Pseudomonas aeruginosa est un pathogène opportuniste responsable d'infections graves chez les individus immunodéprimés et chez les personnes atteintes de mucoviscidose. Cette pathogénicité repose sur de nombreux facteurs de virulence, dont l'un, le système de sécrétion de type III (SSTT) est présent chez un grand nombre de bactéries pathogènes à Gram négatif. Ce système de sécrétion permet à la bactérie d'injecter des effecteurs cytotoxiques directement dans le cytoplasme de la cellule eucaryote cible. Chez P. aeruginosa, le SSTT est constitué d'un appareil de sécrétion, appelé Psc (Pop secretion) permettant le passage des effecteurs à travers les membranes bactériennes, et d'un translocon, codé par l'opéron pcrGVHpopBD, permettant l'injection des effecteurs cytotoxiques dans le cytosol de la cellule eucaryote. Nous avons montré dans le laboratoire que l'isolat clinique CHA de P. aeruginosa est capable d'échapper à l'activité bactéricide des polymorphonucléaires neutrophiles humains (PMNs) et d'induire une mort rapide par oncose des phagocytes (Dacheux et al., 2000). Dans un premier volet, l'utilisation des hématies comme modèle cellulaire m'a permis de montrer que cette oncose est précédée par la formation de pores, de taille estimée entre 28 et 35 Å, dans la membrane cytoplasmique de ces cellules. Des expériences de mutagénèse montrent que la formation de ces pores requiert les protéines PcrV, PopB et PopD. L'analyse par Western blot de membranes isolées d'hématies infectées par P. aeruginosa indiquent que les protéines PopB et PopD constituent le pore de translocation inséré dans la membrane cytoplasmique des cellules eucaryotes. La protéine PcrV, qui n'est jamais retrouvée dans la fraction membranaire d'hématies infectées par P. aeruginosa, agit à la surface de la bactérie comme une « chaperonne extracellulaire » responsable de l'assemblage de PopB et PopD en un complexe hétéro-oligomérique. Le second volet traite du mécanisme d'action des anticorps protecteurs anti-PcrV contre les infections à P. aeruginosa. Des expériences de fractionnement d'hématies infectées par P. aeruginosa en présence de ces anticorps protecteurs a permis d'établir que ces derniers inhibent l'assemblage du pore de translocation du SSTT.

<p>Nedbrytning av organiskt material är en nyckelfaktor som påverkar omvandlingar av de många grundämnen som utgör eller är associerade till just organiskt material. En stor del av nedbrytningen av akvatiskt organiskt material (OM) sker i gränsskiktet mellan sediment och vatten. Eftersom så många biogeokemiska cykler styrs av nedbrytningen av OM är det viktigt att ha kunskap om processer och påverkansfaktorer både på mikro- och makronivå. Mineraliseringshastigheten av OM är en vanligt förekommande mätparameter, men vanligtvis inkluderar mätningarna inte de naturliga processer som kan påverka nedbrytnings-hastigheterna, t.ex. fysiska krafter.</p><p>Syftet med den här studien är att studera mineraliseringshastigheten av det OM som finns naturligt i ytsediment i söt- och brackvatten när det utsätts för fysiska krafter som orsakar förändringar i redox-förhållanden, resuspension eller advektivt porvattenflöde. Fem</p><p>laborativa experiment har utförts för att belysa syftet:</p><p>Åldrat ytsediment från en sötvattens å utsattes för olika redox förhållanden där oxisk respiration, sulfatreduktion respektive metanogenes gynnades. Resultaten visade ingen skillnad i mineraliseringshastighet beroende på behandling. Detta motsäger studier utförda i marina miljöer, där anoxiska förhållanden ger en lägre mineraliseringshastighet än oxiska.</p><p>Vidare gjordes två studier på brackvattensediment där effekten av resuspension var i centrum. Den ena studien fokuserade på frekvens och varaktighet av resuspensionstiderna, den andra på olika typer av sediment. Studierna visade att väldigt korta resuspensionstider med upp till 48 timmars stillhet mellan varje resuspension ökade mineraliseringstakten med fem gånger jämfört med diffusivt utbyte, och mer än dubblerades i jämförelse med kontinuerlig resuspension eller resuspension i långa perioder. Resuspensionen under kort tid var troligen gynnande då resuspension fysiskt stör bildningen av stabila bakteriesamhällen. Mineraliseringshastigheterna i sediment som domineras av väldigt fin, fin eller medium sand visade lika hastigheter, medan grov sand visade en signifikant lägre mineraliseringshastighet. Likheterna mellan de tre första sedimenttyperna kan dock ha påverkats av tillgång på lättnedbrytbart OM då sediment och vatten hämtades in under en algblomning.</p><p>Till sist studerades effekten på mineraliseringshastigheten av advektivt porvattenflöde. Detta gjordes på åldrat sediment dels från en sötvattensbäck dels från en brackvattenstrand. Inget av de två sedimenttyperna visade någon skillnad i mineraliseringshastighet i jämförelse med diffusivt styrda system. Det är i motsats till tidigare marina studier, men är i linje med den första studien, där mineraliseringshastigheten var oberoende av redox-förhållande.</p><p>Den generella slutsatsen från den här studien är nödvändigheten att studera samma aspekter i olika typer av akvatiska system, eftersom responsen verkar vara annorlunda beroende på system, t.ex. söt- brack- och saltvatten. Faktorer som kan förklara de här skillnaderna finns ännu inte, vilket gör att småskaliga studier och modeller blir viktiga verktyg för att utreda detta.</p> / <p>Organic matter mineralisation is a key parameter that affects most other element transformations associated with organic matter. A substantial part of aquatic organic matter (OM) mineralisation takes place at the interface between sediment and water. Understanding OM mineralisation is important at both the micro and macro scales, since it drives many biogeochemical cycles. OM mineralisation rates are widely measured, but generally not all the natural factors possibly affecting the rates, such as physical forcing, are considered.</p><p>This thesis examines the mineralisation rates of indigenous OM in fresh and brackish surface sediments, subjected to different physical forces inducing changed redox conditions, resuspension, and advective pore water flow. Five experiments were performed to this end.</p><p>Aged surface sediment from a freshwater river was subjected to different redox conditions favouring oxic respiration, sulphate reduction, and methanogenesis, respectively. Results indicated no difference in mineralisation rate irrespective of treatment. This contradicts what has been found in marine environments, where anoxic mineralisation rates are lower than oxic ones.</p><p>Further, two studies of resuspension of brackish sediments were performed, one addressing the impact of the frequency and duration of the resuspension events, and the other addressing the impact of resuspension on different types of sediments. The studies found that very brief resuspension events followed by calm periods of up to 48 h increased mineralisation rates by five times compared to diffusion, and more than doubled the rate compared to continuous or long-term resuspension. The short-term events were possibly favoured because resuspension physically disturbs the arrangement of a stable bacteria community. Mineralisation rates on sediments dominated by very fine, fine, or medium-grained sand were the same, while coarse sand displayed a significantly lower rate. The similar rates of the three first sediment types could stem from access to labile OM, due to an ongoing algae bloom when the sediment and water samples were collected.</p><p>Finally, the effect of advective pore water flow on aged sediment from one fresh and one brackish sediment was studied. Neither of the sediments displayed a mineralisation rate different from those occurring in incubations in which only diffusive exchange occurred. This contradicts the findings of previous marine studies, but is in line with the first study, which did not detect different mineralisation rates irrespective of redox conditions.</p><p>The general conclusion is that it is necessary to study the same physical forces in different aquatic environments, since responses appear to differ, for example, between freshwater, brackish, and marine environments. Factors explaining these differences have not yet been expressed, making small-scale studies and modelling a challenge for future research.</p>

<p>Epithelial cell polarisation is a prerequisite for the branching morphogenesis in several organs. Differential screening techniques were used to identify genes, which are upregulated during induction of epithelium in early kidney development. This investigation revealed two separate genes, Nuclear localising protein 1 (Nulp1), a previously undescribed gene with sequence characteristics of the basic helix-loop-helix transcription factor family, and glycoprotein 210 (gp210, POM210), an integral membrane protein constituent of the nuclear pore complex (NPC). Of these, gp210 was found to be upreglated during conversion of mesenchyme to epithelium. </p><p>The nuclear envelope, which demarcates the nuclear region in the eukaryotic cell, consists of an inner and an outer membrane that are fused at the locations for NPCs. These large macromolecular assemblages are tube like structures connecting the cytoplasmic and nuclear compartments of the cell. NPCs serve as the only conduits for exchange of molecular information between these cellular rooms. Electron microscopy techniques have revealed detailed information about the NPC architecture. A number of proteins (nucleoporins) have been characterised and embodied as components of the NPC structure. Active, energy dependent nucleocytoplasmic transport of RNAs and proteins is mediated by a group of soluble receptor proteins, collectively termed karyopherins. </p><p>Gp210 has been suggested to be important for nuclear pore formation. Nevertheless, our analyses showed a limited expression pattern of gp210, with its mRNA and protein largely confined to epithelial cells in the mouse embryo. Furthermore, in several cell lines, gp210 was undetectable. The expression pattern of gp210 was not synchronised with some other nucleoporins, indicating NPC heterogeneity. Characterisation of the structure of the human gp210 gene, including its promoter region, gave insight about possible cell-type specific gene regulatory mechanisms. </p><p>Regulation of molecular traffic between the nucleus and the cytoplasm leads to transcriptional control. Cell specific configuration of the NPC structure, due to diffential expression of gp210, could be involved in this control. Gp210 could be of importance for the development of epithelial cell polarisation.</p>

<p>Cellulose powders from various sources were manufactured and characterized to investigate the influence of their crystallinity index, surface area, and pore volume on sorption phenomena and the relevant pharmaceutical functionality. The influence of the cellulose crystallinity index on moisture sorption was important at low and intermediate relative humidities. At high relative humidities, properties such as surface area and pore volume took precedence in governing the moisture sorption process.</p><p>The theory of physical adsorption of gases onto fractal surfaces was useful for understanding the distribution of water in cellulose and the inner nanoscale structure of cellulose particles. It was found that, as a consequence of swelling, moisture induces a fractal nanopore network in cellulose powders that have a low or intermediate degree of crystallinity. On the other hand, no swelling occurs in highly crystalline cellulose powders and moisture sorption is restricted to the walls of the open pores.</p><p>No correlation was found between the cellulose crystallinity index and the incorporation and release of nicotine in cellulose mixtures. By loading nicotine in highly porous matrices of the Cladophora sp. algae cellulose, higher stability against oxidative degradation, higher loading capacity, and more steady release into an air-stream was achieved than when commercially available microcrystalline cellulose was loaded.</p><p>It was also shown that, by manipulating the structure of cellulose, the undesired hydrolysis of acetylsalicylic acid in mixtures with cellulose can be avoided. It was suggested that a broad hysteresis loop between the moisture adsorption and desorption curves of isotherms at low relative humidities could be indicative of an improved compatibility between acetylsalicylic acid and cellulose.</p><p>In all, this thesis demonstrates how the pharmaceutical functionality of microcrystalline cellulose can be improved via engineering of the structure of native cellulose powders.</p>

GaN nanopore arrays with pore diameters of approximately 75 nm were fabricated by inductively coupled plasma etching (ICP) using anodic aluminum oxide (AAO) films as etch masks. Nanoporous AAO films were formed on the GaN surface by evaporating an Al film onto a GaN epilayer and subsequently anodizing the aluminum. To minimize plasma-induced damage, the template was exposed to CF4-based plasma conditions. Scanning electron microscopy (SEM) analysis shows that the diameter and the periodicity of the nanopores in the GaN were directly transferred from the original anodic alumina template. The pore diameter in the AAO film can be easily controlled by tuning the anodization conditions. Atomic force microscopy (AFM), photoluminescence (PL) and micro-Raman techniques were employed to assess the quality of the etched GaN nanopore surface. Such a cost-effective method to produce nano-patterned GaN template would be useful for growth and fabrication of III-Nitrides based nanostructures and photonic band gap materials. / Singapore-MIT Alliance (SMA)

The search for new materials for hydrogen storage is important for the development of future hydrogen energy applications. In this Thesis, it is shown that new materials with interesting properties can be synthesized by the reaction of hydrogen with various nanocarbon precursors. The thesis consists of two parts. The first part is devoted to studies of hydrogen storage in some metal-organic frameworks (MOFs) and nanostructured carbon materials, while the second part describes synthesis of new materials by the reaction of hydrogen gas with various carbon materials (i.e. fullerene C60, single-walled carbon nanotubes (SWCNTs), and fullerene C60 encapsulated inside SWCNTs (C60@SWCNTs)). Hydrogen adsorption was measured for a set of Zn- and Co-based MOFs at near ambient temperatures. MOFs synthesized using different metal clusters and organic connecting ligands allowed to study effects of different surface area, pore volume, and pore shapes on hydrogen storage parameters. Hydrogen adsorption values in the studied MOFs correlated well with surface area and pore volume but did not exceed 0,75wt.%. Therefore, new methods to improve the hydrogen storage capacity in MOFs were investigated. The addition of metal catalysts was previously reported to improve significantly hydrogen storage in MOFs. In this thesis the effect of Pt catalyst addition on hydrogen adsorption in MOF-5 was not confirmed. Contrary to previous reports, hydrogen adsorption in MOF-5 mixed/modified with Pt catalysts had fast kinetics, correlated well with surface area, and was on the same level as for unmodified MOF-5. New nanostructured carbon materials were synthesized by the reaction between fullerene C60 and coronene/anthracene. Despite negligible surface area these materials adsorbed up to 0,45wt.% of hydrogen at ambient temperatures. The reaction of fullerene C60 with hydrogen gas was studied at elevated temperatures and hydrogen pressures. In situ gravimetric monitoring of the reaction was performed in a broad temperature interval with/without addition of metal catalysts (i.e. Pt and Ni). The reaction resulted in synthesis of hydrogenated fullerenes C60Hx (with x≤56) followed by fullerene cage fragmentation and collapse upon prolonged duration of hydrogen treatment. Possible mechanisms of C60 hydrogenation and fragmentation were discussed. It is demonstrated that reaction of SWCNTs with hydrogen gas at elevated temperatures and hydrogen pressures can be used for nanotube opening, purification from amorphous carbon, side-wall hydrogenation, and partial unzipping of SWCNTs. Some graphene nanoribbons (GNRs) were synthesized as the result of SWCNTs unzipping. A surprising ability of hydrogen to penetrate inside SWNTs and to react with encapsulated fullerene C60 was demonstrated. / Sökandet efter nya material för vätelagring är viktigt för utveckling av framtida väteenergitillämpningar. I denna avhandling visas att nya material med intressanta egenskaper kan syntetiseras genom reaktion av väte med olika nanokolprekursorer. Avhandlingen består av två delar. Den första delen ägnas åt studier av vätelagring i vissa metall-organiska fackverk (så kallade MOFs) och nanostrukturerade kolmaterial medan den andra delen beskriver syntes av nya material genom reaktion av vätgas med olika kolmaterial (dvs. fulleren C60, enkelväggiga kolnanorör (SWCNTs) och fulleren C60 kapslat i SWCNTs (C60 @ SWCNTs)). Väteadsorptionen mättes för ett antal Zn- och Co-baserade MOFs vid rumstemperatur. MOFs syntetiserades med hjälp av olika metallkluster och organiska ligander för att studera effekterna av olika yta, porvolym och porformer på vätelagringsparametrarna. Väteadsorptionsvärden i de studerade MOFs korrelerade väl med yta och porvolym, men översteg inte 0,75wt.%. Därför undersöktes nya metoder för att förbättra kapaciteten för vätelagring i MOFs. Tillsättning av metallkatalysatorer har tidigare rapporterats avsevärt förbättra vätelagring i MOFs. I denna avhandling kunde effekten av en tillsats av Pt-katalysator på väteadsorption i MOF-5 inte bekräftas. I motsats till tidigare rapporter hade väteadsorption i MOF-5 blandad/modifierad med Pt-katalysatorer snabb kinetik och korrelerade väl med arean, men var på samma nivå som för omodifierad MOF-5. Nya nanostrukturerade kolmaterial syntetiserades genom reaktion mellan fulleren C60 och coronene/antracene. Trots försumbar yta adsorberade dessa material upp till 0,45wt.% väte vid rumstemperatur. Reaktionen av fulleren C60 med vätgas studerades vid förhöjda temperaturer och vätetryck. In situ gravimetrisk övervakning av reaktionen utfördes i ett brett temperaturintervall med/utan tillsats av metallkatalysatorer (dvs. Pt och Ni). Reaktionen resulterade i syntes av hydrogenerade fullerener C60Hx (med x≤56) följt av fragmentering och kollaps av fullerenstrukturen vid förlängd varaktighet av vätebehandlingen. Möjliga mekanismer för hydrering och fragmentering av C60 diskuteras. Det har visats att reaktionen mellan SWCNTs och vätgas vid förhöjda temperaturer och vätetryck kan användas för öppning av nanorör, borttagning av amorft kol, funktionalisering av sidoväggar och partiell "blixtlåsöppning" av SWCNTs. Reaktionen kan också syntetisera grafen-nanoband (GNRs) som en följd av att SWCNTs öppnas på längden. En överraskande stor förmåga för väte att tränga in i SWNT och där reagera med inkapslade fullerenmolekyler C60 demonstrerades.

Epithelial cell polarisation is a prerequisite for the branching morphogenesis in several organs. Differential screening techniques were used to identify genes, which are upregulated during induction of epithelium in early kidney development. This investigation revealed two separate genes, Nuclear localising protein 1 (Nulp1), a previously undescribed gene with sequence characteristics of the basic helix-loop-helix transcription factor family, and glycoprotein 210 (gp210, POM210), an integral membrane protein constituent of the nuclear pore complex (NPC). Of these, gp210 was found to be upreglated during conversion of mesenchyme to epithelium. The nuclear envelope, which demarcates the nuclear region in the eukaryotic cell, consists of an inner and an outer membrane that are fused at the locations for NPCs. These large macromolecular assemblages are tube like structures connecting the cytoplasmic and nuclear compartments of the cell. NPCs serve as the only conduits for exchange of molecular information between these cellular rooms. Electron microscopy techniques have revealed detailed information about the NPC architecture. A number of proteins (nucleoporins) have been characterised and embodied as components of the NPC structure. Active, energy dependent nucleocytoplasmic transport of RNAs and proteins is mediated by a group of soluble receptor proteins, collectively termed karyopherins. Gp210 has been suggested to be important for nuclear pore formation. Nevertheless, our analyses showed a limited expression pattern of gp210, with its mRNA and protein largely confined to epithelial cells in the mouse embryo. Furthermore, in several cell lines, gp210 was undetectable. The expression pattern of gp210 was not synchronised with some other nucleoporins, indicating NPC heterogeneity. Characterisation of the structure of the human gp210 gene, including its promoter region, gave insight about possible cell-type specific gene regulatory mechanisms. Regulation of molecular traffic between the nucleus and the cytoplasm leads to transcriptional control. Cell specific configuration of the NPC structure, due to diffential expression of gp210, could be involved in this control. Gp210 could be of importance for the development of epithelial cell polarisation.

Cellulose powders from various sources were manufactured and characterized to investigate the influence of their crystallinity index, surface area, and pore volume on sorption phenomena and the relevant pharmaceutical functionality. The influence of the cellulose crystallinity index on moisture sorption was important at low and intermediate relative humidities. At high relative humidities, properties such as surface area and pore volume took precedence in governing the moisture sorption process. The theory of physical adsorption of gases onto fractal surfaces was useful for understanding the distribution of water in cellulose and the inner nanoscale structure of cellulose particles. It was found that, as a consequence of swelling, moisture induces a fractal nanopore network in cellulose powders that have a low or intermediate degree of crystallinity. On the other hand, no swelling occurs in highly crystalline cellulose powders and moisture sorption is restricted to the walls of the open pores. No correlation was found between the cellulose crystallinity index and the incorporation and release of nicotine in cellulose mixtures. By loading nicotine in highly porous matrices of the Cladophora sp. algae cellulose, higher stability against oxidative degradation, higher loading capacity, and more steady release into an air-stream was achieved than when commercially available microcrystalline cellulose was loaded. It was also shown that, by manipulating the structure of cellulose, the undesired hydrolysis of acetylsalicylic acid in mixtures with cellulose can be avoided. It was suggested that a broad hysteresis loop between the moisture adsorption and desorption curves of isotherms at low relative humidities could be indicative of an improved compatibility between acetylsalicylic acid and cellulose. In all, this thesis demonstrates how the pharmaceutical functionality of microcrystalline cellulose can be improved via engineering of the structure of native cellulose powders.

Reactive Transport Models (RTMs) provide quantitative tools to analyze the interaction between transport and biogeochemical processes in subsurface environments such as aquatic sediments and groundwater flow. A tremendous amount of research has shown the role and impact of scaling behavior of the reactive systems which stems from geologic heterogeneity. Depending on the kinetics of the reactions, different types of formulations have been proposed to describe reactions in RTMs. We introduce a novel quantitative criteria on the range of validity of local equilibrium assumption (LEA) in aquatic sediments with irreversible heterogeneous sorption reactions. Then we present a one-dimensional (1-D) early diagenetic module, MATSEDLAB, developed in MATLAB. The module provides templates for representing the reaction network, boundary conditions and transport regime, which the user can modify to fit the particular early diagenetic model configuration of interest. We describe the theoretical background of the model and introduce the MATLAB pdepe solver, followed by calibration and validation of the model by a number of theoretical and empirical applications. Finally, we introduce a new pore-scale model using lattice Boltzmann (LB) approach. It uses an iterative scheme for the chemical transport-reaction part and recent advances in the development of optimal advection-diffusion solvers within the lattice Boltzmann method framework. We present results for the dissolution and precipitation of a porous medium under different dynamical conditions, varying reaction rates and the ratio of advective to diffusive transport (Pe, Peclet number) for linear reactions. The final set of calculations considers sorption reactions on a heterogeneous porous medium. We use our model to investigate the effect of heterogeneity on the pore-scale distribution of sorption sites and the competition between three different sorption reactions.

Nuclear power generation is being regarded as a solution to ever increasing demand for electricity, and concerns over global warming and climate change due to the use of fossil fuels. Although nuclear power generation is considered to be reliable, economical, clean, and safe, the wastes produced from the nuclear fuel cycle are not, and can remain hazardous for hundreds of thousands of years. An international consensus has developed over the past several decades that deep geologic disposal of low, intermediate, and high level radioactive wastes is the best option to protect the biosphere. In this thesis, both regional scale and sub-regional scale models are created to simulate groundwater flow and transport for a representative Canadian Shield setting, honouring site-specific topography and surface water features. Sub-surface characteristics and properties are derived from numerous geoscience studies. In addition, a regional scale model is developed, centred on the Bruce Nuclear Power Development (BNPD) site near Tiverton, Ontario, and located within the Michigan Basin. Ontario Power Generation (OPG) has proposed a Deep Geologic Repository (DGR) for low & intermediate level waste (L&ILW) at the BNPD site. Paleoclimate simulations using various combinations of parameters are performed for both the Canadian Shield Sub-Regional model, and the Michigan Basin Regional model. Fracture zone permeability is a very important parameter when modelling crystalline rock settings. Migration of a unit tracer representing glacial recharge water can occur to depth in fractures of high permeability. Representative rock compressibility values are necessary as compressibilities are used to calculate storage coefficients, and the one-dimensional loading efficiency; these affect the subsurface propagation of elevated pore pressures due to glacial loading at surface. Coupled density-dependent flow and transport in paleoclimate simulations affects deep flow systems and provides a measure of flow stability, as well as increasing the mean life expectancy at depth. Finally, hydromechanical coupling is a very important mechanism for reducing vertical hydraulic gradients during a glaciation event when a hydraulic boundary condition equal to the pressure at the base of an ice-sheet is applied at ground surface. Pore water velocities are reduced, thereby retarding migration of surface waters into the subsurface environment.