Tripsinas e quimotripsinas, enzimas pertencentes à classe das serina proteinases, são as principais enzimas proteolíticas digestivas presentes no intestino médio de insetos de diversas ordens. Entretanto, enzimas de diferentes insetos possuem propriedades cinéticas distintas, sendo os motivos dessas diferenças especulados. Precipitações por sulfato de amônio das tripsinas de Tenebrio molitor, Diatraea saccharalis e Spodoptera frugiperda mostram que insetos Lepidópteros possuem serina proteinases mais hidrofóbicas, que foi confirmado através de cromatografias de interação hidrofóbica e da análise de acesso do solvente às superfícies protéicas em modelagens tridimensionais de seqüências. Tal fato está relacionado à formação de oligômeros e resistência a defesas de plantas. Inativações por TPCK mostram que quimotripsinas digestivas de S. frugiperda, inseto polífago, reagem duas ordens de grandeza mais lentamente e possui um deslocamento do pH ótimo de modificação em mais de uma unidade quando comparada com dos outros dois organismos, fato relacionado à resistência a cetonas presentes em diversas plantas. A tripsina digestiva de Periplaneta americana foi purificada e microsseqüenciada, resultando na seqüência VSPAFSYGTG e associada a um alérgeno (denominado PaTry), expresso nos cecos e na região anterior do ventrículo. O anticorpo anti-tripsina de M. domestica reconheceu apenas uma banda no intestino de P. americana e foi utilizado para imunocitolocalizar tripsinas nos tecidos epiteliais, demonstrando que esta é secretada por exocitose nos cecos e na região anterior do ventrículo, como esperado. Por último, a atividade majoritária de quimotripsina se localiza surpreendentemente na região posterior do ventrículo de M. domestica. Apesar disso, apenas 28% dessa atividade é perdida através das fezes, pois 31% da atividade enzimática se encontra firmemente aderida à membrana, e 41% na fração celular solúvel (associada ao glicocálice), sendo a atividade solúvel luminal correspondente a apenas 12%, indicando a existência de pelo menos duas espécies moleculares distintas, uma solúvel e uma aderida à membrana, comprovado inativações térmicas das duas atividades (solúvel e aderida à membrana) na presença e na ausência de Triton X-100, sendo que a atividade aderida à membrana apresentou uma maior meia vida com uma cinética de primeira ordem nos dois casos. Ensaio em gel demonstrou que o homogeneizado possui apenas uma banda de atividade quimotríptica de 30 kDa. A atividade solúvel majoritária foi purificada até a homogeneidade, apresentando uma banda de 30 kDa em SDS-PAGE, pH ótimo de 7,4 e é 90% inativada por TPCK 0,1 mM em pH 8,5 em 15 min. Ela prefere substratos contendo Phe em P1, apesar clivar substratos contendo Tyr e Leu. Uma seqüência contígua similar a quimotripsina foi obtida a partir de uma biblioteca de cDNA de intestino médio de M. domestica, formada por 71 ESTs (de 826 seqüências obtidas ao acaso), indicando que esta deve corresponder à atividade majoritária. Essa seqüência, denominada MdChy1, prediz uma proteína madura de 28.639,2 Da e foi clonada e expressa de maneira recombinante em E. coli BL21 (DE-3) Star, sendo utilizada para produção de anticorpos policlonais em coelhos, que reconheceram uma banda de 30 kDa no ventrículo anterior e posterior, mas não no médio. Esses anticorpos foram utilizados para imunomarcações e reconheceram proteínas no lúmem, nas microvilosidades e em pequenas vesículas do epitélio, demonstrando que a quimotripsina é secretada ao lúmem por exocitose e indicando que o MdChy1 corresponde à atividade majoritária de quimotripsina. Análises de expressão em M. domestica indicam a existência de dois conjuntos de serina proteinases digestivas, um expresso na região anterior e um segundo na região posterior do ventrículo. O MdChy1 é expresso na região posterior, local em que se encontra a atividade majoritária de quimotripsina. Uma reconstrução filogenética dos genes similares a quimotripsinas de Drosophila melanogaster e de M. domestica demonstram que a MdChy1 se agrupa com genes expressos no intestino médio, portanto, com função digestiva. / Trypsins and chymotrypsins, serine proteinases enzymes, are the major proteolytic activities present in the midgut of insects. However, enzymes obtained from different insects present different kinetic properties, and the reason for the differences are speculated. Trypsin precipitation of Tenebrio molitor, Diatraea saccharalis and Spodoptera frugiperda with ammonium sulfate showed that Lepidopteran insects possess serine proteinases with a higher superficial hydrophobicity than insects belonging to other orders, which may be associated to oligomerization of enzymes and resistance to inhibitors present in the food. This was confirmed by hydrophobic interaction chromatography and analysis of solvent access to serine proteinases surface. Moreover, inactivations of chymotrypsins by TPCK showed that S. frugiperda chymotrypsins react one order slower and has an optimum pH of modification more than 1 unit higher than chymotrypsins of D. saccharalis and T. molitor, which was related with the resistance of the enzyme to the presence of plant ketones, since S. frugiperda is a polyphagous organism. The digestive trypsin from Periplaneta americana midgut was purified microssequenced, resulting in the sequence VSPAFSYGTG, coincident to the MPA3 allergen (named PaTry), which is expressed in the caeca and anterior ventriculus. Western blot using M. domestica trypsin antisera recognized a single band, and immunohistochemical assays using this antisera showed that the P. americana trypsin is secreted by exocitosys in caeca and anterior ventriculus, which is coincident to the expression data. Although the major M. domestica chymotrypsin activity is present in the posterior ventriculus, only 28% of the activity is lost in feces, because 31% of activity is membrane-bound, and 41% is in the cellular soluble fraction (glycocalix-associated), and only 12% of total activity is soluble in the lumen, indicating the existence of at least two molecular species of chymotrypsins. Thermal inactivations of both activities (soluble and membrane-bound) showed that they may represent two different molecular enzymes, since the membrane-bound activity has a higher half-life than the soluble both in the presence and in the absence of Triton X-100. Both activities presented a linear first-order inactivation kinetic. In gel assays showed the presence of only one activity band in the midgut of 30 kDa. The major soluble activity was purified through one affinitychromatography, and active fractions presented a single 30 kDa band, a optimum pH of 7.4 and was 90% modified by TPCK 0.1 mM at pH 8.5 during 15 min. This enzyme preferentially cleaves substrates containing Phe residues in P1, although it cleaves substrates containing Tyr and Leu. A contig of a chymotrypsin-like sequence was randomly obtained from a cDNA library of M. domestica midguts from 71 ESTs (a total of 826 sequences), indicating that this sequence corresponds to the major activity present in the lumen. This sequence, named MdChy1, predicted a protein with 28639.2 Da which was cloned, recombinantly expressed in E. coli BL21 (DE-3) Star, this recombinant MdChy1 was used to raise polyclonal antibodies in rabbit. A western blot using this antisera recognised a single band in the anterior and posterior ventriculus, but not in the middle. Imunno-gold labeling of epithelium marked proteins in the lumen, at the microvilli and inside small vesicles, demonstrating that chymotrypsin is secreted through exocytosis in M. domestica and reinforcing that MdChy1 corresponds to the major chymotryptic activity found in the midgut. A semi-quantitative RT-PCR of M. domestica serine proteinase-like genes demonstrated that there are two set of genes, one expressed in the anterior and another in the posterior ventriculus, as visualized in western blot. MdChy1 is expressed in the posterior ventriculus, where the major chymotryptic activity is found. A phylogenetic reconstruction of Drosophila melanogaster chymotrypsin-like sequences and M. domestica chymotrypsins showed that MdChy1 branched with sequences expressed in midgut, thus coding proteins involved in digestion.

The main objective of this thesis was to study the anaerobic digestion (AD) of wastewater from a chicken processing facility and of crude glycerol from local biodiesel operations. The AD of these substrates was conducted in bench-scale reactors operated in the batch mode at 35°C. The secondary objective was to evaluate two sources of glycerol as co-substrates for AD to determine if different processing methods for the glycerol had an effect on CH₄ production. The biogas yields were higher for co-digestion than for digestion of wastewater alone, with average yields at 1 atmosphere and 0°C of 0.555 and 0.540 L (g VS added)⁻¹, respectively. Another set of results showed that the glycerol from an on-farm biodiesel operation had a CH₄ yield of 0.702 L (g VS added)⁻¹, and the glycerol from an industrial/commercial biodiesel operation had a CH₄ yield of 0.375 L (g VS added)⁻¹. Therefore, the farm glycerol likely had more carbon content than industrial glycerol. It was believed that the farm glycerol had more impurities, such as free fatty acids, biodiesel and methanol. In conclusion, anaerobic co-digestion of chicken processing wastewater and crude glycerol was successfully applied to produce biogas rich in CH₄.

Dairy farms can apply anaerobic digestion (AD) as a manure management system, while producing renewable energy. Ultimately, this can reduce greenhouse gas (GHG) emissions. There is much research work that has quantified the changes in emissions due to AD. However, important methodologies such as the Intergovernmental Panel on Climate Change (IPCC) Guidelines, rely only on a small sample of the accumulated scientific findings in the field. This thesis improves the robustness of these methodologies by applying data-driven techniques to estimate values of the energy output of AD systems and their consequent effect in GHG emissions. For this purpose, meta-analyses techniques are applied to mathematically combine metrics from 155 non-standardised research publications (i.e. with different boundaries, scopes and functional units). As a first step, a novel database is created by systematically searching for relevant articles and assessing them against defined criteria. The database is divided in two parts. Given that the offset of GHGs is highly dependent on the energy output of AD system, empirical methane yields (i.e. key metric of AD performance) are collected in Part I of the database. GHG released from different farm activities are input to Part II of the database. To quantify the change in emissions from these activities, standard baseline and AD scenarios are defined. The second step of the meta-analysis consists of applying uni- and multi-variate tests to the database. For Part I, methane yields are analysed in terms of type of digesters. From the batch digesters, new maximum methane yields are proposed based on the combined results of 42 peer reviewed articles. These results offer better estimates than default values of methane yields from the 2007 Guidelines of the IPCC, which only consider two studies. For continuously stirred tank digesters and semi-continuous digesters lower methane yields are revealed. Multi-variate analysis of methane yields together with operating conditions and manure composition, enable the identification of clusters. These groups of variables can be useful to build potential AD scenarios in dairy farms. For Part II of the database, relative changes in emissions between the activities in the standardised baseline and AD scenarios, are examined. It is found, through meta-analysis, that replacing raw manure by anaerobically-treated manure (i.e. digestate) in storage tanks and for field- application, mitigates baseline emissions by 38.7% and 6.9%, respectively. These relative changes can be used to estimate emissions from digestate, being more specific and evidence-based than the current methodology from the IPCC. In addition, relative changes found for offset of fossil fuels by biogas generated in the AD scenarios indicate a reduction of baseline emissions by 9.0%. Only methane leaks from digesters significantly increase the baseline emissions (by 7.4%). Finally, results found by meta-analyses of methane yields and changes in emissions are applied to four dairy farm case studies. The work presented in the case studies demonstrates the benefits of enhancing the robustness of methods to estimate the effect of AD on GHG emissions from dairy farms.

La méthanisation par voie sèche possède différents avantages par rapport à la méthanisation par voie humide. Les réacteurs sont plus petits, les besoins en eau sont moindres, la production de digestat et le prétraitement nécessaire sont également moins importants. Cependant, plusieurs études ont démontré que l'eau favorise l'hydrolyse du substrat et permet le transport des sous-produits d'hydrolyse et des nutriments vers les bactéries. Pour mieux comprendre le rôle de l'eau lors de la méthanisation, des tests de digestion sèche et semi-sèche à partir de substrats organiques complexes (déchets alimentaires, paille de riz, déchets de carotte), avec différentes teneurs en matière sèche de substrat traité ont été réalisées. Les résultats confirment que l'eau joue un rôle essentiel sur le taux de production spécifique de méthane, le rendement final de méthane généré et la dégradation de la matière volatile sèche (MVS). Le rendement final de méthane produit dans des conditions semi-sèches et sèches est respectivement de 51% et de 59% inférieur avec la paille de riz et 4% et 41% de moins pour les déchets alimentaires en comparaison avec des conditions humides. Des tests d'inhibition basés sur l'analyse des acides gras volatils (AGV) ont été menées pour étudier les processus d'inhibition spécifiques qui ont lieu avec les substrats sélectionnés à différentes teneurs en matière sèche. Pour le cas de la méthanisation par voie humide des déchets de carotte, aucune accumulation d'AGV a été trouvé, et toutes les concentrations d'AGV étaient inférieurs aux seuils d'inhibition. Une corrélation directe entre la teneur en matière sèche et la concentration totale d'AGV (AGVtot) a été mise en évidence pour la paille de riz et les déchets alimentaires. Pour la paille de riz, une concentration d'AGVtot maximale de 2,1 g / kg a été trouvé pour la voie sèche, 1 g / kg dans les conditions semi-sèche et 0,2 g / kg dans les conditions humides, alors que pour les déchets alimentaires la concentration d'AGVtot était de 10 g / kg à l'état sec, 9 g / kg dans les conditions semi-sèche et 3 g / kg dans les conditions humides. Un modèle mathématique de la méthanisation de substrats organiques complexes dans des conditions sèches et semi-sèche a été proposé pour simuler l'effet de la teneur en matière sèche sur le processus. Les données obtenues à partir d'expériences en mode batch, en termes de production de méthane et de concentration d'AGV, ont été utilisées pour calibrer le modèle proposé. Les paramètres cinétiques de production et d'élimination d'AGV ont été calibrés à l'aide des données expérimentales, et il a été montré qu'ils sont fortement dépendants de la teneur en matière sèche et différent des valeurs de la littérature concernant la méthanisation par voie humide. Cela est dû à l'accumulation d'AGV dans les conditions sèches, ce qui implique d'utiliser des valeurs plus élevées concernant les constantes d'inhibition introduites dans le modèle. Enfin, comme la méthanisation par voie sèche a généralement lieu dans des réacteurs à écoulement piston, une étude historique et critique de la littérature concernant la compréhension du rôle de l'hydrodynamique dans des bioréacteurs à écoulement piston a été réalisée / Dry Anaerobic Digestion (AD) presents different advantages if compared to wet AD, i.e. smaller reactor size, lesser water addition, digestate production and pretreatment needed, although several studies have demonstrated that water promotes substrate hydrolysis and enables the transfer of process intermediates and nutrients to bacterial sites. To better understand the role of water on AD, dry and semidry digestion tests of selected complex organic substrates (food waste, rice straw, carrot waste), with various TS contents of the treated biomass have been carried out in the present study. The results confirm that water plays an essential role on the specific methane production rate, final methane yield and Volatile Solids (VS) degradation. The final methane yield in semi-dry and dry conditions was 51% and 59% lower for rice straw and 4% and 41% lower for food waste, respectively, if compared with wet conditions. Inhibition tests, based on Volatile Fatty Acid (VFA) analysis, were carried out to investigate the specific inhibition processes that take place with the selected substrates at different TS contents. In wet AD of carrot waste no VFA accumulation was found, and all VFA concentrations were lower than the inhibition limits. A direct correlation between TS content and total VFA (TVFA) concentration was noticed for rice straw and food waste AD. For rice straw a maximum TVFA concentration of 2.1 g/kg was found in dry condition, 1 g/kg in semidry conditions and 0.2 g/kg in wet conditions, whereas for food waste the TVFA concentration was 10 g/kg in dry condition, 9 g/kg in semidry conditions and 3 g/kg in wet conditions. A Mathematical model of complex organic substrate AD in dry and semidry conditions has been proposed to simulate the effect of TS content on the process. The data obtained from batch experiments, in terms of methane production and VFA concentrations, were used to calibrate the proposed model. The kinetic parameters of VFA production and degradation, calibrated using the experimental data, resulted highly dependent on the TS content and different from wet AD literature values. This is due to VFA accumulation in dry conditions, which implies higher values of the inhibition factors introduced in the model. Finally, as dry AD takes usually place in Plug Flow (PF) reactors, an historical and critical review on the role of hydrodynamics in PF bioreactors has been carried out

L’utilisation des microalgues dans les filières bioénergies est une thématique qui connait un développement remarquable ces dernières années. Si dans une perspective d’exploitation de masse, elles permettent de répondre plus favorablement aux contraintes qui pèsent sur l’exploitation des biocarburants de première et de deuxième génération, elles se heurtent également à la question de la demande en éléments nutritifs mais aussi à un bilan énergétique défavorable. En conséquence, il apparait difficile de répondre à une exigence de durabilité attendue pour ce nouveau gisement. Ce travail de thèse s’est intéressé à une solution permettant à la fois de recycler les éléments nutritifs présents dans la biomasse et de fournir de l’énergie au système de production voire de transformation : la digestion anaérobie. Les travaux se sont particulièrement focalisés sur l’intégration de la production de microalgues et de la méthanisation au travers de la conversion énergétique de cette biomasse et de la mobilisation des éléments nutritifs vers la culture à l’échelle du laboratoire et à l’échelle pilote. Après avoir identifié les contraintes associées à la biodégradabilité anaérobie des microalgues et les stratégies d’optimisation, nous avons mis en évidence que le potentiel énergétique est contraint par la qualité propre des cellules et une capacité de résistance à la dégradation biologique. L’application de stratégies d’optimisation de cette étape de conversion via l’utilisation de prétraitement thermique a montré qu’il est possible d’augmenter les rendements de production d’énergie et d’éléments minéraux mobilisables vers la culture. L’utilisation d’un écosystème naturel microalgue-bactérie destiné à la production en milieu ouvert et qui utilise un digestat synthétique comme milieu de culture a révélé le rôle déterminant de la flore bactérienne associée en interaction avec les microalgues. Ces résultats ont été évalués dans un système de production à l’échelle pilote préindustrielle en conditions extérieures, conçu et opéré spécifiquement pour répondre à cette problématique. Les caractéristiques propres du bassin de culture déterminent le comportement hydrodynamique du milieu et le comportement physique et écologique de la population phytoplanctonique mobilisée. L’étude de la dynamique des communautés microbiennes, eucaryotes et procaryotes, confirme le potentiel de résilience et de production d’un écosystème complexe soumis aux contraintes de son environnement. Les résultats de ces travaux ouvrent des perspectives de gestion et d’optimisation des procédés intégrant l’algoculture et la méthanisation qui peuvent répondre plus largement à des problématiques environnementales et de production de molécules d’intérêt au-delà des filières énergétiques. / In recent years, there has been an explosion of interest in the use of microalgae as a source of bioenergy. Mass cultivation of microalgae for bioenergy production promises several advantages compared to first and second generation biofuels. However, similar difficulties in terms of nutrient requirements and an unfavourable energy balance are faced. As a consequence, achieving the sustainable levels of microalgal culture required to implement this strategy in the longer term appears problematic. The work presented in this thesis focuses on anaerobic digestion; a solution which allows both recycling of nutrients and supply of energy to the production and downstream processes. In particular, the studies presented here have been directed towards the integration of microalgal culture and methanisation, at both the laboratory and pilot scale. The guiding principle used is conversion of biomass and provision of nutrients to the culture. We first identified the constraints and potential strategies associated with the aerobic biodegradability of microalgae. Next, we demonstrated that the energetic potential of cells is limited by their quality as well as their level of resistance to biological degradation. We have shown that it is possible to optimise the conversion step, increasing energy yields and nutrient mineralisation via a strategy of thermal pretreatment The use of a natural microalgae-bacteria ecosystem which uses a synthetic digestate as culture media, revealed a key role for bacterial flora interacting with microalgae. These results were further tested in a pilot-level production system specifically designed to address these questions. The evidence suggests that the characteristics of the culture pond determine both the hydrodynamic behaviour of the culture and the physical and ecological behaviour of the phytoplanktonic population. A study of the dynamics of the microbial, eukaryotic and prokaryotic communities suggests the presence of a resilient and complex ecosystem, which is influenced by variations in its environment. The results of this work provide opportunities for management and optimisation of processes integrating microalgae cultivation and methanisation beyond bioenergy production, for example liquid wastes treatment and production of high-value byproducts.

Tripsinas e quimotripsinas, enzimas pertencentes à classe das serina proteinases, são as principais enzimas proteolíticas digestivas presentes no intestino médio de insetos de diversas ordens. Entretanto, enzimas de diferentes insetos possuem propriedades cinéticas distintas, sendo os motivos dessas diferenças especulados. Precipitações por sulfato de amônio das tripsinas de Tenebrio molitor, Diatraea saccharalis e Spodoptera frugiperda mostram que insetos Lepidópteros possuem serina proteinases mais hidrofóbicas, que foi confirmado através de cromatografias de interação hidrofóbica e da análise de acesso do solvente às superfícies protéicas em modelagens tridimensionais de seqüências. Tal fato está relacionado à formação de oligômeros e resistência a defesas de plantas. Inativações por TPCK mostram que quimotripsinas digestivas de S. frugiperda, inseto polífago, reagem duas ordens de grandeza mais lentamente e possui um deslocamento do pH ótimo de modificação em mais de uma unidade quando comparada com dos outros dois organismos, fato relacionado à resistência a cetonas presentes em diversas plantas. A tripsina digestiva de Periplaneta americana foi purificada e microsseqüenciada, resultando na seqüência VSPAFSYGTG e associada a um alérgeno (denominado PaTry), expresso nos cecos e na região anterior do ventrículo. O anticorpo anti-tripsina de M. domestica reconheceu apenas uma banda no intestino de P. americana e foi utilizado para imunocitolocalizar tripsinas nos tecidos epiteliais, demonstrando que esta é secretada por exocitose nos cecos e na região anterior do ventrículo, como esperado. Por último, a atividade majoritária de quimotripsina se localiza surpreendentemente na região posterior do ventrículo de M. domestica. Apesar disso, apenas 28% dessa atividade é perdida através das fezes, pois 31% da atividade enzimática se encontra firmemente aderida à membrana, e 41% na fração celular solúvel (associada ao glicocálice), sendo a atividade solúvel luminal correspondente a apenas 12%, indicando a existência de pelo menos duas espécies moleculares distintas, uma solúvel e uma aderida à membrana, comprovado inativações térmicas das duas atividades (solúvel e aderida à membrana) na presença e na ausência de Triton X-100, sendo que a atividade aderida à membrana apresentou uma maior meia vida com uma cinética de primeira ordem nos dois casos. Ensaio em gel demonstrou que o homogeneizado possui apenas uma banda de atividade quimotríptica de 30 kDa. A atividade solúvel majoritária foi purificada até a homogeneidade, apresentando uma banda de 30 kDa em SDS-PAGE, pH ótimo de 7,4 e é 90% inativada por TPCK 0,1 mM em pH 8,5 em 15 min. Ela prefere substratos contendo Phe em P1, apesar clivar substratos contendo Tyr e Leu. Uma seqüência contígua similar a quimotripsina foi obtida a partir de uma biblioteca de cDNA de intestino médio de M. domestica, formada por 71 ESTs (de 826 seqüências obtidas ao acaso), indicando que esta deve corresponder à atividade majoritária. Essa seqüência, denominada MdChy1, prediz uma proteína madura de 28.639,2 Da e foi clonada e expressa de maneira recombinante em E. coli BL21 (DE-3) Star, sendo utilizada para produção de anticorpos policlonais em coelhos, que reconheceram uma banda de 30 kDa no ventrículo anterior e posterior, mas não no médio. Esses anticorpos foram utilizados para imunomarcações e reconheceram proteínas no lúmem, nas microvilosidades e em pequenas vesículas do epitélio, demonstrando que a quimotripsina é secretada ao lúmem por exocitose e indicando que o MdChy1 corresponde à atividade majoritária de quimotripsina. Análises de expressão em M. domestica indicam a existência de dois conjuntos de serina proteinases digestivas, um expresso na região anterior e um segundo na região posterior do ventrículo. O MdChy1 é expresso na região posterior, local em que se encontra a atividade majoritária de quimotripsina. Uma reconstrução filogenética dos genes similares a quimotripsinas de Drosophila melanogaster e de M. domestica demonstram que a MdChy1 se agrupa com genes expressos no intestino médio, portanto, com função digestiva. / Trypsins and chymotrypsins, serine proteinases enzymes, are the major proteolytic activities present in the midgut of insects. However, enzymes obtained from different insects present different kinetic properties, and the reason for the differences are speculated. Trypsin precipitation of Tenebrio molitor, Diatraea saccharalis and Spodoptera frugiperda with ammonium sulfate showed that Lepidopteran insects possess serine proteinases with a higher superficial hydrophobicity than insects belonging to other orders, which may be associated to oligomerization of enzymes and resistance to inhibitors present in the food. This was confirmed by hydrophobic interaction chromatography and analysis of solvent access to serine proteinases surface. Moreover, inactivations of chymotrypsins by TPCK showed that S. frugiperda chymotrypsins react one order slower and has an optimum pH of modification more than 1 unit higher than chymotrypsins of D. saccharalis and T. molitor, which was related with the resistance of the enzyme to the presence of plant ketones, since S. frugiperda is a polyphagous organism. The digestive trypsin from Periplaneta americana midgut was purified microssequenced, resulting in the sequence VSPAFSYGTG, coincident to the MPA3 allergen (named PaTry), which is expressed in the caeca and anterior ventriculus. Western blot using M. domestica trypsin antisera recognized a single band, and immunohistochemical assays using this antisera showed that the P. americana trypsin is secreted by exocitosys in caeca and anterior ventriculus, which is coincident to the expression data. Although the major M. domestica chymotrypsin activity is present in the posterior ventriculus, only 28% of the activity is lost in feces, because 31% of activity is membrane-bound, and 41% is in the cellular soluble fraction (glycocalix-associated), and only 12% of total activity is soluble in the lumen, indicating the existence of at least two molecular species of chymotrypsins. Thermal inactivations of both activities (soluble and membrane-bound) showed that they may represent two different molecular enzymes, since the membrane-bound activity has a higher half-life than the soluble both in the presence and in the absence of Triton X-100. Both activities presented a linear first-order inactivation kinetic. In gel assays showed the presence of only one activity band in the midgut of 30 kDa. The major soluble activity was purified through one affinitychromatography, and active fractions presented a single 30 kDa band, a optimum pH of 7.4 and was 90% modified by TPCK 0.1 mM at pH 8.5 during 15 min. This enzyme preferentially cleaves substrates containing Phe residues in P1, although it cleaves substrates containing Tyr and Leu. A contig of a chymotrypsin-like sequence was randomly obtained from a cDNA library of M. domestica midguts from 71 ESTs (a total of 826 sequences), indicating that this sequence corresponds to the major activity present in the lumen. This sequence, named MdChy1, predicted a protein with 28639.2 Da which was cloned, recombinantly expressed in E. coli BL21 (DE-3) Star, this recombinant MdChy1 was used to raise polyclonal antibodies in rabbit. A western blot using this antisera recognised a single band in the anterior and posterior ventriculus, but not in the middle. Imunno-gold labeling of epithelium marked proteins in the lumen, at the microvilli and inside small vesicles, demonstrating that chymotrypsin is secreted through exocytosis in M. domestica and reinforcing that MdChy1 corresponds to the major chymotryptic activity found in the midgut. A semi-quantitative RT-PCR of M. domestica serine proteinase-like genes demonstrated that there are two set of genes, one expressed in the anterior and another in the posterior ventriculus, as visualized in western blot. MdChy1 is expressed in the posterior ventriculus, where the major chymotryptic activity is found. A phylogenetic reconstruction of Drosophila melanogaster chymotrypsin-like sequences and M. domestica chymotrypsins showed that MdChy1 branched with sequences expressed in midgut, thus coding proteins involved in digestion.

Os teredinídeos são bivalves perfuradores de madeira. Esses animais desenvolveram a capacidade de utilizar a madeira como fonte de nutrientes, mantendo a capacidade de alimentar-se de material em suspensão. A importância relativa da madeira na alimentação em relação aos hábitos suspensívoros, o local onde a digestão de celulose ocorre, e a origem da celulose envolvida no processo (endógena ou exógena), permanecem desconhecidos. O objetivo do trabalho, portanto, é investigar o processo digestivo nesses animais. Nausitora fusticula (Jeffreys, 1860) foi escolhida por ser uma espécie cuja anatomia é bem descrita e por ocorrer em grande abundância no litoral de São Paulo. Os troncos contendo os animais foram coletados no manguezal da Praia Dura, Ubatuba-SP. Testes enzimáticos foram realizados em diferentes órgãos do trato digestivo (glândula digestiva especializada e normal, apêndice armazenador de madeira, intestino, canal anal) e brânquias; sobre amido, laminarina, liquenana, carboximetilcelulose (CMC), celulose microcristalina (Avicel®), maltose e β-glicosidase. A digestão de carboidratos ocorre em todos os órgãos analisados, exceto para celulose microcristalina (Avicel®). As maiores atividades foram encontradas no divertículo digestivo especializado e no apêndice. A presença de atividade enzimática nos ctenídeos aponta para a importância das bactérias da glândula de Deshayes. A digestão de carboximetilcelulose (CMC) ocorre em menor proporção que de outros carboidratos. A madeira é de importância significativa devido a digestão de hemiceluloses. Porém não foi possível determinar se a madeira é mais ou menos importante do que o material filtrado, nem precisamente a origem das enzimas que atuam nestes animais. / Teredinids are wood boring bivalves. They evolved to use wood as a source of nutrient, besides keeping the suspension-feeding habit. The role of wood and plankton in the diet of these animals, the structures in which digestion takes place and the origin of the cellulase (endogenous or exogenous) remain uncertain. Nausitora fusticula (Jeffreys, 1860) was chosen because the funcional anatomy of this species is well described and it’s common inhabitant of the mangroves of São Paulo state. The logs containg N. Fusticula were collected in the mangrove of Praia Dura, Ubatuba, São Paulo Enzymatic activities over starch, carboximetilcellulase (CMC), microcristalinecelulose (Avicel®), lichenan, laminarin, maltose and β-glucosid in different organs of the digestive tract and ctenidia of this species were analyzed. The digestion of were detected in the organs analyzed, mainly on the appendix and the SDD, except for microcristaline cellulose (Avicel®). The enzymatic activities occur mainly in the appendix and the specialized digestive diverticule (SDD). The presence of enzymatic atctivity in the ctenidia suggests the importance of the glands of Deshayes in the digestive process. The digestion of CMC is less significant than of the other carbohydrates. The results suggest that wood plays a significant role in the nutrition of this species, mainly due to digestion of hemicelulloses. Still, it is not possible to know if the wood is more important than the plankton in the diet, or to precisely identify the origin of the cellulase.

Le syndrome métabolique (MS), une association des plus dangereux facteurs de risque pour les maladies cardiovasculaires et le diabète de type 2, est devenu l'un des principaux défis cliniques et de santé publique dans le monde. Un nombre croissant d’évidences s’est accumulé au cours de la dernière décennie, démontrant l'efficacité de certains composés bioactifs alimentaires pour le traitement et la prévention du MS. Néanmoins, la plupart des études d'intervention administre les composés bioactifs sous forme de composés purs, sans considérer que l'interaction entre les bioactifs ajoutés et l'ensemble de la matrice alimentaire peut impacter la bioaccessibilité, la biodisponibilité et, par conséquent, l’efficacité de ces molécules bioactives.L'objectif principal de cette thèse, intégrée dans le projet européen PATHWAY-27, était de formuler des aliments enrichis en composés bioactifs potentiellement efficaces contre le MS, et d'étudier l'effet de la matrice alimentaire sur la bioaccessibilité et la biodisponibilité de ces bioactifs. Cette étude a mis l'accent sur l'utilisation des anthocyanes, de l’acide docosahexaénoïque et, dans une moindre mesure, des bêta-glucanes comme ingrédients bioactifs pour enrichir des produits laitiers et des produits à base d'œuf. Une combinaison des modèles de digestion in vitro et in vivo (chez le porc) a été utilisée.La composition et la structure des matrices alimentaires ont impacté la libération et la solubilisation de substances bioactives au cours de la digestion (bioaccessibilité), tel que démontré in vitro et in vivo. La structure de / Metabolic Syndrome (MS), a constellation of the most dangerous cardiovascular disease and type 2 diabetes mellitus risk factors, has become one of the major clinical and public health challenges worldwide. During the last decade, many bioactives have been proposed as effective for the treatment and prevention of MS. However, most intervention studies administer bioactives as pure compounds, without consider that bioactive-food matrix interactions could deeply impact on the bioaccessibility, bioavailability and hence on the effectiveness of bioactives.The main objective of this thesis, included within the European project PATHWAY-27, was to formulate potential effective bioactive-enriched foods against MS and to investigate the effect of the food matrix on the bioaccessibility and bioavailability of dietary bioactives.In particular, this study focused in the use of dairy and egg-based products as matrices and in the addition of anthocyanins, docosahexaenoic acid and, to a lesser extent, beta glucan as bioactives. A combination of in vitro and in vivo (pig) digestion models was used.Both the structure and the composition of the food matrices impacted the release and the solubilisation of bioactives during digestion (bioaccessibility), as demonstrated in vitro and in vivo. In addition, the structure of the food matrix modulated the final amount of DHA into the systemic circulation of pigs (bioavailability). This study proves that understanding how dietary bioactives interact with the matrix in which they are included in is the basis for the production of effective bioact

Avec 67 Mt de fumiers de bovins récupérés chaque année, la France possède un gisement considérable de substrats agricoles mobilisables et valorisables par méthanisation. Le procédé de méthanisation par voie sèche, discontinu, avec recirculation de lixiviat semble être le mieux adapté à la valorisation de ce type de substrats à forte teneur en matière sèche (>20%). A l’heure actuelle, ce procédé est cependant rare sur le territoire. Afin de permettre et de pérenniser le développement de cette technologie, des verrous techniques et scientifiques doivent être levés, notamment ceux qui portent sur la recirculation des lixiviats. L’objectif de cette thèse est d’optimiser le procédé de méthanisation par voie sèche appliquée aux effluents agricoles (principalement fumiers de bovins), afin d’atteindre les conditions les plus favorables à la production d’un maximum de biogaz, de façon constante et en un minimum de temps en considérant les contraintes relatives à un tel procédé. Dans un premier temps, l’objectif a été de comprendre le rôle du lixiviat dans ce procédé de digestion anaérobie discontinu, d’un point de vue biologique. Pour se faire quatre lixiviats ayant différentes origines ont été utilisés. Deux d’entre eux étaient biologiquement actifs (lixiviats provenant de méthaniseurs) et les deux autres stérilisés. Du point de vue abiotique, il a été montré que pour favoriser la digestion anaérobie, le lixiviat devait avoir un pH adéquat, présenter une concentration suffisante de nutriments et un fort pouvoir tampon. D’un point de vue biotique, deux communautés distinctes de microorganismes évoluent dans le lixiviat et dans le fumier, sans aucun transfert entre ces deux environnements, limitant ainsi le rôle d’inoculation souvent attribué au lixiviat. Dans un deuxième temps, la réalisation d’un plan d’expérience a permis d’identifier, au laboratoire sur pilotes instrumentés, des paramètres de recirculation du lixiviat qui influencent les vitesses de production de méthane. Ainsi, le temps entre les recirculations, le volume recirculé et le ratio lixiviat/substrat initialement introduit jouent sur la forme des cinétiques de production. En actionnant l’un ou l’autre de ces leviers, il serait potentiellement possible d’adapter la production de méthane, en fonction des besoins des systèmes de valorisation du biogaz en place sur ces installations. Enfin, la méthode de tomographie de résistivité électrique a été utilisée, à grande échelle, pour suivre la percolation du lixiviat à travers le massif et mettre en évidence les disparités de distribution du lixiviat dans le massif. Cette étude a montré que la géométrie du réseau de recirculation du lixiviat, consistant en un tuyau perforé parcourant la surface du massif dans le sens de la longueur, ne permettait pas un écoulement homogène du lixiviat dans les digesteurs. Certaines zones n’ayant jamais été humidifiées, la production de méthane se trouve réduite et les rendements amoindris. Cette thèse s’articule autour de plusieurs analyses multi-échelles et complémentaires permettant de mieux comprendre le rôle du lixiviat, d’améliorer sa mise en œuvre et son utilisation pour la digestion anaérobie des fumiers de bovins. / With 67 Mt of cattle manure recovered every year, France has a significant source of agricultural waste to be valorised through anaerobic digestion. Batch mode solid state anaerobic digestion (SSAD) process with leachate recirculation seems to be the most suitable technique to valorise that kind of waste, which contains high total solid content (>20%). Currently, this process is rare on French territory. To develop batch mode SSAD, various technical and scientific barriers must be straightened out, and particularly those concerning leachate recirculation. The objective of this work is to optimize SSAD of agricultural was (mostly cattle manure) by pointing out the most favorable settings that allow producing high volumes of biogas, steadily and within a short time, taking into account the particular technical constraints of this process. First of all, the objective was to better understand the biological role of leachate in the batch mode SSAD process. For that purpose, four leachates with different origins were used. Two of them were biologically active (from existing digesters) while the two others were sterilized. It was demonstrated an effective anaerobic digestion was favored by using a leachate gathering the following abiotic characteristics: an adequate pH, a strong buffer capacity and the presence of the right concentration of nutrients. From the biotic point of view, dedicated communities of microbes were in progress in each liquid and solid environment with nested relationship. The role of leachate as inoculum was then limited. In a second part, the influent parameters of leachate recirculation were identified at laboratory scale, by setting up a design of experiment. It was found that the elapsed time between two recirculations, the recirculated volume of leachate and the initial leachate to substrate ratio introduced in the reactor could modify the shape of methane production rate. By changing one or several of those parameters, it would be possible to control and adapt methane production rate to the specific constraints of one SSAD plant. In the last part, the Electrical Resistivity Tomography (ERT) method was used, at full scale, to monitor the leachate percolation through the solid waste and highlight leachate distribution disparities. It was shown the leachate injection system consisting of a perforated pipe laying on the solid top surface was not efficient to evenly moisten the solid waste. From that observation, it was concluded that cumulated methane production could be improved if areas that were not in contact with leachate could be moistened by using another leachate injection system. This manuscript was based on several multi-scale and complementary analyses that allow a better understanding of the role of leachate during SSAD process and an improvement of its utilization for the anaerobic digestion of cattle manure.

Lorsque l'allaitement est impossible, du lait maternel pasteurisé (LMP) est préférentiellement administré, en particulier aux nouveau-nés hospitalisés. La pasteurisation de Holder (62,5°, 30 min) est appliquée pour des raisons sanitaires mais pourrait réduire l'absorption des lipides via l'inactivation des lipases endogènes du lait. L’homogénéisation du LMP pourrait contrer cet effet négatif en augmentant la surface disponible pour l’adsorption des enzymes. L’objectif de cette thèse était d’étudier l’impact de la pasteurisation de Holder et de l’homogénéisation par ultrasons sur la digestion du LM chez le nouveau-né. Un modèle de digestion in vitro a été mis en place pour évaluer la digestion gastro-intestinale de LM cru (LMC) vs. LMP aux stades « nouveau-né à terme » ou « prématuré ». Une étude clinique a été menée chez des nouveau-nés prématurés pour comparer la digestion gastrique de (A) LMC vs. LMP et (B) LMP vs. LM pasteurisé et homogénéisé (LMPH).La pasteurisation et l’homogénéisation ont modifié la structure initiale du LM, ses cinétiques digestives et sa désintégration structurale. In vitro, la pasteurisation a réduit la lipolyse gastrique au stade à terme, alors qu’aucun impact n'a été observé au stade prématuré. La lipolyse intestinale, in vitro, a été réduite. In vivo, la pasteurisation a accélérée la protéolyse gastrique de la lactoferrine et a réduit celle de l’a-lactalbumine. L'homogénéisation a accéléré la lipolyse et la protéolyse de l'albumine sérique. Concernant les conditions physiologiques, l’activité lipolytique postprandiale était augmentée après adm / When breastfeeding is not possible, pasteurized human milk (PHM) from milk banks is preferentially administered, especially for vulnerable hospitalized newborns. Holder pasteurization (62.5°, 30 min) is applied for sanitary reasons but may reduce fat absorption through inactivation of milk endogenous lipases. This could be counteracted by homogenization of PHM through an increase of the specific surface available for enzyme adsorption. The objective of this thesis was to study the impact of Holder pasteurization and ultrasonic homogenization on the digestion of HM in the newborn. An in vitro dynamic model was used to evaluate the gastrointestinal digestion of raw HM (RHM) vs. PHM at preterm and term stages. A clinical trial was conducted on hospitalized preterm newborns for comparing the gastric digestion of (A) RHM vs. PHM and (B) PHM vs. pasteurized-homogenized HM (PHHM). Pasteurization and homogenization affected the HM initial structure and its digestive kinetics and structural disWhile gastric lipolysis was reduced after pasteurization in term in vitro study, no impact was observed at the preterm stage. Intestinal lipolysis, in vitro, was reduced by pasteurization. Gastric proteolysis was selectively affected by pasteurization, being, in vivo, faster for lactoferrin and slower for a-lactalbumin. Homogenization increased lipolysis and proteolysis of serum albumin. Some physiological gastric conditions were affected by treatments: RHM had enhanced postprandial lipolytic activity and PHHM had a reduced gastric emptying time. The in vivo data described here may help to i