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All types of muscles use Ca2+ as their main intracellular messenger. In skeletal muscle fibers abnormal levels of intracellular calcium result in altered contractile properties, altered energy metabolism, and altered gene expression. Moreover, long term failure of normal Ca2+ homeostasis can lead to cell death of muscle fibers by necrosis and apoptosis. Elevations of intracellular Ca2+ levels are more and more regarded as the reason for pathological changes and muscle fiber damage in Duchenne Muscular Dystrophy (DMD). DMD is a severe recessive x-linked muscle disease caused by mutations in the dystrophin gene. The characteristics of DMD are muscle tissue wasting and fibrosis. Both muscle wasting and intracellular Ca2+ are to be reflected in changes of muscle force. Several Ca2+ conducting channels including transient receptor potential (TRP) channels are supposed to account for the abnormal Ca2+ homeostasis in DMD. Gene expressions of TRP channels have been studied in human and mouse skeletal muscle and among others TRPC3, TRPC6 and TRPV4 channels were found to occur in skeletal muscles. The present study followed the hypothesis that TRPC3, TRPC6 and TRPV4 are functional in skeletal muscle fibers and that they contribute to muscular Ca2+ homeostasis. Further, it was assumed that dysfunction of the mentioned TRP channels contributes to abnormal contractile properties and pathology and of dystrophin-deficient muscle. To study Ca2+ changes in mouse skeletal muscle fibers the fluorescent calcium indicator Fura-2 was used. Further, the technique of Mn2+ quench of Fura-2 fluorescence was applied. Muscle force measurements of mouse soleus and diaphragm strips were performed. To elucidate abnormalities of TRP channel function in dystrophin-deficient muscle, muscles and muscle fibers of mdx mice were studied. Hyperforin, an activator of TRPC6 channels elicited increases of calcium levels in wildtype muscle fibers. These increases were partly inhibited by the TRPC6 inhibitor 1-(5-chloronaphthalenesulfonyl) homopiperazine hydrochloride (ML-9). The TRPC3/TPRC6 activator 1-oleoyl-2-acetyl-sn-glycerol (OAG) resulted in increased calcium entry, which was attenuated by ML-9. 2-aminoethoxydiphenylborane (2-APB), an unspecific TRP channel inhibitor, suppressed calcium entry in muscle fibers under basal conditions. In addition, the specific TRPC3 inhibitor Pyr3, strongly inhibited background calcium entry. The TRPV4 activator 4α-phorbol 12,13-didecanoate (4α-PDD) induced significant increased calcium entry and this increase could be inhibited by the TRPV4 inhibitor HC 067047. During muscle force recordings ML-9 significantly inhibited twitches and tetani and accelerated muscle fatigue during sustained repetitive stimulation. The results indicate that TRPC3, TRPC6 and TRPV4 are functionally expressed in mouse muscle fibers. TRPC3 stays active under the basal conditions and contributes to background calcium entry. In contrast, TRPC6 and TRPV4 did not seem to be active at resting conditions, but could be pharmacologically activated. TRPC6 may play a role to counteract the calcium loss under long-term muscle fatigue. Though TRPC3 and C6 play a role for muscular Ca2+ homeostasis, it is unclear whether and how the two channels associate and cross-talk with each other in skeletal muscle cells. In mdx fibers Pyr3 inhibited background calcium influx stronger that in WT fibers, implying a possible over-activation of TRPC3 channels in mdx muscle fibers. At later stages mdx muscle showed marked decrease in force reflecting muscle wasting. Soleus showed moderate decrease and diaphragm showed severe decrease (more than 60%) in force. Resistance to muscle fatigue was shown in mdx soleus muscle when compared with WT soleus muscle. Diaphragm segments of mdx mice showed very strong resistance to muscle fatigue. The results indicate a substantial loss of muscle mass, an increase in oxidative fiber types and a reduction of fast fatigable muscle fibers. It is concluded that the hypothesis of functional expression of TRPC3, TRPC6 and TRPV4 in mouse skeletal muscle has been confirmed. The results give improved knowledge about the relation of Ca2+ homeostasis, mdx pathology and TRP channels. Diaphragms of old mdx mice show severe muscle weakness but the remaining fibers of the diaphragm showed strong fatigue-resistance. The application of a TRPC3 inhibitor may be a promising treatment to prevent high Ca2+ mediated muscle damage in muscular dystrophy.
Liu–II coal pit is a typical example of China’s deep coal mines which is seriously threatened by groundwater inrush from the underlying carboniferous Taiyuan limestone formation. An exhaustive data set of this confined aquifer exists. The aquifer lies 45 m∼ 60 m below the major coal seam. A traditional artesian aquifer test has been performed in order to assess the hydraulic properties, e.g. transmissivity (T) and storage coefficient (S). This artesian aquifer test is conducted with four simultaneously operating production wells while the discharge of each production well varied with time. The results of this test suggest that the aquifer is heterogeneous. Therefore, the according problems are: (1) how to analyze the artesian aquifer test with linearly declining discharge; (2) how to deal with multiple production wells in an aquifer test; (3) how to adequately consider aquifer heterogeneity. Thus, the objective of this thesis is to solve these problems. 1) As opposed to classical above-ground pumping tests, it is difficult to control the discharge rate of the production well in a deep mine artesian aquifer test since the hydraulic pressure is extraordinary high. Moreover the discharge rate won’t descend rapidly to zero, thus the analytical solution of Jacob and Lohman (1952) type curve for the artesian aquifer test will not be applicable. It is more reasonable to analyze the test as a pumping test with variable discharge. It is considered to rebuild a hydrogeological conceptual model which is similar with Theis (1935) model but with the variable discharge. A general equation for any discharge variability is given. Its application for the linearly declining discharge is presented subsequently, and a type curve of this equation with linearly declining discharge is given as well. After that, a simple numerical model is built by FEFLOW to simulate an artificial pumping test with the linearly declining discharge by assigning different parameter sets for transmissivity and storage coefficient. The type curve method is applied to evaluate transmissivity and storage coefficient for the linearly declining discharge well. The deviation between the given values of transmissivity and storage coefficient in FEFLOW and the values of those calculated by matching point are sufficiently small. Thus, when the discharge of production well declines linearly, a type curve method as an empirical method is reasonable and gives satisfactory values of these hydrogeological parameters. 2) In some cases, it is necessary to conduct a pumping test (or an artesian aquifer test) with several pumping wells (or production wells) which work simultaneously in order to discharge maximum quantity of groundwater. Normally, the superposition method or numerical simulation is applied to analyze the test result. However, a new approach called “Well Generalization Method” is defined and analyzed in this thesis. It is an easy–to–use approach for hydrogeologist to estimate the aquifer parameters while conducting an aquifer test. Since the key point of this approach is using a generalization well to substitute the pumping (or production) wells, it is obvious that this approach will generate the estimated error of parameters. Accordingly, several scenarios are analyzed and discussed based on the artificial type aquifer designed in FEFLOW. A homogeneous aquifer and a heterogeneous aquifer which is generated by geostatistical stochastic simulation technique (see 3)) are discussed separately. As a result, this approach is feasible and applicable under some conditions when the calculated observation well is arranged more than about 2.5 times the scale of the multi–pumping–wells field away from the center of the multi–pumping–wells field, furthermore, the maximum deviation of drawdown resulting from these observation wells will be less than 0.5 m, and the estimated value of transmissivity will be 0.44% smaller than real value. 3) Finally aquifer heterogeneity is addressed, in order to check the introduced method for applicability under realistic conditions. It has been described that aquifer heterogeneity plays a major role in hydrodynamic processes (e.g. de Marsily et al., 1998). Geostatistics which is considered as a useful tool for characterizing the spatial variability of transmissivity is applied to solve this problem. Based on the results of the artesian aquifer test conducted in Liu–II coal pit, a model of spatial variability of transmissivity is developed. Sequentially, the variogram model is applied in ordinary kriging to interpolate the transmissivity distribution, and in sequential Gaussian simulation to simulate a random field of transmissivity data in order to reflect its small scale variability. A comparison of the results of estimation and simulation of transmissivity indicates that the simulated values better reflect the spatial variability, reversely, the estimated values are much smoother.
Bats belong to the most gregarious and diverse mammals with highly complex social behaviors. Despite extensive research on their ecology and social behavior in some bat species, gained insights are restricted to only few of the more than 1300 species. In the recent past, bats have also become a central topic of a different branch of research: Since the 1990s bats came to the fore of virologists and immunologists due to the bats’ apparent importance as reservoir hosts and vectors of several (mostly tropical) diseases. While this research is focused mainly on emerging infectious diseases linked to bats, and their zoonotic potential, little has been invested regarding the link between disease transmission and bat social systems.
In my work, I aim at filling this gap by merging automated daily roosting observations, social network analysis, and a virological screening in Natterer’s bats (Myotis nattereri). In a collaborative approach, my co-workers and I analyzed the social structure of individually marked Natterer’s bats, their astrovirus detection rate and transmission pathways within their colony, as well as roosting interactions between different co-occurring con- and heterospecific bat colonies.
We discovered Natterer’s bats to display a very divergent social network structure that contradicts the findings of previous studies on large fission-fusion groups. Contrary to the modular social network structure found in e.g. primates or other bats species, the social network of Natterer’s bats consists of only one highly interconnected community. Moreover, although the close proximity between bat hosts in the colony should strongly promote direct transmission, we found indications that astrovirus infections follow at least partly an indirect transmission pathway via contaminated roost use. Lastly, our results prove that co-occurring con- and heterospecific bat colonies, e.g. as in this study Natterer’s bats, brown long-eared bats and Bechstein’s bats, can influence each other in their roost use by avoiding conspecific roosts and by being attracted towards those of heterospecifics. This holds implication for the transmission of parasites and pathogens within and between different colonies with opportunities for spillovers. To conclude, this multidisciplinary study led to valuable insights in the hitherto hidden mechanisms within and among bat colonies.
In this thesis we have revisited the formation of the excitonic insulator (EI), which realizes an exciton condensate. In contrast to optically created exciton condensates, the EI forms in thermal equilibrium and is solely driven by the Coulomb attraction between electrons and holes. The EI phase is anticipated to occur near the semimetal-semiconductor (SM-SC) transition at low temperatures. Depending from which side the EI is approached, it forms due to a BCS-type condensation of electron-hole pairs or a Bose-Einstein condensation (BEC) of excitons. The extended Falicov-Kimball model (EFKM) is the minimal model the EI can be described with. This model describes spinless fermions in two dispersive bands (f band and c band), that interact via a local Coulomb repulsion. The EFKM is also used to describe electronic ferroelectricity (EFE). Both phases, the EI and EFE-type ordering, are characterized by a spontaneous f-c hybridization in the EFKM. We have presented the EI phase, the EFE phase, and the orderings they compete with. Moreover, we have determined the ground-state phase diagram of the EFKM. We have focused particularly on the anticipated BCS-BEC crossover within the EI and have analyzed the formation scenarios. The exciton spectrum and the exciton density in the normal phase close to the critical temperature give information about relevant particles and therefore the nature of the transition. We have demonstrated that the whole EI is surrounded by a halo", that is, a phase composed of electrons, holes and excitons. However, on the SM side, only excitons with a finite momentum exist. These excitons appear only in a small number and barely influence the SM-EI transition. This phase transition is driven by critical electron-hole fluctuations, generated by electrons and holes at the Fermi surface. On the SC side, excitons with arbitrary momenta exist. Most notably, we have found the number of zero-momentum excitons to diverge at the SC-EI transition, signaling the BEC of these particles. Within the EI phase, there is a smooth crossover from the BCS regime to the BEC regime. One of the promising candidates to observe the EI experimentally, is the transition-metal dichalcogenide 1T-TiSe2. Strong evidences were found favoring an EI scenario of the charge-density-wave (CDW) formation in this material. However, some aspects point to a lattice instability to drive the CDW transition. We have addressed this issue by analyzing the recently discovered chiral property of the CDW in 1T-TiSe2. We have found that the EI scenario is insufficient to explain a stable, long range chiral charge ordering. Lattice degrees of freedom must be taken into account. In particular, nonlinear electron-phonon coupling and phonon-phonon interaction are crucial. By estimating appropriate model parameters for 1T-TiSe2, we have suggested a combination of excitonic and lattice instability to drive the CDW transition in this material. Experiments in 1T-TiSe2 and other materials suggest that the coupling to the lattice is non-negligible. We have extended therefore the model by an explicit exciton-phonon interaction, and have analyzed crucial effects of this interaction. While the single-particle spectrum is not modified qualitatively, the electron-hole pair spectrum changes significantly. The inclusion of the phonons lead to a massive collective mode in the ordered ground state in contrast to the case for vanishing exciton-phonon coupling, where the mode is acoustic. We have suggested that a gapless collective mode leads to off-diagonal long range order. This questions that the ground state for finite exciton-phonon coupling represents a condensate.
For many years, rangeland ecologists have debated about whether the state of semi-arid and arid rangelands is the expression of an ecological equilibrium or non-equilibrium dynamics reached in response to grazing livestock. Since the problem has been considered at different spatial scales, it is recognised that the competing concepts of equilibrium and non-equilibrium dynamics need to be integrated. Furthermore, the role of environmental variables as vegetation driving factors has long been ignored in the discussion on grazing effects on ecosystems. Present thesis, examines the dependence of plant communities on environmental in particular site-ecological conditions in three ecosystems of Western Mongolia established along a precipitation gradient to detect the vegetation-driving ecological factors involved. Furthermore, grazing impact is exemplary assessed in a desert steppe at additional spatial scales of plant communities and population. At the landscape level, a classification of plant communities in dependence on environmental conditions is carried out. Additionally, the investigations focused on the impact of grazing on soil and on the occurrence of grazing-mediated plant communities. Data were sampled along an altitudinal gradient between 1150 m to 3050 m a.s.l. from arid lowland with desert steppe via semi-arid mountain steppe to humid alpine belt. Within each altitudinal belt, data sampling was carried out along grazing gradients, established from grazing hot spots to areas distant from them. By means of an environmentally based vegetation classification, factors with highest explanation values for largest variation in vegetation were identified and considered as most responsible for vegetation patterns. To validate and affirm the classification, three different statistical methods are applied: environmentally adjusted table work of vegetation relevés supported by cluster analysis of species distribution, detrended correspondence analysis of vegetation data separately from environmental data, and the principle component analysis of only environmental data. Vegetation-driving factors change along the altitudinal gradient from abiotic forces in the desert steppe, as e.g. altitude and soil texture, to abiotic and biotic forces in the alpine belt represented by soil texture, soil nutrients and grazing. Vegetation and soil of all ecosystems respond to grazing but with different patterns and to a different extent. While desert steppe does not indicate grazing communities, mountain steppe demonstrates grazing communities at fertilised sites and alpine belt at nutrients depleted sites. Thus, the grazing sensitiveness of the ecosystems is assumed to be linked with plant productivity and the role of vegetation as site-determining factor (Chapter 2). To examine grazing impact at lower spatial scales on desert steppe as the ecosystem with lowest grazing sensitiveness at the landscape scale, at community scale the total number of species, the total vegetation cover, the percentage of annual species, the cover of annual species, and properties of soil nutrient along gradients of grazing intensity within three different communities were assessed. Vegetation parameters respond to grazing in different ways, and the responses of the same parameters vary between plant communities. Correlations with grazing intensity indicate only partly statistical significance. Significant correlations of grazing intensity with concentrations of soil nutrient point to eutrophication in two communities. A comparison of vegetation and soil properties refers to a greater indirect influence of grazing via increased soil nutrients than the direct effect on vegetation (Chapter 4). At the population level, data about stand density, aboveground biomass, individual plant weight, and the proportion of flowering plants of the dominant dwarf semi-shrub Artemisia xerophytica were collected along a grazing gradient. Soil data were used to distinguish between grazing and edaphic influences. All parameters of Artemisia xerophytica reflect the assumed gradient of grazing intensity up to 800 m distance from the grazing hot spot. As grazing pressure decreases, plant density and total biomass per plot increase. The average shrub weight, an indicator of plant vitality, is related to both: distance from the grazing hot spot and stand density, which may be explained by additional intraspecific competition at higher densities. At a longer distance, these effects are masked by variations in soil parameters determining water availability, leading to quite similar degradation forms. These results are in contrast to other studies carried out at the scale of plant communities which did not detect significant changes along a grazing gradient. One explanation is the different map scale: the study took place only within a single plant community comparing populations of one species (Chapter 3). The comparative study demonstrates that even arid desert steppes of western Mongolia display equilibrial and non-equilibrial properties, depending on the observational scale: while no grazing mediated plant communities could be identified at the landscape scale as predicted by the non-equlilibrium model, at the community level vegetation parameters imply an intermediate position between equilibrium and non-equilibrium system. At the population level, the results clearly reflect the grazing gradient as predicted by the equilibrium model (Chapter 4). As a consequence, the assessment of vegetation dynamics and grazing impact in rangelands requires a multiple-scale approach that duly considers different vegetation properties responding differently to grazing, climatic and edaphic variability at different spatial scales. It is further suggested, that future research should draw comparisons between landscapes that co-evolved with herbivory, and those that did without (Chapter 4).
A slice is an intersection of a hyperplane and a self-similar set. The main purpose of this work is the mathematical description of slices. A suitable tool to describe slices are branching dynamical systems. Such systems are a generalisation of ordinary discrete dynamical systems for multivalued maps. Simple examples are systems arising from Bernoulli convolutions and beta-representations. The connection between orbits of branching dynamical systems and slices is demsonstrated and conditions are derived under which the geometry of a slice can be computed. A number of interesting 2-d and 3-d slices through 3-d and 4-d fractals is discussed.
We present classical and hybrid modeling approaches for genetic regulatory networks focusing on promoter analysis for negatively and positively autoregulated networks. The main aim of this thesis is to introduce an alternative mathematical approach to model gene regulatory networks based on piecewise deterministic Markov processes (PDMP). During somitogenesis, a process describing the early segmentation in vertebrates, molecular oscillators play a crucial role as part of a segmentation clock. In mice, these oscillators are called Hes1 and Hes7 and are commonly modeled by a system of two delay differential equations including a Hill function, which describes gene repression by their own gene products. The Hill coefficient, which is a measure of nonlinearity of the binding processes in the promoter, is assumed to be equal to two, based on the fact that Hes1 and Hes7 form dimers.However, by standard arguments applied to binding analysis, we show that a higher Hill coefficient is reasonable. This leads to results different from those in literature which requires a more sophisticated model. For the Hes7 oscillator we present a system of ordinary differential equations including a Michaelis-Menten term describing a nonlinear degradation of the proteins by the ubiquitinpathway. As demonstrated by the Hes1 and Hes7 oscillator, promoter behavior can have strong influence on the dynamical behavior of genetic networks. Since purely deterministic systems cannot reveal phenomenons caused by the inherent random fluctuations, we propose a novel approach based on PDMPs. Such models allow to model binding processes of transcription factors to binding sites in a promoter as random processes, where all other processes like synthesis, degradation or dimerization of the gene products are modeled in deterministic manner. We present and discuss a simulation algorithm for PDMPs and apply it to three types of genetic networks: an unregulated gene, a toggle switch, and a positively autoregulated network. The different regulation characteristics are analyzed and compared by numerical means. Furthermore, we determine analytical solutions of the stationary distributions of one negatively, and three positively autoregulated networks. Based on these results, we analyze attenuation of noise in a negative feedback loop, and the question of graded or binary response in autocatalytic networks.
The six extraocular muscles (EOMs) are arranged around the eyeball as agonist-antagonist pairs performing the eye movements. The EOMs comprise a distinct muscle group that is fundamentally different from other skeletal muscle, which is reflected on many levels, such as functionality, anatomy as well as in their molecular make-up. Physiologically EOMs are considered superfast, high endurance muscles that are continuously active. In addition, EOMs contain unusual slow-tonic fibers that share features with amphibian and avian slow-tonic fibers. EOMs also express slow/cardiac isoforms of proteins and genes along with the typical isoforms of fast muscle fibers. Another striking hallmark of EOM is their differential involvement in a number of diseases. For instance, EOMs are preferentially spared in Duchenne Muscular Dystrophy (DMD). DMD is the most common fatal, genetic disease in males clinically characterized by progressive muscle wasting. Mutations in the dystrophin gene result in a destabilization of the muscle membrane causing muscle fiber damage. While all other skeletal muscles deteriorate the EOMs remain morphologically and functionally healthy. In the pathogenesis of DMD elevated Ca2+ levels are believed to be an early event and it has been shown that EOMs are protected from pharmacologically induced Ca2+ damage. The goal of this study was to characterize the spared EOMs, in particular their Ca2+ homeostasis, in the context of DMD pathology to reveal new potential therapeutic targets for the disease. A combination of physiological, molecular and biochemical methods was used to investigate the Ca2+ homeostasis of EOMs to demonstrate clear differences compared with the fast limb muscle tibialis anterior (TA). Ca2+ handling of stimulated cultured EOM myotubes suggested more efficient Ca2+ removal from the cytoplasm after induced Ca2+ influx compared with cultured myoblasts from TA. Subsequent mRNA and protein expression analyses of myoblasts and adult muscle tissue revealed high expression levels of many key Ca2+ regulating and buffering proteins in rodent EOMs compared with TA. Among these Ca2+ proteins were slow/cardiac proteins, which normally are not found in fast muscles. For instance, the sarcoplasmic Ca2+ ATPase SERCA2 was elevated along with its regulator phospholamban (PLN). Further, PLN was preferentially endogenously phosphorylated at Thr17 suggesting continuous activation of SERCA2 and possibly the fast isoform SERCA1, the main Ca2+ pumps responsible for removing Ca2+ from the cytoplasm after muscle contraction. Furthermore, Ca2+ buffers, such as calsequestrin (CASQ2) and parvalbumin (PARV) were elevated. These results suggest that EOMs are endowed with a unique and superior Ca2+ homeostasis that facilitates efficient Ca2+ buffering and removal from the cytoplasm. This is in agreement with their continuous and fast activation cycles, as well as with a potential protective mechanism in prevention of Ca2+ overload in DMD. The extreme activity patterns of EOM suggested that a high activity of store-operated Ca2+ entry (SOCE) plays a critical part to replenish Ca2+ for rapid and continuous cycles of contractions. To extend the data on general Ca2+ homeostasis and because of possible implications of store-operated Ca2+ influx and other Ca2+ influx pathways in DMD, the expression patterns of group 1 transient receptor potential (TRP) channels and the proteins Orai1 and STIM1 were studied. The TRP channels, TRPC1, TRPC6 and TRPV4 channel proteins in addition to STIM1 showed higher expression in EOM compared with TA. High TRPC1, TRPV4 and STIM1 levels could play a significant role in the high fatigue resistance, muscle differentiation and SOCE in EOM. In addition, tissue from the mdx mouse model of DMD was investigated. The only channels differentially expressed in mdx EOM compared with normal EOM were TRPM4 and TRPM7 (decreased in mdx EOM) and TRPV4 (increased in mdx EOM). Although, these changes in mdx EOM were of small magnitude, they could point toward subtle compensatory changes related to the disease process. In general, EOMs seem to be unaffected by the disease and inherently protected. In conclusion, the results in this thesis have improved the understanding of the Ca2+ homeostasis in EOMs and suggest that EOM may be better able to prevent prolonged elevation of cytoplasmic Ca2+ levels. These data may help to design new therapeutic approaches targeting Ca2+ handling proteins to ameliorate muscular dystrophy.
In the present thesis, a systematic study of beam driven Alfvén eigenmodes in high-density and low-temperature plasmas of the W7-AS stellarator is performed. The device went out of operation in 2002 and the study is based on stored experimental data. Alfvén instabilities can roughly be divided into ideal MHD Alfvén eigenmodes and those existing due to kinetic effects. The spectrum of ideal MHD Alfvén waves in toroidal fusion devices consists of a continuum of stable waves that are strongly localized. Weakly damped, discrete eigenmodes can exist in gaps of the continuous spectrum which are formed by plasma inhomogeneities and the coupling of Alfvén continua. This allows an identification of ideal MHD Alfvén eigenmodes in terms of their frequency and mode numbers. Kinetic effects can modify this spectrum and cause additional types of eigenmodes, the kinetic Alfvén eigenmodes (KAE) and energetic particle modes (EPM). The goal of this thesis is twofold: (I) identification and description of fast particle driven Alfvén instabilities in W7-AS, and (II) study of energetic particle losses induced by Alfvén instabilities. The reconstruction of the ideal MHD plasma equilibrium for each discharge with sufficient accuracy is the very foundation of all subsequent steps. This is achieved, based on measured plasma parameter profiles that are further refined by validating them to the measurements of other, independent plasma diagnostics. The applied scheme is inspired by an approach of Integrated Data Analysis (IDA) to combine different diagnostic data and provide combined uncertainties. After mode number analysis and eigenmode identification, the theoretically expected, linear growth rate of the instability is calculated where possible, and the various contributions of the fast particle drive to the instability of the mode are identified. Alfvénic activity recorded by the Mirnov diagnostic is analyzed, which consists of a set of spatially distributed coils that measure magnetic fluctuations. On W7-AS, the probes are arranged in three poloidal arrays at different toroidal positions. The spacing between the probes is non-equidistant. In addition, the signals of one probe array are digitized with a different sample rate. These characteristics prohibit the straight-forward use of standard tools available for harmonic analysis. Instead, a new tool has been developed and thoroughly tested. It is a multi-dimensional extension of the Lomb periodogram, able to provide reliable time-resolved frequency and mode number spectra in the case of uneven datapoint spacing. Numerical studies of this periodogram show a good performance with respect to mode number resolution given the low number of available probes, and robustness against perturbations of the signal. Only two of the probe arrays can be used for the analysis of eigenmodes with frequencies >70 kHz, such that for high-frequency phenomena insufficient information about the mode numbers is available. A total of 133 different Alfvén eigenmodes is studied in discharges from different experimental campaigns. A restriction to discharges from various high-beta campaigns with neutral beam heating is required to allow for a realistic reconstruction of plasma equilibrium and velocity distribution functions of energetic particles. The discharges are characterized by high density, ne = 5 x 1019 m-3 to 2.5 x 1020 m-3 at relatively low temperatures of Te = Ti = 150 ... 600 eV. Alfvén eigenmodes often appear transiently in the startup phase of these discharges, where density and heating power are being ramped up. Occasionally, Alfvén eigenmodes are seen in the stationary, high-beta phase in the presence of considerable neutral beam heating. Most of the Alfvén eigenmodes are successfully classified as ideal MHD eigenmodes. 19 global, 47 toroidicity-induced and 8 ellipticity-induced Alfvén eigenmodes (GAEs, TAEs, and EAEs, respectively) are unambiguously identified by their mode numbers and frequencies. Excellent agreement between experimentally observed mode number spectra and theoretically calculated eigenmode structure is shown for a TAE example. Additional 13 events are found to have frequencies inside the EAE gap and could possibly be EAEs. Evidence for high-frequency Alfvén eigenmodes (mirror- and helicity-induced Alfvén eigenmodes) is seen, but can not be proven rigorously due to uncertain mode numbers and the complexity of the Alfvén continuum. The remaining 41 Alfvén eigenmodes can not be classified to be one of the above cases. Reasons are either high frequencies, mode numbers obscured by far-field effects, or mode numbers that could not be related to ideal MHD Alfvén eigenmodes. A selection of these shows indications of strong non-linear wave-particle interactions and are assumed to be EPMs. Kinetic Alfvén eigenmodes are not expected to exist in the experimental conditions that were studied. The radially resolved velocity distribution function is used to describe the parameter regimes in which the modes are observed in terms of the dimensionless parameters vb/vA (beam velocity normalized to the Alfvén velocity) and ßfast/ßth, where beta is the ratio of plasma pressure to magnetic pressure. The first parameter describes through which of the possible resonance velocities particles can interact with the eigenmode. A peculiarity of the fast particle dynamics in fusion devices is that they can resonantly interact with Alfvén eigenmodes through sideband resonances even if v < vA. The second parameter describes the energy content of the destabilizing fast particle population compared to the potentially stabilizing thermal plasma component. These parameters contain relevant information about the instability of an eigenmode and such diagrams are given for all observed modes. In addition to that, the expected linear growth rate of gap modes is calculated based on a theoretical model that extends the ideal MHD by a perturbative, drift-kinetic description of the energy exchange between waves and circulating particles, neglecting the effects of trapped particles. For the discharges under consideration the thermal electron speed is comparable to vA and the electrons provide a significant Landau damping contribution. Due to strong density gradients near the plasma boundary in most of the discharges, the thermal ions can provide a small drive via the spatial inhomogeneity which does not overcome the electron damping, however. The drive by spatial inhomogeneity of thermal ions requires a certain propagation direction of the mode and is equally stabilizing for opposite mode numbers. The fast particles also contribute to the growth rate via spatial inhomogeneity, velocity gradients and velocity anisotropy terms are negligible in W7-AS. Most of the observed GAE or EAE modes have negative mode numbers, which correspond to a propagation direction for which the spatial inhomogeneity of thermal and beam ions is predicted to be stabilizing. A fast particle drive of these modes is not confirmed, whereas the TAEs are found to be strongly destabilized by neutral beam injection. The distribution of plasma parameters for discharges showing TAEs in terms of the dimensionless stability parameters suggests an instability threshold that is qualitatively confirmed by an exploration of the parameter space with the theoretical model. Wave-induced, resonant losses of energetic ions scale linearly with the wave amplitude. To identify them, correlations between ion loss probe signals and wave amplitudes are searched, where correlation times in the order of the slowing-down time of energetic particles are expected. Significant correlations can be established only exceptionally for 3 of the identified ideal MHD Alfvén eigenmodes. Those Alfvén eigenmodes, however, which are assumed to be EPMs frequently show severe losses of energetic ions that are visible in the time traces of the plasma energy as well.
Technological advances in light microscopy have always gone hand in hand with unprecedented biological insight. For microbiology, light microscopy even played a founding role in the conception of the entire discipline. The ability to observe pathogens that would otherwise evade human observation makes it a critical necessity and an indispensable tool to infectious disease research. Thus, the aim of this thesis was to optimize, extend, and functionally apply advanced light microscopy techniques to elucidate spatio-temporal and spatio-morphological components of bacterial and viral infection in vitro and in vivo.
Pathogens are in a constant arms race with the host’s immune system. By finding ways to circumvent host-mediated immune responses, they try to evade elimination and facilitate their own propagation. The first study (publication I) demonstrated that the obligate intracellular pathogen Coxiella burnetii is not just able to infect natural killer (NK) cells, but is actually capable of surviving the harsh degradative conditions in the cytotoxic lymphocyte’s granules. Using live-cell imaging of reporter-expressing Coxiella burnetii, the transient NK cell passage was closely monitored to provide detailed spatio-temporal information on this dynamic process in support of a range of static analyses. Bacterial release from NK cells was pinpointed to a time frame between 24 to 48 hours post-infection and the duration of release to about 15 minutes.
The second approach (publications II-V) aimed at shedding light on the greater spatio-morphological context of virus infection. Thus far, most studies investigating the distribution or tropism of viruses in vivo have used conventional immunohistochemistry in thin sections. Omitting the native spatial context of the infection site in vivo inherently bears the risk of incomplete description. While the microscopic tools and sample preparation protocols needed for volumetric 3D immunofluorescence imaging have recently been made available, they had not gained a foothold in virus research yet. An integral part of this thesis was concerned with the assessment and optimization of available tissue optical clearing protocols to develop an immunofluorescence-compatible 3D imaging pipeline for the investigation of virus infection inside its intact spatio-morphological environment (publication II). This formed the basis for all subsequent volumetric analyses of virus infection in vivo presented here. Consequently, this thesis provided a valuable proof of concept and blueprints for future virus research on the mesoscopic scale of host-pathogen interactions in vivo (publications II-V), using rabies virus (RABV; publications II-IV) and the newly-emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; publication V) as infection models for the nervous system and the respiratory tract, respectively.
Applying and further improving this volumetric 3D imaging workflow enabled unprecedented insights into the comprehensive in vivo cell tropism of RABV in the central (CNS) (publication III) and peripheral nervous system (PNS) (publication IV). Accordingly, differential infection of CNS-resident astrocytes by pathogenic and lab-attenuated RABV was demonstrated (publication III). While either virus variant showed equal capacity to infect neurons, as demonstrated by quantitative image analysis, only pathogenic field RABVs were able to establish non-abortive infection of astrocytes via the natural intramuscular inoculation route. A combined 3D LSFM-CLSM workflow further identified peripheral Schwann cells as a relevant target cell population of pathogenic RABV in the PNS (publication IV). This suggested that non-abortive infection of central and peripheral neuroglia by pathogenic RABV impairs their immunomodulatory function and thus represents a key step in RABV pathogenesis, which may contribute significantly to the establishment of lethal rabies disease.
Finally, utilizing the full volumetric acquisition power of LSFM, a further refined version of the established 3D imaging pipeline facilitated a detailed mesoscopic investigation of the distribution of SARS-CoV-2 in the respiratory tract of the ferret animal model (publication V). Particularly for this newly-emerged pathogen of global concern, in-depth knowledge of host-pathogen interactions is critical. By preserving the complete spatio-morphological context of virus infection in the ferret respiratory tract, this thesis provided the first specific 3D reconstruction of SARS-CoV-2 infection and the first report of 3D visualization of respiratory virus infection in nasal turbinates altogether. 3D object segmentation of SARS-CoV-2 infection in large tissue volumes identified and emphasized a distinct oligofocal infection pattern in the upper respiratory tract (URT) of ferrets. Furthermore, it corroborated a preferential replication of SARS-CoV-2 in the ferret URT, as only debris-associated virus antigen was detected in the lower respiratory tract of ferrets, thus providing crucial information on the spatial distribution of SARS-CoV-2.