Spatial modeling techniques for mapping and characterization of acid sulfate soils

Acid sulfate (a.s.) soils constitute a major environmental issue. Severe ecological damage results from the considerable amounts of acidity and metals leached by these soils in the recipient watercourses. As even small hot spots may affect large areas of coastal waters, mapping represents a fundamental step in the management and mitigation of a.s. soil environmental risks (i.e. to target strategic areas). Traditional mapping in the field is time-consuming and therefore expensive. Additional more cost-effective techniques have, thus, to be developed in order to narrow down and define in detail the areas of interest. The primary aim of this thesis was to assess different spatial modeling techniques for a.s. soil mapping, and the characterization of soil properties relevant for a.s. soil environmental risk management, using all available data: soil and water samples, as well as datalayers (e.g. geological and geophysical). Different spatial modeling techniques were applied at catchment or regional scale. Two artificial neural networks were assessed on the Sirppujoki River catchment (c. 440 km2) located in southwestern Finland, while fuzzy logic was assessed on several areas along the Finnish coast. Quaternary geology, aerogeophysics and slope data (derived from a digital elevation model) were utilized as evidential datalayers. The methods also required the use of point datasets (i.e. soil profiles corresponding to known a.s. or non-a.s. soil occurrences) for training and/or validation within the modeling processes. Applying these methods, various maps were generated: probability maps for a.s. soil occurrence, as well as predictive maps for different soil properties (sulfur content, organic matter content and critical sulfide depth). The two assessed artificial neural networks (ANNs) demonstrated good classification abilities for a.s. soil probability mapping at catchment scale. Slightly better results were achieved using a Radial Basis Function (RBF) -based ANN than a Radial Basis Functional Link Net (RBFLN) method, narrowing down more accurately the most probable areas for a.s. soil occurrence and defining more properly the least probable areas. The RBF-based ANN also demonstrated promising results for the characterization of different soil properties in the most probable a.s. soil areas at catchment scale. Since a.s. soil areas constitute highly productive lands for agricultural purpose, the combination of a probability map with more specific soil property predictive maps offers a valuable toolset to more precisely target strategic areas for subsequent environmental risk management. Notably, the use of laser scanning (i.e. Light Detection And Ranging, LiDAR) data enabled a more precise definition of a.s. soil probability areas, as well as the soil property modeling classes for sulfur content and the critical sulfide depth. Given suitable training/validation points, ANNs can be trained to yield a more precise modeling of the occurrence of a.s. soils and their properties. By contrast, fuzzy logic represents a simple, fast and objective alternative to carry out preliminary surveys, at catchment or regional scale, in areas offering a limited amount of data. This method enables delimiting and prioritizing the most probable areas for a.s soil occurrence, which can be particularly useful in the field. Being easily transferable from area to area, fuzzy logic modeling can be carried out at regional scale. Mapping at this scale would be extremely time-consuming through manual assessment. The use of spatial modeling techniques enables the creation of valid and comparable maps, which represents an important development within the a.s. soil mapping process. The a.s. soil mapping was also assessed using water chemistry data for 24 different catchments along the Finnish coast (in all, covering c. 21,300 km2) which were mapped with different methods (i.e. conventional mapping, fuzzy logic and an artificial neural network). Two a.s. soil related indicators measured in the river water (sulfate content and sulfate/chloride ratio) were compared to the extent of the most probable areas for a.s. soils in the surveyed catchments. High sulfate contents and sulfate/chloride ratios measured in most of the rivers demonstrated the presence of a.s. soils in the corresponding catchments. The calculated extent of the most probable a.s. soil areas is supported by independent data on water chemistry, suggesting that the a.s. soil probability maps created with different methods are reliable and comparable.

Iron(III) as Lewis acid catalyst in organosilicon and carbonyl chemistry

Iron is one of the most common elements in the earth’s crust and thus its availability and economic viability far exceed that of metals commonly used in catalysis. Also the toxicity of iron is miniscule, compared to the likes of platinum and nickel, making it very desirable as a catalyst. Despite this, prior to the 21st century, the applicability of iron in catalysis was not thoroughly investigated, as it was considered to be inefficient and unselective in desired transformations. In this doctoral thesis, the application of iron catalysis in combination with organosilicon reagents for transformations of carbonyl compounds has been investigated together with insights into iron catalyzed chlorination of silanes and silanols. In the first part of the thesis, the synthetic application of iron(III)-catalyzed chlorination of silanes (Si-H) and the monochlorination of silanes (SiH2) using acetyl chloride as the chlorine source is described. The reactions proceed under ambient conditions, although some compounds need to be protected from excess moisture. In addition, the mechanism and kinetics of the chlorination reaction are briefly adressed. In the second part of this thesis a versatile methodology for transformation of carbonyl compounds into three different compound classes by changing the conditions and amounts of reagents is discussed. One pot reductive benzylation, reductive halogenation and reductive etherification of ketones and aldehydes using silanes as the reducing agent, halide source or cocatalyst, were investigated. Also the reaction kinetics and mechanism of the reductive halogenation of acetophenone are briefly discussed.

Metal-Ion-Binding Oligonucleotides: High-Affinity Probes for Nucleic Acid Sequences

Small non-coding RNAs have numerous biological functions in cell and are divided into different classes such as: microRNA, snoRNA, snRNA and siRNA. MicroRNA (miRNA) is the most studied non-coding RNA to date and is found in plants, animals and some viruses. miRNA with short sequences is involved in suppressing translation of target genes by binding to their mRNA post-transcriptionally and silencing it. Their function besides silencing of the viral gene, can be oncogenic and therefore the cause of cancer. Hence, their roles are highlighted in human diseases, which increases the interest in using them as biomarkers and drug targets. One of the major problems to overcome is recognition of miRNA. Owing to a stable hairpin structure, chain invasion by conventional Watson-Crick base-pairing is difficult. One way to enhance the hybridization is exploitation of metal-ion mediated base-pairing, i. e. oligonucleotide probes that tightly bind a metal ions and are able to form a coordinative bonds between modified and natural nucleobases. This kind of metallo basepairs containing short modified oligonucleotides can also be useful for recognition of other RNA sequences containing hairpin-like structural motives, such as the TAR sequence of HIV. In addition, metal-ion-binding oligonucleotides will undoubtedly find applications in DNA-based nanotechnology. In this study, the 3,5-dimethylpyrazol-1-yl substituted purine derivatives were successfully incorporated within oligonucleotides, into either a terminal or non-terminal position. Among all of the modified oligonucleotides studied, a 2-(3,5-dimethylpyrazol-1-yl)-6-oxopurine base containing oligonucleotide was observed to bind most efficiently to their unmodified complementary sequences in the presence of both Cu2+ or Zn2+. The oligonucleotide incorporating 2,6-bis(3,5-dimethylpyrazol-1-yl)purine base also markedly increased the stability of duplexes in the presence of Cu2+ without losing the selectivity.

The effects of mutated cationic amino acid transporter y+LAT1 at the cellular and systemic level

y+LAT1 is a transmembrane protein that, together with the 4F2hc cell surface antigen, forms a transporter for cationic amino acids in the basolateral plasma membrane of epithelial cells. It is mainly expressed in the kidney and small intestine, and to a lesser extent in other tissues, such as the placenta and immunoactive cells. Mutations in y+LAT1 lead to a defect of the y+LAT1/4F2hc transporter, which impairs intestinal absorbance and renal reabsorbance of lysine, arginine and ornithine, causing lysinuric protein intolerance (LPI), a rare, recessively inherited aminoaciduria with severe multi-organ complications. This thesis examines the consequences of the LPI-causing mutations on two levels, the transporter structure and the Finnish patients’ gene expression profiles. Using fluorescence resonance energy transfer (FRET) confocal microscopy, optimised for this work, the subunit dimerisation was discovered to be a primary phenomenon occurring regardless of mutations in y+LAT1. In flow cytometric and confocal microscopic FRET analyses, the y+LAT1 molecules exhibit a strong tendency for homodimerisation both in the presence and absence of 4F2hc, suggesting a heterotetramer for the transporter’s functional form. Gene expression analysis of the Finnish patients, clinically variable but homogenic for the LPI-causing mutation in SLC7A7, revealed 926 differentially-expressed genes and a disturbance of the amino acid homeostasis affecting several transporters. However, despite the expression changes in individual patients, no overall compensatory effect of y+LAT2, the sister y+L transporter, was detected. The functional annotations of the altered genes included biological processes such as inflammatory response, immune system processes and apoptosis, indicating a strong immunological involvement for LPI.