Interactions of natural products with β-lactoglobulins, members of the lipocalin family

Natural products constitute an important source of new drugs. The bioavailability of the drugs depends on their absorption, distribution, metabolism and elimination. To achieve good bioavailability, the drug must be soluble in water, stable in the gastrointestinal tract and palatable. Binding proteins may improve the solubility of drug compounds, masking unwanted properties, such as bad taste, bitterness or toxicity, transporting or protecting these compounds during processing and storage. The focus of this thesis was to study the interactions, including ligand binding and the effect of pH and temperature, of bovine and reindeer β-lactoglobulin (βLG) with such compounds as retinoids, phenolic compounds as well as with compounds from plant extracts, and to investigate the transport properties of the βLG-ligand complex. To examine the binding interactions of different ligands to βLG, new methods were developed. The fluorescence binding method for the evaluation of ligand binding to βLG was miniaturized from a quartz cell to a 96-well plate. A method of ultrafiltration sampling combined with high-performance liquid chromatography was developed to assess the binding of compounds from extracts. The interactions of phenolic compounds or retinoids and βLG were investigated using the 96-well plate method. The majority of flavones, flavonols, flavanones and isoflavones and all of the retinoids included were shown to bind to bovine and reindeer βLG. Phenolic compounds, contrary to retinol, were not released at acidic pH. Those results suggest that βLG may have more binding sites, probably also on the surface of βLG. An extract from Camellia sinensis (L.) O. Kunze (black tea), Urtica dioica L. (nettle) and Piper nigrum (black pepper) were used to evaluate whether βLG could bind compounds from plant extracts. Piperine from P. nigrum was found to bind tightly and rutin from U. dioica weakly to βLG. No components from C. sinensis bound to βLG in our experiment. The uptake and membrane permeation of bovine and reindeer βLG, free and bound with retinol, palmitic acid and cholesterol, were investigated using Caco-2 cell monolayers. Both bovine and reindeer βLG were able to cross the Caco-2 cell membrane. Free and βLG-bound retinol and palmitic acid were transported equally, whereas cholesterol could not cross the Caco-2 cell monolayer free or bound to βLG. Our results showed that βLG can bind different natural product compounds, but cannot enhance transport of retinol, palmitic acid or cholesterol through Caco-2 cells. Despite this, βLG, as a water-soluble binding protein, may improve the solubility of natural compounds, possibly protecting them from early degradation and transporting some of them through the stomach. Furthermore, it may decrease their bad or bitter taste during oral administration of drugs or in food preparations. βLG can also enhance or decrease the health benefits of herbal teas and food preparations by binding compounds from extracts.

Expression of functional GABAc receptors in the brain

γ-aminobutyric acid (GABA) is the main inhibitory transmitter in the nervous system and acts via three distinct receptor classes: A, B, and C. GABAC receptors are ionotropic receptors comprising ρ subunits. In this work, we aimed to elucidate the expression of ρ subunits in the postnatal brain, the characteristics of ρ2 homo-oligomeric receptors, and the function of GABAC receptors in the hippocampus. In situ hybridization on rat brain slices showed ρ2 mRNA expression from the newborn in the superficial grey layer of the superior colliculus, from the first postnatal week in the hippocampal CA1 region and the pretectal nucleus of the optic tract, and in the adult dorsal lateral geniculate nucleus. Quantitative RT-PCR revealed expression of all three ρ subunits in the hippocampus and superior colliculus from the first postnatal day. In the hippocampus, ρ2 mRNA expression clearly dominated over ρ1 and ρ3. GABAC receptor protein expression was confirmed in the adult hippocampus, superior colliculus, and dorsal lateral geniculate nucleus by immunohistochemistry. From the selective distribution of ρ subunits, GABAC receptors may be hypothesized to be specifically involved in aspects of visual image motion processing in the rat brain. Although previous data had indicated a much higher expression level for ρ2 subunit transcripts than for ρ1 or ρ3 in the brain, previous work done on Xenopus oocytes had suggested that rat ρ2 subunits do not form functional homo-oligomeric GABAC receptors but need ρ1 or ρ3 subunits to form hetero-oligomers. Our results demonstrated, for the first time, that HEK 293 cells transfected with ρ2 cDNA displayed currents in whole-cell patch-clamp recordings. Homomeric rat ρ2 receptors had a decreased sensitivity to, but a high affinity for picrotoxin and a marked sensitivity to the GABAC receptor agonist CACA. Our results suggest that ρ2 subunits may contribute to brain function, also in areas not expressing other ρ subunits. Using extracellular electrophysiological recordings, we aimed to study the effects of the GABAC receptor agonists and antagonists on responses of the hippocampal neurons to electrical stimulation. Activation of GABAC receptors with CACA suppressed postsynaptic excitability and the GABAC receptor antagonist TPMPA inhibited the effects of CACA. Next, we aimed to display the activation of the GABAC receptors by synaptically released GABA using intracellular recordings. GABA-mediated long-lasting depolarizing responses evoked by high-frequency stimulation were prolonged by TPMPA. For weaker stimulation, the effect of TPMPA was enhanced after GABA uptake was inhibited. Our data demonstrate that GABAC receptors can be activated by endogenous synaptic transmitter release following strong stimulation or under conditions of reduced GABA uptake. The lack of GABAC receptor activation by less intensive stimulation under control conditions suggests that these receptors are extrasynaptic and activated via spillover of synaptically released GABA. Taken together with the restricted expression pattern of GABAC receptors in the brain and their distinctive pharmacological and biophysical properties, our findings supporting extrasynaptic localization of these receptors raise interesting possibilities for novel pharmacological therapies in the treatment of, for example, epilepsy and sleep disorders.

Epithelial-mesenchymal transition in oral squamous carcinoma cells

In epithelial-mesenchymal transition (EMT), epithelial cells acquire traits typical for mesenchymal cells, dissociate their cell-cell junctions and gain the ability to migrate. EMT is essential during embryogenesis, but may also mediate cancer progression. Basement membranes are sheets of extracellular matrix that support epithelial cells. They have a major role in maintaining the epithelial phenotype and, in cancer, preventing cell migration, invasion and metastasis. Laminins are the main components of basement membranes and may actively contribute to malignancy. We first evaluated the differences between cell lines obtained from oral squamous cell carcinoma and its recurrence. As the results indicated a change from epithelial to fibroblastoid morphology, E-cadherin to N-cadherin switch, and change in expression of cytokeratins to vimentin intermediate filaments, we concluded that these cells had undergone EMT. We further induced EMT in primary tumour cells to gain knowledge of the effects of transcription factor Snail in this cell model. The E-cadherin repressors responsible for the EMT in these cells were ZEB-1, ZEB-2 and Snail, and ectopic expression of Snail was able to augment the levels of ZEB-1 and ZEB-2. We produced and characterized two monoclonal antibodies that specifically recognized Snail in cell lines and patient samples. By immunohistochemistry, Snail protein was found in mesenchymal tissues during mouse embryonal development, in fibroblastoid cells of healing skin wounds and in fibromatosis and sarcoma specimens. Furthermore, Snail localized to the stroma and borders of tumour cell islands in colon adenocarcinoma, and in laryngeal and cervical squamous cell carcinomas. Immunofluorescence labellings, immunoprecipitations and Northern and Western blots showed that EMT induced a progressive downregulation of laminin-332 and laminin-511 and, on the other hand, an induction of mesenchymal laminin-411. Chromatin immunoprecipitation revealed that Snail could directly bind upstream to the transcription start sites of both laminin α5 and α4 chain genes, thus regulating their expression. The levels of integrin α6β4, a receptor for laminin-332, as well as the hemidesmosomal complex proteins HD1/plectin and BP180 were downregulated in EMT-experienced cells. The expression of Lutheran glycoprotein, a specific receptor for laminin-511, was diminished, whereas the levels of integrins α6β1 and α1β1 and integrin-linked kinase were increased. In quantitative cell adhesion assays, the cells adhered potently to laminin-511 and fibronectin, but only marginally to laminin-411. Western blots and immunoprecipitations indicated that laminin-411 bound to fibronectin and could compromise cell adhesion to fibronectin in a dose-dependent manner. EMT induced a highly migratory and invasive tendency in oral squamous carcinoma cells. Actin-based adhesion and invasion structures, podosomes and invadopodia, were detected in the basal cell membranes of primary tumour and spontaneously transformed cancer cells, respectively. Immunofluorescence labellings showed marked differences in their morphology, as podosomes organized a ring structure with HD1/plectin, αII-spectrin, talin, focal adhesion kinase and pacsin 2 around the core filled with actin, cortactin, vinculin and filamin A. Invadopodia had no division between ring and core and failed to organize the ring proteins, but instead assembled tail-like, narrow actin cables that showed a talin-tensin switch. Time-lapse live-cell imaging indicated that both podosomes and invadopodia were long-lived entities, but the tails of invadopodia vigorously propelled in the cytoplasm and were occasionally released from the cell membrane. Invadopodia could also be externalized outside the cytoplasm, where they still retained the ability to degrade matrix. In 3D confocal imaging combined with in situ gelatin zymography, the podosomes of primary tumour cells were large, cylindrical structures that increased in time, whereas the invadopodia in EMT-driven cells were smaller, but more numerous and degraded the underlying matrix in significantly larger amounts. Fluorescence recovery after photobleaching revealed that the substructures of podosomes were replenished more rapidly with new molecules than those of invadopodia. Overall, our results indicate that EMT has a major effect on the transcription and synthesis of both intra- and extracellular proteins, including laminins and their receptors, and on the structure and dynamics of oral squamous carcinoma cells.

Orphan nuclear receptor subfamily NR4A their interplay with other nuclear receptors and functions in osteoblasts

Nurr1, NGFI-B and Nor1 (NR4A2, NR4A1 and NR4A3, respectively) belong to the NR4A subfamily of nuclear receptors. The NR4A receptors are orphan nuclear receptors which means that activating or repressing ligands for these receptors have not been found. NR4A expression is rapidly induced in response to various stimuli including growth factors and the parathyroid hormone (PTH). The studies concerning the NR4A receptors in the central nervous system have demonstrated that they have a major role in the development and function of the dopaminergic neurons of the midbrain and in regulating hypothalamus-pituitary-adrenal-axis. However, the peripheral functions of the NR4A family are largely unknown. Cultured mouse primary osteoblasts, a preosteoblastic cell line and several osteoblastic cell lines were used to investigate the role of NR4A receptors in osteoblasts. NR4A receptors were shown to directly bind to and activate the promoter of the osteopontin gene (OPN) in osteoblastic cells, thus regulating its expression. OPN is a major bone matrix protein expressed throughout the differentiation of preosteoblastic cells into osteoblasts. The activation of the OPN promoter was shown to be dependent on the activation function-1 located in the N-terminal part of Nurr1 and to occur in both monomeric and RXR heterodimeric forms of NR4A receptors. Furthermore, PTH was shown to upregulate OPN expression through the NR4A family. It was also demonstrated that the fibroblast growth factor-8b (FGF-8b) induces the expression of NR4A receptors in osteoblasts as immediate early genes. This induction involved phosphatidylinositol-3 kinase, protein kinase C, and mitogen activated protein kinase, which are all major pathways of FGF signalling. Nurr1 and NGFI-B were shown to induce the proliferation of preosteoblastic cells and to reduce their apoptosis. FGF-8b was shown to stimulate the proliferation of osteoblastic cells through the NR4A receptors. These results suggest that NR4A receptors have a role both in the differentiation of osteoblasts and in the proliferation and apoptosis of preosteoblast. The NR4A receptors were found to bind to the same response element on OPN as the members of the NR3B family of orphan receptors do. Mutual repression was observed between the NR4A receptors and the NR3B receptors. This repression was shown to be dependent on the DNA-binding domains of both receptor families, but to result neither from the competition of DNA binding nor from the competition for coactivators. As the repression was dependent on the relative expression levels of the NR4As and NR3Bs, it seems likely that the ratio of the receptors mediates their activity on their response elements. Rapid induction of the NR4As in response to various stimuli and differential expression of the NR3Bs can effectively control the gene activation by the NR4A receptors. NR4A receptors can bind DNA as monomers, and Nurr1 and NGFI-B can form permissive heterodimers with the retinoid X receptor (RXR). Permissive heterodimers can be activated with RXR agonists, unlike non-permissive heterodimers, which are formed by RXR and retinoic acid receptor or thyroid hormone receptor (RAR and TR, respectively). Non-permissive heterodimers can only be activated by the agonists of the heterodimerizing partner. The mechanisms behind differential response to RXR agonists have remained unresolved. As there are no activating or repressing ligands for the NR4A receptors, it would be important to find out, how they are regulated. Permissiviness of Nurr1/RXR heterodimers was linked to the N-terminal part of Nurr1 ligand-binding domain. This region has previously been shown to mediate the interaction between NRs and corepressors. Non-permissive RAR and TR, permissive Nurr1 and NGFI-B, and RXR were overexpressed with corepressors silencing mediator for retinoic acid and thyroid hormone receptors (SMRT), and with nuclear receptor corepressor in several cell lines. Nurr1 and NGFI-B were found to be repressed by SMRT. The interaction of RXR heterodimers with corepressors was weak in permissive heterodimers and much stronger in non-permissive heterodimers. Non-permissive heterodimers also released corepressors only in response to the agonist of the heterodimeric partner of RXR. In the permissive Nurr1/RXR heterodimer, however, SMRT was released following the treatment with RXR agonists. Corepressor release in response to ligands was found to differentiate permissive heterodimers from non-permissive ones. Corepressors were thus connected to the regulation of NR4A functions. In summary, the studies presented here linked the NR4A family of orphan nuclear receptors to the regulation of osteoblasts. Nurr1 and NGFI-B were found to control the proliferation and apoptosis of preosteoblasts. The studies also demonstrated that cross-talk with the NR3B receptors controls the activity of these orphan receptors. The results clarified the mechanism of permissiviness of RXR-heterodimers. New information was obtained on the regulation and functions of NR4A receptors, for which the ligands are unknown.

Coffee and risk of type 2 diabetes

Type 2 diabetes is one of the diseases that largely determined by lifestyle factors. Coffee is one of the most consumed beverages in the world and recently released data suggest the effects of coffee consumption on type 2 diabetes. The objective of the present study was to evaluate the effects of habitual coffee consumption on various aspects of type 2 diabetes and its most common complications. This study is part of the national FINRISK studies. Baseline surveys were carried out between 1972 and 1997. The surveys covered two eastern regions in 1972 and 1977, but were expanded to include a third region in southwestern Finland in 1982, 1987, 1992, and 1997. The Helsinki capital area was included in the survey in 1992 and 1997 and the Oulu province, in northern Finland, in 1997. Each survey was drawn from an independent random sample of the national register of subjects aged 25-64. In 1997, an additional sample of subjects aged 65-74 was conducted. The blood pressure, weight, and height of subjects were measured. By using self-administered questionnaires data were collected on medical history, socioeconomic factors, physical activity, smoking habits, and alcohol, coffee, and tea consumption. Higher coffee consumption was associated with higher body mass index, occupational physical activity and cigarette smoking, and lower blood pressure, education level, leisure time physical activity, tea consumption and alcohol use. Age, body mass index, systolic blood pressure and current smoking were positively associated with the risk of type 2 diabetes, however, education, and occupational, commuting and leisure time physical activity were inversely associated. The significant inverse association between coffee consumption and the risk of type 2 diabetes was found in both sexes but the association was stronger in women. Coffee consumption was significantly and inversely associated with fasting glucose, 2-hour plasma glucose, fasting insulin, impaired fasting glucose, impaired glucose regulation, and hyperinsulinemia among both men and women and with isolated impaired glucose tolerance among women. Serum gamma-glutamyltransferase modified the association between coffee consumption and incident diabetes. Among subjects with high serum -glutamyltransferase (>75th percentile), coffee consumption showed an inverse association for women, as well as men and women combined. An inverse association also occurred between coffee consumption and the risk of total, cardiovascular disease, and coronary heart disease mortality among patients with type 2 diabetes. The results of this study showed that habitual coffee consumption may be associated with a reduced risk of type 2 diabetes. Coffee consumption may have some effects on several markers of glycemia, and may lower the incident of type 2 diabetes in high normal serum -glutamyltransferase levels. Total, cardiovascular disease, and coronary heart disease mortality rate among subjects with type 2 diabetes may also be reduced by coffee consumption.

Use of biomass fuels in the brick-making industries of Sudan: Implications for deforestation and greenhouse gas emission

The study focuses on the potential roles of the brick making industries in Sudan in deforestation and greenhouse gas emission due to the consumption of biofuels. The results were based on the observation of 25 brick making industries from three administrative regions in Sudan namely, Khartoum, Kassala and Gezira. The methodological approach followed the procedures outlined by the Intergovernmental Panel on Climate Change (IPCC). For predicting a serious deforestation scenario, it was also assumed that all of wood use for this particular purpose is from unsustainable sources. The study revealed that the total annual quantity of fuelwood consumed by the surveyed brick making industries (25) was 2,381 t dm. Accordingly, the observed total potential deforested wood was 10,624 m3, in which the total deforested round wood was 3,664 m3 and deforested branches was 6,961 m3. The study observed that a total of 2,990 t biomass fuels (fuelwood and dung cake) consumed annually by the surveyed brick making industries for brick burning. Consequently, estimated total annual emissions of greenhouse gases were 4,832 t CO2, 21 t CH4, 184 t CO, 0.15 t N20, 5 t NOX and 3.5 t NO while the total carbon released in the atmosphere was 1,318 t. Altogether, the total annual greenhouse gases emissions from biomass fuels burning was 5,046 t; of which 4,104 t from fuelwood and 943 t from dung cake burning. According to the results, due to the consumption of fuelwood in the brick making industries (3,450 units) of Sudan, the amount of wood lost from the total growing stock of wood in forests and trees in Sudan annually would be 1,466,000 m3 encompassing 505,000 m3 round wood and 961,000 m3 branches annually. By considering all categories of biofuels (fuelwood and dung cake), it was estimated that, the total emissions from all the brick making industries of Sudan would be 663,000 t CO2, 2,900 t CH4, 25,300 t CO, 20 t N2O, 720 t NOX and 470 t NO per annum, while the total carbon released in the atmosphere would be 181,000 t annually.

Nitrogen dynamics and nitrogen use efficiency of spring cereals under Finnish growing conditions

Nitrogen (N) is one of the main inputs in cereal cultivation and as more than half of the arable land in Finland is used for cereal production, N has contributed substantially to agricultural pollution through fertilizer leaching and runoff. Based on this global phenomenon, the European Community has launched several directives to reduce agricultural emissions to the environment. Trough such measures, and by using economic incentives, it is expected that northern European agricultural practices will, in the future, include reduced N fertilizer application rates. Reduced use of N fertilizer is likely to decrease both production costs and pollution, but could also result in reduced yields and quality if crops experience temporary N deficiency. Therefore, more efficient N use in cereal production, to minimize pollution risks and maximize farmer income, represents a current challenge for agronomic research in the northern growing areas. The main objective of this study was to determine the differences in nitrogen use efficiency (NUE) among spring cereals grown in Finland. Additional aims were to characterize the multiple roles of NUE by analysing the extent of variation in NUE and its component traits among different cultivars, and to understand how other physiological traits, especially radiation use efficiency (RUE) and light interception, affect and interact with the main components of NUE and contribute to differences among cultivars. This study included cultivars of barley (Hordeum vulgare L.), oat (Avena sativa L.) and wheat (Triticum aestivum L.). Field experiments were conducted between 2001 and 2004 at Jokioinen, in Finland. To determine differences in NUE among cultivars and gauge the achievements of plant breeding in NUE, 17-18 cultivars of each of the three cereal species released between 1909 and 2002 were studied. Responses to nitrogen of landraces, old cultivars and modern cultivars of each cereal species were evaluated under two N regimes (0 and 90 kg N ha-1). Results of the study revealed that modern wheat, oat and barley cultivars had similar NUE values under Finnish growing conditions and only results from a wider range of cultivars indicated that wheat cultivars could have lower NUE than the other species. There was a clear relationship between nitrogen uptake efficiency (UPE) and NUE in all species whereas nitrogen utilization efficiency (UTE) had a strong positive relationship with NUE only for oat. UTE was clearly lower in wheat than in other species. Other traits related to N translocation indicated that wheat also had a lower harvest index, nitrogen harvest index and nitrogen remobilisation efficiency and therefore its N translocation efficiency was confirmed to be very low. On the basis of these results there appears to be potential and also a need for improvement in NUE. These results may help understand the underlying physiological differences in NUE and could help to identify alternative production options, such as the different roles that species can play in crop rotations designed to meet the demands of modern agricultural practices.

Chemical characteristics and behaviour of sediment phosphorus in the northeastern Baltic Sea.

Chemical characteristics and behaviour of sediment phosphorus in the northeastern Baltic Sea Eutrophication is a severe environmental problem in the Baltic Sea, especially in the Gulf of Finland and the Archipelago Sea, and it is enhanced by the release of phosphorus (P) from bottom sediments. The release of P from sediment reserves largely depends on the occurrence of P in different chemical forms and on the prevailing conditions, especially on the presence of oxygen. This study examines the chemical character and the vertical distribution of sediment P in two shallow estuaries, in shallow coastal sediments overlain by oxic near-bottom water, and in poorly oxygenated open sea sediments in the northeastern Baltic Sea. The objective was to evaluate how much of the sediment P is buried and removed from the nutrient cycle, and how much of it is in forms that can be released from the sediment to the overlaying water over time. Relationships between the distribution of the different P forms and the chemical and physical properties of the sediment, sediment pore water, and near-bottom water were determined in order to examine the behaviour of P at the sediment-water interface. The results show that the chemical character of sediment P varied in the different areas. Generally, in the outer estuaries and in the organic-rich coastal areas in the eastern Gulf of Finland, the sediments were higher in P than the sediments in the poorly oxygenated open sea areas in the central and western Gulf. The estuary sediments that received erosion-transported material were characterised by P bound to hydrated oxides of iron and aluminum. Iron-bound P is sensitive to changes in redox-conditions, but part of it was buried in the estuaries, possibly because of high sedimentation rates and incomplete reduction of iron. The open sea sediments in the central and western Gulf of Finland were dominated by apatite-P, which was also abundant in the areas strongly affected by sediment transportation. The burial of sediment P was most effective in the areas rich in apatite-P, which is a relatively stable form of P in sediment. In the eastern Gulf of Finland, organic P forms predominated in the organic-rich sediments. A part of these P forms will be buried, while part will be degraded in the long term, releasing soluble P to the pore water. In the poorly oxygenated areas, iron compounds at the sediment surface are not able to retain P released during mineralisation of organic matter or reduction-induced dissolution of iron-compounds in deep sediment layers. However, in the shallow coastal areas overlain by oxic near-bottom water, the organic-rich surface sediment can also become temporarily reduced and release P from the sediment to the overlaying water. The considerable variation in the chemical composition of sediment P reserves in the northeastern Baltic Sea proved that it is an important factor and should be taken into account when evaluating the release of sediment P and the role of P reserves in bottom sediments in eutrophication.

Structural analyses of (1->3),(1->4)-β-D-glucan of oats and barley

The structures of (1→3),(1→4)-β-D-glucans of oat bran, whole-grain oats and barley and processed foods were analysed. Various methods of hydrolysis of β-glucan, the content of insoluble fibre of whole grains of oats and barley and the solution behaviour of oat and barley β-glucans were studied. The isolated soluble β-glucans of oat bran and whole-grain oats and barley were hydrolysed with lichenase, an enzyme specific for (1→3),(1→4)-β-D-β-glucans. The amounts of oligosaccharides produced from bran were analysed with capillary electrophoresis and those from whole-grains with high-performance anion-exchange chromatography with pulse-amperometric detection. The main products were 3-O-β-cellobiosyl-D-glucose and 3-O-β-cellotriosyl-D-glucose, the oligosaccharides which have a degree of polymerisation denoted by DP3 and DP4. Small differences were detected between soluble and insoluble β-glucans and also between β-glucans of oats and barley. These differences can only be seen in the DP3:DP4 ratio which was higher for barley than for oat and also higher for insoluble than for soluble β-glucan. A greater proportion of barley β-glucan remained insoluble than of oat β-glucan. The molar masses of soluble β-glucans of oats and barley were the same as were those of insoluble β-glucans of oats and barley. To analyse the effects of cooking, baking, fermentation and drying, β-glucan was isolated from porridge, bread and fermentate and also from their starting materials. More β-glucan was released after cooking and less after baking. Drying decreased the extractability for bread and fermentate but increased it for porridge. Different hydrolysis methods of β-glucan were compared. Acid hydrolysis and the modified AOAC method gave similar results. The results of hydrolysis with lichenase gave higher recoveries than the other two. The combination of lichenase hydrolysis and high-performance anion-exchange chromatography with pulse-amperometric detection was found best for the analysis of β-glucan content. The content of insoluble fibre was higher for barley than for oats and the amount of β-glucan in the insoluble fibre fraction was higher for oats than for barley. The flow properties of both water and aqueous cuoxam solutions of oat and barley β-glucans were studied. Shear thinning was stronger for the water solutions of oat β-glucan than for barley β-glucan. In aqueous cuoxam shear thinning was not observed at the same concentration as in water but only with high concentration solutions. Then the viscosity of barley β-glucan was slightly higher than that of oat β-glucan. The oscillatory measurements showed that the crossover point of the G´ and G´´ curves was much lower for barley β-glucan than for oat β-glucan indicating a higher tendency towards solid-like behaviour for barley β-glucan than for oat β-glucan.

Preparation, structural analysis and prebiotic potential of arabinoxylo-oligosaccharides

Arabinoxylo-oligosaccharides (AXOS) can be prepared enzymatically from arabinoxylans (AX) and AXOS are known to possess prebiotic potential. Here the structural features of 10 cereal AX were examined. AX were hydrolysed by Shearzyme® to prepare AXOS, and their structures were fully analysed. The prebiotic potential of the purified AXOS was studied in the fermentation experiments with bifidobacteria and faecal microbiota. In AX extracted from flours and bran, high amounts of a-L-Araf units are attached to the b-D-Xylp main chain, whereas moderate or low degree of substitution was found from husks, cob and straw. Nuclear magnetic resonance (NMR) spectroscopy showed that flour and bran AX contain high amounts of a-L-Araf units bound to the O-3 of b-D-Xylp residues and doubly substituted b-D-Xylp units with a-L-Araf substituents at O-2 and O-3. Barley husk and corn cob AX contain high amounts of b-D-Xylp(1→2)-a-L-Araf(1→3) side chains, which can also be found in AX from oat spelts and rice husks, and in lesser amounts in wheat straw AX. Rye and wheat flour AX and oat spelt AX were hydrolysed by Shearzyme® (with Aspergillus aculeatus GH10 endo-1,4-b-D-xylanase as the main enzyme) for the production of AXOS on a milligram scale. The AXOS were purified and their structures fully analysed, using mass spectrometry (MS) and 1D and 2D NMR spectroscopy. Monosubstituted xylobiose and xylotriose with a-L-Araf attached to the O-3 or O-2 of the nonreducing end b-D-Xylp unit and disubstituted AXOS with two a-L-Araf units at the nonreducing end b-D-Xylp unit of xylobiose or xylotriose were produced. Xylobiose with b-D-Xylp(1→2)-a-L-Araf(1→3) side chain was also purified. These AXOS were used as standards in further identification and quantification of corresponding AXOS from the hydrolysates in high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD) analysis. The prebiotic potential of AXOS was tested in in vitro fermentation experiments. Bifidobacterium adolescentis ATCC 15703 and B. longum ATCC 15707 utilized AXOS from the AX hydrolysates. Both species released L-arabinose from AXOS, but B. adolescentis consumed the XOS formed, whereas B. longum fermented the L-arabinose released. The third species tested, B. breve ATCC 15700, grew poorly on these substrates. When cultivated on pure AXOS, the bifidobacterial mixture utilized pure singly substituted AXOS almost completely, but no growth was detected with pure doubly substituted AXOS as substrates. However, doubly substituted AXOS were utilized from the mixture of xylose, XOS and AXOS. Faecal microbiota utilized both pure singly and doubly substituted AXOS. Thus, a mixture of singly and doubly substituted AXOS could function as a suitable, slowly fermenting prebiotic substance. This thesis contributes to the structural information on cereal AX and preparation of mono and doubly substituted AXOS from AX. Understanding the utilization strategies is fundamental in evaluating the prebiotic potential of AXOS. Further research is still required before AXOS can be used in applications for human consumption.

Lost in Translation : Translation Mechanisms in Production of Cocksfoot Mottle Virus Proteins

The present study focuses on the translational strategies of Cocksfoot mottle virus (CfMV, genus Sobemovirus), which infects monocotyledonous plants. CfMV RNA lacks the 5'cap and the 3'poly(A) tail that ensure efficient translation of cellular messenger RNAs (mRNAs). Instead, CfMV RNA is covalently linked to a viral protein VPg (viral protein, genome-linked). This indicates that the viral untranslated regions (UTRs) must functionally compensate for the lack of the cap and poly(A) tail. We examined the efficacy of translation initiation in CfMV by comparing it to well-studied viral translational enhancers. Although insertion of the CfMV 5'UTR (CfMVe) into plant expression vectors improved gene expression in barley more than the other translational enhancers examined, studies at the RNA level showed that CfMVe alone or in combination with the CfMV 3'UTR did not provide the RNAs translational advantage. Mutation analysis revealed that translation initiation from CfMVe involved scanning. Interestingly, CfMVe also promoted translation initiation from an intercistronic position of dicistronic mRNAs in vitro. Furthermore, internal initiation occurred with similar efficacy in translation lysates that had reduced concentrations of eukaryotic initiation factor (eIF) 4E, suggesting that initiation was independent of the eIF4E. In contrast, reduced translation in the eIF4G-depleted lysates indicated that translation from internally positioned CfMVe was eIF4G-dependent. After successful translation initiation, leaky scanning brings the ribosomes to the second open reading frame (ORF). The CfMV polyprotein is produced from this and the following overlapping ORF via programmed -1 ribosomal frameshift (-1 PRF). Two signals in the mRNA at the beginning of the overlap program approximately every fifth ribosome to slip one nucleotide backwards and continue translation in the new -1 frame. This leads to the production of C-terminally extended polyprotein, which encodes the viral RNA-dependent RNA polymerase (RdRp). The -1 PRF event in CfMV was very efficient, even though it was programmed by a simple stem-loop structure instead of a pseudoknot, which is usually required for high -1 PRF frequencies. Interestingly, regions surrounding the -1 PRF signals improved the -1 PRF frequencies. Viral protein P27 inhibited the -1 PRF event in vivo, putatively by binding to the -1 PRF site. This suggested that P27 could regulate the occurrence of -1 PRF. Initiation of viral replication requires that viral proteins are released from the polyprotein. This is catalyzed by viral serine protease, which is also encoded from the polyprotein. N-terminal amino acid sequencing of CfMV VPg revealed that the junction of the protease and VPg was cleaved between glutamate (E) and asparagine (N) residues. This suggested that the processing sites used in CfMV differ from the glutamate and serine (S) or threonine (T) sites utilized in other sobemoviruses. However, further analysis revealed that the E/S and E/T sites may be used to cleave out some of the CfMV proteins.

Computational Studies on Bimetallic Clusters

The chemical and physical properties of bimetallic clusters have attracted considerable attention due to the potential technological applications of mixed-metal systems. It is of fundamental interests to study clusters because they are the link between atomic surface and bulk properties. More information of metal-metal bond in small clusters can be hence released. The studies in my thesis mainly focus on the two different kinds of bimetallic clusters: the clusters consisting of extraordinary shaped all metal four-membered rings and a series of sodium auride clusters. As described in most general organic chemistry books nowadays, a group of compounds are classified as aromatic compounds because of their remarkable stabilities, particular geometrical and energetic properties and so on. The notation of aromaticity is essentially qualitative. More recently, the connection has been made between aromaticity and energetic and magnetic properties. Also, the discussions of the aromatic nature of molecular rings are no longer limited to organic compounds obeying the Hückel’s rule. In our research, we mainly applied the GIMIC method to several bimetallic clusters at the CCSD level, and compared the results with those obtained by using chemical shift based methods. The magnetically induced ring currents can be generated easily by employing GIMIC method, and the nature of aromaticity for each system can be therefore clarified. We performed intensive quantum chemical calculations to explore the characters of the anionic sodium auride clusters and the corresponding neutral clusters since it has been fascinating in investigating molecules with gold atom involved due to its distinctive physical and chemical properties. As small gold clusters, the sodium auride clusters seem to form planar structures. With the addition of a negative charge, the gold atom in anionic clusters prefers to carry the charge and orients itself away from other gold atoms. As a result, the energetically lowest isomer for an anionic cluster is distinguished from the one for the corresponding neutral cluster. Mostly importantly, we presented a comprehensive strategy of ab initio applications to computationally implement the experimental photoelectron spectra.

Geological factors affecting on after-use of Finnish cut-over peatlands : with implications on the carbon accumulation

In Finland, peat harvesting sites are utilized down almost to the mineral soil. In this situation the properties of mineral subsoil are likely to have considerable influence on the suitability for the various after-use forms. The aims of this study were to recognize the chemical and physical properties of mineral subsoils possibly limiting the after-use of cut-over peatlands, to define a minimum practice for mineral subsoil studies and to describe the role of different geological areas. The future percentages of the different after-use forms were predicted, which made it possible to predict also carbon accumulation in this future situation. Mineral subsoils of 54 different peat production areas were studied. Their general features and grain size distribution was analysed. Other general items studied were pH, electrical conductivity, organic matter, water soluble nutrients (P, NO3-N, NH4-N, S and Fe) and exchangeable nutrients (Ca, Mg and K). In some cases also other elements were analysed. In an additional case study carbon accumulation effectiveness before the intervention was evaluated on three sites in Oulu area (representing sites typically considered for peat production). Areas with relatively sulphur rich mineral subsoil and pool-forming areas with very fine and compact mineral subsoil together covered approximately 1/5 of all areas. These areas were unsuitable for commercial use. They were recommended for example for mire regeneration. Another approximate 1/5 of the areas included very coarse or very fine sediments. Commercial use of these areas would demand special techniques - like using the remaining peat layer for compensating properties missing from the mineral subsoil. One after-use form was seldom suitable for one whole released peat production area. Three typical distribution patterns (models) of different mineral subsoils within individual peatlands were found. 57 % of studied cut-over peatlands were well suited for forestry. In a conservative calculation 26% of the areas were clearly suitable for agriculture, horticulture or energy crop production. If till without large boulders was included, the percentage of areas suitable to field crop production would be 42 %. 9-14 % of all areas were well suitable for mire regeneration or bird sanctuaries, but all areas were considered possible for mire regeneration with correct techniques. Also another 11 % was recommended for mire regeneration to avoid disturbing the mineral subsoil, so total 20-25 % of the areas would be used for rewetting. High sulphur concentrations and acidity were typical to the areas below the highest shoreline of the ancient Litorina sea and Lake Ladoga Bothnian Bay zone. Also differences related to nutrition were detected. In coarse sediments natural nutrient concentration was clearly higher in Lake Ladoga Bothnian Bay zone and in the areas of Svecokarelian schists and gneisses, than in Granitoid area of central Finland and in Archaean gneiss areas. Based on this study the recommended minimum analysis for after-use planning was for pH, sulphur content and fine material (<0.06 mm) percentage. Nutrition capacity could be analysed using the natural concentrations of calcium, magnesium and potassium. Carbon accumulation scenarios were developed based on the land-use predictions. These scenarios were calculated for areas in peat production and the areas released from peat production (59300 ha + 15 671 ha). Carbon accumulation of the scenarios varied between 0.074 and 0.152 million t C a-1. In the three peatlands considered for peat production the long term carbon accumulation rates varied between 13 and 24 g C m-2 a-1. The natural annual carbon accumulation had been decreasing towards the time of possible intervention.

An approach to palaeoseismicity in the Olkiluoto (sea) area during the early Holocene

Olkiluoto Island is situated in the northern Baltic Sea, near the southwestern coast of Finland, and is the proposed location of a spent nuclear fuel repository. This study examined Holocene palaeoseismicity in the Olkiluoto area and in the surrounding sea areas by computer simulations together with acoustic-seismic, sedimentological and dating methods. The most abundant rock type on the island is migmatic mica gneiss, intruded by tonalites, granodiorites and granites. The surrounding Baltic Sea seabed consists of Palaeoproterozoic crystalline bedrock, which is to a great extent covered by younger Mesoproterozoic sedimentary rocks. The area contains several ancient deep-seated fracture zones that divide it into bedrock blocks. The response of bedrock at the Olkiluoto site was modelled considering four future ice-age scenarios. Each scenario produced shear displacements of fractures with different times of occurrence and varying recovery rates. Generally, the larger the maximum ice load, the larger were the permanent shear displacements. For a basic case, the maximum shear displacements were a few centimetres at the proposed nuclear waste repository level, at proximately 500 m b.s.l. High-resolution, low-frequency echo-sounding was used to examine the Holocene submarine sedimentary structures and possible direct and indirect indicators of palaeoseismic activity in the northern Baltic Sea. Echo-sounding profiles of Holocene submarine sediments revealed slides and slumps, normal faults, debris flows and turbidite-type structures. The profiles also showed pockmarks and other structures related to gas or groundwater seepages, which might be related to fracture zone activation. Evidence of postglacial reactivation in the study area was derived from the spatial occurrence of some of the structures, especial the faults and the seepages, in the vicinity of some old bedrock fracture zones. Palaeoseismic event(s) (a single or several events) in the Olkiluoto area were dated and the palaeoenvironment was characterized using palaeomagnetic, biostratigraphical and lithostratigraphical methods, enhancing the reliability of the chronology. Combined lithostratigraphy, biostratigraphy and palaeomagnetic stratigraphy revealed an age estimation of 10 650 to 10 200 cal. years BP for the palaeoseismic event(s). All Holocene sediment faults in the northern Baltic Sea occur at the same stratigraphical level, the age of which is estimated at 10 700 cal. years BP (9500 radiocarbon years BP). Their movement is suggested to have been triggered by palaeoseismic event(s) when the Late Weichselian ice sheet was retreating from the site and bedrock stresses were released along the bedrock fracture zones. Since no younger or repeated traces of seismic events were found, it corroborates the suggestion that the major seismic activity occurred within a short time during and after the last deglaciation. The origin of the gas/groundwater seepages remains unclear. Their reflections in the echo-sounding profiles imply that part of the gas is derived from the organic-bearing Litorina and modern gyttja clays. However, at least some of the gas is derived from the bedrock. Additional information could be gained by pore water analysis from the pockmarks. Information on postglacial fault activation and possible gas and/or fluid discharges under high hydraulic heads has relevance in evaluating the safety assessment of a planned spent nuclear fuel repository in the region.

Exploring privacy for ubiquitous computing: Tools, methods and experiments

Ubiquitous computing is about making computers and computerized artefacts a pervasive part of our everyday lifes, bringing more and more activities into the realm of information. The computationalization, informationalization of everyday activities increases not only our reach, efficiency and capabilities but also the amount and kinds of data gathered about us and our activities. In this thesis, I explore how information systems can be constructed so that they handle this personal data in a reasonable manner. The thesis provides two kinds of results: on one hand, tools and methods for both the construction as well as the evaluation of ubiquitous and mobile systems---on the other hand an evaluation of the privacy aspects of a ubiquitous social awareness system. The work emphasises real-world experiments as the most important way to study privacy. Additionally, the state of current information systems as regards data protection is studied. The tools and methods in this thesis consist of three distinct contributions. An algorithm for locationing in cellular networks is proposed that does not require the location information to be revealed beyond the user's terminal. A prototyping platform for the creation of context-aware ubiquitous applications called ContextPhone is described and released as open source. Finally, a set of methodological findings for the use of smartphones in social scientific field research is reported. A central contribution of this thesis are the pragmatic tools that allow other researchers to carry out experiments. The evaluation of the ubiquitous social awareness application ContextContacts covers both the usage of the system in general as well as an analysis of privacy implications. The usage of the system is analyzed in the light of how users make inferences of others based on real-time contextual cues mediated by the system, based on several long-term field studies. The analysis of privacy implications draws together the social psychological theory of self-presentation and research in privacy for ubiquitous computing, deriving a set of design guidelines for such systems. The main findings from these studies can be summarized as follows: The fact that ubiquitous computing systems gather more data about users can be used to not only study the use of such systems in an effort to create better systems but in general to study phenomena previously unstudied, such as the dynamic change of social networks. Systems that let people create new ways of presenting themselves to others can be fun for the users---but the self-presentation requires several thoughtful design decisions that allow the manipulation of the image mediated by the system. Finally, the growing amount of computational resources available to the users can be used to allow them to use the data themselves, rather than just being passive subjects of data gathering.