Diffusive gradients in thin film (DGT) technique is applied to determine pore water mercury concentrations in river sediments. DGT devices have been a useful indicator of dissolved metals in aqueous systems, although it is not as well developed for measuring mercury. DGT devices were evaluated for three different ion exchange resins for adsorption of mercury. After a series of laboratory experiments, 3-Mercaptopropyl Functionalized Silica Gel (3M) was chosen as an effective resin layer. Laboratory experiments showed that the resin strongly associated with dissolved Hg²⁺. DGT probes were tested with sediments from the South River (Virginia, USA) in the laboratory and the time dependent deployment verified an uptake of mercury to the probes and established an effective diffusion coefficient for site specific utilization. Multiple piston and sediment probes were deployed in the South River in-situ to determine overlying water Hg concentrations and sediment pore water Hg concentration profiles. The DGT devices were successful in measuring Hg concentrations in-situ. / text

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No description available.

The mammalian Na+/H+ exchanger isoform 1 (NHE1) is a ubiquitous membrane protein that exchanges one intracellular H+ for an extracellular Na+, thereby regulating cell pH and volume. NHE1 catalytic activity is mediated by a transmembrane (TM) domain with 12 transmembrane segments. We performed cysteine scanning mutagenesis on TMVI (Asn227–Ile249) of NHE1. Each residue of TMVI was mutated into a cysteine in the background of a cysteineless NHE1 protein. MTSET and MTSES are sulfhydryl reactive membrane impermeable compounds able to react with accessible cysteines. Asp238Cys, Pro239Cys, and Glu247Cys expressed inactive NHE1. Asn227Cys, Ile233Cys, and Leu243Cys were strongly inhibited by MTSET, suggesting their pore lining properties. More mutations were introduced to characterize critical residues in TMVI. The Glu248Gln and Leu243Ala mutants were more susceptible to limited proteolytic attack by trypsin suggesting an altered conformation. The results suggest that Glu248 and Leu243 are important in protein structure, stability, and folding.

The purpose of this study was to assess the decay resistance of wood modified with a variety of chemicals and to attempt to further understand the mechanism by which chemical modification protects wood from decay. Corsican pine (Pinus nigra) sapwood was modified with three cyclic anhydrides; succinic anhydride, alkenyl succinic anhydride (a derivative of succinic anhydride with a 16-18 carbon alkenyl chain) and phthalic anhydride, and with two more widely studied modifying chemicals; acetic anhydride and butyl isocyanate. All reactions were carried out using pyridine as solvent and catalyst. Modified wood was tested against decay fungi in a pure culture test against basidiomycete fungi (Coniophora puteana, Gloeophyllum trabeum, Trametes versicolor and Pycnoporus sanguineus) under different moisture content regimes, an unsterile soil soft rot test, a fungal cellar test and a field trial. Butyl isocyanate proved the most effective modifying chemical at protecting wood from decay, followed by acetic anhydride and then alkenyl succinic anhydride. Uneven distribution of the modifying chemical in wood was evident using each of these three chemicals, particularly in the case of acetic anhydride. Despite its apparent ability to control decay by basidiomycete fungi, alkenyl succinic anhydride was unable to completely protect wood from soft rot fungi. Phthalic and succinic anhydride modifications both proved susceptible to hydrolysis and leaching, and neither were effective as wood protection chemicals. Phthalic anhydride modified wood performed well in the pure culture test, apparently through biocidal action, but was susceptible to decay in unsterile conditions. The approach made in this study to understanding the mechanism of protection was to analyse physical properties of the modified wood cell wall. This involved the measurement of adsorption isotherms, volumetric swell due to water soak, and cell wall pore size (using the solute exclusion technique). Neither the moisture content of modified wood nor its cell wall moisture content (measured as the fibre saturation point from the adsorption analysis) provided a good explanation of decay resistance. In several cases, the relationship between volumetric swell (due to water soak) and weight loss (to a given fungus in pure culture) was found to be consistent between modification types. From this it is concluded that the extent by which water swells modified wood is important to decay resistance. A reduction in cell wall pore volume was measured using the solute exclusion technique, though no further conclusions could be drawn from this test. It is proposed that the mechanism of resistance to decay by basidiomycete fungi involves the blocking of cell wall pores, which restricts the access of degradative agents released by decay fungi. The amount by which wood swells is important in this theory since this will determine by how much transient pores in modified wood can open, and whether enough space is created to bypass this blocking effect. The possibility of the role of site substitution in decay resistance is not discounted, and may contribute to decay resistance, particularly against white rot fungi. Pore blocking is not thought to be the mechanism of protection against soft rot fungi. In this case the substitution and shielding of decay susceptible sites are thought to be more important.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 4 uppsatser.

Pore forming toxins (PFTs) are a large group of proteins found mainly in bacteria with some exceptions found in animals. They bind and form pores in their target membranes and form pores, which leads to cell death. Among these are cholesterol-dependent cytolysins (CDC), which require the presence of cholesterol to bind target membranes. Mitilysin (Mly), a protein of interest in this project, belongs to the CDC group of pore forming toxins. It is produced by the bacterium Streptococcus mitis, a pathogen closely related to Streptococcus pneumoniae, found in human oral cavity, which causes several diseases such as Viridans Group Streptococcal (VGS) toxic shock syndrome and endocarditis. Mly is a homologue of the toxin Pneumolysin, which is produced by S. pneumoniae. However, the mechanism of pore formation is not well known. The purpose of this project is to understand the mechanism of CDC pore formation, focusing on the key amino acid residues that are responsible for transitioning from Mly pre-pore to pore state. The findings will aid in the design of inhibitors of pore formation as potential anti-bacterial drug candidates. The major goal of the project was to determine the 3-dimensional (3D) structure of assembled Mly pore. Mly is expressed in E.coli and purified by Ni-NTA affinity chromatography. Pore formation is confirmed by a hemolysis assay and negative stain-transmission electron microscopy. Mly pores are vitrified, analyzed and imaged in a cryo-electron microscope. 2D images were processed to generate a 3D density map. However, our Mly pore 3D map was incomplete due to lack of 2D projection angles resulting from preferred orientation of pore particles during sample preparation. To overcome this problem, we aim to use DNA origami, which requires His-tagged Mly. We were able to determine that His-tagged Mly retains its pore formation ability.

Benefited from the efficiency of hydraulic fracturing and horizon drilling, the production of unconventional oil and gas resources, such as shale gas and tight oil, has grown quickly in 21th century and contributed to the North America oil and gas production. Although the new enhancing oil recover (EOR) technologies and strong demand spike the production of unconventional resources, there are still unknowns in recovery mechanisms and phase behavior in tight rock reservoirs. In such environment, the phase behavior is altered by high capillary pressure owing to the nanoscale pore throats of shale rocks and it may also influence minimum miscibility pressure (MMP), which is an important parameter controlling gas floods for CO2 injection EOR. To investigate this influence, flash calculation is modified with considering capillary pressure and this work implements three different method to calculate MMP: method of characteristics (MOC); multiple mixing cell (MMC); and slim-tube simulation. The results show that CO2 minimum miscibility pressure in nanopore size reservoirs are affected by gas-oil capillary pressure owing to the alternation of key tie lines in displacement. The values of CO2-MMP from three different methods match well. Moreover, in tight rock reservoirs, the heterogeneous pore size distribution, such as the ones seen in fractured reservoirs, may affect the recovery mechanisms and MMP. This work also investigates the effect of pore size heterogeneity on multicomponent multiphase hydrocarbon fluid composition distribution and its subsequent influence on mass transfer through shale nanopores. According to the simulation results, compositional gradient forms in heterogeneous nanopores of tight reservoirs because oil and gas phase compositions depend on the pore size. Considering that permeability is small in tight rocks and shales, we expect that mass transfer within heterogeneous pore size porous media to be diffusion-dominated. Our results imply that there can be a selective matrix-fracture component mass transfer during both primary production and gas injection secondary recovery in fractured shale rocks. Therefore, molecular diffusion should not be neglected from mass transfer equations for simulations of gas injection EOR or primary recovery of heterogeneous shale reservoirs with pore size distribution. / Master of Science / The new technologies to recover unconventional resources in oil and gas industry, such as fracturing and horizontal drilling, boosted the production of shale gas and tight oil in 21st century and contributed to the North America oil and gas production. Although the new technologies and strong demand spiked the production of tight oil resources, there are still unknowns of oil and gas flow mechanisms in tight rock reservoirs. As we know, the oil and gas resources are stored in the pores of reservoir formation rock. During production process, the oil and gas are pushed into production wells by formation pressure. However, the pore radius of shale rock is extremely small (around nanometers), which reduces the flow rate of oil and gas and raises capillary pressure in pores. The high capillary pressure will alter the oil and gas phase behavior and it may influence the value of minimum miscibility pressure (MMP), which is an important design parameter for CO2 injection (an important technology to raise production). To investigate this influence, we changed classical model with considering capillary pressure and this modified model is implemented in different methods to calculate MMP. The results show that CO2 -MMP in shale reservoirs are affected by capillary pressure and the results from different methods match well. Moreover, in tight rock reservoirs, the heterogeneous pore size distribution, such as fractures in reservoirs, may affect the flow of oil and gas and MMP value. So, this work also investigates the effect of pore size heterogeneity on oil and gas flow mechanisms. According to the simulation results, compositional gradient forms in heterogeneous nanopores of tight reservoirs and this gradient will cause diffusion which will dominate the other fluid flow mechanisms. Therefore, we always need to consider molecular diffusion in the simulation model for shale reservoirs.

The increasing complexity of oil and gas reservoirs has led to the need of a better understanding of the processes governing the rock properties. Traditional theoretical and empirical models often fail to predict the behavior of carbonates, tight gas sands and shale gas, for example. An essential part of the necessary investigation is the study of the phenomena occurring at the pore scale. In this direction, the so-called digital rock physics is emerging as a research field that offers the possibility of imaging the rock pore space and simulating the processes therein directly. This report describes our work on developing algorithms to simulate viscous and electric flow through a three dimensional Cartesian representation of the porous space, such as those available through X-ray microtomography. We use finite differences to discretize the governing equations and also propose a new method to enforce the incompressible flow constraint under natural boundary conditions. Parallel computational codes are written targeting performance and computer memory optimization, allowing the use of bigger and more representative samples. Results are reported with an estimate of the error bars in order to help on the simulation appraisal. Tests performed using benchmark samples show good agreement with experimental/theoretical values. Example of application on digital modeling of cement growth and on multiphase fluid distribution are also provided. The final test is done on Bentheimer, Buff Berea and Idaho Brown sandstone samples with available laboratory measurements. Some limitations need to be investigated in future work. First, the computer potential fields show anomalous border effects at the open boundaries. Second, a minor problem arises with the decreased convergence rate for the velocity field due to the increased number of operations, leading to the need of a more sophisticated preconditioner. We intend to expand the algorithms to handle microporosity (e.g. carbonates) and multiphase fluid flow. / text

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