Grâce au développement des technologies de métagénomique au cours des dix dernières années, il a été constaté que les micro-organismes représentent la plus grande ressource de diversité métabolique et génétique sur Terre. En effet, un gramme de sol contient 109 cellules bactériennes et 103-104 différentes espèces bactériennes. Certaines sont en mesure de réaliser des réactions enzymatiques conduisant à la dégradation complète de certains polluants toxiques pour l'environnement comme les composés organiques tels que la quinoléine. Cependant, l'immense réservoir de molécules et enzymes microbiennes n'a pas encore été exploité, car plus de 99% d'entre elles ne sont, pour l'instant, pas cultivables in vitro. Mon travail s'inscrit dans le cadre d'une collaboration entre l'Université SJTU (Shanghai Jiao Tong Université en Chine) et le groupe de G. M.E (Génomique Microbienne Environmentale) du laboratoire Ampère à l'Ecole Centrale de Lyon. Nos partenaires à l'Université SJTU ont construit un réacteur de dénitrification à l'échelle du laboratoire capable de dégrader la quinoléine en retirant la demande chimique en oxygène. Un nouvel outil appelé "Genefish" a été developpé dans notre laboratoire comme une méthode alternative de la métagénomique pour aider à la découverte de nouveaux gènes d'intérêt industriel ou environnemental. A la suite des premiers travaux réalisés dans notre laboratoire, ma thèse présentée ici comporte deux parties.Dans la première partie de ce travail, nous avons étudié le potentiel de dégradation de la quinoléine présente dans les bactéries d'un sol de référence largement étudié au laboratoire. Pour cela nous avons mis en place des expériences de microcosme qui visent à révéler la diversité potentielle des bactéries responsables de la dégradation de la quinoléine. Des analyses comparatives des profils RISA (Ribosomal Intergenic Spacer analysis) nous ont permis de mettre en évidence des changements dans la structure de la communauté des bactéries du sol incubé en conditions aérobie et anaérobie en présence de quinoléine. La dégradation de la quinoléine a été confirmée par technique de GC/MS (Gas Chromatography-Mass Spectrometry). Les travaux futurs seront de vérifier la communauté de bactéries responsables de la dégradation de quinoléine en utilisant la technique de NGS (Next Generation Sequencing).Le deuxième objectif de ma thèse a été d'utiliser Genefish dont la finalité est de capturer des gènes ciblés (le gène bcr qui serait responsable de la degradation de quinoléine dans le réacteur de nos partenaires) dans l'ADN métagénomique extrait du sol. Genefish consiste à élaborer une souche d'E.coli incluant un plasmide de capture permettant de pêcher les gènes recherchés dans un échantillon d'ADN metagénomique par recombinaison homologue. Le plasmide de capture comprend une cassette de deux gènes toxiques pour la souche qui activés par induction chimique vont permettre la sélection positive directe des clones recombinants, et deux sites multiples de clonage dans lesquels sont insérées les zones de recombinaison qui vont jouer le rôle d'hameçons. Nous avons testé la capacité de Genefish à capturer des produits PCR du gène bcr, l'efficacité de recombinaison reste faible à cause de la persistance de plusieurs copies du plasmide suicide dans la cellule après l' évenement de recombinaison. Par conséquent, trois stratégies ont été essayées pour améliorer l'efficacité: la co-électroporation, la ségrégation de plasmide et la construction de plasmide suicide en mono-copie. Finalement, la stratégie de la ségrégation plasmidique fonctionne mais l'efficacité de recombinaison est encore trop faible peut-être due à l'incertitude des modèles de recombinaison homologue. Les travaux futurs se concentreront sur l'amélioration des fréquences de recombinaison par transfert de fragments du plasmide de capture dans le chromosome de la souche Genefish.

Blueberry spanworm, Itame argillacearia (Packard), is an important defoliator of wild (syn. ‘lowbush’) blueberry in north-eastern North America. Identification of I. argillacearia sex pheromone(s) could be useful for monitoring, mating disruption or mass trapping, as a way to improve integrated pest management programs for this pest. Thus, the main goal of this study was to identify sex pheromone(s) of I. argillacearia. The courtship, mating and oviposition patterns of I. argillaceara, was studied in the laboratory. GC/MS, GC/EAD and EAG analysis of pheromone gland extracts, in combination with y-tube experiments and two field trapping studies confirmed the chiral-alkenyl-epoxide, (3R,4S)-epoxy-(Z,Z)-6,9-17:H and tri-ene, (Z,Z,Z)-3,6,9-17:H as the major female-produced sex pheromone components. Contech Wing traps® placed at canopy level were effective for capturing male I. argillacearia moths.

A wide range of organic compounds are released from building and furnishing products and these have the potential to adversely affect indoor air quality. There are growing international requirements for testing and controlling these emissions for the protection of public health. The test methods require specialist analytical chemistry facilities based on thermal desorption/gas chromatography/mass spectrometry (TD/GC/MS). This project has addressed the need for better performance and greater automation of the analysis, as well as development of simpler screening tests. A variety of products were tested using screening techniques, with an emission cell method being used as a reference test. Short duration tests, using a micro-scale chamber at slightly elevated temperature, were shown to have the potential to predict emissions occurring during longer term reference tests. Multi-sorbent air sampling tubes, that have the potential to extend the volatility range of compounds determined by a single TD/GC/MS analysis, were compared with Tenax TA tubes specified by current standard methods. This showed no difference in performance for the range of compounds for which Tenax is optimal, with improved performance for a number of more volatile compounds. The determination of formaldehyde was investigated using 2-hydroxymethylpiperidine as a derivatising agent, followed by TD/GC/MS. The results showed the possibility of this method being developed as an alternative to the current standard method that involves solvent elution and liquid chromatography. The performance of a newly developed time-of-flight mass spectrometer was compared with a standard quadrupole instrument. This showed its potential, with the use of re-collection, to extend the concentration range of compounds quantified from a single air sample, of particular benefit for the determination of carcinogens. New compound identification software was applied to increase automation of analysis of the TD/GC/MS data. Good correlation with manual processing was achieved, demonstrating the possibility of routine application to material emissions testing.

It has been discovered during the past few years that demosponges of the order Verongida such as Aplysina cavernicola exhibit chitin-based skeletons. Verongida sponges are well known to produce bioactive brominated tyrosine derivatives. We could recently demonstrate that brominated compounds do not exclusively occur in the cellular matrix but also in the skeletons of the marine sponges Aplysina cavernicola and Ianthella basta. Our measurements imply that these yet unknown compounds are strongly, possibly covalently bound to the sponge skeletons. In the present work, we determined the skeletal amino acid composition of the demosponge A. cavernicola especially with respect to the presence of halogenated amino acids. The investigations of the skeletons before and after MeOH extraction confirmed that only a small amount of the brominated skeleton-bound compounds dissolves in MeOH. The main part of the brominated compounds is strongly attached to the skeletons but can be extracted for example by using Ba(OH)2. Various halogenated tyrosine derivatives were identified by GC-MS and LC-MS in these Ba(OH)2 extracts of the skeletons.

Dans le but d'évaluer la contamination des atmosphères intérieures et extérieures induite par les usages non agricoles de pesticides, deux approches complémentaires ont été mises en oeuvre : l'utilisation de capteurs passifs de type Tenax TA pour réaliser des prélèvements d'air, et l'utilisation de cheveux employés comme biomarqueurs d'exposition. Des campagnes de mesures ont été menées sur plusieurs sites à la suite de traitements de désherbage ou de désinsectisation ainsi quedans des logements. Les échantillons d'air et de cheveux ont été extraits respectivement par thermodésorption et par extraction solide-liquide, avant d'être analysés en chromatographie gazeuse couplée à la spectrométrie de masse (GC-MS). Une augmentation du niveau de contamination de l'air extérieur et intérieur et l'existence de transferts entre ces deux milieux ont pu être observées après l'application de pesticides. Dans les logements, des pesticides actuellement employés mais aussi des pesticides interdits et persistants ont été détectés. Plusieurs pesticides ont également été détectés dans les cheveux, mais l'exposition humaine à ces derniers n'a pas pu toujours être corrélée à une contamination de l'air.

Nitrocellulose is the main component in many types of ammunition, propellants and explosives. The principles of production for nitrocellulose have not changed much since the 19th century when it started being industrially produced for this purpose. The character of the nitrocellulose has a large effect on the end products abilities. The aim of this study was to develop a method that would be able to characterise and distinguish between nitrocellulose from different manufacturers to be able to relate the character of the nitrocellulose to the properties of ammunition, propellants and explosives. Samples were dissolved in acetone and analysed by GC/MS and data were then analysed by multivariable statistics. FTIR was also used to characterise the nitrocellulose. Results from both methods showed very small differences when chromatograms and spectra were analysed. This study shows that GC/MS and FTIR are not suitable for this type of characterisation. The differences between the data were not sufficient to be able to separate the samples from each other. / Nitrocellulosa är den viktigaste komponenten i många typer av ammunition, drivmedel och sprängämnen. Principerna för produktionen av nitrocellulosa har inte förändrats mycket sedan det börjades produceras industriellt för detta ändamål på 1800 talet. Karaktären av nitrocellulosa har en stor inverkan på slutproduktens egenskaper. Syftet med denna studie var att utveckla en metod som skulle kunna karaktärisera och skilja mellan nitrocellulosa från olika tillverkare för att kunna relatera karaktären av nitrocellulosa till egenskaperna hos ammunition, drivmedel och sprängämnen. Proverna löstes i aceton och analyserades med GC/MS och data analyserades med multivariabel statistik. FTIR användes också för att karakterisera nitrocellulosan. Resultaten för båda proverna visade mycket små skillnader när kromatogram och spektra analyserades. Denna studie visar att GC/MS och FTIR inte är lämpliga för denna typ av karaktärisering. Skillnaderna i data var inte tillräckliga för att kunna skilja proverna från varandra.

Investigating Neolithic pottery and vessel use could elucidate the duality between the farming Funnel Beaker Culture and the hunter-gathering Pitted Ware Culture during the Neolithic. The two archaeological groups differ on several accounts that are of great importance when interpreting past societies. However, it is the suggested differential subsistence economies that are of specific interest for this particular investigation. A comparative study based on the absorbed fatty acids in the ceramic material from two different Neolithic sites addresses the food cultures of the farming subsistence and the contrasting, contemporary hunter-gatherer society and the differences in resource-use. The investigation argues that food acts as an active social binder, and stress the importance of incorporating this aspect when discussing past cultures. The results of the analyses display difference in vessel use between the two sites as well as an intra-site difference at Korsnäs. It is argued that these differences are indicative of deviating food-cultures and spatial organisation at Korsnäs respectively. These results are combined with the previously conducted osteological analyses and stable isotopic analyses an approach that contribute to a more dynamic understanding of the Neolithic food cultures than what has been available before. Investigating Neolithic pottery and vessel use could elucidate the duality between the farming Funnel Beaker Culture and the hunter-gathering Pitted Ware Culture during the Neolithic. The two archaeological groups differ on several accounts that are of great importance when interpreting past societies. However, it is the suggested differential subsistence economies that are of specific interest for this particular investigation. A comparative study based on the absorbed fatty acids in the ceramic material from two different Neolithic sites addresses the food cultures of the farming subsistence and the contrasting, contemporary hunter-gatherer society and the differences in resource-use. The investigation argues that food acts as an active social binder, and stress the importance of incorporating this aspect when discussing past cultures. The results of the analyses display difference in vessel use between the two sites as well as an intra-site difference at Korsnäs. It is argued that these differences are indicative of deviating food-cultures and spatial organisation at Korsnäs respectively. These results are combined with the previously conducted osteological analyses and stable isotopic analyses an approach that contribute to a more dynamic understanding of the Neolithic food cultures than what has been available before.

Biological processes in living organisms consist of a vast number of different molecular networks and interactions, which are complex and often hidden from our understanding. This work is focused on recovery of such details for two quite distant examples: acclimation to extreme freezing tolerance in Siberian spruce (Picea obovata) and detection of proteins associated with prostate cancer. The first biological system in the study, upon P. obovata, is interesting by this species ability to adapt and sustain extremely low temperatures, such as -60⁰C or below. Despite decades of investigations, the essential features and mechanisms of the amazing ability of this species still remains unclear. To enhance knowledge about extreme freezing tolerance, the metabolome and proteome of P. obovata’s needles were collected during the tree’s acclimation period, ranging from mid August to January, and have been analyzed. The second system within this study is the plasma proteome analysis of high risk prostate cancer (PCa) patients, with and without bone metastases. PCa is one of the most common cancers among Swedish men, which can abruptly develop into an aggressive, lethal disease. The diagnostic tools, including PSA-tests, are insufficient in predicting the disease’s aggressiveness and novel prognostic markers are urgently required. Both biological systems have been analyzed following similar steps: by two-dimensional difference gel electrophoresis (2D-DIGE) techniques, followed by protein identification using mass spectrometry (MS) analysis and multivariate methods. Data processing has been utilized for searching for proteins that serve as unique indicators for characterizing the status of the systems. In addition, the gas chromatography-mass spectrometry (GC-MS) study of the metabolic content of P.obovata’s needles, from the extended observation period, has been performed. The studies of both systems, combined with thorough statistical analysis of experimental outcomes, have resulted in novel insights and features for both P. obovata and prostate cancer. In particular, it has been shown that dehydrins, Hsp70s, AAA+ ATPases, lipocalin and several proteins involved in cellular metabolism etc., can be uniquely associated with acclimation to extreme freezing in conifers. Metabolomic analysis of P. obovata needles has revealed systematic metabolic changes in carbohydrate and lipid metabolism. Substantial increase of raffinose, accumulation of desaturated fatty acids, sugar acids, sugar alcohols, amino acids and polyamines that may act as compatible solutes or cryoprotectants have all been observed during the acclimation process. Relevant proteins for prostate cancer progression and aggressiveness have been identified in the plasma proteome study, for patients with and without bone metastasis. Proteins associated with lipid transport, coagulation, inflammation and immune response have been found among them.

Recent developments in converting biomass to bio-chemicals and liquid fuels provide a promising sight to an emerging biofuels industry. Biomass can be converted to energy via thermochemical and biochemical pathways. Thermal degradation processes include liquefaction, gasification, and pyrolysis. Among these biomass technologies, pyrolysis (i.e. a thermochemical conversion process of any organic material in the absence of oxygen) has gained more attention because of its simplicity in design, construction and operation. This research study focuses on comparative assessment of two types of pyrolysis processes and catalytic upgrading of bio-oil for production of transportation fuel intermediates. Slow and fast pyrolysis processes were compared for their respective product yields and properties. Slow pyrolysis bio-oil displayed fossil fuel-like properties, although low yields limit the process making it uneconomically feasible. Fast pyrolysis, on the other hand, show high yields but produces relatively less quality bio-oil. Catalytic transformation of the high-boiling fraction (HBF) of the crude bio-oil from fast pyrolysis was therefore evaluated by performing liquid-phase reactions at moderate temperatures using Pt/HZSM-5 catalyst. High yields of upgraded bio-oils along with improved heating values and reduced oxygen contents were obtained at a reaction temperature of 200°C and ethanol/HBF ratio of 3:1. Better quality, however, was observed at 240 °C even though reaction temperature has no significant effect on coke deposition. The addition of ethanol in the feed has greatly attenuated coke deposition in the catalyst. Major reactions observed are esterification, catalytic cracking, and reforming. Overall mass and energy balances in the conversion of energy sorghum biomass to produce a liquid fuel intermediate obtained sixteen percent (16 wt.%) of the biomass ending up as liquid fuel intermediate, while containing 26% of its initial energy.

Human health is a complex and wide-ranging subject far beyond nutrition and physical exercise. Still, these factors have a huge impact on global health by their ability to prevent diseases and thus promote health. Thus, to identify health risks and benefits, it is necessary to reveal the underlying mechanisms of nutrition and exercise, which in many cases follows a complex chain of events. As a consequence, current health research is generating massive amounts of data from anthropometric parameters, genes, proteins, small molecules (metabolites) et cetera, with the intent to understand these mechanisms. For the study of health responses, especially related to physical exercise and nutrition, alterations in small molecules (metabolites) are in most cases immediate and located close to the phenotypic level and could therefore provide early signs of metabolic imbalances. Since there are roughly as many different responses to exercise and nutrients as there are humans, this quest is highly multifaceted and will benefit from an interpretation of treatment effects on a general as well as on an individual level. This thesis involves the application of chemometric methods to the study of global metabolic reactions, i.e. metabolomics, in a strategy coined predictive metabolomics. Via the application of predictive metabolomics an extensive hypothesis-free biological interpretation has been carried out of metabolite patterns in blood, acquired using gas chromatography-mass spectrometry (GC-MS), related to physical exercise, nutrition and diet, all in the context of human health. In addition, the chemometrics methodology have computational benefits concerning the extraction of relevant information from information-rich data as well as for interpreting general treatment effects and individual responses, as exemplified throughout this work. Health concerns all lifestages, thus this thesis presents a strategic framework in combination with comprehensive interpretations of metabolite patterns throughout life. This includes a broad range of human studies revealing metabolic patterns related to the impact of physical exercise, macronutrient modulation and different fitness status in young healthy males, short and long term dietary treatments in overweight post menopausal women as well as metabolic responses related to probiotics treatment and early development in infants. As a result, the studies included in the thesis have revealed metabolic patterns potentially indicative of an anti-catabolic response to macronutrients in the early recovery phase following exercise. Moreover, moderate differences in the metabolome associated with cardiorespiratory fitness level were detected, which could be linked to variation in the inflammatory and antioxidaive defense system. This work also highlighted mechanistic information that could be connected to dietary related weight loss in overweight and obese postmenopausal women in relation to short as well as long term dietary effects based on different macronutrient compositions. Finally, alterations were observed in metabolic profiles in relation to probiotics treatment in the second half of infancy, suggesting possible health benefits of probiotics supplementation at an early age. / Embargo until 2012-06-01