La biomasse lignocellulosique est composée d’hémicelluloses à hauteur de 30%. Les hémicelluloses sont elles-mêmes composées de saccharides, qui sont de véritables plateformes chimiques car ils peuvent être dérivés en de nombreux produits différents dont l’intérêt porté à leur égard est grandissant. Dans le cadre d’une bioraffinerie papetière, les hémicelluloses ont été solubilisées sous forme de monosaccharides et d’oligosaccharides via une étape d’autohydrolyse. Des traitements d’hydrolyse secondaire acide et enzymatique ont ensuite été appliqués à l’hydrolysat dans différentes conditions afin d’hydrolyser un maximum d’oligosaccharides en monosaccharides dans le premier cas, et un maximum de xylanes en xyloses dans le second cas. Ces traitements ont été optimisés pour permettre une application à un pilote industriel. / Lignocellulosic biomass is made of 30% of hemicelluloses. Hemicelluloses are themselves made of saccharides that are true platform chemicals due to their ability to be transformed into many different products. Within the context of a biorefinery, hemicelluloses were solubilized as monosaccharides and oligosaccharides after a water pre-hydrolysis treatment. Secondary acid and enzymatic hydrolysis treatments were further applied to the obtained hydrolysate to depolymerize as much oligosaccharides as possible to monosaccharides (acid hydrolysis) and to depolymerize as much as xylans as possible to xyloses (enzymatic hydrolysis). Treatments were optimized to pilot scale.

The Southern Ocean (ca. 20% of the world ocean surface) is a key place for the regulation of Earth climate thanks to its capacity to absorb atmospheric carbon dioxide (CO2) by physico-chemical and biological mechanisms. The biological carbon pump is a major pathway of absorption of CO2 through which the CO2 incorporated into autotrophic microorganisms in surface waters is transferred to deep waters. This process is influenced by the extent of the primary production and by the intensity of the remineralization of organic matter along the water column. So, the annual cycle of sea ice, through its in situ production and remineralization processes but also, through the release of microorganisms, organic and inorganic nutrients (in particular iron)into the ocean has an impact on the carbon cycle of the Southern Ocean, notably by promoting the initiation of phytoplanktonic blooms at time of ice melting. The present work focussed on the distribution of organic matter (OM) and its interactions with the microbial network (algae, bacteria and protozoa) in sea ice and ocean, with a special attention to the factors which regulate the biological carbon pump of the Southern Ocean. This thesis gathers data collected from a) late winter to summer in the Western Pacific sector, Western Weddell Sea and Bellingshausen Sea during three sea ice cruises ARISE, ISPOL-drifting station and SIMBA-drifting station and b) summer in the Sub-Antarctic and Polar Front Zone during the oceanographic cruise SAZ-Sense. The sea ice covers were typical of first-year pack ice with thickness ranging between 0.3 and 1.2 m, and composed of granular and columnar ice. Sea ice temperature ranging between -8.9°C and -0.4°C, brines volume ranging between 2.9 to 28.2% and brines salinity from 10 to >100 were observed. These extreme physicochemical factors experienced by the microorganisms trapped into the semi-solid sea ice matrix therefore constitute an extreme change as compared to the open ocean. Sea ice algae were mainly composed of diatoms but autotrophic flagellates (such as dinoflagellates or Phaeocystis sp.) were also typically found in surface ice layers. Maximal algal biomass was usually observed in the bottom ice layers except during SIMBA where the maxima was localised in the top ice layers likely because of the snow and ice thickness which limit the light available in the ice cover. During early spring, the algal growth was controlled by the space availability (i.e. brine volume) while in spring/summer (ISPOL, SIMBA) the major nutrients availability inside sea ice may have controlled algal growth. At all seasons, high concentrations of dissolved and particulate organic matter were measured in sea ice as compared to the water column. Dissolved monomers (saccharides and amino acids) were accumulated in sea ice, in particular in winter. During spring and summer, polysaccharides constitute the main fraction of the dissolved saccharides pool. High concentrations of transparent exopolymeric particles (TEP), mainly constituted with saccharides, were present and their gel properties greatly influence the internal habitat of sea ice, by retaining the nutrients and by preventing the protozoa grazing pressure, inducing therefore an algal accumulation. The composition as well as the vertical distribution of OM in sea ice was linked to sea ice algae. Besides, the distribution of microorganisms and organic compounds in the sea ice was also greatly influenced by the thermodynamics of the sea ice cover, as evidenced during a melting period for ISPOL and during a floodfreeze cycle for SIMBA. The bacteria distribution in the sea ice was not correlated with those of algae and organic matter. Indeed, the utilization of the accumulated organic matter by bacteria seemed to be limited by an external factor such as temperature, salinity or toxins rather than by the nature of the organic substrates, which are partly composed of labile monomeric saccharides. Thus the disconnection of the microbial loop leading to the OM accumulation was highlighted in sea ice. In addition the biofilm formed by TEP was also involved in the retention of cells and other compounds(DOM, POM, and inorganic nutrients such as phosphate and iron) to the brine channels walls and thus in the timing of release of ice constituents when ice melts. The sequence of release in marginal ice zone, as studied in a microcosm experiments realized in controlled and trace-metal clean conditions, was likely favourable to the development of blooms in the marginal ice zone. Moreover microorganisms derived from sea ice (mainly <10 µm) seems able to thrive and grow in the water column as also the supply of organic nutrients and Fe seems to benefit to the pelagic microbial community. Finally, the influence of the remineralization of organic matter by heterotrophic bacterioplankton on carbon export and biological carbon pump efficiency was investigated in the epipelagic (0-100 m) and mesopelagic(100-700 m) zones during the summer in the sub-Antarctic and Polar Front zones (SAZ and PFZ) of the Australian sector (Southern Ocean). Opposite to sea ice, bacterial biomass and activities followed Chl a and organic matter distributions. Bacterial abundance, biomass and activities drastically decreased below depths of 100-200 m. Nevertheless, depth-integrated rates through the thickness of the different water masses showed that the mesopelagic contribution of bacteria represents a non-negligible fraction, in particular in a diatom-dominated system./ L’océan Antarctique (± 20% de la surface totale des océans) est un endroit essentiel pour la régulation du climat de notre planète grâce à sa capacité d’absorber le dioxyde de carbone (CO2) atmosphérique par des mécanismes physico-chimique et biologique. La pompe biologique à carbone est un processus majeur de fixation de CO2 par les organismes autotrophes à la surface de l’océan et de transfert de carbone organique vers le fond de l’océan. Ce processus est influencé par l’importance de la production primaire ainsi que par l’intensité de la reminéralisation de la matière organique dans la colonne d’eau. Ainsi, le cycle annuel de la glace via sa production/reminéralisation in situ mais aussi via l’ensemencement de l’océan avec des microorganismes et des nutriments organiques et inorganiques (en particulier le fer) a un impact sur le cycle du carbone dans l’Océan Antarctique, notamment en favorisant l’initiation d’efflorescences phytoplanctoniques dans la zone marginale de glace. Plus précisément, nous avons étudié les interactions entre le réseau microbien (algues, bactéries et protozoaires) et la matière organique dans le but d’évaluer leurs impacts potentiels sur la pompe biologique de carbone dans l’Océan Austral. Deux écosystèmes différents ont été étudiés : la glace de mer et le milieu océanique grâce à des échantillons prélevés lors des campagnes de glace ARISE, ISPOL et SIMBA et lors de la campagne océanographique SAZ-Sense, couvrant une période allant de la fin de l’hiver à l’été. La glace de mer est un environnement très particulier dans lequel les microorganismes planctoniques se trouvent piégés lors de la formation de la banquise et dans lesquels ils subissent des conditions extrêmes de température et de salinité, notamment. Les banquises en océan ouvert étudiées (0,3 à 1,2 m d’épaisseur, températures de -8.9°C à -0.4°C, volumes relatifs de saumure de 2.9 à 28.2% et salinités de saumures entre 10 et jusque >100) étaient composées de glace columnaire et granulaire. Les algues de glace étaient principalement des diatomées mais des flagellés autotrophes (tels que des dinoflagellés ou Phaeocystis sp.) ont été typiquement observés dans les couches de glace de surface. Les biomasses algales maximales se trouvaient généralement dans la couche de glace de fond sauf à SIMBA où les maxima se trouvaient en surface, probablement en raison de l’épaisseur des couches de neige et de glace, limitant la lumière disponible dans la colonne de glace. Au début du printemps, la croissance algale était contrôlée par l’espace disponible (càd le volume des saumures) tandis qu’au printemps/été, la disponibilité en nutriments majeurs a pu la contrôler. A toutes les saisons, des concentrations élevées en matière organique (MO) dissoute et particulaire on été mesurées dans la glace de mer par rapport à l’océan. Des monomères dissous (sucres et acides aminés) étaient accumulés dans la glace, surtout en hiver. Au printemps et été, les polysaccharides dissous dominaient le réservoir de sucres. La MO était présente sous forme de TEP qui par leurs propriétés de gel modifie l’habitat interne de la glace. Ce biofilm retient les nutriments et gêne le mouvement des microorganismes. La composition et la distribution de la MO dans la glace étaient en partie reliées aux algues de glace. De plus, la thermodynamique de la couverture de glace peut contrôler la distribution des microorganismes et de la MO, comme observé lors de la fonte de la glace à ISPOL et lors du refroidissement de la banquise à SIMBA. La distribution des bactéries n’est pas corrélée avec celle des algues et de la MO dans la glace. En effet, la consommation de la MO par les bactéries semble être limitée non pas par la nature chimique des substrats mais par un facteur extérieur affectant le métabolisme bactérien tel que la température, la salinité ou une toxine. Le dysfonctionnement de la boucle microbienne menant à l’accumulation de la MO dans la glace a donc été mis en évidence dans nos échantillons. De plus, le biofilm formé par les TEP est aussi impliquée dans l’attachement des cellules et autres composés aux parois des canaux de saumure et donc dans la séquence de largage lors de la fonte. Cette séquence semble propice au développement d’efflorescences phytoplanctoniques dans la zone marginale de glace. Les microorganismes originaires de la glace (surtout ceux de taille < 10 μm) semblent capables de croître dans la colonne d’eau et l’apport en nutriments organiques et inorganiques apparaît favorable à la croissance des microorganismes pélagiques. Enfin, l’influence des activités hétérotrophes sur l’export de carbone et l’efficacité de la pompe biologique à carbone a été évaluée dans la couche de surface (0-100 m) et mésopélagique (100-700 m) de l’océan. Au contraire de la glace, les biomasses et activités bactériennes suivaient les distributions de la chlorophyll a et de la MO. Elles diminuent fortement en dessous de 100-200 m, néanmoins les valeurs intégrées sur la hauteur de la colonne d’eau indiquent que la reminéralisation de la MO par les bactéries dans la zone mésopélagique est loin d’être négligeable, spécialement dans une région dominée par les diatomées.

Cette thèse s’inscrit dans une thématique de recherche visant à synthétiser des moléculesamphiphiles présentant des propriétés bioactives, pouvant être mises à profit dans diversesapplications biomédicales ou encore dans le domaine de l’agrochimie. Les molécules amphiphilessont alors les propres actrices de leur formulation de par leurs propriétés d’auto-association et debioactivité (concept dit « d’économie moléculaire »). Dans ce contexte, la première partie de cetravail a été consacrée à la synthèse de molécules amphiphiles modèles dérivées de D-glucose etde N-acétyl-D-glucosamine. La voie de synthèse choisie pour les obtenir a été une aminationréductrice régiosélective à partir de chaînes alkylamine de différentes longueurs (6, 12 et 16atomes de carbone). Leur caractérisation a été réalisée par RMN et spectrométrie de masse. Ladeuxième partie de ce travail a été orientée vers l’étude du comportement auto-associatif desmolécules à base de D-glucose en solution aqueuse, seules, ou en mélange avec un phospholipidemodèle. Une organisation à différentes échelles de taille a été mise en évidence par les techniquesde diffusion de la lumière, microscopie électronique en transmission et grâce à la modélisation dedonnées expérimentales obtenues en diffusion des rayons X aux petits angles. / This work is part of a research program on the synthesis of amphiphilic molecules havingbioactive properties, which could be used in biomedical applications or in agrochemistry.Amphiphilic molecules could be the own actor of their formulation because of the dual propertyof bioactivity and self-assembly. In this context, the first part of this work concerns the synthesisof model amphiphilic molecules derived from D-glucose and N-acetyl-D-glucosamine. The chosenway to synthesize these molecules was a regioselective reductive amination from alkylaminechains of different lengths (6, 12 and 16 carbon atoms). Compounds were characterized by NMRand Mass Spectrometry. The second part of this work was oriented towards the study of the selfassemblyproperties of molecules derived from D-glucose in an aqueous solution, alone, or mixedwith a model phospholipid. An organization with different sizes was shown with severaltechniques: light diffusion, transmission electronic microscopy, and thanks to the establishment ofa model from experimental small-angle X-ray scattering data. When the amphiphilic moleculewith 12 atoms of carbon on this hydrocarbonated chain is studied alone in a solution, ellipsoidalmicelles seem to be present, mixed with bigger aggregates (~100 nm). However, when this sameamphiphilic molecule is used in a mix with a model phospholipid, a size diminution of theassembly was observed with the increase of amphiphilic molecules in the formulations.

No description available.

No description available.

Thesis (Ph. D.)--Institute of Paper Chemistry, 1972. / Includes bibliographical references (leaves 156-162).

Molecular recognition at biomembranes is one of the more poorly understood aspects of fundamental research in physical organic chemistry. Our aim was to improve our understanding of the molecular recognition of polysaccharides at biomembranes, in particular developing synthetic lipids that will recognise and report on the presence of glycosaminoglycans (GAG polysaccharides), like heparin and hyaluronic acid. Elevated levels of hyaluronic acid have been implicated in bladder carcinoma and osteoarthritis, and the use of heparin for medical applications is well documented. We synthesised a boronic acid capped lipid that also bore a fluorinated fluorescent reporter group, which could report on multivalent recognition events at bilayer membranes by fluorescent quenching and changes in the lateral distribution of the reporter groups. These preliminary studies showed these boronic acid capped fluorinated lipids gave a fluorescent signal upon interaction with simple mono- and poly- saccharides, albeit with unexpectedly weak binding to these saccharides. To understand and quantify the weaker binding of saccharides to membrane bound boronic acids a series of novel fluorescent and chromogenic lipids were synthesised that bore the reporter group close to the boronic acid. These studies revealed several underlying factors that had important roles in the recognition of oligosaccharides by boronic acid capped lipids. For the first time the effect of the bilayer on saccharide/boronic acid recognition was quantified, with the membrane weakening the interaction 33-fold. We were able to propose a model for the interaction of saccharides for membrane bound boronic acids that explained many of these unexpected observations.We also devised a parallel approach using GAGs to open or close synthetic membrane channels. Using a GAG to switch on the release of an ion or dye would generate a fluorescent signal that amplifies the original recognition event and improves sensitivity for GAGs. Proof-of-principle studies using palladium ions to open dye-transporting channels were successful and these studies were followed by the synthesis of boronic acid-capped cholates. Incorporation of boronic acid-capped cholates into membranes caused changes in the rate of release of alkali metal ions, which caused an enclosed fluorescent dye to give a signal, in the presence or absence of saccharides. These compounds successfully gave a response to the simple saccharide D-fructose but gave no response to other saccharides tested, including various hyaluronic acids. Although we were not able to develop a selective sensor for GAGs, we have developed a model for saccharide/boronic acid interactions that is a valuable addition to the physical organic chemistry of membranes.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第19754号 / 農博第2150号 / 新制||農||1038(附属図書館) / 学位論文||H28||N4970(農学部図書室) / 32790 / 京都大学大学院農学研究科食品生物科学専攻 / (主査)教授 安達 修二, 教授 入江 一浩, 教授 保川 清 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Phospholipid bilayers constitute the primary structural element of biological membranes, and as such, they play a central role in biochemical and biophysical processes at the cellular level, including cell protection, intercellular interactions, trans-membrane transport, cell morphology, and protein function, to name a few. The properties of phospholipid bilayers are thus of great interest from both experimental and theoretical standpoints. Although experiments have provided much of the macroscopic functions and properties of biological membranes, insight into specific mechanisms at the molecular level are seldom accessible by conventional methods. To obtain a better understanding of biochemical and biophysical processes at the molecular level involving phospholipid bilayers, we apply molecular simulation methods to investigate the complexity of the membrane matrix using atomistic models. Here, we discuss three specific biological processes that are associated with biological membranes: 1) membrane stabilization, 2) membrane phase behavior, and 3) fatty acid-induced toxicity in cell membranes. For membrane stabilization, molecular dynamics studies were performed for mixed phospholipid bilayers containing two of the most prevalent phospholipids (phosphatidylcholine and phosphatidylethanolamime) in biological membranes. We presented structural and dynamics properties of these systems, as well as the effect of stabilizing agents, such as trehalose, on their properties. Furthermore, we performed a comprehensive analysis of the phase transition of lipid bilayers and investigated the interactions of stabilizing agents (glucose or trehalose) with lipid bilayers under dehydrated conditions to understand the mechanisms for preservation of cellular systems. For membrane phase behavior, a comprehensive study of the structural properties of saturated and monounsaturated lipid bilayers near the main phase transition were investigated using molecular dynamics simulations. In this study, we demonstrated that atomistic simulations are capable of capturing the phase transformation process of lipid bilayers, providing a valuable set of molecular and structural information at and near its transition state. Lastly, the third study investigated the mechanism for fatty acid-induced toxicity by integrating in vitro and in silico experiments to reveal the biophysical interactions of saturated fatty acid (palmitate) with the cellular membranes and the role of trehalose and unsaturated fatty acids (oleate and linoleate) in preventing changes to the membrane structure. Knowledge gained from this study is essential in the prevention and treatment of obesity-associated cirrhosis diseases. / Ph. D.

Notre travail s'effectue dans le but de fournir une méthode pour permettre le séquençage des oligosaccharides, des biopolymères jouant un rôle clé dans le domaine de la santé comme dans certains domaines industriels tels que l'énergie ou l'alimentation.Les méthodes utilisées pour séquencer les protéines sont limitées pour l'étude des oligosaccharides.En revanche, nous montrons que l'alliance entre la méthode expérimentale de spectroscopie d'action (IRMPD) et les calculs théoriques est une méthode prometteuse pour le séquençage des oligosaccharides.Notre méthode théorique consiste à obtenir des minima de la surface d'énergie potentielle.Les spectres infrarouges de ces minima sont calculés avec la DFT et en utilisant une grande base.Les spectres calculés sont alors comparés aux spectres expérimentaux afin d'obtenir des informations sur la structure des constituants ou la composition du mélange dans l'échantillon.Notre approche alliant les calculs théoriques aux mesures IRMPD s'est avérée particulièrement efficace pour obtenir les structures des mono ou disaccharides présents dans l'échantillon.De plus elle permet d'identifier des signatures spécifiques à des anomères ou à des conformères / Our work aims to develop a method to allow the sequencing of oligosaccharides, which are biopolymers playing a key role in the field of Health as in several industrial fields such as energy or nutrition.The methods used for sequencing proteins are limited in the study of oligosaccharides.However, we show that the combination of action spectroscopy experimental method (IRMPD) and theoretical calculations is a promising method to sequence oligosaccharides.Our theoretical method consist of obtaining minima of the potential energy surface.The infrared spectra of these minima are computed with DFT and a large basis.The calculated spectra are then compared to the experimental ones to gain informations on the structure of the compounds or on the composition of the mixture in the sample.Our approach combining theoretical computations to IRMPD measurements is particularly effective to obtain the structures of mono and disaccharides present in the sample.Moreover, it allows to identify specific signatures of anomers and conformers