Feed intake assessment is a valuable tool for herd management decisions. The use of markers, either internal or external, is currently the most used technique for estimating feed intake in production animals. Three experiments were conducted with beef and dairy cattle. In dairy cows fed a corn silage based diet with 45% concentrate, the average fecal recovery (FR) of TiO2 was higher than FR of Cr2O3 and both FR were more than unity. The FR was unaffected by the fecal sampling procedure but, estimates for dry-matter digestibility (DMD) and fecal output (FO) were affected. The Cr2O3 + indigestible acid detergent fiber (iADF) marker pair produced accurate dry-matter intake (DMI) estimates. In steers fed diets with different forage sources FR of TiO2 was close to 1 and this marker produced adequate FO estimates. The FR was affected by the forage source that composed the diet and none of the marker pairs produced accurate DMI estimates. In young Nelore bulls fed corn silage or Tifton-85 hay based diets with varying F:C ratios, the average FR of internal markers acetyl bromide lignin (ABL), indigestible neutral detergent fiber (iNDF), iADF and cutin was different from 100%. Markers Cr2O3 and TiO2 had FR lower and higher than 100%, respectively. The combination of internal and external markers to estimate DMI produced satisfactory and accurate results, particularly Cr2O3 based pairs with iNDF and iADF. Internal markers ABL and cutin deserve more attention. The GRAB sampling procedures yielded accurate DMD, FO and DMI estimates, which were as good as or better than BULK sampling procedures. Regardless of the fecal sampling method and the composition of the diet, it is necessary to establish the FR of the markers to be used in each experiment, in order to obtain correct estimates. None of the markers had complete FR consistent throughout the 3 experiments. Cutin and ABL had lower than unity FR on all diets and failed to produce accurate DMD estimates. When either one was paired with Cr2O3 or TiO2, DMI estimates were also not accurate. Of the indigestible fibers, iNDF and iADF, the later was more accurate in estimating DMI when paired with Cr2O3. Consistently throughout the experiments, FR was lower than and higher than unity for internal and external markers, respectively. Corrected FO estimates were accurate for Cr2O3 on various diets under GRAB sampling. The same was not true for TiO2, which even after FR correction was applied failed to produce accurate FO estimates consistently. The method of dosing the external markers is extremely important and greatly affects and determines results. Whichever the method, it must allow the animals to display normal feeding behavior and not affect performance. The GRAB sampling procedures can replace TFC (once FR is established) which may open new possibilities for pasture based or collectively housed animals. / A determinação do consumo de alimentos é uma valiosa ferramenta na hora da tomada de decisões de manejo do rebanho. O uso de marcadores, sejam internos ou externos, é atualmente a técnica mais utilizada para estimar o consumo em animais de produção. Três experimentos foram conduzidos. Em vacas de leite alimentadas com silagem de milho com 45% de concentrado, a recuperação fecal (RF) média de TiO2 foi maior do que a RF de Cr2O3 e ambas foram maiores do que a unidade. A RF não foi afetada pelo método de coleta de fezes, mas, as estimativas de digestibilidade da matéria seca e produção fecal (PF) foram. A dupla de marcadores Cr2O3+i fibra detergente ácido indigestível (iADF) produziu estimativas de consumo de matéria seca (CMS) acuradas. Em novilhos alimentados com diferentes fontes de forragem, a RF do TiO2 foi próxima a 1 e este marcador produziu estimativas de PF adequadas. A RF foi afetada pela fonte de forragem que compunha a dieta e nenhum dos marcadores produziu estimativas de CMS acuradas. Em tourinhos Nelore alimentados com dietas compostas de silagem de milho ou feno de Tifton-85 e diferentes relações de volumoso:concentrado, a RF média dos marcadores internos lignina brometo de acetila (LBA), fibra detergente ácido indigestível (iFDN), (iFDA) e cutina foi diferente de 100%. Os marcadores Cr2O3 e TiO2 tiveram RF menor e maior que 100%, respectivamente. A combinação de marcadores internos e externos para estimar o CMS produziu resultados acurados e satisfatórios, principalmente as duplas Cr2O3 e iFDN ou iFDA. Os marcadores internos LBA e cutina merecem mais estudos. O método de coleta GRAB produziu estimativas de DMS, PF e CMS acuradas, as quais foram iguais ou melhores que as produzidas pelo método de coleta BULK. Independentemente do método de coleta de fezes e da composição da dieta, é necessário estabelecer a RF real dos marcadores que serão usados em experimento para obter estimativas corretas. Nenhum dos marcadores teve RF completa e consistente nos 3 experimentos. A cutina e LBA tiveram RF menor do que a unidade em todas as dietas e falharam em produzir estimativas acuradas de DMS. Quando qualquer dos dois foi pareado com Cr2O3 ou TiO2 as estimativas de CMS também não foram acuradas. Das fibras indigestíveis, iFDN e iFDA, a segunda foi mais acurada em estimar o CMS quando pareada com Cr2O3. As estimativas de PF corrigida foram acuradas para Cr2O3 em diferentes dietas sob metodologia de coleta GRAB. O mesmo não foi observado para o TiO2, que produziu estimativas enviesadas inclusive após a correção. O método de dosagem dos marcadores externos é extremadamente importante já que afeta e determina em grande medida os resultados. Qualquer que seja o método, este deve permitir ao animal comportar-se e alimentar-se normalmente sem comprometer seu desempenho. Os métodos de coleta GRAB podem substituir a coleta total de fezes (CTF) (após determinação da RF) o que poderá abrir novas possibilidades para estudos com animais em pastagem ou alojados em baias coletivas.

Les plantes sont des organismes sessiles qui ne peuvent fuir des conditions souvent défavorables et doivent par conséquent s’adapter à un environnement hostile pour survivre. La cutine partie intégrante de la cuticule qui joue un rôle de barrière pour la plante est un polymère lipidique constitué principalement d’acides gras en C16 et C18 hydroxylés et époxydés reliés entre eux par des liaisons ester mettant en jeu les fonctions carboxyl et ω-hydroxyl des acides gras. La cutine ne joue pas seulement un rôle de barrière physique mais joue un rôle de réservoir de molécules possédant des propriétés physiologiques fondamentales. Grâce à des approches biochimiques et génétiques, nos travaux ont permis de mettre en évidence AtEH1, une époxyde hydrolase responsable de la formation des diols incorporés dans la cutine d’Arabidopsis thaliana. Ces diols sont décrits dans la littérature comme intervenant dans les interactions plante-pathogène. Nous avons également montré que ces composés ainsi que d’autres dérivés d’acides gras sont perçus par la plante. Nous avons identifié et caractérisé CYP77B1, une époxygénase d’acide gras qui a un rôle potentiel à jouer dans la formation d’acides gras polyhydroxylés incorporés dans la cutine. / Plants are sessile organisms that are not able to escape from difficult environmental conditions and therefore have to adapt to multiple abiotic and biotic stress to survive. Cutin is a part of the cuticle which plays a major role as a barrier for the plant. It’s a lipid polymer composed mainly by hydroxylated and epoxidized C16 and C18 fatty acids linked together by ester links involving the carboxyl and ω-hydroxyl functions of those fatty acids. Cutin plays also a role as a reservoir of molecules with fundamental physiological properties. With biochemical and genetic approaches, we characterized AtEH1, an epoxide hydrolase responsible for the formation of diols incorporated in Arabidopsis thaliana cutin. These diols are described as being involved in plant-pathogen interactions. We also showed that these compounds as well as others fatty acids derivatives are perceived by plants. We have also identified and characterized CYP77B1, an epoxidase that has a potential role in the formation of polyhydroxylated fatty acids incorporated in cutin.

La cutine est un polymère d'acides gras oxydés et de glycérol propre aux plantes. Elle forme la matrice structurale de la cuticule qui recouvre l'épiderme des parties aériennes et joue un rôle vital pour les plantes en empêchant la dessiccation. La biosynthèse du polymère de cutine a été étudiée chez la plante modèle Arabidopsis thaliana. Des mutants perte-de-fonction pour la monooxygénase de type cytochrome P450 CYP77A4 ont été isolés. L'analyse de lignées transgéniques exprimant le gène rapporteur GUS sous le contrôle du promoteur de CYP77A4 a montré que le gène était exprimé essentiellement dans les organes floraux et les graines. L'analyse de la cutine dans divers organes a permis de démontrer que le gène était essentiel pour la synthèse d'un acide gras trihydroxylé en C18 présent dans les polyesters des embryons. Une méthode permettant la séparation de l'embryon et des téguments des graines en quantité suffisante pour analyser la cutine a été mise au point. Le profil de monomères des embryons mutants a montré que CYP77A4 est une époxygénase de la voie de biosynthèse des monomères de cutine en C18. L'étude de la physiologie des mutants a par ailleurs permis de démontrer que les acides gras trihydroxylés de la cuticule de l'embryon jouent un rôle important dans la germination de la graine en conditions de stress salin. Dans une deuxième étude, des mutants perte-de-fonction et des suexpresseurs pour le gène d'Arabidopsis BODYGUARD (BDG) codant une protéine de la superfamille des hydrolases à repliement α/β ont été caractérisés. L'analyse des polyesters dans ces lignées a permis de montrer que cette protéine jouait en fait un rôle dans la biosynthèse de la cutine. / Cutin is a polymer of oxidized fatty acids and glycerol specific to plants. It forms the structural matrix of the waxy cuticle covering the epidermis of the aerial parts and plays a vital role in plants by preventing desiccation. Biosynthesis of cutin polymer was studied in the model plant Arabidopsis thaliana. Mutant loss-of-function monooxygenase type cytochrome P450 CYP77A4 were isolated. The analysis of transgenic lines expressing the GUS reporter gene under the control of the promoter of CYP77A4 showed that the gene was expressed mainly in floral organs and seeds. The analysis of various organs in the cutin demonstrated that the gene was essential for the synthesis of a C18 trihydroxy polyesters present in seed polyesters (9,10,18-trihydroxyoctadecenoic acid). A method for the separation of the embryo and seed coat allowing to analyze embryo polyesters was developed. The trihydroxy C18 fatty acid was found to be the major cutin embryo monomer. Profile of cutin monomers in mutant embryos showed that CYP77A4 is an epoxygenase in the biosynthetic pathway of C18 cutin monomers. The study of the physiology of the mutants also showed that the trihydroxy- fatty acids of the embryo cuticle play an important role in the germination of the seed under conditions of salt stress. In a second study, mutant loss-of-function and overexpressors for the Arabidopsis gene BODYGUARD encoding a protein of the α / β hydrolase fold superfamily have been characterized. Analysis of polyesters in these lines showed that this protein, whose role in the formation of the cuticle was not understood, plays in fact a role in cutin biosynthesis.

No description available.

No description available.

Soil organic matter (SOM) contains about twice the amount of carbon in the atmosphere. With global changes, the potential shifts in SOM quantity and quality are a major concern. Due to its heterogeneity, SOM remains largely unknown in terms of its molecular composition and responses to climatic events. Traditional bulk soil analysis cannot depict the structural changes in SOM. This thesis applies two complementary molecular-level methods, i.e., SOM biomarker gas chromatography/mass spectrometry (GC/MS) and nuclear magnetic resonance (NMR) spectroscopy, to examine the origin and degradation of various SOM components in grassland and temperate forest soils, and to investigate the shifts in microbial community and SOM composition with both laboratory- and field-simulated global changes, such as frequent freeze-thaw cycles, increasing soil temperatures, elevated atmospheric CO2 levels, and nitrogen (N) deposition. This thesis has several major findings. First, as the most active component in soil, microbial communities were sensitive to substrate availability changes resulting from prolonged soil incubation, freeze-thaw-induced cell lyses, N fertilization and increased plant inputs under elevated CO2 or soil warming. Microbial community shifts have direct impacts on SOM decomposition patterns. For instance, an increased fungal community was believed to contribute to the enhanced lignin oxidation in an in situ soil warming experiment as the primary degrader of lignin in terrestrial environments. Second, contrast to the conventional belief that aromatic structure was recalcitrant and stable in SOM, ester-bond aliphatic lipids primarily originating from plant cutin and suberin were preferentially preserved in the Canadian Prairie grassland soil profiles as compared with lignin-derived phenols. Cutin- and suberin-derived compounds also demonstrated higher stability during soil incubation. With an increased litter production under elevated CO2 or global warming, an enrichment of alkyl structures that had strong contributions from leaf cuticles was observed in the Duke Forest Free Air CO2 Enrichment (FACE) and soil warming experiments, suggesting an accumulation of plant-derived recalcitrant carbon in the soil. These results have significant implications for carbon sequestration and terrestrial biogeochemistry. Overall, this thesis represents the first of its kind to employ comprehensive molecular-level techniques in the investigation of SOM structural alterations under global changes.

Soil organic matter (SOM) contains about twice the amount of carbon in the atmosphere. With global changes, the potential shifts in SOM quantity and quality are a major concern. Due to its heterogeneity, SOM remains largely unknown in terms of its molecular composition and responses to climatic events. Traditional bulk soil analysis cannot depict the structural changes in SOM. This thesis applies two complementary molecular-level methods, i.e., SOM biomarker gas chromatography/mass spectrometry (GC/MS) and nuclear magnetic resonance (NMR) spectroscopy, to examine the origin and degradation of various SOM components in grassland and temperate forest soils, and to investigate the shifts in microbial community and SOM composition with both laboratory- and field-simulated global changes, such as frequent freeze-thaw cycles, increasing soil temperatures, elevated atmospheric CO2 levels, and nitrogen (N) deposition. This thesis has several major findings. First, as the most active component in soil, microbial communities were sensitive to substrate availability changes resulting from prolonged soil incubation, freeze-thaw-induced cell lyses, N fertilization and increased plant inputs under elevated CO2 or soil warming. Microbial community shifts have direct impacts on SOM decomposition patterns. For instance, an increased fungal community was believed to contribute to the enhanced lignin oxidation in an in situ soil warming experiment as the primary degrader of lignin in terrestrial environments. Second, contrast to the conventional belief that aromatic structure was recalcitrant and stable in SOM, ester-bond aliphatic lipids primarily originating from plant cutin and suberin were preferentially preserved in the Canadian Prairie grassland soil profiles as compared with lignin-derived phenols. Cutin- and suberin-derived compounds also demonstrated higher stability during soil incubation. With an increased litter production under elevated CO2 or global warming, an enrichment of alkyl structures that had strong contributions from leaf cuticles was observed in the Duke Forest Free Air CO2 Enrichment (FACE) and soil warming experiments, suggesting an accumulation of plant-derived recalcitrant carbon in the soil. These results have significant implications for carbon sequestration and terrestrial biogeochemistry. Overall, this thesis represents the first of its kind to employ comprehensive molecular-level techniques in the investigation of SOM structural alterations under global changes.