Mathematical models on the impact of noise and dyadic molecular structures on the properties of a cardiac myocyte

In cardiac myocytes (heart muscle cells), coupling of electric signal known as the action potential to contraction of the heart depends crucially on calcium-induced calcium release (CICR) in a microdomain known as the dyad. During CICR, the peak number of free calcium ions (Ca) present in the dyad is small, typically estimated to be within range 1-100. Since the free Ca ions mediate CICR, noise in Ca signaling due to the small number of free calcium ions influences Excitation-Contraction (EC) coupling gain. Noise in Ca signaling is only one noise type influencing cardiac myocytes, e.g., ion channels playing a central role in action potential propagation are stochastic machines, each of which gates more or less randomly, which produces gating noise present in membrane currents. How various noise sources influence macroscopic properties of a myocyte, how noise is attenuated and taken advantage of are largely open questions. In this thesis, the impact of noise on CICR, EC coupling and, more generally, macroscopic properties of a cardiac myocyte is investigated at multiple levels of detail using mathematical models. Complementarily to the investigation of the impact of noise on CICR, computationally-efficient yet spatially-detailed models of CICR are developed. The results of this thesis show that (1) gating noise due to the high-activity mode of L-type calcium channels playing a major role in CICR may induce early after-depolarizations associated with polymorphic tachycardia, which is a frequent precursor to sudden cardiac death in heart failure patients; (2) an increased level of voltage noise typically increases action potential duration and it skews distribution of action potential durations toward long durations in cardiac myocytes; and that (3) while a small number of Ca ions mediate CICR, Excitation-Contraction coupling is robust against this noise source, partly due to the shape of ryanodine receptor protein structures present in the cardiac dyad.

Substrata Uralica : Studies on Finno-Ugrian Substrate in Northern Russian Dialects

The thesis consists of five articles and an introduction. It treats the problems of the Uralic substrate, most notably, the substrate toponyms, in the Russian dialects of Arkhangelsk region. The articles contribute to the general linguistic discussion concerning the nature of linguistic substrate and the outcome of language shift and to the onomastic discussion concerning the etymologisation and ethnic interpretation of substrate toponymy. Among the questions the articles scrutinised are the following: 1) How may phonetic and morphosyntactic substrate interference be verified? 2) How typical is the transfer of vocabulary in the case of a language shift? 3) How the borrowing of toponymy and appellative vocabulary are connected in the case of a language shift? 4) How does the etymologisation of the toponyms differ from the etymologisation of appellatives? 5) How reliable can the toponymic etymologies be? 6) How can the substrate language be identified? It is found that the substrate interference that can be meaningfully studied, from the point of view of historical linguistics, is predominantly lexical and not related to phonetics and morphosyntax, as presumed in many handbooks. New methods are outlined for the identification of substrate languages separately from the lexical, phonological and typological point of view by using the substrate toponymy as the main source of information on extinct languages. A reliability scale for the toponymic etymologies is developed that helps to identify the kinds of etymologies containing ethnohistorically meaningful information. The study also sheds light on questions related to Uralistics and Slavistics. The most important of these are the following: 1) Which Uralic languages were spoken in North Russia prior to Slavic? 2) When did the Slavicisation of the Finno-Ugrian population take place in the area of the Arkhangelsk Region? 3) What is the significance of the Finno-Ugrian substrate in northern Russian dialects to comparative Uralistics? 4) Are there any traces of pre-Uralic substrate languages in north-eastern Europe? The Finnic substrate languages, already identified by earlier studies, seem to have consisted of two groups, one of which was closest to the southern Finnic. Also, language(s) close to Sámi in some respects though not identical with it where spoken in pre-Slavic North Russia.

Noise sensitivity medical, psychological and genetic aspects

Noise can be defined as unwanted sound. It may adversely affect the health and well-being of individuals. Noise sensitivity is a personality trait covering attitudes towards noise in general and a predictor of noise annoyance. Noise sensitive individuals are more affected by noise than less sensitive individuals. The determinants and characteristics related to noise sensitivity are rather poorly known. The risk of health effects caused by noise can be hypothesized to be higher for noise sensitive individuals compared to those who are not noise sensitive. A cardiovascular disease may be an example of outcomes. The general aim of the present study was to investigate the association of noise sensitivity with specific somatic and psychological factors, including the genetic component of noise sensitivity, and the association of noise sensitivity with mortality. The study was based on the Finnish Twin Cohort of same-sex twin pairs born before 1958. In 1988 a questionnaire was sent to twin pairs discordant for hypertension. 1495 individuals (688 men, 807 women) aged 31 88 years replied, including 573 twin pairs. 218 of the subjects lived in the Helsinki Metropolitan Area. Self-reported noise sensitivity, lifetime noise exposure and hypertension were obtained from the questionnaire study in 1988 and other somatic and psychological factors from the questionnaire study in 1981 for the same individuals. In addition, noise map information (1988 1992) from the Helsinki Metropolitan Area and mortality follow-up 1989 2003 were used. To evaluate the stability and validity of noise sensitivity, a new questionnaire was sent in 2002 to a sample of the subjects who had replied to the 1988 questionnaire. Of all subjects who had answered the question on noise sensitivity, 38 % were noise sensitive. Noise sensitivity was independent of noise exposure levels indicated in noise maps. Subjects with high noise sensitivity reported more transportation noise exposure than subjects with low noise sensitivity. Noise sensitive subjects reported transportation noise exposure outside the environmental noise map areas almost twice as often as non-sensitive subjects. Noise sensitivity was associated with hypertension, emphysema, use of psychotropic drugs, smoking, stress and hostility, even when lifetime noise exposure was adjusted for. Monozygotic twin pairs were more similar with regards noise sensitivity than dizygotic twin pairs, and quantitative genetic modelling indicated significant familiality. The best fitting genetic model provided an estimate of heritability of 36 %. Follow-up of subjects in the case-control study showed that cardiovascular mortality was significantly increased among noise sensitive women, but not among men. For coronary heart mortality the interaction of noise sensitivity and lifetime noise exposure was statistically significant in women. In conclusion, noise sensitivity has both somatic and psychological components. It does aggregate in families and probably has a genetic component. Noise sensitivity may be a risk factor for cardiovascular mortality in women.

Regio- and stereoselectivity of oxidative coupling reactions of phenols : Spirodienones as construction units in lignin

Dimeric phenolic compounds lignans and dilignols form in the so-called oxidative coupling reaction of phenols. Enzymes such as peroxidases and lac-cases catalyze the reaction using hydrogen peroxide or oxygen respectively as oxidant generating phenoxy radicals which couple together according to certain rules. In this thesis, the effects of the structures of starting materials mono-lignols and the effects of reaction conditions such as pH and solvent system on this coupling mechanism and on its regio- and stereoselectivity have been studied. After the primary coupling of two phenoxy radicals a very reactive quinone me-thide intermediate is formed. This intermediate reacts quickly with a suitable nucleophile which can be, for example, an intramolecular hydroxyl group or another nucleophile such as water, methanol, or a phenolic compound in the reaction system. This reaction is catalyzed by acids. After the nucleophilic addi-tion to the quinone methide, other hydrolytic reactions, rearrangements, and elimination reactions occur leading finally to stable dimeric structures called lignans or dilignols. Similar reactions occur also in the so-called lignification process when monolignol (or dilignol) reacts with the growing lignin polymer. New kinds of structures have been observed in this thesis. The dimeric com-pounds with so-called spirodienone structure have been observed to form both in the dehydrodimerization of methyl sinapate and in the beta-1-type cross-coupling reaction of two different monolignols. This beta-1-type dilignol with a spirodienone structure was the first synthetized and published dilignol model compound, and at present, it has been observed to exist as a fundamental construction unit in lignins. The enantioselectivity of the oxidative coupling reaction was also studied for obtaining enantiopure lignans and dilignols. A rather good enantioselectivity was obtained in the oxidative coupling reaction of two monolignols with chiral auxiliary substituents using peroxidase/H2O2 as an oxidation system. This observation was published as one of the first enantioselective oxidative coupling reaction of phenols. Pure enantiomers of lignans were also obtained by using chiral cryogenic chromatography as a chiral resolution technique. This technique was shown to be an alternative route to prepare enantiopure lignans or lignin model compounds in a preparative scale.

The Pseudomonas syringae-derived HrpA pilins - molecular characterization and biotechnological application of the transcripts

Many Gram-negative bacteria pathogenic to plants and animals possess type III secretion systems that are used to cause disease. Effector proteins are injected into host cells using the type III secretion machineries. Despite vigorous studies, the nature of the secretion signal for type III secreted proteins still remains elusive. Both mRNA and proteinaceous signals have been proposed. Findings on coupling of translation to secretion by the type III secretion systems are also still contradictory. This study dealt with the secretion signal of HrpA from Pseudomonas syringae pathovar tomato. HrpA is the major component of the type III secretion system-associated Hrp pilus and a substrate for the type III secretion systems. The secretion signal was shown to reside in the first 15 codons or amino acids, a location typical for type III secretion signals. Translation of HrpA in the absence of a functional type III secretion system was established, but it does not exclude the possibility of coupling of translation to secretion when the secretion apparatus is present. The hrpA transcripts from various unrelated plant pathogenic bacteria were shown to be extremely stable. The biological relevance of this observation is unknown, but possible explanations include the high prevalence of HrpA protein, an mRNA secretion signal or timing of secretion. The hrpA mRNAs are stable over a wide range of temperatures, in the absence of translating ribosomes and even in the heterologous host Escherichia coli. The untranslated regions (UTRs) of hrpA transcripts from at least 20 pathovars of Pseudomonas syringae are highly homologous, whilst their coding regions exhibit low similarity. The stable nature of hrpA messenger RNAs is likely to be due to the folding of their 5 and 3 UTRs. In silico the UTRs seem to form stem-loop structures, the hairpin structures in the 3 UTRs being rich in guanidine and cytosine residues. The stable nature of the hrpA transcript redirected the studies to the stabilization of heterologous transcripts and to the use of stable messenger RNAs in recombinant protein production. Fragments of the hrpA transcript can be used to confer stability on heterologous transcripts from several sources of bacterial and eukaryotic origin, and to elevate the levels of production of the corresponding recombinant proteins several folds. hrpA transcript stabilizing elements can be used for improving the yields of recombinant proteins even in Escherichia coli, one of the most commonly used industrial protein production hosts.

The Human UDP-Glucuronosyltransferases: Studies on Substrate Binding and Catalytic Mechanism

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Thyroid Hormone Control of Cardiac Substrate Metabolism

Thyroid hormone (TH) plays an important role in maintaining a homeostasis in all the cells of our body. It also has significant cardiovascular effects, and abnormalities of its concentration can cause cardiovascular disease and even morbidity. Especially development of heart failure has been connected to low levels of thyroid hormone. A decrease in TH levels or TH-receptor binding adversely effects cardiac function. Although, this occurs in part through alterations in excitation-contraction and transport proteins, recent data from our laboratory indicate that TH also mediates changes in myocardial energy metabolism. Thyroid dysfunction may limit the heart s ability to shift substrate pathways and provide adequate energy supply during stress responses. Our goals of these studies were to determine substrate oxidation pattern in systemic and cardiac specific hypothyroidism at rest and at higher rates of oxygen demand. Additionally we investigated the TH mediated mechanisms in myocardial substrate selection and established the metabolic phenotype caused by a thyroid receptor dysfunction. We measured cardiac metabolism in an isolated heart model using 13Carbon isotopomer analyses with MR spectroscopy to determine function, oxygen consumption, fluxes and fractional contribution of acetyl-CoA to the citric acid cycle (CAC). Molecular pathways for changes in cardiac function and substrate shifts occurring during stress through thyroid receptor abnormalities were determined by protein analyses. Our results show that TH modifies substrate selection through nuclear-mediated and rapid posttranscriptional mechanisms. It modifies substrate selection differentially at rest and at higher rates of oxygen demand. Chronic TH deficiency depresses total CAC flux and selectively fatty acid flux, whereas acute TH supplementation decreases lactate oxidation. Insertion of a dominant negative thyroid receptor (Δ337T) alters metabolic phenotype and contractive efficiency in heart. The capability of the Δ337T heart to increase carbohydrate oxidation in response to stress seems to be limited. These studies provided a clearer understanding of the TH role in heart disease and shed light to identification of the molecular mechanisms that will facilitate in finding targets for heart failure prevention and treatment.

Substrate Selectivity and Molecular Adaptation in the Outer Membrane Proteases of Yersinia pestis and Salmonella enterica

Proteolysis is important in bacterial pathogenesis and colonization of animal and plant hosts. In this work I have investigated the functions of the bacterial outer membrane proteases, omptins, of Yersinia pestis and Salmonella enterica. Y. pestis is a zoonotic pathogen that causes plague and has evolved from gastroenteritis-causing Yersinia pseudotuberculosis about 13 000 years ago. S. enterica causes gastroenteritis and typhoid fever in humans. Omptins are transmembrane β-barrels with ten antiparallel β-strands and five surface-exposed loops. The loops are important in substrate recognition, and variation in the loop sequences leads to different substrate selectivities between omptins, which makes omptins an ideal platform to investigate functional adaptation and to alter their polypeptide substrate preferences. The omptins Pla of Y. pestis and PgtE of S. enterica are 75% identical in their amino acid sequences. Pla is a multifunctional protein with proteolytic and non-proteolytic functions, and it increases bacterial penetration and proliferation in the host. Functions of PgtE increase migration of S. enterica in vivo and bacterial survival in mouse macrophages, thus enhancing bacterial spread within the host. Mammalian plasminogen/fibrinolytic system maintains the balance between coagulation and fibrinolysis and participates in several cellular processes, e.g., cell migration and degradation of extracellular matrix proteins. This system consists of activation cascades, which are strictly controlled by several regulators, such as plasminogen activator inhibitor 1 (PAI-1), α2-antiplasmin (α2AP), and thrombin-activatable fibrinolysis inhibitor (TAFI). This work reveals novel interactions of the omptins of Y. pestis and S. enterica with the regulators of the plasminogen/fibrinolytic system: Pla and PgtE inactivate PAI-1 by cleavage at the reactive site peptide bond, and degrade TAFI, preventing its activation to TAFIa. Structure-function relationship studies with Pla showed that threonine 259 of Pla is crucial in plasminogen activation, as it prevents degradation of the plasmin catalytic domain by the omptin and thus maintains plasmin stability. In this work I constructed chimeric proteins between Pla and Epo of Erwinia pyrifoliae that share 78% sequence identity to find out which amino acids and regions in Pla are important for its functions. Epo is neither a plasminogen activator nor an invasin, but it degrades α2AP and PAI-1. Cumulative substitutions towards Pla sequence turned Epo into a Pla-like protein. In addition to threonine 259, loops 3 and 5 are critical in plasminogen activation by Pla. Turning Epo into an invasin required substitution of 31 residues located at the extracellular side of the Epo protein above the lipid bilayer, and also of the β1-strand in the N-terminal transmembrane region of the protein. These studies give an example of how omptins adapt to novel functions that advantage their host bacteria in different ecological niches.

Benthic-pelagic coupling in the northern Baltic Sea: importance of bioturbation and benthic predation

Benthic-pelagic coupling describes processes that operate across and between the seafloor and open-water ecosystems. In soft-sediment communities, bioturbation by sediment-dwelling and epibenthic organisms may strongly shape habitat characteristics and influence processes, e.g. biogeochemical cycling, which supplies bioavailable nutrients to pelagic primary producers. In addition, benthic fauna may mediate benthic-pelagic coupling by affecting the survival and hatching of zooplankton dormant eggs in the sediment. In the shallow waters and seasonally fluctuating environment of the Baltic Sea, emergence from the seafloor essentially contributes to the dynamics of zooplankton pelagic populations. In this thesis, I examine how benthic organisms with different functional traits affect the link between the benthic and pelagic systems in the northern Baltic Sea. By means of experimental laboratory studies, the effects of sediment-dwelling (Monoporeia affinis, Macoma balthica and Marenzelleria spp.) and nectobenthic (Mysis spp.) taxa on the survival and hatching of zooplankton benthic eggs and on benthic nutrient fluxes and sediment structure were investigated. In the predation studies, the nectobenthic mysids Mysis spp. preyed upon benthic eggs of the cladoceran Bosmina longispina maritima (syn. B. coregoni maritima), both in pelagic and benthic environments. Of the sediment-dwelling species, the amphipod M. affinis and the bivalve M. balthica reduced the number of cladoceran eggs in the sediment, whereas the polychaetes Marenzelleria spp. had no effects on cladoceran eggs. Both M. balthica and M. affinis also increased the mortality rates of benthic eggs of copepods and rotifers. It was estimated that zooplankton eggs provide an additional carbon source for food-limited benthic communities. The results indicate that predation pressure on zooplankton benthic eggs may be strong, but varies widely depending on the season and the functional characteristics of the macrofauna. Macoma balthica buried cladoceran eggs and a fluorescent tracer from the sediment surface to a depth of 3 4 cm, indicating efficient sediment mixing. In contrast, the other taxa had fewer effects on particle distributions. In addition to organic matter mineralization, particle mixing is crucial to the success of benthic recruitment of zooplankton, since only eggs close to the sediment surface may hatch. Macoma balthica and M. affinis altered the patterns of zooplankton emergence from the sediment. In general, the highest emergence rates were observed in the absence of macroscopic fauna, and M. balthica exerted a stronger suppressive effect than M. affinis. Moreover, copepods were less severely affected than cladocerans, while only one species (Temora longicornis) clearly benefited from the presence of the macrofauna. These differences probably result from species-specific differences in the resistance of eggs to disturbances. The results show that benthic fauna may considerably alter the patterns of zooplankton emergence from the seafloor, thereby shaping zooplankton pelagic populations. The semi-motile M. balthica and Marenzelleria spp. increased the fluxes of phosphate and ammonium from the sediment to the water, whereas the motile M. affinis and Mysis mixta had a contrasting effect. In the eutrophied Baltic Sea, efficient internal cycling of bioavailable nutrients forms a strong feedback inhibiting the recovery of the ecosystem. Based on the results, a change in species dominance from the two motile taxa, susceptible to oxygen deficiency, to the more tolerant semi-motile taxa provides additional feedback, strengthening internal nutrient cycling and accelerating eutrophication, with deteriorating near-bottom oxygen conditions and changes in the benthic communities. In shallow-water ecosystems, benthic nutrient regeneration plays a key role in determining the overall productivity of the ecosystem. In addition, the results of this study show that the communities in the benthos may essentially contribute to the structure of those in the plankton.

Observations of the solar wind-magnetosphere-ionosphere coupling

In this thesis, the solar wind-magnetosphere-ionosphere coupling is studied observationally, with the main focus on the ionospheric currents in the auroral region. The thesis consists of five research articles and an introductory part that summarises the most important results reached in the articles and places them in a wider context within the field of space physics. Ionospheric measurements are provided by the International Monitor for Auroral Geomagnetic Effects (IMAGE) magnetometer network, by the low-orbit CHAllenging Minisatellite Payload (CHAMP) satellite, by the European Incoherent SCATter (EISCAT) radar, and by the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite. Magnetospheric observations, on the other hand, are acquired from the four spacecraft of the Cluster mission, and solar wind observations from the Advanced Composition Explorer (ACE) and Wind spacecraft. Within the framework of this study, a new method for determining the ionospheric currents from low-orbit satellite-based magnetic field data is developed. In contrast to previous techniques, all three current density components can be determined on a matching spatial scale, and the validity of the necessary one-dimensionality approximation, and thus, the quality of the results, can be estimated directly from the data. The new method is applied to derive an empirical model for estimating the Hall-to-Pedersen conductance ratio from ground-based magnetic field data, and to investigate the statistical dependence of the large-scale ionospheric currents on solar wind and geomagnetic parameters. Equations describing the amount of field-aligned current in the auroral region, as well as the location of the auroral electrojets, as a function of these parameters are derived. Moreover, the mesoscale (10-1000 km) ionospheric equivalent currents related to two magnetotail plasma sheet phenomena, bursty bulk flows and flux ropes, are studied. Based on the analysis of 22 events, the typical equivalent current pattern related to bursty bulk flows is established. For the flux ropes, on the other hand, only two conjugate events are found. As the equivalent current patterns during these two events are not similar, it is suggested that the ionospheric signatures of a flux rope depend on the orientation and the length of the structure, but analysis of additional events is required to determine the possible ionospheric connection of flux ropes.

Dynamics of free-running, pump-modulated and coupled semiconductor and solid-state lasers

The output of a laser is a high frequency propagating electromagnetic field with superior coherence and brightness compared to that emitted by thermal sources. A multitude of different types of lasers exist, which also translates into large differences in the properties of their output. Moreover, the characteristics of the electromagnetic field emitted by a laser can be influenced from the outside, e.g., by injecting an external optical field or by optical feedback. In the case of free-running solitary class-B lasers, such as semiconductor and Nd:YVO4 solid-state lasers, the phase space is two-dimensional, the dynamical variables being the population inversion and the amplitude of the electromagnetic field. The two-dimensional structure of the phase space means that no complex dynamics can be found. If a class-B laser is perturbed from its steady state, then the steady state is restored after a short transient. However, as discussed in part (i) of this Thesis, the static properties of class-B lasers, as well as their artificially or noise induced dynamics around the steady state, can be experimentally studied in order to gain insight on laser behaviour, and to determine model parameters that are not known ab initio. In this Thesis particular attention is given to the linewidth enhancement factor, which describes the coupling between the gain and the refractive index in the active material. A highly desirable attribute of an oscillator is stability, both in frequency and amplitude. Nowadays, however, instabilities in coupled lasers have become an active area of research motivated not only by the interesting complex nonlinear dynamics but also by potential applications. In part (ii) of this Thesis the complex dynamics of unidirectionally coupled, i.e., optically injected, class-B lasers is investigated. An injected optical field increases the dimensionality of the phase space to three by turning the phase of the electromagnetic field into an important variable. This has a radical effect on laser behaviour, since very complex dynamics, including chaos, can be found in a nonlinear system with three degrees of freedom. The output of the injected laser can be controlled in experiments by varying the injection rate and the frequency of the injected light. In this Thesis the dynamics of unidirectionally coupled semiconductor and Nd:YVO4 solid-state lasers is studied numerically and experimentally.

Residual noise covariance for Planck low-resolution data analysis

Aims: Develop and validate tools to estimate residual noise covariance in Planck frequency maps. Quantify signal error effects and compare different techniques to produce low-resolution maps. Methods: We derive analytical estimates of covariance of the residual noise contained in low-resolution maps produced using a number of map-making approaches. We test these analytical predictions using Monte Carlo simulations and their impact on angular power spectrum estimation. We use simulations to quantify the level of signal errors incurred in different resolution downgrading schemes considered in this work. Results: We find an excellent agreement between the optimal residual noise covariance matrices and Monte Carlo noise maps. For destriping map-makers, the extent of agreement is dictated by the knee frequency of the correlated noise component and the chosen baseline offset length. The significance of signal striping is shown to be insignificant when properly dealt with. In map resolution downgrading, we find that a carefully selected window function is required to reduce aliasing to the sub-percent level at multipoles, ell > 2Nside, where Nside is the HEALPix resolution parameter. We show that sufficient characterization of the residual noise is unavoidable if one is to draw reliable contraints on large scale anisotropy. Conclusions: We have described how to compute the low-resolution maps, with a controlled sky signal level, and a reliable estimate of covariance of the residual noise. We have also presented a method to smooth the residual noise covariance matrices to describe the noise correlations in smoothed, bandwidth limited maps.