Spatial and temporal variability in midge (Nematocera) assemblages in shallow Finnish lakes (60−70 °N) : community-based modelling of past environmental change

Multi- and intralake datasets of fossil midge assemblages in surface sediments of small shallow lakes in Finland were studied to determine the most important environmental factors explaining trends in midge distribution and abundance. The aim was to develop palaeoenvironmental calibration models for the most important environmental variables for the purpose of reconstructing past environmental conditions. The developed models were applied to three high-resolution fossil midge stratigraphies from southern and eastern Finland to interpret environmental variability over the past 2000 years, with special focus on the Medieval Climate Anomaly (MCA), the Little Ice Age (LIA) and recent anthropogenic changes. The midge-based results were compared with physical properties of the sediment, historical evidence and environmental reconstructions based on diatoms (Bacillariophyta), cladocerans (Crustacea: Cladocera) and tree rings. The results showed that the most important environmental factor controlling midge distribution and abundance along a latitudinal gradient in Finland was the mean July air temperature (TJul). However, when the dataset was environmentally screened to include only pristine lakes, water depth at the sampling site became more important. Furthermore, when the dataset was geographically scaled to southern Finland, hypolimnetic oxygen conditions became the dominant environmental factor. The results from an intralake dataset from eastern Finland showed that the most important environmental factors controlling midge distribution within a lake basin were river contribution, water depth and submerged vegetation patterns. In addition, the results of the intralake dataset showed that the fossil midge assemblages represent fauna that lived in close proximity to the sampling sites, thus enabling the exploration of within-lake gradients in midge assemblages. Importantly, this within-lake heterogeneity in midge assemblages may have effects on midge-based temperature estimations, because samples taken from the deepest point of a lake basin may infer considerably colder temperatures than expected, as shown by the present test results. Therefore, it is suggested here that the samples in fossil midge studies involving shallow boreal lakes should be taken from the sublittoral, where the assemblages are most representative of the whole lake fauna. Transfer functions between midge assemblages and the environmental forcing factors that were significantly related with the assemblages, including mean air TJul, water depth, hypolimnetic oxygen, stream flow and distance to littoral vegetation, were developed using weighted averaging (WA) and weighted averaging-partial least squares (WA-PLS) techniques, which outperformed all the other tested numerical approaches. Application of the models in downcore studies showed mostly consistent trends. Based on the present results, which agreed with previous studies and historical evidence, the Medieval Climate Anomaly between ca. 800 and 1300 AD in eastern Finland was characterized by warm temperature conditions and dry summers, but probably humid winters. The Little Ice Age (LIA) prevailed in southern Finland from ca. 1550 to 1850 AD, with the coldest conditions occurring at ca. 1700 AD, whereas in eastern Finland the cold conditions prevailed over a longer time period, from ca. 1300 until 1900 AD. The recent climatic warming was clearly represented in all of the temperature reconstructions. In the terms of long-term climatology, the present results provide support for the concept that the North Atlantic Oscillation (NAO) index has a positive correlation with winter precipitation and annual temperature and a negative correlation with summer precipitation in eastern Finland. In general, the results indicate a relatively warm climate with dry summers but snowy winters during the MCA and a cool climate with rainy summers and dry winters during the LIA. The results of the present reconstructions and the forthcoming applications of the models can be used in assessments of long-term environmental dynamics to refine the understanding of past environmental reference conditions and natural variability required by environmental scientists, ecologists and policy makers to make decisions concerning the presently occurring global, regional and local changes. The developed midge-based models for temperature, hypolimnetic oxygen, water depth, littoral vegetation shift and stream flow, presented in this thesis, are open for scientific use on request.

Cellular Membranes as a Playground for Semliki Forest Virus Replication Complex

All positive-strand RNA viruses utilize cellular membranes for the assembly of their replication complexes, which results in extensive membrane modification in infected host cells. These alterations act as structural and functional scaffolds for RNA replication, providing protection for the viral double-stranded RNA against host defences. It is known that different positive-strand RNA viruses alter different cellular membranes. However, the origin of the targeted membranes, the mechanisms that direct replication proteins to specific membranes and the steps in the formation of the membrane bound replication complex are not completely understood. Alphaviruses (including Semliki Forest virus, SFV), members of family Togaviridae, replicate their RNA in association with membranes derived from the endosomal and lysosomal compartment, inducing membrane invaginations called spherules. Spherule structures have been shown to be the specific sites for RNA synthesis. Four replication proteins, nsP1-nsP4, are translated as a polyprotein (P1234) which is processed autocatalytically and gives rise to a membrane-bound replication complex. Membrane binding is mediated via nsP1 which possesses an amphipathic α-helix (binding peptide) in the central region of the protein. The aim of this thesis was to characterize the association of the SFV replication complex with cellular membranes and the modification of the membranes during virus infection. Therefore, it was necessary to set up the system for determining which viral components are needed for inducing the spherules. In addition, the targeting of the replication complex, the formation site of the spherules and their intracellular trafficking were studied in detail. The results of current work demonstrate that mutations in the binding peptide region of nsP1 are lethal for virus replication and change the localization of the polyprotein precursor P123. The replication complex is first targeted to the plasma membrane where membrane invaginations, spherules, are induced. Using a specific regulated endocytosis event the spherules are internalized from the plasma membrane in neutral carrier vesicles and transported via an actin-and microtubule-dependent manner to the pericentriolar area. Homotypic fusions and fusions with pre-existing acidic organelles lead to the maturation of previously described cytopathic vacuoles with hundreds of spherules on their limiting membranes. This work provides new insights into the membrane binding mechanism of SFV replication complex and its role in the virus life cycle. Development of plasmid-driven system for studying the formation of the replication complex described in this thesis allows various applications to address different steps in SFV life cycle and virus-host interactions in the future. This trans-replication system could be applied for many different viruses. In addition, the current work brings up new aspects of membranes and cellular components involved in SFV replication leading to further understanding in the formation and dynamics of the membrane-associated replication complex.

Missing-In-Metastasis (MIM) regulates cell morphology by promoting plasma membrane and actin cytoskeleton dynamics

The cells of multicellular organisms have differentiated to carry out specific functions that are often accompanied by distinct cell morphology. The actin cytoskeleton is one of the key regulators of cell shape subsequently controlling multiple cellular events including cell migration, cell division, endo- and exocytosis. A large set of actin regulating proteins has evolved to achieve and tightly coordinate this wide range of functions. Some actin regulator proteins have so-called house keeping roles and are essential for all eukaryotic cells, but some have evolved to meet the requirements of more specialized cell-types found in higher organisms enabling complex functions of differentiated organs, such as liver, kidney and brain. Often processes mediated by the actin cytoskeleton, like formation of cellular protrusions during cell migration, are intimately linked to plasma membrane remodeling. Thus, a close cooperation between these two cellular compartments is necessary, yet not much is known about the underlying molecular mechanisms. This study focused on a vertebrate-specific protein called missing-in-metastasis (MIM), which was originally characterized as a metastasis suppressor of bladder cancer. We demonstrated that MIM regulates the dynamics of actin cytoskeleton via its WH2 domain, and is expressed in a cell-type specific manner. Interestingly, further examination showed that the IM-domain of MIM displays a novel membrane tubulation activity, which induces formation of filopodia in cells. Following studies demonstrated that this membrane deformation activity is crucial for cell protrusions driven by MIM. In mammals, there are five members of IM-domain protein family. Functions and expression patterns of these family members have remained poorly characterized. To understand the physiological functions of MIM, we generated MIM knockout mice. MIM-deficient mice display no apparent developmental defects, but instead suffer from progressive renal disease and increased susceptibility to tumors. This indicates that MIM plays a role in the maintenance of specific physiological functions associated with distinct cell morphologies. Taken together, these studies implicate MIM both in the regulation of the actin cytoskeleton and the plasma membrane. Our results thus suggest that members of MIM/IRSp53 protein family coordinate the actin cytoskeleton:plasma membrane interface to control cell and tissue morphogenesis in multicellular organisms.

The role of productivity in the ecological and evolutionary dynamics of predator-prey interaction

Productivity is predicted to drive the ecological and evolutionary dynamics of predator-prey interaction through changes in resource allocation between different traits. However, resources are seldom constantly available and thus temporal variation in productivity could have considerable effect on the species' potential to evolve. To study this, three long-term microbial laboratory experiments were established where Serratia marcescens prey bacteria was exposed to predation of protist Tetrahymena thermophila in different prey resource environments. The consequences of prey resource availability for the ecological properties of the predator-prey system, such as trophic dynamics, stability, and virulence, were determined. The evolutionary changes in species traits and prey genetic diversity were measured. The prey defence evolved stronger in high productivity environment. Increased allocation to defence incurred cost in terms of reduced prey resource use ability, which probably constrained prey evolution by increasing the effect of resource competition. However, the magnitude of this trade-off diminished when measured in high resource concentrations. Predation selected for white, non-pigmented, highly defensive prey clones that produced predation resistant biofilm. The biofilm defence was also potentially accompanied with cytotoxicity for predators and could have been traded off with high motility. Evidence for the evolution of predators was also found in one experiment suggesting that co-evolutionary dynamics could affect the evolution and ecology of predator-prey interaction. Temporal variation in resource availability increased variation in predator densities leading to temporally fluctuating selection for prey defences and resource use ability. Temporal variation in resource availability was also able to constrain prey evolution when the allocation to defence incurred high cost. However, when the magnitude of prey trade-off was small and the resource turnover was periodically high, temporal variation facilitated the formation of predator resistant biofilm. The evolution of prey defence constrained the transfer of energy from basal to higher trophic levels, decreasing the strength of top-down regulation on prey community. Predation and temporal variation in productivity decreased the stability of populations and prey traits in general. However, predation-induced destabilization was less pronounced in the high productivity environment where the evolution of prey defence was stronger. In addition, evolution of prey defence weakened the environmental variation induced destabilization of predator population dynamics. Moreover, protozoan predation decreased the S. marcescens virulence in the insect host moth (Parasemia plantaginis) suggesting that species interactions outside the context of host-pathogen relationship could be important indirect drivers for the evolution of pathogenesis. This thesis demonstrates that rapid evolution can affect various ecological properties of predator-prey interaction. The effect of evolution on the ecological dynamics depended on the productivity of the environment, being most evident in the constant environments with high productivity.

The role of cyclase-associated protein (CAP) in actin dynamics during cell motility and morphogenesis

The highly dynamic remodeling of the actin cytoskeleton is responsible for most motile and morphogenetic processes in all eukaryotic cells. In order to generate appropriate spatial and temporal movements, the actin dynamics must be under tight control of an array of actin binding proteins (ABPs). Many proteins have been shown to play a specific role in actin filament growth or disassembly of older filaments. Very little is known about the proteins affecting recycling i.e. the step where newly depolymerized actin monomers are funneled into new rounds of filament assembly. A central protein family involved in the regulation of actin turnover is cyclase-associated proteins (CAP, called Srv2 in budding yeast). This 50-60 kDa protein was first identified from yeast as a suppressor of an activated RAS-allele and a factor associated with adenylyl cyclase. The CAP proteins harbor N-terminal coiled-coil (cc) domain, originally identified as a site for adenylyl cyclase binding. In the N-terminal half is also a 14-3-3 like domain, which is followed by central proline-rich domains and the WH2 domain. In the C-terminal end locates the highly conserved ADP-G-actin binding domain. In this study, we identified two previously suggested but poorly characterized interaction partners for Srv2/CAP: profilin and ADF/cofilin. Profilins are small proteins (12-16 kDa) that bind ATP-actin monomers and promote the nucleotide exchange of actin. The profilin-ATP-actin complex can be directly targeted to the growth of the filament barbed ends capped by Ena/VASP or formins. ADF/cofilins are also small (13-19 kDa) and highly conserved actin binding proteins. They depolymerize ADP-actin monomers from filament pointed ends and remain bound to ADP-actin strongly inhibiting nucleotide exchange. We revealed that the ADP-actin-cofilin complex is able to directly interact with the 14-3-3 like domain at the N-terminal region of Srv2/CAP. The C-terminal high affinity ADP-actin binding site of Srv2/CAP competes with cofilin for an actin monomer. Cofilin can thus be released from Srv2/CAP for the subsequent round of depolymerization. We also revealed that profilin interacts with the first proline-rich region of Srv2/CAP and that the binding occurs simultaneously with ADP-actin binding to C-terminal domain of Srv2/CAP. Both profilin and Srv2/CAP can promote nucleotide exchange of actin monomer. Because profilin has much higher affinity to ATP-actin than Srv2/CAP, the ATP-actin-profilin complex is released for filament polymerization. While a disruption of cofilin binding in yeast Srv2/CAP produces a severe phenotype comparable to Srv2/CAP deletion, an impairment of profilin binding from Srv2/CAP results in much milder phenotype. This suggests that the interaction with cofilin is essential for the function of Srv2/CAP, whereas profilin can also promote its function without direct interaction with Srv2/CAP. We also show that two CAP isoforms with specific expression patterns are present in mice. CAP1 is the major isoform in most tissues, while CAP2 is predominantly expressed in muscles. Deletion of CAP1 from non-muscle cells results in severe actin phenotype accompanied with mislocalization of cofilin to cytoplasmic aggregates. Together these studies suggest that Srv2/CAP recycles actin monomers from cofilin to profilin and thus it plays a central role in actin dynamics in both yeast and mammalian cells.

Actin Dynamics in Muscle Cells

In every cell, actin is a key component involved in migration, cytokinesis, endocytosis and generation of contraction. In non-muscle cells, actin filaments are very dynamic and regulated by an array of proteins that interact with actin filaments and/or monomeric actin. Interestingly, in non-muscle cells the barbed ends of the filaments are the predominant assembly place, whereas in muscle cells actin dynamics was reported to predominate at the pointed ends of thin filaments. The actin-based thin filament pointed (slow growing) ends extend towards the middle of the sarcomere's M-line where they interact with the thick filaments to generate contraction. The actin filaments in muscle cells are organized into a nearly crystalline array and are believed to be significantly less dynamic than the ones in other cell types. However, the exact mechanisms of the sarcomere assembly and turnover are largely unknown. Interestingly, although sarcomeric actin structures are believed to be relatively non-dynamic, many proteins promoting actin dynamics are expressed also in muscle cells (e.g ADF/cofilin, cyclase-associated protein and twinfilin). Thus, it is possible that the muscle-specific isoforms of these proteins promote actin dynamics differently from their non-muscle counterparts, or that actin filaments in muscle cells are more dynamic than previously thought. To study protein dynamics in live muscle cells, I used primary cell cultures of rat cardiomyocytes. My studies revealed that a subset of actin filaments in cardiomyocyte sarcomeres displays rapid turnover. Importantly, I discovered that the turnover of actin filaments depends on contractility of the cardiomyocytes and that the contractility-induced actin dynamics plays an important role in sarcomere maturation. Together with previous studies those findings suggest that sarcomeres undergo two types of actin dynamics: (1) contractility-dependent turnover of whole filaments and (2) regulatory pointed end monomer exchange to maintain correct thin filament length. Studies involving an actin polymerization inhibitor suggest that the dynamic actin filament pool identified here is composed of filaments that do not contribute to contractility. Additionally, I provided evidence that ADF/cofilins, together with myosin-induced contractility, are required to disassemble non-productive filaments in developing cardiomyocytes. In addition, during these studies we learned that isoforms of actin monomer binding protein twinfilin, Twf-1 and Twf-2a localise to myofibrils in cardiomyocytes and may thus contribute to actin dynamics in myofibrils. Finally, in collaboration with Roberto Dominguez s laboratory we characterized a new actin nucleator in muscle cells - leiomodin (Lmod). Lmod localises towards actin filament pointed ends and its depletion by siRNA leads to severe sarcomere abnormalities in cardiomyocytes. The actin filament nucleation activity of Lmod is enhanced by interactions with tropomyosin. We also revealed that Lmod expression correlates with the maturation of myofibrils, and that it associates with sarcomeres only at relatively late stages of myofibrillogenesis. Thus, Lmod is unlikely to play an important role in myofibril formation, but rather might be involved in the second step of the filament arrangement and/or maintenance through its ability to promote tropomyosin-induced actin filament nucleation occurring at the filament pointed ends. The results of these studies provide valuable new information about the molecular mechanisms underlying muscle sarcomere assembly and turnover. These data offer important clues to understanding certain physiological and pathological behaviours of muscle cells. Better understanding of the processes occurring in muscles might help to find strategies for determining, diagnosis, prognosis and therapy in heart and skeletal muscles diseases.

Dynamics of Finnish starlings in 1951-2005 : from monitoring to population modelling

Farmland bird species have been declining in Europe. Many declines have coincided with general intensification of farming practices. In Finland, replacement of mixed farming, including rotational pastures, with specialized cultivation has been one of the most drastic changes from the 1960s to the 1990s. This kind of habitat deterioration limits the persistence of populations, as has been previously indicated from local populations. Integrated population monitoring, which gathers species-specific information of population size and demography, can be used to assess the response of a population to environment changes also at a large spatial scale. I targeted my analysis at the Finnish starling (Sturnus vulgaris). Starlings are common breeders in farmland habitats, but severe declines of local populations have been reported from Finland in the 1970s and 1980s and later from other parts of Europe. Habitat deterioration (replacement of pasture and grassland habitats with specialized cultivation areas) limits reproductive success of the species. I analysed regional population data in order to exemplify the importance of agricultural change to bird population dynamics. I used nestling ringing and nest-card data from 1951 to 2005 in order to quantify population trends and per capita reproductive success within several geographical regions (south/north and west/east aspects). I used matrix modelling, acknowledging age-specific survival and fecundity parameters and density-dependence, to model population dynamics. Finnish starlings declined by 80% from the end of the 1960s up to the end of the 1980s. The observed patterns and the model indicated that the population decline was due to the decline of the carrying capacity of farmland habitats. The decline was most severe in north Finland where populations largely become extinct. However, habitat deterioration was most severe in the southern breeding areas. The deteriorations in habitat quality decreased reproduction, which finally caused the decline. I suggest that poorly-productive northern populations have been partly maintained by immigration from the highly-productive southern populations. As the southern populations declined, ceasing emigration caused the population extinction in north. This phenomenon was explained with source sink population dynamics, which I structured and verified on the basis of a spatially explicit simulation model. I found that southern Finnish starling population exhibits ten-year cyclic regularity, a phenomenon that can be explained with delayed density-dependence in reproduction.

Spirometric studies on the adult general population of Helsinki : bronchodilation responses, determinants, and intrasession repeatability of FEV1, FEV6, FVC, and forced expiratory time

Spirometry is the most widely used lung function test in the world. It is fundamental in diagnostic and functional evaluation of various pulmonary diseases. In the studies described in this thesis, the spirometric assessment of reversibility of bronchial obstruction, its determinants, and variation features are described in a general population sample from Helsinki, Finland. This study is a part of the FinEsS study, which is a collaborative study of clinical epidemiology of respiratory health between Finland (Fin), Estonia (Es), and Sweden (S). Asthma and chronic obstructive pulmonary disease (COPD) constitute the two major obstructive airways diseases. The prevalence of asthma has increased, with around 6% of the population in Helsinki reporting physician-diagnosed asthma. The main cause of COPD is smoking with changes in smoking habits in the population affecting its prevalence with a delay. Whereas airway obstruction in asthma is by definition reversible, COPD is characterized by fixed obstruction. Cough and sputum production, the first symptoms of COPD, are often misinterpreted for smokers cough and not recognized as first signs of a chronic illness. Therefore COPD is widely underdiagnosed. More extensive use of spirometry in primary care is advocated to focus smoking cessation interventions on populations at risk. The use of forced expiratory volume in six seconds (FEV6) instead of forced vital capacity (FVC) has been suggested to enable office spirometry to be used in earlier detection of airflow limitation. Despite being a widely accepted standard method of assessment of lung function, the methodology and interpretation of spirometry are constantly developing. In 2005, the ATS/ERS Task Force issued a joint statement which endorsed the 12% and 200 ml thresholds for significant change in forced expiratory volume in one second (FEV1) or FVC during bronchodilation testing, but included the notion that in cases where only FVC improves it should be verified that this is not caused by a longer exhalation time in post-bronchodilator spirometry. This elicited new interest in the assessment of forced expiratory time (FET), a spirometric variable not usually reported or used in assessment. In this population sample, we examined FET and found it to be on average 10.7 (SD 4.3) s and to increase with ageing and airflow limitation in spirometry. The intrasession repeatability of FET was the poorest of the spirometric variables assessed. Based on the intrasession repeatability, a limit for significant change of 3 s was suggested for FET during bronchodilation testing. FEV6 was found to perform equally well as FVC in the population and in a subgroup of subjects with airways obstruction. In the bronchodilation test, decreases were frequently observed in FEV1 and particularly in FVC. The limit of significant increase based on the 95th percentile of the population sample was 9% for FEV1 and 6% for FEV6 and FVC; these are slightly lower than the current limits for single bronchodilation tests (ATS/ERS guidelines). FEV6 was proven as a valid alternative to FVC also in the bronchodilation test and would remove the need to control duration of exhalation during the spirometric bronchodilation test.

Atrial Electric Signal During Sinus Rhythm in Lone Paroxysmal Atrial Fibrillation

Atrial fibrillation (AF) is the most common tachyarrhythmia and is associated with substantial morbidity, increased mortality and cost. The treatment modalities of AF have increased, but results are still far from optimal. More individualized therapy may be beneficial. Aiming for this calls improved diagnostics. Aim of this study was to find non-invasive parameters obtained during sinus rhythm reflecting electrophysiological patterns related to propensity to AF and particularly to AF occurring without any associated heart disease, lone AF. Overall 240 subjects were enrolled, 136 patients with paroxysmal lone AF and 104 controls (mean age 45 years, 75% males). Signal measurements were performed by non-invasive magnetocardiography (MCG) and by invasive electroanatomic mapping (EAM). High-pass filtering techniques and a new method based on a surface gradient technique were adapted to analyze atrial MCG signal. The EAM was used to elucidate atrial activation in patients and as a reference for MCG. The results showed that MCG mapping is an accurate method to detect atrial electrophysiologic properties. In lone paroxysmal AF, duration of the atrial depolarization complex was marginally prolonged. The difference was more obvious in women and was also related to interatrial conduction patterns. In the focal type of AF (75%), the root mean square (RMS) amplitudes of the atrial signal were normal, but in AF without demonstrable triggers the late atrial RMS amplitudes were reduced. In addition, the atrial characteristics tended to remain similar even when examined several years after the first AF episodes. The intra-atrial recordings confirmed the occurrence of three distinct sites of electrical connection from right to left atrium (LA): the Bachmann bundle (BB), the margin of the fossa ovalis (FO), and the coronary sinus ostial area (CS). The propagation of atrial signal could also be evaluated non-invasively. Three MCG atrial wave types were identified, each of which represented a distinct interatrial activation pattern. In conclusion, in paroxysmal lone AF, active focal triggers are common, atrial depolarization is slightly prolonged, but with a normal amplitude, and the arrhythmia does not necessarily lead to electrical or mechanical dysfunction of the atria. In women the prolongation of atrial depolarization is more obvious. This may be related to gender differences in presentation of AF. A significant minority of patients with lone AF lack frequent focal triggers, and in them, the late atrial signal amplitude is reduced, possibly signifying a wider degenerative process in the LA. In lone AF, natural impulse propagation to LA during sinus rhythm goes through one or more of the principal pathways described. The BB is the most common route, but in one-third, the earliest LA activation occurs outside the BB. Susceptibility to paroxysmal lone AF is associated with propagation of the atrial signal via the margin of the FO or via multiple pathways. When conduction occurs via the BB, it is related with prolonged atrial activation. Thus, altered and alternative conduction pathways may contribute to pathogenesis of lone AF. There is growing evidence of variability in genesis of AF also within lone paroxysmal AF. Present study suggests that this variation may be reflected in cardiac signal pattern. Recognizing the distinct signal profiles may assist in understanding the pathogenesis of AF and identifying subgroups for patient-tailored therapy.

Irritable bowel syndrome in the general population : epidemiology, comorbidity and societal costs

Background: Irritable bowel syndrome (IBS) is a common functional gastrointestinal (GI) disorder characterised by abdominal pain and abnormal bowel function. It is associated with a high rate of healthcare consumption and significant health care costs. The prevalence and economic burden of IBS in Finland has not been studied before. The aims of this study were to assess the prevalence of IBS according to various diagnostic criteria and to study the rates of psychiatric and somatic comorbidity in IBS. In addition, health care consumption and societal costs of IBS were to be evaluated. Methods: The study was a two-phase postal survey. Questionnaire I identifying IBS by Manning 2 (at least two of the six Manning symptoms), Manning 3 (at least three Manning symptoms), Rome I, and Rome II criteria, was mailed to a random sample of 5 000 working age subjects. It also covered extra-GI symptoms such as headache, back pain, and depression. Questionnaire II, covering rates of physician visits, and use of GI medication, was sent to subjects fulfilling Manning 2 or Rome II IBS criteria in Questionnaire I. Results: The response rate was 73% and 86% for questionnaires I and II. The prevalence of IBS was 15.9%, 9.6%, 5.6%, and 5.1% according to Manning 2, Manning 3, Rome I, and Rome II criteria. Of those meeting Rome II criteria, 97% also met Manning 2 criteria. Presence of severe abdominal pain was more often reported by subjects meeting either of the Rome criteria than those meeting either of the Manning criteria. Presence of depression, anxiety, and several somatic symptoms was more common among subjects meeting any IBS criterion than by controls. Of subjects with depressive symptoms, 11.6% met Rome II IBS criteria compared to 3.7% of those with no depressiveness. Subjects meeting any IBS criteria made more physician visits than controls. Intensity of GI symptoms and presence of dyspeptic symptoms were the strongest predictors of GI consultations. Presence of dyspeptic symptoms and a history of abdominal pain in childhood also predicted non-GI visits. Annual GI related individual costs were higher in the Rome II group (497 ) than in the Manning 2 group (295 ). Direct expenses of GI symptoms and non GI physician visits ranged between 98M for Rome II and 230M for Manning 2 criteria. Conclusions: The prevalence of IBS varies substantially depending on the criteria applied. Rome II criteria are more restrictive than Manning 2, and they identify an IBS population with more severe GI symptoms, more frequent health care use, and higher individual health care costs. Subjects with IBS demonstrate high rates of psychiatric and somatic comorbidity regardless of health care seeking status. Perceived symptom severity rather than psychiatric comorbidity predicts health care seeking for GI symptoms. IBS incurs considerable medical costs. The direct GI and non-GI costs are equivalent to up to 5% of outpatient health care and medicine costs in Finland. A more integral approach to IBS by physicians, accounting also for comorbid conditions, may produce a more favourable course in IBS patients and reduce health care expenditures.

Dynamic nature of proteins - interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.

Molecular dynamics studies of nanoparticle impacts

This thesis concerns the dynamics of nanoparticle impacts on solid surfaces. These impacts occur, for instance, in space, where micro- and nanometeoroids hit surfaces of planets, moons, and spacecraft. On Earth, materials are bombarded with nanoparticles in cluster ion beam devices, in order to clean or smooth their surfaces, or to analyse their elemental composition. In both cases, the result depends on the combined effects of countless single impacts. However, the dynamics of single impacts must be understood before the overall effects of nanoparticle radiation can be modelled. In addition to applications, nanoparticle impacts are also important to basic research in the nanoscience field, because the impacts provide an excellent case to test the applicability of atomic-level interaction models to very dynamic conditions. In this thesis, the stopping of nanoparticles in matter is explored using classical molecular dynamics computer simulations. The materials investigated are gold, silicon, and silica. Impacts on silicon through a native oxide layer and formation of complex craters are also simulated. Nanoparticles up to a diameter of 20 nm (315000 atoms) were used as projectiles. The molecular dynamics method and interatomic potentials for silicon and gold are examined in this thesis. It is shown that the displacement cascade expansionmechanism and crater crown formation are very sensitive to the choice of atomic interaction model. However, the best of the current interatomic models can be utilized in nanoparticle impact simulation, if caution is exercised. The stopping of monatomic ions in matter is understood very well nowadays. However, interactions become very complex when several atoms impact on a surface simultaneously and within a short distance, as happens in a nanoparticle impact. A high energy density is deposited in a relatively small volume, which induces ejection of material and formation of a crater. Very high yields of excavated material are observed experimentally. In addition, the yields scale nonlinearly with the cluster size and impact energy at small cluster sizes, whereas in macroscopic hypervelocity impacts, the scaling 2 is linear. The aim of this thesis is to explore the atomistic mechanisms behind the nonlinear scaling at small cluster sizes. It is shown here that the nonlinear scaling of ejected material yield disappears at large impactor sizes because the stopping mechanism of nanoparticles gradually changes to the same mechanism as in macroscopic hypervelocity impacts. The high yields at small impactor size are due to the early escape of energetic atoms from the hot region. In addition, the sputtering yield is shown to depend very much on the spatial initial energy and momentum distributions that the nanoparticle induces in the material in the first phase of the impact. At the later phases, the ejection of material occurs by several mechanisms. The most important mechanism at high energies or at large cluster sizes is atomic cluster ejection from the transient liquid crown that surrounds the crater. The cluster impact dynamics detected in the simulations are in agreement with several recent experimental results. In addition, it is shown that relatively weak impacts can induce modifications on the surface of an amorphous target over a larger area than was previously expected. This is a probable explanation for the formation of the complex crater shapes observed on these surfaces with atomic force microscopy. Clusters that consist of hundreds of thousands of atoms induce long-range modifications in crystalline gold.

Molecular Dynamics Simulations of Homogeneous Nucleation

Nucleation is the first step in a phase transition where small nuclei of the new phase start appearing in the metastable old phase, such as the appearance of small liquid clusters in a supersaturated vapor. Nucleation is important in various industrial and natural processes, including atmospheric new particle formation: between 20 % to 80 % of atmospheric particle concentration is due to nucleation. These atmospheric aerosol particles have a significant effect both on climate and human health. Different simulation methods are often applied when studying things that are difficult or even impossible to measure, or when trying to distinguish between the merits of various theoretical approaches. Such simulation methods include, among others, molecular dynamics and Monte Carlo simulations. In this work molecular dynamics simulations of the homogeneous nucleation of Lennard-Jones argon have been performed. Homogeneous means that the nucleation does not occur on a pre-existing surface. The simulations include runs where the starting configuration is a supersaturated vapor and the nucleation event is observed during the simulation (direct simulations), as well as simulations of a cluster in equilibrium with a surrounding vapor (indirect simulations). The latter type are a necessity when the conditions prevent the occurrence of a nucleation event in a reasonable timeframe in the direct simulations. The effect of various temperature control schemes on the nucleation rate (the rate of appearance of clusters that are equally able to grow to macroscopic sizes and to evaporate) was studied and found to be relatively small. The method to extract the nucleation rate was also found to be of minor importance. The cluster sizes from direct and indirect simulations were used in conjunction with the nucleation theorem to calculate formation free energies for the clusters in the indirect simulations. The results agreed with density functional theory, but were higher than values from Monte Carlo simulations. The formation energies were also used to calculate surface tension for the clusters. The sizes of the clusters in the direct and indirect simulations were compared, showing that the direct simulation clusters have more atoms between the liquid-like core of the cluster and the surrounding vapor. Finally, the performance of various nucleation theories in predicting simulated nucleation rates was investigated, and the results among other things highlighted once again the inadequacy of the classical nucleation theory that is commonly employed in nucleation studies.

Trade Liberalization, Heterogeneous Firms and Industrial Dynamics

This master thesis studies how trade liberalization affects the firm-level productivity and industrial evolution. To do so, I built a dynamic model that considers firm-level productivity as endogenous to investigate the influence of trade on firm’s productivity and the market structure. In the framework, heterogeneous firms in the same industry operate differently in equilibrium. Specifically, firms are ex ante identical but heterogeneity arises as an equilibrium outcome. Under the setting of monopolistic competition, this type of model yields an industry that is represented not by a steady-state outcome, but by an evolution that rely on the decisions made by individual firms. I prove that trade liberalization has a general positive impact on technological adoption rates and hence increases the firm-level productivity. Besides, this endogenous technology adoption model also captures the stylized facts: exporting firms are larger and more productive than their non-exporting counterparts in the same sector. I assume that the number of firms is endogenous, since, according to the empirical literature, the industrial evolution shows considerably different patterns across countries; some industries experience large scale of firms’ exit in the period of contracting market shares, while some industries display relative stable number of firms or gradually increase quantities. The special word “shakeout” is used to describe the dramatic decrease in the number of firms. In order to explain the causes of shakeout, I construct a model where forward-looking firms decide to enter and exit the market on the basis of their state of technology. In equilibrium, firms choose different dates to adopt innovation which generate a gradual diffusion process. It is exactly this gradual diffusion process that generates the rapid, large-scale exit phenomenon. Specifically, it demonstrates that there is a positive feedback between firm’s exit and adoption, the reduction in the number of firms increases the incentives for remaining firms to adopt innovation. Therefore, in the setting of complete information, this model not only generates a shakeout but also captures the stability of an industry. However, the solely national view of industrial evolution neglects the importance of international trade in determining the shape of market structure. In particular, I show that the higher trade barriers lead to more fragile markets, encouraging the over-entry in the initial stage of industry life cycle and raising the probability of a shakeout. Therefore, more liberalized trade generates more stable market structure from both national and international viewpoints. The main references are Ederington and McCalman(2008,2009).

Electrocardiographic parameters of ventricular repolarization : modifiers and the prognostic value

Electric activity of the heart consists of repeated cardiomyocyte depolarizations and repolarizations. Abnormalities in repolarization predispose to ventricular arrhythmias. In body surface electrocardiogram, ventricular repolarization generates the T wave. Several electrocardiographic measures have been developed both for clinical and research purposes to detect repolarization abnormalities. The study aim was to investigate modifiers of ventricular repolarization with the focus on the relationship of the left ventricular mass, antihypertensive drugs, and common gene variants, to electrocardiographic repolarization parameters. The prognostic value of repolarization parameters was also assessed. The study subjects originated from a population of more than 200 middle-aged hypertensive men attending the GENRES hypertension study, and from an epidemiological survey, the Health 2000 Study, including more than 6000 participants. Ventricular repolarization was analysed from digital standard 12-lead resting electrocardiograms with two QT-interval based repolarization parameters (QT interval, T-wave peak to T-wave end interval) and with a set of four T-wave morphology parameters. The results showed that in hypertensive men, a linear change in repolarization parameters is present even in the normal range of left ventricular mass, and that even mild left ventricular hypertrophy is associated with potentially adverse electrocardiographic repolarization changes. In addition, treatments with losartan, bisoprolol, amlodipine, and hydrochlorothiazide have divergent short-term effects on repolarization parameters in hypertensive men. Analyses of the general population sample showed that single nucleotide polymorphisms in KCNH2, KCNE1, and NOS1AP genes are associated with changes in QT-interval based repolarization parameters but not consistently with T-wave morphology parameters. T-wave morphology parameters, but not QT interval or T-wave peak to T-wave end interval, provided independent prognostic information on mortality. The prognostic value was specifically related to cardiovascular mortality. The results indicate that, in hypertension, altered ventricular repolarization is already present in mild left ventricular mass increase, and that commonly used antihypertensive drugs may relatively rapidly and treatment-specifically modify electrocardiographic repolarization parameters. Common variants in cardiac ion channel genes and NOS1AP gene may also modify repolarization-related arrhythmia vulnerability. In the general population, T-wave morphology parameters may be useful in the risk assessment of cardiovascular mortality.