contact, and their fission-fusion social dynamics, may explain the lengthiness of the process. Second, we investigated sleeping site selection patterns of northern pigtailed macaques over a period of 14 months by testing the hypotheses of random selection, predation avoidance, and food proximity. We identified a total of 107 sleeping sites with a low rate of reuse (N = 15 reused sleeping sites). Macaques sleeping sites were characterized by a low availability of large and tall trees and their selection pattern was not random: they slept more often in familiar areas, with a greater number of stems and a higher canopy height. These sleeping site characteristics were likely selected as an anti-predator strategy; however, food proximity also played a key role in sleeping site selection. Macaques often slept within or close to a feeding site, and selected their sleeping sites following food distribution. Third, we documented movement, ranging, and foraging patterns of northern pigtailed macaques based on 14 months of observation, and we used Hidden Markov Models (HMM) and Characteristic Hull Polygons to analyze these patterns in regard to fruit availability. Macaques’ home ranges encompassed a total of 599 ha and spanned through a natural dry-evergreen forest and a plantation forest. Our results showed that active foraging increased with higher native fruit availability, while macaques moved from foraging state to transiting to plantations and surrounding edge areas during periods of lower availability of native fruits. Accordingly, the macaques’ diet shifted from fleshy to dry fruits, such as the introduced Acacia species. Our results showed that the diet and movement ecology adaptations of northern pigtailed macaques in this degraded forest fragment were primarily dependent on availability of native fruit species, and that foraging strategies in the Sakaerat troop differed from northern pigtailed macaque populations inhabiting the nearby primary forest of Khao Yai National Park. Fourth, we illustrated a modeling approach of seed shadows, which incorporated field-collected data on the Sakaerat troop. We adapted a deterministic model of seed deposition with random components. We parameterized the model with macaque feeding behavior (i.e. consumed fruit species, seed treatments), gut and cheek pouch retention time, feeding and sleeping site location, daily activity, and movement patterns based on monthly fruit availability (analyzed with HMM). We found that northern pigtailed macaques dispersed many medium- to large-seeded species, across long distances in the degraded native forest and toward plantation forests (mean of dispersal distance > 500 m with a maximum range of 2300 m), and produced complementary seed shadows, with a sparse distribution of seeds spat out locally (mean > 50 m with a maximum range of 870 m). Our results showed that northern pigtailed macaques are effective seed dispersers in this degraded habitat. Overall, our findings provide novel insights regarding northern pigtailed macaques’ adaptability to habitat degradation, which include selection of numerous sleeping sites following food availability, use of exotic Acacia species in plantations to cope with native fruit scarcity, and use of large home range. These behavioral profiles result in long-distance dispersal events, giving an overview of their contributions to forest restoration and maintenance of ecosystem functions within their ranges. Our results bring a significant contribution to the current knowledge of the ecology and factors affecting ranging patterns, resource use, and seed dispersal effectiveness of the northern pigtailed macaque classified as vulnerable but still poorly-known, and constitute an essential starting point toward designing appropriate conservation strategies. [less ▲]

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See detailWar in the darkness: biological alternatives to control wireworms
La Forgia, Diana ULiege

Doctoral thesis (2020)

Wireworms (Coleoptera : Elateridae) are common polyphagous soil-dwelling pest that feed on roots and tubers of many crops of high economical value. The use of pesticides is not always efficient because ... [more ▼]

Wireworms (Coleoptera : Elateridae) are common polyphagous soil-dwelling pest that feed on roots and tubers of many crops of high economical value. The use of pesticides is not always efficient because even a low density of wireworms can affect the field and be responsible for important economical damage. The withdrawal of many insecticide formulations (including neonicotinoids), leaves producers without control methods. They call for the development of efficient, cost-effective and environmentally-friendly solutions. In Chapter I, we list the existing alternatives to pesticides: they include natural enemies, biological agents and semiochemicals. We also discuss the potential of several associations of alternatives, such as the attractand-kill strategy that couple the use of microbial agents with semiochemicals. The aims pursued during the past four years of research were the development of such an attract-and-kill strategy of wireworm’s control. To do so, several sub-goals have been set : (a) developing behavioral assays on the wireworm orientation behavior (b) profiling volatile organic compounds (VOCs) released in the rhizosphere of maize (c) evaluating the role of the identified VOCs on wireworms foraging behavior (d) developing an attract-and-kill based on VOCs, associated with entomopathogenic nematodes (EPNs). In Chapter III, the main aim was the research of maize odors that could be attractive for wireworms. After field trials, we tested the hypothesis according to which different maize varieties have differential susceptibility/attraction to wireworms because they emit different VOCs from the roots. The work was focused on the VOCs quantification from the roots of two maize varieties having experienced contrasted levels of wireworm infestation in the field. We showed that the least susceptible variety released a more diverse blend of VOCs, including large amounts of hexanal, heptanal and 2,3-octenanedione. Behavioral assays showed that wireworms were strongly attracted to VOCs released by maize roots. However, when wireworms were offered both maize varieties, no preference was detected, contrasting with the field results. In Chapter IV, we investigated whether wireworms are able to use VOCs as cues to assess the suitability of maize plants that are already under attack by conspecifics. Seven compounds from plants and larvae have been identified, amongst which 2-Pentylfuran was present in high quantity, particularly in treatments where larvae were present. Behavioral assays in dual-choice olfactometer showed a significant attraction to 2- Pentylfuran. Finally, in Chapter V, we describe an attract-and-kill method using EPNs as biocontrol agent against wireworms. We first compared the efficiency of several EPN strains through classical screening laboratory assays (contact application of EPNs). Then, we developed an attract-and-kill system proposing alginate beads filled with EPNs and spiked with potato extract to larvae. The potato extract was previously tested as attractive for wireworms and easy to produce and to use in the laboratory tests. We found that the ingestion of these beads led to higher mortality rates. This method also demonstrated some signs of reduction of the wireworms metabolism. Through this work, we were able to deeper study the wireworms orientation behavior in terms of attraction to susceptible maize varieties. We showed that VOCs are part of the cues for the host plant detection. Still regarding the behavior, the larvae aggregation with conspecifics on plant roots was highlighted for the first time, opening an important research path. Finally, the development of the attract-and kill system combining VOCs with EPNs showed a long-term reduction of wireworms activity that needs to be tested in the field. The results obtained during these years of research will certainly open new paths in the study of the aggregation, the cues for the host selection and preference that could be combined to other biocontrol methods. In particular, the results open new perspectives on the development of a more efficient attract-andkill with the combination of more specific VOCs like 2-Pentylfuran and other EPNs strains. The pursuit of this research could lead to effective and innovative solution in wireworms control. [less ▲]

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See detailL’haptoglobine comme outil pronostique chez le bovin.
Severin, Marion ULiege

Master's dissertation (2020)

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See detailEffects of climate change on dairy farming systems: evaluation and impacts of heat stress on dairy cow in Tunisia
Amamou, Hajer ULiege

Doctoral thesis (2020)

The main objective of the research carried out within the framework of this thesis was to assess the risks related to climate change (CC), in particular heat stress (HS) in dairy cattle in Tunisia, and to ... [more ▼]

The main objective of the research carried out within the framework of this thesis was to assess the risks related to climate change (CC), in particular heat stress (HS) in dairy cattle in Tunisia, and to identify measures or indicators that could reveal the tolerance of dairy cows to HS. In the first study, an enquiry was conducted among 566 dairy farmers throughout Tunisia. The objective was to focus on Tunisian dairy farmers’ perceptions of the risks and the actions taken to cope with changes attributable to CC. A total of 70 diagnostic variables relating to farm characteristics, resources, management, performances and profit, in addition to CC risk perception and adaptation strategies, were used and analysed. A typology based on multivariate statistical analysis was carried out using variables related to the land, feed resources, labour and infrastructure. Four groups of dairy systems were identified. The largest proportions of farmers around 70% belonged to the landless dairy systems (Clusters 1 and 2), whereas the minority of farmers belonged to medium-sized (18%, Cluster 3) and large-sized (12%, Cluster 4) farm systems that specialized in milk production. The analyse of results showed that almost all the farmers in all the clusters perceived that the greatest impact of CC would be on cow performance and forage production. The study of the attitudes of the farmers towards adaptation to CC reveals that they sought, as a priority, to modify and adapt their current livestock housing infrastructure. Other identified strategies were related to the storage of forage reserves, the purchase of fodder and the promotion of irrigated areas. Although the CC-related concerns varied among the farming clusters, dairy farmers focus on short-term environmental modifications rather than longer-term actions to address CC effects. In the second study, the aspects of vulnerability to HS for dairy cattle farming systems in Tunisia was investigated for dressing adequate actions to combat CC effects. In order to do so, historical milk test-day records from official milk recording collected during 7 years were merged with historical temperature and humidity data provided by public weather stations. The results showed that dairy farms in Tunisia are exposed annually for 4 to 5 months with temperature-humidity index (THI) values above 72. Overall, the statistical models used in this study have shown that the tipping points (thresholds) of the THI at which milk yield started to decline ranged between 65 and 67. The largest milk decline per unit of THI above threshold values was 0.135±0.01 kg for multiparous cows. The milk losses estimated only during the 3 months of the summer period were 110 and 142 kg/cow in north and south, respectively. Individual cow response to heat load were estimated using random regression model and been considered as key measures of dairy farming system sensitivity assessment to HS. The results reveal the high sensitivity of Tunisian Holstein cows to HS especially in dairy farms characterized by large herd size and high level of milk production. In the third study, an on-farm experimental protocol was set up on 4 commercial dairy farms during summer (HS) and autumn (thermo-neutral) periods using direct physiological, on-barn temperature and relative humidity, milk yield and milk composition measurements. This study aimed to investigate the effects of HS on physiological and production parameters of dairy cows. When the THI went from an average value of 54 in autumn to 77 in summer, respiration rate (RR) and skin temperature (ST) increased by 2.3- and 1.3-fold higher, whereas milk yield per milking decreased by 24%. The results showed a linear relationship between THI and all physiological traits and an increases in RR (+2 breaths/min), ST (+0.5°C) and rectal temperature (RT) (+0.04°C) per increase in one THI unit. Inversely, milk, fat and protein yields showed a drop of 0.13 kg, 0.4 g and 0.3 g per milking per increase in one THI unit, respectively. Methodology of cluster analysis allowed to classify dairy cows into two clusters where 82% of cows belonged to Cluster 1 of heat-sensitive, whereas only 18% of cows belonged to Cluster 2 of heat-tolerant. The reaction norm models conducted to quantify the individual responses of cows across the trajectory of THI during the HS period revealed that heat-tolerant cows tended to have higher RR, ST, and RT and lower to almost no decrease in milk yield compared to heat-sensitive cows. The results also suggested that RR could be used as a reliable indicator for thermo-tolerance. In conclusion, this thesis shows that the CC-related concerns were linked to economic rather than climatic factors and adaptation strategies were focused on short-term environmental modifications to address CC effects in the Tunisian dairy farms. Moreover, dairy farms especially those characterized by large herd size and high level of milk production are highly sensitive to HS in Tunisia. At the individual scale, the RR might be used as an indicator for thermo-tolerance in order to assess HS and predict the thermal status in dairy cows. Only a small proportion (18%) of dairy cows were identified as heat-tolerant in our experiment. Overall, this thesis demonstrated that HS is a current problem in Tunisian dairy farms. Moreover, considering the CC, the severity and duration of HS will increase in the future, which would consequently lead to worsening economic losses. Our results highlight the need to implement immediate and proper management strategies to alleviate HS impacts, as well as future developments in animal breeding and dairy system sustainability to address the CC-related risks. [less ▲]

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See detailPrevention of African Swine Fever Virus: evasion mechanism, vaccine development and adjuvant for animal vaccine
Wu, Jing ULiege

Doctoral thesis (2020)

African swine fever (ASF) is a viral disease caused by African swine fever virus (ASFV), which leads high mortality in domestic pigs and wild boar. The occurrence of ASFV in affected countries often ... [more ▼]

African swine fever (ASF) is a viral disease caused by African swine fever virus (ASFV), which leads high mortality in domestic pigs and wild boar. The occurrence of ASFV in affected countries often provokes severe economic losses and ecological consequences. Lack of knowledge concerning the diversity of ASFV strains and the puzzling virus-host interactions involved in infection and immunity hinders the development of vaccines and complicates the control and eradication of ASF. Currently, there is no commercially available vaccine. In recent years, the prevalence of ASFV makes it urgent to acquire more knowledge and tools for protection against ASFV. In this thesis, we discussed the prevention of ASF from the following three aspects: immune evasion mechanism, vaccine development, and adjuvant for animal vaccine. Firstly, we demonstrated the action mechanism of DP96R gene of ASFV, which is one of the viral virulence factors. Results showed that DP96R of ASFV China2018/1 strain blocks the cytosolic cGAS-STING-TBK1 signaling pathway by inhibiting the activation of both TBK1 and IKKβ, thus down-regulating the expression of type I IFNs and inflammatory cytokines. This provides insightful information for further investigation to better understand the mechanism of immune evasion of ASFV. Secondly, we utilized dual expression vector to construct recombinant DNA plasmids encoding ASFV main structural genes, B646L (p72), E183L (p54), CP204L (p30), EP402R (CD2v) respectively, and genetic adjuvants (IRF3-5D, TBK1), then evaluated the induced immune responses following the administration of the DNA cocktail vaccines in mice. The results suggested ASFV DNA cocktail vaccines based on appropriate antigen genes and TBK1 as a genetic adjuvant offer a promising strategy for the development of ASFV vaccines. Thirdly, the action mechanism of new animal vaccine adjuvant pUC18-CpG was investigated. It stimulates RAW 264.7 mainly through the TBK1-mediated signaling pathway, causing the up-regulation of interferons and pro-inflammatory cytokines. It showed great adjuvanticity in mice and induced antigen-specific cytokine expression towards a Th1 based immune response. A better understanding of the pUC18-CpG is helpful for the promotion of its clinical application. In conclusion, we revealed a new immune evasion mechanism of ASFV, constructed a new type of ASFV DNA vaccine, and deepened our understanding of animal vaccine adjuvant (pUC18-CpG), which will provide theoretical knowledge and technical support for the prevention and control of ASF. [less ▲]

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See detailDevelopment of a modelling approach for characterization and prediction of bacterial spoilage microbiota dynamics in perishable foodstuffs
Cauchie, Emilie ULiege

Doctoral thesis (2020)

Food waste is currently a major problem since it is estimated that about one third of the food produced in the world is discarded before it is consumed. The reasons for these food losses and waste are ... [more ▼]

Food waste is currently a major problem since it is estimated that about one third of the food produced in the world is discarded before it is consumed. The reasons for these food losses and waste are varied and one cause is the bacterial spoilage, rendering foods unacceptable for consumption. The study of the dynamics of bacterial spoilage populations and the prediction of their dynamics would therefore be interesting to better understand and anticipate this phenomenon. This research focused on the study of predictive models for spoilage bacteria of fresh meat and meat products, considered as highly perishable foodstuffs. The two working matrices were pork minced meat and white pudding, considering variations in storage conditions (temperature and packaging). The first chapter of this thesis provides a general overview of bacterial spoilage of meat and meat products, as well as factors that may promote or limit its development. The different techniques used in this study to characterize and modelize the dynamics of spoilage microbiota are also described. This research was then divided into four main areas that are discussed in the other chapters: (1) describing the spoilage bacterial microbiota naturally present in the matrices studied; (2) characterizing the spoilage bacteria of interest for these products; (3) developing and validating predictive models with one or more bacteria; (4) and studying the metabolome of minced meat inoculated by spoilage microorganisms of interest. These studies have demonstrated the interest of combining results from classical microbiology and 16S rDNA-based metagenetic to monitor and predict the dynamics of spoilage microbiota. For the white pudding, the bacteria of interest were Brochothrix thermosphacta, Carnobacterium maltaromaticum, Lactobacillus spp. (Lb. fuchuensis, Lb. graminis, Lb. oligofermentans), Lactococcus lactis, Leuconostoc mesenteroides, Pseudomonas psychrophila, Pseudomonas sp., Psychrobacter spp. (Psy. okhotskensis, Psy. urativorans), Raoultella terrigena and Serratia sp. For minced pork samples they were B. thermosphacta, Lb. algidus, Lc. piscium, Leuconostoc spp. (Ln. inhae, Ln. gelidum), Photobacterium spp. (Ph. kishitanii, Ph. phosphoreum) and Pseudomonas spp. (Ps. fragi, Ps. fluorescens, Ps. psychrophila). The type of packaging and storage temperature have a significant effect on the different dynamics, as well as the food companies and the production batches analyzed. Some of these bacteria of interest were then inoculated on sterile and non-sterile matrices, stored at different temperatures and packaging. The growth parameters to each bacterium were collected: maximum growth rate, lag time, minimum and maximum bacterial populations, time to reach the stationary phase, time to reach the spoilage threshold, minimum growth temperature, etc. Packaging seems to have the greatest impact on the maximum growth rate, itself having the greatest influence on the microbiological shelf life of the foods studied. Based on these data, good adjustments were obtained for the growth simulations, but overestimations were often observed. The same observations could be made by comparing the simulations performed on the white pudding with those available from software (ComBase and Sym'Previus). For minced pork, the data obtained allowed the development of three species interaction models based on the Lotka-Volterra (prey-predator model) and the modified Jameson models. The simulations obtained were validated by monitoring the spoilage microbiota of naturally contaminated pork minced meat matrices. The modified Jameson model obtained the best adjustments, although the prey-predator approach seems to be an interesting interaction model for complex microbiota. However, these proposals for models with three or more spoilage bacteria need to be validated by more experimental repetitions. Finally, metabolomic analyses (1H-NMR), in collaboration with CIRM-CHU, were performed in order to monitor the metabolites produced by inoculated bacteria in sterile minced pork samples. The dynamics of the metabolome for sterile non-inoculated matrices was also monitored. The different metabolomic patterns and metabolites produced were highlighted according to the inoculated bacteria and the food packaging. Moreover, the storage temperature seems to have the lowest impact on the metabolome. Development of predictive models based on data obtained by multi-omics analyses, combined with classical microbiology, provide an interesting approach. Further research on the development of complex models integrating the dynamics of two or more spoilage bacteria, interacting with each other and with the natural microbiota of foodstuffs, will be also an important step for better understanding and anticipating the bacterial spoilage of perishable foodstuffs. [less ▲]

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See detailAgro-industrial feed ingredients, a novel approach to enhance intestinal health in weaned piglets: from in vitro to in vivo perspectives
Uerlings, Julie ULiege

Doctoral thesis (2020)

Weaning is a critical transition period in pig production with major dietary, behavioural and environmental challenges leading to tremendous physiological, immunological and microbiological changes in the ... [more ▼]

Weaning is a critical transition period in pig production with major dietary, behavioural and environmental challenges leading to tremendous physiological, immunological and microbiological changes in the piglet’s intestines. This multifactorial process predisposes the piglets to subsequent intestinal disturbances and infections, resulting in poor performance and diarrhoea. To tackle the current problematic expansion of antibiotic resistance, nutritional management is yet another promising strategy to alleviate intestinal disorders around weaning. By-products from the agro-industrial sector and, to a lesser extent, whole cereals and roots, are major sources of dietary fibres suitable for livestock feeding. These native sources of ingredients could represent potential prebiotic candidates due to the heterogeneous dietary fibre components embedded in their cell wall matrix. These feed ingredients, regarded as environmental-friendly, socially accepted and more economic and sustainable than antimicrobials and isolated fibre fractions, are therefore of upmost interest. However, among potential dietary strategies, mainly purified fibre fractions have been accepted and promoted, while the prebiotic capacities of several cereals, roots and corresponding by-products remain to be investigated. We therefore hypothesised that the prebiotic effects of these feed ingredients could reach or overcome the ones of isolated fibre fractions. For this purpose, 36 fibre-rich feed ingredients were first tested in a three-step in vitro model of the piglet’s gastro-intestinal tract for their prebiotic potential (objective 1), measuring the gas kinetics, short-chain fatty acid and microbiota profiles in the fermentation broth as indicators of prebiotic activity. Several feed ingredients such as chicory pulp, citrus and orange by-products, rye bran and soybean hulls, with complex structural composition varying in soluble and insoluble dietary fibres and distinct constituent sugars, positively modulated health-related microbiota communities in the fermentation broths, reaching or overcoming the prebiotic effect of their corresponding purified fraction and/or inulin. Purified fractions were ranked as highly fermentable, with inulin displaying the most interesting prebiotic profile as butyrogenic ingredient. Subsequently, the six most promising ingredients were tested via a functional in vitro fermentation – cell culture assay (objective 2) combining the in vitro batch fermentation model with cultured intestinal porcine epithelial cells (IPEC-J2), for their barrier-enhancing and immunomodulatory effects. Inulin and its fermentation metabolites promoted the intestinal barrier function via up-regulated expressions of tight and adherens junction genes. Chicory pulp fermentation supernatant enhanced the intestinal barrier integrity and seemed to induce anti-inflammatory and pro-apoptotic regulations in comparison to inulin, while the fermentation supernatants of chicory root, citrus pulp, rye bran and soybean hulls only showed minor immunomodulatory effects. These in vitro assays led to preliminary conclusions that allowed the selection of the most promising ingredients for the third objective of the thesis, i.e. evaluating the inclusion of citrus pulp (0.2 % and 2 %) and inulin (0.2 %) in the feed of newly weaned piglets in vivo. The aim was to provide insights into their capacities to modulate intestinal fermentation, ecology, morphology, inflammation and permeability, with the purpose of improving gut health at weaning, and hence, reducing the incidence of infections. We observed that citrus pulp improved gut morphology and promoted colonic fermentation at weaning without depressing growth performance or impairing the inflammatory response and the intestinal barrier function. Colonic health-associated microbiota communities were notably enhanced in both the early and late post-weaning stages under citrus pulp supplementation at 2 %. A decline in colonic branched-chain fatty acids, concomitant with greater acetate proportions, was also observed and could account for a possible reduction of proteolytic fermentation in newly weaned piglets following citrus pulp inclusion at 2 %. Moreover, greater villus height to crypt depth ratios were observed following citrus pulp (0.2 % and 2 %) and inulin supplementations, which might suggest the capacity of the ingredients to cope with epithelial damage during the weaning transition. Citrus pulp could therefore be considered as a valuable nutritional strategy for future inclusion in the weaner diet. In summary, this thesis improved our understanding of dietary fibre management around weaning using whole cereals, roots and by-products from the agro-industrial sector. The heterogeneous sources of endogenous dietary carbohydrates present in these feed ingredients, causing a more gradual degradation, could effectively maintain fermentation throughout the entire hindgut. Several types of feed ingredients may therefore be promising alternatives to antimicrobials and pure fibre fractions, to reduce the prevalence of post-weaning diarrhoea. Nevertheless, a challenge trial could better recreate the conditions encountered in commercial production at weaning and might provide a clearer picture of the preventive or curative effects of these feed ingredients against pathogen infection at weaning. Alternatively, using the functional fermentation – cell culture model, other feed ingredients and their fermentation metabolites may be tested for their bioactive properties for future inclusion in young mammalian diets. [less ▲]

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See detailStudy on the processing technology of iced roasted sweet potato and its sensory characteristics and nutritional peculiarities
Hou, Feina ULiege

Doctoral thesis (2020)

Nowadays, fresh sweet potato is greatly influenced by seasonality and unable to be consumed all year. The roast sweet potato in market is usually made by personal, so the quality, safety and nutrition ... [more ▼]

Nowadays, fresh sweet potato is greatly influenced by seasonality and unable to be consumed all year. The roast sweet potato in market is usually made by personal, so the quality, safety and nutrition cannot be guaranteed effectively. In addition, roasted sweet potato is hard to storage and has a short shelf-life, what’s more, the price of roast sweet potato is high due to its seasonality, thus reducing consumers’ desire to buy it. Therefore, a new iced roasted sweet potato product which has a long shelf-life, good taste, and high nutritional value should be developed to meet the needs of consumers. Firstly, we studied on changes in nutritional and functional value of roasted sweet potato during roasting and selected the special cultivar of roasted sweet potato. There were significant differences in the proximate and nutritional composition of the fresh and roasted sweet potatoes from the different cultivars. The results showed that fresh and roasted sweet potatoes were both rich in protein and dietary fiber, with low gross energy and fat. After roasting, the starch and protein contents declined, while total phenolic content and antioxidant activity were increased, and most of vitamins are preserved. In addition, the comprehensive nutritional value of Yanshu No.25 ranked first. Secondly, we optimized the processing technology of roasted sweet potatoes. The results showed that roasting time, roasting temperature and roasting speed affected the measured responses, and the optimal roasting conditions included a roasting time of 40 min, a roasting temperature of 235°C, and a roasting speed of 40 rad/min. Under the optimal conditions, the result of reducing sugar content is 47.79±0.43 g/100g DW, the result of vitamin C content is 60.25±0.67 mg/100 g DW. In addition, 38 volatile compounds were identified in roasted sweet potato by GC-MS, 2-methyl butanal was the main aromatic compound. Low-field NMR results showed that roasting changes the water distribution, the proportion of free water increased and relaxation times (T2) were decreased after roasting process. Thirdly, the effects of different freezing temperature on structure, moisture distribution, sensory, and nutritional characteristics of iced roasted sweet potato was studied. The results of ice crystals formation and microstructure showed that the tissues were severely damaged at freezing temperature of -18 °C, which took the longest freezing time (5.09 h). What’s more, the samples of -18 °C showed softer texture (hardness 454.39 g) and darker color (L* value 86.50) than that of the -40 °C and -70 °C frozen samples. The analysis of NMR and drip loss demonstrated that the condition of -18 °C freezing maintained less the intracellular water content. Moreover, with the freezing temperature increased, vitamin C and TPC content was decreased significantly, while protein and dietary fiber content did not show significant change. In conclusion, quality of the roasted sweet potato is better under the quick-frozen condition. According to this dissertation, these investigations about raw sweet potato and roasted sweet potato qualities lead to a better understanding of the influence of processing technology on roasted sweet potato and propose new insight in improving the quality of sweet potato products. In spite of the extensive available information about the effect of roasting in different sweet potato cultivars, much of the work is essentially descriptive. What’s more, Maillard and other reactions during roasting process of sweet potatoes are complicated, and the formation of characteristic flavor is more complex, which requires further research. More basic research is still needed to elucidate the underlying mechanisms of reaction during roasting and freezing. [less ▲]

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See detailContribution à l’étude de la réponse immune contre les dermatophytes à l’aide d’un modèle murin d’infection à Trichophyton benhamiae.
Heinen, Marie-Pierre ULiege

Doctoral thesis (2020)

Dermatophytoses are widespread superficial skin mycosis known to affect more than 20% of the human population, making them the most common fungal infections. Pathogenic dermatophytes are specialized ... [more ▼]

Dermatophytoses are widespread superficial skin mycosis known to affect more than 20% of the human population, making them the most common fungal infections. Pathogenic dermatophytes are specialized filamentous fungi that exhibit the capacity to invade keratinized tissues and produce infections that are generally restricted to the stratum corneum, hair, and nails. Despite their superficial localization, these fungi induce an immune response that remains poorly documented as compared to that observed with other fungal infections. Although the ability of dermatophytes to induce innate response is documented, little is known about the adaptive immune responses against these fungi. Furthermore, the inoculation route in most in vivo models used for studying the immune response against dermatophytes fails to mimic the natural epicutaneous infection or even induce observable skin lesions. Some clinical case studies, however, have shown that resolution of dermatophytoses is associated with the development of cell-mediated immunity with T helper (Th) type 1 polarization. At the beginning of this work, despite the crucial role of Th17 response in many other fungal diseases, particularly at mucosal surfaces, no study had yet experimentally documented Th17 response in dermatophytoses. In this regard, a relevant mouse model of dermatophytosis had just been developed at the Laboratory. In the first part of this work, by comparing Trichophyton benhamiae acute superficial dermatophytosis in WT and Rag2−/− mice, we evidenced that TCR-mediated immunity is critical for the optimal control of acute dermatophytosis and that adaptive immunity is polarized to both Th1 and Th17 responses. Using IL-17A-deficient, IFN-γ-deficient and IL-17A and IFN-γ double-deficient mice we next evidenced that theses two pathways function in a complementary manner, with the Th17 antifungal response acting on dermatophyte clearance and the Th1 one being involved in both fungal clearance and Th17-inflammation down-modulation. In mammals, it is generally accepted that, besides an increased epidermal turnover, the two main effector and regulatory mechanisms in the fight against opportunistic fungal skin infections are the cytotoxic and phagocytic activity of polymorphonuclear neutrophil (PMN)s, as well as the production of antimicrobial peptides (AMP)s at the site of infection. PMNs and AMP have long been known as key elements of the cutaneous innate immune system, but interest in these has drastically increased with the discovery of the Th17 pathway, particularly in fungal infections. Indeed, in skin and mucosal defence against fungi, IL-17 and IL-22, the major’s cytokines of Th17 family, have essential role for promoting PMN mobilization and regulating AMP production at the site of infection. Both attraction of PMNs and production of AMPs occur upon infection with dermatophytes and have been associated with host protection in human and experimental infections but the implication of the different immune components in the triggering of these two defences mechanisms had so far never been studied in acute superficial dermatophytosis. In the second part of this work, we evidenced for the first time that while in situ PMN attraction and AMP production can occur without the intervention of TCR-mediated immunity, this last significantly contributes to optimally strengthen these two defense mechanisms in acute superficial dermatophytosis. We next demonstrated that innate and Th17-secreted IL-17A significantly contributed to increase the in situ PMN attraction and that the actions of PMNs significantly contribute to decrease the fungal loads. We also evidenced that, while single IL-17A and IFN-γ deficiencies had no impact on the AMP production in our model of superficial T. benhamiae infection, a double IFN-γ and IL-17A deficiency significantly decreased it. These two lasts observations suggest not only a preponderant role of a Th17-secreted non-IL-17 cytokine, probably IL-22, in the AMPs production but also possible synergistic actions of this unknow cytokine with IL-17A and also with IFN-γ on the AMPs production, particulary in the case of IFN-γ and IL-17A deficiencies respectively. In parallel with these experiments, we infected the various aforementioned strains of mice after having depleted them in PMN, and we evidenced that the action of the PMNs contributed significantly to reduce the fungal loads but that other mechanisms, such as the local AMP production, certainly helped to reduce the fungal skin load and prevent the dissemination of the dermatophyte beyond the skin, especially in the case of deficiencies affecting the cutaneous PMNs infiltration. Taken together these data suggest that, during acute superficial dermatophytosis, Th17 immune response contributes to the fungal clearance by strengthening the innate in situ PMN infiltration and AMP production, with preponderant roles of IL-17A on the PMN recruitement and of an other Th17-secreted cytokine, probably IL-22, on AMP production, alone or in synergy with IL-17A or IFN-γ. [less ▲]

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Morou Madougou, Amadou ULiege

Doctoral thesis (2020)

Livestock breeding is an important activity in agriculture in Niger. This sector is facing huge problems, such as the weak productivity of the animals, the weak investment, the feeding and watering ... [more ▼]

Livestock breeding is an important activity in agriculture in Niger. This sector is facing huge problems, such as the weak productivity of the animals, the weak investment, the feeding and watering difficulty and the recurrent sanitary problems. Niger is a landlocked country with an area of 1,267,000 km², whose southernmost border is more than 600 km from the sea (Gulf of Guinea) and according to National Institute of statistics (INS), Niger has a population of 19,124,884. In Niger, which is a predominantly agro-pastoral country, breeding is performed by nearly 87% of the active population either as a main activity or as a secondary activity after agriculture. Breeding is a determining factor in the context of food security and poverty reduction. On average, it contributes to household income at a level of 15% and to food security at a level of 25%. In Niger, the animal species supplying milk are: cattle, goats, camelids and sheep. The main cattle breeds involved in milk production come from several local breeds from Bos taurus (Kouri) and Bos indicus (Azawak, Bororo, Djelli, Goudali). There are mainly three major national dairy sectors, namely peri-urban, rural and ranching..The average milk production is 2.4 l/ cow / day in the rainy season compared to 2 l in the dry and cold season and 1.4 l in the dry and hot season. Analysis of the evolution of dietary pattern shows a tendency towards increased consumption of dairy products in West Africa, particularly in urban areas, where populations with no dairy consumption pattern have rapidly adopted them. The development of the dairy sector requires a real consideration of the control of health risks to ensure the health of the consumer, the quality and hygiene of the products. Poor hygiene control is the main source of contamination since several foodborne pathogens can be transmitted by raw milk. There are few data on the microbiological quality of raw milk in Niger. Therefore, the raw milk microbiota from three collection centres (Kollo, Hamdallaye and Say) and three farms (Toukounous, Kirkissoye and Niamey) in Niger have been evaluated using two methods, the classical microbiology and metagenetic. The objective of this study was to assess the microbiological quality of raw milk produced in Niger and compare it with similar production methods in other countries. To perform this, we enumerated microorganisms that indicates the hygiene quality and safety of raw milk (coliforms, Escherichia coli and Staphylococcus aureus) and then we performed metagenetics analyzes in order to obtain a global image of the microbiota. The use of metagenetic analysis aimed to get an insight of indigenous bacterial compositions and to enhance the safety and quality of raw milk with high-throughput sequencing technology through 16S rDNA metagenetics (also called metagenomics analysis targeting 16S ribosomal DNA). We wanted also to assess the presence of antibiotics residues, the levels of hygiene indicator bacteria and the occurrence of coagulase positive Staphylococcus. Data collected in this study may be useful for an exposure assessment of Niger inhabitants to foodborne pathogens present in raw milk. Samples were submitted to classical microbiology for Aerobic Total Microbiological Counts (ATMC) at 30°C, the enumeration of coagulase positive Staphylococcus and E. coli (ECC) and total coliforms counts (TCC), while metagenetic analysis was performed on the same samples. V1–V3 hypervariable 16S rDNA amplicon libraries were prepared for each sample and sequenced with MiSeq Illumina sequence (V3 kit). Taxonomical assignment and clustering were performed with Mothur using SILVA database. Metagenetic analysis of sequencing data for the V1-V3 region of 16S rDNA resulted in the identification of dominant populations and in the evaluation of their relative abundance. In descending order of abundance, the following phyla were recovered: Proteobacteria, Firmicutes and Actinobacteria. The main species encountered were Acinetobacter, Staphylococcus, Klebsiella, Escherichia spp, Lactobacillus spp, Lactococcus spp and a part of the whole population was composed of isolates issued from environmental origin, as Enhydrobacter spp and Kocuria spp. Taxonomical assignment and clustering were performed with Mothur using SILVA database. Screening of antibiotic residues was performed using a standardized biological test kit form, the Delvotest®. In total, of the 192 samples of raw milk, 19 (10.1%) were positive. s. A voluntary survey of raw milk consumers was performed to learn about foodborne disease. Following the answers of interviewed consumers, a rate of 25% foodborne illness among people who consume raw milk directly out of 194 survey respondents was detected. The results show that hygiene rules are not respected in the production of raw milk and that raw milk is directly consumed without any heat treatment before consumption. This presents a serious public health risk. In conclusion, the quality of raw milk can be improved by using the good hygiene practice during milking, collection and transport of raw milk and only the heat treatment of the milk can help to limit health risks for consumers. [less ▲]

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See detailContribution à la mise en évidence des facteurs influençant le succès de l’introduction du robot de traite au pâturage
Lessire, Françoise ULiege

Doctoral thesis (2020)

Le développement de la traite robotisée a représenté un changement majeur dans le secteur laitier que ce soit au niveau du quotidien des éleveurs, pour les vétérinaires et conseillers en élevage ou ... [more ▼]

Le développement de la traite robotisée a représenté un changement majeur dans le secteur laitier que ce soit au niveau du quotidien des éleveurs, pour les vétérinaires et conseillers en élevage ou l’industrie laitière. Ce changement touche un nombre croissant d’exploitations au point qu’en Belgique, 2017, une nouvelle installation de traite sur 2 était robotisée (Fedagrim, 2019). Dès les années 2000, s’est posée la question de la possibilité de poursuivre le pâturage dans les exploitations robotisées. La réponse à cette interrogation est difficile car liée à différents contextes, par exemple l’obligation de pâturer pour des questions de bien-être animal pendant une certaine période de l’année en Suède, alors que dans certains pays d’élevage plus extensif comme la Nouvelle Zélande ou l’Irlande, le pâturage est incontournable. Les publications relatives à ces questions sont donc conjoncturelles. La première publication intégrée dans cette thèse a recensé les différents systèmes développés dans 7 pays qui ont participé au projet Européen AUTOGRASSMILK. Rapidement, il a été établi que le robot de traite associé au pâturage générait moins de traites. En effet, 2,7 traites automatisées par vache et par jour peuvent être enregistrées en moyenne à l’étable, alors qu’en système pâturant, la fréquence de traite atteint difficilement plus de 2 traites par jour. La gestion de la circulation des animaux vers le robot est généralement plus difficile au pâturage, expliquant la diminution de cet indicateur de performances. Alors qu’à l’étable, le retour vers le robot met en jeu un comportement individuel, en prairie, l’instinct grégaire des animaux se marque davantage, avec pour conséquence une répartition des traites moins homogène sur la journée. D’autres facteurs entrent également en jeu : les vaches sont soumises à d’autres contraintes, telles que la distance au robot, la disponibilité en eau, les aléas climatiques…Les facteurs influençant la circulation des animaux au pâturage peuvent être classés en paramétrables (que l’exploitant peut modifier) et non paramétrables (sur lesquels l’exploitant n’a pas de contrôle). La partie expérimentale de ce travail est divisé en trois parties. Le premier volet concerne les facteurs paramétrables permettant la combinaison du robot et du pâturage, le deuxième volet étudie les facteurs climatiques, non paramétrables et le dernier fait la synthèse des précédentes parties. Le premier article fait l’état des lieux des différentes stratégies mises en place en Europe pour aménager un robot de traite en prairie. La deuxième publication a eu pour objectif de vérifier si les modalités d’attribution de concentré avaient un impact sur la fréquentation du robot par les vaches au pâturage. En effet, à l’étable, il est reconnu que la circulation des animaux est améliorée par la distribution de quantités variables de concentrés. Vérifier l’impact de cette distribution dans un système de robot au pâturage a donc paru judicieux. La gestion des grands troupeaux semble facilitée par les systèmes robotisés. En effet, l’automatisation de la traite permet de suppléer à la demande en main d’œuvre nécessaire pour la gestion d’un troupeau de telles tailles. De plus, la génération de rapports et les différentes alarmes disponibles permettraient de faciliter la surveillance des animaux avec des interventions humaines limitées. Les troisième et quatrième études ont visé à évaluer la possibilité de pratiquer le pâturage dans deux troupeaux de plus de 100 animaux et de vérifier l’intérêt économique de cet aménagement. Les animaux en prairie sont davantage soumis aux aléas climatiques susceptibles de modifier leur comportement. Or, dans le contexte du réchauffement climatique, les épisodes de stress thermiques deviennent plus fréquents. L’objectif de la cinquième étude a été de quantifier les impacts de conditions météorologiques contrastées sur les déplacements, la production laitière et le temps de rumination des vaches laitières en système 100% pâturant. [less ▲]

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See detailTrophic ecology of Southern Ocean sea stars: Influence of environmental drivers on trophic diversity
Le Bourg, Baptiste ULiege

Doctoral thesis (2020)

Like in the rest of the world, climate change impacts the Southern Ocean, but not in the same way in all regions of this ocean. Changes in sea ice cover around the Antarctic continent are one of the most ... [more ▼]

Like in the rest of the world, climate change impacts the Southern Ocean, but not in the same way in all regions of this ocean. Changes in sea ice cover around the Antarctic continent are one of the most visible manifestations. For example, sea ice cover has decreased significantly in the Western Antarctic Peninsula while it tends to increase slightly on the rest of the coastline of the continent. These changes in environmental conditions influence the functioning of the ecosystems of this ocean. In particular, the disappearance or persistence of sea ice in a region where it was seasonally present may prevent the appearance of summer phytoplankton blooms, thus impacting the dynamics of krill populations and their predators in the pelagic environment. The benthic environment will also be disturbed by environmental modifications resulting from climate change, as organic matter fluxes toward this compartment will be affected. Sea stars (Echinodermata: Asteroidea) are a key component of Southern Ocean benthos, with 12% of the known sea star species living there. In temperate environments, this taxon may play an important role in the functioning of ecosystems with its trophic interactions controlling the populations of other organisms, which themselves have a large effect on the ecosystems. This group is considered to be quite resistant to changes of seawater temperature in the Antarctic environment. However, it will likely be affected by changes of environmental conditions and functioning of food webs. Indeed, a reduction in the abundance or disappearance of common prey can lead to an increased competition in sea star assemblages. In order to determine the ecological role of sea stars in the Southern Ocean and to understand how they might be impacted by climate change, a study of their trophic ecology and of the factors controlling it is necessary. Therefore, the objectives of this PhD thesis were to determine the trophic role of sea stars in the Southern Ocean, and how environmental factors such as turbidity, depth and sea ice impact their trophic diversity. To do so, stable isotope values of carbon (δ13C), nitrogen (δ15N) and sulfur (δ34S) were analysed in tissues of sea star sampled across the Southern Ocean (n = 2454 individuals, plus data on 204 individuals from the literature or shared by colleagues). A significant proportion of the sea star samples came from collections archived in institutions and/or museums, which significantly increased the spatial and temporal coverage of the study. However, most of these samples were preserved in ethanol, and some have been previously fixed with formaldehyde. Preservative fluids may alter the stable isotope values of biological tissues. Therefore, the impact of the preservation method on the stable isotope values in sea star tissues was studied (chapter 3). A two year-long experiment showed that it was possible to mathematically correct the effect of preservative fluids on stable isotope values in sea stars, making it possible to use archived samples for trophic ecology studies. In order to better understand the potential importance of sea stars in the ecosystems of the Southern Ocean, the food web of subantarctic Macrocystis pyrifera (Phaeophyceae, Laminariales; or “kelp”) forests was reconstructed by analysing stable isotope values in invertebrate (19 taxa, including 6 sea star taxa) and primary producer tissues sampled in the Kerguelen Islands (chapter 4). Mixing models did not highlight major Macrocystis pyrifera consumers and showed that the food web is supported by pelagic organic matter and live (with the exception of kelp) or detrital micro/macrophytobenthos. This suggests that sea stars do not have the same ecological function in Macrocystis pyrifera forests from subantarctic regions than in those from more temperate regions, where they control grazer populations. The results also show that sea stars are not only top predators in the food chain. On the one hand, some species may occupy lower trophic positions. On the other hand, their trophic niches may not overlap: some species rely more on the food chain supported by pelagic production and others on the food chain supported by benthic (including detrital) production. Following this analysis of an entire food web, isotopic niches of sea stars were compared at a local scale, and the possible relationship between ontogenetic changes, i.e. changes during growth, and trophic ecology were studied (chapter 5). The analysis of stable isotope values in sea stars sampled in Ezcurra Inlet (Admiralty Bay, King George Island, South Shetland Islands, chapter 5) showed that the size, and especially the central disc radius, can be linked to stable isotope values in some species, indicating the occurrence of ontogenetic changes in the diet of these species. This was observed only in some species, and notably omnivore species, for which the trophic position increased with body size. The relationship between the disc radius and the trophic ecology may be explained by larger sea stars being able to evert their stomach over larger areas and thus consume larger prey and/or prey with higher trophic level. For sediment feeding and potentially suspension feeding species, the relationship between size and stable isotope values was usually not observed, suggesting lower variability of the trophic ecology between size classes in these species. The analysis of stable isotope values in sea stars sampled in Ezcurra Inlet also indicates that the diet variability of some sea star species may be important, which in part determines their interspecific trophic interactions. The turbidity generated by the terrestrial inputs provided by meltwater run-off from terrestrial glaciers results in an important environmental gradient from the inner to the outer Ezcurra Inlet, which determines the habitat conditions and the characteristics of the resources available for sea stars. Some species may adapt their diet depending on those variable conditions. Interspecific interactions are also impacted. Indeed, the Diplasterias brandti and Odontaster validus species have more different δ13C values (i.e. more different food sources) and lower isotopic niche overlap in the inner inlet, where high turbidity occurs, than in the outer, where turbidity is lower. Similarly, the size of the isotopic niche of Odontaster validus is smaller in the inner Ezcurra Inlet than in the outer. This is probably the result of a more limited availability and diversity of resources in the inner inlet. This may lead to the constriction of Odontaster validus isotopic niche and to resource segregation that may limit interspecific competition between the few species able to survive in these unfavourable conditions. In the chapter 6, the impact of trophic group, depth, sea ice concentration and sea ice season duration on the trophic ecology of sea stars was assessed thanks to a global analysis of the dataset at the scale of the whole Southern Ocean. The Southern Ocean was subdivided into different benthic ecoregions according to environmental (seabed temperature, sea ice, bathymetry) and biotic data (species distribution), to study biogeographic variations in the trophic ecology of sea stars. This subdivision notably highlighted the separation between Antarctic and Subantarctic environments, with the different δ13C values in organic matter from the surface in Subantarctic and Antarctic waters being reflected in tissues from benthic sea stars. In this chapter, the compilation of the available information on their diet allowed to make a classification of sea star taxa from the Southern Ocean into trophic groups, ranging from suspension feeders to predators of active prey. The differences of stable isotope values between trophic groups and their variability in some of them suggested a diversity of food sources and/or of feeding strategies between and within trophic groups. These results confirm that, contrary to what is sometimes stated in the literature, sea stars in the Southern Ocean show a great trophic diversity. Depth has important effects on the trophic ecology of sea stars, both across the entire Southern Ocean and within ecoregions. Indeed, coastal sea stars may exploit food webs supported by a variety of pelagic and benthic primary producers while deeper sea stars may depend on the sedimentation of the surface primary production. Coastal sea stars are then characterised by a high diversity of food sources, while deeper sea stars have a higher diversity of trophic positions than coastal ones. The lower diversity and availability of food sources in deep waters may induce the diversification of sea star feeding behaviours (e.g. omnivory, predation, sediment feeding), which would reduce competition between species. The impact of sea ice on the trophic ecology of sea stars was also investigated. The sympagic communities may be used as a food source by sea stars in case high sea ice concentrations. Furthermore, increasing reliance on degraded phytodetritus during longer periods of sea ice cover may occur in several trophic groups. This may dampen the impacts of sea ice presence on resource availability during long periods of sea ice cover. Our results also suggest that multiple relationships do exist between sea ice and the diet of benthic consumers, but they are not easy to interpret. Finally, not all of them are consistent across ecoregions, probably as a result of their contrasted oceanographic features. In addition, the impacts of the environmental parameters may differ between trophic groups, highlighting the importance of trophic diversity to predict the sensitivity of sea stars to future environmental changes, whether natural or anthropogenic. To summarise, the studies of this thesis show that the trophic ecology of sea stars from the Southern Ocean is impacted by a combination of intrinsic (body size, trophic group) and extrinsic features (turbidity, depth, sea ice). Information on the influence of environmental parameters may provide hypotheses regarding the possible impacts of climate change on sea stars and on their role in benthic food webs of the Southern Ocean. Indeed, the environmental parameters may influence the trophic ecology of sea stars and the trophic interactions between taxa thanks to their impact on resource availability. The lower diversity and availability of food sources in turbid and deep waters have been considered as potential sources of diversification of feeding behaviours to avoid competition between species. By contrast, their greater availability in less turbid and coastal environments allows the consumption of similar prey with limited risks of competition. Sea ice has more variable impacts on resource availability, being an habitat for sympagic communities and inducing phytoplankton blooms after its break up, but inhibiting them in case of persistence. Consequently, changes in the ice cover and its dynamics because of climate change will induce changes in the resource availability for the Southern Ocean benthos. Similarly, changes in turbidity in coastal areas as a result of modifications in the dynamics of terrestrial glaciers could have consequences on resource availability in this type of environment. These changes are likely to modify the trophic interactions between sea star taxa, with an increase or decrease of the importance of competition, which may result in modifications of the structure of sea star assemblages in the Southern Ocean. [less ▲]

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See detailStudy on flavor composition and factors influencing the formation of volatile compounds in stewed pork
Han, Dong ULiege

Doctoral thesis (2020)

The traditional stewed pork is a famous sauce pickled product in China and often produced by stewing the fresh pork in aged brine. Here, the aged brine included water and various ingredients such as salt ... [more ▼]

The traditional stewed pork is a famous sauce pickled product in China and often produced by stewing the fresh pork in aged brine. Here, the aged brine included water and various ingredients such as salt, sugar, spices, soy sauce and cooking wine. Because of its unique sensory characteristics, for example tender texture, bright colour and rich flavour, the stewed pork is appreciated by consumers. However, the traditional stewed pork also has faced a number of potential problems in recent years. Among them, the most important is the volatilization and loss of flavour compounds. In order to solve this problem, the flavour compounds in the stewed pork were fully analysed and a new processing technology were proposed. Firstly, the flavour compounds profile and odour-active compounds in the stewed pork from four local brands, Dahongmen (DHM), Daoxiangcun (DXC), Henghuitong (HHT) and Tianfuhao (TFH), were evaluated by GC-MS/O and E-nose combined with chemometrics analysis. A total of 62 volatile compounds were identified and quantified in all pork samples, and 24 of them were considered as odour-active compounds because their OAVs were greater than 1. According to principal components analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) of GC-MS/O and E-nose data, the stewed pork samples were divided into three groups (DHM, HHT, and DXC-TFH). The PLS-DA result showed that 9 odour-active compounds (heptanal, nonanal, 3-carene, D-limonene, β-phellandrene, p-cymene, eugenol, 2-ethylfuran and 2-pentylfuran) were confirmed to the potential flavour markers for the discrimination of stewed pork products. Secondly, the effects of different pork breeds on the aroma profiles of boiled pork were investigated. The three varieties of pigs are Tibetan, Sanmenxia and Duroc × (Landrace × Yorkshire). The volatile compounds and odour-active compounds in boiled pork from three different breeds of pigs were identified and quantified using gas chromatography-olfactometry-mass spectrometry (GC-MS/O) and odour activity values (OAVs). A total of 61 volatile compounds were identified, among which 25 compounds were selected as odour-active compounds in boiled pork. Hexanal, nonanal, 1-octen-3-ol, dimethyl disulphide, heptanal, 2-pentylfuran and 2-ethylfuran were the important contributors to the whole flavour of boiled pork. The flavour profile was determined by E-nose based on principal component analysis (PCA). This result showed that boiled pork from the three pig breeds could be clearly distinguished. The radar chart of response value of E-noes sensors displayed the boiled pork from different pig breeds had significantly different flavour, and that boiled pork from the fore leg and hind leg muscles of pigs had similar aroma compositions. The above analyses showed the different pig breeds had a greater influence on flavour of boiled pork than pigs in different parts, and the GC-MS/O combined with E-nose was a feasible method to determine and distinguish the volatile profiles of different varieties of pork samples. Besides, the influence of different seasoning recipes (SP1: stewing pork in water, SP2: stewing pork with water and salt, SP3: stewing pork with water, salt and spices, SP4: stewing pork with water, salt, spices and soy sauce, SP5: stewing pork with water, salt, spices, soy sauce and sugar, SP6: stewing pork with water, salt, spices, soy sauce, sugar and cooking wine) on volatile profiles and sensory evaluation of stewed pork were studied. The GC-MS/O and two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GC × GC-TOFMS) were applied to detect the flavour profile in stewed pork form different seasoning recipes. The stewed pork processed using SP1 and SP2 had the most abundant volatile compounds, especially aldehydes. Which indicated that the cooked pork with water and salt promoted lipid oxidation and amino acid degradation. Samples SP3, SP4, SP5 and SP6 were close each other in PC1-PC2, whereas samples SP3 was located on the opposite side of samples SP4, SP5 and SP6 in PC1-PC3 using PCA. It was showed that the addition of spices had a significant influence on the flavour of stewed pork. Sensory evaluation revealed the stronger spicy odour, caramel odour and soy sauce odour were presented in samples SP3, SP4, SP5 and SP6. These results were consistent with the results of partial least squares regression (PLSR). Finally, the volatile compounds and non-volatile compounds of stewed pork with different processing methods (TS: traditional stewing, TSE: traditional stewing with enzymatic degradation, TSE: traditional stewing with enzymatic degradation and Maillard reaction, HS: high-temperature stewing, HSE: high-temperature stewing with enzymatic degradation, HSEM: high-temperature stewing with enzymatic degradation and Maillard reaction) were analysed. The high-temperature stewed pork (HS, HSE and HSEM) had a higher content of volatile composition than traditional stewed pork (TS, TSE and TSEM), especially sample HSEM. The traditional and high-temperature stewed pork samples clearly distinguished by E-nose method. The contents of umami amino acids (UAAs), sweet amino acids (SAAs) and bitter amino acids (BAAs) of high-temperature stewed pork were higher significantly (P < 0.05) than those of traditional stewed pork, of which the content of Asp and Glu related to umami taste were the most in sample HS and HSEM. The high-temperature stewed pork showed the lower contents of 5’-nucleotides and fatty acids (FAs) than traditional stewed pork. It was concluded that the pork with high-temperature stewing (HS, HSE and HSEM) could be used as an effective method to improve the taste and odour of stewed pork, moreover, sample HSEM had a great advantage in the formation of odour compounds. [less ▲]

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See detailDevelopment of novel aptasensors for the detection of mycotoxins
Guo, Xiaodong ULiege

Doctoral thesis (2020)

Mycotoxins contaminants, one of the most serious global challenges, have been attracted more and more attention from International Agency for Research on Cancer (IARC) of the World Health Organization ... [more ▼]

Mycotoxins contaminants, one of the most serious global challenges, have been attracted more and more attention from International Agency for Research on Cancer (IARC) of the World Health Organization (WHO) and scientists in food safety sciences. Many countries and organizations have established the maximum contamination level of the main mycotoxins at very low values. Traditional analytic strategies are mainly based on instrumental quantitative method and immunoassays approaches. Aptamer, a novel molecules recognition element like or even superior to antibodies, has attracted more and more attentions for scientists. Therefore, specific aptamers could be employed to construct biosensors for the detection of mycotoxins. The objective of this thesis is to develop novel aptamer-based biosensors for sensitive determination of trace levels of mycotoxins and to provide a promising application of these aptasensors for more hazard factors in food safety sciences. The main contents and results are as follows: (1) Aptamer-based biosensor for detection of mycotoxins Mycotoxins are a large types of secondary metabolites appeared by fungi, they pose a great hazard and toxic reactions to human and animals. A majority of countries and regulators, such as European Union, have established series of requirements and set the maximum tolerated levels. The development of high sensitive and specific analytical platform for mycotoxins is much in demand to address new challenges for food safety in worldwide. Due to the superiority of simple, rapid, and low-cost characteristics, aptamer-based biosensors are successfully developed for the detection of various mycotoxins with high sensitivity and selectivity compared with traditional instrumental methods and immunological approaches. In this article, we discuss and analyze the development of aptasensors for mycotoxins determination in food and agricultural products during the last eleven years and cover the literatures from the first report in 2008 until today. In addition, challenges and future trends for the selection of aptamers towards various mycotoxins and aptasensors for multi-mycotoxins analysis are summarized. Given the promising development and potential application of aptasensors, the future researches will witness the great practicability of aptamer-based biosensor for food safety field. (2) A qPCR aptasensor for sensitive detection of aflatoxin M1 Aflatoxin M1 (AFM1), one of the most toxic mycotoxins, imposes serious health hazards. AFM1 had previously been classified as a group 2B carcinogen (IARC, 1993) and has been classified as a group 1 carcinogen by the International Agency for Research on Cancer (IARC) of the World Health Organization (WHO) (IARC, 2002). Determination of AFM1 thus plays an important role for quality control of food safety. In this work, a sensitive and reliable aptasensor was developed for the detection of AFM1. The immobilization of aptamer through a strong interaction with biotin–streptavidin was used as a molecular recognition element, and its complementary ssDNA was employed as the template for a real-time quantitative polymerase chain reaction (RT-qPCR) amplification. Under optimized assay conditions, a linear relationship (ranging from 1.0×10-4 to 1.0 µg L-1) was achieved with a limit of detection (LOD) down to 0.03 ng L-1. In addition, the aptasensor developed here exhibits high selectivity for AFM1 over other mycotoxins and small effects from cross-reaction with structural analogs. The method proposed here has been successfully applied to quantitative determination of AFM1 in infant rice cereal and infant milk powder samples. Results demonstrated that the current approach is potentially useful for food safety analysis, and it could be extended to a large number of targets. (3) A novel graphene oxide-based aptasensor for amplified fluorescent detection of aflatoxin M1 in milk powder In this paper, a rapid and sensitive fluorescent aptasensor for the detection of aflatoxin M1 (AFM1) in milk powder has been developed. Graphene oxide (GO) was employed to quench the fluorescence of carboxyfluorescein-labelled aptamer and protect the aptamer from nuclease cleavage. Upon the addition of AFM1, a formation of AFM1/aptamer complex resulted in the aptamer detached from the surface of GO, then the aptamer was cleaved by DNase I and the target AFM1 was released for a new cycle, which led to a great signal amplification and high sensitivity. Under optimized conditions, the GO-based detection of the aptasensor exhibited a linear response to AFM1 in a dynamic range from 0.2 to 10 μg/kg, with a limit of detection (LOD) of 0.05 μg/kg. Moreover, the developed aptasensor showed a high specificity towards AFM1 without interference from other mycotoxins. In addition, the technique has been successfully applied for detection of AFM1 in infant milk powder samples. This aptasensor proposed here offers a promising technology for food safety and can be extended to various targets. (4) Graphene oxide driven fluorescent aptasensor for the detection of fumonisin B1 Fumonisin B1 (FB1), one of the most toxic mycotoxins, has been designated as possible 2B group carcinogen by the International Agency for Research on Cancer (IARC) in 2002. Therefore, simple, sensitive and specific approaches for the detection of FB1 are much in demand. In this study, a novel aptasensor was introduced for FB1 analysis based on graphene oxide (GO) and DNase I signal amplification. GO was adopted as a fluorescence quencher against ROX-modified aptamer and a protectant for the aptamer from cleavaging by DNase I for subsequent target cycling and signal amplification detection. This proposed sensing strategy exhibited a good linearity for FB1 determination in the dynamic range from 0.5 to 20 ng mL-1 with a good correlation of R2 = 0.995. Its detection of limit was established at 0.15 ng mL-1 (S/N = 3). The specific analysis indicated that this aptasensor was selective for FB1 other than other mycotoxins. In addition, the practical application in real samples of this aptasensor for the detection of FB1 was investigated. The sensing platform proposed here was useful for a potential application in the field of food safety for mycotoxins analysis. (5) Articles highlights and future perspective By using the novel aptamer-based biosensors, we developed several approaches for the detection of the most toxic mycotoxins for food safety. In addition, these sensing strategies could be applied for more hazard factors determination by simple replacement of the specific aptamers. More importantly, though the practical applicability, feasibility, and accuracy of these proposed aptasensors were investigated and evaluated through the analysis of the spiked samples experiments, the future’s researches were needed for a validation of these aptasensors with real contaminated samples to determine the performances such as limit of detection and quantification, precision, trueness, accuracy, etc. Through the method validation, these aptasensors will be widely used for the detection of mycotoxins. In addition, future direction will focus on the simplification of analytic principle and devices and the combination of novel aptamers with new materials and techniques to improve the analytical performance and market practicality of aptasensors. [less ▲]

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See detailHow to value labor in agricultural production: a case study in the Red River Delta, Vietnam
Nguyen Thi Hai Ninh, ULiege

Doctoral thesis (2020)

In Vietnam rural area, agricultural production is still a main occupational activity of millions laborers and be major income source of them. Despite this important role, it is often debated that the most ... [more ▼]

In Vietnam rural area, agricultural production is still a main occupational activity of millions laborers and be major income source of them. Despite this important role, it is often debated that the most concerning issue in labor market of Vietnam rural areas is job creation. In other word, the actual capacity of agriculture to create new employment is rather low compare to non-agricultural sectors. This issue leads to the large migration of young, experienced and skilled laborers from rural to urban areas as well as from agriculture to non-agricultural sectors. As a consequence, agricultural labor in many provinces of the country are mostly un-trained and the old aged. This shortage of skilled laborers not only directly affects agricultural production at farm household level but also is a challenge to the implementation of rural renewal targets of the Vietnamese Government. Furthermore, the lack of new job creation for agricultural works in parallel with poor skilled and old aged result in the low wage rate of laborers who work in agricultural sector. This wage rate is equivalent to two-third of the wage of employees in industrial sector, and 50% of the wage of those working in service sector. Not only wage, other forms of value of agricultural employees such as social protection, working condition are also less concerned by employers in rural labor market and the current Vietnam Labor Code neither. In order cope with the shortage of skilled farm labor, rural households in the Red River delta diversify their use of labor by combining family laborers with hired laborers for agricultural activities. Family labor source contains both family farm laborers and family non-farm laborers but still participating in farming activities of the household, especially in the peak season. Within 220 households of the three provinces investigated in this thesis, the highest proportion of family farm laborers is over 45 years old and women are discovered to mostly in charge in agricultural production, especially in rice farming. That is because more non-farm jobs opportunities open for young, healthy, and skilled men rather than women. Hired laborers in agriculture in Bac Ninh, Hai Duong and Thai Binh provinces are divided into two types, seasonal hired laborers and permanent hired laborers. Seasonal laborers are often hired to work in peaking time. In rice farming households, seasonal hired laborers usually work for short period of time such as for the land preparing, transplanting, and harvesting. In clam farming households, seasonal laborers are widely rent in preparing clam plots and harvesting. In general, women are observed to work in seasonal hiring more frequently than men in both household groups. However, seasonal hired laborers are not detected in pig farming group. Alternatively, laborers in this group are hired on a permanent or longer-term basis, normally from three months to a year. When using hired laborers in agricultural production, farm households give the laborers payment that are equivalent to their labor value. Of these payment, wage is considered as the most important value of hired laborers. Basically, the wage is paid in two methods, daily wage for seasonal laborers and monthly wage for permanent ones. The daily wage is applied for farming activities which last within a few days such as manual transplanting, manual harvesting in rice farming or clam harvesting. The daily wage may be paid in piece for activities such as land preparation and spraying pesticide. Whereas, the monthly wage is common for laborers in pig farming and clam plot guarding. The wage is counted for 30 working days. Average monthly wage of a hired laborer is 161 USD in pig farming and 175 USD in clam farming. Thus, wage rate of hired farm labor in the study sites is equivalent to 70% and 66% of the wage of laborers in industrial and service sector, respectively. A part from the wage, there are different forms of labor values paid by the householders through remuneration such as drink, lunch, bonus for good performance and support for sickness. Such remuneration can be paid in cash or in kind which ranges from 0.3 to 9 USD. For hired laborers, labor welfare usually is a luxury metric as they work in farm households with only verbal agreement. Without written contract, they receive no health insurance and social insurance support. Despite the rather low in wage and labor welfare, hired laborers still present the satisfaction with their employment. Wage is a work feature which contributes the most to their satisfaction, relation with householder is the second important factor. This relationship proves a crucial function of social relation in driving labor supply and demand in agricultural labor market rather than an economic one. Similar to many developing countries, imperfect information is a typical characteristic of the agricultural labor market of the Red River delta, Vietnam. This imperfection influences labor demand in terms of raising cost for monitoring hired laborers of farm households. On the other side, labor migration is considered as a determinant impacting on labor supply of the rural labor market. This study discovers a positive correlation between remittance of migrated laborers sending home and wage paid to hired laborers in the pig and clam farming groups. Conversely, the more development of agricultural machinery renting market, the less value that householders have to pay for hiring manual farm laborers. In addition to these external determinants, farm size of household, gender and work experience are internal factors which impact on the wage rate that hired laborers can receive. Among the three household groups, the wage of hired laborers in the clam farming is 3.9% higher than the one in the rice farming group. In order to increase the labor value in agricultural production, several interventions by central government and local authorities at different levels in the Red River delta should be taken into account: (1) including agricultural wage laborers into the governance of labor code; (2) promoting the operation of employment service centers in rural areas; (3) improving work skill of farm laborers above 40 years old through training courses which connect with labor demand in the rural labor market. [less ▲]

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See detailBiodiversity and ecosystem services in tropical forests: the role of forest allocations in the Dja area, Cameroon
Lhoest, Simon ULiege

Doctoral thesis (2020)

Due to human-driven environmental changes, planet Earth has entered the new Anthropocene era, with major impact on biological diversity recognized as the sixth mass extinction period. The concepts of ... [more ▼]

Due to human-driven environmental changes, planet Earth has entered the new Anthropocene era, with major impact on biological diversity recognized as the sixth mass extinction period. The concepts of biodiversity and ecosystem services (ES) have risen to objectify and measure the human impacts on ecosystems and the many-fold contributions of ecosystems to human well-being. Among global terrestrial ecosystems, tropical forests are particularly important for the conservation of biodiversity and for the provision of ES. Agricultural conversion, logging, hunting, commercial poaching and over-harvesting lead to deforestation, degradation and defaunation of tropical forests, with highly variable consequences depending on many local factors. In Central Africa in particular, biodiversity and ES have been far less studied than in other tropical regions, despite the vital roles of these tropical forests in the livelihood of tens of millions of people in a context of high poverty. A better understanding of the determinants of biodiversity and ES in Central Africa is crucial for improving human well-being and the resilience of forest ecosystems. Despite the still relatively preserved tree cover across the region, biodiversity and ES may differ depending on forest land management and allocations. Therefore, the objective of this thesis is to assess the conservation value of tropical forests in southeastern Cameroon, as well as the supply of ES and use by local populations, in three contrasted forest allocations: a protected area, a Forest Stewardship Council (FSC)-certified logging concession, and three community forests. First, we assessed the conservation value of the three forest allocations, examining species richness and composition of two taxonomic groups: mammals inventoried with 44 camera traps, and dung beetles inventoried with 72 pitfall traps (Chapter 2). We also aimed to identify the determinants of forest conservation value, disentangling the effects of forest allocations, proximity to human settlements (villages and roads), and local forest habitat. Mammal and dung beetle species showed lower species richness in the community forests than in the protected area, and intermediate values in the logging concession. Proximity to human settlements and disturbance was negatively correlated to species richness of both groups, negatively correlated with species body size, and associated to the loss of the most threatened mammal species. The high species variability among forest allocations (i.e., spatial turnover) suggests that any conservation initiative should integrate many sites to protect a multitude of species, and not only large isolated areas. The high conservation value of the protected area has been confirmed, and the logging concession can play a complementary role in conservation strategies through landscape connectivity. In contrast, community forests are particularly defaunated due to their proximity to roads and villages, but they still provide wild proteins to local populations. Second, we assessed the perceptions of the supply of ES by tropical forests to local populations, and the determinants of these perceptions (Chapter 3). We evaluated the significance and abundance of ES by conducting a questionnaire survey with 225 forest stakeholders. The most significant ES perceptions were provisioning services (93% of respondents) and cultural services (68%), while regulating services were much less reported (16%). The perceptions of ES abundance were relatively homogeneous among forest allocations and respondents. Bushmeat provision has been identified as the only significant ES for local populations that is not supplied in high abundance. Third, we depicted the use of ES by local populations in three villages, and we evaluated its determinants and sustainability (Chapter 4). We used diverse interviews and field surveys to assess three provisioning services (bushmeat, firewood, and timber) and five cultural services (cultural heritage, inspiration, spiritual experience, recreation, and education). On average, local populations consumed 56 kg of bushmeat person–1 year–1 (hunting zones covering on average 213 km² per village), 1.17 m³ of firewood person–1 year–1 (collection zones on average 4 km² per village), and 0.03 m³ of timber person–1 year–1. On average, 59% of respondents recognized the importance of cultural services. The main determinants of ES use were forest allocations, population size, and deforestation rate, and we also showed slight differences between Baka and Bantu people in the use of cultural services. Firewood and timber have been shown to be used sustainably by local populations in this area, whereas bushmeat hunting and consumption have exceeded sustainability thresholds. Finally, the main findings of the thesis are summarized and their practical implications are discussed, in particular for the role of forest allocations (Chapter 5). The potential reconciliation between conservation and the sustainable use of tropical forests is discussed. Methodological feedbacks are given for the use of mammals and dung beetles as biodiversity indicators. Research perspectives are presented for a better understanding of the interactions between biodiversity and ES. Finally, different perspectives for integrating the concept of ES in tropical forest management are given: for instance, identifying and resolving conflicts among stakeholders, raising awareness, making decisions, or evaluating the effectiveness of conservation measures. In particular, ES are increasingly used in concrete management applications, such as FSC-certification, payments for environmental services, UNESCO Man and Biosphere Reserves, and various development projects. [less ▲]

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See detailMigrant workers in industrial zones and return migration: Case studies in Que Vo and Yen Phong industrial zones of Bac Ninh province and Van Thang commune of Nong Cong district, Thanh Hoa province, Vietnam
Ngo Trung Thanh, ULiege

Doctoral thesis (2020)

It is clear that the important role of labor migration in development reflected through the impacts of remittance currently exists in many countries around the world. The complexed nature of migration ... [more ▼]

It is clear that the important role of labor migration in development reflected through the impacts of remittance currently exists in many countries around the world. The complexed nature of migration that needs to interpret in a dynamic context and a changing society. Reviewing literature demonstrates the discourses of the motives of migration across many migration theories. Then, there are plenty of discussions of the motives of migration added from empirical research. However, there is still a lack of literature that requires discussion on why the domestic migrants leave their homes to work at places considered as exploitative and degrading, like industrial zones. In addition, migration is understood as an in and out process. Attempts have been made to explain the motive of out-migration, but few ones focus on return migration. Furthermore, existing literature focuses more on international return migration than internal return migration and the theories of return migration are subject to various debates. Since 1975, after the reunion of Vietnam, the government enforced a policy to restructure the population which led to inter-province migration. Many studies have been conducted on migration ever since, but few focused on return migration. This research survey 310 migrant workers in Que Vo and Yen Phong industrial zones of Bac Ninh province, and 68 returnees in Van Thang commune, Nong Cong district, Thanh Hoa province of Vietnam. Face to face interviews with two designed questionnaires have been applied to those samples. One is for migrant workers and the other is for returnees. Besides, some qualitative methods are also applied for supplementing the data collected by the questionnaires. Through those principle methods, this study found that the motives of migrant workers are complex. Push and pull theory by itself is not enough to explain these motives. The addition of the new economic theory of migration labor has made the explanation of migration motives more complete. Also, the research illustrated that the factors pushing rural people outmigration are, firstly, the local shortage of non-agricultural jobs, causing migrant workers to find alternatives in Bac Ninh industrial zones. More importantly, there is a shortage of cash for daily consumption. This itself, agricultural production, a prominent feature of rural areas, cannot be solved. Interestingly, the economic status of the household before the migration is not considered clearly as a push factor. But, migration to industrial zones is the rural youths’ way of life. Experiencing in these zones aspires those people due to a life different from the areas of origin, acted as a pull factor. Furthermore, migrant workers are all attracted by high labor demand that created easier access to employment in the industrial zones of Bac Ninh. This study also found that social network acts as both push and pull factor for immigrating to the industrial zones. Furthermore, it revealed that migrant workers, a major labor force for industrial zones, now face challenges created by the unstable model of development. The sustainability of the development of industrial zones in Bac Ninh is threatened by the fact that these zones follow the footloose of their development model exposed in the 1990s. Additionally, this study found that migrant workers in industrial zones in Bac Ninh faced a trade-off between accepting a hard life and accumulating capitals as well as experiences for an expected better one afterward. Furthermore, the migration undertaken by migrant workers in industrial zones of Bac Ninh seems to be circular. Regarding return migration, this study demonstrated that the motive to return not only results from potential failures related to the increased living costs of the future married life but also associates with children left behind at the home village with stayers. Returnees are all driven by a filial obligation to their parents, shaped by the norms or culture of the home community. Non-farm employment opportunities around home villages are more of a motive to return for single migrants. This study also found that women play an important role in agriculture development in Van Thang. This sector is likely a buffer for the negative impacts of the return while the returnees seek better nonfarm employment around their home villages. [less ▲]

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See detailEconomic analysis of small scale freshwater aquaculture production and its product marketing channels in agro-aquaculture system in Hai Duong province, Vietnam
Nguyen Van Huong, ULiege

Doctoral thesis (2020)

VAC stands for the first three letters of three words: Garden (V), pond (A), cage (C), referring to a smallintensively farming ecosystem model to solve the shortages of food and develop rural economy in ... [more ▼]

VAC stands for the first three letters of three words: Garden (V), pond (A), cage (C), referring to a smallintensively farming ecosystem model to solve the shortages of food and develop rural economy in Vietnam. It has been shaped and developed for nearly four decades since Vietnam finished the wartimes and reunification in 1975. At first, the VAC economy may seem to be small, and just a "informal economy". However, it has been soon become an important role for the strategy of self-sufficient food and economic development to overcome difficulties and hardships of transition period in the past. Since Vietnam approved the autonomous role of household economy after the revolution of “Doi Moi”, the VAC model has been widespread promoted and exploited by many local provincial authorities and farmers in over the country. Hai Duong province is one of the provinces, which has encouraged farm households to develop the VAC model since begin of the 1980s when it first was introduced in the Red River Delta in Vietnam. As impacted VAC ecosystem model, many types of fish farming have been practiced in Hai Duong where emerges to many zones of concentrated aquaculture production converted from rice fields. With the introduction of fish in the existing agricultural systems, farmers have diversified the farming practices in the optimal manner of land use to improve the nutritional food status, increase household income, and create more employment. This leads to the fish production becoming very diverse, complex and dynamic in Hai Duong province. The study has designed to understand the diversifications of the integrated small scale aquaculture (SSA) production models in the Red River Delta. The study results show that four models have been found such as single commercially-intensive fish production system (FS), Animal Fish system (AF), New VAC system and traditional VAC system with different characteristics. Despite these SSA models are differed from one another, they are all in favoured of producing food for farmers’ home consumption or/ and commercial products for cash income in parallel reduction the seasonal situation of unemployment in rural areas. Particularly, the economic efficiency of the SSA models has made a great contribution to improve the farm households’ economic condition in the rural in Hai Duong province, Vietnam. These freshwater SSA models are considerably dynamic and diversified by household strategies. In general, they have good efficiency in terms of job creation, food production, and economic benefits. The study also shows that the AF model has the highest economic return while the FS model obtains the lowest. The new VAC and traditional VAC models are significantly diversified to generate different sources of onfarm income. Whereas the new VAC model with a focus on high market value species has higher economic efficiency than the traditional VAC model. This reflects VAC can be developed to in a manner that can generate more cash income for the rural farm households in Hai Duong. Besides, the SSA models have been more intensified and developed the different species of marketable fish to supply to increasingly market demand, fish farmers have been being still faced to many challenges and difficulties of marketing their fish products such as lacks of outlets and marketing channels available at local markets, shortages of storing facilities, means of transportation, and market volatility. These problems require to more governmental interventions on both production and marketing to assist small scale aquaculture production to maintain as a strategic tool to develop the local economy as well as provide farm households a sustainable livelihoods. The supports might be focus on enhancing the production management skills, and market organized in both wholesale and retail markets that would be the most appropriate measures to facilitate the SSA models more developing in Hai Duong province. [less ▲]

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See detailDeveloping decision-support tools with economic and environmental interests for the dairy sector using milk mid-infrared spectrometry
Delhez, Pauline ULiege

Doctoral thesis (2020)

Maintaining satisfying economic outcomes and limiting environmental impacts are key challenges in dairy farming today and this requires good decision-making regarding actions to make on farms. The ... [more ▼]

Maintaining satisfying economic outcomes and limiting environmental impacts are key challenges in dairy farming today and this requires good decision-making regarding actions to make on farms. The analysis of milk by Fourier-transform mid-infrared (MIR) spectrometry provides valuable information on milk composition. This technique has already demonstrated qualities to support decision-making, for example, through the well-established predictions of milk fat and protein contents or the latest development of prediction models for novel traits. However, its full potential remains partly uninvestigated. Hence, the objective of this thesis was to contribute to the development of decision-support tools with economic and environmental interests for the dairy sector using milk MIR spectrometry. The research conducted in the framework of this thesis covered three different approaches of using MIR for decision support: (1) the development of a MIR calibration equation to predict a trait of interest, (2) the development of a test-day model to predict milk MIR spectra for management purposes, and (3) the combination of MIR-predicted data with other data streams as a means of providing additional information for decision-making. First, we explored different strategies to predict the pregnancy status of dairy cows (pregnant vs. open) in Australia using milk MIR spectra and partial least squares discriminant analysis. Correctly identifying the pregnancy status of cows is imperative for a profitable dairy farm. Early pregnancy could not be detected satisfactorily, but promising results were obtained using MIR spectra recorded 151 days or more after insemination (i.e., mid- and late gestation), with the area under the receiver operating characteristic curve of 0.76 on the testing set. A potential application that needs to be explored further is the development of a screening tool to detect mid- to late-term fetal abortion. Secondly, we studied the ability of a test-day mixed model to predict milk MIR spectra from first parity Holstein cows for management purposes (e.g., for the detection of problems, simulations, predictions of future data). The spectral data used for modeling originated from the Walloon milk recording database. The average correlation between observed and predicted values of each spectral wavenumber was 0.85 for the modeling set and ranged from 0.36 to 0.62 for different scenarios that corresponded to situations with more or less information known about the cows. Correlations between milk fat, protein and lactose contents predicted from the observed spectra and from the modeled spectra ranged from 0.83 to 0.89 for the modeling set and from 0.32 to 0.73 for the scenarios. These results demonstrated a moderate but promising ability to predict milk MIR spectra using a test-day model. Different improvements of the model are possible before potential practical applications that could have economic or environmental implications for dairy farming, depending on the MIR traits subsequently predicted from the modeled spectra. Thirdly, we investigated the univariate relationships (correlations) between dairy cow enteric methane (CH4) production (g/day) predicted from milk MIR spectra and 42 technico-economic variables from 206 Walloon dairy herds over a period of 8 years. Enteric CH4 is an important part of the carbon footprint of milk production. Significant correlations ranged between |0.06| and |0.38|. Low MIR CH4 production tended to be associated with more extensive or suboptimal management practices, which could lead to lower profitability. The observed weak correlations suggest intricate interactions between MIR CH4 and technico-economic variables due to the use of real farm data with large variability in management practices. This implies the need for further research to unravel these complex relationships for a better understanding of factors associated with CH4 production on dairy farms in order to better target mitigation strategies. Lastly, we discussed, in the light of the research carried out in this thesis, strengths as well as issues and considerations regarding the development of decision-support tools using milk MIR. In particular, key strengths of MIR are the low cost and rapidity of the technology as well as the standard procedures for milk sample collection and analysis, allowing the acquisition of MIR data on a large scale for the development of various customized tools to assist decision-making on dairy farms. Issues and considerations covered the prediction of indirect MIR traits, the quality and variability of spectral and reference data, the choice and validation of models, the utilization of MIR indicators, the study of MIR traits in the population, the timing of milk sampling, and the uptake of MIR tools by farmers. In conclusion, this thesis contributed (1) to establish the first steps of the development of new MIR tools and studies to support decision-making in dairy farming with potential economic and environmental benefits; and (2) to gain insight into the benefits and considerations of using milk MIR for the development of decision-support tools. [less ▲]

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See detailEtude de la mise en place des services pérennes de vaccination animale en milieu rural en République Démocratique du Congo : Cas de lEtude de la mise en place des services pérennes de vaccination animale en milieu rural en République Démocratique du Congo : Cas de la maladie de Newcastle dans trois provinces du Sud-Ouest
Lwapa Embele Isenge, Francis ULiege

Doctoral thesis (2020)

The Democratic Republic of Congo (DRC) has a population living mostly in rural areas (70%). Most of this rural population (80%) are agro-pastoralists. For these households, livestock farming constitutes a ... [more ▼]

The Democratic Republic of Congo (DRC) has a population living mostly in rural areas (70%). Most of this rural population (80%) are agro-pastoralists. For these households, livestock farming constitutes a form of on-farm savings that can be mobilized in case of need. Endemic infectious diseases that can be prevented by vaccination regularly threaten the main domestic animal species kept by these households. Furthermore, following the evaluation of the Performance of the Veterinary Services of DRC carried out by the OIE in 2011, these diseases, in particular the Newcastle disease in chickens, the peste des petit ruminants, the foot-and-mouth disease, the contagious bovine pleuropneumonia, anthrax and blackleg in ruminants and rabies in dogs, were ranked as priorities. At the dawn of the year 2020, no systematic control measures for these diseases had been taken at the national level. The establishment of sustainable animal vaccination services in DRC is an urgent necessity. In this situation, one way of establishing effective and sustainable vaccination services would be to establish schemes for recovering costs of vaccination from the users of the services. This doctoral research investigates the appropriateness and modalities of setting up paid animal vaccination services in a rural Congolese context marked by poverty and difficult access. Semi-structured individual interviews (SSII), focus group discussions (FGD) and stated preference surveys were used across four studies to identify the requirements for the implementation of animal vaccination services based on the user-pay principle and the One Health (OH) approach. This study used the vaccination of village chickens against Newcastle disease in three provinces of the southwestern part of DRC as a case study. This vaccination used the I-2 ND vaccine produced locally by the Kinshasa Veterinary Laboratory. This vaccine is thermostable and can be administered by eye drop. To conduct a participatory evaluation of the paid vaccination campaigns of village chickens against Newcastle disease in Kongo Central province, 12 FGD and 160 SSII were organized in four sites (study 1). This participatory process led to the design of a grid for evaluating the performance of animal vaccination services. In order to analyze the demand for paid animal vaccination services, identify preferences and understand the behavior of livestock keepers, a discrete choice experiment was carried out in eight sites out of 320 livestock keepers (study 2). To carry out a participatory evaluation of the value of OH approaches in the development of animal health services in DRC, 15 FGD and 100 SSII were conducted among professionals from Environmental Services (ES), Veterinary Services (VS) and Public Health Services (PHS) in five territories in three provinces (study 3). The expectations and benefits identified by the Congolese stakeholders were compared to the benefits of the OH approach as currently theorized in the scientific literature. This step was followed by the development of an evaluation protocol adapted from the one proposed by the Network for Evaluation of One Health (NEOH). In order to evaluate the synergy between village chicken vaccination networks and public health vaccination networks, 12 FGD and 288 SSII were conducted in six public health zones in three selected territories (study 4). The evaluations of 15 vaccination networks run by Community-Based Health Workers (CBHW) and 15 networks run by public veterinarians were carried out separately on the basis of the evaluation grid proposed by study 1. The results of the two evaluations were then compared. The assessment grid highlighted four strengths in favor of the sustainability of the paid vaccination service for village chickens organized by the Centre Agronomique et Vétérinaire Tropical de Kinshasa (CAVTK) in Kongo Central province. These were the interest expressed by chicken keepers, the perceived efficacy of the vaccine, the availability of the vaccine and the ease of vaccine use. Two weaknesses were identified, namely the poor access of chicken keepers to information and the low motivation of vaccinators. According to the assessment grid developed in this study, the paid vaccination campaign for village chickens in Kongo Central province obtained a performance score of 62.8%, with a diversity of scores between zones (study 1). Farmers preferred a paid vaccination service for village chickens, carried out according to an imposed calendar and administered by a public veterinarian (study 2). SV, SE and PHS professionals in DRC identified four of the eight benefits of the OH approach as described in the literature. Application of the adapted protocol for evaluating the OH approach showed that in DRC, there is a strong implantation of OH thinking and the OH sharing spirit, but a low level of OH learning, OH planning and OH working in the field (study 3). CBHW and veterinarians encountered the same difficulties in the field. CBHW felt that their involvement in the vaccination of village chickens had changed the collaborative relationship between the VS, ES and PHS. In general, according to the assessment grid established here, CBHW scored better (84±3%) than public veterinarians (76±8%). However, only vaccine efficacy criterion showed a significant difference. Furthermore, CBHW teams had achieved an average activity radius of 43.5±30.5 km and public veterinarians an average activity radius of 6.6±4.0 km. The priorities for improving the animal vaccination service seem to be awareness raising among animal keepers and increasing the motivation of vaccinators. The profile of paid animal vaccination service should be adapted to the expectations of farmers while meeting the technical requirements of vaccination. The public veterinarian will supervise the vaccination activities, which will be implemented by trained CBHW, through collective campaigns at fixed periods of the year. The acceptable price would allow the service to be fixed on a sustainable basis and could be increased if confidence in the service provided increases. In the DRC, the professionals of the VS, ES and PHS were willing to work together to reinforce each other and to achieve their common ideal, which is the well-being of the communities they serve. The success of such an approach would require the rejuvenation of veterinary staff in rural areas and the assignment of qualified veterinary professionals capable of designing and co-managing joint activities with the managers of ES and PHS. The results of this thesis showed that village chicken keepers in these three provinces have adopted the user-pay principle for organizing the vaccination of their chickens. The amount collected by the vaccination services could contribute to the partial financing of vaccination activities. It will be used on the one hand to renew vaccine stocks and on the other hand to pay the vaccinators. The performance achieved by CBHW in vaccinating village chickens is proof that the OH approach can help VS to set up sustainable animal vaccination services in DRC. It will be able to solve the problem of sensitization among animal keepers, motivating vaccinators and the lack of human resources. It will provide a partial solution to the cold chain problem. The financial and material resources provided by the CAVTK and the research funds of this thesis have shown that DRC’s veterinary services need to develop a public-private partnership (PPP) for the implementation of activities in favor of animal health. Such a partnership could help these services to boost animal vaccination by making vaccines and cold chains available at the local VS. The failures of vaccination of village chickens observed in some places have shown that the implementation of sustainable animal vaccination services in DRC must not only face organizational, logistical and financial obstacles but must also prevent biological causes of vaccination failures. These failures will have an impact on animal keepers' appreciation of the vaccine's effectiveness and will reduce the rate of adoption of vaccination by them. On the organizational, logistical and financial level, this study showed that three pillars, namely user-pays principle, One Health approach and public-private partnership, could ensure the financing, sustainability and logistics of these services as well as the accessibility of these services to a significant number of animal keepers in the country. Laboratories must be involved upstream of animal vaccination in order to find appropriate vaccine strains, to determine the vaccination status of the herds to be vaccinated, to diagnose possible immunosuppressive diseases in the herds concerned and finally to develop appropriate vaccine strategies. It is also important that support programs be set up to teach animal keepers good animal husbandry practices and biosecurity measures. These are the conditions for an animal vaccination to be effective and for the proposed services to be organized in a sustainable way. [less ▲]

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See detailIn vitro study of the impacts of exposure to mixtures of endocrine disrupting chemicals on the aryl hydrocarbon and steroid receptor transcriptional activity
Doan, Thi-Que ULiege

Doctoral thesis (2020)

Chemicals are undoubtedly important and beneficial for our modern life. As a result, we are exposed to mixtures of chemicals in our daily life through applying them for food production and preservation ... [more ▼]

Chemicals are undoubtedly important and beneficial for our modern life. As a result, we are exposed to mixtures of chemicals in our daily life through applying them for food production and preservation and for supporting human and animal health and recreation. However, risk assessment for the consumer is usually based on a chemical-by-chemical approach. Among these chemicals, endocrine disruptors (EDs) are of concern, in particular because they are able to alter the function(s) of the endocrine system, leading to adverse health effects in organism or (sub) population levels. In vitro Chemically Activated LUciferase gene eXpression (CALUX) assays involving several transgenic reporter cell lines are interesting tools to study the impacts of exposure to mixtures of EDs and their components on the transcriptional activity of the master xenobiotic receptor, which is the aryl hydrocarbon receptor (AhR), as well as the steroid (estrogen (ER), androgen (AR), progesterone (PR), and glucocorticoid (GR)) receptors. Three mixtures were being investigated as examples of compound groups of human everyday exposure to chemicals: (1) the “total POP mixture” consisting of 29 POPs (persistent organic pollutants) prevalent in Scandinavian human blood, (2) the “ED mixture” containing 18 potential EDs dominantly found in Wallonia raw water intended for drinking water production, and (3) the “polyphenol mixture” containing seven food-based polyphenols. The concentration of each component in the mixture was based on human-relevant exposure such as fold human blood level (the POP mixture), fold maximum quantified concentration in raw water (the ED mixture), or fold recommended intake dose from food supplements (the polyphenol mixture). Specific aims of the project were: (a) evaluating species (rat and human) and/or tissue-specific (hepatocytes and mammary gland) AhR responses to the POP mixture and the polyphenol mixture and their components, (b) profiling the endocrine disrupting activities of the EDs and the mixture thereof prevalent in raw water using AhR and steroid receptors, (c) identifying interactions among the chemicals (additive, antagonistic or synergic effects) on the transcriptional activity of the receptors, (d) identifying the actual chemical(s) the most active in the mixtures, and (e) predicting the effect of the mixtures based on the activity of single compounds. The results showed that 16 out of 29 POPs contaminating human blood were AhR antagonists. The total POP mixture also showed an AhR antagonistic activity although it contained each compound at the concentration below its lowest-observed-effect concentration (LOEC). Chlorinated compounds were the drivers of the activity of the total POP mixture, among which PCB-118 and PCB-138 contributed for 90% of the total POP mixture effect. From the 18 EDs prevalent in raw water, chlorpyrifos, bisphenol A, fluoranthene, phenanthrene, and benzo(a)pyrene demonstrated significant activities on several receptors. Noticeably, benzo(a)pyrene mixed with dioxin TCCD induced a synergistic response in AhR- i reporter human mammary gland cells (DR-T47-D), 10-fold higher than the cells’ response to TCDD alone, at a concentration which could be a realistic blood level after a food contamination incident or in a high exposed sub-population. The mixture of the 18 EDs compounds exerted AhR and ER agonistic activities, which can be explained by the activities of benzo(a)pyrene and bisphenol A in the mixture. While the rat AhR reporter cells (DR-H4IIE) was more sensitive to POP exposure, we showed for the first time that the AhR endogenous ligand FICZ, a tryptophan derivative was more potent than TCDD in the human AhR (DR- HepG2) (40 times more potent than TCDD) while both exhibited a similar potency in the rat cells (after 6h exposure). Two isoflavones (daidzein and genistein) induced a higher AhR agonistic/synergistic activity in the rat cells, while the others (a flavonol (quercetin) and two flavones (baicalin and chrysin), curcumin, and the mixture of the seven polyphenols) caused a stronger AhR antagonistic response in the human cells. Quercetin and resveratrol were the strongest AhR antagonists in the human cells, which contributed most for the antagonistic activity of the polyphenol mixture. Dose-response curves were predicted successfully by concentration addition and general concentration addition models for the POP mixture, while both concentration addition and independent action performed well for estimating the effect of the polyphenol mixture, indicating the additive activity of the components in these mixtures. The results suggested that the endocrine disrupting activities of chemicals in human daily life exposure could involve more than one mechanism: their (anta-) agonistic effects on different receptors with the potential for additive, inhibitory or synergistic effects of mixtures thereof should be considered in risk assessment. [less ▲]

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See detailEcomorphology and biomechanics of cetacean backbone in an evolutionary context
Gillet, Amandine ULiege

Doctoral thesis (2020)

Cetaceans (whales, dolphins, and porpoises) represent the most speciose taxon of extant marine mammals and exhibit a tremendous ecological disparity. Although all cetaceans possess a streamlined and ... [more ▼]

Cetaceans (whales, dolphins, and porpoises) represent the most speciose taxon of extant marine mammals and exhibit a tremendous ecological disparity. Although all cetaceans possess a streamlined and hydrodynamic body adapted to their aquatic environment, they also have a wide phenotypic variability at the level of body size, body shape and fin shape. Moreover, the different species exhibit extraordinary disparity in the shape of their vertebral column. As whales and dolphins swim with dorso-ventral oscillations of their backbone, modifications of their vertebral morphology should impact their ability to swim in different kinds of habitats. However, relationships between the vertebral morphology, swimming performances, ecology, and evolutionary history of cetaceans remain uncertain. This thesis aims at providing concrete elements regarding the causes and consequences of the large morphological variability of the cetacean backbone. To this purpose, we computed the largest database of cetacean vertebral morphology ever created by quantifying the vertebral shape of 73 species (i.e., 80 % of extant diversity). These morphological data were combined to backbone biomechanics and swimming kinematics data and were analysed in both evolutionary and ecological contexts. Our results demonstrate that both ecological and phylogenetic factors are associated to vertebral shape. We identified two distinct phenotypic evolutionary patterns: non-delphinoids and delphinoids. Non-delphinoids are a paraphyletic group comprising several cetacean clades: mysticetes, sperm whales, beaked whales, and 'river dolphins'. They are all characterised by a low number of elongated vertebrae, resulting in relatively flexible backbones. In this clade, inshore species retained a small body size while offshore species evolved towards an increased body size accompanied by a slightly increased vertebral count (pleomerism). The small size of riverine species ensures manoeuvrability in complex environments while gigantism of offshore species provides adaptation to deep diving, long distance migrations, and bulk-feeding. Delphinoids form a monophyletic group comprising three families: Monodontidae (narwhals and belugas), Phocoenidae (porpoises) and Delphinidae (oceanic dolphins), the most species-rich cetacean family. They all possess an extremely modified vertebral morphology, unique among mammals, by having an extraordinary high number of disk-shaped vertebrae while retaining a small body size. In this clade, inshore species have a lower vertebral count than offshore species. Within delphinoids, the closely related porpoises (Phocoenidae) and oceanic dolphins (Delphinidae) have clearly distinct vertebral morphology and follow slightly different phenotypic trajectories along the habitat gradient, probably reflecting parallel evolution with similar responses to same constraints. Furthermore, similar morphological adaptations are found between coastal and offshore ecotypes in the common bottlenose dolphin (Tursiops truncatus) suggesting that similar constraints act both at the micro- and macroevolutionary levels. The extreme vertebral count increase and associated vertebral shortening observed in offshore delphinoids increases the stiffness of their backbone. These modifications provide enhanced body stability and allow delphinoids to use higher tailbeat frequencies in an energetic efficient manner, resulting in higher swimming speed. These new functional abilities allowed small delphinoids to exploit scattered oceanic resources in a new way and can be considered as key innovations that supported their explosive radiation and ecological success. [less ▲]

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See detailEtude du potentiel herbicide des extraits végétaux des espèces xero-halophytes Tunisiennes et détermination de leurs modes d’action.
Ben Kaab, Sofiène ULiege

Doctoral thesis (2020)

Les adventices constituent une contrainte majeure pour l’agriculture. En effet, connues par leur pouvoir allélopathique important, ces adventices peuvent causer des dommages économiques sévères atteignant ... [more ▼]

Les adventices constituent une contrainte majeure pour l’agriculture. En effet, connues par leur pouvoir allélopathique important, ces adventices peuvent causer des dommages économiques sévères atteignant 34% dans les grandes cultures. Dans cette optique, suite à la forte limitation des herbicides chimiques sur le marché et plus spécifiquement le retrait progressif du glyphosate, la demande du public pour des herbicides alternatifs d'origine biologique et davantage respectueux de l’environnement, est croissante. Cette thèse s’inscrit dans la politique de minimiser l’utilisation des herbicides chimiques principalement le glyphosate. Les travaux de recherche effectué dans le cadre de cette thèse ont permis de sélectionner 2 extraits végétaux à forte activité herbicide à savoir, l’extrait phénoliques de Cynara cardunculus et l’huile essentielle de Rosmarinus officinalis. Par la suite nous avons procédé à un fractionnement bio-guidé afin de déterminer les composés bioactifs majoritaires. Ainsi, la myricitrine extraite de C. cardunculus a été identifiée pour la première fois comme molécule à potentiel herbicide. Ensuite, nous avons élaboré une nouvelle formulation à base de ces deux extraits végétaux sélectionnés qui pour la première fois améliore en même temps leurs efficacités et leurs stabilités. Finalement, l’étude des modes d’action de l’extrait phénolique de C. cardunculus a été réalisé par l’analyse des paramètres physiologiques et biochimiques de la plante cible traitée par nos deux extraits végétaux et en même temps par l’étude de l’interaction des molécules bioactives avec la membrane lipidique de Arabidopsis thaliana. [less ▲]

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See detailImpact of climatic zones and agricultural practices in Burkina Faso on Anopheles gambiae s.l.: studies using "omic" approaches.
Zoure, Abdou ULiege

Doctoral thesis (2020)

Malaria remains a public health challenge. A child dies of malaria every two minutes in the world. The pathogen agent (Plasmodium) is transmitted to humans by Anopheles mosquitos’ bites including ... [more ▼]

Malaria remains a public health challenge. A child dies of malaria every two minutes in the world. The pathogen agent (Plasmodium) is transmitted to humans by Anopheles mosquitos’ bites including Anopheles gambiae sensus lacto (s.l.) (Giles, 1902) as the main vector in Sub-Saharan Africa. A review of the literature reveals that in West Africa and particularly in Burkina Faso, this vector has developed resistance to the main insecticide used for vector control. In addition, the environment such as agriculture practices including pesticide use and climate (both temperature and rainfall) increase insecticide pressure and could also influence the abundance, diversity of mosquitoes and the effectiveness of their control as human disease vector. Firstly, a genomic approach was carried out by targeting three climatic zones and two agricultural pressure conditions, namely the major presence of cotton crops or not. This study showed that the network of phylogenetic tree haplotypes did not reveal any distinct genetic structure related to climatic or agricultural conditions. Similarly, an absence of gene flow and population differentiation and an excess of rare mutations have been revealed. Then the microbiota of the midgut was investigated by a metagenomic approach and revealed that proteobacteria (97.2%) was the dominant bacterial phylum. The most abundant genera were Enterobacter (32.8%) followed by Aeromonas (29.8%), Pseudomonas (11.8%), Acinetobacter (5.9%) and Thorsellia (2.2%). Seven bacterial species refractories to Plasmodium infection have been detected and already proposed as promising symbiotic agents for control by para transgenesis. Finally, a proteomic analysis was developed and allowed to find an almost similar distribution of the biological functions of proteins identified according to climatic conditions or agricultural practices (insecticide pressure). No systematic impact of the diversity of climatic regions or targeted insecticide pressures was identified following the analysis of the expression variations of the proteomes studied (1182 proteins identified and 648 involved in targeted metabolic pathways). This study provides the first proteomic characterization of whole individuals of An. gambiae in Burkina Faso. Further in-depth research should be considered in order to successfully strengthen vector control strategies and understand the interactions between vector mosquitoes and their environment in different ecological niches. [less ▲]

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See detailEvolution des modes de consommation alimentaires à Kinshasa : enjeux pour la filière manioc en zone périurbaine
Bonkena Bokombola, Papy ULiege

Doctoral thesis (2020)

This study examines the value chains of cassava leaves and chikwangue, in light of the evolution of food consumption patterns, population growth and urbanization in the city of Kinshasa. The analysis of ... [more ▼]

This study examines the value chains of cassava leaves and chikwangue, in light of the evolution of food consumption patterns, population growth and urbanization in the city of Kinshasa. The analysis of the evolution of culinary and food practices, considering its historical roots, has made it possible to identify current innovations and trends in food consumption patterns. It was based on an in-depth documentary analysis of the various reports on consumption carried out in Kinshasa. Certain documents and works published before the independence of the country have also been of great help in locating certain historical landmarks. The analysis of the value chain was made possible thanks to an empirical study carried out with direct and indirect actors in both urban and peri-urban areas of Kinshasa. Thus, a survey at the level of producers, processors, traders, service providers and state service agents was carried out to identify the functioning of the value chain taking into account its environment. Another household-level survey aimed at identifying the end market and identifying the drivers of demand for cassava leaves and its potential. The analysis of the changing eating habits of the people of Kinshasa reveals a specific culture linked to the history of the formation and evolution of social, economic and cultural identities. Food consumption in the city of Kinshasa highlights the influence of cultural mixing in culinary and food practices. The population of Kinshasa is cosmopolitan; the original heterogeneity now rooted in a native majority and the mixing with foreign cultures have favored the appearance of a particular urban culture in Kinshasa and new eating styles. The telltale signs of the evolution of culinary and food practices in Kinshasa were already perceptible before independence. Kinshasa cuisine has been developed on the basis of cultural, pre-colonial, colonial and more recently global influences. Current trends show that the people of Kinshasa are seeking to adapt by emphasizing a few innovations, both in terms of consumption and distribution (food supply). These innovations are recognized as an unavoidable phenomenon linked to urbanization. They were achieved gradually, and they remain strongly marked by the history of consumers' social positions. This evolution in food demand and consumption has important consequences on the food problem of the country in general and of the city of Kinshasa in particular. As the food styles of city dwellers differ from those of rural people, one of the essential questions for the future is to know under what conditions the agricultural supply of the country or of peri-urban areas can contribute to satisfy the urban demand of Kinshasa (in constant evolution) ? This question is not limited to estimating whether the quantities of food produced will be sufficient in the future to feed the populations of the city of Kinshasa. It also refers to the conditions for adapting this offer to the new requirements of city dwellers in this city, taking into account in particular their income, their way of life, and their socio-cultural models. Indeed, the food of the Kinois of tomorrow, in quantity and in quality, will be partly dependent on the capacity of the Congolese food system in general and Kinshasa in particular to innovate, from the seed to the plate. The household survey showed that cassava leaves and chikwangue have strong symbolic and cultural value. There are several methods of preparing “pondu” according to the provinces, the most common of which are: pondu ya madesu (cassava leaves with beans), limbondo (laid bicarbonates) and saka saka or matamba (cassava leaves) without baking soda or beans). In terms of variety, the majority of consumers (72%) choose the Manihot glazziovi. Projecting demand over 5 to 10 years, places potential demand for cassava leaves at 863,615 tonnes in 2022 and 1,070,221 tonnes in 2027; that of the chikwangue is estimated at 334,307 tonnes in 2022 and 414,285 tonnes in 20227. Survey results show that the cassava leaf and chikwangue value chains are driven by several actors. Certain actors (direct and service providers) contribute to the proper functioning of the value chain while others (State service agents in particular) are illustrated by the phenomenon of racketeering, thus contributing to the increase in product prices at the end of the chain. The value chain and the “contracts” between the actors and the stakeholders respond to economic logics and constraints embedded in social logics of security (being able to still work tomorrow, having good contacts with people we will need) rather than optimization (earning the maximum today). The transformation of the leaves and the chikwangue is still rudimentary. Stakeholders are using less sophisticated techniques. Since research has invested little in these value chains, the experience of industrialization is currently in its infancy. The marketing of these products remains an almost informal activity with a strong presence of women. All actors in the value chain make profits, which attests to economic profitability at the level of each link. The leaf value chain achieves an added value of around USD 8.0 / kg of leaves. However, processing is the activity that creates the most value and, therefore, processors are the ones who take the largest share (at least 90%). For the same quantity, the value added in the chikwangue value chain is evaluated at USD 1.19 / kg, the largest portion of which is captured by the processor of cassava roots into kimpuka (36.13%) and the trader retailer (36.13%). The agrifood market value chains of cassava leaves and chikwangue face many constraints in terms of production, marketing and processing. Despite these various constraints, these two value chains have significant assets, linked in particular to the ecology of cassava, to transport infrastructure (Kinshasa is well connected to its hinterland thanks to national road 1, the path to iron and the Congo river) and to the geographic proximity and accessibility to the urban market. Beyond the advantages, several opportunities arise and can be capitalized on to boost the commercial activities of the cassava leaf and chikwangue value chains. Among other things, we can note: urban demand, international demand for cassava products, the symbolic and cultural value of the product, taking cassava value chains into account in various projects and programs in the eastern part of the country, and the existence of scientific institutions and research and management centers. [less ▲]

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See detailAnalyse des typologies d’élevage et des performances des bovins en vue d’évaluer des stratégies de développement des ressources génétiques bovines au Mali
Touré, Abdoulaye ULiege

Doctoral thesis (2020)

L'élevage représente une activité importante dans l'économie du Mali où la production bovine est destinée tant à la consommation interne qu’à l’exportation vers certains pays de la sous-région ... [more ▼]

L'élevage représente une activité importante dans l'économie du Mali où la production bovine est destinée tant à la consommation interne qu’à l’exportation vers certains pays de la sous-région. Actuellement, l’élevage périurbain se développe autour des grandes villes, notamment de Bamako. Ainsi, dans le souci d’assurer une autosuffisance en lait et le développement de cette filière, l’État du Mali a encouragé la constitution d’un réseau de collecte et accompagné la construction d’unités de transformation du lait. A ces actions s’ajoutent l’importation de génisses et/ou de taureaux à haut potentiel laitier et la promotion de l’insémination artificielle (IA). Malgré ces efforts, le secteur laitier est confronté à des difficultés telles que la faible productivité des animaux, la faiblesse des investissements, l’insuffisance de ressources fourragères et la récurrence de problèmes sanitaires. Les présents travaux de thèse doctorale s’intéressent à deux systèmes d’élevage au Mali: la production laitière périurbaine autour de Bamako et l’élevage extensif bovin au Nord du Mali. Ils partagent les défis mentionnés plus haut mais diffèrent par l’implication des acteurs, l’orientation économique des productions et la disponibilité des intrants (infrastructures, ressources financières, alimentaires et vétérinaires). Ces différents contextes nécessitent des besoins distincts en matière de gestion des ressources génétiques. Dans l’objectif de compréhension et d’amélioration de ces systèmes, le présent travail se propose de caractériser les races bovines élevées au Mali en vue de leurs valorisations. Pour ce faire, deux entités géographiques ont été concernées par cette étude: - La zone périurbaine de Bamako dans le but de déterminer (i) la typologie des élevages bovins, (ii) les performances de production et de reproduction des animaux (iii) et les préférences relatives des éleveurs pour certains caractères phénotypiques guidant le choix des races. - La zone sahélienne au Nord du Mali afin (iv) d’évaluer les performances zootechniques de la race zébu Azawak afin d’envisager son éventuelle spécialisation en race locale laitière. Afin de caractériser l’élevage des bovins dans la zone périurbaine de Bamako en termes de motivations socio-économiques, de pratiques d’élevage et de gestion des ressources génétiques, une enquête a été conduite auprès de 52 exploitations. Dans cette étude, une Analyse en Composante Principale (ACP) et une Classification Ascendante Hiérarchique (CAH) ont permis de dégager trois groupes d’éleveurs selon les modes de conduite des troupeaux. Un premier groupe mène de petits élevages pastoraux (50% de l’échantillon). Il est principalement constitué d’élevages traditionnels recourant aux races locales. Près de 95% des éleveurs de ce groupe sont analphabètes et la grande majorité d’entre eux (90%) ne pratique pas d’autres activités économiques non agricoles. Les animaux sont élevés dans des parcs communautaires sans aucun suivi des services vétérinaires. Le deuxième groupe présente un profil intermédiaire avec un système agropastoral dominant (40% de l’échantillon). Une intensification de la production laitière caractérisée par l’utilisation de meilleures infrastructures (parc individuel), de l’IA et/ou du croisement, et le recours aux services vétérinaires (88,5% des éleveurs) sont observés dans ce groupe. L’objectif principal des éleveurs de ce groupe est la production laitière. Le troisième groupe est caractérisé par de grands troupeaux mobiles (10% de l’échantillon). Les éleveurs de ce groupe présentent une orientation plus économique de leurs activités, qui se caractérise par la recherche d’une production laitière, la pratique de l’embouche bovine, la vente d’animaux sur pieds et l’exportation vers d’autres pays. Dans le but d’approfondir cette étude typologique, une analyse zootechnique a été réalisée sur les pratiques d’élevage. Ainsi, une seconde étude a été conduite dans la même zone entre janvier 2012 et décembre 2015 auprès des 17 éleveurs disposant d’un registre de suivi des activités d’élevage. Cette étude a permis de caractériser les performances de production et de reproduction des races bovines du système périurbain de Bamako. Les résultats ont montré une durée de l’intervalle entre les vêlages de 433 ± 115 jours pour les vaches de races locales Peul et Maure, contre 460 ± 80 jours pour les vaches issues de croisements avec les races exotiques. Cependant, la race locale zébu Azawak, dont le berceau se situe au nord du Mali, conduite dans les conditions d’élevage périurbaines, présente des performances de production inférieure à celles des autres races bovines locales. Sa production laitière par lactation a été de 636 ± 433 kg contre 681 ± 411 kg pour le zébu Peul. En vue de proposer une stratégie d’amélioration de la production laitière des races bovines au Mali, une troisième étude a été menée. Elle a permis d’estimer les valeurs que les éleveurs attribuent à différents critères d’élevage par la méthode d'analyse conjointe multi-attributs. Cette étude a concerné 120 éleveurs bovins dans la région périurbaine de Bamako. L'estimation économétrique de la fonction d'utilité des éleveurs a été réalisée à l’aide d’un modèle Logit conditionnel et la disposition à payer pour certains attributs a été calculée par le rapport entre chaque coefficient d’utilité des caractères et celle de l’unité monétaire. Le « consentement à payer » le plus élevé a été observé pour la race adaptée au système de production à faible niveaux d’intrants avec une valeur supplémentaire de 163€, composée de 70€ pour la forte résistance aux maladies, 69€ pour la faible demande alimentaire et 24€ pour une production laitière jugée supérieure. Pour investiguer davantage la possibilité pour le milieu périurbain d’opérer une sélection phénotypique sur une race pure de vache locale à tendance laitière (zébu Azawak), une autre enquête a été conduite dans cinq communes rurales du cercle de Ménaka en zone sahélienne du Mali. La collecte des données a porté sur 1129 animaux. L’âge au premier vêlage a été de 50 ± 11 mois avec un intervalle entre vêlages de 16 ± 4 mois. Afin de s’affranchir de l’usage de systèmes de pesée dans d’éventuels processus de sélection, des systèmes barymétriques ont été évalués. Les corrélations du poids avec le périmètre thoracique (r = 0,95) et la hauteur au garrot (r = 0,94) ont été les plus élevées. Des équations barymétriques ont été établies pour chaque catégorie animale (veau/velle, génisse/taurillon, vache/taureau) au moyen de régressions polynomiales du poids (y) sur le périmètre thoracique (x). Dans le cadre de la diffusion et du suivi des performances pondérales du zébu Azawak, cette mensuration mériterait d’être considérée à l’avenir. Cette étude a montré l’importance de l’élevage des bovins du type traditionnel dans ce milieu. Elle a caractérisé les performances de production et de reproduction de la race zébu Azawak. La compréhension des caractéristiques de ce système d’élevage permettra leur prise en compte au niveau des programmes d’amélioration génétique. Au regard des paramètres de reproduction intéressants du zébu Azawak, son introduction en milieu périurbain de Bamako pourrait servir de tremplin pour stimuler l’élevage bovin laitier surtout pour le type extensif traditionnel. En conclusion, l’ensemble des études permet d’avancer que le recours aux vaches croisées et/ou des races exotiques ne permet pas d’améliorer à elles seules la productivité des exploitations bovines au Mali. Il est dès lors nécessaire de développer une politique appropriée pour mieux planifier une stratégie adéquate d'amélioration de la production laitière par de croisements favorables à un développement durable de la production. La mise en place d’un schéma de croisement des races locales avec des races laitières étrangères impliquant tous les acteurs de la filière constituerait une stratégie possible à la gestion durable des races locales comme un pilier essentiel de ce schéma. [less ▲]

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See detailContribution à la biologie du virus de Schmallenberg chez les ruminants
Bayrou, Calixte ULiege

Doctoral thesis (2020)

On the autumn 2011, the Friedrich Loeffler Institute (Germany) isolate the genetic material of a hitherto unknown virus which is associated with an unexplained syndrome of fever, drop of milk and diarrhea ... [more ▼]

On the autumn 2011, the Friedrich Loeffler Institute (Germany) isolate the genetic material of a hitherto unknown virus which is associated with an unexplained syndrome of fever, drop of milk and diarrhea reported in the dairy farms from the Netherlands and Northwest Germany. The newcomer was named Schmallenberg virus based on the geographical origin of the first positive samples. It belongs to the Orthobunyavirus genus. For the first time in Western Europe, an arbovirus of this group circulates among ruminants. Such an emergence is, by many ways, similar to the type 8 Bluetongue virus emergence in 2006 and is one indication that the global infectious diseases dynamic is changing in Europe. Thus, understanding and documenting the Schmallenberg virus emergence, in that context, is of great importance. The present thesis is part of this approach and aim to contribute to the knowledge and the understanding of the virus biology and the associated disease. It is comprised of three studies that investigate the problematic at three different levels. The first study is a description of the lesions found in the bovine fetus after the transplacental passage of the virus. This study is a confirmation that the lesions are limited to the neurologic and myo-arthro-skeletal systems. The two characteristic lesions associated with the in-utero infection are the micromyelia and the arthrogryposis. The study strongly suggests that the key element of the pathogeny of these lesions is the virus-induced destruction of the spinal cord motoneurons. The second study follows the seroprevalence of the virus in the wild deer populations in Wallonia from 2012 to 2017. The study substantiates the hypothesis of a hypo-endemic installation of the virus with cyclic pulsations. This particular endemic state has been described for close viruses. It is characterized by several years of low-level circulation followed by one year of higher circulation. Moreover, according to this study, deer are not the main reservoir of the virus. The populations of wild ruminants do participate to the circulation of the virus. Nevertheless, they have a minor impact on the global dynamic of the Schmallenberg virus circulation. The third study focuses on one of the main effectors of the interferon response, the Mx1 protein. The aim is to describe the effect of the latter on the viral cycle. By comparing, in vitro, Mx1 proteins from different mammals (bovine, canine, equine, porcine Mx proteins), the study shows an antiviral effect for the four tested proteins. However, the canine Mx1 is significantly less active. The second main result is the observation of a not previously described dose-dependent effect of the Mx antiviral effect. Those three studies, because they explore the Schmallenberg virus biology from different angles, provide a broad overview of the questions raised by the Schmallenberg virus emergence. [less ▲]

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See detailParamètres génétiques des ruminants et typologie socioéconomique des élevages en milieu rural Burundais
Manirakiza, Josiane ULiege

Doctoral thesis (2020)

Livestock systems in developing countries are influenced by environmental, socio-economic and cultural factors. In Burundi, this sector has evolved, due to: (1) high human population and land pressure ... [more ▼]

Livestock systems in developing countries are influenced by environmental, socio-economic and cultural factors. In Burundi, this sector has evolved, due to: (1) high human population and land pressure which has led to a regression and degradation of pastoral resources due to the competition with agriculture, (2) actions of livestock services and rural development projects which promoted the crossbreeding of local breeds and the extension of fodder crops (3) epidemics and health crises that have impeded the actions of development of monogastric species and (4) competition between food for the latter and for human. Latest development policies in this sector were focused on ruminants, especially on small scale dairy cattle farming and crossing the local goat with bucks of Boer blood. However, these policies have not been accompanied by any structure for control and rational risk management. Aimed at providing a scientific basis for the sustainable management of these resources, this thesis attempts to (1) characterize zootechnical performances of animals in their production systems, (2) evaluate the relevance of farmers’ organizations as farmers-field-schools for the sustainable improvement and management of animal resources and (3) evaluate genetic parameters of the local goat for the feasibility of a breeding program. To characterize cattle and goat zootechnical performances in their production systems, we established a mapping of genetic types and production systems according to eco-climatic conditions. To this end, preliminary surveys were conducted in 201 and 319 cow and goat farmers. In cattle breeding, we observed a progressive shifting from the traditional extensive system of the local breed to small-scale dairy farming of Holstein crossbreds in the mixed crop-livestock system. These changes were more obvious in the humid and densely populated central highlands than in the boundary lowlands with a long dry season. We then characterized more finely the racial composition of the crossed animals and evaluated the effect of the crossing level on the milk production of these animals. Statistical analyses showed an increase in milk production as the Holstein blood increase, significant but lower than theoretically expected. In goat breeding, results showed a trend in production systems similar to that observed in cattle farming, but at a lesser extent. Indeed, farmers of humid highlands tended to raise small herds composed of indigenous and crossbred animals and to adopt mixed crop-livestock system, whereas those of dry lowlands had large herds composed mainly of indigenous animals grazing freely in communal pastures. Further, Boer crossbreds were significantly heavier and greater in size compared to local breeds, although the level of improvement was below the theoretically expected. In terms of the relevance of farmers-field-schools for improvement and sustainable management of animal resources, we assessed farmers' perceptions on the two species and estimated the annual gross margin per cattle and goat. Surveys were carried out on 105 and 160 dairy and goat farmers respectively. In cattle farming, results showed a positive effect of farmers-field-schools in the adoption of technologies and improvement of productivity per animal, although measures to consolidate them are still required. In goat breeding, three groups of farmers were identified. The first group gathers poor households whom the sustainable participation in these organizations is limited by excessive sales of goats. The second regroups well-off farmers with high arable land who planned to convert a part of goat-flock into a cow. The last group is composed of successful members of farmers-field-schools and have high goat herds received from a project of research development for genetic improvement of the local goat breed. They plan to continue goat farming in the future but showed their willingness to reduce their goat herd size. The annual gross margin per goat was significantly higher in the latter group than in the other groups. Dairy farmers have shown their willingness to continue to participate in such organizations even the end of external funding. Inversely, the results showed that the sustainability of such organizations for goat breeding program could be compromised because farmers with high farm size tend to adopt cattle farming, which is supposed to be more profitable than that of goats. These are often raised by poor households. The integration of other economic activities into these associations has been proposed to generate rapid incomes and so to protect goat from excessive sales and improve the welfare of farmers. Further, this socioeconomic context does not allow an advanced selection based on the breeding value of animals; a selection based on the phenotypic value for body weight and survival of kids is proposed. Indeed, results showed that these traits were responsible for the low productivity estimated for many goat keepers. To evaluate if this phenotypic selection would be of interest, the last study aimed to estimate the genetic parameters of growth and survival of goat kids of the local breed in rural areas. Estimates heritability, repeatability and genetic correlations indicate that the response of phenotypic selection of body weight and size would be modest and null for kid survival. All of these results show that the low productivity of most livestock farms due to low herd size and weak capacities of farmers, jeopardizes sustainable management of cattle and goat resources in Burundi. Farmers’ organizations could contribute to empower smallholder’s capacities and improve animal productivity if measures of their consolidation are established. Genetic parameters were less favorable for a phenotypic selection. Improving the breeding conditions and setting up a complementary program of selection based on the breeding value are proposed; selected bucks could be then diffused in the farmers’ organizations. A long-term commitment for all stakeholders of the sector is required for technical and financial support of integrated farmers’ organizations [less ▲]

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See detailRoles of Tax and HBZ proteins in post-transcriptional control of cellular gene expression
Vandermeulen, Charlotte ULiege

Doctoral thesis (2020)

HTLV-1 is a retrovirus capable of inducing severe pathologies such as the adult T-cell leukemia/lymphoma (ATLL) and the HTLV-1 associated myelopathy/ tropical spastic paraperesis (HAM/TSP). HTLV- 1 is a ... [more ▼]

HTLV-1 is a retrovirus capable of inducing severe pathologies such as the adult T-cell leukemia/lymphoma (ATLL) and the HTLV-1 associated myelopathy/ tropical spastic paraperesis (HAM/TSP). HTLV- 1 is a positive stranded RNA virus encoding typical retroviral genes as well as essential regulatory and accessory genes. Two of them, Tax and HBZ, have been more and more in the spotlights for playing crucial roles in the virus persistence and oncogenicity. The majority of HTLV-1 Tax and HBZ studies have focused on the impact of the oncoproteins on transcriptional events. Con- sequently, little is known in the case of post-transcription, including splicing. Aberrant splicing is common in cancer cells and people living with HTLV-1 display altered splicing patterns. Here, we uncovered potential roles of HTLV-1 Tax and HBZ proteins in the regulation of alternative splicing events (ASEs) upon HTLV-1 infection. By using Jurkat cells inducibly expressing Tax or HBZ, we identi ed Tax and/or HBZ dependent alternative splicing events. Tax and HBZ had globally opposite e ects on splicing (Tax fosters inclusion and HBZ exclusion). However, the shared ASEs triggered by Tax and HBZ are regulated similarly. We also noticed that the viral Tax and HBZ proteins impact di erent set of genes at the transcriptional and splicing level and alternatively spliced genes were enriched for known cancer genes. Next, we investigated AS events in HTLV-1 infected individuals. Interestingly, several ASEs shared between T cells expressing Tax or HBZ and people living with HTLV-1 highlighted genes already known for their role in HTLV-1 leukemogenesis. New targets of HTLV-1 were also discov- ered. Of particular interest, we show that the protein tyrosine phosphatase receptor type c gene (PTPRC) encoding CD45, a critical regulator of immune response, is controlled by alternative splicing in Tax and HBZ expressing cells as well as in ATLL patients. We built a comprehensive interactome map of Tax and HBZ with cellular host proteins and identi ed 44 and 111 new protein-protein interactions for Tax and HBZ, respectively. Interestingly, Tax and HBZ interact with RNA binding Proteins having diverse functions on mRNA fate. This may indicate a global regulation of gene expression throughout mRNA life. Finally, we further investigated one partner of Tax in particular, U2AF65, a crucial protein in- volved in alternative splicing. While a precise mechanism on how Tax modulates U2AF65-dependent splicing still needs to be fully determined, our study highlights U2AF65 as a potential major player in HTLV-1 biology. [less ▲]

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See detailQuelle est la perception de l’avortement chez les éleveurs ovins-caprins en Belgique?
Janssen, Pierre ULiege

Master's dissertation (2020)

The abortion rate for small ruminants is usually estimated at 5%. In Belgium, for example, there is no systematic abortion census for this sector and this figure is currently difficult to confirm ... [more ▼]

The abortion rate for small ruminants is usually estimated at 5%. In Belgium, for example, there is no systematic abortion census for this sector and this figure is currently difficult to confirm. According to the most recent studies on abortions of small ruminants, the notion of multifactorial has been put forward and the value of a differential diagnosis of abortion causes has been noted. The preface of this study lists the infectious and non-infectious causes of abortion in Belgium. For each factor, the means of transmission, the risk of zoonosis, the clinical signs, the diagnostic tests, the treatment and prevention have been analyzed. The originality of this work lies mainly in the fulfilment of an online questionnaire sent to small ruminant breeders. The aim of this questionnaire is to asses the situation with regards to abortion in this sector in Belgium. This study is a first and had never been carried out before. The analysis of the results of this study has enabled us to establish the profile of small ruminant breeders in Belgium (Wallonia), to give an estimate of the number of abortion cases, to know the feeding behaviour as well as the biosecurity and sanitary measures followed by the breeders. All these factors were analyzed in order to identify possible causes explaining the abortion rate. This study also revealed the measures that would be judicious to implement in order to increase diagnosis and in the long term to reduce the number of abortions in Belgium. [less ▲]

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See detailAn in-depth study of random forests methodologies for short biomarker signature discovery
Debit, Ahmed ULiege

Doctoral thesis (2020)

Biomarker signatures in cancer are generally defined as a single or a combined alteration of genes associated with a defined biological tumor phenomenon. These signatures are providing clinicians with ... [more ▼]

Biomarker signatures in cancer are generally defined as a single or a combined alteration of genes associated with a defined biological tumor phenomenon. These signatures are providing clinicians with significant information to improve our understanding of cancer biology. Furthermore, with a validated specificity and sensitivity, molecular signatures can be used as a clinical tool for screening, predicting progression, and treatment response. Next generation sequencing technologies allow us to measure the expression profile of the genes with high resolution. Thanks to advances in bioinformatics techniques and the emergence of advanced statistical approaches, deriving biomarker signatures by mining such data has become increasingly popular. In this thesis, we propose a comprehensive pipeline for Short Biomarker Signature Discovery (sBSD) in cancer. The major challenge is to design a stable set of genes, as small as possible, that accurately predicts learned patterns. Furthermore, this thesis covers important aspects related to the application of machine learning techniques and bioinformatics approaches to gene expression data. Our proposed strategy focuses on the stability of methods, clinical interpretation of results, and applicability in the context of gene expression data. The scientific contributions in this work have been divided into four parts. First, an evaluation of the robustness of Feature Selection (FS) methods for RNA-seq data is performed. The robustness of FS methods has been reported to be crucial for signature discovery for clinical purposes. It is usually assessed by investigating how different resamplings of a training set affect the final set of selected genes. The novelty of our assessment method is the introduction of another type of data perturbation coming from the change in RNA-seq normalization method. Consequently, the proposed method evaluates the robustness of FS methods based on the change in resampling partition, and the change in normalization method. Two stability scores are developed in this sense: Stability Per Resampling (SPR), and Stability Per Normalization (SPN). We evaluated the robustness of 17 state-of-the-art FS methods based on such scores using three RNA-seq datasets. Second, we integrate random forest algorithm into our sBSD pipeline. It mainly fits the purpose of identifying the best signature and its alternatives. Since the original RF algorithm proposed by (Breiman Leo, 2001), several variations to RFs have been made available via the R Project for Statistical Computing, including orthogonal and oblique methods. The aim for this part is thus to assess the AUC reproducibility of 15 RF variants based on two hyper-stability scores: Hyper-stability Resampling dependent Score HRS and the Hyper-stability Signature dependent Score HSS. In particular, we focus on the question of how AUC stability can help to decide on the best predictive RF strategy in the context of Short Biomarker Signature Discovery. Third, we introduce a heuristic filtering strategy that aims to filter out less performing combinations in signatures before calculating their AUC values. This strategy overcomes computational problems related to exhaustively testing all possibilities, a daunting task for initially large signatures. Application to two datasets containing the expression of circulating miRNAs in tumor and normal samples, identifies optimal or near-optimal solutions (the best signature or its alternatives), with drastically decreased computation time. Finally, special attention is given to the interpretation of the resulting RF model, associated with the best signature. The best signature the sBSD pipeline identifies can be used as a screening, predictive, or prognostic tool for cancer. We provide some ways for interpreting signature-based RF models by deriving compact sets of rules. Although not entirely satisfactory, according to preliminary results and performance of the set of rules, it paves the way to future work in which an acceptable tradeoff between performance and interpretability can be sought. [less ▲]

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See detailImproving jujube fruit yield estimation by assimilating a remotely sensed leaf area index into the WOFOST model
Bai, Tiecheng ULiege

Doctoral thesis (2020)

Jujube fruit has important nutritional and medicinal qualities and is one of the most economically valuable fruits in China. Field-scale jujube fruit yield estimation using site-specific techniques can ... [more ▼]

Jujube fruit has important nutritional and medicinal qualities and is one of the most economically valuable fruits in China. Field-scale jujube fruit yield estimation using site-specific techniques can provide indicators of the reasons for yield gaps, which could be promising to better understand spatial yield variation in jujube orchards, thereby analysing the possible causes to improve fruit orchard management decision-making. Both remote sensing and assimilation methods have been widely used for yield assessments of annual crops. There are few reports focusing on the use of assimilation methods to estimate yields for fruit crops, especially jujube trees. The main goal of this thesis is to make full use of the advantages of crop growth models and remote sensing technology to improve the accuracy of jujube fruit yield estimation. The first aim is to introduce phenological length into the yield regression model, based on a remotely sensed vegetation index, to enhance the accuracy of yield estimation. The second aim is to develop and evaluate remote sensing assimilation methods to reduce the uncertainty of key input parameters or state variables in the jujube growth simulation process, thereby improving yield estimation at the field scale for local jujube orchards. Firstly, the performance of the calibrated WOFOST (World Food Studies) model was evaluated by simulating jujube fruit tree growth in potential mode. The model was calibrated and validated using data collected in field experiments performed in three growth seasons. The validated errors of –2, –3, and –3 days were detected in different phenological development stages corresponding to emergence, flowering, and maturity. Simulated growth dynamics of leaves, stems, fruits, total biomass, and leaf area index (LAI) agreed well with measured values, showing R2 (coefficient of determination) values of 0.95, 0.98, 0.99, 0.99, and 0.95, and RMSE (root mean square error) values of 0.14, 0.33, 0.37, 0.62 t ha–1 and 0.19 m2 m–2, respectively. In order to estimate the yields of jujube orchards of different ages, the weight of initial new organs in each growing season (new buds and roots) was introduced as the initial total crop dry weight (TDWI), which was set as an average value for orchards of the same age. The R2 and RMSE of the field-scale yield estimation for 181 orchards were 0.22 and 1.07 t ha–1 (16.3%) for 2016, 0.04 and 1.33 t ha–1 (17.2%) for 2017, respectively. Although the calibrated WOFOST model can provide a fundamental strategy for simulating the growth of jujube fruit trees, there may still be some uncertainty in the method of setting the fixed TDWI for the same aged jujube orchards, resulting in a slightly low estimation accuracy. Secondly, this thesis evaluated the yield estimation performance of regression methods based on remotely sensed vegetation indices that are widely used for crop yield estimation. An approach that used the phenological length to improve remotely sensed estimates of inter-annual variability for yields was explored and tested. The optimal time for determining jujube yield estimation was during the fruit filling period, which showed higher R2 between vegetation indices (VIs) and fruit yields. The average VIs from 16 July to 15 August represented the best performance for yield estimation, with an average R2 value of 0.75 for NDVI (Normalized Difference Vegetation Index), 0.61 for SAVI (Soil-adjusted Vegetation Index), 0.47 for NDWI (Normalized Difference Water Index), and 0.44 for EVI (Enhanced Vegetation Index), respectively. The potential of using Landsat-NDVI for jujube yield estimation, combined with the phenological length, was proved based on observed fruit yields of 181 jujube orchards, showing a validated R2 of 0.64 and RMSE of 0.73 t ha–1 (11.1%) for 2016, 0.71 and 0.73 t ha–1 (9.5%) for 2017, respectively. Thirdly, this study presented an attempt to assimilate a single LAI at near to maximum vegetative development stage, derived from Landsat satellite data, into a calibrated WOFOST model to improve fruit yield estimation at the field scale. The assimilation after forcing LAI improved the yield estimation performance compared with the unassimilated simulation, showing a R2 of 0.62 and RMSE of 0.74 t ha–1 (11.3%) for 2016, and R2 of 0.59 and RMSE of 0.87 t ha–1 (11.3%) for 2017, respectively. Finally, the main contribution of this study was to develop a SUBPLEX algorithm to assimilate a time series of remotely sensed LAI during the main growth stages into the calibrated WOFOST model, and compared the yield estimation accuracy of the SUBPLEX algorithm with a widely used Ensemble Kalman Filter (EnKF) assimilation. The results showed that both SUBPLEX and EnKF assimilations significantly improved yield estimation performance compared with the un-assimilated simulation. The SUBPLEX (R2 = 0.78, RMSE = 0.64 t ha−1 (8.3%) and RPD (Standard Deviation (SD)/RMSE) = 2.13) also showed slightly better yield estimation accuracy compared with EnKF assimilation (R2 = 0.66, RMSE = 0.79 t ha−1 (10.2%) and RPD = 1.73). The study provides a new assimilation scheme based on a SUBPLEX algorithm to employ remotely sensed data and a crop growth model to improve field-scale jujube fruit yield estimates. In summary, this thesis highlighted that the proposed forcing method is a suitable choice when only one remote sensing image is available at near to the maximum vegetative developmental stage. Remote sensing regression methods can be recommended when two satellite images of the fruit filling stage are available and applied only to specific areas. The EnKF and SUBPLEX methods are highly recommended when multiple remote sensing images from emergence to maturity are available. The SUBPLEX method usually exhibited better performance and stability because the accuracy of the EnKF method depended on whether the phenological time was clear. The assimilation methods may be the most promising fruit crop yield estimation methods to use in the future due to their good mechanism. [less ▲]

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See detailStrain engineering and process design for continuous surfactin production in biofilm bioreactors with Bacillus subtilis 168
Brück, Hannah ULiege

Doctoral thesis (2020)

Biofilm bioreactors show promise for continuous microbial biosurfactant production due to the natural robustness of self-immobilized cells and the possible design of processes avoiding foam formation. The ... [more ▼]

Biofilm bioreactors show promise for continuous microbial biosurfactant production due to the natural robustness of self-immobilized cells and the possible design of processes avoiding foam formation. The widely used bacterial strain B. subtilis 168 has the potential to produce surfactin, a powerful biosurfactant with exceptional biological activities and various industrial applications. However, B. subtilis 168 exhibits only poor biofilm formation capacities and thus entails limited cell adhesion capacities. In order to improve the natural cell immobilization of B. subtilis 168 to adapt this strain better to biofilm cultivation, filamentous mutant strains with restored exopolysaccharide (EPS) production were generated. The impacts of the genetic modifications were evaluated through colonization assays and by measuring the biofilm formation capacity under low shear stress in a drip-flow reactor (DFR). Subsequently, the most performant strains were selected and cultivated in a newly designed continuous trickle-bed biofilm bioreactor containing highly structured metal packing elements for biofilm formation. Moreover, a bacterial growth model was built able to describe the growth dynamics of the planktonic cells and the biofilm in the system. The colony development was strongly affected by filamentous cell growth and EPS production which was manifested through an enhanced surface spreading and colonization capacity. In the DFR and trickle-bed biofilm bioreactor, the EPS+ mutants showed significantly increased performances regarding the biofilm formation and surfactin production capacities. Whereas cell filamentation had a minor impact on the processes, but contributed to a better cell cohesion in the biofilm and led to reduced cell detachment during the cultivation. Thus, EPS production and filamentous cell growth contributed considerably to an improved process performance in the system. In addition, continuous fermentation has shown to be favorable for a high surfactin productivity. The experimental data from the trickle-bed biofilm bioreactor were in good accordance with those obtained by simulations with the developed growth model. Hence, the growth model has been successfully validated and could be used for further process optimization. [less ▲]

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See detailImpacts de la pollution diffuse en milieu agricole sur la qualité des eaux de surface à l’échelle du bassin versant de l’oued Joumine : Application de différentes approches de modélisation
Boukari, Amira ULiege

Doctoral thesis (2019)

The protection of the aquatic environment while managing the risk of water scarcity is challenging, mainly in regions with limited adaptation capacity. There is an increasing need to improve existing ... [more ▼]

The protection of the aquatic environment while managing the risk of water scarcity is challenging, mainly in regions with limited adaptation capacity. There is an increasing need to improve existing monitoring networks and to establish early warning system of future trends of water quality in order to ensure a sustainable use of water resources. A specific concern is given to nonpoint source pollution from agriculture, which is often the main source of water quality degradation in rivers. In this work, we focused on the Joumine river basin (418 km2), a rural catchment situated north Tunisia dominated by agricultural activities and exposed to eutrophication problems. Aiming to present an assessment framework of the spatial–temporal water quality variability and quantify “pressure-impact” relationships, we proposed a physically-based modelling approaches involving the use of an agro-hydrological model (SWAT) and a river ecosystem model (PEGASE), operating at the watershed scale.We also analysed the utility and feasibility of coupling the two selected models in order to assess the contribution of the coupled approach in improving the modelling predicting capacity. The study highlighted the impact of agriculture in nitrate transfer and the vulnerability of Joumine water to contamination with pesticides molecules, such as simazine and epoxiconazole. It showed the seasonal behavior of the catchment and helped in identifying exposed areas to nutrients and pesticides export. The simulated concentration patterns of the studied elements showed that climate and farming practices are important factors in controlling the fate of agricultural pollutants. Results have also emphasized the contribution of different pollution sources such as livestocks and urban releases. It also proved that the PEGASE model, initially designed for temperate regions, could be used to simulate water quality in semiarid context. Some discrepancies between simulated and measured concentrations were improved by coupling with the SWAT model on a daily time step. Such application test of the two models coupling for nitrogen transfer simulation helped to identify the needs for developing an integrated interface in PEGASE allowing data communication with SWAT. These findings demonstrate that the adopted assessment approach in investigating the behavior of the studied hydrosystem can be a useful support to develop an appropriate surface water quality management program. Better results could be reached by checking sources of uncertainties and improving the validation step. This demonstrate the need to enhance the existing database with high monitoring frequency, particularly in periods of high transfer. The study of prospective scenarios of future trends in climate and land use, as well as extending the coupling method for other water quality variables will be interesting. [less ▲]

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See detailMapping and characterization of protein interactome networks
Desbuleux, Alice ULiege

Doctoral thesis (2019)

Numerous complex networks composed of diverse interactions, either physical interactions or functional associations, between macromolecules underlie most cellular functions. The sets of physical and ... [more ▼]

Numerous complex networks composed of diverse interactions, either physical interactions or functional associations, between macromolecules underlie most cellular functions. The sets of physical and functional associations are respectively defined as biophysical and genetic interactome networks. Mapping and characterizing biophysical and genetic interactome networks is necessary, albeit not sufficient, to understand complex genotype to phenotype relationships. However, as current individual interactome maps remain incomplete, their organization remains mysterious and the relationships between distinct maps are unclear. Moreover, understanding the nature of the interactions elucidated by each of these maps is essential to accurately interpret the functional relevance of their integration. Saccharomyces cerevisiae is one of the few organisms for which systematic genetic and biophysical maps have been generated at genome scale, making it possible to compare them. For my PhD thesis, my colleagues and I focused on protein interactome networks, and provided the first annotation of an expanded map of the yeast binary protein interactome. We first assessed the coverage of the yeast binary interactome network by generating an inventory of all protein-protein interactions reported in public repositories. Using comprehensive experimental validations, we identified and selected the datasets with a majority of binary direct interactions. Assembling a binary interactome network of only ~7,000 interactions from the literature highlighted the imperative need to systematically expand the coverage of the yeast binary interactome network. To that end, we expanded an available ORFeome collection, to assemble a nearly complete collection, and used it to systematically test all possible protein pairs to produce a new systematic binary map, YI-II. We revealed biological properties that govern the organization of the cellular interactome by integrating the expanded yeast binary interactome map with genetic network maps. Our results support recent observations, that the majority of interactions in the interactome are likely of a different nature, with most being more transient, potentially involved in context-specific regulatory processes. An understanding of the properties that govern integration of genetic and biophysical maps, as provided by this study, would be key to not only understand known genotype to phenotype relationships but identify novel ones. [less ▲]

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See detailAnalyse sociotechnique et organisationnelle du programme de sélection du bovin N’Dama au Sénégal
Camara, Younouss ULiege

Doctoral thesis (2019)

The objective of this thesis was to evaluate the N'Dama cattle breeding program in Senegal by questioning its organization, its appropriation by breeders and the involvement of other stakeholders. These ... [more ▼]

The objective of this thesis was to evaluate the N'Dama cattle breeding program in Senegal by questioning its organization, its appropriation by breeders and the involvement of other stakeholders. These elements determine the sustainability of low-input breeding programmes in developing countries. Our approach is based on the assumption that, in order to understand the problem of sustainability of these programs, a multidisciplinary analysis must be carried out. This analysis thus proposes to consider the sustainability of this programme as being based on different prerequisites integrating the inclusion of genetics among other innovations in the agricultural system (hypothesis 1), the practices, objectives and normative considerations of farmers (hypothesis 2), the involvement of stakeholders and the visions of designers in relation to the strategies developed (hypothesis 3). The results thus made it possible to analyse the links between the genetic innovation adopted and the practices of farmers, but also with their strategies according to their relations with other stakeholders and their expectations regarding the roles of each. [less ▲]

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See detailIdentification and characterization of two genome-specific repetitive elements from Gossypium A and D genomes
Lu, Hejun ULiege

Doctoral thesis (2019)

Gossypium genus divides into eight diploid genomic groups, where the differential amplification of lineage-specific transposable elements (TEs) underlies the three-fold genome size variation of the ... [more ▼]

Gossypium genus divides into eight diploid genomic groups, where the differential amplification of lineage-specific transposable elements (TEs) underlies the three-fold genome size variation of the different genomes. Genomic specific TEs propagation accounts for the genome size gap between A and D genomes. Though multiple versions of the genome sequencing assemblies of the A genome, D genome, and tetraploid genomes have been released. It is also challenging to assemble the complete genome avoiding unanchored scaffolds remaining, due to the massive repetitive sequences scattered around the whole genome. Especially in the tetraploid cotton, homologous fragments from A- and D-sub genome are difficult to be distinguished and correctly anchored in genomes. The research on genome-specific TEs between A and D genomes can uncover the mechanisms of cotton genome speciation and evolution, assist tetraploid genome assembling and potentially artificial apply them in genome editing. Fluorescence in situ hybridization (FISH) is a versatile tool to visualize the distribution of sequences in chromosomes and plays a vital role in recent cytogenetic research. More and more repetitive sequences in the cotton genome were reported recently and identified with FISH. Combining with bioinformatics analysis, we identified and characterized two genome-specific repetitive sequences from Gossypium A and D genomes respectively. This will promote a better understanding of the mechanism of genome evolution, and support genome-specific markers to facilitate genome accurately assembling. The main contents and results are as follows: (1) Discovery and Annotation of a Novel Transposable Element Family in Gossypium Fluorescence in situ hybridization (FISH) is an efficient cytogenetic technology to study chromosome structure. Transposable element (TE) is an important component in eukaryotic genomes and can provide insights in the structure and evolution of eukaryotic genomes. A FISH probe derived from bacterial artificial chromosome (BAC) clone 299N22 generated brilliant signals on all 26 chromosomes of the cotton diploid A genome (AA, 2x=26) but very few on the diploid D genome (DD, 2x=26). All 26 chromosomes of the A sub genome (At) of tetraploid cotton (AADD, 2n=4x=52) also gave positive signals with this FISH probe, whereas very few signals were observed on the D sub genome (Dt). Sequencing and annotation of BAC clone 299N22, revealed a novel Ty3/gypsy transposon family, which was named as CICR. This family is a significant contributor to size expansion in the A (sub) genome but not in the D (sub) genome. Further FISH analysis with the LTR of CICR as a probe revealed that CICR is lineage-specific, since massive repeats were found in A and B genomic groups, but not in C–G genomic groups within the Gossypium genus. Molecular evolutionary analysis of CICR suggested that the transposon family silenced in 1–1.5 million years ago (MYA), when the tetraploid cottons formed. Furthermore, A genomes are more homologous with B genomes, and the C, E, F, and G genomes likely became divided from a common ancestor prior to 3.5–4 MYA, the time when CICR appeared. The genomic variation caused by the insertion of CICR in the A (sub) genome may have played an important role in the speciation of organisms with A genomes. The CICR family is highly repetitive in A and B genomes of Gossypium, but absent in the C–G genomes. The differential amount of CICR family in At and Dt will aid in partitioning sub genome sequences for chromosome assemblies during tetraploid genome sequencing and will act as a method for assessing the accuracy of tetraploid genomes by looking at the proportion of CICR elements in resulting pseudochromosome sequences. The timeline of the expansion of CICR family provides a new reference for cotton evolutionary analysis, while the impact on gene function caused by the insertion of CICR elements will be a target for further analysis of investigating phenotypic differences between A genome and D genome species. (2) Identification of a Genome-specific Repetitive Element in the Gossypium D genome The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5 genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling. [less ▲]

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See detailStudy on interfacial and techno-functional properties of milk fat globule membrane: Role of Cholesterol
Malik, Priyanka ULiege

Doctoral thesis (2019)

Fat in milk and cream is present as tiny droplets, which are enveloped by a thin membrane known as milk fat globule membrane (MFGM). This protective envelope appears as a complex assembly of proteins ... [more ▼]

Fat in milk and cream is present as tiny droplets, which are enveloped by a thin membrane known as milk fat globule membrane (MFGM). This protective envelope appears as a complex assembly of proteins, lipids and other minor compounds. It originates from the plasma membrane of secretory cells of the mammary gland and contains cholesterol and cholesterol esters. MFGM has very important functional and nutritional properties, intervening in dairy technology as well as in the formulation of certain food products. Various studies on the surface properties of the MFGM have been carried out with a particular view to linking them to its techno-functional properties. While techniques for cholesterol reduction and milk fat fractionation have been developed or are under development, there does not appear to be any relevant scientific information on the effect of cholesterol removal on properties of the MFGM. The present work aimed to characterize the impact of MFGM fraction composition on the interfacial and techno-functional properties of MFGM, and to deepen the understanding regarding role of cholesterol. First, fractions of MFGM were extracted at different stages. Their chemical composition as well as their physicochemical properties were then characterized. Differences in composition were observed between the fractions, which affects the surface properties, both in adsorption kinetics, mechanical properties and rheological properties of the interfacial films. In an attempt to better understand specific interfacial properties of the various components of MFGM, their monolayers were characterized using a Langmuir film balance. Fractions of MFGM were separated into lipids (total and polar lipids) and defatted membrane. The interfacial properties of these components have been characterized at the air / water interface. The interfacial properties of MFGM and polar lipids were also characterized at the oil / water interface. By using the compression isotherm, the surface elasticity of the components of the MFGM were calculated. MFGM polar lipids have been found to have relatively high surface elasticity, confirming their potential to help stabilize food systems. Cholesterol was removed from MFGM using β-cyclodextrin (β CD) and methyl β-cyclodextrin (MβCD). The use of ß CD in dairy products is approved by many regulatory agencies around the world. A lower concentration of MβCD eliminated cholesterol more effectively from MFGM compared to ß CD. The properties of low-cholesterol MFGM were compared to the native MFGM. The lipid classes and fatty acid composition were found to be modified due to the removal of cholesterol, resulting in different surface properties of low- cholesterol MFGM. Emulsions were finally prepared using MFGM and low cholesterol MFGM. A relationship could be established between the values of equilibrium surface tension and the stability of emulsions vis-a-vis creaming. The lower the value of the equilibrium surface tension, the lesser is the creaming. Moreover, the stability of the emulsions obtained by whipping of the emulsions could be related to the elasticity modulus. The higher the elasticity modulus, the greater the stability of the whipped emulsions. [less ▲]

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See detailDrêches d’alcool de riz dans l’alimentation du porc : réponses de l’animal et du microbiote intestinal
Nguyen Cong, Oanh ULiege

Doctoral thesis (2019)

Rice distillers’ by-product (RDP) is a coproduct from rice fermentation process in the alcohol production and it is a widely used feedstuff in Vietnam and in Asia. But its adequate incorporation into pig ... [more ▼]

Rice distillers’ by-product (RDP) is a coproduct from rice fermentation process in the alcohol production and it is a widely used feedstuff in Vietnam and in Asia. But its adequate incorporation into pig diets is still questionable. The objective of this study was to investigate RDP production, their nutritional value and inclusion effects on nutrient digestibility, growth performance, blood profiles, carcass characteristics, meat quality and colonic microbiota of weaned and/or finishing pigs. Therefore, four main experiments were performed according to results outlined below. Production, nutritive value and use of rice distiller’s by-product as feeding for pig raising in Northern Vietnam were investigated in Experiment 1. A total of 120 rice alcohol producers classified by production scales (large, medium and small) were interviewed. Additionally, RDP samples were collected from nine representative producers to analysis their daily chemical composition for one week of storage. Our results indicate that an amount of 3.3 tons dry matter (DM) of RDP was obtained per producer per year. A positive correlation between quantity of RDP production and pig number raised in the household was established (p < 0.05). Amounts of rice distillers’ by-product used in the daily diet of swine in all three household’s scales gradually decreased from pregnant to lactating sows (28 and 18% DM) and varied for fattening pigs (25 to 34% DM). RDP was a rich source in crude protein (26.2% DM), lactic acid (2.3 g/100 g fresh matter), phosphorus (7.5 g/kg DM), iron (104 mg/kg DM) and gross energy (20.4 MJ/kg DM). Its nutritive values were stable under ambient condition during a week (p > 0.05). In experiment 2, nutrient digestibility and energy value of ordinary (ORDP) and glutinous (GRDP) rice distillers’ by-product in growing pigs was evaluated. Glutinous by-product especially showed higher level in crude protein (31% DM) in comparison with RDPO (20% DM). Inclusion of ORDP in diets fed to pigs tended to increase DM intake (p = 0.054) but decreased apparent digestibility of gross energy (p < 0.001) and of crude protein (p < 0.04); while inclusion of GRDP in diets fed to pigs decreased DM intake (p < 0.001) et tended to decrease apparent digestibility of crude protein. Both GRDP and ORDP products negatively affected apparent digestibility of ether extract. Digestible and metabolizable energy of ORDP and GRDP were 17.0 and 16.6, and 17.7 and 17.1 MJ/kg DM, respectively. To study growth performance, nutrient digestibility, blood profile and intestinal microbiota of weaned piglets fed diets containing increasing levels of RDP, Experiment 3 was designed. Weaned piglets fed diets with increasing inclusion levels (0, 15, and 30 % DM) of RDP tended (p ≤ 0.07) to produce higher average daily gain, and lower (p = 0.08) feed conversion ratio; numerically lower apparent total tract digestibility and apparent ileal digestibility of nutrient components were observed; blood parameters were within the normal ranges. However, gene amplicon profiling of 16S rRNA revealed that colonic microbiota composition of weaned piglets changed by inclusion of RDP, and RDP in a favorable way modulated gastrointestinal microbiota composition and improved piglet performance. Finally, in Experiment 4, growth performance, carcass quality characteristics and intestinal microbiota profiles in finishing pigs fed diets with different inclusion levels of RDP were evaluated. Inclusion of RDP (0, 15, and 30 % DM) in finishing pig diets increased average daily gain (p < 0.01) and backfat thickness (p < 0.05). 16S ribosomal RNA gene amplicon profiling showed that RDP was associated with a modulation of colonic microbiota composition and induced an improvement of animal growth and fat deposition. In conclusion, RDP was rich in high quality crude protein and other nutrients and was a suitable feed for pigs. RDP modulated colonic microbiota, which led to trends for improvement in animal growth and fat deposition. Additionally, in a local context RDP used in pig diet improved economical efficiency. [less ▲]

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See detailEvaluation des performances techniques de l'irrigation au Burkina Faso
Kambou, Donkora ULiege

Doctoral thesis (2019)

In Burkina Faso, faced with the persistence of severe climatic conditions that compromise mainly rain-fed agricultural production, the development of irrigation appeared as a promising alternative to ... [more ▼]

In Burkina Faso, faced with the persistence of severe climatic conditions that compromise mainly rain-fed agricultural production, the development of irrigation appeared as a promising alternative to secure, intensify and increase sustainably agricultural production. However, one of the main constraint to irrigation development is the availability of water, scarcity or shortage of water on irrigated areas. This research contributed to the reflection on the problem of water on irrigated areas in Burkina Faso through the evaluation of the technical performance indicators, the irrigation management analysis and the irrigators organizational efficiency, while first examining the general context of the development of irrigation. The study shows that overall, relatively large quantities of water fall in Burkina Faso. However, the distribution of this water in time and space is very uncertain and does not guarantee a good rainy season for agricultural production. The implementation of water harvesting techniques and the practice of supplemental irrigation would help secure agricultural production during the rainy season. This random rainfall context justifies the choice of producers and policies to develop irrigated agriculture. Irrigation in Burkina Faso is essentially gravity and is poorly developed, with 33% of areas developed on an irrigable area of 233,500 ha. Efforts are made in the construction of irrigation infrastructures. However, irrigation management is poorly controlled and producers poorly organized to ensure the proper management of water and the maintenance of hydraulic infrastructures. Furthermore, if the water used for irrigation does not present any risk for crops and soil, on the other hand, poor management of fertilizers and pesticides has been highlighted, which could have negative consequences for the environment in more or less long term. In order to evaluate irrigation performance, a bibliographic synthesis allowed to review and clarify the concepts of water use efficiency and productivity according to their fields of application as well as the irrigation systems and the tools to be used for best management of irrigation. The results show that water application efficiencies were less than 20% at Savili, and between 41 and 55% at Mogtédo. Water use efficiencies ranged from 1.12 to 3.4 kg m-3 for Allium Cepa (onion) in three networks, 0.31 kg m-3 for Zea mays (corn) at Mogtedo, and 0.34 kg m-3 for Phaseolus vulgaris (green beans) at Savili. The modeling of the theoretical and actual irrigation schedules shows that, compared with the theoretical irrigation schedule, the actual schedule in the typical and illegal irrigation networks applied irrigation too often, with crops receiving water long before they had exhausted the available soil-water supply. The amount applied was similar at the two sites (58 mm in the Savili and Mogtéto Typical network, respectively, and 43 mm in the Mogtédo illegal network) and the method of irrigation was also similar (filling furrows or small basins). Poor irrigation management resulted in significant water loss, estimated to be 2,999,923 m3/year for the Mogtédo and Savili sites. The main reason for this underperformance seems to be related to technical and organizational failures by producers. This study highlights the waste of water for irrigation and the strong water competition between typical and illegal irrigation networks. Thus, the problem of water on the irrigated areas in Burkina Faso is not directly related to the lack of water but especially to the poor water management. Improving the performance of irrigated areas around small reservoirs may require: - strengthen the technical, organizational and operational capacities of farmers; - improve the technical quality of land development; - privatize the water supply of the irrigated perimeters, so that the farmer benefits from the water service. [less ▲]

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See detailEtude des conditions de la formation de sporidies chez le champignon biofongicide Pseudozyma flocculosa CBS 16788
Zaki, Omran ULiege

Doctoral thesis (2019)

Pseudozyma flocculosa est un champignon reconnu comme agent de lutte biologique très efficace contre la maladie du blanc (l’oïdium) du concombre, de tomates du rosier de serre. Malgré les avantages ... [more ▼]

Pseudozyma flocculosa est un champignon reconnu comme agent de lutte biologique très efficace contre la maladie du blanc (l’oïdium) du concombre, de tomates du rosier de serre. Malgré les avantages offerts par P. flocculosa sur le plan de la lutte biologique, l'utilisation de ce champignon reste largement limitée par rapport à celle des fongicides chimiques. La méthode utilisée actuellement pour la production de propagules de P. flocculosa est la culture submergée. Les sporidies produites par cette technique montrent une faible résistance au rayonnement UV et une faible longévité par rapport aux sporidies issues de la culture sur milieu solide. Ces faiblesses pourraient avoir un impact négatif sur l'efficacité de ce mycofongicide. Pour mieux comprendre les raisons de ces faiblesses, une comparaison morphologique a été réalisée entre les sporidies submergées et les sporidies aériennes issues d’une fermentation solide en utilisant plusieurs approches microscopiques. Les analyses réalisées par microscopie électronique à balayage et à transmission montrent que la paroi cellulaire des sporidies submergées est mince avec une surface lisse contrairement aux sporidies aériennes qui ont une paroi épaisse avec une surface verruqueuse et cassante. Cette épaisseur est due à la présence d'une couche externe riche en mélanine. D’autres éléments tels que la densification du cytoplasme et du noyau semblent indiquer une dormance plus aboutie chez les sporidies issues de la culture en milieu solide. Le fait que les sporidies submergées n'atteignent pas ce stade de dormance pourrait être la principale cause de leur vulnérabilité aux conditions défavorables. Une technologie de production des sporidies aériennes transférable à l’échelle industrielle a donc été mise au point. Cette technologie combine les avantages de la production en culture submergée et sur milieu solide. Les conditions optimales de croissance (température, aération, humidité et pH) pour a production du mycélium en culture submergée ont été définies. Une étape de sporulation sur support adapté comme le son épuisé a ensuite été mise au point. Ce procédé a permis de donner une poudre de sporidies de concentration 2x109 CFU/g. [less ▲]

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See detailTraining and performance monitoring in elite eventing horse
Kirsch, Katharina ULiege

Doctoral thesis (2019)

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See detailDevelopment and efficacy evaluation of novel adhesive pesticide nano-delivery systems
Sun, Changjiao ULiege

Doctoral thesis (2019)

Developing new eco-friendly pesticides is the foundation for preventing major biological disasters and ensuring food security. However, it has been estimated that 70% to 90% of the applied pesticides are ... [more ▼]

Developing new eco-friendly pesticides is the foundation for preventing major biological disasters and ensuring food security. However, it has been estimated that 70% to 90% of the applied pesticides are either lost in the air or run-off, which has caused many adverse effects, such as pest resistance, risk to humans and non-target organisms and environmental contamination. In the recent decade, the development of nanopesticide formulations has shown a great potential to improve the performance of pesticides by constructing nano-delivery systems. Moreover, in terms of the crop foliage microstructure, the surface of nanoparticles can be easily modified by affinity groups to improve adhesion and decrease the loss from crop foliage. In this PhD thesis, we aimed at developing new formulations of avermectin (Av). In order to decrease the organic solvent pollution and prevent premature degradation of avermectin, stable and controlled release of pesticide, formulations with high affinity for crop foliage and long retention time on crop foliage were constructed to increase the effective utilization rate of pesticides and minimize loss to the environment. The efficacy of the nanoformulations was evaluated as well on pests and non-target species. First, surfactant-modified mesoporous activated carbon (MAC) was employed to absorb Av in order to improve its photo-stability and allow for sustained release of avermectin. Sodium dodecyl sulfate (SDS) modified MAC had excellent absorption of avermectin, and the absorption could be represented by the Langmuir isotherm model. The Av-MAC-SDS delivery system significantly improved sustained release of avermectin and also effectively inhibited the photo-degradation of avermectin. Then, biocompatibility and biodegradable polylactic acid (PLA) was employed as the carrier material. Tannic acid (TA), a bioadhesive natural molecule, was applied to modify abamectin nano-delivery systems to enhance retention time on foliage. The nanoparticles showed excellent continuous sustained release and photo-stability. Compared with unmodified nanopesticides, the retention rate of modified nanoparticles on the foliage was remarkably enhanced by more than 50% and indoor toxicity with dipping method against Myzus persicae L. was also increased. Finally, insecticidal activity of PLA-based nano-formulated abamectin was examined on the pea aphid, Acyrthosiphon pisum (Hemiptera: Aphididae), and the aphid predator Adalia bipunctata (Coleoptera: Coccinellidae). A Potter Precision Laboratory Spray Tower was used to conduct direct spray laboratory bioassays. A comparable insecticidal effect of TA modified nanoformulation was observed compared to commercial emulsifiable concentrate (EC) against the aphid. And the nanoformulations had lower stomach toxicity on non-target lady beetles. These results are expected to be beneficial to develop novel leaf-adhesive nanopesticides with high retention time and bioavailability. [less ▲]

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See detailImpacts of migration on agricultural development in Red River Delta, Vietnam
Nguyen Thi Minh Khué, ULiege

Doctoral thesis (2019)

This thesis explores the impacts of rural migration on agricultural production in the context of 30 years after the Đổi Mới (renovation) reform based on a systematic survey of a Vietnamese village, key ... [more ▼]

This thesis explores the impacts of rural migration on agricultural production in the context of 30 years after the Đổi Mới (renovation) reform based on a systematic survey of a Vietnamese village, key informant interviews and participatory observation. All data was collected in Mai Thon Village, Bac Ninh province, a typical Red River Delta village. It features the comparative perspective, comparing the situations of household groups participating in different types of migration and non-migrant households and the impact thereof on their agricultural production. This thesis shows that the increasing rural out-migration flows have become more circular with the development of infrastructure. Normally, migrants send remittances back home and bring food from their homes back to the city. Moving back and forth, the migrants themselves are the key factors of rural-urban continuum. Migration has, therefore, become an important generator of change in farming in Mai Thon village. Remittance plays a central role in local household income and shows a positive case of remittance spending in farming activities. The groups involved in diversified migration types made more remittances to overcome farming constraints than other groups. The remittance used for agricultural production is four times higher than for non-farm. Agricultural production and non-agricultural production are complementary to each other in household earning activities. The majority of migrant households keep their paddy fields and manage to maintain agricultural production on their land in the context of labour lost due to migration in multiple ways including partial abandon, partial leasing, partial lending and partial producing. Agricultural land and farm work, however, are retained as a stable resource, a guarantee of subsistence or a safety net for rural people while boosting their autonomy. In terms of an agricultural production choice, most of Mai Thon households keep rice production as the fundamental agricultural activity, while cash-crop cultivation and livestock raising are vastly reduced. The thesis also explores the expansion of multifunctional households and multi-spatial households to maintain agriculture under the influence of migration. Moreover, households with a migrant labourer continue agricultural production, giving priority to home consumption, which encourages Mai Thon households to keep farming on a small-scale, using local varieties or breeds with a higher nutritional value, enabling better local resource usage and hence more environmentally friendly for their own family and friends. This reaction shows the interesting resistance of peasant farmers in a context of global food crisis, not only in terms of food security but also food safety and food sovereignty. Most migrants prefer declaring their status as “peasants” and “village members” to keep their sense of social security, meanwhile integrating the outside world as “flexible peasants”. As a result, rural households become multi-site households with multiple job holdings and the village becomes a hybrid village where the traditional institutions have mixed with modern ones. This implies that although migration would be considered as a supplemental strategy for agriculture production to increase household security and autonomy, decentralised rural industries provide rural people with close-by extra job opportunities beyond farming, which could prompt people to continue farming. Even though family farming has an important role in rural household livelihoods, the contribution of agriculture to farmer incomes and rural development depends on the active participation of youth who are the potential labour force. In Mai Thon, a wide range of constraints discourage the youth active participation in agricultural production activities includes: Inadequate credit facilities, low and unstable returns from agricultural investment, the drudgery of agriculture work and availability of employment alternatives Indeed, those constraints have complex interlinks with each other. The prospects for success in the future lie in the fact that despite farming low return, most rural youths still engage in agriculture and consider it as their way of life. [less ▲]

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See detailVariabilité interannuelle des échanges nets de CO2 d’une forêt tempérée dominée par le hêtre : rôle des facteurs climatiques, physiologiques et phénologiques
Hurdebise, Quentin ULiege

Doctoral thesis (2019)

This thesis is dedicated to the study of climatic, physiological and phenological causes of the interannual variability (IAV) of the net CO2 exchange (or net ecosystem productivity (NEP)) of a temperate ... [more ▼]

This thesis is dedicated to the study of climatic, physiological and phenological causes of the interannual variability (IAV) of the net CO2 exchange (or net ecosystem productivity (NEP)) of a temperate forest. Until today, temperate forests act as a carbon sink. They absorb more carbon than they emit at annual scale without perturbations. However, the intensity of the sink is highly variable from one year to another and the causes of this variability remain to be explored. Furthermore, the fate of this sink itself is uncertain under the current climate change. This is why it is essential to study NEP variability in these ecosystems. To do so, a measurement station was set up in 1996 at the heart of a beech-dominated forest in east Belgium. The forest also contains numerous coniferous species (Douglas fir, spruce, silver fir,...). The mean NEP over the studied period (1997-2016) was around 411 gC/(m².an). The forest acted as a CO2 sink every single year. The range of the IAV was around 348 gC/(m².an). No trend was observed for the annual NEP. For the monthly NEP, an increasing trend was observed in April. At the opposite, trends were observed for climatic (drier, sunnier and hotter spring and autumn, more precipitation in summer), phenological (shortening of the leafed period and of the carbon uptake period) and physiological (reduction of the quantum efficiency) variables. In particular, it was shown the climate evolution impacted negatively beech phenology (earlier senescence without a significant advance of leaf out) and positively coniferous phenology (earlier carbon uptake start). Combined with the lack of interannual trend for the photosynthetic capacity, these results suggest the lack of trend for annual NEP is essentially due to forest heterogeneity. The analysis of annual NEP and its interactions with climatic, phenological and physiological variables has brought to light the role of the previous year climate conditions. More specifically, it was shown that a hot and dry summer the previous year diminish the growing season length, the photosynthetic capacity, the quantum efficiency and the annual NEP of the forest for the current year. These processes may likely be explained by the sensitivity to previous year climatic conditions of carbon allocation (directly or through carbon storage) to the fruits, the leaves, the wood or the roots. The main recommendation of the thesis for the future of the research at the Vielsalm station was to deepen the understanding of the carbon allocation processes that are likely controlling the forest annual NEP variability. Before studying the IAV of the NEP, the validity and representativeness of the data were checked. In this context, the canopy proximity variability (due to tree growth and measurement height changes) impact on eddy covariance measurements was explored. No significant impact was observed for CO2 turbulent transport at the Vielsalm station. However, the CO2 flux was impacted suggesting an evolution of the composition of the area contributing to the measured fluxes. As a second step, the heterogeneity of the forest had, therefore, to be considered. A robust methodology was developed in order to allow the comparison of the measured CO2 flux for the whole period despite canopy proximity variability. The thesis underlines the necessity, in the context of the climate change, to continue to measure the productivity, the phenology and the physiology at the Vielsalm station and to start collecting auxiliary measurements in order to confirm the obtained results and the formulated hypothesis. [less ▲]

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See detailEffects of dietary fiber and heat stress on cholesterol and bile acids metabolism in pigs
Fang, Wei ULiege

Doctoral thesis (2019)

Cholesterol, as a vital role in the human and animal body, is an essential component of all cell membranes and serves as precursors for steroid hormones, bile acids (BAs) and vitamin D. Cholesterol ... [more ▼]

Cholesterol, as a vital role in the human and animal body, is an essential component of all cell membranes and serves as precursors for steroid hormones, bile acids (BAs) and vitamin D. Cholesterol homeostasis is maintained by a subtle balancing act among synthesis, absorption, and excretion. Conversion to BAs from cholesterol is the major route for cholesterol excretion. Furthermore, BAs, as signaling molecules, can coordinate hepatic lipids and energy homeostasis through the nuclear receptor farnesoid X receptor (FXR), and the plasma membrane-bound bile acid receptor (TGR5). In this study, we investigated the effects of dietary fiber and heat exposure on cholesterol and bile acids metabolism in pigs. Pigs are recognized as excellent biomedical models for human research and the highly conserved metabolic and physiological responses to a severe heat load amongst species make it an ideal model to further extend our knowledge on thermal biology. In addition, pigs are important agricultural species, thus results will likely have important implications in both human health and pig production. Firstly, soluble dietary fibers (DFs) have been known for their cholesterol-lowering effects for a long time and thereby they are suggested as healthy dietary supplements to reduce the risk of cardiovascular diseases, etc. Pectin, a fruit-extracted DF, can increase fecal excretion of BAs to divert cholesterol to synthesize bile acids. In Chapter 3, we demonstrated the lipid-lowering effect of pectin even in pigs fed with a conventional corn-soybean meal diet with a normal level of fat. By profiling intestinal BAs and mapping BAs sensors and transporters along the length of intestine, we for the first provided the molecular evidence to support that the ileum and jejunum are the major gut section for BAs re-absorption in pigs. Based upon these data, it shown a great similarity between human and pig regarding intestinal BAs transportation. Pectin in a diet with a normal level of fat did not influence the BAs synthesis and excretion, however, it did upregulate intestine BAs sensors and transporters in the ileum and cecum. Secondly, we investigated the effect heat stress on cholesterol in pigs. In heat-stressed pigs, lipid metabolism is unique, in contrast to pair-fed counterparts. However, the mechanism of HS acting on cholesterol metabolism remains unclear. In the study, a temperature of 33°C does stress the growing pigs, indicating by 50% reduced feed intake and 300% respiratory rate; however, it did not cause obvious damages. Likewise, we found that, in short-term HS, liver cholesterol synthesis was reduced but serum cholesterol level was increased. Long-term HS pigs leaded to cholesterol metabolism alteration in the liver, uptake had reduced and cholesterol distribution to other tissues had increased (Chapter 4). Thirdly, we performed an experiment on BA profiling when pigs were exposed to heat stress (Chapter 5). Bile acids are critical for cholesterol homeostasis and new roles in metabolism have been demonstrated recently. In short-term HS (Chapter 5a), liver taurocholates, including taurolithocholic acid (TLCA), taurochenodeoxycholic acid (TCDCA), tauroursodeoxycholic acid (TUDCA), taurohyodeoxycholic acid (THDCA) and taurohyocholic acid (THCA) were elevated on d3, which at the functional level. In contrast, In Chapter 5b, taurine-conjugated BAs (TCBA) were reduced in serum and liver after 21d heat exposure. Several TCBAs, such as TUDCA and THDCA, are known as chaperons to inhibit classic endoplasmic reticulum (ER) stress. This could be deleterious to normal function of cells experiencing heat stress. In addition, the long-term HS pigs caused a decreased expression of genes involved in BA synthesis and conjugation as well as efflux and flux transport in liver, which are not caused by feed restriction. It is the first study to comprehensively characterize BA profiles in compartments important to maintain BA homeostasis after heat stress. In summary, this thesis increased the understanding of cholesterol and bile acids metabolism when pigs supplemented dietary pectin and exposed HS, respectively. Dietary pectin reduced serum cholesterol levels and increased transepithelial transport of BAs in the caecum and apical transport of BAs in the ileum. These results suggested site-specific regulatory effects of pectin on BAs transport in the gut. In addition, heat exposure triggered cholesterol metabolism variations which are not caused by reduced feed intake. These have helped us to develop a different understanding of HS influencing cholesterol and BA metabolism. Furthermore, heat stress has profound impacts on liver TCBAs, which independently of nutrient intake, might serve as elements to protect cells damage during heat stress. [less ▲]

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Li, Minmin ULiege

Doctoral thesis (2019)

Pesticides are components used to protect crops from pests and disease in fields but also in the food chain allowing securing the food supply with the efficient use of ever-scarcer natural resources. The ... [more ▼]

Pesticides are components used to protect crops from pests and disease in fields but also in the food chain allowing securing the food supply with the efficient use of ever-scarcer natural resources. The FAO estimated an average of 26% to 40% of crop yields that are lost annually due to weeds, pests and diseases. To ensure safety and sustainability with pesticide use, the fundamental principle lies behind the EU and China pesticide legislation. It is very important to combine the protection of human health, wildlife and the environment with the improvement of agricultural productivity. Also, the assessment for novel chiral postharvest pesticides is necessary to follow their future in food and environment. Therefore, in this thesis, we firstly investigated the analysis methods, the limits of quantification (LOQs) were estimated to be 1.0 μg/kg for 2,4-D, carbendazim, thiabendazole, and prochloraz, and 1.5 μg/kg for iprodione in food matrices. The mean recoveries were in the range of 70.4-113.9%. The analysis uses the ultra-performance convergence chromatography coupled with triple quadruple mass spectrometry (UPC2-MS/MS) following by the QuEChERs as sample preparation. The coefficients of determination (r2) exceeded 0.9954 in the solution calibration and all matrix-matched calibrations, and the LODs of CYF enantiomers were 2.8-4.9 μg/kg and the LOQ was 50 μg/kg. Acceptable average recoveries were within 84.95% to 119.9% at three concentration levels and the RSDs ranged from 0.75% to 9.36% of all cases. Based on chemometric methods, the residue levels of these five pesticides in commercial juice may be further decreased using a reconstitution step. Afterward, the PF of the peeling process was the lowest with degradation of (+) -CYF and (-) -CY by around 65.4% and 66.2%, respectively. The reduction of CYF enantiomers in the process of fermentation was in accordance with the first-order of kinetics, in which the half-lives of (-) -CYF and (+) -CYF were 4.25, 4.05 days in apple wine making, and 3.18, 3.19 days in apple vinegar-making, respectively. Also, the degradation dynamics of CYF followed first-order kinetics. Under aerobic conditions, the differences in black soil, krasnozem and fluvo-aquic soil were significantly different (p < 0.05). Finally, the CYF enantiomers selectively recognize proteins and affect metabolic pathways. This mechanism of interfering hormones was found to be up-regulated by the estrogen receptor family protein FAM102A by proteomic analysis. Preliminary studies have shown that the development of (+)-CYF is more active and less toxic than rac-CYF. However, the toxicity of (+)-CYF to bees requires longer observation duration, at least over 48 hours. In summary, this thesis increased the understanding of the chemometric-assisted method, especially their time saving during extracting and cleaning. The supercritical fluid chromatography combined with tandem mass spectrometry support a perfect separation with the advantages of low viscosity, high separation efficiency, and environmental benefits. From the food processing factor data, we found that the residue levels of water-soluble pesticides in commercial juice may be further decreased using a reconstitution step. Apples with pesticide residue levels lower than the maximum residue levels can be assessed, and the resulting apple juice can be consumed directly. In addition, they easily degraded other compounds and these compounds could be converted into each other, the enantioselective usually occurred in the enzyme, especially in chiral environment. Through bioassay and protein experiments, chiral pesticides expressed enantioselective toxicity, which may be due to differences in binding between with protein and chiral structure. [less ▲]

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See detailHeavy metals in Chinese raw cow milk: spatial distribution and relationships with silage and environmental factors
Zhou, Xuewei ULiege

Doctoral thesis (2019)

Milk and dairy products play important roles in human diets. Owing to the increasing consumption of milk and dairy products in China, the enhanced national production of milk and the presence of polluting ... [more ▼]

Milk and dairy products play important roles in human diets. Owing to the increasing consumption of milk and dairy products in China, the enhanced national production of milk and the presence of polluting industrial activities that could directly or indirectly contaminate milk with heavy metals, there is a need to screen for the presence of heavy metals and to assess the potential health risks of consuming contaminated milk. Therefore, this thesis conducts a large-scale research to study the spatial variability of heavy metals contents in raw cow’s milk produced in the 11 main producing areas in China. This research also estimates from a limited set of records the relationships between the content of heavy metals in individual cow’s milk, drinking water, feed and soil to isolate pathways potentially responsible for the milk contamination. Moreover, this thesis aims also to assess the human health risk of consuming contaminated milk by calculating using theoretical approach the hazard quotient (HQ). As the analysis cost to measure the contents of heavy metals in milk is high, there is an interest to find a cheap proxy. This one could be related to the milk composition. Therefore, the correlation values between the heavy metals’ contents in milk and the main milk components were also estimated in this thesis. The concentrations of heavy metals were measured in 1,043 bulk milk samples, 60 individual cow milk samples, 46 drinking water samples, 6 silage and soil samples and 40 TMR samples. All samples were analyzed by inductively coupled plasma mass spectrometry after microwave assisted acid digestion, except for soil samples, which were analyzed by atomic absorption spectrometry and atomic fluorescence spectrometry. The main results of this thesis are as follows: (1) The average concentrations of Pb, As and Cd in bulk milk were 1.74 μg/L, 0.32 μg/L and 0.05 μg/L, thus suggesting limited cause for concern regarding heavy metal contamination in milk produced in China. Only 12 bulk milk samples (1.15%) exceeded the maximum residue limit (MRL) of Pb set by the European Union. There is no expected health risk when those average and highest levels were used to calculate HQ values. Indeed, those values were always lower than 1. (2) Regional variability was observed in the Pb, As and Cd contamination in milk. A higher heterogeneity of heavy metal content in milk was observed within areas than between areas. The content of Pb and Cd in individual milk samples from industrial areas was significantly higher than that in agricultural areas, but the content of As was significantly lower. This result suggested that industrial activities (i.e., steel production, waste incineration plant and cement plant) lead to potential Pb and Cd contamination in milk, thus confirming the need to know the micro-environment of the farm to interpret the observed contents of heavy metals. (3) The ingestion of contaminated feed, water and soil by cows can induce the production of contaminated milk. Weak correlation values were obtained from As concentrations between water and bulk milk (r ranged from 0.12 to 0.45). As content in individual cow’s milk samples was positively correlated with the content in water (r = 0.37). Conversely, Cd in milk was negatively correlated with Cd in water. Nearly no relation (r ranged from -0.03 to 0.09) was found between Pb levels in water and milk. This result indicated that drinking water may be the main source of As contamination in raw milk. Weak positive correlations were observed between heavy metals in milk and silage. The content of Pb in individual cow milk samples was positively correlated with Pb in silage (r = 0.54). Heavy metals in silage appeared to be the main source of heavy metals in raw milk. Moderate positive correlation values were found for Cr (r = 0.60) and Cd (r = 0.66) between milk and soil, and negative values were observed for Cr (r = -0.60) and Cd (r = -0.75) in water. Those correlations suggested that water and soil contaminate milk differentially. (4) No strong relationships were observed between the content of heavy metal and milk composition. However, weak positive correlations were found between Pb and protein in milk (r = 0.11), and Cr and protein in milk (r = 0.18). Cd content in individual cow’s milk was weak positively correlated with lactose. Beyond these, heavy metals and milk composition showed zero or negative correlations. Thus, milk protein appeared to be more affected by heavy metal pollution than other milk components. In conclusion, this thesis highlights the presence of heavy metals at low quantities in milk produced in China. Therefore, there is a need to define a sampling protocol to screen dairy farms with a potential to produce contaminated milk, to ensure that high quality milk is provided to consumers. Unfortunately, the results obtained in this thesis were not sufficient to propose a detailed sampling procedure, because information on the micro-environment (such as the presence of industrial activities or the type of industry) around the farm was lacking. Such knowledge was highlighted in this thesis to be the most important factor to illustrate the sources of heavy metals in raw milk. Moreover, there is also a need to increase the sample size to provide higher confidence in the relationships described in this thesis. [less ▲]

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See detailImpact of bifidobacteria and oligosaccharides from bovine milk on virulence of two intestinal pathogenic bacteria and on child gut microbiota
Bondue, Pauline ULiege

Doctoral thesis (2019)

The most abundant bifidobacteria found in breastfed infant feces are able to metabolize human milk oligosaccharides (HMO), by cleaving the α-glycosidic bonds of fucoses and sialic acids, as well as the β ... [more ▼]

The most abundant bifidobacteria found in breastfed infant feces are able to metabolize human milk oligosaccharides (HMO), by cleaving the α-glycosidic bonds of fucoses and sialic acids, as well as the β-glycosidic bonds in the HMO core. The whey obtained from cow’s milk contains complex oligosaccharides, also called bovine milk oligosaccharides (BMO), especially 3’-sialyllactose (3’SL). BMO are structurally very similar to HMO and share some common properties. Because they are of bovine origin, Bifidobacterium crudilactis FR/62/b/3 and Bifidobacterium mongoliense FR/49/f/2, two bifidobacterial strains isolated from a raw cow’s milk cheese, could encode the enzymes necessary to digest them. In addition, the fermentation of carbohydrates by bifidobacteria could produce some metabolites able to modulate the virulence of intestinal pathogens. Because in vivo experimentations are difficult and limited by obvious ethical reasons, some in vitro digestive models have been developed. Among all models, the simulator of the human intestinal microbial ecosystem (SHIME®) represents all parts of digestive tract and seems particularly adapted to evaluate the interactions between the pre/probiotics and the microbiota of young children. This research was divided into three main axes: -Ability of B. crudilactis FR/62/b/3 and B. mongoliense FR/49/f/2 to metabolize BMO (genome analysis: study 2; BMO fermentation: studies 1 and 2). -Virulence gene expression analysis of intestinal pathogens after contact with cell-free spent media (CFSM; containing potential antivirulent metabolites) obtained from BMO fermentation by B. crudilactis FR/62/b/3 and B. mongoliense FR/49/f/2 (studies 1 and 2). -Challenges in a toddler SHIME® model inoculated with prebiotic (3’SL), probiotic (B. crudilactis FR/62/b/3), synbiotic (3’SL+B. crudilactis FR/62/b/3) and CFSM (metabolites): impact on the microbiota (study 3). Genome analysis revealed that B. mongoliense DSM 21395 has a more sophisticated enzymatic pathway for BMO digestion compared to B. crudilactis LMG 23609. B. crudilactis FR/62/b/3 and B. mongoliense FR/49/f/2 were able to grow on media supplemented with BMO or 3’SL as the main source of carbohydrates. The CFSM issued from the fermentation of 3’SL by these two bifidobacteria significantly down-regulated the virulence gene expression of enterohaemorrhagic Escherichia coli (EHEC) O157:H7 and Salmonella enterica serotype Typhimurium, respectively. Those obtained from fermentation of BMO (in whey) by B. mongoliense FR/49/f/2 significantly down-regulated the virulence gene expression of EHEC O157:H7. Finally, the synbiotic combination of 3’SL and B. crudilactis FR/62/b/3 tested in the toddler SHIME® model, in which specific bacterial populations proper to each colon are developed, tended to a bifidogenic effect. In conclusion, the glycobiome of B. mongoliense DSM 21395 seemed more adapted to BMO digestion to that of B. crudilactis DSM 23609. However, the synbiotic combination of 3’SL and B. crudilactis FR/62/b/3 led to interesting in vitro results by decreasing the virulence gene expression of intestinal pathogens and by having a bifidogenic effect on the microbiota implemented in the gastrointestinal system. In addition, the toddler SHIME® model developed in this work shares both infant and adult microbiota properties and seems appropriate to study the interactions between the pre/probiotics and the microbiota of young children. [less ▲]

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See detailLarge-scale predictions of methane emission and body weight as tools contributing potentially to the genetic improvement of environmental sustainability of milk production
Vanrobays, Marie-Laure ULiege

Doctoral thesis (2019)

Maximizing profitability of dairy farms ensuring also mitigation of cattle environmental footprint is a major concern in milk production. Improvement of dairy cows’ feed efficiency is of interest to ... [more ▼]

Maximizing profitability of dairy farms ensuring also mitigation of cattle environmental footprint is a major concern in milk production. Improvement of dairy cows’ feed efficiency is of interest to achieve this goal as feed costs contribute largely to the variable costs in dairy sector and because feed efficiency is related to environmental concerns. As feed efficiency of dairy cows is influenced by several interconnected factors, many aspects of research could be addressed to improve it. For that, ample volume of reliable data from a lot of cows is required. Methane emission and body weight of lactating dairy cows have large influence on feed efficiency. However, these traits are difficult to measure at large scale in commercial farms. Therefore, the objective of this thesis was to improve predictions of daily methane emissions from milk mid-infrared spectra and body weights of lactating dairy cows in order to study the genetic variability of these traits and to investigate the opportunity of using them as tools to improve environmental sustainability of milk production. First, predictions of methane from milk mid-infrared spectra were improved by introducing the lactation stage information into the calibration process of the prediction equation in order to take into account the expected metabolic status of the cow. As milk mid-infrared spectra are collected routinely during milk recording, this equation allows to predict methane emissions of dairy cows at a large scale and at an individual level. High throughput screening of dairy cows for methane was conducted with mid-infrared methane predictions. Also, correlations between milk mid-infrared predicted methane and milk fatty acids were predicted throughout lactation. These correlations changed across lactation and these variations were related with the metabolic origins of milk fatty acids and then with the expected metabolic status of the cows over lactation allowing to confirm that integration of lactation stage in methane mid-infrared prediction equation was useful. Thereafter, a model was built to predict body weight of dairy cows throughout lactation from body weights estimated from linear conformation traits recorded at least once during the lactation. These predictions could be associated with milk production and composition as well as animal characteristics to estimate new traits related to feed efficiency like dry matter intake. Finally, this thesis demonstrated that methane emission and body weight of cows fulfill all criteria to be included in a breeding program in order to improve feed efficiency of dairy cows. To conclude, this thesis has shown that predictions of methane emission and body weight of dairy cows are traits of interest for widespread screening of herds in order to develop genetic selection tools to improve environmental sustainability of milk production. [less ▲]

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See detailMulti-tracer approach to apprehend feeding ecology of grey seals and harbour seals in the North Sea
Damseaux, France ULiege

Doctoral thesis (2019)

For several decades, the North Sea has been impacted by climate- and other human-driven changes such as chemical and noise pollution, marine traffic and intensive fishing activities. Indeed, the North Sea ... [more ▼]

For several decades, the North Sea has been impacted by climate- and other human-driven changes such as chemical and noise pollution, marine traffic and intensive fishing activities. Indeed, the North Sea contributes to 4-5% of the world fish production with more than 5 million of tons of fish per year and is considered as one of the most productive fishing area in the world. This may be a real problem for the renewal of some fish species that play an important role in the food chain such as sandeels (Ammodytidae). They are the trophic link between plankton and marine mammals as grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina); both piscivorous and sympatric species that inhabit much of the coasts and continental shelf waters of the North Sea. Classifying foraging resources and foraging distributions of marine mammals in relation to anthropogenic activities and environmental conditions is important to guide marine conservation. This study provided a rare opportunity to determine the poorly known 1) ecological niche partitioning and competition between sympatric grey seals and harbour seals and 2) temporal variations in their feeding ecology in the changing environment of the North Sea by using a multi-tracer approach - with stable isotope ratios of carbon, nitrogen and sulphur and mercury and selenium concentrations - to test one of the most pertinent ecological questions of our time: How do populations respond to environmental changes? As such, we have been able to 1) identify current, short-term and long-term variations in foraging resources and spatial distributions of sympatric grey seals and harbour seals in the North Sea, 2) describe influence of prey abundance variations on their foraging habits, 3) identify potential human infrastructures that may influence their foraging activities and 4) clarify the important use of a multi-tracer approach in ecological studies. In undertaking these analyses, we have identified substantial variations in foraging resources and spatial distributions of grey seals and harbour seals sampled along the German and Scottish coasts in the North Sea. Moreover, our results suggested a high degree of plasticity in foraging resources for harbour seals and in foraging spatial distribution for grey seals to pronounce environmental changes in the North Sea. Finally, we perceived wind farms as important areas for seal foraging activities in the southern North Sea. [less ▲]

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See detailClimatic niche evolution within tropical tree lineages: the case of the Erythrophleum genus (Fabaceae - Caesalpinioideae) in Africa
Gorel, Anaïs ULiege

Doctoral thesis (2019)

In Africa, while some plant groups and specifically genera are strictly associated to specific biomes, evidence of widely distributed genera transcending biome or habitat boundaries have also been ... [more ▼]

In Africa, while some plant groups and specifically genera are strictly associated to specific biomes, evidence of widely distributed genera transcending biome or habitat boundaries have also been reported for herbaceous plants and for tree genera. In this thesis, we aim at understanding the evolutionary processes that allowed particular tropical tree lineages to adapt to contrasted environmental conditions and occur in vast areas. While a diversity of methods at different phylogenetic and spatial scales can provide complementary insights, detailed analyses of well-resolved clades are needed to build robust generalizations about niche evolution and biome shifts. Therefore, from species distribution modeling to hard physiological measurements, we attempt to disentangle the processes explaining the vast distribution of Erythrophleum (Fabaceae), a tropical tree genus widely distributed in Africa, Australia and China. A synthesis is first provided on the Erythrophleum species in Africa (Chapter 2). Erythrophleum encompasses two forest species and two savanna species. The forest species are morphologically similar and sold for timber under the same commercial name, Tali, but genetics revealed contrasted distribution. Erythrophleum ivorense is restricted to the wet coastal forest, while Erythrophleum suaveolens occurs over vast areas from the moist forest up to gallery forests in the savanna. Secondly, we use species distribution models to determine the bioclimatic constraints on the distribution of the Erythrophleum species and gene pools (Chapter 3). Our results support the substantial role of climate in niche evolution, and speciation, within the genus. Erythrophleum has managed to adapt to extremely contrasted climates, resulting in a distribution encompassing several biomes, from the wet forest to the dry forest and the savanna. Ecophysiological (Chapter 4) and experimental (Chapter 5) approaches are then used to get a functional understanding of the niche evolution within Erythrophleum. We find that, for the two forest species, the shift into drier environments was associated with a coordinated evolution of the xylem resistance to embolism, controlled by subtle adaptations in wood anatomical traits, and desiccation delay strategies at stem and leaf levels. Finally, after confronting our results with previous studies on congeneric species, we conclude that, for certain tree lineages, the lability of drought tolerance traits, specifically those related to xylem protection, is an important functional path allowing to transcend habitat and biome boundaries (Chapter 6). We then discuss the generalization of the niche evolution pattern we detected for Erythrophleum to other African genera. Comparing the niche of 1439 woody species at the continental scale, we provide new evidence supporting the niche evolution within many woody genera in tropical Africa (20% of the 532 studied genera). [less ▲]

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See detailImpact of microbial composition on volatolomic profile of Cambodian fermented beverage: from natural to synthetic communities
Ly, Sokny ULiege

Doctoral thesis (2019)

This thesis addressed issues related to rice wine production development in Cambodia. The choice of alcoholic ferment starter is one of the most influencing factors on the yield and quality of the ... [more ▼]

This thesis addressed issues related to rice wine production development in Cambodia. The choice of alcoholic ferment starter is one of the most influencing factors on the yield and quality of the alcoholic beverage. The microbial composition of starters varied according to the regions where they were produced and was influenced by the environment and the material used. Through this study, a first rRNA pyro-sequencing to study the microbiota of traditional Cambodian starters was developed. The results of Chapter 3.1 highlighted the impact of the composition of the microbiota on the profile of the synthesized aromatic compounds. The dominant strains, mainly the filamentous fungus Rhizopus oryzae, the yeast Saccharomyces cerevisiae and the lactic acid bacteria Lactobacillus plantarum have been identified. These three strains have been reported to significantly affect the aromatics profile of the wine. The results of Chapter 3.2 detailed the important role of these three strains in the process of replacing the natural community. The aromatic profile was complementary to that of the natural community (Dombea); moreover, some unpleasant aromas have been reduced when using the controlled and known synthetic community. Another part of the study highlighted the importance of choosing the type of device used for biofilm cultivation to favour its attachment. Chapter 3.3 focused on the evaluation of the fermentation system on the attachment of Trichoderma spp. and the production of hydrophobins. In this respect, two fermentation systems (SFE, DFR) were evaluated. All the results showed the importance of the choice of the device for the biofilm culture, especially in the case of the study of microbial interactions. Thus, the alternative bioreactor design makes it possible to understand and better control the interaction as well as the structuration of the synthetic community studied. Biofilm reactors have made it possible to better control the complex morphology of the mycelium. The results of this study could be considered as a promising avenue for the development of rice wine fermentation technology in Cambodia. [less ▲]

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Egyptien, Sophie ULiege

Master of advanced studies dissertation (2019)

Honeybee semen conservation is of worldwide scientific interest with increasing urgency to improve results in order to conserve biodiversity. Gamete cryopreservation from selected lines is of growing ... [more ▼]

Honeybee semen conservation is of worldwide scientific interest with increasing urgency to improve results in order to conserve biodiversity. Gamete cryopreservation from selected lines is of growing interest also. Indeed, selection of bees tolerant to varroa is one of the main actual objectives in honeybee research. Cryobanking of these gametes will be exploitable internationally by simple transport. In order to improve cryopreservation, different parameters are studied such as influence of drone age. To study this criterion, we need a method to raise large numbers of drones of known age without impairing the colony’s stability. We also need objective characteristics of semen quality. One of these is semen viability studied by epifluorescence or flow cytometry using SYBR-14 and propidium iodide dyes. This report describes the development of this technique and first attempts of cryopreservation. It also details the first steps of validation of the fluorescent supravital staining by flow cytometry as a reference to test new dyes. We can conclude that the rearing method allows to raise large numbers of drones of known age and needs to be tested again during the next breeding season and that the flow cytometry technique needs to be further validated with comparison to epifluorescence microscopy. [less ▲]

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See detailMécanisme de biosynthèse et production de l'astine, un pentapeptide cyclique non-ribosomique de Cyanodermella asteris
Vassaux, Antoine ULiege

Doctoral thesis (2019)

Astin C is a cyclic peptide assembled through a nonribosomal mechanism by a NonRibosomal Peptide Synthetase (NRPS). This nonribosomal peptide displays promising therapeutic properties including anti-tumor ... [more ▼]

Astin C is a cyclic peptide assembled through a nonribosomal mechanism by a NonRibosomal Peptide Synthetase (NRPS). This nonribosomal peptide displays promising therapeutic properties including anti-tumor and anti-inflammatory activities. For decades, this compound was only extracted from the roots of Aster tataricus, a well-known plant in traditionnal japanese and chinese medicine. Recently, Cyanodermella asteris, a fungal endophyte of this plant, was demonstrated to be able to synthesize astin C. This discovery offers new opportunities for the production of this compound of interest. Nonetheless the very low growth rate of this endophytic fungus is an obstacle limiting the astin C production. In this study, two distinct approaches were conjointly considered to upscale the production rate of this compound. The first strategy was related to an optimization of the homologous production from C. asteris. For this purpose, an innovative cultivation system has been developed enabling to grow the fungus exclusively on a stainless steel support. This cultivation condition turned out to be favorable both for the fungal biomass development and for the astin C production. In order to further optimize this process, the effects of several culture parameters (i.e. support pre-treatment procedure, inoculum type, pH, medium composition) on the astin C production rates was investigated. Under optimized conditions, astin C yields were further enhanced, constituting a first step towards the development of an astin C production process at industrial scale. Meanwhile, a study was conducted in order to develop a heterologous expression system for astin C production in yeast. The identification, through bioinformatics analyses, of the genes involved in the astin biosynthesis was a precondition for the development of this approach. Once these genes have been identified, a literature review has enabled to compile the molecular tools applicable for the cloning of NRPS long lenght sequence, and to select a proper host to heterologously express them. The whole sequence or a truncated one have been transfered respectively to Saccharomyces cerevisiae or Yarrowia lipolytica. In both considered yeasts, a heterologous expression of the foreign sequences was confirmed. In S. cerevisiae, the synthesis of the astin NRPS could not be demonstrated. On the other hand, in Y. lipolytica, for the first time, the production of a NRPS-type structure was detected. Although no nonribosomal peptide was detected, this study enabled to overcome several of the hurdles limiting the development of a astin heterologous production way in yeast. [less ▲]

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See detailCharacterisation of toxins from animal venoms by mass spectrometry
Degueldre, Michel ULiege

Doctoral thesis (2019)

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François, Anne-Christine ULiege

Master of advanced studies dissertation (2019)

INTRODUCTION : L’hypoglycine A est une toxine environnementale responsable d’intoxications sévères chez certains mammifères. Possédant la structure d’un acide aminé branché ,elle est transformée en un ... [more ▼]

INTRODUCTION : L’hypoglycine A est une toxine environnementale responsable d’intoxications sévères chez certains mammifères. Possédant la structure d’un acide aminé branché ,elle est transformée en un métabolite toxique : le méthylènecyclopropylacétyl-CoA. Cette métabolisation est réalisée grâce à un système enzymatique présent dans la majorité des cellules eukaryotes. Le microbiote intestinal est capable de métaboliser les acides aminés branchés grâce à un système enzymatique similaire à celui utilisé pour métaboliser l’hypoglycine A. La question du rôle du microbiote lors d’intoxication à l’hypoglycine A se pose. Premièrement, la toxine est-elle capable de modifier le microbiote ? Est-ce que cette modification agit comme un acteur dans le processus pathophysiologique des différentes espèces cibles ? Et deuxièmement, cette toxine est-elle métabolisée par le microbiote ? Est-ce que ce métabolisme peut expliquer la sensibilité individuelle face à cette intoxication ? Ce mémoire propose une étude préliminaire visant à observer les changements du microbiote lors d’intoxication à cette toxine. MATERIEL ET METHODES : Grâce à un simulateur de l’écosystème microbien intestinal humain, une intoxication à l’hypoglycine A a été reproduite . Les modifications du microbiote, la concentration de certains acides gras volatils produits par le microbiote sont observées ainsi que la stabilité de la toxine dans ce simulateur. RESULTATS: Des modifications du microbiote sont observées comme la disparition des Lachnospiraceae, l’apparition des Enterobacteriaceae et l’installation d’une dysbiose observée, entre autre, par une diminution générale de la production des acides gras volatils. La concentration de la toxine semble instable dans le système. D’autres études seront nécessaires afin de confirmer ces observations. [less ▲]

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See detailAnalyzing the genetic diversity in Walloon and European Piétrain pig populations using pseudo-phenotypes, pedigree and SNP marker data
Wilmot, Hélène ULiege

Master's dissertation (2019)

This study aims to infer the origin of the Piétrain breed, to estimate the diversity of the Walloon Piétrain population and to analyze the existing genetic diversity of different European Piétrain ... [more ▼]

This study aims to infer the origin of the Piétrain breed, to estimate the diversity of the Walloon Piétrain population and to analyze the existing genetic diversity of different European Piétrain populations. For these purposes, pedigree and pseudo-phenotypes (i.e. deregressed estimated breeding values) of the Walloon population and genotypes of several European populations were analyzed. The Multi-Dimensional Scaling (MDS) based on genotypes did not allow to have an exact assumption of the Piétrain breed origin. However, it suggested the involvement of different local English (e.g. Berkshire) and Spotted breeds. To have an insight of the Walloon genetic diversity, different pedigree parameters of boars provided to progeny testing were then analyzed. The average inbreeding coefficient was 2.74%, the effective population size (Ne) was 223 and the genetic diversity parameter was 97.96%. The genetic diversity found in the Walloon population seemed therefore relatively high. Gene flows, relatively uncommon between farms, were also studied by a MDS based on the opposite of kinship coefficients. A Principal Component Analysis (PCA) based on pseudo-phenotypes provided complementary information about breeding objectives as it was found that owners focused on meat or growth traits. It could therefore be suggested to the Belgian Piétrain program, based on the boar’s semen cryopreservation, to sample representative boars in the population regarding its genetic and phenotypic diversities. Moreover, as one owner provided 55% of the tested boars, owners should equally contribute to progeny testing. Finally, different European and an American Piétrain populations were analyzed through genotypes. Inbreeding estimations and Runs of Homozygosity (ROHs) stated that Dutch and American populations, supposedly held by commercial firms, were more inbred and uniform. More exchanges of animals should be done in these populations to avoid bottleneck in the future. [less ▲]

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See detailInitiatives locales: entre territorialisation et administration des enjeux alimentaires
Feyereisen, Marlène ULiege

Doctoral thesis (2019)

Depuis les années 1980, une série d’évènements remet en question le modèle alimentaire productiviste et sa capacité à construire la durabilité. Ces enjeux stimulent la construction d’initiatives ... [more ▼]

Depuis les années 1980, une série d’évènements remet en question le modèle alimentaire productiviste et sa capacité à construire la durabilité. Ces enjeux stimulent la construction d’initiatives alimentaires qui focalisent sur la qualité des produits (par ex. agriculture biologique, commerce équitable, slow food, circuits courts, local). Parmi ces initiatives alimentaires, l’alimentation locale construit la qualité sur base de la proximité. Mais ces initiatives, si elles tentent de construire un système alimentaire durable, font aussi face à certaines limites. De nombreux travaux montrent notamment comment les initiatives locales reproduisent certaines inégalités qui remettent en question leur capacité à construire des relations entre les acteurs du système alimentaire qui soient à la fois justes pour l’environnement et pour les humains. Dans le sillon de ces travaux, cette thèse tente de mieux comprendre de quelle manière les initiatives de production, commercialisation et distribution alimentaires locales participent à construire la durabilité du système alimentaire. Pour ce faire, deux initiatives locales sont analysées avec une approche de sociologie pragmatique (théorie de l’acteur-réseau et économie des conventions), combinée avec une approche territoriale : les Grosses légumes et la Coopérative fermière de la Gaume. Ces deux initiatives qui évoluent sur le même territoire rendent compte de deux processus de construction du territoire et des enjeux alimentaires : un processus de territorialisation et un processus d’administration. L’analyse rend compte de rapports de force entre ces deux manières de se lier au territoire, et montre que les réseaux qui adoptent un processus d’administration tendent à limiter la capacité d’action de ceux qui adoptent un processus de territorialisation. Le rôle des pouvoirs publics et de leurs instruments est ici déterminant. Ces dynamiques ont pour conséquence de réduire la capacité du territoire à construire un système alimentaire durable et à répondre aux enjeux de justice sociale. Les résultats de cette thèse invitent à déplacer le regard et penser la durabilité non plus au niveau des initiatives locales, mais à celui du territoire. Plusieurs pistes construites sur base des apprentissages de cette thèse sont alors esquissées. [less ▲]

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See detailEn quoi l’instauration d’une nouvelle modalité d’existence intensive à des non-humains participe à un glissement dans l’écologie des relations ? Le cas de la conservation des lémuriens à Madagascar et de ses enjeux
Emond, Pauline ULiege

Master's dissertation (2019)

Le présent travail s’intéresse aux relations imposées entre l’homme et les autres êtres vivant dans les actions de conservation. Plus précisément, il traite des possibles transformations dans ... [more ▼]

Le présent travail s’intéresse aux relations imposées entre l’homme et les autres êtres vivant dans les actions de conservation. Plus précisément, il traite des possibles transformations dans l’attachement des humains à la nature qui découle de l’instauration de nouveaux modes d’existence intensifs de l’animal pour sa protection. En abordant le cas des lémuriens à Madagascar et du système des aires protégées, ce mémoire tente de mettre en évidence les enjeux gravitant autour de la sauvegarde d’une espèce et des systèmes de conservation de la nature. Passant par les thèmes de la gouvernance, de la patrimonialisation et de la construction identitaire, il cherche à comprendre comment ces nouvelles représentions qui élaborent les non-humains aux yeux des humains. Il est le résultat d’un stage d’immersion au sein d’une aire protégée malgache spécialisé dans la recherche et l’étude des lémuriens. Et a été suivi d’une enquête de terrain orienté vers l’évolution de l’écologie des relations des Malgaches avec les lémuriens et la biodiversité. [less ▲]

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See detailLa politique « zéro déchet » dans le secteur de la restauration en Belgique
Van de Walle, Aurélie ULiege

Master's dissertation (2019)

Notre société nous poussant généralement à la surconsommation, nous générons dès lors inutilement une quantité phénoménale de déchets au travers de la consommation de produits que nous utilisons ... [more ▼]

Notre société nous poussant généralement à la surconsommation, nous générons dès lors inutilement une quantité phénoménale de déchets au travers de la consommation de produits que nous utilisons, emballages compris. Pas moins de 70 000 kg de déchets seraient produits chaque année en moyenne par un restaurant traditionnel. Cependant, des solutions permettant la réduction et la valorisation de la quantité de déchets générés au sein des restaurants/cafés ont été envisagées par certains prestataires de service, acteurs qui feront l’objet d’une étude conjointe avec leurs consommateurs. Le présent travail aborde, d’une part, un premier volet relatif à la sociologie pragmatique qui a pour objectif d’analyser les justifications, en tant que synonyme de « motivations » et de « motifs d’engagement », des prestataires de service à lancer une démarche entrepreneuriale dans le secteur de la restauration « zéro déchet » ainsi que celles des consommateurs à fréquenter leurs établissements. D’autre part, un second volet relatif à la communication des prestataires de service à destination de leurs consommateurs portera plus particulièrement sur la place occupée par la politique du « zéro déchet ». L’analyse s’effectuera non seulement au travers des thèmes de communication (énoncés lors des entretiens et communiqués sur les sites web) et des stratégies de communication (mises en œuvre par les prestataires de service afin d’attirer leurs consommateurs) mais également au travers de la communication sur place. [less ▲]

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See detailCharacterization of GPR1/FUN34/YaaH proteins and acetate metabolism in the microalga Chlamydomonas reinhardtii
Durante, Lorenzo ULiege

Doctoral thesis (2019)

The green microalga C. reinhardtii has been widely adopted as a model to study the dynamic metabolism of photosynthetic organisms. The successful research in the last decades has provided significant ... [more ▼]

The green microalga C. reinhardtii has been widely adopted as a model to study the dynamic metabolism of photosynthetic organisms. The successful research in the last decades has provided significant advances in understanding the regulation of carbon metabolism in this facultative photo-autotrophic model, however, the process of metabolite transport across the membranes remains poorly described. In particular, although the exchanges occurring between the intracellular compartments account for the majority of total transport, the characterization of membrane proteins in this alga is very limited. In this work, we investigated general aspects of acetate metabolism in C. reinhardtii and the characterization of five genes coding proteins belonging to the GPR1/FUN34/YaaH (GFY) family. Here, we provide several lines of evidence to implicate CrGFY1-5 as channels which share structural homology with bacterial succinate-acetate channels and specifically localize to microbodies, which are surprisingly distinct from the glyoxylate cycle-containing peroxisomal microbodies. In silico structural models, gene expression profiling, and in vivo fluorescence localization of all five isoforms support this role and also argue in favor of possible redundant functions. The additional parts of this work present different analyses related to acetate metabolism aspects investigated through the use of the toxic analogous fluoroacetate, the cellular fitness during anaerobic period and the acetate-dependent lipid accumulation along with other physiological analyses. [less ▲]

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See detailInnovations agricoles endogènes : le cas du fruit de la passion au Burundi et comparaison avec le Rwanda et le Kenya
Bashangwa Mpozi, Bosco ULiege

Doctoral thesis (2019)

Passion fruit production in East Africa has involved adoption of endogenous innovations for promoting productivity and improving income generation. These endogenous innovations are common in major passion ... [more ▼]

Passion fruit production in East Africa has involved adoption of endogenous innovations for promoting productivity and improving income generation. These endogenous innovations are common in major passion fruit producing areas in Burundi (Matongo and Isare), Rwanda (Nyamagabe and Rulindo) and Kenya (Embu and Meru). This study analyzed the importance of such endogenous agricultural innovations incorporating passion fruit in Burundi by comparing them to Rwanda and Kenya. The specific objectives of the study were to: i) analyze the socio-economic and agroecological importance of cropping systems incorporating passion fruit, ii) identify the changes introduced by adoption of passion fruit production at the level of the family farm and the community, iii) identify the actors participating in the implementation of passion production, and iv) analyze the constraints faced by passion fruit farmers. The study involved field surveys of innovative farmers in the three countries and interviews were conducted with non-agricultural stakeholders who favored the implementation of this crop. The study focused on the analysis of farm-level transformations and the dynamics induced at the community or territory level adopting passion fruit production. The results indicate high adoption of passion fruit in small farms with an average size of 0.9 ha in Burundi, 0.8 ha in Rwanda and 2.7 ha in Kenya. These small farms are further subdivided into several parcels occupied by different crops: on average, 3 plots are occupied by the passion fruit in Burundi against 1 plot in Rwanda and Kenya. There is an average of 4 plots occupied by other crops in Burundi and Kenya compared to 3 plots in Rwanda. In general, passion fruit was found to occupy an average of 39% of the farmers land area in Burundi compared to 28% in Rwanda and 25% in Kenya. This large spatial occupation, in a context of land shortage, could lead to a gradual decline in areas devoted to other crops. In Burundi only 18% of the land occupied by passion fruit was occupied by other crops compared to 64% in Rwanda and 95% in Kenya. The abandonment of other crops can be avoided by the practice of very predominant crop associations in Burundi. The adoption of passion fruit had led to changes in production systems. Thus we observe the emergence of two great culture systems: a system with the passion fruit and a system without the passion fruit. In Burundi, crop association is favored while in Rwanda and Kenya farmers prefer monoculture. The associated system makes it possible to diversify agricultural production, sources of income and reduce the risks associated with monoculture. In addition, the intercropping passion fruit with agroforestry trees improves soil fertility and conservation. It also provides forages, maintains permanent soil cover, helps erosion control and reduces disease and pest pressure. In addition to changes observed at the farm level, the passion fruit has made it possible to create new activities in the study areas, new markets even outside the production areas. This has brought forth the emergence of new players involved in production, marketing, processing and services. The economic analysis indicates that the cost of production for passion fruit in monoculture was very high in Kenya (1,989 USD/ha/year) compared to Burundi (1,123 USD/ha/year) and Rwanda (1,067 USD/ha/year). This is explained by significant investments in labor inputs and labor costs that are very high in Kenya. However, the production of passion fruit in monoculture creates wealth with positive gross value added in Burundi (3,417 USD/ha), Rwanda (3,808 USD/ha) and Kenya (7,039 USD/ha). Moreover, in Burundi, the associated system values the land better thanks to its very high added value (3955 USD/ha) than that observed in monoculture (3417 USD/ha). In light of these results, promoting the adoption of passion fruit using the intercropping system would address the multiple challenges facing smallholder farmers in East Africa. [less ▲]

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See detailAnalyse fonctionnelle et suivi temporel des communautés végétales de la toiture verte extensive du bâtiment Terra (Gembloux) et étude expérimentale de la facilitation du sedum
Rivière, Lucie ULiege

Master's dissertation (2019)

The abiotic conditions imposed by an extensive green roof are similar to those of a dry lawn. Green roofs can therefore support habitats similar to these lawns. However, the vegetation dynamic of an ... [more ▼]

The abiotic conditions imposed by an extensive green roof are similar to those of a dry lawn. Green roofs can therefore support habitats similar to these lawns. However, the vegetation dynamic of an extensive green roof is still poorly studied. This work fits in this context and is structured around two axes. The first part studies the evolution and the structure of plant communities on the TERRA Research Centre’s green roof. This extensive green roof was sown two years ago. Three points are analysed: the influence of substrate depth and sunlight exposure on the canopy, Ellenberg’s indicators and community CSR strategies. The results indicate that the abundance and specific richness of the roof increased during these two years. Substrate depth and sunlight exposure influence vegetation cover and the distribution of CSR strategies, but this is not the case for Ellenberg’s indicators. It is observed that ruderal species spread more than stress tolerant species in more stressful areas. This observation is not in line with the analogous habitat hypothesis. The second part studies the facilitation effect of sedum through a pot experimentation. The objective of this experimentation is to determine whether the sedum's facilitating effect is more pronounced with certain species or strategies C, S or R. The variables analysed are germination, survival, leaf count and photosynthetic capacity. The results indicate that the sedum acts more like a competitor and that proximity to the sedum increases competition. These two experiments provide additional knowledge on the dynamic of the functioning of green roofs. The study of the evolution of the roof indicates that ruderal species are to be favoured in the most stressful areas. Analysis of interspecific interaction suggests that sedum does not act as a nearby facilitator in slightly less stressful areas. [less ▲]

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See detailRecombinant protein production in the yeast Yarrowia lipolytica
Vandermies, Marie ULiege

Doctoral thesis (2019)

Les protéines recombinantes (rProt) revêtent une importance capitale (comme produit fini et comme catalyseur) dans les domaines de la pharmaceutique, de la chimie, des cosmétiques, de l'alimentation ... [more ▼]

Les protéines recombinantes (rProt) revêtent une importance capitale (comme produit fini et comme catalyseur) dans les domaines de la pharmaceutique, de la chimie, des cosmétiques, de l'alimentation humaine et animale, et du traitement des déchets. Pour des raisons de qualité, une partie de ces protéines est produite par des systèmes-hôtes levuriens, tels Saccharomyces cerevisiae et Pichia pastoris (syn. Komagataella sp.). Outre ces hôtes établis, la levure non-conventionnelle Yarrowia lipolytica représente une usine cellulaire prometteuse pour la production de rProt. En effet, Y. lipolytica synthétise et sécrète des protéines de manière substantielle, jusqu’à 1–2 g·L-1. De plus, certains des inconvénients inhérents à ses prédécesseurs (hyperglycosylation élevée, effet Crabtree, dépendance au méthanol pour induire l'expression hétérologue) sont absents chez Y. lipolytica. Néanmoins, un manque de vue d'ensemble et d'outils spécifiques pour répondre aux exigences de cette levure l’empêchent toujours d'atteindre son plein potentiel de production de rProt. Dans le cadre de cette thèse, deux problèmes majeurs de la production de rProt chez Y. lipolytica ont été sélectionnés et traités : l’absence de promoteurs inductibles pratiques et la difficulté à maîtriser le dimorphisme au cours des processus en bioréacteur. Ces deux problèmes d’ordre pratique ont été résolus suite à la découverte et au détournement d’un gène de sa fonction primaire. Dans un premier temps, l'identification et la caractérisation du gène EYK1 dans le cadre du métabolisme de l'érythritol et de l'érythrulose chez Y. lipolytica ont conduit au développement de promoteurs régulés par ces polyols. Leur facilité d'utilisation et leur polyvalence se révèlent correspondre aux critères de production d'une large gamme de rProt. En utilisant une souche-hôte et des plasmides adaptés à l'expression inductible par l'érythritol et l'érythrulose, environ 45 000 U·mL-1 de lipase CalB sécrétée – le rendement le plus élevé jamais atteint chez la levure – ont été obtenus en 24 h dans un bioréacteur planctonique en mode batch. Deuxièmement, la découverte du gène YlHsl1 a permis d’obtenir des cellules mutantes bloquées dans une morphologie pseudohyphale (ne pouvant plus changer de conformation en réponse à des stimuli environnementaux). Ces cellules s’adaptent parfaitement à la croissance à l’état immobilisé au sein du bioréacteur, ce qui constitue un atout supplémentaire pour les bioprocédés continus et simplifie le traitement en aval des protéines sécrétées. Enfin, le système d'expression induit par l'érythritol développé pour Y. lipolytica au cours de cette thèse a été directement comparé pour la première fois à celui de P. pastoris, pour leur capacité à produire des rProt (ici la lipase CalB). La comparaison a révélé un titre de lipase CalB sécrétée 5 fois plus élevé dans les cultures en bioréacteur de Y. lipolytica que dans celles de P. pastoris, confirmant l'efficacité de Y. lipolytica pour la production de rProt. [less ▲]

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See detailLe microdosage d’engrais : une technique d’amélioration des moyens d’existence des producteurs pauvres au Sahel. Cas des exploitations agricoles à base de mil et de sorgho au Mali
Sissoko, Penda ULiege

Doctoral thesis (2019)

Millet and sorghum are the main sources of food for the Sahelian populations. They represent the most important cereals in Mali, both in terms of cropping area and their consumption by rural households ... [more ▼]

Millet and sorghum are the main sources of food for the Sahelian populations. They represent the most important cereals in Mali, both in terms of cropping area and their consumption by rural households. They are largely self-consumed in rural households and almost totally sold on the domestic market to supply the urban population. However, the observed yields for these two crops in the traditional system are low compared to that of corn and rice. These yields depend not only on climatic and soil conditions but also on producers’ socio-economic constraints. To find solutions to these constraints, agricultural research in the Sahel, for decades, has aimed to improve millet and sorghum productivity by developing technical packages adapted to the different agro-ecological zones in order to reach food and nutritional security (FNS) for populations and to contribute to poverty reduction. Localized fertilization at planting hole or fertilizer microdosing technique is one of the innovations developed by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) to address (respond) the socio-economic constraints of producers in order to be adopted and disseminated in the Sahelian and Sudano-Sahelian areas of West Africa (Mali, Burkina Faso, Niger). In Mali, fertilizer micro-dosing technique on millet and sorghum is carried by farmers out manually or mechanically with use a disk drill. The study of the thesis was about the exploration of the effects of the introduction of fertilizer microdosing technique in millet and sorghum farming systems in the Sahelian and Sudano-Sahelian regions of Mali (Koulikoro, Segou and Mopti). It focuses first on the vulnerability of millet and sorghum cropping systems in research sites; then assesses the adoption and performance of the cultivation systems based on manual and mechanical fertilizer microdosing techniques compared to the conventional system (farmer practice) at plot level. Then, it analyzed the determinants of millet and sorghum productivity using these techniques. The identification of determinants and assessment of the effects of the large-scale adoption of the fertilizer microdosing technique on food and nutrition security (FNS) on farms were analyzed. Finally, the sustainability of the fertilizer microdosing technique was analyzed in order to propose technical and policy measures to help and facilitate its adoption by farmers. Survey was done from a sample (360) of farms based on diagnostic and monitoring surveys during two cropping seasons. Descriptive statistics, analysis of variance (ANOVA) and parametric analyses models were used to analyze data collected using SPSS, STATGRAPHICS and STATA software’s. Analyzing producers' perceptions using diagnostic surveys showed that rainfall variability, soil poverty and lack of agricultural equipment’s were the main risks to the productivity of cropping systems based on millet and sorghum. Fertilizer microdosing is the most widely used (76%) among the main strategies developed by producers to reduce the vulnerability of their crops. Results of the follow-up surveys showed an adoption rate of 69% for microdosing techniques at the level of the interviewed farmers. Better results on technical-economic indicators were obtained on plots adopting these techniques compared to farmers practice. These performances were observed through significant increases in millet and sorghum grain yields, higher net margins and higher values of labor productivity and of family workday and economic profitability rate values around 100% for manual technique and almost doubled (200%) on plots adopting mechanical technique. Results also indicated that the large-scale adoption of fertilizer microdosing technique by farmers contributes to the improvement of the Food and Nutritional Security by a better coverage of cereal needs of adopting farms. Determinants analysis of adoption showed that variables concerning farmer perception on mineral fertilizer cost reduction, yield increase, access to fertilizer subsidy, reduction of food shortage and improved household incomes affect significantly and positively the decision to adopt fertilizers microdosing techniques. The economic, social and agro-ecological sustainability of the fertilizer microdosing technique in farming systems based on millet and sorghum should be ensured through: (i) availability and adoption of this technical innovation by producers, (ii) producers' access to mineral fertilizer and its appropriate use on fields, (iii) mechanical equipment availability for producers to reduce the difficulty of manual labor, (iv) strict respect of the agricultural calendar, (v) institutional support to producers through partial subsidies of production (inputs and equipment’s) and also economic incentives for credit access. [less ▲]

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See detailHydrolysable tannins: promising grass based silage additives for more environmentally friendly dairy systems?
Herremans, Sophie ULiege

Doctoral thesis (2019)

Today, the livestock sector has to address multiple concerns. Being criticized for its environmental impact and competition for land use, a better efficiency at transforming vegetal proteins into animal ... [more ▼]

Today, the livestock sector has to address multiple concerns. Being criticized for its environmental impact and competition for land use, a better efficiency at transforming vegetal proteins into animal proteins while limiting food-feed competition is now one of its main challenges. Several strategies have been identified to improve nitrogen use efficiency (NUE) and reduce environment damage of livestock production; the use of plant secondary compounds such as tannins is one of them. These natural molecules can bind with proteins and protect them against degradation by micro-organisms. Their action can thus help improve nitrogen efficiency and reduce nitrogen losses. Our meta-analysis conducted on 58 experiments showed that tannins are generally ineffective at improving zootechnical performances but a shift in N excretion was observed, urinary N being reduced in favor of faecal N. However, hydrolysable tannins and the effect of tannins addition before ensiling have been little studied to date, unlike condensed tannins. This thesis thus aimed at testing the following hypotheses : i) hydrolysable tannin extracts can reduce proteolysis both in grass-based silage and rumen, ii) hydrolysable tannin extract added before ensiling can improve nitrogen use efficiency in lactating dairy cows. The first experimental results showed that hydrolysable tannin extracts were effective at reducing ammonia-nitrogen content of silages suggesting a reduction of proteolysis. NH3-N proportion was reduced by 12 to 18% with oak tannin and up to 16% with chestnut tannin. Tannins also decreased ruminal nitrogen degradability of grass silage during enzymatic in vitro trial and in an artificial rumen. Proteolysis reduction thanks to oak tannin extract linearly increased with tannin dose in silage. The best dose range for oak and chestnut tannin extracts in silage seems to be around 30 g/kg of dry matter (DM) of forage. From 50g/kg DM, tannins showed a detrimental effect on in vitro organic matter digestibility. The second part of the work revealed that oak tannins extract (added at 26g/kg DM in grass before ensiling) had no effect on nitrogen use efficiency of lactating dairy cows. However, a shift from urine to faecal nitrogen was observed in this trial in presence of oak tannins. This strategy can thus be adopted to decrease the environmental impact of ruminant protein feeding. This experiment also documented the use of the “nitrogen isotopic discrimination” proxy to compare nitrogen use efficiency of two contrasting diets. The results indicated that the proxy would specifically sign the N partitioning at the metabolic level rather than the overall NUE, the latter also being impacted by digestive processes. The greatest interest of tannins would thus lie in their positive impact on environment preservation. The addition of tannin before ensiling seemed pointless in our conditions as compared to direct feeding given that the benefit from protecting proteins in silo did not persist in the rumen. The influence of pH on stability of hydrolysable tannin-protein complexes seems contradictory to literature data on condensed tannins. The specificity of tannin-protein complexes to both tannin and protein structures is a great challenge in the understanding of tannin impacts and the development of tannin applications in ruminant feeding. [less ▲]

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See detailPhenotypic plasticity of corn leaf aphid Rhopalosiphum maidis under elevated temperature and CO2
Chen, Yu ULiege

Doctoral thesis (2019)

In the current context of global climate change, the world average temperature and carbon dioxide (CO2) concentration in the atmosphere has steadily increased. Climate change is also predicted to increase ... [more ▼]

In the current context of global climate change, the world average temperature and carbon dioxide (CO2) concentration in the atmosphere has steadily increased. Climate change is also predicted to increase the frequency and magnitude of extreme heat events, which will involve great challenges for most of the ectotherm organisms, such as aphids. As a worldwide pest insect, corn leaf aphid, Rhopalosiphum maidis caused significant damage on cereal crops such as barley, corn, and wheat. R. maidis is also a vector of plant viruses including sugarcane mosaic virus, maize dwarf mosaic virus, which result in economic losses. Similar to all ectotherms, aphids have acute sensory capability for detecting temperature variations. Their small size and high mass-specific metabolic rates makes them sensitive to energy and water balance during exposure to extremes. In this study, thermal tolerance of R. maidis under extreme high temperatures across differential life stages were tested. The critical high temperature (CHT) of R. maidis was between 39.0 to 40.0 °C according kinds of feeding treatments. The upper lethal temperatures (ULTs) of R. maidis were significantly different between feeding and no feeding treatments. In addition, the ULTs varied significantly across life stages with highest ULTs values for 4th instars. Feeding significantly increased the thermal tolerance of aphids. R. maidis exhibit wing polyphenism in response to poor habitat quality. Polyphenism is an important form of adaptation in an adverse environment. Five developmental stages of aphids with increased population densities were investigated under two kinds of temperature patterns. Crowding was found to directly impact winged induction. The 1st and 2nd nymphs were more sensitive for alate morphs induction under high density. In addition, temperature played a significant role in wing production, with the 26/39 °C temperature setting inducing higher alate morphs and survival. The increase in concentrations of CO2 not only affects plant growth and development, but also impacts the emission of plant organic volatile compounds. During the dual choice bioassays, the winged and wingless aphids were more attracted by the VOCs of barley seedlings cultivated under ambient CO2 concentrations (aCO2; 450ppm) than barley seedlings cultivated under elevated CO2 concentrations (eCO2; 800ppm), nymphs were not attracted by the VOCs of eCO2 barley seedlings. While 16 VOCs were identified from aCO2 barley seedlings, only 9 VOCs were found from eCO2 barley seedlings. The effect of elevated CO2 on feeding behavior of R. maidis on barley seedlings was tracked using electrical penetration graph (EPG). The nutrient content of host plant and the developmental indexes of aphids under eCO2 and aCO2 conditions were examined. Barley seedlings under eCO2 concentrations had lower contents of crude protein and amino acids. EPG analysis showed plants cultivated under eCO2 influenced the aphid feeding behavior, by prolonging the total pre-probation time and the ingestion of passive phloem sap. Moreover, fresh body weight, fecundity and intrinsic population growth rate of R. maidis was significantly decreased in eCO2 in contrast to aCO2 condition. Our reasearch provide a new perspective on understanding plant-insect herbivore interactions under climate change. [less ▲]

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See detailDevelopment of equations to predict methane eructed by lactating cows from milk mid-infrared spectra
Vanlierde, Amélie ULiege

Doctoral thesis (2019)

Au regard du contexte climatique actuel, tous les secteurs, y compris l’agriculture, doivent œuvrer pour réduire leurs émissions de gaz à effet de serre (GES) dans l’intérêt commun. Le méthane (CH4) est ... [more ▼]

Au regard du contexte climatique actuel, tous les secteurs, y compris l’agriculture, doivent œuvrer pour réduire leurs émissions de gaz à effet de serre (GES) dans l’intérêt commun. Le méthane (CH4) est l’un des GES majeur et représente une part importante des émissions attribuées au secteur agricole. En effet, ce gaz est notamment naturellement produit lors du processus de digestion des ruminants. Supprimer cette production entérique de CH4 de la part des bovins n’est physiologiquement pas envisageable mais des leviers d’action permettent d’impacter son niveau d’émission comme: l’alimentation donnée aux animaux, la gestion du troupeau ou la sélection génétique des individus les plus efficients. Cependant un point crucial dans cette démarche est de pouvoir quantifier ces émissions de CH4 à grande échelle de façon individuelle. Les méthodes de mesures existantes (chambres respiratoires, méthode du gaz traceur SF6, etc.) sont souvent lourdes à mettre en œuvre et difficiles ou impossibles à appliquer à de larges populations d’individus. Disposer d’un proxy pour estimer aisément ces émissions présente un grand intérêt. Les travaux détaillés dans cette thèse de doctorat sont consacrés au développement d’équations visant à estimer les émissions journalières et individuelles de CH4 à partir de spectres moyen infrarouge (FT-MIR) de lait. En effet, d’un point de vue métabolique, des mécanismes de fermentation ruminale vont influencer à la fois les émissions de CH4 et la composition du lait notamment au niveau de la matière grasse. Le spectre FT-MIR de lait reflète la composition chimique du lait qui est déjà prélevé et analysé en routine dans le cadre du paiement du lait et du contrôle laitier. Après l’établissement d’une première relation (n = 77) confirmant la pertinence d’établir un lien entre le spectre FT-MIR du lait et les émissions de CH4 des vaches laitières, diverses étapes ont permis d’améliorer et d’affiner le modèle de prédiction. Par la suite, le stade de lactation des animaux a été tenu en compte dans un nouveau modèle prédictif (n = 446) via une modification spectrale. En effet, les variations de mobilisation des ressources corporelles des animaux au fil de la lactation impactent fortement l’origine des acides gras du lait et donc également la relation entre le spectre FT-MIR du lait et les émissions de CH4. Cette adaptation a permis d’obtenir des prédictions d’émissions de CH4 cohérentes d’un point de vue zootechnique au fil de la lactation L’ajout de nouvelles données de référence présentant une spécificité zootechnique (race, stade de lactation, ration alimentaire, etc.) mal représentée au préalable dans le jeu de calibration a permis d’améliorer la qualité du modèle prédictif ainsi que son potentiel d’application (n = 532). L’acquisition de telles données a été possible via la mise en œuvre d’essais expérimentaux ciblant des régimes alimentaires ou des animaux spécifiques, mais également via le biais de collaborations internationales. Ceci a permis de mettre en évidence l’importance de couvrir la variabilité locale avant d’appliquer le modèle afin de garantir la pertinence de la prédiction obtenue. Les premières versions de l’équation de prédiction ont été développées sur base de valeurs de référence de CH4 obtenues grâce à la méthode utilisant le SF6 comme gaz traceur. Afin de confirmer les résultats obtenus, une nouvelle équation a été développée, basée cette fois uniquement sur des mesures de CH4 obtenues en chambres respiratoires. Cette technique est en effet reconnue comme le « gold standard » pour mesurer le CH4 émis par les bovins. Ces données ont été récoltées par des équipes de recherche européennes et elles ont pu être mises en commun par le biais de collaborations. Cependant elles n’avaient pas été collectées dans le but de développer une telle équation et ne présentaient donc pas une gamme de variabilité idéale dans cette optique. Malgré cela, grâce au nombre conséquent de données collectées (n = 584), les résultats statistiques obtenus ont montré une tendance sensiblement similaire aux précédents résultats et ont donc permis de confirmer le potentiel du spectre FT-MIR de lait comme proxy pour estimer les émissions de CH4 à grand échelle. La tentative de validation externe de l’équation de prédiction basée sur les données SF6 par les données collectées en chambres respiratoires (et vice versa) n’a pas donné de résultats satisfaisants. Les données de référence des modèles respectifs provenaient de pays, de races, de régimes alimentaires, etc. différents donc les jeux de données de calibration ne couvraient pas les informations des jeux de données utilisés comme validation. Après avoir considéré et écarté à ce stade la nécessité de modifier les valeurs CH4 de référence pour tenir compte d’un potentiel biais dû à la méthode de référence entre les mesures SF6 et les chambres respiratoires, de nouvelles équations combinant l’ensemble des données disponibles (méthode du traceur SF6 et chambres respiratoires) ont été développées (n = 1089). Enfin, toujours dans un but d’améliorer la qualité des prédictions obtenues, des données phénotypiques pertinentes et aisément disponibles en routine ont été ajoutées au spectre FT-MIR de lait comme valeurs prédictives. Le modèle présentant les meilleures performances statistiques est actuellement celui basé sur les 1089 données de références et qui tient en compte également du stade de lactation, de la production laitière, de la race et de la parité des animaux (R² et erreur standard de cross-validation de respectivement 0.68 et 57 g de CH4/jour). Les modèles développés offrent un grand potentiel d’application de par leur facilité d’obtenir des estimations des émissions de CH4 à grand échelle. Avant de pouvoir envisager de les utiliser de façon concrète, leurs performances devront être validées sur le terrain et les conditions d’applicabilité permettant d’assurer la pertinence des prédictions obtenues doivent encore être bien définies. [less ▲]

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