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See detailEffects of tree species diversity and drought on ecosystem functioning in a young forest
Rahman, Md Masudur ULiege

Doctoral thesis (2018)

Warmer and drier conditions are expected globally and regionally in the future due to climate change. In Belgium, a 50% decrease in summer precipitations and an increase in winter precipitations are ... [more ▼]

Warmer and drier conditions are expected globally and regionally in the future due to climate change. In Belgium, a 50% decrease in summer precipitations and an increase in winter precipitations are expected. The drier conditions have the potential to influence forest ecosystem functioning, both aboveground and belowground. Further, more drought events could result in more frequent soil drying-rewetting events, which could influence the CO2 emissions (“Birch effect”). Mature forests are already experiencing adverse effects of climate change on tree growth, tree mortality and species composition. Studies suggested that ecosystems with higher tree species diversity could be more resistant and resilient to stress conditions, such as drought. Therefore, mixed planting may be an option to mitigate drought effects to forest ecosystems. The overall objective of this thesis was to assess the combined effects of tree species admixture and drought on different above- and belowground processes in a young forest plantation. In this study, combined effects of mixed planting and precipitation reduction (hereafter “drought”) on different above- and belowground processes around central oak (Quercus robur. L.) and beech (Fagus sylvatica L.) trees were investigated in 6-7 years old plantations (FORBIO). Oak and beech were planted in monocultures or admixed with 1-3 other functionally dissimilar tree species (tree species admixture gradient from 1 to 4). Three drought and three control plots (3 m × 3 m) around oak and beech trees were established at every admixture levels. Rainout shelters were installed in drought plots to intercept about 50% of the precipitation. Different aboveground variables such as plant growth, leaf traits, crown damage and belowground variables such as soil organic matter decomposition, nutrient availability, microbial biomass, C and N mineralization were measured over two growing seasons. Further, tree species admixing and drought legacy effects on soil microbial biomass and activity were measured under oak. Tree species admixing influenced different variables but the effects were not consistent between oak and beech. Tree species admixing reduced the height and increased the specific leaf area of beech, but did not influence any of the belowground variables measured. For oak, reduced crown damage from pests and pathogens, decreased leaf Al, Na and Zn contents, and increased soil N and total exchangeable cations were observed with higher tree species admixture level. Further, tree species admixing to oak influenced soil microbial community composition, and drought legacy reduced soil microbial biomass, soil respiration and bacterial growth but not fungal growth rates. Upon soil drying and rewetting, tree species admixing to oak did not influence bacterial growth and soil respiration rates but drought legacy reduced both bacterial growth and soil respiration. There were significant interactions between tree species admixing and drought for several variables such as organic matter decomposition, leaf Cu and N contents, net nitrification, potential respiration, MBC, metabolic potential of bacteria, qmic fungal to bacterial growth ratio etc. These interactions were mainly driven by the drought effects on monocultures and two species mixtures, indicating that tree species admixtures had offset the drought effects in three and four tree species mixture. Results from this study suggest that both tree species admixing and drought have the potential to influence ecosystem processes in young forests. Results also indicate that tree species admixing could offset the effects of drought on different ecosystem processes, thus stabilize ecosystem process under drought. Further, drought and drought legacy may reduce soil microbial activity, hence drought followed by precipitation (drying-rewetting) would not increase the CO2 emissions from soils. Overall, both oak and beech could benefit from admixing of functionally dissimilar tree species. Therefore, planting oak and beech in mixtures could be an option for forest management in the face of climate change. [less ▲]

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See detailIdentification de nouvelles fonctions des métalloprotéases par détermination de leur répertoire de substrats : Applications aux aminoprocollagène peptidases
Leduc, Cédric ULiege

Doctoral thesis (2018)

Manuscrit de thèse + Tableaux supplémentaires au manuscrit .

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See detailEarly life programming of piglets' microbiota and gut health by maternal dietary fibre supplementation
Leblois, Julie ULiege

Doctoral thesis (2018)

Post-weaning diarrhoea (PWD) is a widespread disease causing loss of weight and mortality of the piglets. To cure or prevent PWD, the treatment of pigs with antibiotics is frequent. The overuse of these ... [more ▼]

Post-weaning diarrhoea (PWD) is a widespread disease causing loss of weight and mortality of the piglets. To cure or prevent PWD, the treatment of pigs with antibiotics is frequent. The overuse of these substances led to the appearance of multi-resistant bacteria, raising public health issues. Thus, finding sustainable alternatives to antibiotics for PWD curation is of major importance. Most research focusses on the use of substances like prebiotics able to affect the microbiota of the piglets, as gut microbiota is responsible for the maturation of the intestinal immune system. Promoting a beneficial microbiota as early in life as possible is a good strategy for a better future health and a lower prevalence of PWD. Our hypothesis was that using dietary fibres (wheat bran and resistant starch) in the diet of sows would alter their microbiota and in turn affect their piglets’ microbiota and future health. In addition, the ability of the two fibre sources to alter milk composition, also affecting piglets’ performances and health, was tested. This hypothesis was challenged with two animal experiments. Results indicated that wheat bran (WB) and resistant starch (RS) had the ability to alter sows’ microbiota during gestation but not anymore during lactation, possibly limiting a differential microbial transfer to their offspring. These two dietary fibre slightly altered milk composition. Maternal wheat bran had the ability to increase the villus height and villus to crypt ratio in the small intestine of the progeny, while resistant starch increased the gene expression of tight junction proteins at weaning. These two fibre sources included in a high level in sows’ diets did not affect their performance or their piglets’, making their use in animal diets realistic. A second objective of the thesis was to unravel whether the diet of sows could program the metabolism of piglets for later life, using them as model for human. For this, piglets were challenged with a high fat diet in order to induce low-grade inflammation and/or obesity symptoms. After 7 weeks on a high fat diet, piglets had an increased backfat thickness and higher serum cholesterol levels. The main findings are that feeding sows resistant starch increased the total sum of short-chain fatty acids (SCFA) production in the caecum and colon of their progeny, which is beneficial but did not affect the microbiota of the pigs. Moreover, maternal RS diet seemed to increase the barrier function of the colon due to a higher gene expression of tight junction proteins while the maternal effects on intestinal inflammation were contradictory for TNF-α and IFN-γ. It seems thus that the maternal diet had the ability to decrease gut permeability. However, the high fat diet did not alter the microbiota of the pigs, nor was it affected by the maternal diet. In conclusion, using dietary fibre in sows’ diet had the ability to alter their own microbiota during gestation and milk composition, but the impact on the piglet’s microbiota was rather limited. It could be thus interesting to use these diets on piglets’ themselves after birth to promote the establishment of beneficial bacteria. Although effects on the microbiota were limited, the maternal diet seemed to affect some aspects of the health of their progeny in later life. [less ▲]

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See detailIdentifying primate parasites in the Ecuadorian Amazon: A tool for Public Health and Conservation
Martin, Sarah ULiege

Doctoral thesis (2018)

Non-human primates (NHPs) have coevolved with parasites. However factors such as loss and fragmentation of habitat, pet trade or bushmeat hunting have changed the diversity and intensity of these ... [more ▼]

Non-human primates (NHPs) have coevolved with parasites. However factors such as loss and fragmentation of habitat, pet trade or bushmeat hunting have changed the diversity and intensity of these parasites and exposed NHPs to novel parasites from humans, livestock and wildlife. This study focused on gastrointestinal parasites in New World monkeys. Indeed, gastrointestinal parasites can heavily impact the health and behavior of NHPs, and most studies on NHPs’ parasites have focused on Old World primates. Therefore, our study aimed to fill some gap of this research topic on New World monkeys. In order to accomplish this, we used two techniques to determine the diversity of gastrointestinal parasites in the Western Amazon of Ecuador, and see if they are a potential reservoir of zoonotic parasites.After reviewing the various classes of parasites affecting NHPs, we studied two groups of Capuchins (Cebus albifrons), one captive and one free-ranging, where we looked how parasitism is affected by host-intrinsic and extrinsic factors. We found microscopically 6 genera of gastrointestinal parasites, the most prevalent being Strongyloides sp. (76.9%), followed by Hymenolepis sp. (38.5%) and Prosthenorchis elegans (11.5%). Zoonotic parasites such as Entamoeba histolytica/nuttalli/dispar/moskovskii/ and Capillaria sp. where found only in a minority of the animals tested (3.8%). Adults (6) showed higher parasite richness than the subadults (5) and juveniles (3). Faecal egg/cyst counts were not significantly different between captive and free-ranging individuals, or between sexes or age groups. The free-ranging group had a little higher prevalence than the captive group, but this difference was not significant, maybe due to limited sampling. Additionally, our study demonstrated that a serial sampling of 3 samples per individual significantly increased the test sensitivity. Secondly, we tried to correlate parasites richness and intensity with behaviour as an intrinsic factor. For this, we focused on two captive groups of Woolly monkeys (Lagothrix lagotricha), one living in a small enclosure (SE) and the other in a large one (LE). We correlated the size of the enclosure, parasite transmission and social contact through social network analysis. In both groups, an increased number of social contacts per individual and a higher clustering coefficient were associated with a higher parasite richness. Adults (2.3), subadults (3) and juveniles (2.5) did not differ in number of parasites harboured (F = 3.321, p = 0.078), but between sexes, females (3) harboured more parasites than males (2) (F = 17.481, p = 0.002). The SE group harboured slightly more parasites (6) than the LE group (5), but this difference was not statistically significant (F = 4.601, p = 0.058). However the FEC for Strongyloides sp. was significantly higher in the SE group (range 1 to 477) than in the LE group (range 0 to 12) (F = 6867.753, p < 0.001). Thus a smaller enclosure seems to be consistent with a higher number of parasites in individuals. As for the first study with capuchins, if we increase sampling maybe parasite richness can increase as well. We also found that parasite richness of central adult individuals increased the parasite load within the group. Therefore, maintaining the health of central individuals may be an obvious and practical method to increase group health. Finally, we evaluated the presence of gastrointestinal parasites in two populations of NHPs (captive and free-ranging) including ten NW monkey species: Alouatta seniculus, Ateles belzebuth, Callicebus discolor, Callicebus luficer, Cebuella pygmaea, Cebus albifrons, Cebus apella, Lagothrix lagotricha, Saguinus fuscicollis, and Saimiri sciureus). We then focused on the molecular identification of Entamoeba histolytica in these ten species to assess the role of these primate populations as potential reservoirs of zoonotic parasites. Microscopic identification allowed the identification of 10 parasites of gastrointestinal parasites and molecular identification (conventional PCR) pointed two individual woolly monkeys who had Entamoeba histolytica. We also identified Entamoeba nuttalli (the NHP Entamoeba), again in a woolly monkey. In our study, in accordance with other studies, we found that host biology (such as age, sex, and primate species) may influence the parasite diversity harboured. Most parasites found in our study where also found in OW monkeys, but some were specific to the neotropical area. Most parasites in our study are widely distributed and have numerous hosts, while others are restricted to some NHPs. Host age and sex may influence parasite richness, but their effect varies depending on the parasite species and on the NHP host. The sensitivity to parasite infestation of NHPs captive or in close contact with humans is related to several extrinsic factors (home range overlap, disturbed habitat, human contact, poor environmental enrichment, contaminated food, among others) and intrinsic factors (social contacts) that increase the diversity and prevalence of parasites. However, free-ranging NHPs have developed strategies such as self-medication to decrease the number of parasites or alleviate their effect. Although we did not observe this kind of behaviour, we observed ad libitum in captive Cebus albifrons and Ateles belzebuth sequences of rubbing onions and eating sand, which is also considered as self-medication behaviour. Our study also demonstrated the importance of a serial sampling, which allows to find a higher number of parasite species per NHP species. However, we did not find some of the regular parasites found in other studies, maybe because of the microscopic technique employed. Molecular identification also increased the prevalence of Entamoeba sp., from 14.7 % to 57.5 %. As a contribution to regulation perspectives, we proposed a series of strategies such as environmental education for tourists and local population itself, or such as technical training for caretakers, or basic health major procedures such as treatment administration to implement in NHPs facilities or in communities in close contact with NHPs. Finally, one general recommendation should be essential for Ecuador, and this is to establish a national network for wildlife diseases’ surveillance to enhance the detection of infectious and zoonotic diseases and protect wildlife populations, domestic animals and humans. [less ▲]

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See detailSoil structure exploration and measurement of its macroscopic behavior for a better understanding of the soil hydropedodynamic functionalities
Smet, Sarah ULiege

Doctoral thesis (2018)

Air permeability and water conductivity are fundamental physical properties when it comes to the soil functions across the environment. The water conductivity and the air permeability as functions of the ... [more ▼]

Air permeability and water conductivity are fundamental physical properties when it comes to the soil functions across the environment. The water conductivity and the air permeability as functions of the soil’s degree of saturation (K(θ) and ka(ɛ), respectively) are only discretely measurable, and the use of models is necessary to obtain continuous expressions of these functions. Most models however consider the soil pore network structure as a fitting parameter although it is public knowledge that K(θ) and ka(ɛ) depend mostly on the soil microstructure, which is, none the less, unique between samples with homogeneous texture. New ways of studying K(θ) and ka(ɛ) are needed. The direct soil pore space visualization is a promising avenue to lead us to objectifying soil physics. The X-ray microtomographic technique (X-ray µCT) is now widely used by soil scientists and delivers 3D grayscale images of objects composed by materials of different densities. When dealing with a porous medium such as the natural soil, the X-ray µCT images need to be cautiously and expertly processed to obtain realistic feature quantification. A parallel, but however perquisite, objective of this dissertation is to statistically compare the effects of various image processing on the final X-ray µCT image features quantification. We simulated grayscale images to be processed to conclude about the image processing methodology we applied in our research. The overall objective of this dissertation is to explore the relationships between one microscopic soil structure (the volume of the smallest visible pore is 0.0004 mm³) and its macroscopic functionalities, such as its water conductivity and air permeability. More specifically, we confirmed that the use of 3D X-ray µCT data enables a better estimation of the soil water retention curve near saturation through the identification of the largest soil pores. These are indeed often by-passed with pressure plate’s laboratory measurements because of various artefacts. We also identified microscopic pore space morphological parameters that explained the soil saturated hydraulic conductivity, and microscopic porosity distribution measures that explained the soil air permeability. The final X-ray µCT image features quantification depends on the applied image processing, as stated, but also, clearly, on the image resolution. We concluded that working with a higher resolution would not necessarily lead to a higher degree of knowledge because resolution is sample-size dependent, and one pore size distribution could moreover be sufficiently visible at low resolution. We however observed that the pore network morphological and topological connectivity increases with resolution. Finally, we highlighted the imperfections of the capillary theory applied to soil through scanning the same soil samples at various water contents. As hypothesized, the pore network connectivity seems to play an important role in the pore accessibility to draining. After having studied the effects of the soil pore network structure on the soil hydrodynamic properties, we turned the question around and evaluated the effects of the chemical soil composition (organic carbon and free forms of iron) on the very same soil pore network structure. This dissertation therefore discusses the advantages and limitations of the use of X-ray microtomography to study soils for a more realistic understanding of the soil hydropedodynamic processes. [less ▲]

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See detailAdvancing agricultural monitoring for improved yield estimations using SPOT-VGT and PROBA-V type remote sensing data
Durgun, Yetkin Özüm ULiege

Doctoral thesis (2018)

Accurate and timely crop condition monitoring is crucial for food management and the economic development of any nation. However, accurately estimating crop yield from the field to global scales is a ... [more ▼]

Accurate and timely crop condition monitoring is crucial for food management and the economic development of any nation. However, accurately estimating crop yield from the field to global scales is a challenge. According to the global strategy of the World Bank, in order to improve national agricultural statistics, crop area, crop production, and crop yield are key variables that all countries should be able to provide. Crop yield assessment requires that both an estimation of the quantity of a product and the area provided for that product should be available. The definition seems simple; however, these measurements are time consuming and subject to error in many circumstances. Remote sensing is one of several methods used for crop yield estimation. The yield results from a combination of environmental factors, such as soil, weather, and farm management, which are responsible for the unique spectral signature of a crop captured by satellite images. Additionally, yield is an expression of the state, structure, and composition of the plant. Various indices, crop masks, and land observation sensors have been developed to remotely observe and control crops in different regions. This thesis focuses on how much low spatial resolution satellites, such as Project for On Board Autonomy Vegetation (PROBA V), can contribute to global crop monitoring by aiding the search for improved methods and datasets for better crop yield estimation. This thesis contains three chapters. The first chapter explores how an existing product, Dry Matter Productivity (DMP), that has been developed for Satellites Pour l’Observation de la Terre or Earth observing Satellites VeGeTation (SPOT VGT), and transferred to PROBA V, can be improved to more closely relate to yield anomalies across selected regions. This chapter also covers the testing of the contribution of stress factors to improve wheat and maize yield estimations. According to Monteith’s theory, crop biomass linearly correlates with the amount of Absorbed Photosynthetically Active Radiation (APAR) and constant Radiation Use Efficiency (RUE) downregulated by stress factors such as CO2, fertilization, temperature, and water stress. The objective of this chapter is to investigate the relative importance of these stress factors in relation to the regional biomass production and yield. The production efficiency model Copernicus Global Land Service Dry Matter Productivity (CGLS DMP), which follows Monteith’s theory, is modified and evaluated for common wheat and silage maize in France, Belgium, and Morocco using SPOT VGT for the 1999–2012 period. The correlations between the crop yield data and the cumulative modified DMP, CGLS DMP, Fraction of APAR (fAPAR), and Normalized Difference Vegetation Index (NDVI) values are analyzed for different crop growth stages. The best results are obtained when combinations of the most appropriate stress factors are included for each selected region, and the modified DMP during the reproductive stage is accumulated. Though no single solution can demonstrate an improvement of the global product, the findings support an extension of the methodology to other regions of the world. The second chapter demonstrates how PROBA V can be used effectively for crop identification mapping by utilizing spectral matching techniques and phenological characteristics of different crop types. The study sites are agricultural areas spread across the globe, located in Flanders (Belgium), Sria (Russia), Kyiv (Ukraine), and Sao Paulo (Brazil). The data are collected for the 2014–2015 season. For each pure pixel within a field, the NDVI profile of the crop type for its growing season is matched with the reference NDVI profile. Three temporal windows are tested within the growing season: green up to senescence, green up to dormancy, and minimum NDVI at the beginning of the growing season to minimum NDVI at the end of the growing season. In order of importance, the crop phenological development period, parcel size, shorter time window, number of ground truth parcels, and crop calendar similarity are the main reasons behind the differences between the results. The methodology described in this chapter demonstrates the potentials and limitations of using 100 m PROBA V with revisiting frequency every 5 days in crop identification across different regions of the world. The final chapter explores the trade off between the different spatial resolutions provided by PROBA V products versus the temporal frequency and, additionally, explores the use of thermal time to improve statistical yield estimations. The ground data are winter wheat yields at the field level for 39 fields across Northern France during one growing season 2014–2015. An asymmetric double sigmoid function is fitted, and the NDVI values are integrated over thermal time and over calendar time for the central pixel of the field, exploring different thresholds to mark the start and end of the cropping season. The integrated NDVI values with different NDVI thresholds are used as a proxy for yield. In addition, a pixel purity analysis is performed for different purity thresholds at the 100 m, 300 m, and 1 km resolutions. The findings demonstrate that while estimating winter wheat yields at the field level with pure pixels from PROBA V products, the best correlation is obtained with a 100 m resolution product. However, several fields must be omitted due to the lack of observations throughout the growing season with the 100 m resolution dataset, as this product has a lower temporal resolution compared to 300 m and 1 km. This thesis is a modest contribution to the remote sensing and data analysis field with its own merits, in particular with respect to PROBA V. The experiments provide interesting insight into the PROBA V dataset at 1 km, 300 m, and 100 m resolutions. Specifically, the results show that 100 m spatial resolution imagery could be used effectively and advantageously in agricultural crop monitoring and crop identification at local – field level – and regional – the administrative regions defined by the national governments – levels. Furthermore, this thesis discusses the limitations of using a low resolution satellite, such as the PROBA V 100 m dataset, in crop monitoring and identification. Also, several recommendations are made for space agencies that can be used when designing the new generation of satellites. [less ▲]

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See detailDetection and identification of viruses infected in wheat and its pests
Zhang, Peipei ULiege

Doctoral thesis (2018)

Wheat is the second important crop in the world, nevertheless its production is hampered by viral diseases causing severe economic losses. More than 50 wheat viruses have been reported so far. Some of the ... [more ▼]

Wheat is the second important crop in the world, nevertheless its production is hampered by viral diseases causing severe economic losses. More than 50 wheat viruses have been reported so far. Some of the viruses cause similar symptoms and their observation in the field does not allow the identification of the virus species. Some wheat samples with the known symptoms but could not detect the known virus, some wheat samples exhibit new symptoms. Identification of the species and biological characteristics of the wheat viruses is the key to control the occurrence of wheat viral diseases. Planthopper s are also the limiting factors in wheat production due to sapping the plants and transmitting wheat viruses. But there is little information about the commensal viruses in planthoppers. The objective of this thesis is to detect and identify the viruses infected in wheat and its pests to enlarge the understanding of wheat pathogen and insect viruses, providing a basis for prevention and control of wheat viral disease. The main contents and results are as follows: (1) A multiplex RT-PCR system for simultaneous detection of four wheat viruses Wheat dwarf virus (WDV), barley yellow striate mosaic virus (BYSMV), rice black-streaked dwarf virus (RBSDV) and northern cereal mosaic virus (NCMV) are four viruses infecting wheat and causing similar symptoms. A multiplex reverse transcription polymerase chain reaction (m-RT-PCR) protocol has been developed for the simultaneous detection and discrimination of these viruses. The protocol uses a specific primer set for each virus to amplify four distinct DNA fragments of 273, 565, 783 and 1,296 bp, amplified known viruses of RBSDV, BYSMV, WDV and NCMV, respectively. Annealing temperature, concentrations of dNTP, Taq polymerase and Mg2+ were optimized for the m-RT-PCR. The detection limit of the assay was up to 10-2 dilution. The amplification specificity of these primers was tested against a range of field samples from different parts of China, where RBSDV, BYSMV, WDV and NCMV have been detected. This study fulfills the need for a rapid and specific wheat virus detection that also has the potential for investigating the epidemiology of these viral diseases. (2) Identification of a new wheat virus To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) using RT-PCR. A sample that tested negative for the three viruses was selected for small RNA sequencing. Twenty-five million sequences were generated, among which 5% were of viral origin. A novel polerovirus was discovered and temporarily named wheat leaf yellowing-associated virus (WLYaV). The full genome of WLYaV corresponds to 5,772 nucleotides (nt), with six AUG-initiated open reading frames, one non-AUG-initiated open reading frame and three untranslated regions, showing typical features of the family Luteoviridae. Sequence comparison and phylogenetic analyses suggested that WLYaV had the closest relationship with sugarcane yellow leaf virus (ScYLV), but the identities of full genomic nucleotides and deduced amino acid sequence of coat protein (CP) were 64.9% and 86.2%, respectively, below the species demarcation threshold (90%) in the family Luteoviridae. Furthermore, agroinoculation of Nicotiana benthamiana Domin leaves with a cDNA clone of WLYaV caused yellowing symptoms on the plant. Our study discovered a new polerovirus that is associated with wheat leaf yellowing disease, which would help to identify and control pathogens of wheat. (3) Identification of two novel totiviruses in white-backed planthopper There is little information about the commensal viruses infecting the white-backed planthopper, Sogatella furcifera Horváth, although it is an important agricultural pest. Two novel double-stranded RNA virus species belonging to the family Totiviridae were identified using high throughput sequencing and tentatively named Sogatella furcifera totivirus 1 and 2 (SfTV1 and SfTV2). Their complete genomes consist of 6,310 and 6,303 nt, respectively, showing typical genomic features with viruses in the family Totiviridae. Identity, phylogenetic and sequence analyses showed that SfTV1, SfTV2 and three other insect viruses may form a proposed novel genus of family Totiviridae. Vertical transmission of the two viruses was highly efficient, and they were detected in all insect tissues and developmental stages, with the highest titers in the adult and in the hemolymph and reproductive organs. To our knowledge, this is the first report of viruses in the family Totiviridae found in a hemipteran insect. (4) Identification of a new partitivirus in small brown planthopper In the present study, a novel partitivirus, tentatively named laodelphax striatellus associated partitivirus (LsPV), was identified in Laodelphax striatellus Fallén by RNA-sequencing. Its genome contains two segments of double stranded RNA (dsRNA), dsRNA1 (1,775 nucleotides) encoded a putative RNA-dependent RNA polymerase (RdRp) of 538 amino acids. dsRNA2 (1,575 nucleotides) encoded a putative coat protein (CP) of 440 amino acids. LsPV has similar genomic size, conserved motifs, and close phylogenetic relationships with members of Gammapartitivirus genus within the family Partitiviridae, the identities were only 28.6-70.9% for RdRp and 20.2-59.5% for CP, indicating that it is a new species of this genus. This is the first report of a complete genomic sequences of partitivirus from an insect. (5) Identification of a new iflavirus in small brown planthopper A novel iflavirus, tentatively named laodelphax striatellus iflavirus 3 (LsIV3), was identified in Laodelphax striatellus Fallén by total RNA-sequencing, and its genome sequence was confirmed by Sanger sequencing. The complete genome consisted of 10,831 nucleotides with a poly-A tail and included one open reading frame, encoding a 361.7-kD polyprotein. Conserved motifs for structural proteins, helicase, protease, and RNA-dependent RNA polymerase were identified by aligning the deduced amino acid sequence of LsIV3 with several other iflaviruses. The genome has the highest identity with another planthopper iflavirus, nilaparvata lugens honeydew virus-3 (39.7%), under the species demarcation threshold (90%). Results of the identities and phylogenetic analysis based on the deduced amino acid sequences of the complete polyprotein of LsIV3 and other iflaviruses, indicated that LsIV3 is a new species belonging to the family Iflaviridae. [less ▲]

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See detailAnaesthesia refinement for the laboratory rhesus macaque
Bertrand, Henri ULiege

Doctoral thesis (2018)

Non-human primates (NHPs) are considered an optimal model for some areas of biomedical research. However, their use raises major ethical concerns and NHPs should only be used when other animal models are ... [more ▼]

Non-human primates (NHPs) are considered an optimal model for some areas of biomedical research. However, their use raises major ethical concerns and NHPs should only be used when other animal models are considered unsuitable. Providing anaesthesia for experimental invasive procedures in laboratory animals, including NHPs is a legal and ethical obligation in Europe (Article 14 of European Directive 2010/63/10). However, the nature of anaesthetics can not only negatively influence the scientific data that is being collected but also the primates’ welfare by depressing their vital functions and possibly delaying reintroduction in social group. Hence, the anaesthesia protocol should consider both the welfare of the animal, and the scientific objectives of the study. A review of the scientific literature from 2010 to 2015 was performed to identify current anaesthesia methods used in NHPs for experimental invasive procedures. This review highlighted that isoflurane and ketamine (alone or combination with other anaesthetics) were the most frequently used anaesthetics in NHPs. However, this review also showed an underreporting, of details of the anaesthetic protocols used. This information that should be considered critical not only from a scientific perspective but also because of public concerns related to the use of NHPs. Ketamine has a wide therapeutic index in NHPs but is associated with dysphoria and delirium during emergence, tissue irritation and can cause long-term neurological impairment. Isoflurane, with its low cost and low toxicity, is widely for general anaesthesia in a range of laboratory animal species. Isoflurane anaesthesia is associated with a relatively rapid recovery, which enables an early initial neurological assessment to be carried out, and supportive treatment to be implemented if necessary. Refinement of the use of anaesthetics that have less prolonged depressant effects, or are reversible with specific antagonists could therefore be beneficial for primate welfare. Three alternative combinations of injectable agents, which would avoid the use of ketamine, were assessed. The choice of the agents was based on the potiential for reversing their activity, their short duration of action and also their safety for tissues. A combination of fentanyl-midazolam- medetomidine (10μg/kg-1; 0.5mg.kg-1; 20μg.kg-1) by the intramuscular route provided an easily reversible immobilization with a rapid and good quality recovery. Cardiovascular and respiratory parameters were moderately depressed compared to ketamine; Heart rate (beats/min) (Ket=119±18; FMM=89±17; p=0.0066), systolic blood pressure (mmHg) (Ket=109±10; FMM=97±10; p=0.0313), and respiratory rate (breaths/min) (Ket=39±9; FMM=29±10; p=0.0416). Two other combinations: fentanyl-fluanisone-midazolam (0.031mg.kg-1; 1mg.kg-1; 0.5 mg.kg-1) and alfaxalone-medetomidine- midazolam (2mg.kg-1; 20μg.kg-1; 0.3mg.kg-1) were also assessed. These two combinations were either less reliable or provided a prolonged sedation that was not reversible with current available antagonists. Abstract 5 The volatile agents most recently introduced into clinical practice, such as sevoflurane and desflurane, have a lower solubility in the blood associated with shorter recovery and a possible better recovery than isoflurane. General anaesthesia with either sevoflurane or desflurane had similar cardiovascular effects, mainly a moderate hypotension that was easily manageable with administration of additional intravenous fluids or by administration of vasopressor agents. Recovery from sevoflurane and desflurane was more rapid than isoflurane, however no significant difference between sevoflurane and desflurane was found. The quality of recovery was assessed using a clinical scoring scheme, but despite a trend showing a better recovery profile with desflurane, no significant statistical difference was found between the treatment groups. The combination of fentanyl-medetomidine-midazolam and the use of modern volatile agents resulted in a rapid recovery and hence a more rapid resumption of normal food and water intake as well as a faster reintroduction to the animal’s social group, potentially decreasing the risk of violent hierarchical conflict. However further studies to evaluate the possible interference of these alternative regimens with different types of neurophysiological research should be performed, to enable better interpretation of scientific data obtained from animals. [less ▲]

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See detailEffect of long-term fertilization strategies on microbial community composition in a 35-year field experiment of Chinese Mollisols
Ma, Mingchao ULiege

Doctoral thesis (2018)

Long-term intensive fertilizations are often accompanied by inefficiences that result in pollution and soil degradation of Mollisols in northeast China, especially the overuse of inorganic nitrogen (N ... [more ▼]

Long-term intensive fertilizations are often accompanied by inefficiences that result in pollution and soil degradation of Mollisols in northeast China, especially the overuse of inorganic nitrogen (N) input. Organic manure can improve soil quality and may be potential as substitution of N fertilizer. However, we know less about the impacts of inorganic fertilizer and organic manure applications on microbial community composition, which functions as sensitive indicators for soil biological fertility. To broaden our knowledge, high throughput pyrosequencing and quantitative PCR were used to explore the responses of soil property and microbial community composition to long-term fertilization strategies. Soils were collected from a 35-year experimental field of Chinese Mollisols with six treatments: 1) no fertilizer (CK), 2) inorganic phosphorus and potassium fertilizer (PK), 3) inorganic N, P and K fertilizer (NPK), 4) manure (M), 5) inorganic P, K fertilizer plus manure (MPK), and 6) inorganic N, P, K fertilizer plus manure (MNPK). Treatments 1), 2) 3) and 5) were analyzed for bacterial and fungal community, and treatments 1), 3), 4) and 6) were used for arbuscular mycorrhizal fungi (AMF). All fertilization strategies significantly changed soil properties and increased the crop yields, with the highest increase observed in chemical fertilizers plus manure treatments. The application of manure also had beneficial effects on soil acidification alleviation and soil organic matter (OM) accumulation, while long-term chemical fertilizer application (NPK and PK) significantly decreased soil pH. With regards to microbial abundance, 16S rRNA gene copies were significantly increased in MPK regime. Compared with CK, long-term MPK application indicated a good effect on the soil shift from “fungal-based” to healthier one, namely “bacterial-based” soil, by decreasing ITS gene copy numbers and increasing the Bacteria-to-Fungi ratio, while chemical fertilization application exhibited the opposite pattern. Furthermore, the community richness indices (CHAO1 and ACE) in MPK regime were also higher than those in other regimes, probably indicating resilience of microbial diversity and stable agroecosystem. The diversity and richness of AMF were negatively affected by chemical fertilizer applications, likely resulting in a reduction of mutualism in plant–AMF symbiosis; however, a reverse trend was observed for the application of manure. Regarding bacterial community composition, Proteobacteria, Acidobacteria, Actinobacteria and Verrucomicrobia were dominated phyla, and phylun Ascomycota was absolutely dominated in fungi in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota and Glomeromycota. The community composition considerably varied by different fertilization strategies at each taxonomic level. NPK application might induce the incidence rate of disease, because more harmful fungal taxa were overrepresented in this regime, such as order Chaetothyriales, family Chaetothyriaceae, Genuses Corynespora, Bipolaris, Pleosporaceae, Cyphellophora, Sphingomonas and Xanthomonas. Although such of them were not crop pathogens, their present in soil would no doubt increase the environmental risk. Additionlly, NPK application might cause a loss of plant-fungal symbioses, N loss in soil and greenhouse gas emission, probably due to the shift of classes Leotiomycetes and Eurotiomycetes. In contrast, more taxa with positive impact on soil quality were overrepresented in MPK regime, including phyla Proteobacteria, Bacteroidetes, class Alphaproteobacteria, family Claroideoglomeraceae, and genera Variovorax, Chthoniobacter, Massilia, Lysobacter, Claroideoglomus, Catelliglobosispora and Steroidobacter. These beneficial bacteria were in association with plant growth promotion, OM accumulation, P acquisition, pathogen suppression, and soil enzyme activity arising. In summary, different fertilization strategies led to distinct variances in microbial community composition. Such shifts primarily derived from the changes of soil pH and OM. Our findings determined the responses of microbial community composition to long-term application of inorganic fertilizer and organic amendment, and highlighted the benefits of substitution of inorganic N fertilizer by manure for sustainable development of agriculture in Chinese Mollisols. [less ▲]

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See detailVery High Resolution & 3D Remote Sensing Data for Supporting Forestry in Wallonia. What Resolution? What Scale? What Purpose?
Bonnet, Stéphanie ULiege

Doctoral thesis (2018)

The forest, which represents one-third of the Earth surface, has always been in close interaction with human societies. Forests provide many environmental services: soil and water resources protection ... [more ▼]

The forest, which represents one-third of the Earth surface, has always been in close interaction with human societies. Forests provide many environmental services: soil and water resources protection, reduction of impact of gas emissions, biodiversity reservoir and conservation... Concerns about global changes add to social functions such as recreational activities or wood production and about forest management and silviculture practices. The need for information about the forest resource has never been greater to ensure a sustainable management. The description of the forest stands (location, extent, composition, structure ...) and their dendrometric characterization (dominant height, number of trees per hectare, mean quadratic circumference, basal area and volume per hectare ...) have become crucial prerequisites indispensable for planning. Remote sensing enables information acquisition over large areas and overcomes the capacity and accessibility limitations inherent in field data collection, which mobilizes significant human and financial resources. The Walloon forest is characterized by a great diversity of situations and preoccupations: type of owner, structure, composition, spatial distribution, stations, fragmentation, silvicultural practices. This diversity makes it particularly relevant to use remote sensing as an information acquisition tool. This thesis lies in this context. The main purpose was the implementation of different types of three-dimensional remote sensing data to determine how they could contribute properly to forest management in Wallonia. First, we considered the use of low-density and regional-scale Airborne Laser Scanning (ALS) data in combination with the data collected by the Walloon Regional Forest Inventory. This combination has shown its potential for quantifying coniferous forest attributes, coupled with regional allometry built on the inventory database. In parallel with the importance of coniferous forest, a major concern is the development of a close-to-nature forestry, promoting natural regeneration. The presence of gaps in the stands is therefore essential information. We focused on a robust mapping of gaps in broadleaved forests from high-density ALS data. To complete our progression in the use of three-dimensional data, we focused on data acquired by drones. Our study showed their effectiveness in detecting (dominant, co-dominated, dominated) trees in coniferous stands as a basis for quantifying forest attributes. The potential use and relevance of several photogrammetric products (ortho- or rectified images, digital surface model, and correlation maps) have been tested to detect individual trees as a basis for forest characterization. We investigated the association of the individual tree detection approach and the area-based approach for the assessment of forest attributes with drone data. As a conclusion, we argue the importance of a strong interaction between the different kind of remote sensing data as indispensable support for forest managers. [less ▲]

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See detailIntroduction to elephant ecophysiology: principles, methods and case studies on forest elephant (Loxodonta africana cyclotis) crop raiders in Gabon
Ngama, Steeve ULiege

Doctoral thesis (2018)

Biodiversity is becoming scarce at the start of this third millennium because of human activities, which have already led to the disappearance of many species. Many more species are threatened to ... [more ▼]

Biodiversity is becoming scarce at the start of this third millennium because of human activities, which have already led to the disappearance of many species. Many more species are threatened to extinction in the short or medium term. This threat leads scientists devoted to conservation biology to use new disciplines such as ecophysiology to strengthen species conservation efforts. This thesis presents a first attempt to apply the principles of ecophysiology to forest elephants (Loxodonta Africana cyclotis). This biological model was chosen both because of its emblematic character and because these endangered species raid and damage crops. This thesis integrates ecophysiology into elephant conservation efforts through two dimensions: a theoretical and an experimental. In the first part which covers the theoretical dimension and involves all elephant species, the thesis reviews the concept of animal ecophysiology. Results from bibliographic investigations reveal disagreements among specialists in the definition of animal ecophysiology. In this thesis we consider animal ecophysiology as the science that studies the resilience ability of animals and mechanisms governing their physiology and behavior within their natural environments. It is characterized by the simultaneous use of many techniques such those from molecular biology, endocrinology or nutrition. With regard to elephants, results show that crop raiding by itself is a multidimensional threat that complicates the implementation of strategies for conserving these animals. The experimental part of this thesis involves only forest elephants. Results first reveal that food selection by elephants might be influenced by their parasitic status and not stress hormone levels. Next, our research shows that the presence of fruiting trees may increase crop damage by elephants. However, deterrence methods in farm areas tend to decrease crop damage by elephants. These results also highlight the fact that steep fields might limit elephant movements and prevent them from damaging crops. Our research also show that beehives can only be effective as long-term elephant deterrents when they are occupied by densely populated bee colonies, which are active and able to cope with the small hive beetle pest. In addition, we have demonstrated that to effectively use chili pepper as a deterrent it is necessary to use technics and/or apparatus that target the animal face which seems to be the most sensitive elephant body part toward chili pepper. Therefore, this thesis is a step forward in the use of animal ecophysiology principles for the study and conservation of elephants. It presents news data on the understanding of factors that might underlie crop damage by elephants. It highlights mechanisms that govern interactions between elephants and their environment, and the influence of physiology and health in their food selections. This thesis is also a progress in the ability of developing and implementing mitigation strategies against elephant crop raiders, for the benefit of these animals’ conservation. [less ▲]

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See detailExposition des travailleurs aux résidus de pesticides sur les fleurs coupées et sur les produits horticoles
Toumi, Khaoula ULiege

Doctoral thesis (2018)

Persons who, during their professional tasks, come in contact with pesticide residues are exposed by various routes, with possible negative effects on their health. The aim of the thesis is to evaluate ... [more ▼]

Persons who, during their professional tasks, come in contact with pesticide residues are exposed by various routes, with possible negative effects on their health. The aim of the thesis is to evaluate the exposure risks of two categories of workers indirectly exposed to pesticide residues (parent compounds and metabolites): Belgian florists and Tunisian market gardeners. As a first step, the exposure of Belgian florists to pesticide residues present on cut flowers was studied. A survey of florists reveals that, despite a fairly long work period, they do not protect themselves enough from contact with residues. The analysis of residues on cut flowers most sold in Belgium has shown that they are highly contaminated, with 107 residues of different pesticides were detected on 90 samples. By wearing cotton gloves by florists, it has been established that 111 residues of different pesticides could be transferred from the flowers to the hands. In the worst case, the estimated systemic exposure of florists to four active substances exceeds (at maximum concentrations) the acceptable threshold values (AOEL). The bio-monitoring approach conducted with Belgian florists and a reference group led to the conclusion that the florists' urine is significantly more contaminated and that a linear relationship exists between dermal exposure to residues and urinary excretion. The same methodological approach, except biomonitoring, was used to assess the exposure of Tunisian market garden workers to pesticide residues. The survey reveals that the majority of workers doesn't generally protect themselves during the re-entry tasks despite an extended daily working time. The wearing of cotton gloves, combined with the sampling and analysis of residues on the handled horticultural products, demonstrated that chili pepper and tomato samples are contaminated by pesticide residues, with 7 exceedances of EU MRL. A total of 57 and 63 pesticide residues were detected on gloves worn by workers during harvesting in tomato and chili pepper greenhouses, respectively. The systemic exposure of workers harvesting tomatoes and chili peppers exceeds (at maximum concentrations) their AOEL values, for 9 and 15 pesticides, respectively. The study has thus demonstrated that Belgian florists and Tunisian workers are exposed during their usual tasks to significantly high amounts of pesticide residues whose toxicological properties suggest that they could have on long-term negative effects on health. [less ▲]

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See detailCan satellites help organic crops certification?
Denis, Antoine ULiege

Doctoral thesis (2018)

Organic agriculture products are in increasing demand globally principally because, compared to conventional products, organic food is seen to be healthier and organic farming is more respectful of the ... [more ▼]

Organic agriculture products are in increasing demand globally principally because, compared to conventional products, organic food is seen to be healthier and organic farming is more respectful of the environment by avoiding the use of synthetic chemical fertilizers and pesticides, and it excludes genetically modified organisms. Organic labelled farming products have to comply with established international standards and rules, and, in particular, organic producers have to be certified annually by organic certification bodies. One of the challenges of this certification process is the efficient targeting of the relatively small percentage of fields declared to be organic that must effectively be subject to an in situ inspection. The main objective of the present research, the first of its kind, is to assess how spatial remote sensing may support the organic crop certification process. This research is based on the hypothesis that the differences in treatments between organically and conventionally managed crop fields, primarily the differences in fertilization and crop protection, would result in biochemical and biophysical differences between the fields. Among these differences, some are supposed to be observable by spatial remote sensing derived indices. Consequently, these indices could be used at the beginning of the field certification process to target for priority in situ control fields declared as organic but that would show on satellite imagery an appearance that is closer to conventional fields. Such a technique would provide organic certification bodies with a supplementary and independent means of control which might be particularly useful for large farms and in production regions located in remote areas where the certification process might be more difficult and costly. In order to address this objective, 3 case studies were elaborated. The first case study focuses on wheat and maize in central-eastern Germany and consists of an exploratory approach combining a wide range of both in situ measurements and satellite sensors of various spatial and spectral resolutions. The second case study has a main purpose to assess the robustness of the method developed in the first case study over years and regions. It consisted in repeating the method on the German study site for the following cropping season for wheat and maize, and, for wheat exclusively, on a region located in central France. Near operational conditions were simulated by a limited use of satellite images. The third case study focuses on organic cotton in Burkina Faso and has a primary purpose of assessing the method’s efficiency in the context of a developing country where rural areas are sometimes more difficult to reach, making the use of remote sensing particularly relevant. Results show that the efficiency of the proposed method varies greatly depending on the situation. Indeed, in some situations, it appeared that biochemical and biophysical differences between organically and conventionally managed fields may exist at given crop growth stages and are sufficiently pronounced to enable a complete discrimination between organic and conventional management modes through various simple indices derived from multispectral satellite images. In other situations however, the discrimination appeared to be far more difficult and required the complementarity of different types of indices integrated in multivariate linear models. Given these mixed results and the limited representativeness of the 3 case studies compared to the diverse contexts where the developed method is supposed to be used in operationally, it appeared that there is simultaneously both room for optimism but also considerable uncertainty with regard to whether spatial remote sensing could effectively contribute to ensuring that crop fields declared as organic are truly organic. [less ▲]

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See detailImpact du partenariat public-privé pour la délégation de gestion du service de l'eau d'irrigation. «Cas du projet El Guerdane dans la région du Souss-Massa»
Maatala, Nassreddine ULiege

Doctoral thesis (2018)

Over the past decade, the use of the Public-Private Partnership (PPP) by the Moroccan Government has undergone remarkable development in many activity sectors, particularly, infrastructure, agriculture ... [more ▼]

Over the past decade, the use of the Public-Private Partnership (PPP) by the Moroccan Government has undergone remarkable development in many activity sectors, particularly, infrastructure, agriculture, energy, ports, transportation... etc. This type of partnership in the irrigation sector was initiated in 2005 and concerned the El Guerdane project in the Souss-Massa area. This project commissioning started in 2009; the irrigation of this perimeter was essentially based on pumping water from the aquifer. In addition, the importance of water withdrawals, given the scarcity of inputs, has led to a continuous decline in the water table levels (from 1.5 to 2 m /year). At this rate, the medium and the long term future of the 10,000 ha of citrus was seriously threatened. As a result, the idea of safeguarding this sector came up and was undertaken by the Government. The project to safeguard the citrus-growing area of El Guerdane consists of an annual volume of water transfer estimated to 45 million m3 from the Aoulouz-Chakoukane dam to irrigate 10 000 ha of plantations in the the project’s area. Since the commissioning of the El Guerdane project, the Moroccan Government has continued to implement similar projects all over the country. Unfortunately, the Government did not benefit from the return on experience based on completed projects’ assessment in order to come out with corrective measures that could have been adopted either within the program’s framework or switch for other types of partnership. In this research, we went through several aspects to evaluate the impact of this public-private partnership program. Accordingly, these aspects concern the financial and the agronomic valorization of irrigation water, the farmers' net income, the technical efficiency of farms and the technical and economic efficiency of the use of irrigation water. In order to study the project’s impact on the aspects already mentioned, we have selected and defined a control perimeter that did not benefit from this program (the Issen perimeter). In addition, we defined a representative sample to avoid the exogenous factors’ effect on our results (the propensity score matching method). Our sample was selected using the software R.3.1.0 and SPSS 23. Furthermore, the impact evaluation was carried out by the double difference method. In this work, we have been interested in qualitative aspect related to the regulation of the El Guerdane project that has been realized in the form of public-private partnership thanks to the interviews carried out with the different actors of this project (farmers, private partner, Government, Regional Office of Agricultural Development, etc.). The estimation of the scores related to the different types of efficiency was carried out using the FRONTIER 4.1 software by choosing a stochastic parametric model and by using a functional Translog form. The analysis of the irrigation water valorization determinants was carried out using an ordinary regression model by the GRETL software, while the analysis of the determinants of the efficiency scores was carried out by a Tobit model using the same software to take into consideration the truncated criterion of the dependent variable. The survey concerned 130 citrus growers in both perimeters studied. For the El Guerdane perimeter, the financial valorization increased from a negative level of -0.637 DH /m3 in 2009 to a positive level of 2.19 DH /m3 in 2016. The agronomic valuation level has improved in the El Guerdane perimeter from 2.59 Kg / m3 in 2009 to 3.65 Kg/m3 in 2016. In 2009, water price and farm size are positively correlated with the level of irrigation water valorization, while the participation in the public-private partnership program is negatively correlated with this aspect (irrigation water valorization). In 2016 only the farms’ size impacts the irrigation water valorization in both perimeters. This partnership program was able to improve the financial valorization of irrigation water by 2.1 Dh / m3, the agronomic valorization by 1.05 Kg / m3 and the farmers net income by 10 902 Dh / ha. The farms technical efficiency is affected only by their areas in 2009 and 2016. The technical efficiency of irrigation water use is positively impacted by farm size and negatively impacted by the public-private partnership program in 2009; also, the technical efficiency of irrigation water use is negatively correlated to water price in 2016. The economic efficiency of irrigation water use is negatively correlated to the participation in the public-private partnership program in the year of 2009. However, it was negatively impacted by the water price in 2016 and positively impacted by the partnership program in the same year. The project monitoring shows that during the exploitation years ,all the indicators maintain a positive trend resulting in a record level for some of them such as the volumes taken and distributed to the users. Despite the negative impact of the public-private partnership program on several aspects, in 2009 or in 2016, the social cost of the El Guerdane project remains a significant component that could justify the use of this type of collaboration. Therefore, the use of this mode of management for the irrigation water service will be more relevant if the aspect of the technical supervision of the farmers is taken over by the private partner. [less ▲]

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See detailRôle des petites entreprises de produits artisanaux traditionnels dans le développement local: cas de la périphérie de Hanoi-Vietnam.
Nguyen, Thi Thu Hien ULiege

Doctoral thesis (2018)

With a history of more than 1000 years, the traditional handicraft products of Vietnam have been developed in the several provinces along the country. The most popular production model of handicrafts is ... [more ▼]

With a history of more than 1000 years, the traditional handicraft products of Vietnam have been developed in the several provinces along the country. The most popular production model of handicrafts is small and medium enterprises (SMEs). Majority of which are located in the sub-urban of the large cities. This study aims to understand the roles of the small and medium enterprises in the local economic and social development in the periphery of Hanoi through the data collection on employment, labours and relations with local partners in traditional villages. Furthermore, it helps to identify the current situation of the traditional handcraft small enterprises on the employment aspects, the gender issues at work and their local socio-economic networks. The study conducted surveys on 50 SMEs and 157 employees in three districts of the periphery of Hanoi, on three typical and well-known traditional handicraft sectors of Vietnam from 2014 to 2016. Data were analysed by both qualitative and quantitative methods. The results showed that these SMEs have a significant contribution to the local job creation. They also play an important role in the development of local economic and social networks. For employment-related aspects, it exists gender discrimination in workforce. Related to the issues of the quality of work, one survey was conducted to assess the employees’ job satisfaction in the targeted enterprises. Women are more satisfied than men about the family-work balance, while men appreciate more the salary/payment criteria. About the relations among the traditional handcraft small enterprises, collaboration and competition among them have coexisted. This leads to the local economic and social network development, as well as to establish a cluster zone in this area. These results help to understand the contribution of these SMEs to local development. [less ▲]

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See detailLepilemur mittermeieri, une espèce menacée du nord-ouest de Madagascar: écologie et enjeux de conservation
Wilmet, Leslie ULiege

Doctoral thesis (2018)

Tropical forests are home to the widest variety of organisms, currently estimated at around 50% of all species on the planet. They also provide important ecosystemic services, particularly in terms of ... [more ▼]

Tropical forests are home to the widest variety of organisms, currently estimated at around 50% of all species on the planet. They also provide important ecosystemic services, particularly in terms of global climate regulation, storage of vast amounts of carbon and oxygen production. Unfortunately, they are also extremely threatened by increased anthropogenic pressure, both direct and indirect. Indeed, deforestation and habitat fragmentation are considered to be the main threats to biodiversity today. Madagascar, one of the world’s main “hotspots” of biodiversity, has not been spared; about 90% of the island’s forest cover has disappeared and the current deforestation rates remain very high. The Island, a world priority in terms of conservation material, is notably home to an endemic group of primates, lemurs, who are completely linked to their forest habitat and for whom the state of conservation is particularly alarming. This research project focuses on the impact of forest fragmentation on a strictly tree-dwelling species of primate in Madagascar. The study model, Lepilemur mittermeieri, is a small, little-known, folivorous and nocturnal primate, who is threatened with extinction (IUCN, 2012) and is restricted to the Ampasindava peninsula, north-west of Madagascar. This lepilemur is completely dependent on the forests of the peninsula, whose area is continuously shrinking under anthropogenic pressure. L. mittermeieri can be considered the archetype of a tree-dwelling species of primate with small distribution areas and whose habitat is threatened. The general objective of this research is to explore the ecology of L. mittermeieri and the conservation issues related to its preservation. This work is based on three specific objectives: one, to collect the first data on this species; two, to understand habitat use by L. mittermeieri; and three, to examine the future of the species in a fragmented forest environment. This work is therefore carried out on two scales, that of the individual and that of the distribution area, the Ampasindava peninsula. At the individual scale, we studied the species ecology by focusing on the range and sleeping sites features, as well as the diet of the species and the social structure. By radio-tracking, we were able to follow about twenty individuals and highlight that the average range of L. mittermeieri is around 2 ha. We identified, on average, 4.7 sleeping sites per individual, mostly clusters of vegetation, always occupied by a single individual and almost never shared over time. Sleeping sites are mainly located in the core area of the home range. L. mittermeieri diet is diverse, with a minimum of 77 vegetable species, some of which are more commonly consumed. The species seems rather solitary, but not especially territorial as ranges overlap, even between males. At the scale of the Ampasindava peninsula, this study shows that L. mittermeieri is found in fragments of different size, altitude and forest type. We found a density of 1.4 individuals/ha, which could represent a total population of some 10.000 individuals if the hypothesis of homogeneity within different forest fragments is confirmed. This first estimate must be taken with precaution. We also calculated an increasing rate of deforestation on the peninsula, reaching 3.14%/year between 2000 and 2014. This is confirmed by a significant reduction in the number of forest core areas and increasing fragmentation. L. mittermeieri is present in narrow forest strips indicating that the species still has the resources to survive. There is no obvious indication that the long-term survival of the species is assured. To conclude, this work highlights the extent and speed of deforestation and fragmentation of forest habitats on the Ampasindava peninsula. The recent development of a rare earth mining project is increasing the pressure on biodiversity in this region. This work emphasizes the importance and the urgency of implementing an action plan for the conservation of L. mittermeieri. [less ▲]

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See detailRecherche et caractérisation de symbioses microbiennes chimiosynthétiques ou digestives chez des crustacés amphipodes associés à des accumulations végétales en milieux marins côtier et profonds.
Trevisan, Mélissa ULiege

Doctoral thesis (2018)

Widespread in coastal and deep-sea habitats, plant remains constitute abundant and attractive food sources especially for the macrofauna and particularly for small-sized amphipod crustaceans. These ... [more ▼]

Widespread in coastal and deep-sea habitats, plant remains constitute abundant and attractive food sources especially for the macrofauna and particularly for small-sized amphipod crustaceans. These detritic habitats favour the development of bacterial symbioses by specialized members of the macrofauna to exploit alternative energy sources as reduced compounds through chemosynthesis and refractory compounds through specific heterotrophic digestive microflora. In the present work, 12 deep-sea wood fall amphipod species of the genus Onesimoides (3 species) and Bathyceradocus (9 species) from Indo-Pacific Ocean were compared to 3 Gammarus (2 species) and Gammarella (1 species) species from Mediterranean sea-grass litter (Posidonia oceanica). All species being supposed detritivorous and depending on a detritic plant substrate, the comparison points were focussed on their diet specificities, as well as on the presence and roles of the eventual microbial (epibiotic or digestives) associations they harbour on their integument or in their gut. The genetic diversity of symbionts was investigated in the gut microflora of Onesimoides, Gammarus and Gammarella species. The results confirm that all the amphipod species examined nourish on plant detritus, mainly from monocots, in their habitat and benefit directly or indirectly of the plant substrate. They would have however the ability to degrade and assimilate cellulose through endogenous cellulases that are ancestral and widespread among the Arthropod group. This is supported by the progressive alteration of the plant cell walls (PCWs) as observed along the transit. In addition, all the plant debris had undergone microbial degradation in submarine conditions (not terrestrial) prior to their ingestion by amphipods. The degradation stage and the type of involved microbes vary not only with the substrate, the habitat or the collection site but mainly with the amphipod group or species. It is well known that degradation is a “microbial conditioning” of plant detritus. It results in 1) an increase then decrease of the decomposer abundance (endophytes/epiphytes) with the PCW degradation progress, 2) an increased accessibility of residual cellulose and, finally, 3) an increase then decrease of the nutritional value and N-content of the residues. The results suggest that the degradation state of the ingested plant substrate determines the true diet of the species and strongly influences the development of digestives microflora that may complement the host diet by providing nitrogen and thus allowing the host feed on residual substrate of very poor nutritional value. Considering these criteria, the examined amphipod species could be classified according to a representative sequence. The Gammarus species feeding on freshly “conditioned” seagrass leaf litter, complete their diet by endophytic/epiphytic microorganisms (mainly hyphae from the black septate fungus) and find support on a poorly developed microflora with resident bacteria (γ-proteobacteria) together with transitory bacteria (α-proteobacteria). In contrast, Gammarella fucicola feeds on old litter at the end of the degradation process and complete its diet by the activity of an important and diversified digestive bacterial microflora that resident on its hindgut lining. It is very similar in the Onesimoides species that are associated to deep-sea sunken wood but ingest, as G. fucicola, residues of lignified (vascular) tissues of monocots after deep microbial alteration (bacteria, fungi). In addition, the microflora of both genus exhibited some common features, among which the involvement of 2 common groups of bacteria (γ-proteobacteria, Bacteriodetes). Such similarities strongly support the supposed symbiotic and mutualistic character of both microflora. Finally, only the Bathyceradocus sp. seems to be different. They also mainly ingest deeply altered lignified tissues of monocots but do not possess any digestive bacterial microflora. They possibly complement their diet by eating epibiotic microorganisms (bacteria, fungi) that colonize their mouthparts and/or by the help of trichomycetes anchored on their hindgut wall. The present study illustrates the importance of alternate and successive roles of microorganisms, small-sized macrofauna and microbial symbionts in the gradual, step-by-step, alteration of plant substrates in the sea, to the terminal degradation stage of the most recalcitrant elements of wood and lignified tissues of monocotyledons. [less ▲]

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See detailCaractérisation structurale et fonctionnelle du domaine de fixation à la chitine de la chitotriosidase de macrophage humain
Crasson, Oscar ULiege

Doctoral thesis (2018)

Chitin is an important structural component of cell walls and exoskeletons of numerous organisms. Chitin binding proteins are closely related to those structures. They are associated to chitin stability ... [more ▼]

Chitin is an important structural component of cell walls and exoskeletons of numerous organisms. Chitin binding proteins are closely related to those structures. They are associated to chitin stability, remodelling, recognition, metabolism and tens of biological functions. ChBD, the chitin binding domain of the human chitotriosidase (HCHT) attracted our attention due to a considerable lack of information regarding this domain. Based on literature, CBMs are known to influence significantly the behaviour of their cognate catalytic domains. We wanted to verify if it was the case for ChBD and to determine in which manner this phenomenon could occur. We investigated the biochemical function of ChBD by chitin binding studies. We analysed the structure of the CBM and defined a binding mechanism in accordance to previous publications and our experimental data. A phylogenetic analysis was used to determine the evolution path of HCHT and its constitutive domains. Altogether, our results make the link between chitin, innate immunity, ChBD and HTCH appearance. [less ▲]

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See detailMeasuring and Modeling Spatio-Temporal Soil Moisture Dynamics at the Field Scale with Plastic Mulching in Dryland Agriculture
Chen, Baoqing ULiege

Doctoral thesis (2018)

Drylands include arid, semi-arid, and dry sub-humid ecosystems characterized by low and irregular rainfall and high evapotranspiration. Drylands cover about 41% of the Earth’s land surface and are home to ... [more ▼]

Drylands include arid, semi-arid, and dry sub-humid ecosystems characterized by low and irregular rainfall and high evapotranspiration. Drylands cover about 41% of the Earth’s land surface and are home to more than 30% of the total global population. Water shortages and low soil water content (SWC) in dryland seriously limit crop production, especially when irrigation is not available (i.e., rain-fed agriculture). Moreover, because of the long duration of drought and intense water pulses, drylands usually experience intense soil moisture fluctuation (SMF), which leads to a high risk of soil degradation. Plastic mulching (PM) has been developed as an effective measure to alleviate drought in rain-fed drylands. Although soil water dynamics under PM have been widely studied, most of our knowledge is derived from measurements at the point scale, which only represent a small portion of whole soil profiles. There is still a lack of knowledge regarding spatial variations in SWC and SMF. ‘From points to profile’ not only allows for a deeper understanding of the effects of PM on soil moisture dynamics, it also lays the foundation for further understanding soil processes driven by soil moisture dynamics, improves the sensing and modeling strategies for soil processes, improves PM practices, and further contributes to the development of dryland agriculture. In this dissertation, we adopted a research route including field measurements, model optimization, and model prediction to quantify how partial PM affects soil moisture dynamics in space and time simultaneously. Specifically, we first measured the soil moisture using point-scale methods in the field; second, we optimized two-dimensional (2D) simulation methods using measured point-scale soil water data. Finally, spatio-temporal soil moisture dynamics were predicted using optimized 2D simulation; at the same time, electrical resistivity tomography (ERT) was applied to verify the 2D simulation results. For the first part of our research, we mainly aimed to address how PM influences the soil water dynamics at the point scale. At the same time, we also aimed to identify the effects of PM on crop yield, water use efficiency (WUE), and economic benefits. Considering plastic pollution, a PM method called one film for two years (PM2) was proposed in this study, and comparisons were conducted among no mulch (NM), traditional PM, and PM2. According to two years of field experiments, we found that PM and PM2 are effective in improving the soil moisture content during the growing season. Compared to NM, the PM treatment led to yield improvements of 12.1% and 25.0% in the two experimental years. Compared to PM, similar average soil moisture contents, maize yields, and WUE were recorded in PM2, but economic profits were improved because of savings on plastic film, tillage costs, and labor costs. Moreover, because the amount of plastic residue was reduced by half and no tillage was adopted to prevent the incorporation of plastic residue into soil in PM2, PM2 has potential to promote the sustainable development of drylands. In the second part, we aimed to optimize simulation to reproduce soil water dynamics in fields with PM with the measured soil water data in the field. Considering the dominant role of rainfall infiltration in rain-fed agriculture, we developed a simulation approach that uses a bare strip boundary, a plastic strip boundary, and a planting hole boundary (BPH) to consider the effects of rainfall canopy redistribution and film side infiltration. We compared this approach’s performance to that of two others that were developed by previous researchers: a BP- approach that uses a bare strip boundary and a plastic strip boundary without considering film side infiltration and rainfall canopy redistribution and a BP+- approach that uses a bare strip and a plastic strip that considers film side infiltration by increasing rainfall infiltration in the bare strip. Our results that showed BP and BP+ failed to reproduce soil water dynamics in field, while BPH showed good performance. This result suggests that is necessary to take into account changing canopy redistribution, crop growth, and film side infiltration in simulations by numerically solving the Richards equation using PM. Finally, we quantified the field-scale spatial variations in SWC and SMF with the optimized simulation strategy and ERT measurements. The modeling results indicated that the highest SWC appeared in the zone near the planting hole. The center zone of the plastic strip was drier, and the bare strip was the driest. Compared to NM, PM not only improved the SWC in the plastic strip but also improved the SWC in the bare strip. The modeling and ERT results suggested that the application of PM resulted in contrasting SMF between the mulched strip and the bare strip in PM, and the SMF in the mulched strip was relatively constant compared to that in the bare strip. Nevertheless, when the SMF was compared between PM and NM using Hydrus 2D, we found that PM reduced the SMF of the whole soil profile compared to NM, meaning that the PM not only alleviated the SMF in the mulched strip but also alleviated it in the bare strip. In this dissertation, the spatio-temporal soil water dynamics were addressed using PM at the field scale in a maize field, which was located in a semi-arid, rain-fed area with sandy loam soil. As the development of new PM methods and materials is ongoing and spatio-temporal soil water dynamics may change with changing soil and climate conditions, further studies on different PM methods and materials in different climate and soil conditions may be necessary. In a broad sense, improving crop yield, economic benefits, and sustainability is important for the development of dryland agriculture. Our study contributes to improving these factors by improving PM methods to ensure higher economic benefits and sustainability, improving the modeling of soil water transport, laying the foundation to model other processes related to crop production and environmental sustainability, and providing soil water dynamics information in a high spatio-temporal resolution, which is necessary to further improve PM methods and regulate the soil processes driven by soil water dynamics. Even with this knowledge, improving plastic technology and developing dryland agriculture still have a long way to go. In particular, we are facing a revolution in PM technology from the pursuit of yield and economic benefits to the pursuit of higher yields, economy benefits, and environmental sustainability. Long-term experiments are necessary to clarify the influences of PM on the environment other than yield improvements. Supplementary studies are still needed in the future in order to select effective and sustainable PM strategies for the agriculture of the future. [less ▲]

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See detailInvestigations of aphid saliva composition and role in plant – insect interactions: focus on Sitobion avenae and Myzus persicae
Zhang, Yong ULiege

Doctoral thesis (2018)

Aphid is one of the most important and destructive agricultural group of pests in the world. Currently, aphid is mainly controlled by chemical pesticides, resulting in serious impacts on human health and ... [more ▼]

Aphid is one of the most important and destructive agricultural group of pests in the world. Currently, aphid is mainly controlled by chemical pesticides, resulting in serious impacts on human health and environmental safety. Cultivating and using insect-resistant host plant varieties is an important approach for the sustainable control of wheat aphids, but due to few understanding of the interaction mechanisms between aphids and hosts, it still lacks aphid resistance varieties. Aphid saliva play important roles in the interactions with plant. Some studies have identified several salivary effectors from Acyrthosiphon pisum pea aphid and Myzus persicae peach aphid inducing plant defense responses. However, few studies have been reported on the roles of Sitobion avenae grain aphid saliva, which is one of the most important cereal pests. In our studies, the role of S. avenae watery saliva in host plant resistance induction was firstly examined by infiltrating aphid saliva into wheat leaves. Strong SA-dependent and moderated JA defensive responses were observed. The fecundity and the intrinsic increase rate of the S. avenae population significantly decreased after feeding on wheat leaves infiltrated with aphid saliva. In a choice test, saliva-infiltrated wheat had obvious repellent effects on aphids. The feeding behavior of S. avenae on saliva-treated wheat was also negatively affected, including shorter feeding time on phloem and longer penetration activity. These findings directly demonstrated the invovlment of S. avenae salivary components in the induction of wheat resistance against aphids and the important roles of watery saliva in aphid-plant interactions. To investigate the aphid saliva composition, the transcriptome of the whole salivary glands of S. avenae was sequenced. Among the 33,079 identifed unigenes, 526 unigenes were predicted to encode secretory proteins, and some of their orthologs have been proved to play important roles in aphid-host interactions. Gene expression analysis showed that the 15 most highly expressed putative secretory proteins and glutathione-S-transferase 1 are specifcally expressed in salivary glands. These findings firstly provide insight into the identifcation of potential effector molecules in S. avenae saliva and further understanding of the saliva impact in aphid-wheat interactions. In the next step, the species and function of salivary effectors in S.avenae were identified by RNA interference (RNAi) via oral delivery. The knockdown of laccase 1 (Lac1) was performed to demonstrate that the genes in aphid salivary gland can be successfully silenced by feeding dsRNA directly. Lac 1 from S. avenae (SaLac 1) was highly expressed in the salivary gland. After feeding on aphid-resistant wheat with a high total phenol content, the expression level of SaLac 1 increased significantly. RNAi by oral feeding successfully inhibited the transcript levels of SaLac 1, and the knockdown of Lac 1 significantly decreased the survival rate of S. avenae on aphid-resistant wheat. Our study demonstrated that S. avenae Lac1 was was essential for the aphid to adapt to resistant plant and oral delivery of gene-specific dsRNA successfully silenced the target gene in salivary gland of S. avenae. Beside the cereal aphid, further investigations were performed to the M. persicae and plant interactions. Direct effects of SA and JA exposure on the green peach aphid, Myzus persicae physiology were investigated developping a proteomic approach. SA and JA treatments induced variation in several regulated proteins that were mainly associated with stress responses, protein synthesis, energy metabolism and cytoskeleton. This study was the first to demonstrate that beside the fundamental roles in the regulation of plant developmental processes and stress responses, plant signal molecules SA and JA can also modulate physiological status of aphid as a second target, providing new insight into aphid-plant interactions. [less ▲]

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See detailImplication de la toxine beta2 de Clostridium perfringens dans le syndrome de l’entérotoxémie bovine.
Lebrun, Maude ULiege

Doctoral thesis (2018)

Cattle enterotoxaemia is an acute to hyperacute syndrome, which is characterized by the sudden death of the cattle and the presence of hemorrhagic lesions in the small intestine. Under the stimulus of ... [more ▼]

Cattle enterotoxaemia is an acute to hyperacute syndrome, which is characterized by the sudden death of the cattle and the presence of hemorrhagic lesions in the small intestine. Under the stimulus of misunderstood triggering factors, the enteroxaemia is associated with an exponential overgrowth of Clostridium perfringens in, often limited, small intestine segments and the production of toxins acting locally or systemically. Among the numerous potentially implicated toxins in the genesis of these lesions, the beta2 toxin (CPB2) deserves special attention. Discovered in piglets suffering from necrotic enteritis (Gibert et al., 1997), it was thereafter detected in other animal species suffering of various diseases, but also in healthy animals. Two alleles were quickly defined (1) consensus cpb2, associated to swines’ strains able to produce CPB2 and atypical cpb2, detected in strains from other species and a priori unable to express CPB2 (Jost et al., 2005). The strains that could produce CPB2 were widely distributed but the real implication of this toxin in intestinal diseases is not yet clarified. In cattle, the results of a study on intestinal ligated loops in our lab, suggested a synergistic effect of alpha and beta2 toxins to explain the hemorrhagic lesions observed in this assay (Manteca et al., 2000). The present work, begun in 2000, is the continuation of this study. The global goal was to determine wether the CPB2 toxin was associated, or not, with the cattle enterotoxaemia observed in field conditions. Prior to realizing a case/ control study, we had to produce and purify a CPB2 toxin from cattle strains and we had to have specific tools able to detect the cpb2 gene and the corresponding toxin. The whole work was organized in 6 studies. The 3 first studies served to create new and adapted tools to detect the cpb2 gene and the corresponding CPB2 toxin from cattle C. perfringens strains. The 3 last studies investigated the prevalence of cpb2 gene and ability of the cattle strains to produce CPB2 toxin in vitro in conventional and veal calves farms. [less ▲]

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See detailFunctional characterization of Arabidopsis HMA4 P-type ATPases
Lekeux, Gilles ULiege

Doctoral thesis (2018)

Transition metals play a vital role in the development and survival of photosynthetic organisms. Therefore, plants require a metal homeostasis network to control their inner metal concentration despite ... [more ▼]

Transition metals play a vital role in the development and survival of photosynthetic organisms. Therefore, plants require a metal homeostasis network to control their inner metal concentration despite variation in metal supply. The HMA4 membrane protein has a central role in the zinc homeostasis network of the model plant Arabidopsis thaliana. This PIB-2 ATPase loads zinc (and cadmium) from the pericycle cells into the xylem in roots. It is involved in zinc hyperaccumulation as well as zinc and cadmium hypertolerance in the pseudometallophyte Arabidopsis halleri. In particular, the enhanced expression of HMA4 in A. halleri compared to A. thaliana triggers a higher translocation of metal from root to shoot. As a PIB ATPase, the HMA4 architecture consists of a transmembrane domain, two cytoplasmic catalytic domains, the actuator domain and the ATP-binding domain divided in a nucleotide-binding domain and a phosphorylation domain, as well as N- and C-terminal cytosolic extensions. Thanks to high conservation level within the P-type ATPases, the role of the HMA4 cytoplasmic catalytic domains can be inferred from well characterized pumps of the family. In contrast, the function of its terminal cytosolic extensions as well as the metal permeation mechanism through the membrane remains elusive. A combined in vivo and in vitro functional characterization pointed out the importance of high affinity Zn2+ binding to the HMA4 N- terminal extension C27CxxE31 motif and the C-terminal extension di-Cys motifs for the function of the protein in plants. This study also suggested the presence in the C-terminal extension of a signal for the HMA4 localization in the plasma membrane. Finally, the high divergence of coding sequence between the A. thaliana and A. halleri HMA4 C-terminal extensions does not result in major functional differences between the two proteins, at least when expressed in A. thaliana. Moreover, a structural analysis by homology modeling of the HMA4 transmembrane region highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. The analysis newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, the comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. Altogether this work significantly advanced our understanding of the function of HMA4, a key protein of the zinc homeostasis network in plants. [less ▲]

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See detailSorbs1 is specifically involved in venous and lymphatic vascular development through the regulation of endothelial cells properties
Bacquelaine Veloso, Alexandra ULiege

Doctoral thesis (2018)

A large number of studies have shown that the Sorbs1 adaptor protein, as well as the other members of the SoHo family, are involved in the regulation of cytoskeletal dynamics. Consequently, these members ... [more ▼]

A large number of studies have shown that the Sorbs1 adaptor protein, as well as the other members of the SoHo family, are involved in the regulation of cytoskeletal dynamics. Consequently, these members participate in numerous cytoskeleton-dependent cellular processes, such as cellular migration and adhesion. However, the biological processes in which SoHo proteins perform their cytoskeleton regulatory functions remain unknown. The aim of this study was to uncover the potential role of Sorbs1 in vascular development, a biological process that is highly dependent on endothelial cell cytoskeleton morphogenesis. To this end, we used CRISPR/Cas9- and morpholino-based inactivation of Sorbs1 in the zebrafish model. Both approaches demonstrate that Sorbs1 is required for secondary sprouting and subsequent formation of venous angiogenic and lymphangiogenic structures that specifically derive from the cardinal vein. However, Sorbs1 depletion does not affect arterial angiogenesis development. Mechanistically, we show that Sorbs1 controls endothelial cell properties such as migration and adhesion by regulating the activity of RhoA, a member of the RhoGTPase family. Surprisingly, the knock-down of another member of the SoHo family, Sorbs2, has no significant impact on venous or lymphatic angiogenesis. In contrast to Sorbs1, Sorbs2 is specifically required for endothelial cell migration from the dorsal aorta and for proper intersegmental vessel development. Altogether, we were able to identify for the first time a developmental function of Sorbs1 in venous and lymphatic angiogenesis. [less ▲]

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See detailGermline mutations in Bos taurus
Harland, Chad ULiege

Doctoral thesis (2018)

De novo mutation (dnm) in the germline is a fundamental biological process that is the source of all population genetic variation. In this thesis, we have exploited the unique population structure of ... [more ▼]

De novo mutation (dnm) in the germline is a fundamental biological process that is the source of all population genetic variation. In this thesis, we have exploited the unique population structure of cattle to select pedigrees of three (parents, proband and >1 grand-offspring) and four (plus grandparents) generations to identify and characterise germline dnm. We have also looked at the impact of recent dnms on the genetic load of the cattle population, using forward and reverse genetics to identify the causative mutations responsible for major defects in cattle populations including embryonic lethality. In the first study, we utilised five pedigrees to identify SNP and small insertion-deletion (INDEL) dnms, assign them to a parent of origin and determine the stage of development at which they occurred. We determined the dnm rate in cattle to be ~1.2x10-8 per base pair per generation, with 2.5 paternal dnms for each maternal dnm. We showed that 30% and 50% of the dnms in sperm and eggs respectively are mosaic in the parental DNA, occurring early in embryonic development. By simulation we show that this is incompatible with a constant mutation rate through gametogenesis and best fits a 20x higher mutation rate for the first four cell divisions of the fertilised egg. This paper is currently in review with a preprint available on BioRxiv (Harland et al. 2017a). In a second study, we looked at the rate of dnm in the wider population and for the presence of inter- individual variation in the rate. We utilised the complete Damona dataset of 131 three generation pedigrees identifying ~7,500 dnms, confirming the previously observed degree of mosaicism and our dnm rate of 1.2x10-8 per bp per generation in a wider sample. We observe several outliers in the population, with 5-17x the average number of dnms occurring during embryo development, along with distinct mutational signatures. For one outlier pedigree, we identified two candidate causative mutations that are in the process of characterising. In addition, we detect a significant environmental effect from the use of reproductive technologies, such as in vitro fertilisation and maturation, on the rate of dnm during early embryo development. (Harland et al. 2017b, in preparation). In the third study, we turned our attention to alternative forms of dnm. Utilising the full dataset, we identified five cases of de novo transposition of an endogenous retrovirus family K (ERVK) element, with three of the five events occurring within the germ-line of a single individual, and two of the three in the same gamete. This indicates that the ERVK family is presently active in the bovine genome with an average de novo transposition rate of ~1 event per 50 gametes, but there is strong evidence for considerable inter-individual variation. We identified ~1,600 polymorphic ERVs resulting from the activity of these elements in the cattle population. One recent de novo transposition of an ERVK element in the APOB gene is responsible for the lethal monogenic Cholesterol Deficiency disorder in cattle. This transposition has reached a minor allele frequency (MAF) of 2.8% in the European population (Harland et al. 2017c, in preperation). In a fourth study, we describe a dominant deleterious missense dnm in the Prolactin gene (PRL) that caused heat stress, abnormal hair growth and a failure to milk in ~2,000 affected offspring of a single bull. This set of phenotypes is opposite to those observed in ‘slick’ cattle, which show increased heat tolerance, short hair and potentially increased milk production. We demonstrate that the slick phenotype in Senepol cattle is due to a dominant frameshift mutation in the Prolactin receptor gene, and is an example of a beneficial variant that has undergone positive selection within a population (Littlejohn et al. 2014). The large number of affected cattle for the PRL mutation demonstrates how a rare dnm can rapidly increase in frequency within a population when it is present in an elite sire used for artificial insemination. For examples of other recent dnms, we turned to the Belgian Blue population and investigated recessive junctional epidermolysis bullosa. This lead to the identification of a breed specific, premature stop-gain mutation in the laminin, alpha 3 gene with a MAF of 1%, thus allowing the development of a direct genetic test for the disorder (Sartelet & Harland et al. 2015). We then used whole genome sequences (WGS) obtained on Illumina HiSeq’s to search for embryonic lethal (EL) mutations segregating in the New Zealand dairy and Belgian Blue beef cattle populations using a reverse genetic approach. We genotyped >40,000 cattle for 296 loss of function (LOF) and 3,483 potentially deleterious missense variants that were breed specific, and identified variants with a significant deficiency in homozygous mutant animals. Nine of these variants were confirmed to be EL by genotyping 200 carrier x carrier trios and demonstrating the absence of homozygous offspring. The MAF of these variants was between 1.2% and 6.6%. We estimate that 15% of the tested LOF and 6% of the missense events are EL reducing the fertility of dairy cattle (Charlier et al. 2016). [less ▲]

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See detailThe contract farming as a determinant promoting tea production and marketing at farm household in Vietnam: a case study in Phu Tho province
Le Thi Kim, Oanh ULiege

Doctoral thesis (2018)

Tea contributes substantially to Vietnam’s annual exports, helps creating job opportunities and raises farmer’s income. However, tea farmers face many difficulties and are highly vulnerable due to their ... [more ▼]

Tea contributes substantially to Vietnam’s annual exports, helps creating job opportunities and raises farmer’s income. However, tea farmers face many difficulties and are highly vulnerable due to their scattered tea areas, poor farm management, weak disease control, and unstable market. Numerous studies proved that contract farming brings many opportunities for farmers such as access to credit and inputs, together with access to a reliable market. Nevertheless, until now, there has not been any thorough research on the benefits of contract farmers on tea production in in Phu Tho province. This thesis, therefore, aims to analyze efficiency of tea contract farming in Phu Tho and identify if contract farming improves farmers’ income. The study conducted in three different groups of full, semi and non-contract farmers. The results show that: 1) The more full contract farmers produce, the higher income they get, even though their selling price might be lower than the other groups; 2) Tea price of full contract farmers was the lowest, while that of non-contract farmers was the highest; 3) Average land area of full contract model was the highest in the three studied groups and owned by the processing plant whereas semi and non-contract farmers are self-ownership. Land was provided to full contract farmers with special conditions that semi and non-contract model found it is likely unable for them to engage; 4) Full contract farmers’ tea yield was the highest in three farmer groups thanks to the high quality of input materials; 5) Contract farmers were generally satisfied with tea production inputs and tea marketing activities; 6) Contract farming helped promoting black tea value chain in Phu Tho province. Nevertheless, contract farmers still face various disadvantages such as low prices, requirements for high-quality, and obliged relationship with the companies. In addition, it appears various factors affecting tea contract farming in Phu Tho province. Based on the above findings, there are some important recommendations as follows: firstly, the terms in the contract should be improved; secondly, the role of local governments should be enhanced; thirdly, the government should implement different measures to promote tea contract farming; fourthly, the success of full contract farming model should also be promoted more widely; and fifthly, semi contract farming model should be improved and promoted. [less ▲]

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See detailUnraveling the mechanisms behind the packaging of RNA into exosomes
Pérez Boza, Jennifer ULiege

Doctoral thesis (2018)

Exosomes are small extracellular vesicles of endosomal origin of about 100nm of diameter. They are used by the cells to transfer information and can contain a wide range of biomolecules. Among many others ... [more ▼]

Exosomes are small extracellular vesicles of endosomal origin of about 100nm of diameter. They are used by the cells to transfer information and can contain a wide range of biomolecules. Among many others, exosomes carry coding and non-coding RNAs. The aim of this study is to unravel the mechanisms behind the exosomal encapsulation of these biomolecules. For that purpose, we have approached this question from three different points of view. First, we studied the differences between cellular and exosomal RNA in order to determine if the class, sequence and function of the RNA molecules determine their encapsulation. Then, we assessed if two RNA binding proteins (Ago2 and GW182), often localized in the site of exosome formation, regulate the loading and export of microRNAs. Finally, we investigated how the chemotherapeutic drug Epirubicin initiates a response in the cell that leads to the exosomal over export of miR-503. In the first part of this study, we have characterized the RNA content of cellular and exosomal RNA on human endothelial cells in depth. Unlike many other profiling studies already published, we have used healthy primary cells to show the basal composition of RNA sub-classes and to find the motifs significantly more present in cells or in exosomes basally. Regarding coding genes, we have shown that mRNA genes can be classified into four different groups depending on the relative export of their regions. Moreover, we proved that RNA duos derived from the same locus and microRNA-mRNA target pairs are found at almost the same ratio in both cells and exosomes. Finally, we have also proven that, even though microRNAs are by far the most studied class of RNAs in exosomes, they represent a very small amount of the total RNA content of these vesicles thus setting the basis to promote a switch in exosomal RNA research towards longer RNAs. In the second part of this thesis, we have been able to conclude that neither AGO2 nor GW182 are involved in general processes of microRNA export based on motif recognition. Finally, in the third and last part, we have identified a new mechanism regulating microRNA export. Under basal conditions, both ANXA2 and hnRNPA2B1 bind to miR-503 in a stable partnership. Epirubicin mediates the export of miR-503 by inducing the separation of hnRNPA2B1 from the complex. In a parallel mechanism, the chemotherapeutic drug induces a reduction in the expression of hnRNPA2B1 that acts as a backup of the main complex-destabilization leading to miR-503 exosomal export. [less ▲]

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See detailAnalyse des risques liés à l’emploi des pesticides et mesure de la performance de la lutte intégrée en culture de tomate au Burkina Faso
Son, Diakalia ULiege

Doctoral thesis (2018)

In Burkina, tomato (Solanum lycopersicum L.) cultivation plays a very important socio-economic role. However, its production faced many constraints, like insect pests attacks wich can induce crop losses ... [more ▼]

In Burkina, tomato (Solanum lycopersicum L.) cultivation plays a very important socio-economic role. However, its production faced many constraints, like insect pests attacks wich can induce crop losses ranging from 50 to 100%. The inventory of the entomofauna carried out in 2015, 2016 and 2017 in the communes of Kouka, Faramana, Ouahigouya and Bobo-Dioulasso, by using yellow water traps, has shown that the main pest families of tomato in Burkina Faso are Aleyrodidae, Aphididae, Acrididae, Agromyzidae, Arctiidae, Gelechiidae, Noctuidae and Tephritidae. Useful insects from Coccinellidae, Reduviidae, Ichneumonidae, Sphecidae and Pompilidae families have also been identified. To combat these pests, producers mainly used chemical control, while surveys carried out in 2015 and 2016 among 316 tomato producers in order to characterize farmers' agricultural and phytosanitary practices, showed a high illiteracy rate (70%) and a low training level of producers (9%). Ninety percent of pesticides used by tomato producers are purchased in local markets without guarantee of conformity or quality and 71% of them are formulated for cotton crop. Lambda-cyhalothrin was the most used active substance. The doses used by producers were higher than those recommended and more than 70% of market gardeners do not observe any measure of adequate protection during pesticides use. Deadlines without preharvest treatment are not respected and empty containers of pesticides are left in fields after treatments. The frequency treatment indicator (FTI) showed a high dependence of producers to pesticides whereas the evaluation of predictive exposure with the predictive operator exposure model (UK POEM), showed a high exposure of producers to pesticides, with predictive exposure levels ranging from 0.0105 mg / kg bw / day to 1.7855 mg / kg bw / day, several times higher than the acceptable operator exposure level (AOEL). The study also showed that exposure could be greatly reduced if the required personal protective equipment (PPE) is worn. Samples of tomato fruits, water and soil collected from producers in Kouka and Bobo-Dioulasso and analyzed by PRIMORIS laboratory (Belgium) showed a contamination of tomatoes and soils with pesticide residues. The most active substances found were lambda-cyhalothrin, profenofos and chlorpyrifos-ethyl. Only chlorpyrifos-ethyl showed a residue level above its maximum residue limit (MRL) in tomatoes (360% of MRL), without acute intoxication risk for consumers according to the calculations of the Predictable Short Term Intake (PSTI). However, continuous consumption of fruits with high pesticide residue concentrations could lead to adverse effects on human health, as once ingested, chlorpyrifos passes rapidly from intestines to bloodstream where it is distributed to the rest of the body. To reduce chemical pesticides use in tomato production, the effectiveness of three biopesticides (BIO K 16, H-N and PiOL) was assess in 2015-2016 in the commune of Kouka.This study showed that a good combination of chemical pesticides with biopesticides provides best fruit protection and highest yields compared to conventional chemical control. The combination Bacillus thuringiensis-abamectin has provided both the best fruit protection and the highest tomato yield (2 kg/m²). In order to mitigate the problem of producer exposure to pesticides, IPM trials based on tomato crop in association with aromantic plants (basil, garlic, onion) were compared to the usual practices of producers, in the commune of Bobo-Dioulasso. All IPM practices yielded the best results in terms of crop protection and yields with low use of nitrogen fertilizers and plant protection products compared to producers practices. The tomato-onion association provided the best fruit yield (3 kg / m²) compared to peasant and other IPM practices. Awareness-raising and producers training measures on better agricultural and phytosanitary practices and implementation of IPM methods are necessary to prevent producer, or consumers’ exposure to pesticides and damage to the environment in Burkina Faso. [less ▲]

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See detailApplication des progestagènes à la gestion hormonale de la reproduction chez la femelle bovine de la race N'Dama au Gabon
Okouyi M’foumou W’otari, Marcel ULiege

Doctoral thesis (2018)

Three experiments were conducted between 2013 and 2015 in the Nyanga ranch (Gabon) to gain up-to-date, more comprehensive knowledge about the breed and more details about the effects of using progestogens ... [more ▼]

Three experiments were conducted between 2013 and 2015 in the Nyanga ranch (Gabon) to gain up-to-date, more comprehensive knowledge about the breed and more details about the effects of using progestogens on the oestrus, follicular growth, ovulation and gestation rates in this female. At the start of the study, their genital tracts and ovaries were palpated and an initial vaginoscopy was carried out when the progesterone-based hormone treatments were vaginally administered in the form of a CIDR®. The presence of a corpus luteum was checked at this point by ultrasound examination. The basic protocol was: CIDR-PGF2α-eCG administered over nine days. A PGF2α was administered by intramuscular injection (IM) to each animal two days before the CIDR® was removed. On the day the device was removed, equine Chorionic Gonadotropin (eCG) was administered by IM and a second vaginoscopy was carried out to determine the animals’ degree of tolerance to the CIDR. To assess the effects of the eCG on the sexual behaviour and ovulation of the female N’Dama, the animals were split into five experimental batches; a control batch, (0UI of eCG, n=26) and four batches which received increasing doses of eCG when the CIDR was removed; batch 1 (300 UI, n=25), 2 (400 UI, n=24), 3 (500 UI, n=23) and 4 (600 UI, n = 23). From the day the CIDR® was removed, referred to as D0, the animals were permanently visually observed (24h/24) for seven days. The number of ovulations was determined by the number of corpus lutea observed on the ovaries when the animal was slaughtered between D7 and D10 after the end of treatment. To assess the diameter of the preovulatory follicle and the time of ovulation, an ultrasound examination of each ovary was conducted to identify and measure the diameter of the follicles on the day the CIDR® was removed (D0) and 2, 3, 4 and 5 days later. The animals were slaughtered between 7 and 10 days following removal of the CIDR®. To assess the effects of the time of insemination and administration of GnRH during the AI on gestation rates of female N’Dama, the animals were split into two groups, labelled G1 and G2 (nG1 = nG2 = 84) which were inseminated 48 hours and 72 hours, respectively, after removal of the CIDR®. During insemination, half of the animals (GnRH +) in each group were treated with 4.2 µg buserelin acetate. The other half were untreated and represented the control group (GnRH-), receiving 1ml of physiological serum. A pregnancy diagnosis was carried out by manual palpation and ultrasound 45 days after insemination. The statistical analysis of the data was conducted using the SAS version 9.1 software. The data were processed using a general linear model (GLM) and by logistical regression, and the results were expressed as a LSMEAN ± ES. The female N’Dama tolerated the CIDR® device relatively well. The average onset of oestrus after the end of treatment was 48,6 ± 5,3 hours, which is within the 48 to 72-hour interval indicated in the marketing authorisation for the product. Oestrus lasted on average 9.9 ± 2 hours, in keeping with the literature. These two parameters were not affected by the administration of eCG at the end of treatment. The percentage of silent oestrus (28.4 %) and anovulatory oestrus (4.5%) demonstrate that it would be advisable to take other signs into account to confirm oestrus in the female N’Dama. In line with the literature, the use of eCG reduces the percentage of silent oestrus or oestrus which is not followed by ovulation. The administration of eCG at the end of progesterone-based treatment (CIDR-PG) influences the follicular and ovulation characteristics of the female N’Dama. The follicle growth rate (FGR) varied from 0.9 ± 0.4 mm / day in untreated animals and 1.0 ± 0.4mm/day in animals which received eCG. The diameter of the preovulatory follicle was between 5.8 and 12.2 mm. The average ovulation rate (90.2 %) and multiple ovulation rate (18.3 %) increased as the dose of eCG increased. After the end of treatment, ovulation occurred on average 83.7 ± 14.4 hours later. Administration of eCG at the end of treatment contributed to further synchronising the time of ovulation within the 72 to 96-hour period, i.e., which would point towards routinely implementing a single, 72-hour insemination. The gestation rate of 48.8 % obtained on the first AI carried out 78 hours after the end of treatment was satisfactory. In this case, the administration of GnRH at the time of AI did not influence the gestation rate. During oestrus caused by progestogens, the female N’Dama presents oestrus, ovulation and gestation rates which are not significantly different to those observed in other Bos taurus. [less ▲]

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See detailEtude des propriétés physicochimiques des matières grasses d’Irvingia gabonensis et de Dacryodes edulis en vue de leur intégration dans des formulations alimentaires
Yamoneka Wasso, Juste ULiege

Doctoral thesis (2018)

Irvingia gabonensis seed and Dacryodes edulis pulp contain significant proportions of fats, used in central and west Africa in several food formulations. In order to promote their valorization at an ... [more ▼]

Irvingia gabonensis seed and Dacryodes edulis pulp contain significant proportions of fats, used in central and west Africa in several food formulations. In order to promote their valorization at an industrial scale, their physicochemical properties were evaluated. The results showed that I. gabonensis seed fat (IGF) is a lauric fat, solid at room temperature stable in β 'form. This fat could be used in several oil blends as base stock with many applications. D. edulis pulp oil (DPO) is a liquid oil with many potential uses as cooking oil or liquid oil in industrial blends oils. The high solid fat content of IGF at 37°C, and its complete melting around 40°C is the limiting factor for its direct valorization in several food formulations. In order to overcome this constraint, it was blended with DPO and other three liquid oils. The binary blends containing 20%, 30% of IGF and 80%, 70% of rapeseed and groundnut oils showed similar hardness and SFC with fats extracted from commercial margarine. The interesterified blend containing 90% of IGF and 10% of DPO showed a melting behavior similar to that of cocoa butter. This suggested the blend could be used as cocoa butter substitute in confectionary industry. The valorization of these two oils in food industry could promote the organization of their sectors for a better contribution to the local economy [less ▲]

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See detailInfluence of combined environmental constraints on photochemical capacity and CO2 fluxes in a temperate managed grassland.
Digrado, Anthony ULiege

Doctoral thesis (2018)

Increase in agricultural production to insure food security and energy demand by 2050 might result in higher greenhouse gas emissions (GHG) from the agricultural sector. Managed grasslands, however, offer ... [more ▼]

Increase in agricultural production to insure food security and energy demand by 2050 might result in higher greenhouse gas emissions (GHG) from the agricultural sector. Managed grasslands, however, offer the opportunity to offset some of the GHG emission through the storage of carbon in terrestrial systems by photosynthesis. Photosynthesis, however, is highly sensitive to environmental conditions. Especially, plant ability to harvest and use light energy for photochemistry can be impaired by abiotic stresses. While numerous studies have focused on the impact of environmental constraints on ecosystem carbon fluxes, the influence on ecosystem photochemical capacity is understudied. The main goals of this thesis was to evaluate how environmental constraints impacted the grassland photochemical capacity and how variations in processes involved in light reactions of photosynthesis influenced ecosystem carbon fluxes. Frequent chlorophyll fluorescence measurements were conducted over a two-year period, on three grassland species (Lolium perenne L., Taraxacum sp., and Trifolium repens L.). The ecosystem photochemical capacity was estimated from measurements performed on the three grassland species. In addition, monitoring CO2 fluxes was performed by eddy covariance. Our results showed that photochemical capacity of the primary grasslands species exhibited diurnal and seasonal variations. The monocot L. perenne and the dicots (Taraxacum and T. repens) exhibited different acclimation strategies. All species exhibited the onset of energy dissipation mechanisms within the photosystem II but expressed contrasted response in the photosystem I efficiency. As a result, the ecosystem also exhibited variations in its ability to harvest and use photon energy. The strongest declines in photochemical capacity were observed in summer when abiotic stresses such as high light and high air temperature were combined. However, decrease in photochemical capacity did not result in a decreased ability to fix carbon in the grassland. The maintenance of carbon assimilation despite the onset of energy dissipation mechanisms can be explained by the higher availability of light energy under these conditions. In the final section of this PhD thesis, we discuss how future experiments can improve our knowledge in plants functional ecology and in the relationship between the photochemical capacity and ecosystem carbon fluxes. We also discuss how these results can benefit GHG mitigation strategies and how plants influence GHG balance through other routes than photosynthesis. [less ▲]

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See detailEffets des gènes FLOWERING LOCUS T (FT) et TWIN SISTER OF FT (TSF) sur le développement racinaire d’Arabidopsis thaliana
Mathieu, Laura ULiege

Doctoral thesis (2018)

Flowering is a critical step in plant development. It is induced by various signals produced in response to environmental and endogenous cues, such as photoperiod, temperature or plant age. A master ... [more ▼]

Flowering is a critical step in plant development. It is induced by various signals produced in response to environmental and endogenous cues, such as photoperiod, temperature or plant age. A master flowering signal is the FLOWERING LOCUS T (FT) protein, which is produced in the leaves and transported through the phloem toward the shoot apical meristem, where it triggers the morphogenesis switch. The biological question examined in this thesis is whether the systemic effect of FT encompasses the roots, coordinating their growth with the aerial part. We used the model species Arabidopsis thaliana (L.) Heynh., where FT shares its function with a paralog, TWIN SISTER OF FT (TSF). In the first part of our work, we designed a hydroponic rhizotron device suitable for growing adult plants of Arabidopsis: Rhizoponics. Using this setup, we observed that a photoperiodic treatment that induces flowering of Col-0 wild type plants also promotes development of the root system. However, this increase also occurs in ft-10 tsf-1 double mutant, thus independently of FT and TSF proteins. In the second part of our work, we analyzed the organization and maintenance of the root apical meristem, and the branching of primary root. Experiments were performed with ft-10 tsf-1 and 35S:FT seedlings grown in vitro, using several reporter genes to study auxin signaling and transport. We observed a higher number of distal stem cell layers in primary root columella of the ft-10 tsf-1 mutant and an increased branching of the primary root in the 35S:FT line. These results suggest that FT/TSF promote cell differentiation at root tip and priming of lateral roots, two processes that are regulated by auxin. We confirmed, using pDR5:GUS and pDR5:GFP reporter genes, that FT/TSF interfere with auxin homeostasis at the primary root tip. The most intriguing result is the absence of the auxin efflux carrier PIN3 in the columella of the primary root in the ft- 10 tsf-1 mutant. This phenotype could not be explained neither by transcriptional repression of PIN3 nor by protein endocytosis. We analyzed different processes where PIN3 modulates auxin flux to induce tissue differential growth, such as gravitropism, phototropism and apical hook development. We observed that the responses of the 35S:FT seedlings were slightly accentuated compared to Col-0, suggesting PIN3 activation by FT.All together, our results indicate that the systemic proteins FT/TSF have an effect on auxin signaling in root tip and could stimulate root branching at floral transition. [less ▲]

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See detailPREBIOTIC POTENTIAL OF NOVEL NON-DIGESTIBLE CARBOHYDRATES FOR PREVENTION AND CONTROL OF SALMONELLA TYPHIMURIUM IN PIGS
Tran, Thi Hanh Tham ULiege

Doctoral thesis (2018)

Foodborne diseases have drawn increasing attention around the world. Salmonelloses are the second most common zoonosis in humans after campylobacteriosis in the European Union (EU). Pig, after poultry, is ... [more ▼]

Foodborne diseases have drawn increasing attention around the world. Salmonelloses are the second most common zoonosis in humans after campylobacteriosis in the European Union (EU). Pig, after poultry, is the second most important domestic animal species associated the outbreaks of salmonellosis in humans. In addition, pig production is the most important among the principal domestic animal species in the world. A supply of the consummers’ market with Salmonella-free pig meat would be important to animal production, as well as to human food safety. The control of this pathogen in pigsties by prebiotics is an approach that deserves consideration. A wide range of molecules including non-digestible carbohydrates have attracted increasing interest to prevent the harmful effects of pathogens such as Salmonella enterica. The aim of this research thesis is to assess the in vitro and in vivo potential of some novel carbohydrates to reduce Salmonella Typhimurium infections in weaned piglets. Firstly, an in vitro batch fermentation system was improved by including mucus. This study investigated whether the survival of a wider number of intestinal bacterial populations is impacted by the presence of mucus and whether this dependence on mucus is influenced by the fermented ingredient. The introduction of mucins affected many microbial genera and fermentation patterns. Mucins increased final gas production with inulin and shifted short-chain fatty acid molar ratios. Lactobacillus spp. and Bifidobacterium spp. were decreased with mucins. In contrast, Proteobacteria, Verrucomicrobia, Ruminococcaceae, Bacteroidaceae (including Bacteroides spp.), and Akkermansia spp. were increased. In addition, Proteobacteria and Lachnospiraceae were promoted in the mucus compared with the broth, while Ruminococcaceae decreased. However, this impact of mucus on microbial genera and fermentation patterns was independent of the fermentation substrate. The improved in vitro fermentation model of the pig intestines was used to assess prebiotic potential of novel non-digestible carbohydrates (NDCs) and their influence on Salmonella Typhimurium. Inulin, cellobiose, pectic- (POS), isomalto- (IMO), xylo-(XOS) oligosaccharides, and gluconic acid (GLU) were fermented for 72 h. None of the tested NDCs did inhibit Salmonella Typhimurium counts compared to control. However, inulin and IMO displayed prebiotical properties, since they supported the highest Lactobacillus and Bifidobacterium populations after 12 and 24 h of fermentation. Cellobiose and GLU also promoted Lactobacillus populations, but not Bifidobacteria. Looking at the fermentation patterns, GLU was weakly fermented but was the fastest fermenting NDC with the highest butyrate molar ratio. POS was slowly fermented, while XOS was poorly fermented. Cellobiose yielded the highest lactate molar ratio. Finally, based on the results from the second in vitro trial and data obtained on mice, two promising prebiotics, IMO and POS were chosen to evaluate their prebiotical properties in an in vivo Salmonella Typhimurium challenge using a Trojan piglet model. IMO could be potential a prebiotic to improve performance, strengthen serum immune system, and decrease the Salmonella prevalence in piglets. POS did not present these properties. It is concluded that although all tested NDCs did not reduce Salmonella Typhimurium growth, IMO seems the most promising prebiotic in terms of fermentation patterns, host responses, transmission and colonization of Salmonella in piglets. Cellobiose and GLU were only tested in in vitro system, but owing to their specific fermentation patterns, they deserve some attention and could also be assessed in vivo to confirm their action on pathogens. [less ▲]

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See detailSingle-cell approaches for the characterization of microbial population dynamics in bioprocesses
Baert, Jonathan ULiege

Doctoral thesis (2018)

Some evidences show that a clonal population of microbial cells exhibits variation at their physiological level. For this reason, several methods that allow cellular characterization with a single-cell ... [more ▼]

Some evidences show that a clonal population of microbial cells exhibits variation at their physiological level. For this reason, several methods that allow cellular characterization with a single-cell resolution have been strongly developed this last decade. For instance, flow cytometry is a reliable analytic method to study the complex distribution of physiologies occurring among microbial populations. This so called “phenotypic heterogeneity” has been extensively discussed in the scientific literature and remains a hot topic for biotechnology development suggesting that clonal cells have not the same ability to synthesize a product of interest during bioprocesses course. However, phenotypic heterogeneity patterns are not commonly interpreted in term of biological performances. Therefore, the current main challenges in single-cell techniques lies in an accurate understanding of the sources of biological inefficiency through a relevant interpretation of the phenotypic heterogeneity occurring in microbial populations. For this purpose, this work investigates the potentialities of both genetically encoded and exogenous biosensors to support the implementations of innovative optimization strategies considering biological traits of cell factories. Moreover, correlation between cell population heterogeneity and bioreactor heterogeneity has also been addressed by studying the response of biosensors under intensive culture conditions that occurs in industrial bioreactors. Thus, thanks to a deep analysis of biosensor signals, this work point out the added value brought by the single-cell concepts and make possible a better understanding of microbial physiology in bioprocesses conditions. Additionally, in parallel with an extended experimental strategy, this work proposed an original formalism in order to valorize the different component of single-cell technology and to facilitate its transfer towards industrial applications. Finally, beside challenges in link with biosensors signals interpretation, flow cytometry analysis leads to the high-throughput characterization of cell suspension and then, provides thousands of data. This high information diversity compels to cope with strong data management challenges. Actually, the question is: “How structure and treat single-cell data to improve their interpretations accuracy? In this frame, this study demonstrates the potential of single-cell distribution statistical treatment to rationally discriminate cellular samples which present different biological traits. In that way, we shown experimentally that the higher performant biological system can also be the more heterogeneous which is in opposite to the paradigm stating that only homogenous population are attractive for bioprocess applications. In a nutshell, this work set up the basis to study the relation between phenotypic heterogeneity and biological performance through the discussion of serval fundamental and applied concepts. That supports the proposal of rational optimization strategies while considering biological inputs and ensuring the valorization of single-cell concept as a response to current major industrial challenges. [less ▲]

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See detailBioefficacité d'Ocimum spp. (Lamiaceae) pour une gestion intégrée des ravageurs en cultures maraîchères.
Yarou, Boni ULiege

Doctoral thesis (2018)

Les pesticides de synthèse utilisés pour lutter contre les ravageurs des cultures maraîchères en Afrique de l’Ouest demeurent un problème compte tenu de leur nocivité sur l’homme et l’environnement, en ... [more ▼]

Les pesticides de synthèse utilisés pour lutter contre les ravageurs des cultures maraîchères en Afrique de l’Ouest demeurent un problème compte tenu de leur nocivité sur l’homme et l’environnement, en plus de la sélection de populations résistantes chez ces ravageurs. Cependant, la flore ouest-africaine regorge de nombreuses plantes aux potentiels biocides qui pourraient constituer une alternative à l’utilisation de ces pesticides de synthèse. Cette thèse s’inscrit dans une politique de valorisation de légumes traditionnels du genre Ocimum dans la gestion des ravageurs des cultures maraîchères. Ainsi, l’effet des espèces Ocimum gratissimum L. et O. basilicum L. (Lamiaceae) sur le comportement de pucerons et de Lépidoptères a été évalué à partir des huiles essentielles – utilisées sous forme de diffuseurs – et des plantes entières utilisées comme plantes associées. Dans un premier temps, un inventaire de l’entomofaune associée au basilic tropical (O. gratissimum) réalisé dans les conditions du Sud-Bénin a permis de mettre en évidence la présence de 52 familles d’insectes. Les plus abondantes par ordre décroissant du nombre d’individus par famille sont les Formicidae, les Coccinellidae, les Acrididae, les Lygaeidae, les Pentatomidae, les Chrysomelidae, les Megachilidae et les Halictidae. Au sein de ces familles, figurent aussi bien des ennemis naturels (Coccinellidae, Syrphidae, Braconidae) que des pollinisateurs (Megachilidae, Halictidae) et des ravageurs (Pentatomidae, Acrididae). Ensuite, l’effet biocide d’O. gratissimum et O. basilicum a été étudiée. Au laboratoire, les huiles essentielles et les plants d’Ocimum disposés à proximité des plants de tomate (Solanum lycopersicum L.) réduisent significativement l’activité de ponte de Tuta absoluta Meyrick. Aussi, les huiles essentielles peuvent réduire le potentiel reproducteur des pucerons, tandis que dans un système d’association culturale, les plants d’Ocimum induisent une activité répulsive sur les pucerons et peuvent aussi impacter la reproduction de ces pucerons. Au champ, seul l’effet du basilic tropical a été testé sur les trois principaux ravageurs du chou (Brassica oleracea L.) – Hellula undalis Fabricius, Plutella xylostella L., Spodoptera littoralis Boisduval. Cette association basilic tropical-chou permet non seulement de réduire l’abondance de ces ravageurs, mais aussi l’importance des dégâts sur les parcelles associées. Le potentiel biocide de ces légumes traditionnels sur les ravageurs des cultures maraîchères et l’importance de l’entomofaune utile associée à ces plantes, peuvent dès lors présenter un moyen de gestion intégrée des ravageurs en cultures maraîchères afin d’améliorer la qualité sanitaire des produits et la santé des populations. [less ▲]

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See detailEtude du potentiel des enzymes de Cynara cardunculus L. en technologie fromagère
Ben Amira, Amal ULiege

Doctoral thesis (2018)

L’objectif des travaux entrepris au cours de cette thèse visait à identifier, extraire et caractériser les enzymes coagulants des fleurs de Cynara cardunculus L., en vue de les valoriser dans la ... [more ▼]

L’objectif des travaux entrepris au cours de cette thèse visait à identifier, extraire et caractériser les enzymes coagulants des fleurs de Cynara cardunculus L., en vue de les valoriser dans la technologie des produits laitiers. Dans une première étape, deux lots de fleurs, collectés à deux stades de maturation, ont été comparés d’un point de vue biochimique et enzymatique, afin de sélectionner le lot approprié pour une meilleure production d’enzymes coagulants. Les fleurs collectées au milieu du stade de maturation (fin du mois de juin) ont alors été sélectionnées pour la suite des travaux. Les critères de sélection étaient basés sur la composition chimique des fleurs, les activités enzymatiques des extraits coagulants, ainsi que sur les propriétés texturales des caillés produits. Dans une deuxième étape, le contenu enzymatique des fleurs a été identifié par une approche protéomique. L’étude a révélé la présence de 4 cardosines (A, E, G et H), dont la cardosine A qui a une spécificité d’action similaire à celle de la chymosine. L’absence des autres cardosines (B, C, D et F) constitue un avantage pour la réduction de l’activité protéolytique excessive, responsable de l’amertume et des défauts de texture des fromages. La partie suivante de la thèse a concerné l’étude de l’extraction de la présure de C. cardunculus et son application dans le processus de coagulation du lait. Cette étude était divisée en deux parties complémentaires. Dans un premier temps, nous nous sommes intéressés à évaluer l’effet du pH d’extraction sur les propriétés techno-fonctionnelles des extraits bruts des fleurs. Dans un deuxième temps, les conditions d’extraction de la présure ont été optimisées par méthodologie des surfaces de réponses, en vue de maximiser son activité coagulante. Les conditions optimales étaient alors sélectionnées. L’efficacité de l’extrait coagulant a été testée dans la coagulation de deux types de laits bovins (cru et reconstitué), en appliquant deux doses d’extrait coagulant (0,5 mg et 1 mg/10 mL de lait). Les résultats ont montré des propriétés viscoélastiques et des fermetés des gels élevées, similaires à ceux d’une chymosine commerciale. Pour terminer, l’étude des propriétés technologiques des gels était accompagnée d’une évaluation de la qualité des fromages produits, afin de confirmer l’aptitude de la présure extraite dans les conditions optimisées, à remplacer avec succès la chymosine. Cette dernière partie visait également à sélectionner une concentration en sel appropriée au cours du saumurage, pour obtenir une meilleure qualité du produit final. Par conséquent, les propriétés physico-chimiques, texturales et rhéologiques, ainsi que le niveau de protéolyse dans les fromages, saumurés à différentes concentrations en sel, ont été déterminés. Les résultats ont permis de sélectionner une concentration en sel de 15 %, pour la quelle d’excellentes propriétés ont été obtenues, en termes de rendement fromager, texture et viscoélasticité après 28 jours de stockage (4°C). En conclusion, la présente thèse a contribué par l’optimisation des conditions d’extraction, à la production d’un extrait enzymatique doté d’une activité spécifique maximale, permettant de produire d’excellentes qualités de coagulums et des fromages saumurés. Ces résultats satisfaisants pourraient offrir de nouvelles opportunités de production d’une « présure végétale » compétitive, par rapport aux enzymes animales ou microbiennes. [less ▲]

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See detailAspects of acoustic communication in Serrasalmidae
Melotte, Geoffrey ULiege

Doctoral thesis (2018)

In Teleostei, the evolution of the ability to produce sounds has provided a great diversity of sonic mechanisms, even at the intrafamilial level. However, the constraints modulating the evolution of sound ... [more ▼]

In Teleostei, the evolution of the ability to produce sounds has provided a great diversity of sonic mechanisms, even at the intrafamilial level. However, the constraints modulating the evolution of sound-producing mechanisms and hearing structures are very little supported by comparative anatomy studies and it is not determined in fish if the evolutionary constraints are related to intraspecific communication or environmental characteristics. Serrasalmidae (Characiformes) are neotropical freshwater fishes inhabiting most of the major river systems in South America. This family is currently divided into three clades: the « pacu », the « Myleus » and the « piranha » clades. The ability to produce sounds has been reported in some species belonging to the « piranha » clade, within the genera Pygocentrus and Serrasalmus. The ability to detect sounds has been reported only in Pygocentrus nattereri. This thesis aims to improve our knowledge on acoustic communication in the family Serrasalmidae. The main goal was to determine, in a phylogenetic context, whether soundproducing and -detecting apparatuses coevolved within this family. The hypothesis is that the species having developped the most complex sound-producing mechanisms also improved their ability to discriminate different types of sounds. An alternative hypothesis is that auditory ablities are more related to the biology of fishes: carnivorous species would have better hearing than herbivorous species to locate their living prey. The ability to produce and detect sounds was therefore investigated using different techniques in a large panel of serrasalmid species. The ability to produce sounds is uneven in the family Serrasalmidae. In the « pacu » clade, Piaractus brachypomus produces single low frequency pulses by contracting its hypaxial musculature. In the « Myleus » clade, several species belonging to the genera Myleus and Myloplus produced no sound, whatever the experimental conditions. In the « piranha » clade, Pygopristis denticulata and Catoprion mento produce sounds composed of a varying number of pulses. They possess a sonic muscle extending from the second rib to the first rib (P. denticulata) or to the swimbladder (C. mento). Pygocentrus spp. and Serrasalmus spp., as well as Catoprion mento, are able to utter drumming sounds (tonal vocalizations characterized by the presence of harmonics in the power spectrum) when hand-held. Sonic muscles of the genera Pygocentrus and Serrasalmus originate at the base of the second rib and attach to a tendon surrounding the swimbladder ventrally. Investigation of the auditory system morphology in various serrasalmid species showed that the hearing structures (otoliths and Weberian ossicles) are similar in overall shape and position in all the species investigated. Moreover, hearing range and hearing sensitivity are quite comparable among the species, despite differences in life-history traits (vocal vs. nonvocal and herbivorous vs. carnivorous species). Therefore, hearing capacities are not related to the ability to produce sounds or to the diet. Acoustic communication appears to be of importance within carnivorous species since the most sensitive hearing range covers the frequency spectrum of acoustic signals. However, hearing ability is not related to the capacity to emit sounds. The auditory system seems to be highly conserved within this family, suggesting that it was shaped by other constraints than acoustic communication. Sonic organs developed secondarily in the most derived species and could be related to their radiation. [less ▲]

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See detailBeech wood Fagus sylvatica hydrolysates as feedstocks for Chlorella biomass, fatty acid and pigment production
Miazek, Krystian ULiege

Doctoral thesis (2018)

This thesis evaluates the possibility of using wood hydrolysates as feedstocks for microalgae growth and production of industrially valuable compounds such as fatty acids and pigments. Moreover, the ... [more ▼]

This thesis evaluates the possibility of using wood hydrolysates as feedstocks for microalgae growth and production of industrially valuable compounds such as fatty acids and pigments. Moreover, the effect of lignocellulosic hydrolysates, organic substances typically present in lignocellulosic hydrolysates, as well as minor co-products, on growth and accumulation of target compounds in microalgae cultures is described. Firstly, beech wood dilute-acid (H2SO4) hydrolysate as a feedstock for Chlorella growth, fatty acid and pigment production, was tested. Hydrolysis of beech wood with the use of sulfuric acid produced a hydrolysate containing numerous organic compounds such as sugars, acetate, phenolics and furans. In order to elucidate the effect of wood hydrolysate on Chlorella culture, different components of hydrolysate were tested separately or in the mixture. Amongst compounds tested, glucose and acetate supported Chlorella growth, xylose, mannose, galactose, 2-F and HMF were inhibitory, arabinose and rhamnose were neutral. Results of this thesis show that beech wood acid hydrolysate after neutralization with NaOH can strongly improve Chlorella growth at lower loadings due to the presence of acetate and glucose, readily consumed in Chlorella culture. However, the same hydrolysate added at higher loadings can be inhibitory or even lethal for Chlorella. Interestingly, compounds tested separately and identified as inhibitory for Chlorella growth, seemed not to be responsible for inhibitory effect of wood hydrolysate. They are either at concentrations too low to cause inhibition (2F, HMF, mannose, galactose) or their inhibitory effect is nullified in the presence of glucose and acetate (xylose, mannose). Neutralized sulfuric acid loadings caused inhibition of Chlorella growth. It shows that inorganic compounds added for preparation of wood hydrolysate can also affect microalgae growth. However, neutralized sulfates were only partially responsible for inhibitory activity of wood hydrolysate, showing that wood hydrolysate also contains other substances responsible for growth inhibition. Nevertheless, neutralized wood hydrolysate proved to support Chlorella growth during mixotrophic and heterotrophic cultivation, on condition that wood hydrolysate loading is optimized to avoid toxic threshold. This thesis shows that neutralized wood acid hydrolysate can be used as an organic carbon feedstock for microalgae to produce fatty acids and pigments. The addition of 12% wood hydrolysate (Hyd12%) into photoautotrophic culture, improved by nearly 100% fatty acid productivity in comparison to control. Moreover, pigment content in Chlorella culture growing on wood hydrolysate in the presence of light, was the highest from all carbon-based profiles. Supplementation of Chlorella culture with Hyd12% in dark resulted in fatty acid productivity at comparable level to photoautotrophic control, showing that wood hydrolysate can also become an alternative feedstock for microalgae cultivation in case of lack of light. Wood acid hydrolysate can serve as a supplement to improve fatty acid and pigment productivity during mixotrophic Chlorella cultivation. It can also constitute a source of carbon for fatty acid and pigment production during heterotrophic Chlorella cultivation, although it should be taken in consideration that the presence or lack of light was an important factor affecting composition of fatty acids and pigments in Chlorella culture, cultivated on a neutralized wood acid hydrolysate. Secondly, enzymatic beech wood hydrolysate as a feedstock for Chlorella growth, fatty acid and pigment production, was tested. Beech wood solids were pretreated with NaOH at high temperature to partially remove xylose and Klason lignin, and enable production of glucose during subsequent enzymatic hydrolysis. A 10% neutralized wood enzymatic hydrolysate containing glucose (TGP-Enz10), was tested on Chlorella growth during heterotrophic cultivation and compared with microalgae growth in a medium containing synthetic glucose (TGP). Results show that enzymatic hydrolysate enabled Chlorella growth in the dark for biomass, fatty acid and pigment production due to the presence of glucose, although the productivity obtained was smaller, if compared to heterotrophic cultivation in a synthetic TGP medium. Partial growth inhibition and diminished productivity in wood hydrolysate supplemented Chlorella culture was due to the presence of neutralized citrate buffer. Neutralized citrate buffer (TGP-Cit10) was found to partially inhibit heterotrophic growth and also strongly suppress mixotrophic growth in Chlorella culture. This buffer was also shown to alter fatty acid composition and to slightly affect ChlTotal/CarTotal ratio during heterotrophic cultivation. Heterotrophic Chlorella cultivation with TGP-Enz10 showed that wood enzymatic hydrolysate can constitute a potential feedstock for microalgae cultivation, although the composition of the buffer used during enzymatic hydrolysis should be taken into consideration. Finally, advantages and disadvantages of using different wood hydrolysates as feedstocks for microalgae cultures, are discussed. [less ▲]

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See detailEvolution et adaptation fonctionnelle des arbres tropicaux : le cas du genre Guibourtia Benn.
Tosso, Dji-ndé Félicien ULiege

Doctoral thesis (2018)

La présente thèse s’intéresse aux mécanismes à l’origine de la diversification des espèces d’arbres tropicaux. Elle utilise le genre Guibourtia Benn. (Fabaceae-Detarioideae) comme modèle biologique afin ... [more ▼]

La présente thèse s’intéresse aux mécanismes à l’origine de la diversification des espèces d’arbres tropicaux. Elle utilise le genre Guibourtia Benn. (Fabaceae-Detarioideae) comme modèle biologique afin de comprendre les mécanismes historiques, biologiques et environnementaux, à l'origine de la diversité de ce genre aux niveaux interspécifique et intraspécifique. Plus particulièrement, elle vise à : (1) étudier au niveau interspécifique, le rôle relatif des forces évolutives neutres et de sélection dans la diversification du genre Guibourtia en combinant une phylogénie moléculaire avec la caractérisation des traits et les niches écologiques des espèces ; et (2) au niveau intraspécifique, questionner les causes de la différenciation des populations de trois espèces de Guibourtia. Au niveau interspécifique, la phylogénie datée basée sur le séquençage du génome chloroplastique complet a globalement confirmé la taxonomie actuelle (espèces généralement monophylétiques). Elle a montré une diversification au milieu du Miocène en trois clades qui sont décrits aujourd’hui comme des sous-genres (Guibourtia, Gorskia et Pseudocopaiva). Elle démontre en outre que deux espèces américaines sont issues d’une migration de l’Afrique vers l’Amérique à la fin du Miocène. Il est également apparu que certains traits morphologiques ont été sélectionnés de manière convergente au sein des différents clades du genre Guibourtia en fonction des niches climatiques des espèces. Ce dernier résultat a été consolidé au moyen d’une expérimentation écophysiologique prouvant que la lumière constitue un important facteur de sélection et de différenciation adaptative entre trois espèces (G. ehie, G. coleosperma et G. tessmannii). Au niveau intraspécifique, une étude de phylogéographie de deux espèces a permis de mettre en évidence que les barrières biogéographiques chez G. ehie et les gradients climatiques chez G. coleosperma, auraient contribué à la différenciation génétique des populations. En outre, cette étude montre une forte différenciation entre les populations de G. ehie d’Afrique de l’Ouest et d’Afrique centrale en lien avec quelques traits morphologiques, ce qui préjuge de l’existence d’une nouvelle espèce. Enfin, chez G. tessmannii, espèce aux fruits déhiscents et graines arillées, nous avons identifié les principaux disperseurs dont les calaos (Ceratogymna atrata ) qui pourraient contribuer à une dispersion à longue distance, influençant la structure spatiale de la variation génétique des populations. Cette thèse en utilisant le genre Guibourtia comme modèle d’étude a apporté de nouveaux éléments à la compréhension des mécanismes qui génèrent la diversité au sein des espèces d’arbres. Elle fournit en outre des connaissances originales sur des espèces inscrites en annexe II de la CITES. [less ▲]

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See detailGenetic Relationships between Methane-related Traits and Milk Composition in Lactating Dairy Cows
Kandel, Purna ULiege

Doctoral thesis (2018)

Methane (CH4) emission is one of the most important environmental traits from dairy cows. Genetic selection programs aiming to mitigate CH4 emissions require the estimation of genetic parameters ... [more ▼]

Methane (CH4) emission is one of the most important environmental traits from dairy cows. Genetic selection programs aiming to mitigate CH4 emissions require the estimation of genetic parameters, correlations with other economically important traits and predicted selection response of these traits. In first part of this thesis, CH4 emissions (g/d; PME) were predicted from several milk fatty acid based prediction equations using mid-infrared (MIR) spectra of milk samples from Holstein cows. The heritability of PME was moderate and ranged from 0.21 to 0.40. The sires genetic variability were large enough to respond selection pressure. In second part and to minimize prediction errors, genetic parameters were estimated from direct prediction of CH4 (i.e. based on SF6 measurements) from milk MIR spectra. Predicted CH4 intensity (PMI, g/kg of milk) was derived from the ratio of CH4 (g/d) value divided by the total milk yield recorded for the considered test-day which is a trait that is comparable across different production systems. The relationship between PMI and milk yield (MY) was curvilinear and the distribution of PMI being non-normal, it was log-transformed (LMI) in further analyses. The genetic analyses were performed using two genetic models with or without random within-herd lactation curve effects along with random permanent and additive genetic effects. The results showed that the model with random within-herd lactation curve effects had a better fitting. The heritability of PME was 0.26 and PMI was 0.27. The contribution of random herd-specific lactation curve effects to the total variance also suggested an impact of herd specific management on the CH4 emission traits. After confirming genetic component of CH4 traits, genetic correlations of these traits with milk production traits were explored and expanded to second lactation. The phenotypic correlations between PME and MY, fat yield and protein yield were not different than zero but with LMI, the phenotypic correlations were highly negative. The genetic correlation was low negative between PME and milk production traits but high negative with LMI. The intra-lactation heritability and correlation were changing across lactation suggested there was dynamic relationship between CH4 traits and milk production traits. After demonstrating correlation between milk production traits, the genetic correlation between CH4 traits and functional traits [fertility, body condition score (BCS), longevity], health traits (udder health) and type traits were estimated. There were positive correlations between CH4 emission traits and functional trait suggested there were tradeoffs between these traits in selection. The ingestion ability related type traits had positive genetic correlations with PME but negative genetic correlation with LMI. Finally, using the current Walloon selection index and by selecting PME and LMI, the emission traits responded by a reduction in CH4 emission, without jeopardizing in milk production traits but having negative consequences in fertility, BCS and longevity. In conclusion, this study shows the feasibility to adapt the selection index to mitigate the CH4 emitted by dairy cows. [less ▲]

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See detailGenomics, Metagenomics and Phylogenomics of Cyanobacteria
Cornet, Luc ULiege

Doctoral thesis (2018)

This PhD thesis concerns the genomics, metagenomics and phylogenomics of Cyanobacteria. It is composed of five main parts, of which four are result manuscripts. In the first part (i.e., Introduction), I ... [more ▼]

This PhD thesis concerns the genomics, metagenomics and phylogenomics of Cyanobacteria. It is composed of five main parts, of which four are result manuscripts. In the first part (i.e., Introduction), I review a decade of cyanobacterial phylogeny and molecular dating. I show that, in spite of a considerable literature, the global topology of the cyanobacterial tree is incongruent across 9 of the 12 recent studies. I also raise the issue that cyanobacterial datings are all based on ambiguous fossils, since no genomic data are available for unambiguous fossil calibration points. The second part deals with the problem of public genome contamination. I analyzed 440 genomes of Cyanobacteria with a consensus approach of five methods (two based on ribosomal genes and three based on complete genome analysis), and determined that >5% cyanobacterial genomes are contaminated by foreign DNA. The next two parts are metagenomic analyses. The first metagenomic study is a pipeline for properly assembling complete genomes from non-axenic cultures. To this end, I used 17 cyanobacterial cultures from the BCCM/ULC collection of the ULiège and assembled metagenomic reads into 15 genomes with a very low level of contaminants and a high level of completeness. The second metagenomic study deals with the new field of phylometagenomics. Hence, I developed a new syntenic algorithm designed for metagenomes in mind, and applied it to the study of lichenized Cyanobacteria. I found 90 syntenic and collinear genes shared between 28 Nostocales genomes, including 12 new photobiont metagenomes. The subsequent phylogenetic analysis showed a relatively high level of congruence among these genes. Finally, the last part of the thesis is a large constrained SSU rRNA (16S) tree intended to serve as a guide in organism selection for future sequencing projects. It revealed 31 clusters of Cyanobacteria that are completely devoid of representative genomes (<0.1%). Altogether, the results of this PhD work lay the ground for a better phylogenomic study of the Cyanobacteria, taking advantage of new key organisms. [less ▲]

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See detailIdentification of elicitors inducing resistance in wheat against Zymoseptoria tritici and characterization of the subsequent triggered defense-signaling pathways
Le Mire, Géraldine ULiege

Doctoral thesis (2018)

The implementation of biocontrol products in integrated pest management strategies is a major challenge today in the transition to sustainable and environment-friendly agro-ecosystems. In particular, the ... [more ▼]

The implementation of biocontrol products in integrated pest management strategies is a major challenge today in the transition to sustainable and environment-friendly agro-ecosystems. In particular, the use of natural elicitors, also called plant resistance inducers, represents an interesting alternative to conventional fungicides. Elicitors are natural immune-stimulating compounds which offer the advantage to indirectly target a broad spectrum of pathogens by enhancing the defensive state of the plant. Yet today, wheat is one of the most cultivated crops in the European Union and still requires fungicide protection every year for the control of a harmful disease: Septoria tritici Blotch (STB), caused by the fungal pathogen Zymoseptoria tritici. At a time when few elicitor products are available on the market for the sustainable management of crop diseases, the objective of this thesis project was to screen and identify innovative elicitors able to preventively protect wheat against the STB disease. Greenhouse trials successfully demonstrated the ability of λ-carrageenan, cytosine-phosphate-guanine oligodesoxynucleotide motifs (CpG-ODN), Spirulina platensis, glycine betaine and ergosterol to protect wheat by up to 70 % against the pathogen Z. tritici. These results are promising as previous research has indeed demonstrated the elicitor properties of these five compounds on other plant species and/or animals. Besides, no direct anti-fungal activity was recorded during in vitro experiments towards the disease. The risk of resistance development of the pathogen to these potential elicitors can thus be considered as low. Furthermore, the defense mechanisms of wheat were successfully demonstrated to be significantly induced following treatment with each of these formulated compounds. The relative expression of 23 plant defense genes was analyzed by qRT-PCR at 1, 2 and 3 days after plant treatment. Defense mechanisms involving the two hormones salicylic acid (SA) and jasmonic acid (JA) were triggered in treated wheat. These hormones play a key role in the transduction of defense signals throughout the plant. In addition, the protection efficacy of the two preferential candidates (λ-carrageenan and Spirulina) was investigated in the field during two successive years. Numerous parameters, among which environmental conditions, plant developmental stage, plant genotype and disease pressure, can indeed cause a variability of elicitor protection efficacy under practical conditions. Unfortunately, important contrasts in disease pressures and extreme weather conditions did not allow confirming the elicitor potential of the corresponding treatments on field. Finally, the potential effect of the formulation on the eliciting activity was characterized in order to rule out the possibility of interference by the selected adjuvants. Additional greenhouse experiments showed that a water solution containing only the adjuvants was as efficient to protect wheat against STB as plants treated with formulated or non-formulated λ-carrageenan. These last results highlighted the necessity of developing an appropriate formulation at an early stage before elicitor screening. Overall, the findings of this research study could open the way to the development of innovating biocontrol products based on λ-carrageenan for the sustainable protection of wheat against Zymoseptoria tritici. [less ▲]

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See detailDevelopment of an attenuated recombinant vaccine against Cyprinid herpesvirus 3
Boutier, Maxime ULiege

Doctoral thesis (2018)

The cyprinid herpesvirus 3 (CyHV-3, genus Cyprinivirus, family Alloherpesviridae, order Herpesvirales) is the aetiological agent of a highly contagious and lethal disease affecting koi and common carp ... [more ▼]

The cyprinid herpesvirus 3 (CyHV-3, genus Cyprinivirus, family Alloherpesviridae, order Herpesvirales) is the aetiological agent of a highly contagious and lethal disease affecting koi and common carp (Cyprinus carpio). Common carp is currently the third most important fish species of aquaculture with a world production between 3 and 5 million tons per year. A safe and efficacious attenuated vaccine compatible with mass vaccination is needed to control CyHV-3. In this thesis, we produced an ORF56-57 double deleted (Δ56-57) attenuated recombinant vaccine candidate using prokaryotic mutagenesis. The safety of this vaccine candidate was demonstrated using in vivo bioluminescent imaging system (IVIS), qPCR, and histopathological examination. In comparison to the parental wild type strain, the vaccine candidate replicated at lower levels and spread less efficiently to secondary sites of infection. Transmission experiments allowing contamination through water with or without additional physical contact between fish demonstrated that the vaccine candidate has a reduced ability to spread from vaccinated fish to naïve sentinel cohabitants. Finally, challenge experiments demonstrated that the vaccine candidate induces a protective mucosal immune response at the portal of entry. The first part of this thesis led to the rational development of a recombinant attenuated vaccine against CyHV-3 compatible with mass vaccination of carp. In the second part of this thesis, the relative contributions of ORF56 and ORF57 to the safety and efficacy profile of the Δ56-57 vaccine candidate have been assessed by producing and phenotyping viruses individually deleted for ORF56 or ORF57. Inoculation of these viruses to carp demonstrated that the deletion of ORF56 did not affect virulence, whereas the absence of ORF57 led to an attenuation comparable to, though slightly less than, that of the Δ56-57 vaccine candidate. To demonstrate further the role of ORF57 as a key virulence factor, a mutant retaining the ORF57 region but unable to express the ORF57 protein was produced by inserting multiple in-frame stop codons into the coding region. Analysis of this virus in vivo revealed a safety and efficacy profile comparable to that of the double deleted virus. These findings show that CyHV-3 ORF57 encodes an essential virulence factor. CyHV-3 is considered as the prototype of the genus Cyprinivirus which encompasses a growing list of phylogenetically related viruses causing massive economical losses to the aquaculture sector. This thesis led for the first time to the identification of an essential virulence factor of CyHV-3 and to the demonstration that recombinant viruses deleted for this gene are potential vaccine candidates. All cypriniviruses described to date encode orthologues of CyHV-3 ORF57. Consequently, the present work opens new perspectives for the development of recombinant attenuated vaccines against this economically important viral genus. [less ▲]

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See detailImpact of Murid Herpesvirus 4 Imprinting against Heterologous Respiratory Immunopathologies
Dourcy, Mickael ULiege

Doctoral thesis (2017)

Gammaherpesvirus (ɣ-HVs) infections are highly prevalent in both human and animals. They persist in their host by establishing and maintaining latent infections. Murid herpesvirus 4 (MuHV-4) is a wild ... [more ▼]

Gammaherpesvirus (ɣ-HVs) infections are highly prevalent in both human and animals. They persist in their host by establishing and maintaining latent infections. Murid herpesvirus 4 (MuHV-4) is a wild rodent pathogen that can be used as a model of ɣ-HV infection in the laboratory mouse. Like other ɣ-HVs, MuHV-4 profoundly imprints the host immune system to allow completion of its biological cycle. In particular, MuHV-4-induced modulations have been shown to confer bystander protection against heterologous secondary infections. Type 2 respiratory immunopathologies are of major interest in public health, specifically in developped countries. Notably, allergic asthma affects more than 300 million people worldwide and hSRV (human respiratory syncytial virus) inactivated vaccine-induced Th2 immunopathology substantially delays the development of vaccines against this virus which is yet the main infectious agent of bronchopneumopathies in children and olders. According to the hygiene hypothesis, epidemiological studies suggest that late primoinfections to human ɣ-HVs are correlated to an increased risk of allergic sensitization later in life. Using the MuHV-4 model, the in vivo impact of a ɣ-HV infection was tested against the development of on one hand, allergic airway inflammation induced by house dust mites (HDM) allergens (study 1) and on the other hand, anti-pneumovirus Th2 immunopathology, using Pneumonia virus of mice (PVM) to faithfully mimic the original hRSV disease in homologous host-virus model (study 2). Our results have shown that MuHV-4-infected mice are protected from the development of both allergic and vaccine-induced type 2 immune disorders. Moreover, MuHV-4-infected mice were also clinically protected from the subsequent heterologous infection with PVM. Finally, the protective mechanism against HDM allergic asthma was deciphered; pulmonary MuHV-4 lytic infection causes the severe depletion of the alveolar niche which is repopulated by bone marrow-derived monocytes. These latter cells then differentiate into alveolar macrophages (AMs) that are both phenotypically and functionally distinct from resident AMs. Indeed, in previously MuHV-4 infected mice, these monocyte-derived AMs express regulatory functions to block the activation of dendritic cells involved in allergic sensitization, therefore, conferring protection against allergic airway inflammation. In conclusion, the present thesis has unambiguously unraveled that ɣ-HV infection can protect the host against the development of main public health-related respiratory type 2 immune disorders. Replacement of embryonic AMs by regulatory monocytes is thus a major feature underlying the long-term training of the lung immunity after infections, and could provide a possible mechanistic explanation for the hygiene hypothesis. Altogether, this work opens interesting perspectives for the prevention of respiratory type 2 immunopathologies. [less ▲]

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See detailBovine brucellosis in Argentina: current situation and intraherd simulation model
Aznar, Maria Natalia ULiege

Doctoral thesis (2017)

Bovine brucellosis is an infectious disease, which can negatively affect cattle productivity and human health. It is endemic in Argentina, where 0.8% of cattle and 12% of farms are infected, having this ... [more ▼]

Bovine brucellosis is an infectious disease, which can negatively affect cattle productivity and human health. It is endemic in Argentina, where 0.8% of cattle and 12% of farms are infected, having this percentages remained stable throughout the years. This thesis studies the disease in the country. At first a review on the Argentine situation is presented, which leads to two remarkable aspects: brucellosis remains endemic and it is not possible to reach its eradication. In order to to clarify those points, four main studies were performed. The study 1 is an analysis of cattle movement that showed that there are some districts potential spreaders of the disease while others have more at risk of introduction. The study 2 constitutes an estimation of the brucellosis prevalence and identification of the risk factors associated with an increased occurrence, which helps to improve the knowledge of the epidemiology of the disease in the country. When assessing the situation at the provinces under study, a spatial cluster of infected farms was detected. In that region, farms are considerably large, having lowanimal densities and few movements. Those factors probably correlate with infrequent veterinary control and poor sanitary conditions of the herds. Special attention should be paid to those zones sharing these characteristics since there is high chance of finding clusters of the disease. In the study 3 a method for evaluating some farmers' and veterinarians' management practices in relation to brucellosis and for assessing the vaccination campaign and coverage is developed. It shows that the vaccination campaign is globally well implemented, but the immunization coverage and some management practices should be improved. Finally, the study 4 develops an intra herd simulation model. Its aim is to predict the effects of the disease and to test different control and eradication strategies in different situations. As brucellosis is a contagious disease, when introducing one infected animal in a free herd, it might become endemic. In the case of endemic farms that do not eliminate the reactors, all the tested vaccination strategies produce a reduction in the disease outputs (abortions, infectious deliveries, new infected and born infected) whereas when no vaccination is applied, the outputs remain stable. The isolation of heifers from the general herd reduces the disease outputs by a half. Despite it, if the reactors are not eliminated the sources of infection are kept in the herd. Therefore, a strategy of elimination of infected animals has to be applied. Independently from the chosen vaccination strategy, applying serological tests of high sensitivity and specificity with immediate elimination of reactors produces a dramatic reduction in the disease prevalence. These results might explain the fact that the disease keeps on being endemic in Argentina. Since for achieving eradication at country level, other measures additional to vaccination have to be applied, the mandatory elimination of infected cattle could be taken into account. Summarizing all these issues, it can be concluded that, although there are good regulations to control and eradicate bovine brucellosis in Argentina. The prevalence is not so high and stable throughout the years and, some improvements have to be made in order to achieve eradication. This thesis attempted to assess the Argentine current situation and to provide tools for policy makers and farmers to obtain that goal.   [less ▲]

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See detailThe virion transmembrane proteome: a glance to the evolution and to the biology of Cyprinid herpesvirus 3
Vancsok, Catherine ULiege

Doctoral thesis (2017)

Cyprinid herpesvirus 3 (CyHV-3) is the etiological agent of a highly contagious and lethal disease affecting koi and common carp worldwide. Beyond its economic importance, this virus turned out to be an ... [more ▼]

Cyprinid herpesvirus 3 (CyHV-3) is the etiological agent of a highly contagious and lethal disease affecting koi and common carp worldwide. Beyond its economic importance, this virus turned out to be an interesting subject for fundamental research and is currently considered as the archetype of Alloherpesviridae. The divergence of this family with the Herpesviridae is ancestral, with almost no significant homology between CyHV 3 genes and those of Herpesviridae. Consequently, the extensive knowledge acquired for the latter cannot be used to predict CyHV 3 biological features. Virion transmembrane proteins (VTPs) are well documented in Herpesviridae for their involvement in crucial processes such as entry, immune evasion, morphogenesis and egress of progeny virions from the host cells. In contrast, very little is known about the functions of these proteins in CyHV 3 or in any of the alloherpesviruses. The main objective of this thesis was to provide a first functional characterization of CyHV-3 virion transmembrane proteome. The experimental work performed is summarized in two main chapters. The first study aimed to update the list of known CyHV-3 VTPs and to determine those that are essential to viral growth in vitro. Using mass spectrometry approaches and mutagenesis experiments, we identified 16 VTPs in the CyHV-3 FL strain, among which 8 turned out to be essential to viral growth in vitro. The non-essential VTPs were further assessed quantitatively for their relative importance in vitro and in vivo. ORF25, ORF64, ORF108, ORF132, ORF136, ORF148, and ORF149 were shown to affect viral growth in vitro; while the lack of ORF148 or ORF25 caused attenuation to a minor or major extent in vivo, respectively. Finally, we showed that a mutant lacking ORF25 was highly attenuated but induced a moderate immune protection under the conditions tested. Bioinformatic analyses suggested that CyHV-3 ORF27 encodes a VTP. However, no protein corresponding to this ORF was detected in our proteomic analyses. Analyses of genome sequence and protein expression demonstrate that the FL strain, like several other laboratory strains, do not express ORF27 due to presence of various mutations, while it encodes a VTP in field strains. These observation led us to hypothesize that the deletion of ORF27 could confer a selective advantage to viral growth in vitro, while the expression of a functional pORF27 could confer a selective advantage in vivo. These hypotheses were addressed by producing recombinant viruses. In vitro, the CyHV 3 strain lacking ORF27 expression was shown to have a replicative advantage, especially during co-infection with a viral strain expressing this protein. In contrast, in vivo, no difference between both genotypes could be detected in the experimental conditions tested. This observation suggests that the biological functions of ORF27 cannot be revealed in the laboratory conditions used. In conclusion, this thesis provides a first functional characterization of the virion transmembrane proteome of CyHV-3. It represents a firm basis for further research on alloherpesvirus VTPs. [less ▲]

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See detailTransmission des phytovirus associés aux pucerons: une approche multitrophique
Bosquée, Emilie ULiege

Doctoral thesis (2017)

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See detailNew therapeutic approaches for malignant pleural mesothelioma targeting DNA repair and transforming growth factor TGF-alpha
Staumont, Bernard ULiege

Doctoral thesis (2017)

Malignant pleural mesothelioma (MPM) is an aggressive cancer of the pleura mainly caused by asbestos fibers exposure. MPM is notably characterized by a very poor prognosis and current treatments ... [more ▼]

Malignant pleural mesothelioma (MPM) is an aggressive cancer of the pleura mainly caused by asbestos fibers exposure. MPM is notably characterized by a very poor prognosis and current treatments, including radiation and chemotherapy, are unsatisfactory. As genomic analyzes show that the major mutations occurring in MPM cells pertain to checkpoint control and DNA repair, a first part of this thesis addresses the DNA damage response and the mechanisms of DNA repair in several MPM cell lines. In this study, we show that gamma ionizing radiation (IR) induces cell cycle arrest of MPM cells at the G2-M checkpoint. We also demonstrate that MPM cells are driven prematurely towards mitosis following the abrogation of IR-induced G2 arrest by the checkpoint inhibitor UCN-01, however without a significant induction of cell death. To avoid excessive genomic instability, DNA repair mechanisms are likely to play a key role in such DNA-damaging conditions. We therefore evaluate here the efficiencies of the two main DNA double-strand break repair mechanisms, non-homologous end-joining (NHEJ) and homologous recombination (HR) and highlight differences in such repair activities among MPM cell lines and in comparison to control mesothelial cells. We underline an efficient HR repair in MPM cells, opening the door to additional investigations that might reveal an addiction to activated DNA repair pathways and thereby render MPM cells hypersensitive to targeted combination therapies. In the second part of this thesis, we perform a pre-clinical study investigating the resistance of MPM to a particular epigenetic-based therapy associating the histone deacetylase (HDAC) inhibitor valproic acid (VPA) and doxorubicin. By comparing MPM cell lines with a differential sensitivity to this combination chemotherapy, this study suggests a correlation between transforming growth factor-alpha (TGF-α) expression and resistance to treatment. We further confirm the role of TGF-α in chemoresistance by modulating its expression in highly- and poorly responsive MPM cell lines. In addition, pharmacological inhibition of TGF-α’s receptor (EGFR or epidermal growth factor receptor) by tyrosine kinase inhibitors gefitinib and erlotinib improves the efficacy of VPA+doxorubicin in vitro. Dual HDAC-EGFR inhibitor CUDC-101 furthermore synergizes with doxorubicin to induce apoptosis in vitro and to slow down tumor growth in two different MPM mouse models, emphasizing its therapeutic potential and opening new prospects for combination therapies associating HDAC and EGFR inhibition against MPM. With two different approaches, this thesis provides a better understanding of MPM resistance to chemo- and radiotherapies and offers clues for new therapeutic strategies based on DNA repair pathways and dual HDAC-EGFR/TGF-α inhibition. [less ▲]

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See detailStudy of plant-aphid interactions in Gabonese vegetable crops and biological control perspectives
Bayendi Loudit, Sandrine ULiege

Doctoral thesis (2017)

Periurban agriculture increased vegetables production in the cities. A survey was conducted in three market gardening in Libreville and Owendo cities to register crop and pesticides diversity uses by ... [more ▼]

Periurban agriculture increased vegetables production in the cities. A survey was conducted in three market gardening in Libreville and Owendo cities to register crop and pesticides diversity uses by farmers. The most abundant cultivated species throughout the year appeared to be amaranth (Amaranthus ama L. Amaranthaceae). The most important pests were aphids (Hemiptera: Aphididae) and some beetles (Coleoptera). To control the pests, conventional neurotoxic insecticides were used with effect on environment and human health. In order to identify the occurring insects in the selected areas, a monitoring of insects was carried out during two years on amaranth, roselle, tomato (Lycopersicon esculentum M., Solanaceae) and cabbage (Brassica oleracea L., Brassicaceae). Entomological abundance and diversity were assessed through weekly trapping and visual observations from July to August each year. Insects were collected, identified at the taxonomic level of the family, and classified into three categories: pests, beneficials and associated insects to agriculture. Eighty four families belonging to height orders were recorded with 7910 and 3148 sampled individuals in 2012 and 2013 respectively. The predominant insect families were in both years Aphididae, Cecidomyiidae (Diptera) and Chrysomelidae (Coleoptera) for pests, Dolichopodidae (Diptera), Staphylinidae (Coleoptera) and Coccinellidae (Coleoptera) for beneficials, and Muscidae (Diptera), Psychodidae (Diptera) and Formicidae (Hymenoptera) for associated insects. As aphids are the most important pests, further study at species level and in relation to predatory beneficials were assessed on vegetable crops in 2013 in two periurban gardening sites. The Aphis craccivora Koch aphid was the most abundant aphid species observed infesting amaranth in both sites. The other aphid species were Lipaphis erysimi Kaltenbach, Myzus persicae Sulzer, Aphis fabae Scopoli and Aphis gossypii Glover. Moreover, seven species of natural enemies were trapped, mainly predatory hoverflies (Diptera: Syrphidae) and ladybirds (Coleoptera; Coccinellidae). A. craccivora Koch is known to be a vegetable pest. Its recent identification as pest in amaranth motivated us to study their multitrophic interactions. Since relationships between aphids and host plants could be related to symbiont and feeding behaviour. A. craccivora endosymbiont bacteria and saliva protein diversity were analysed to explain plant–aphid interactions. Indeed, Buchnera aphidicola was found. Some proteins were only identified in solid and soluble saliva, while others originated from Serratia sp. endosymbiont. Two of the identified proteins are involved in plant-pathogen interactions: calmodulin and elongation factor Tu. To control A. craccivora which causes several crop damages, volatile organic compounds (VOC) have been studied. Only aphid alarm pheromone (E)-β-farnesene (EβF) was identified and quantified. Its effect on escape behaviour in aphids has been demonstrated on three species. A. craccivora responded more strongly than the two other Aphidinae (M. persicae and A. fabae) species with 78% of the individuals initiated dispersal behavior at 500 ng dose of EβF. In another laboratory study, the repellency effect of (E)-β-farnesene, methyl salicylate and two essential oils of basil species (Ocimum gratissimum L. and Ocimum basilicum L. Lamiaceae) were determined, while no repellent effect was observed. Also, aphid populations were reduced by exposure to EβF and O. gratissimum essential oil. This study is one of the few to explore the description of insects in the market gardens of Libreville. This could contribute to the elaboration of the sustainable development strategies of pest control in the zones. [less ▲]

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See detailPLUMAGE DIVERSITY IN BASAL PARAVIANS
Lefevre, Ulysse ULiege

Doctoral thesis (2017)

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See detailCarte interactomique entre l'oncoprotéine Tax du virus HTLV-1 et les protéines à domaines PDZ.
Blibek, Karim ULiege

Doctoral thesis (2017)

HTLV-1 (Human T-cell Leukemia Virus) is the etiologic agent of human adult T-cell leukemia (ATL) and tropical spastic paraparesis (TSP). More than 20 million people worldwide are infected with the HTLV-1 ... [more ▼]

HTLV-1 (Human T-cell Leukemia Virus) is the etiologic agent of human adult T-cell leukemia (ATL) and tropical spastic paraparesis (TSP). More than 20 million people worldwide are infected with the HTLV-1 virus, but only about 5 % develop the associated pathologies. At present, efforts are invested in the search for treatments that may improve the survival expectancy of patients infected by the HTLV-1 virus. The diagnosis of HTLV-1 infection is hampered by the viral genome latency (up to 40 years) and treatment options are limited. To propose novel therapeutic opportunities, it thus is necessary to better understand the host molecular mechanisms perturbed by the HTLV-1 infection. The HTLV-1 genome encodes for the Tax-1 protein, which confers the transforming ability of the virus. The Tax-1 protein is known as the transactivator factor of the HTLV-1 virus genome expression (TransActivator of pX region). It is also involved in the destabilization of several molecular mechanisms within the host, leading to cellular transformation. Tax-1 protein displays several functional domains and interacts with a wide range of cellular proteins. In particular, the Tax-1 protein sequence contains, at its carboxy-terminal end, a motif of four amino acids able to interact with PDZ domain (PSD95-DLG1-ZO1) containing proteins. It has been demonstrated that deletion of the PDZ binding motif (PBM) of the Tax-1 protein leads to a decrease of its oncogenic capacity in vitro. Cellular proteins containing PDZ domains are involved in the formation of cellular junctions, synapses and in cellular receptors assembly. Some of PDZ proteins are capable of relaying extracellular signals and participate in the control of proliferation. The human genome codes for at least 150 proteins with PDZ domains. However, the specificity of the oncoprotein Tax-1 to target these proteins remains unknown. In this study, we have mapped The Tax-1 - PDZ interactome using a combination of several methods. We reveal that Tax-1 selectively target a number of PDZ domains-containing proteins potentially involved in HTLV-1 pathogenesis. We validated our approach by focusing on the role of SDCBP and LNX2 proteins in HTLV-1 biology. Our work also demonstrated that the Tax-1-PDZ interactome might represent an attractive therapeutic target for HTLV-1-induced diseases. [less ▲]

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See detailCaractérisation ontogénique, phénotypique et fonctionnelle des macrophages interstitiels pulmonaires après exposition à des composés bactériens
Sabatel, Catherine ULiege

Doctoral thesis (2017)

Respiratory mucosal surfaces are continuously exposed to harmless antigens and immunostimulatory molecules of microbial origin. According to the « self/non self » and « danger » theories, this should ... [more ▼]

Respiratory mucosal surfaces are continuously exposed to harmless antigens and immunostimulatory molecules of microbial origin. According to the « self/non self » and « danger » theories, this should normally result in the developpment of unwanted immune responses towards these inhaled antigens such as Th2-mediated allergic responses. This is however not the case in most people. The hygiene hypothesis postulates that living in an environment rich in microbial components paradoxically protects from airway allergy, implying the existence in the lung of suppressive mechanisms triggered by these immunogenic signals. In this study, we showed that synthetic bacterial DNA rich in unmethylated CpG motifs (CpG) has the unique ability to significantly increase the population of lung interstitial regulatory macrophages (IM) from CCR2-independent monocytes residing in the lung or mobilized from the spleen. Moreover these CpG-induced IM demonstrated a hypersuppressive profile as they produced more IL-10 than their steady state counterparts. Using mice models of airway allergy we showed that the transfert of IM isolated from CpG-treated mice recapitulated the protective effects of CpG when administered before allergen sensitization or challenge. This IM-mediated protection was dependant from IL-10 as CpG-induced Il10-/- IM had no protective effect. The expansion of pulmonary regulatory IM from CCR2-independent pulmonary and splenic monocytes upon CpG exposure could be a possible mechanism by which exposure to an environment rich in microbial products protects against asthma. [less ▲]

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See detailEtude de la transmission du gammaherpèsvirus murin 4: importance de la glycoprotéine gp150 et développement de stratégies antivirales basées sur l'utilisation du cidofovir
Zeippen, Caroline ULiege

Doctoral thesis (2017)

Gammaherpèsviruses are important pathogens in human medicine. Indeed, Epstein Barr virus and Kaposi Sarcoma associated herpesvirus are responsible for numerous lymphoproliferative diseases and cancers ... [more ▼]

Gammaherpèsviruses are important pathogens in human medicine. Indeed, Epstein Barr virus and Kaposi Sarcoma associated herpesvirus are responsible for numerous lymphoproliferative diseases and cancers. Murid Herpesvirus-4 (MuHV-4) is usually used as a model for human gammaherpèsviruses. Until now, the major limitation of this model was the absence of transmission in laboratory animals. Recently, a sexual transmission of MuHV-4 has been described in laboratory mice. This observation allows, on the one hand, to study mechanisms underlying natural transmission, such as cellular trospism, importance of viral proteins, or immunity response during this part of the cycle. On the other hand, this transmission model allows to test efficiency of measures to reduce transmission. Indeed, herpesvirus are archetype of persistant viruses as infection persists lifelong once established. Studying mechanisms underlying transmission and how to use these mechanisms to reduce it efficiently is therefore of primordial importance. In a first study, we focussed on the biological relevance of mechanisms described previously in vitro. Indeed, a MuHV-4 glycoprotein, gp150, has been shown to participate to the release of infectious particles from cells and to evasion of humoral immunity, two functions that could be important for the virus during transmission. Our results showed that gp150 is essential for an efficient sexual transmission of the MuHV-4. Indeed, gp150 promotes the release of infectious particles from infected vaginal epithelial cells. These results has been published in Journal of Virology in July 2017. In a second study, the same model was used to test efficiency of an antiviral molecule to reduce sexual transmission of the MuHV-4. A nucleotide analogue, the cidofovir, was administrated to mice according to different protocols. A daily administration of cidofovir reduced drastically genital shedding, but also prevent completely infection of naive mice after sexual contact. Finally, a single injection of cidofovir, administered 24 hours after sexual contact, reduced significantly transmission. Altogether, in this work, we used a transmission model of a gammaherpèsvirus in two differents studies: the first foccused on glycoprotein implicated during the transmission and established the importance of a single viral glycoprotein for an efficient transmission. The second study highlighted the efficiency of antiviral drugs to prevent infection by gammaherpesviruses. [less ▲]

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See detailDesign of a hydraulic nozzle with a narrow droplet size distribution
De Cock, Nicolas ULiege

Doctoral thesis (2017)

Nowadays, pesticides use is necessary to satisfy the growing demand for agricultural products. During pesticide spray application, the agricultural mixture containing the active ingredient is fragmented ... [more ▼]

Nowadays, pesticides use is necessary to satisfy the growing demand for agricultural products. During pesticide spray application, the agricultural mixture containing the active ingredient is fragmented to a cloud of droplets of various sizes and speeds. The droplet size distribution within the spray affects the efficiency of the treatment. According to the target, a specific droplet size should be used. However, hydraulic nozzles usually used in field application produce sprays with a wide droplet size distribution containing an important proportion of small or too large droplets. This results in non-optimal application and therefore losses of product into the environment. This statement conducted the research as early as in the 60’s to create the rotary atomizer. This device is able to produce narrow droplet size distribution using Plateau-Rayleigh break up mechanism. The characteristics of the produced spray by the rotary atomiser can be tuned by adjusting the rotational speed and the volumetric flow rate. Although offering agronomic and environmental qualities this has not met success for the application of plant protection products in field crops because of their cost, size and complexity. The aim of the thesis was the design of a hydraulic nozzle with the rotary atomizer qualities and without the constraints of rotating parts. Unlike the rotary atomizer which has two control variables, the developed hydraulic nozzle will have a narrower operating range, thus a specific geometry has to be design for each kind of treatment. The new hydraulic nozzle design is composed by an inlet pipe ending perpendiculary on a plate. There is a thin opening at the junction between the pipe and the plate. The edge of the plate is constituted of channels formed by structures. These channels aim to divide the liquid sheet in multiple jets. The breakup of these jets into droplets generate a narrow droplet size distribution. The thesis can been seen as a roadmap providing design tools at each step starting from the determination of an optimal droplet size according to the kind of treatment and ending with a nozzle geometry. The prediction of the optimal droplet size according to the treatment was done using integrated modelling approach of the spray transport and retention by the plant. As each spray requires a specific nozzle geometry, an analytical model of the flow on the nozzle was developed. This model allows the determination of geometry according to the desired spray. Finally, a prototype of nozzle has been built. The measurement of the spray characteristics of the prototype was realized using a developed high-speed imaging technique providing the droplet size and speed. The prototype showed results in term of narrowing of the droplet size distribution. [less ▲]

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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See detailThyroid hormone action and disruption in the brain: Xenopus as a model to study disruption of thyroid hormone availability on early brain development
Mughal, Bilal Babar ULiege

Doctoral thesis (2017)

Thyroid hormones (TH) are essential for normal brain development in vertebrates. Disruption of TH action, either due to genetic and/or environmental factors, has been implicated in neurological defects ... [more ▼]

Thyroid hormones (TH) are essential for normal brain development in vertebrates. Disruption of TH action, either due to genetic and/or environmental factors, has been implicated in neurological defects such as autism, attention deficit hyperactivity disorders (ADHD) and IQ loss. On average, over 30 anthropogenic chemicals are present in all American women, with 15 being ubiquitous, including in pregnant women. Many of these chemicals are demonstrated or suspected TH disruptors. A representative mixture of these 15 common chemicals was established at concentrations reported in human amniotic fluid and an in vivo larval reporter (GFP) assay was used to determine integrated TH transcriptional responses. Dose-dependent effects of short-term (72 h) exposure to single chemicals and the mixture were found. Gene expression analysis on dissected brains showed significant changes in TH related genes including receptors, deiodinases and neural differentiation markers. Immunohistochemistry confirmed the mixture exposure action on neural proliferation as well as neuron and oligodendrocyte size. Mixture exposed tadpoles also displayed dose-dependent reductions in mobility. As TH signalling is strongly conserved across vertebrates these results suggest that ubiquitous chemical mixtures could be exerting adverse effects on foetal human brain development. Genetic disruption is also evident in the Allan-Herndon-Dudley (AHD) syndrome where, in humans, the mutation of the brain specific TH transporter (THT), monocarboxylate transporter 8 (MCT8), leads to severe intellectual disability. The lack of neurological phenotype in mice model of Mct8 deficiency has driven the need for characterisation and generation of various non-rodent models. The Xenopus mct8 and additional TH transporters of interest were cloned and characterised. Protein alignment and bootstrap analysis showed that Xenopus mct8 is closer to its mammalian orthologue than its teleost counterparts. Radiolabelled hormones in vitro uptake assay confirmed Xenopus mct8 active transport of both T3 and T4 bi-directionally. As to the thyroid precursor molecules, diiodotyrosine (DIT) and monoiodotyrosine (MIT), both human and Xenopus mct8, showed active efflux, but no influx. Using real-time quantitative PCR (RT-qPCR) and in situ hybridization, specific expression of the mct8 was observed in the brain, with increasingly strong expression as development progressed. Using the before mentioned in vitro assay, effects of common environmental xenobiotics on MCT8 function were assessed. In conclusion, these results show that Xenopus TH transporters are functional and display marked spatio temporal expression patterns. These features make them interesting targets to elucidate their roles in determining TH availability during embryonic development. Xenopus laevis was used a model of choice in these experiments. X. laevis is ideal for studying TH signalling due to its thyroid dependent metamorphosis, a stage comparable to birth in humans. Further, X. laevis is a popular amphibian model for studying vertebrate embryogenesis and development. Reference genes are essential for gene expression analysis when using RT-qPCR, and there is a lack of ad hoc reference genes for X. laevis. Using previously published RNA-seq data on different X. laevis stages, top 14 candidate gene were identified with respect to their expression levels as a function of developmental stage and degree of variation. Using RT-qPCR, the stability of these genes was evaluated and optimized reference gene pair combinations established for studying 1) development (early whole embryos), 2) brains at later stages (metamorphosis and adult), and 3) thyroid signalling. [less ▲]

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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See detailUtilisation de drêches artisanales dans l’alimentation des porcs : le cas des drêches d’alcool de riz au nord du Vietnam
Nguyen Cong, Oanh ULiege

Master of advanced studies dissertation (2017)

L’objectif de cette étude était d’évaluer la production de drêches d’alcool de riz et leur utilisation comme aliment en élevage porcin dans trois provinces (Hai Duong, Hung Yen et Bac Giang) du Nord du ... [more ▼]

L’objectif de cette étude était d’évaluer la production de drêches d’alcool de riz et leur utilisation comme aliment en élevage porcin dans trois provinces (Hai Duong, Hung Yen et Bac Giang) du Nord du Vietnam. Au total, 120 producteurs d'alcool classés par échelle de production (grand, moyen et petit) ont été enquêtés de janvier à août 2015. De plus, 63 échantillons de drêches d’alcool de riz ont été prélevés dans les zones étudiées pour déterminer les composants nutritionnels sur une période de stockage d’une semaine. La production annuelle de drêches d’alcool de riz en matière sèche était d’environ 4,8±0,3 ; 3,0±0,2 et 2,1±0,2 tonnes respectivement par grand producteur, producteur moyen et petit producteur (p<0,001). Une corrélation positive entre l’échelle de la production d’alcool et le nombre de porcs présents dans l’atelier de production porcine a été mise en évidence (p<0,05). La quantité de drêches d’alcool de riz utilisée en ration quotidienne des truies dans les trois échelles était réduite progressivement du stade de gestation au stade de lactation et variable pour le porc à l'engraissement. Les drêches d’alcool de riz ont été riches en protéines brutes (26,2% MS), en acide lactique (2,27% en matière humide), en phosphore (7,45 g/kg MS), en fer (104 mg/kg MS) et en énergie brute (20,41 MJ/kg MS). En outre, les valeurs nutritives ont été stables sous des conditions ambiantes pendant une semaine (p>0,05). [less ▲]

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See detailImpacts comparés de trois régimes fonciers sur la biodiversité et la biomasse forestière au sud-est du Cameroun
Fonteyn, Davy ULiege

Master's dissertation (2017)

Terrestrial ecosystems are currently facing an unprecedented biodiversity crisis. In the future, and specifically in the tropics, land use changes will have the greatest impacts on biodiversity. The aim ... [more ▼]

Terrestrial ecosystems are currently facing an unprecedented biodiversity crisis. In the future, and specifically in the tropics, land use changes will have the greatest impacts on biodiversity. The aim of this master thesis was to assess biodiversity for trees (forest structure and composition) and animals (composition) in three different land tenures in the semi-deciduous forests of South-East Cameroon. The Dja Reserve represents the control never logged, while the community forests are considered as the highest disturbance level. The sites sampled inside the certified FSC logging concession were at an intermediate location along the disturbance gradient depending on time since logging. In the 36 forest plots, more than 17 000 trees were measured and identified at the species level to assess the tree biodiversity. In the 44 camera traps installed for 3 months, the 4 329 detection events allowed assessing animal biodiversity. Regarding tree biodiversity, the community forests hold relatively high species richness (in contrasts to our expectations) specifically for pioneer species. Though a great part of the animal diversity is retained inside the logging concession, the Dja Reserve holds the richest and most abundant animal communities. Selective logging can thus retain a substantial part of biodiversity compared to areas entirely dedicated to protection. Finally, community forests, although defaunated and structurally disturbed, still answer the social and economical demands of the local communities. [less ▲]

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

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

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

Doctoral thesis (2017)

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

Doctoral thesis (2017)

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

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

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