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Hepatitis C virus (HCV) assembly and production is closely linked to lipid metabolism. Indeed, lipid droplets (LD) have been shown to serve as a platform for HCV assembly. To investigate the effect of HCV on the host cell proteome, 2D-gelelectrophoresis with subsequent MALDI-TOF mass spectrometry of HCV replicating and the corresponding control cells were done. Based on this analysis, it was found out that HCV-replicating Huh7.5 cells revealed lower amounts of TIP47 (tail interacting protein of 47kD) compared to HCV-negative cells. TIP47, a cytoplasmic sorting factor, has been shown to be associated with lipid droplets. As it is known that HCV-replication and assembly takes place at the so called ”membranous web” that is composed of LDs and rearranged ER-derived membranes, it was tempting to investigate the role of TIP47 in HCV life-cycle. Western blot analysis did reveal that overexpression of TIP47 in HCV replicating Huh7.5 cells leads to decreased amounts of the HCV core protein while the levels of non-structural protein (NS)5A and intracellular HCVgenomes are increased. Moreover, in TIP47 overproducing cells higher amounts of infectious HCV particles are secreted. Vice versa, inhibition of TIP47 expression by siRNA results in a decreased level of intracellular NS5A, increased amounts of intracellular core and less infectious viral particles in the supernatant. In addition, complete silencing of TIP47 by lentiviral transduction abolishes HCV replication that can be restored by transfection of these cells with a TIP47 expression construct. It has been shown recently that apoE binds to NS5A and that this interaction plays an important role for the HCV life cycle (Benga et al., 2010). The C-terminal part of TIP47 harbours a 4 helix bundle motif and displays high homology to the N-terminus of apoE. Therefore, we investigated the interaction of NS5A and TIP47. Confocal double immunofluorescence microscopy revealed that a fraction of NS5A colocalizes with TIP47. Coimmunoprecipitation experiments and a yeast-two-hybrid screening confirmed the interaction between NS5A and TIP47 and deletion of the N-terminal-TIP47-PAT domain abolishes this interaction. From this we conclude that the TIP47-NS5A interaction is required for virus morphogenesis. Moreover, TIP47 can bind to Rab9 and this is relevant for targeting the viral particle out of the cell. In accordance to this, TIP47 was identified to be associated to the viral particle. Mutants of TIP47 that fail to bind Rab9 reveal lower amounts and a changed distribution of the HCV core protein. Furthermore, we could see that the core staining colocalizes with subcellular structures that were identified as autophagosomes using a p62-specific antibody which is a specific autophagosome-marker. Based on this, we hypothized that destruction of the Rab9 binding domain misdirects the viral particle towards the lysosomal compartment.
For the first time it could be shown that TIP47 interacts with NS5A and is associated to the viral particle, therefore plays a crucial role for the virus morphogenesis and secretion of the viral article.
Taken together, these results indicate that TIP47 is an essential cellular factor for the life cycle of HCV Abstract and might be used as target for antiviral treatment, e.g. by targeting the NS5A-TIP47 interaction, based on small molecules that mimic the NS5A-specific sequence that binds to TIP47 which might result in a competition of the TIP47/NS5A interaction.
The universal biological energy currency adenosine triphosphate (ATP) is synthesized by the F1Fo-ATP synthase in most living organisms. The overall structure and function of F-type ATPases is conserved in the different organisms. The F1Fo-ATP synthase consist of two domains; the soluble F1 complex has the subunit stoichiometry α3β3γδε and the membrane embedded Fo complex consists of subunits ab2c10-15 in its simplest form found in bacteria. F1 and Fo both function as reversible rotary motors that are connected by a central stalk (γε) and a peripheral stalk (b2δ).
For ATP synthesis, the electrochemical energy formed by a proton or sodium ion gradient is required. The ion translocation across the Fo subcomplex induces torque in the motor part of the enzyme (cnγε), which causes conformational changes in the α3β3 domain leading to ATP synthesis from ADP and inorganic phosphate (Pi) catalyzed in the β-subunits. ATP hydrolysis causes a reverse torque in the Fo subcomplex triggering uphill ion translocation from cytoplasm to periplasm, and the enzyme functions as an ion pump.
The ATP synthesis mechanism is well understood, since several high-resolution structures of F1 are available. In contrast, the ion translocation mechanism across the membrane, mediated by the Fo subcomplex, is not understood in its structural detail.
Subunit a and the c-ring form an ion pathway, but subunit b is needed to form an active ion translocation pathway in both H+- and Na+-dependent systems. Several high-resolution structures of c-rings have provided insights in the ion translocation mechanism. The different ion translocation models based on biochemical, biophysical and structural analysis are in agreement in the fact that ions are translocated through a periplasmic ion access pathway in subunit a to the middle of the membrane and there to the binding site of a c-subunit. After almost a whole rotation of the c-ring the ion returns into the a-c interface, where it can be released to the cytoplasm. In the different models the cytoplasmic access pathway has been proposed to be located in subunit a, at the a-c interface or within the c-ring. The driving force of torque generation has been proposed to be the pH gradient or membrane potential. Several biochemical studies show that a conserved arginine in helix four of subunit a (R226 in Ilyobacter tartaricus or R210 in Escherichia coli)plays a critical role in the ion translocation. The arginine has been proposed to function as an electrostatic separator between the cytoplasmic and periplasmic pathways and as a mediator of the ion exchange into the c-ring ion-binding site.
Structural data of a related enzyme (V1Vo-ATPase from Thermus thermophilus) has provided insight into the helical arrangement of the ion translocating subunits I and Lring (related to subunit a and the c-ring). These structures indicated a small interface between subunit I and the L-ring, and two four-helix bundles in the N-terminal domain of subunit I were proposed to build the periplasmic and cytoplasmic ion pathways. To comprehend the ion-translocation and torque generation mechanism in F1Fo-ATP synthase, structural data of an intact a-c complex is needed.
The goal of this work was to obtain structural data of subunit a, most preferably in a complex with the c-ring or additionally with subunit b. Therefore, a new purification procedure for the I. tartaricus Fo-subcomplex, heterologously expressed in E. coli cells, was established. The purified Fo was characterized biochemically and by Laserinduced liquid bead ion desorption mass spectrometry (LILBID-MS). These analyses showed that pure and completely assembled Fo containing all its subunits in the correct stoichiometry (ab2c11) was obtained. The purified Fo complex was stable at 4°C for several months and at room temperature in the presence of lipids for several weeks. A lipid analysis was performed by thin-layer chromatography (TLC) to investigate the qualitative lipid composition of I. tartaricus whole lipid extract and various I. tartaricus F1Fo isolates. The whole lipid extract contained PC, PG and PE lipids and probably cardiolipin. PC, PG and PE lipids were bound to wild type I. tartaricus F1Fo, whereas recombinant I. tartaricus F1Fo did not have any bound lipids, but was able to bind the synthetic lipids POPC and POPG if they were provided during the purification.
For subsequent structural studies the purified Fo was subjected to two-dimensional (2D) crystallization trials. Vesicles and sheets tightly packed with protein and crystals with a rare plane group for I. tartaricus c11 (p121) were obtained. The c-ring was visible in the CCD images, and immunogold-labeling revealed the presence of the His-tagged a-subunit in the reconstituted vesicles. Furthermore, atomic force microscopy (AFM) imaging showed protein densities next to the c-rings, which protruded less from the membrane (0.4±0.1 nm) than the c-ring (0.7±0.1 nm). These protein densities presumably belonged to subunit a.
Cryo-electronmicroscopy (cryo-EM) was used to collect data of the p121 crystals and a merged projection density map was calculated to 7.0 Å resolution. The unit cell of the crystals (81 × 252 Å) contained two asymmetric units with three c-rings in each and next to the c11-rings new prominent densities were visible. In each extra density up to 7 transmembrane helices were visible, belonging to the stator subunit a and/or subunit b. To elucidate whether there are conserved elements in the three extra densities non-crystallographic averaging was applied using a single-particle approach.
Six possible arrangements for the c-rings and the extra densities were identified and used for the averaging. The extra densities were enhanced only in one of the possible arrangements. The average showed a four-helix bundle and a fifth helix in close proximity to the c-ring. Two more helices were present in each position but their position was ambivalent. The data obtained in this work provides the first insight in the helical arrangement in the a-c interface of F1Fo-ATP synthase.
Detailed knowledge of reaction mechanisms is key to understanding chemical, biological, and biophysical processes. For many reasons, it is desirable to comprehend how a reaction proceeds and what influences the reaction rate and its products.
In biophysics, reaction mechanisms provide insight into enzyme and protein function, the reason why they are so efficient, and what determines their reaction rates. They also reveal the relationship between the function of a protein and its structure and dynamics.
In chemistry, reaction mechanisms are able to explain side products, solvent effects, and the stereochemistry of a product. They are also the basis for potentially optimizing reactions with respect to yield, enhancing the stereoselectivity, or for modifying reactions in order to obtain other related products.
A key step to investigate reaction mechanisms is the identification and characterization of intermediates, which may be reactive, short-lived, and therefore only weakly populated. Nowadays, the structures of those can in most cases only be hypothesized based on products, side products, and isolable intermediates, because intermediates with a life time of less than a few microseconds are not accessible with the commonly used techniques for structure determination such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy.
In this thesis, two-dimensional infrared (2D-IR) spectroscopy is shown to be a powerful complement to the existing techniques for structure determination in solution. 2D-IR spectroscopy uses a femtosecond laser setup to investigate interactions between vibrations - analogous to 2D-NMR, which investigates the interactions between spins. Its ultrafast time resolution makes 2D-IR spectroscopy particularly well suited for the two topics investigated in this thesis: Structure Determination of Reactive Intermediates and Conformational Dynamics of Proteins.
Structure Determination of Reactive Intermediates: The focus of this thesis is using polarization-dependent 2D-IR (P2D-IR) spectroscopy for structure determination of N-crotonyloxazolidinone (referred to as 1), a small organic compound with a chiral oxazolidinone, known as Evans auxiliary, and its reactive complexes with the Lewis acids SnCl4 and Mg(ClO4)2. Chiral oxazolidinones in combination with Lewis acids have frequently been used in stereoselective synthesis for over 30 years. Nevertheless, the detailed mechanisms are in many cases xvi ABSTRACT still mere hypotheses and have not yet been experimentally proven. By accurately measuring the angles between the transition dipole moments in the molecules using an optimized P2D-IR setup and comparing the results to DFT calculations, the conformation of 1 and the conformation and coordination of the main complexes with SnCl4 and Mg(ClO4)2 are unequivocally identified and analyzed in depth. Structural details, such as a slight twist in the solution structure of 1, are detected using P2D-IR spectroscopy; these cannot be inferred from NMR spectroscopy or DFT calculations. In addition to the main Lewis acid complexes, complexes in low concentration are detected and tentatively assigned to different conformations and complexation geometries. The knowledge of those structures is essential for rationalizing the observed stereoselectivities. Additionally, a method is introduced that enables structure determination of molecules in complex mixtures and even in the presence of molecules with similar spectral properties and in high concentration. This work sets the stage for future studies of other substrate-catalyst complexes and reaction intermediates for which the structure determination has not been possible to date.
Conformational Dynamics of Proteins: Exchange 2D-IR spectroscopy allows the investigation of fast dynamics without disturbing the equilibrium of the exchanging species. It is therefore well suited to investigate fast dynamics of proteins and to reveal the speed limit of those. The temperature dependence of the conformational dynamics between the myoglobin substates A1 and A3 in equilibrium is analyzed. The various substates of myoglobin can be detected with FTIR spectroscopy, if carbon monoxide is bound to the heme. From previous studies it is known that the exchange rates at room temperature are in the picosecond time range, well suited to be investigated by 2D-IR spectroscopy. In the temperature range between 0 °C and 40 °C only a weak temperature dependence of the exchange rate in the myoglobin mutant L29I is observed in the present study. The exchange rate approximately doubles from 15 ns-1 at 0 °C to 31 ns-1 at 40 °C. It turned out that the conformational dynamics correlates linearly with the solvent viscosity, which itself is temperature dependent. Comparing our results to measurements at cryogenic temperatures, the linear relation between exchange time constant for this process and the viscosity is shown for the temperature range between -100 °C and 40 °C (corresponding to a viscosity change of 14 orders of magnitude). Thus, it is proven that the dynamics of the conformational switching are mainly determined by solvent dynamics, i.e., the protein dynamics are slaved to the solvent dynamics. This is the first time slaving is observed for such fast processes (in the picosecond time range). The observation implies a long-range structural rearrangement between the myoglobin substates A1 and A3. In addition, the exchange for other mutants and wild type myoglobin is analyzed qualitatively and found to agree with the conclusions drawn from L29I myoglobin.
Savanna regions in West Africa are valuable cultural landscapes and provide a wide range of ecosystem services for human well-being and are frequently affected by human-induced disturbances. Aside from agricultural activities (crop production and animal husbandry), the harvesting of timber and non-timber forest products is crucial for household income, alimentation and medicinal purposes. Most indigenous woody species have undergone increasing anthropogenic pressure as social and economic conditions have changed dramatically during recent decades, resulting in further habitat fragmentation and increased disturbance severity. Human land use activities influence growth conditions for plants by altering various abiotic factors, such as light, nutrient availability and water supply. They are found to alter demographic parameters (e.g., germination, seedling and sapling growth, survival and mortality rates) of woody plant individuals and alter the structure and stability of populations. The degree of anthropogenic disturbance varies between land-cover types, distance to settlements, and protection status. In the context of land-use change, there is an urgent need to better understand and evaluate the impact of land-use on savanna vegetation, particularly on the population biology of common savanna woody species. A major conclusion to be drawn from this thesis is that land use influences savanna vegetation in a complex way and does not necessarily lead to a decline or loss of tree populations and species. It is rather that in a constantly changing landscape, as a result of human-induced disturbances, populations of ubiquitous and some common species can be stable over time. The abundance of some species tends to decline consistently, whereas others benefit from human disturbance. Moreover, the study provides an insight into the structure and dynamics of common, dominant and less dominant savanna woody plants in a communal and a protected area. There is a need for further basic studies to assess the impact of land use and ecological preferences of all species, including repeated density studies that look at survivorship and transition probabilities over a number of seasons as well as longterm in-situ experiments in settlement areas in order to better understand woody plant populations in settlement areas as the few remaining semi-natural sites are likely to decrease in the future. A challenge will be the development of strategies to protect species within a landscape under cultivation.
An exciting in vivo function of ATP-sensitive potassium channels in substantia nigra dopamine neurons Ð Implications for burst firing and novelty coding ÐPhasic burst activity is a key feature of dopamine (DA) midbrain neurons. This particular pattern of excitation of DA neurons occurs via a synaptically triggered transition from low-frequency background spiking to transient high-frequency discharges. Burst-firing mediated phasic DA release is critical for flexible switching of behavioural strategies in response to unexpected rewards, novelty and other salient stimuli. However, the cellular and molecular bases of burst signalling in distinct DA subpopulations of the substantia nigra (SN) or the ventral tegmental area (VTA) are unknown.
DA neuron excitability is controlled by synaptic network inputs, neurotransmitter receptors and ion channels, which generate action potentials and determine frequency and pattern of electrical activity in a complex interplay. ATP-sensitive potassium (K-ATP) channels are widely expressed throughout the brain, where in most cases they are believed to act as metabolically-controlled 'excitation brakes' by matching excitability to cellular energy states. However, their precise physiological in vivo function in DA neurons remains elusive.
To study burst firing and the underlying ionic mechanisms with single cell resolution, in vivo single-unit recordings were combined with juxtacellular neurobiotin labelling as well as immunohistochemical and anatomical identification of individual DA neurons. In vivo recordings were performed in adult isoflurane-anaesthetised wildtype (WT) and global K-ATP channel knockout mice, lacking the pore forming Kir6.2 subunit (Kir6.2-/-). In addition, DA cell-selective functional silencing of K-ATP channel activity in vivo was established using virus-mediated expression of dominant-negative Kir6.2 subunits. Careful control experiments ruled out any significant contributions from nonDA neurons as transduction was effectively limited to SN DA neurons rather than affecting those cells that innervate them. Virus-based K-ATP channel silencing in combination with juxtacellular recording and labelling was achieved to define the electrophysiological phenotype of individually identified, virally-transduced DA neurons in vivo.
Single-unit recordings revealed that K-ATP channels Ð in contrast to their conventional hyperpolarising role Ð in a subpopulation of DA neurons located in the medial SN (m-SN) act as cell-type selective gates for excitatory burst firing in vivo. The percentage of spikes in bursts was threefold reduced in Kir6.2-/- compared to WT mice. Classification of firing patterns based on visual inspection of autocorrelation histograms and on a newly developed spike-train-model confirmed the dramatic shift from phasic burst to tonic single-spike oscillatory firing in Kir6.2-/-. This significant decrease of burstiness was selective for m-SN DA neurons and was not exhibited by DA cells in the lateral SN or VTA. Virus-based K-ATP channel silencing in vivo unequivocally demonstrated that the activity of postsynaptic K-ATP channels was sufficient to disrupt bursting in m-SN DA neuron subtypes. Patch-clamp recordings in brain slices indicated an essential role of K-ATP channels for NMDA-mediated in vitro bursting. In accordance with previous studies in DA midbrain neurons, NMDA receptor stimulation triggered burst-like firing in m-SN DA cells in vitro, but only when K-ATP channels were co-activated in these neurons.
K-ATP channel-gated burst firing in m-SN DA neurons might be functionally relevant in awake, freely moving mice. To explore the behavioural consequences of SN DA neuron subtype-selective K-ATP channel suppression, spontaneous open field (OF) behaviour of mice with bilateral K-ATP silencing across the whole SN (medial + lateral) or in only the lateral SN was tested. Analysis of WT and global Kir6.2-/- mice showed reduced exploratory locomotor activity of Kir6.2-/- in a novel OF environment. Remarkably, K-ATP channel silencing in m-SN DA neurons phenocopied this novelty-exploration deficit, indicating that K-ATP channel-gated burst firing in medial but not lateral SN DA neurons is crucial for WT-like novelty-dependent exploratory behaviour.
In summary, a novel role of K-ATP channels in promoting the excitatory switch from tonic to phasic firing in vivo in a cell-type specific manner was discovered. The present PhD thesis provides several important insights into the pivotal function of K-ATP channels in medial SN DA cells, which project to the dorsomedial striatum, for burst firing and its important consequences for context-dependent exploratory behaviour.
In collaboration with two other research groups transcriptional up-regulation of K-ATP channel and NMDA receptor subunits and high levels of in vivo burst firing were detected in surviving SN DA neurons from Parkinson's disease (PD) patients Ð providing a potential link of K-ATP channel activity to neurodegenerative pathomechanisms of PD. Using high-resolution fMRI imaging another study in humans has recently identified distinct DA midbrain regions that are preferentially activated by either reward or novelty. Taken together, these human data and the results of the present PhD thesis suggest that burst-gating K-ATP channel function in SN DA neurons impacts on phenotypes in disease as well as in health.
The role of the Ca2+-dependent protease calpain in the diabetes-associated platelet hyperreactivity
(2012)
Platelets from diabetic patients are characterised by hyperreactivity resulting in exaggerated adhesion, aggregation and thrombus formation which contribute to the development of cardiovascular complications known to be one of the main causes of diabetes-related mortality. One of the mechanisms suggested to be involved in the diabetes-related platelet hyperactivation is the increased [Ca2+]i which leads to the overactivation of Ca2+-dependent proteases, the calpains. Among the calpain isoforms expressed in platelets the two ubquitiously expressed μ- and m-calpain are thought to play an important role in physiological and pathophysiological processes. Particularly μ-calpain is known to be involved in many steps of physiological platelet activation such as aggregation, adhesion, secretion, and signalling. However, we could show that diabetes was associated with an enhanced activation of both μ- and m-calpain in platelets
In the first part of the study we focussed on the characterization of the molecular mechanism regulating calpain activity. Indeed, although Ca2+ is considered to be the main regulator of the proteolytic activity of the conventional calpains, other mechanisms such as the presence of phospholipids and phosphorylation have been reported to affect their activity. Since most studies reported the phosphorylation of m-calpain we were interested to see whether μ-calpain activity might be also affected by phosphorylation. We could show that the activity of μ-calpain was enhanced by the PKC activator PMA suggesting its possible regulation by phosphorylation. However, whether PKC directly targeted μ-calpain remains unclear. Given that substrate recognition is important for a protease to process its substrate and since no common consensus could be attributed to calpain substrates, our next interest was to understand the mechanism regulating the recognition of its substrates by calpain. Since phosphorylation has been reported to protect different proteins from calpain degradation we investigated whether the calpain substrate CD31 could be phosphorylated in platelets and whether this could affect its recognition by calpain. Although we could show that the tyrosine phosphorylation of CD31 was increased after activation of platelets by thrombin and that this effect was attenuated in platelets from diabetic patients, tyrosine phosphorylation of CD31 seemed to have no effect on its sensitivity to calpain-mediated proteolysis.
After the analysis of the mechanism regulating calpain activity as well as its interaction with its substrates, our next interest was the identification of new calpain substrates in platelets. Since a previous study from our group showed that PPARγ agonists could indirectly reverse the diabetes-associated calpain activation we performed DIGE analysis of platelet samples from diabetic patients before and after PPARγ agonist treatment. Using this approach we could identify four novel calpain substrates in platelets: Integrin-linked kinase (ILK), α parvin, CLP36 and septin-5. Next, we assessed the effect of calpain-mediated cleavage on the function of these newly identified proteins. We could show that μ-calpain was essential for the dissociation of ILK from the IPP complex and its activation while m-calpain-mediated cleavage led to its cleavage and inactivation. Functionally, we also showed that μ-calpain was involved in platelet adhesion while m-calpain was important for spreading.
The next protein we analysed was septin-5, a small GTPase known to regulate platelet degranulation by association with other septins and syntaxin-4. We found that the interaction between septin-5 and syntaxin-4 was inhibitory for platelet degranulation. We could demonstrate that the μ-calpain-mediated cleavage dissociated septin-5 from syntaxin 4 and led to increased secretion of platelet α-granules. Next, we investigated the in vivo role of calpain in the diabetes-associated platelet hyperreactivity. We induced diabetes in mice and could reproduce calpain activation in platelets such as that found in human. Indeed, calpain activation in murine platelets also led to the cleavage of several calpain substrates including ILK and septin-5. Moreover, platelets from diabetic mice demonstrated an increased aggregation and thrombus formation in vivo. Treatment of the animals with the calpain inhibitor A-705253 (30 mg/kg/day for 10 days) significantly restored platelet function and substrate cleavage. In conclusion, in this part of the study, we could show that the increased calpain-dependent α-granule secretion and platelet adhesion may account for the enhanced vascular proliferation and thrombus formation in diabetes and calpain inhibition represents a promising way to prevent atherothrombosis development.
In the last part of the study we analysed another enzyme known to play a crucial role in diabetes, the AMPK which is an energy-sensing kinase known to be impaired in diabetes. We could show that the two catalytic subunits AMPK α1 and α2 are expressed in platelets. The AMPKα2 seemed to be the subunit involved in platelet activation since AMPKα2-deficient mice demonstrated a defect in clot retraction and the stabilization of the thrombus while the animals showed a normal bleeding time. Mechanistically, we showed in platelets that the upstream kinase of AMPKα2 is LKB1 which was activated by thrombin stimulation via a PI-3K-dependent pathway. AMPKα2 then phosphorylated the Src-family kinase Fyn, which is responsible for the phosphorylation of its substrate β3 integrin on Tyr747. These data indicate that AMPKα2, by affecting Fyn phosphorylation and activity, plays a key role in platelet αIIbβ3 integrin signalling, leading to clot retraction and thrombus stability. Although the effect of diabetes in the AMPK-dependent pathway could not be investigated we assume that the dysregulation of this pathway may account for the thrombus destabilization and enhanced embolization encountered in diabetes.
In this thesis, various aspects on the theoretical description of ultracold bosonic atoms in optical lattices are investigated. After giving a brief introduction to the fundamental concepts of BECs, atomic physics, interatomic interactions and experimental procedures in chapter (1), we derive the Bose-Hubbard model from first principles in chapter (2). In this chapter, we also introduce and discuss a technique to efficiently determine Wannier states, which, in contrast to current techniques, can also be extended to inhomogeneous systems. This technique is later extended to higher dimensional, non-separable lattices in chapter (5). The many-body physics and phases of the Bose-Hubbard is shortly presented in chapter (3) in conjunction with Gutzwiller mean-field theory, and the recently devised projection operator approach. We then return to the derivation of an improved microscopic many-body Hamiltonian, which contains higher band contributions in the presence of interactions in chapter (4). We then move on to many-particle theory. To demonstrate the conceptual relations required in the following chapter, we derive Bogoliubov theory in chapter (5.3.4) in three different ways and discuss the connections. Furthermore, this derivation goes beyond the usual version discussed in most textbooks and papers, as it accounts for the fact, that the quasi-particle Hamiltonian is not diagonalizable in the condensate and the eigenvectors have to be completed by additional vectors to form a basis. This leads to a qualitatively different quasi-particle Hamiltonian and more intricate transformation relations as a result. In the following two chapters (7, 8), we derive an extended quasi-particle theory, which goes beyond Bogoliubov theory and is not restricted to weak interactions or a large condensate fraction. This quasi-particle theory naturally contains additional modes, such as the amplitude mode in the strongly interacting condensate. Bragg spectroscopy, a momentum-resolved spectroscopic technique, is introduced and used for the first experimental detection of the amplitude mode at finite quasi-momentum in chapter (9). The closely related lattice modulation spectroscopy is discussed in chapter (10). The results of a time-dependent simulation agree with experimental data, suggesting that also the amplitude mode, and not the sound mode, was probed in these experiments. In chapter (11) the dynamics of strongly interacting bosons far from equilibrium in inhomogeneous potentials is explored. We introduce a procedure that, in conjunction with the collapse and revival of the condensate, can be used to create exotic condensates, while particularly focusing on the case of a quadratic trapping potential. Finally, in chapter (12), we turn towards the physics of disordered systems derive and discuss in detail the stochastic mean-field theory for the disordered Bose-Hubbard model.
The ongoing debate on deforestation in the tropics usually points out agriculture and logging as the main causes. The two activities are often linked and the trails created by logging com-panies with their heavy machines are afterwards used by farmers to penetrate deep into the forest and cultivate. Shifting cultivation is a widespread agricultural practice in the tropics and its sustainability is often a matter of controversy. It is necessary to investigate forest recovery after shifting cultivation, analyze its succession stages for comparison with regeneration after natural disturbance, and evaluate its role for discussing the hazards of deforestation.
The study of systems whose properties are governed by electronic correlations is a corner stone of modern solid-state physics. Often, such systems feature unique and distinct properties like Mott metal-insulator transitions, rich phase diagrams, and high sensitivity to subtle changes in the applied conditions. Whereas the standard approach to electronic structure calculations, density functional theory (DFT), is able to address the complexity of real-world materials but is known to have serious limitations in the description of correlations, the dynamical mean-field theory (DMFT) has become an established method for the treatment of correlated fermions, first on the level of minimal models and later in combination with DFT, termed LDA+DMFT.
This thesis presents theoretical calculations on different materials exhibiting correlated physics, where we aim at covering a range in terms of systems --from rather weakly correlated to strongy correlated-- as well as in terms of methods, from DFT calculations to combined LDA+DMFT calculations. We begin with a study on a selection of iron pnictides, a recently discovered family of high-temperature superconductors with varying degree of correlation strength, and show that their magnetic and optical properties can be assessed to some degree within DFT, despite the correlated nature of these systems. Next, extending our analysis to the inclusion of correlations in the framework of LDA+DMFT, we discuss the electronic structure of the iron pnictide LiFeAs which we find to be well described by Fermi liquid theory with regard to many of its properties, yet we see distinct changes in its Fermi surface upon inclusion of correlations. We continue the study of low-energy properties and specifically Fermi surfaces on two more iron pnictides, LaFePO and LiFeP, and predict a topology change of their Fermi surfaces due to the effect of correlations, with possible implications for their superconducting properties. In our last study, we close the circle by presenting LDA+DMFT calculations on an organic molecular crystal on the verge of a Mott metal-insulator transition; there, we find the spectral and optical properties to display signatures of strong electronic correlations beyond Fermi liquid theory.
With the increasing energies and intensities of heavy-ion accelerator facilities, the problem of an excessive activation of the accelerator components caused by beam losses becomes more and more important. Numerical experiments using Monte Carlo transport codes are performed in order to assess the levels of activation. The heavy-ion versions of the codes were released approximately a decade ago, therefore the verification is needed to be sure that they give reasonable results. Present work is focused on obtaining the experimental data on activation of the targets by heavy-ion beams. Several experiments were performed at GSI Helmholtzzentrum für Schwerionenforschung. The interaction of nitrogen, argon and uranium beams with aluminum targets, as well as interaction of nitrogen and argon beams with copper targets was studied. After the irradiation of the targets by different ion beams from the SIS18 synchrotron at GSI, the γ-spectroscopy analysis was done: the γ-spectra of the residual activity were measured, the radioactive nuclides were identified, their amount and depth distribution were detected. The obtained experimental results were compared with the results of the Monte Carlo simulations using FLUKA, MARS and SHIELD. The discrepancies and agreements between experiment and simulations are pointed out. The origin of discrepancies is discussed. Obtained results allow for a better verification of the Monte Carlo transport codes, and also provide information for their further development. The necessity of the activation studies for accelerator applications is discussed. The limits of applicability of the heavy-ion beam-loss criteria were studied using the FLUKA code. FLUKA-simulations were done to determine the most preferable from the radiation protection point of view materials for use in accelerator components.
In dieser Arbeit werden Schmelz- und Anreicherungsprozesse des Erdmantels, sowie Kristallisationsereignisse der Erdkruste zweier ausgewählter Gebiete in Namibia und Spanien mithilfe geochemischer Methoden rekonstruiert und in einen zeitlichen Zusammenhang gebracht. Ein Vergleich der gewonnenen Ergebnisse beider Kompartimente soll dabei weitere Informationen liefern inwieweit Prozesse des Erdmantels und der Erdkruste miteinander verknüpft waren. Insbesondere soll ein weitere Beitrag zur aktuellen Diskussion geliefert werden, bei der sich das sogenannte „pulsed growth“ und „steady accumulation“ Modell gegenüberstehen (siehe Zusammenstellung Pearson et al., 2007). Zudem tragen die neu gewonnenen Daten dazu bei, die regionalen geologischen Gegebenheiten im besonderen Hinblick auf die geotektonische Geschichte besser zu verstehen.
Das Gibeon Kimberlit Feld befindet sich in der tektonischen Einheit des Rehoboth Terranes in Namibia und ist gekennzeichnet von Vulkanismus vor etwa 72.5 Ma (Davies et al., 2001), der Granat Peridotite und krustale Xenolithe mit an die Oberfläche beförderte. Eine klare Einordnung des Rehoboth Terranes in die Gesamtheit des Süd Afrikanischen Plattenverbunds ist noch nicht vollständig geklärt.
Die Südöstliche vulkanische Provinz in Spanien (SEVP) mit besonderem Hinblick auf die Region um Casas de Tallante stellt das zweite Probengebiet für diese Arbeit dar. Vor etwa 2.6 Ma (Bellon et al., 1983) kam es zur Extrusion von alkali-basaltischen Schmelzen, die zahlreiche Spinell / Plagioklas Peridotite mit sich brachten. Tufflagen, sowie die Matrix der Basalte ermöglichen einen Einblick in die untere Kruste der Region.
Untersuchungen der Erdmantelproben aus Namibia auf ihre Haupt- und Spurenelementchemie, sowie Lu-Hf und Sm-Nd Isotopie zeigten, dass zwei verschiedene Manteltypen vorliegen („N“ und „σ“ Typ), die zu einem Zeitpunkt um etwa 850 Ma („N“) und 1.9 Ga („σ“) angereichert wurden. Eine letzte Anreicherung beider Typen fand vermutlich während der Pan–Afrikanischen Orogenese um etwa 450 Ma statt. Die Reinterpretation eines zuvor publizierten Datensatzes (Pearson et al., 2004), suggeriert, dass es zu einer ersten Verarmung der σ Peridotite um etwa 2.9 Ga kam.
Untersuchungen der U-Pb und Hf Isotopie an Zirkonen aus der unteren Kruste des Probengebiets in Namibia ergaben, dass es zur Bildung von juvenilem Krustenmaterial vermutlich bereits im Archaikum kam (wie bereits vorgeschlagen durch z.B. Hoal et al., 1995; Franz et al., 1996), sowie in den Zeiträumen von 2.3 bis 2.7 und 1.5 bis 1.6 Ga, mit jeweils anschließendem krustalem Recycling und Krustenmischung. Eine Übereinstimmung von Mantel- und Krustenevents konnte für die Zeiträume von etwa 1.8, 0.8 - 0.9 Ga und 0.4 – 0.5 Ga gefunden werden. Eine mögliche erste Verarmung des σ Mantels wird bestätigt durch Zirkonalter im Bereich von 2.7 bis 2.9 Ga.
Die Analyse ausgewählter Spinell / Plagioklas Peridotite aus der SEVP, ergaben, dass ein heterogener Mantel mit mindestens 3 verschiedenen Typen vorliegt. Eine Korrelation der Lu-Hf Isotopie von 3 Proben dieses Probensatzes, sowie den Hf Isotopien einer weiteren Probe von Bianchini et al. (2011) suggerieren, dass es eventuell zu einem Verarmungsereignis zu einem Zeitpunkt von etwa 550 Ma kam. Sr Isotopien von Klinopyroxenen und Plagioklasen im Vergleich ergaben, dass die Sr Isotopie der Plagioklase, im Gegensatz zu den Klinopyroxenen, von denen der Alkali Basalte überprägt wurden.
Zirkonanalysen aus Lokalitäten innerhalb der SEVP (U-Pb, Hf) ergaben ein weitreichendes Altersspektrum, beginnend bei etwa 2-3 Ma bis hin ins Archaikum (2.7 bis 2.9 Ga) mit Provenance Ursprung aus Gondwana und dem Arabisch-Nubischen Schild. Die Kombination der U-Pb Altersinformationen mit den entsprechenden Hf Isotopien, zeigten, dass es vermutlich bereits im Archaikum zu juveniler Krustenbildung kam. Zirkone > 100 µm datieren den Zeitpunkt der Eruption der Alkali Basalte mit Altern um etwa 2.6 Ma und Hf Isotopien, die einem leicht verarmten Mantel entsprechen. Ein mögliches Verarmungsereignis im Erdmantel zu einem Zeitpunkt von etwa 550 Ma, ist im Einklang mit Krustenrecycling zu selbigem Zeitpunkt.
Die neugewonnenen Daten dieser Arbeit unterstützten das „pulsed growth“ Modell.
Literatur
Bellon, H., Bordet, P. and Montenat, C., 1983. Chronology of the Neogene Magmatism from Betic Ranges (Southern Spain). Bulletin De La Societe Geologique De France, 25(2): 205-217.
Bianchini, G., Beccaluva, L., Nowell, G.M., Pearson, D.G. and Siena, F., 2011. Mantle xenoliths from Tallante (Betic Cordillera): Insights into the multi-stage evolution of the south Iberian lithosphere. Lithos, 124(3-4): 308-318.
Davies, G.R., Spriggs, A.J. and Nixon, P.H., 2001. A non-cognate origin for the Gibeon kimberlite megacryst suite, Namibia: Implications for the origin of Namibian kimberlites. Journal of Petrology, 42(1): 159-172.
Franz, L., Brey, G.P. and Okrusch, M., 1996b. Steady state geotherm, thermal disturbances, and tectonic development of the lower lithosphere underneath the Gibeon Kimberlite Province, Namibia. Contributions to Mineralogy and Petrology, 126(1-2): 181-198.
Hoal, B.G., Hoal, K.E.O., Boyd, F.R. and Pearson, D.G., 1995. Age constraints on crustal and mantle lithosphere beneath the Gibeon kimberlite field, Namibia. South African Journal of Geology, 98(2): 112-118.
Pearson, D.G., Irvine, G.J., Ionov, D.A., Boyd, F.R. and Dreibus, G.E., 2004. Re-Os isotope systematics and platinum group element fractionation during mantle melt extraction: a study of massif and xenolith peridotite suites. Chemical Geology, 208(1-4): 29-59.
Pearson, D.G., Parman, S.W. and Nowell, G.M., 2007. A link between large mantle melting events and continent growth seen in osmium isotopes. Nature, 449(7159): 202-205.
Die Wechselwirkung zwischen zwei verschiedenartigen Wellenphänomenen in einer Höhe von ca. 10 bis 100 km, der mittleren Atmosphäre, ist das zentrale Thema der vorliegenden Arbeit. Schwerewellen entstehen durch Oszillationen der Luft in einer stabil geschichteten Atmosphäre. Durch die Vielzahl von Schwerewellen-Paketen, die in der Troposphäre durch Gebirge, Gewitter, Fronten und andere dynamische Prozesse angeregt werden, wird Energie und Impuls in die mittleren Atmosphäre transportiert. Durch den turbulenten Zerfall von brechenden Schwerewellen wird auf die mittlere Strömung eine Kraft ausgeübt, welche im Bereich der Mesopause bei ca. 90 km maximal wird. Daraus resultiert die sogenannte interhemispherische residuelle Zirkulation, die in der Mesosphäre den Sommer- mit dem Winterpol verbindet und die beeindruckend kalte Sommer-Mesopause mit Temperaturen von unter −140°C verursacht. Thermische Gezeiten sind ein weiterer wichtiger Teil in der Dynamik der mittleren Atmosphäre. Sie werden durch die Erwärmung der Tagseite der Erde angeregt und sind globale Schwingungen mit Perioden von 24 Stunden und harmonischen Vielfachen. Mit Wind- und Temperatur-Amplituden von bis zu 50 m/s und 30 K dominieren sie die Tagesvariabilität im Mesopausen-Bereich.
In der Mesosphäre wird die Wechselwirkung zwischen Schwerewellen und thermischen Gezeiten wichtig. Dort wird durch die Gezeitenwinde das Brechen von Schwerewellen zeitlich moduliert und eine periodische Kraft erzeugt, welche auf die Gezeiten rückwirkt. Doch selbst unter Zuhilfenahme modernster Hochleistungsrechner kann in komplexen Zirkulationsmodellen nur ein Bruchteil des turbulenten sowie des Wellen-Spektrums aufgelöst werden. Der Effekt der nichtaufgelösten Skalen, wie Turbulenz und Schwerewellen, muss somit in effizienter Weise parametrisiert werden. Üblicherweise wird in Schwerewellen-Parametrisierungen die horizontale und zeitliche Variation des Hintergrundmediums vernachlässigt. Es entsteht eine vertikale Säule, in der sich stationäre Schwerewellen-Züge instantan nach oben ausbreiten. Es ist jedoch äußerst fraglich, inwieweit eine solche Beschreibung, auf der ein Großteil früherer Untersuchungen basiert, für das Ergründen der Schwerewellen-Gezeiten-Wechselwirkung hinreicht. Für diese Arbeit wurde deswegen das Ziel gesetzt, die Defizite der konventionellen Beschreibung der Schwerewellen-Ausbreitung in realistischen Gezeiten zu quantifizieren.
Die "Ray Tracing"-Methode wird auf die Problemstellung der Schwerewellen-Gezeiten-Wechselwirkung angewendet. In der "Ray Tracing"-Methode werden Schwerewellen-Pakete entlang ihrer Ausbreitungspfade explizit verfolgt und Veränderungen der Schwerewellen-Eigenschaften durch den Einfluss der Hintergrundströmung berücksichtigt. Vom Autor wurde das globale "Ray Tracing"-Modell RAPAGI (RAy PArameterization of Gravity-wave Impacts) entwickelt und mit realistischen Gezeitenfeldern aus dem Zirkulationsmodell HAMMONIA (HAmburg MOdel of the Neutral and Ionized Atmosphere) betrieben. In verschiedenen "Ray Tracing"-Experimenten wird für ein einfaches Schwerewellen-Ensemble gezeigt, wie horizontale Gradienten des Hintergrundmediums sowie dessen Zeitabhängigkeit wesentlichen Einfluss auf die Ausbreitung und Dissipation von Schwerewellen nehmen. Zum einen führt die durch Gezeitenwellen hervorgerufene Transienz zu einer tageszeitlichen Modulation der absoluten Schwerewellen-Frequenz.
Die dadurch induzierten Variationen der horizontalen Phasengeschwindigkeit der Schwerewellen können die anfängliche Phasengeschwindigkeit um bis zu eine Größenordnung übertreffen und folgen dem Verlauf des Hintergrundwindes. Die kritische Filterung von Schwerewellen wird durch diese Modulation abgeschwächt, was im Vergleich zu konventionellen Schwerewellen-Parametrisierungen zu einer im Mittel um 30 % geringeren Kraftwirkung auf die Gezeiten führt. Zum anderen werden durch horizontale Gradienten in der gesamten Hintergrundströmung Schwerewellen-Pakete horizontal abgelenkt. Wellen, die gegen die Hintergrundströmung laufen, werden in der Stratosphäre in die Maxima der Wind-Jets hineingeführt. Durch dieses Verhalten wird analog zum Fermatschen Prinzip der geometrischen Optik die Laufzeit der Schwerewellen in der mittleren Atmosphäre minimiert. Es entsteht eine Fokussierung von Schwerewellen-Feldern, bei gleichzeitiger Zunahme der horizontalen Wellenzahl in den Experimenten im Mittel um ca. 10 %. Dadurch reduziert sich der Schwerewellen-Impulsfluss und die mittlere und ebenfalls die periodische Kraft auf die Hintergrundströmung im Mittel um weitere 20 % bis 30 %. Konventionelle Schwerewellen-Parametrisierungen scheinen somit die Kraftwirkung von brechenden Schwerewellen zu uberschätzen. Aus den Ergebnissen der Arbeit wird klar, dass Schwerewellen-Parametrisierungen nicht "blind" für jede Untersuchung genutzt werden können. Alle Annahmen und Näherungen in Parametrisierungen müssen je nach Zielstellung neu getestet werden.
There is increasing evidence that climate change will have a severe impact on species’ distributions by altering the climatic conditions within their present ranges. Especially species inhabiting stream ecosystems are expected to be strongly affected due to warming temperatures and changes in precipitation patterns. The aim of this thesis was to
investigate how distributions of aquatic insects, i.e., benthic stream macroinvertebrates would be impacted by warming climates. The methods comprised of an ensemble forecasting technique based on species distribution models (SDMs) and climate change scenarios of the Intergovernmental Panel on Climate Change of the year 2080. Future model projections were generated for a wide variety of species from a number of taxonomic orders for two spatial scales: a stream network within the lower mountain ranges of Germany, and the entire territory across Europe. In addition, the effect of the modelling technique on habitat suitability projections was investigated by modifying the choice of study area (continuous area vs. stream network) and the choice of predictors (standard vs. corrected set).
Projections of future habitat suitability showed that potential climate-change impacts would be dependent on species’ thermal preferences, and with a similar pattern for both spatial scales. Future habitat suitability was projected to remain for most or all of the modelled species, and species were projected to track their climatically suitable conditions by shifting uphill along the river continuum within the lower mountain ranges, and into a north-easterly direction across Europe. Cold-adapted headwater and high-latitude species were projected to lose suitable habitats, whereas gains would be expected for warm-adapted river and low-latitude species along the river continuum and across Europe, respectively. Additionally, habitat specialist species in terms of endemics of the Iberian Peninsula were identified as potential climate-change losers, highlighting their restricted habitat availability and therefore vulnerability to warming climates.
The main findings of this thesis underline the high susceptibility of stream macroinvertebrates to ongoing climate change, and give insights into patterns of possible consequences due to changes in species’ habitat suitability. Concerning the methodology, a clear recommendation can be given for future modelling approaches of stream macroinvertebrates by building models within a stream network and with a careful choice of environmental predictors, to reduce uncertainties and thus to improve model projections.
The tumor suppressor programmed cell death 4 (Pdcd4) exerts its function by inhibiting protein translation initiation. Specifically, it displaces the scaffold protein eukaryotic initiation factor 4G (eIF4G) from its binding to the eukaryotic initiation factor 4A (eIF4A). Thereby, Pdcd4 inhibits the helicase activity of eIF4A, which is necessary for the unwinding of highly structured 5’ untranslated regions (UTRs) of messenger RNAs (mRNAs) often found in oncogenes like c-myc to make them accessible for the translation machinery and subsequent protein production. Overexpression of Pdcd4 inhibits tumorigenesis in vitro and in vivo and inversely, Pdcd4 knockout mice show enhanced tumor formation. In line, Pdcd4 is lost in various tumor types and proposed as prognostic factor in colon carcinomas. Unlike most other tumor suppressors that are rendered nonfunctional by mutations (e.g., p53), Pdcd4 loss is not attributable to mutational inactivation. It is regulated via translational repression by microRNAs and increased degradation of the protein under tumor promoting, inflammatory conditions and mitogens. Specifically, proteasomal degradation of Pdcd4 is controlled by p70 S6 Kinase (p70S6K)-mediated phosphorylation in its degron sequence (serines 67, 71 and 76). Stimulation of the PI3K-AKT-mTOR pathway by growth factors, hormones and cytokines initiates p70S6K activity. Phosphorylated Pdcd4 is subsequently recognized by the E3 ubiquitin ligase beta-transducin repeats-containing protein (β-TrCP) and marked with a polyubiquitin tail to be detected by the 26S proteasome for degradation. β-TrCP represents the substrate specific recognition subunit of the ubiquitin ligase complex responsible for protein-protein interaction with Pdcd4 as substrate for ubiquitin transfer and subsequent proteasomal disassembly.
The first part of the present work aimed at identifying novel stabilizers of the tumor suppressor Pdcd4 in a high throughput screen (HTS). As assay design, a fragment of Pdcd4 from amino acid 39 to 91, containing the phosphorylation sensitive degron sequence, was fused to a luciferase reporter gene construct. Stable expression of this Pdcd4(39-91)luciferase (Pdcd4(39-91)luc) fusion protein in HEK 293 cells served as read-out for the Pdcd4 protein amount to be detected in a high throughput compatible cell-based assay. Loss of Pdcd4(39-91)luc was induced by treatment with 12-O-
tetradecanoylphorbol-13-acetate (TPA), a phorbolester, which activates the PI3K signaling cascade leading to degradation of Pdcd4. The cut-off for hit definition was set at >50% activity in rescuing the Pdcd4(39-91)luc signal from TPA-induced degradation. Activity was calculated relative to the difference of DMSO- and TPA-treated cells (ΔDMSO-TPA = RLUDMSO-RLUTPA). Initial screening of a protein kinase inhibitor library (PKI) revealed hit substances expected to show Pdcd4 stabilizing activity by inhibition of kinases involved in Pdcd4 downregulation, e.g., the mTOR inhibitor rapamycin, the PI3K inhibitors wortmannin and LY294002 and the PKC inhibitors GF 109203X and Ro 31-8220.
The Molecular Targets Laboratory (MTL) of the National Cancer Institute (NCI) in Frederick, USA, hosts one of the largest collections of crude natural product extracts as well as a big substance libraries from pure synthetic sources. Screening of over 15 000 pure compounds and over 135 000 natural product extracts identified 46 pure and 42 extract hits as Pdcd4 stabilizers. For nine synthetic and six natural product derived compounds (after bioassay-guided fractionation), dose-dependent activities for recovering the TPA-induced Pdcd4(39-91)luc loss defined IC50s in the low micromolar range. Most importantly, these compounds were confirmed to stabilize endogenous Pdcd4 protein levels from forced degradation as well. This result proved the assay design to be highly representative for endogenous cellular mechanisms regulating Pdcd4 protein stability. The next step was to stratify the hit substances according to their likely mechanism of action to be located either up- or downstream of the p70S6K-mediated phosphorylation of Pdcd4. Therefore, phosphorylation of S6, as proto-typical p70S6K target, was analyzed and uncovered two natural derived compounds to influence p70S6K activity. Four substances did not affect p70S6K phosphorylation activity and were therefore considered to stabilize Pdcd4 by acting downstream, i.e. on the β-TrCP-mediated proteasomal degradation.
In the second part of this work, one of these compounds, namely the sesquiterpene lactone erioflorin, isolated by bioassay-guided fraction from the active extract of Eriophyllum lanatum, Asteraceae, was further characterized in detail with respect to its molecular mechanism of action. Erioflorin dose-dependently protected both Pdcd4(39-91)luc and endogenous Pdcd4 protein from TPA-induced degradation with IC50s of 1.28 and 2.64 μM, respectively. Pdcd4 stabilizing activity was maximal at 5 μM erioflorin. Up to this concentration, erioflorin was verified not to inhibit p70S6K activity. In addition, it was observed that erioflorin rescued Pdcd4(39-91)luc from both, wild type and constitutively active p70S6K-mediated downregulation. Only wild type p70S6K was inhibitable by the mTOR inhibitor rapamycin which served as an upstream acting control. To study the next section of Pdcd4 regulation, i.e. recognition by the E3 ubiquitin ligase β-TrCP, Pdcd4(39-91)luc and endogenous Pdcd4 were immunoprecipitated from whole cell extracts with the corresponding antibodies. In this key experiment, treatment with TPA increased overexpressed β-TrCP binding to both and this coimmunoprecipitation could be strongly reduced by erioflorin treatment. This result strongly pointed to an inhibitory mechanism of the β-TrCP specific binding to Pdcd4 by erioflorin. In addition, erioflorin disrupted the binding of in vitro transcribed/translated β-TrCP to Pdcd4 in an in vitro interaction assay to exclude nonspecific intracellular signals. Furthermore, polyubiquitination of Pdcd4 was decreased by erioflorin treatment as well. To clarify questions regarding specificity of erioflorin for the E3 ubiquitin ligase β-TrCP, stability of another important β-TrCP target was explored, i.e. the tumor suppressor inhibitor of kappa B alpha (IκBα). Indeed, the tumor necrosis factor alpha (TNFα)-mediated loss of IκBα could be prevented by erioflorin cotreatment. On the other hand, the E3 ubiquitin ligase von Hippel Lindau protein (pVHL) was left unaffected as its target hypoxia inducible factor 1 alpha (HIF-1α) could not be stabilized from oxygen-dependent degradation by erioflorin treatment. These results argued strongly for erioflorin being a specific inhibitor of β-TrCP-mediated protein degradation. Functional consequences of erioflorin treatment were investigated by observing its influence on the transcriptional activities of the transformation marker activator protein 1 (AP-1, an indirect downstream target of Pdcd4) and nuclear factor κB (NF-κB which is directly inhibited by IκBα). Indeed, erioflorin showed significant inhibition of AP-1 and NF-κB reporter constructs at 5 μM, a concentration for which an impact on cell viability was excluded. Finally to characterize the significance of erioflorin in a cell-based tumorigenesis assay, the highly invasive colon carcinoma cell line RKO was tested in a two dimensional migration assay. Erioflorin was discovered to significantly lower cell migration in a wound closure assay.
In conclusion, development of a high throughput compatible cell-based reporter assay successfully identified novel substances from pure synthetic and natural product derived background as potent stabilizers of the tumor suppressor Pdcd4. In addition, this work aimed at elucidating the detailed mechanism of action of the sesquiterpene lactone erioflorin from Eriophyllum lanatum, Asteraceae. Erioflorin was discovered to inhibit the E3 ubiquitin ligase β-TrCP, thereby preventing protein degradation of tumor suppressors like Pdcd4 and IκBα. This may offer the possibility to more specifically target protein degradation and generate less adverse side effects by blocking a particular E3 ubiquitin ligase compared to general proteasome inhibition.
Identification of translationally deregulated proteins during inflammation-associated tumorigenesis
(2012)
The translation of mRNAs into proteins is an elaborate and highly regulated process. Translational regulation primarily takes place at the level of initiation. During initation the eukaryotic initiation factors (eIFs) form a complex that binds to the 5’end of the mRNA to scan for a start codon. Once recognized, the ribosome is recruited to the mRNA and protein synthesis starts. Initiation of translation can basically occur via two distinct mechanisms, i.e. cap-dependent and cap-independent that is mediated via internal ribosome entry sites (IRESs). The former is mediated by a 5’cap structure composed of a 7-methylguanylate which is added to every mRNA during transcription and recruits the initiation complex. IRES-dependent translation involves elements within the 5’untranslated region (UTR) of the mRNA that mostly bind IRES trans-acting factors (ITAFs) which associate either with the initiation complex or with the ribosome itself and consequently allow for internal initiation of translation.
During tumorigenesis the demand for proteins is increased due to rapid cell growth, which consequently requires enhanced translation. Many factors that regulate translation are overexpressed in tumors. Moreover, signaling pathways that trigger translation or further hyperactivated by the surrounding tumor microenvironment. This environment is largely generated by infiltration of immune cells such as macrophages that secrete cytokines and other mediators to promote tumorigenesis. As the effects of inflammatory conditions on the translation of specific targets are only poorly characterized, my study aimed at identifying translationally deregulated targets during inflammation-associated tumorigenesis.
For this purpose, I cocultured MCF7 breast tumor cells with conditioned medium of activated monocyte-derived U937 macrophages (CM). Polysome profiling and microarray analysis identified 42 targets to be regulated at the level of translation. The results were validated by quantitative PCR and one target - early growth response 2 (EGR2) - was chosen for in depth analysis of the mechanism leading to its enhanced translation.
In order to identify upstream signaling molecules causing enhanced EGR2 protein synthesis the cytokine profile of CM was analyzed and the impact of several cytokines on EGR2 translation was examined. Preincubation of CM with neutralizing antibodies revealed that lowering interleukin 6 (IL-6) had only little effect, whereas depletion of IL 1β significantly reduced EGR2 translation. This finding was corroborated by the fact that treatment with recombinant IL-1β enhanced EGR2 translation to virtually the same extend as CM. Further experiments revealed that this effect was mediated via the p38-MAPK signaling cascade.
Interestingly, I observed that the mTOR inhibitor rapamycin, which reduces cap-dependent translation, specifically stimulated EGR2 translation. This result argued for an IRES-dependent mechanism that might account for EGR2 translation. The use of bicistronic reporter assays verified this hypothesis. In line with the above mentioned results, CM, IL-1β and p38-MAPK induced EGR2-IRES activity.
Since IRESs commonly require ITAFs to mediate translation initiation, the binding of proteins to the 5’UTR was analyzed using mass spectrometry. Among others, several previously described ITAFs, such as polypyrimidine tract-binding protein (PTB) and heterogeneous nuclear ribonucleoprotein A1 (hnRNP-A1) were identified to directly bind to the EGR2-5’UTR. Furthermore, overexpression of hnRNP-A1 enhanced EGR2-IRES activity whereas a dominant negative form of hnRNP-A1 significantly decreased it, thus, showing its importance for EGR2 translation.
In summary, my data provide evidence that EGR2 expression can be controlled by IRES-dependent translational regulation, which is responsive to an inflammatory environment. The identified mechanism may not be exclusive for one target but might be representative for gene expression regulation mechanisms during tumorigenesis. This is of special interest for the treatment of cancer patients and development of more specific therapies to reduce tumor outcome.
Chemical contamination of the environment and thus of aquatic ecosystems is steadily increasing. Whenever environmental pollutants enter a water body, they affect not only the water, but also the sediment. Substances that bind to sediment particles can be stored for a long time, whereby sediments act as sinks for some contaminants. Therefore, sediment
assessments often more accurately describe the contamination of a water body than investigations of the water itself. Among environmental chemicals, endocrine disrupting compounds (EDCs) have gained more and more attention in recent years. Since they interfere with endocrine systems and may disturb reproduction, they endanger the survival of populations or even species. Hazardous substances enter the aquatic environment by different pathways, with sewage treatment plants (STPs) belonging to the most important contamination sources.The main objective of this work is a comprehensive sediment assessment of predominantly small surface waters in the German federal state of Hesse. The 50 study sites, located in 44 different creeks and small rivers, are situated in the densely populated and economically important Frankfurt/Rhine-Main area, as well as in rural and less urbanized regions.
Chemical analytical data, provided by the Hessian Agency for the Environment and Geology (HLUG), indicated different contamination levels of the study sites. In order to investigate the general toxicity of the sediment samples, the oligochaete Lumbriculus variegatus and the midge Chironomus riparius were exposed to whole sediments and apical endpoints regarding biomass, survival, and reproduction were determined. In further experiments, special attention was paid to the contamination with endocrine active compounds. For this purpose, the reproductive success of the New Zealand mudsnail Potamopyrgus antipodarum was analyzed after exposure to whole sediments. Additionally, a yeast-based reporter gene assay was applied with sediment eluates to assess the estrogenic and androgenic activity of the samples. Biotest results were compared with chemical analysis data to investigate whether the test organisms reflect the measured pollution of the study sites and if the observed effects can be explained by chemical contamination.
Five study sites, all located less than 1 km downstream of a STP discharger, were selected for further investigations based on the results of the sediment monitoring. The sediments from these sites were conspicuous due to their general toxic and/or estrogenic activity. In order to investigate whether the observed effects can be ascribed to the effluents, an active biomonitoring study was conducted with the mudsnail P. antipodarum and the zebra mussel Dreissena polymorpha, exposed at study sites located up- and downstream of the discharger.
In addition to endocrine activity, genotoxic effects were investigated using the comet assay and the micronucleus assay. Endocrine activity was examined based on the reproductive output of P. antipodarum and the content of vitellogenin-like proteins in D. polymorpha. Yeast-based reporter gene assays were used to estimate the endocrine potential (estrogen, anti-estrogen, anti-androgen, dioxin-like) of sediment and water samples.
22% of the 50 sediments showed ecologically relevant effects in the biotests with L. variegatus and C. riparius. Only one sediment caused a relevant effect on both test organisms, while the other ten positively tested sediments affected either L. variegatus or C. riparius, probably due to differences in inter-species sensitivities. This suggests that a combination of different biotests is necessary for a comprehensive evaluation of sediment toxicity. 78% of the sediments caused a significantly increased number of embryos in P. antipodarum, which could be ascribed to estrogenic contamination of the sediment samples. An increase in the number of embryos by 60%, as observed in this study, and an associated increase in population size may result in the displacement of other, less competitive species.
In the in vitro tests, 66% of the sediments showed estrogenic activity and 68% showed androgenic activity. Maximum observed values were 40.9 ng EEQ/kg sediment (EEQ = estradiol equivalent) for estrogenic and 93.4 ng TEQ/kg sediment (TEQ = testosterone equivalent) for androgenic activity. Natural and synthetic hormones as well as alkylphenols were the major contributors to the total estrogenicity of environmental samples in several other studies, and are likely responsible for a large part of the estrogenic activity in this case as well. Similarly, androgenic activity is mainly due to natural steroids and their metabolites.
Bioassay results reflect the analytically measured contamination levels at the study sites only very infrequently. This can be ascribed to the occurrence of integrated effects of chemical mixtures present in the sediments. Additionally, effects of substances not included in the analytical program or of substances present in concentrations below the detection limit of the chemical analytical investigations as well as varying bioavailabilities might be relevant. The fact that a large part of the observed effects cannot be explained by the chemical contamination demonstrates the need for effect studies in ecotoxicological sediment assessments.
In order to identify possible causes for the effects observed in the sediment monitoring, e.g. contamination sources, the area types (urban fabrics, arable lands, pasturages, etc.) of the catchment areas belonging to the study sites were analyzed. No significant differences were found between the area profiles of the sampling sites with and without effects in the biotests.
The results indicate that the contamination responsible for the observed effects can be ascribed to different sources. Furthermore, study sites whose sediments exerted significant effects in biotests were located in anthropogenic as well as in predominantly natural areas. The active biomonitoring study at STPs revealed genotoxic and endocrine effects only sporadically.
However, in the in vitro tests considerable endocrine activities of sediment and water samples were determined. No conclusive picture emerges as to whether the observed effects occur more frequently downstream of the dischargers, and thus could be attributed to a contamination by sewage. This indicates that contamination sources other than STP dischargers, for example agricultural runoff, may contribute to the observed effects. Weaker effects and biological activities downstream of a discharger compared to an upstream site might be ascribed to a dilution effect by the effluents. A comparison of the measured in vitro estrogenicity with exposure studies described in the literature shows that adverse effects in aquatic organisms can be expected at the EEQ concentrations determined in the present study.
The results of the sediment monitoring and the STP study revealed a widespread endocrine pollution of small surface waters in Hesse. The fact that the bioassay results only rarely reflect study site contamination as determined by chemical analysis demonstrates the need for effect studies in comprehensive sediment assessments. In some cases STP dischargers increased, in other cases they decreased the observed in vivo effects and in vitro activity of environmental samples. Transferring the results obtained in laboratory studies to the field, adverse effects on aquatic ecosystems can be expected. The study illustrates the need for restrictive measures that contribute to the removal or reduction of environmental pollutants.
For the identification of substances that have so far not been linked to adverse effects on the environment, methods such as effect-directed analyses (EDA) or toxicity identification evaluation (TIE) should be increasingly applied in future studies. Furthermore, bioassays for the assessment of endocrine activity should be implemented in standardized monitoring programs.
From the dawn of civilization, a multitude of religious has developed each very complex. These great differences among religions make it difficult to find a least common denominator or to talk at length of religion in general. On the other hand, focusing on just one specific religion often causes us to ignore or underestimate some of the very broad traits that religions seem to share. The fact remains that we will make no headway into the question of what makes a specific religion a religion if we do not seek some characteristics common to all religions.
Religion is usually associated with the supernatural or the divine.505 However, the notion of a supernatural realm does not occur in the non-theistic schools of Buddhism and functions in very different ways, say, in Taoism, Hinduism, and Islam. These shortcomings suggest that religion is notoriously difficult to define. To me, religion is any action taken through every aspect of our being to release us from our weakness or imperfection, and bring us closer to the divine reality. In other words, it is a human inner desire or activity to unite with an absolute being.
The examination of the intellectual dimension of religion that is, its key beliefs is most beneficial when it is guided and informed. Since epistemology is the theory of knowledge, one would therefore expect epistemological discussions of religion to concentrate on the question whether one could have knowledge of religious beliefs. Religious epistemology is simple to say that it is the epistemology of distinctively religious beliefs, but that will not be helpful in the absence of a definition of religious beliefs.
Philosophers of religion might consider the epistemology of religious belief, pondering questions about the sources and justifications of religious knowledge. Fundamental questions regarding the nature of knowledge are likely to arise in any culture. After all, everyone has some stake in distinguishing truth from error, wisdom from ignorance, and the path to knowledge from the path to ignorance. Epistemologists have discussed, in addition to the defining conditions and the sources of knowledge, the extent of human knowledge. They have asked how far human knowledge can extend. Many philosophers find it obvious that we know at least some things, if only things about personal experiences or household physical objects. Others have claimed, however, that we really have no knowledge. Such philosophers admit that people typically feel confident that they have some knowledge, but these philosophers insist that our apparent cases of knowledge are mere illusions. Many epistemologists aim not to set knowledge beyond our reach or to escape the quest for knowledge but rather to make many of our ordinary claims to knowledge more secure by explaining knowledge. They seek to explain what knowledge consists in and how we get it.506
Therefore, a good deal of the task of general epistemology is to understand the nature of the various truth-relevant merits which beliefs can possess, the necessary and sufficient conditions for beliefs to possess those merits, and the virtues of mind and practice requisite and apt for their presence merits such as being reliably formed, being warranted, being entitled, being scientific, being rational, being justified and indeed being true.
Epistemology in Western philosophical tradition has until recently offered a prominent definition of knowledge that analyzes knowledge into three essential components: justification, truth, and belief. According to this analysis, propositional knowledge is, by definition, justified true belief. Epistemologists typically focus on propositional knowledge. Knowledge that something is the case, as opposed to knowledge of how to do something. The content of propositional knowledge can be expressed in a proposition, that is, what is meant by a declarative sentence. Knowledge how to do something is by contrast, a skill or competence in performing a certain task. Within the last few decades, philosophers have discovers that these three conditions are not really sufficient for knowledge; something else is required. Genuine knowledge requires not only truth and belief, but also the satisfaction of the belief condition be appropriately related to the satisfaction of the truth condition. That is, on the traditional approach, genuine knowledge requires that a knower have an “adequate indication” that a believed proposition is true. The required “adequate indication”507 of truth, according to Plato, Kant, and many other philosophers, is evidence indicating that a proposition is true. These philosophers thus hold that knowledge must be based on evidence, or justifying reason.
The kind of justification crucial to knowledge is called epistemic justification. Even if knowledge requires justification, a justified belief can be false. In allowing for justified false beliefs, contemporary epistemologists endorse fallibilism about justification. Reformed epistemologists contend that belief in the existence of God can, in some circumstances, have an epistemic status high enough to render it worthy of acceptance even if it has no support from the arguments of natural theology or from any other beliefs. The views of Alston and Mavrodes are sometimes said to display an affinity with Reformed epistemology, and Nicholas Wolterstorff has made significant contributions to its development. But Plantinga has clearly been the leading contemporary advocate of this school of thought in religious epistemology. During the earlier phase of their development, Plantinga concentrated on defending the view that theistic belief can be in certain conditions, is justified or rationally held even in the absence of any propositional evidence or supporting argument.508
For the conviction that theistic belief is properly basic, foundationalists carry out a reconstructive project that would put our revised doxastic structures on foundations so firm that they could withstand rather than ignore skeptical challenges. That is, for the classical foundationlist theistic belief requires support from propositional evidence or argument if it is to be rationally or justifiably held. However, it is fairly clear that belief in God’s existence does not satisfy this criterion; it is neither self-evident nor incorrigible nor evident to the sense for humans at any time in this life.
The question of justification attracts philosophers especially in contemporary epistemology. And controversy of this question focuses on the meaning of ‘justification’ as well as on the substantive conditions of a belief’s being justified in a way appropriate to knowledge. William Alston, for instance, has introduced a non-deontological normative concept of justification that relies mainly on the notion of what is epistemically good from the view-point of maximizing truth and minimizing falsity. Alston link epistemic goodness to a belief’s being based on adequate grounds in the absence of overriding reason to the contrary. But for some epistemologists “Epistemic justification” means simply “evidential support” of certain sort.509 To say that s is epistemically justifiable to some extent for you is, on this view, just to say that s is supportable to some extent by your overall evidential reason. According to epistemologist, knowledge entails beliefs, so that I cannot know that such and such is the case unless I believe that such and such is the case.
Robert Audi mentioned that knowledge arises in experience. It is constituted by conclusively justified true belief, meaning that: the believer may be justified by psychological certain of the true proposition in question and this proposition is so well-grounded as to be itself propositionally certain. And knowledge constitute by such belief may be called epistemic certainty. When we come to religious knowledge, Audi says that religious propositions are simply beyond the scope of human knowledge. But the point is why would it be thought that no religious propositions are known? The most common ground for holding this view is namely, that religious propositions, such as that God exists, cannot be known either a priori or on the basis of experience. The concept of justification or evidence would occur with the concept of belief in a more complex analysis of the concept of knowledge.510
In recent decades, questions of knowledge seem to have been marginalized by question of justification. As a matter of fact, however, epistemological discussion of religious belief, at least since the Enlightenment has tended to focus, not on the question whether religious belief has warrant, but whether it is justified. More precisely, it has tended to focus on the question whether those properties are enjoyed by theistic belief - the belief that there exists a person like the God of traditional Christianity, Judaism, and Islam: an almighty, all knowing, wholly benevolent and loving spiritual person who has created the world. The main epistemological question about religious belief, therefore, has been the question whether or not religious belief in general and theistic belief in particular is rational or rationally acceptable, or whether it is justified?
In its primary sense, rationality is a normative concept that philosophers have generally tried to characterize in such a way that, for any action, belief, or desire, if it is rational we ought to choose it. Rationality is the use of reason to reach a certain level of reasonableness or unreasonableness. Many positive characterizations of rational beliefs have been proposed by beliefs that are either self-evident or derived from self-evident beliefs by a reliable procedure and beliefs that are consistent with the overwhelming majority of one’s beliefs.511 Analytic epistemology in the twentieth century was conducted as if there were a part from truth itself - just one truth-relevant merit in beliefs, that one typically called either “justification or rationality;”512 and since there was a great deal of disagreement on the answer to that question, there was a great flowering of theories of justification, or theories of rationality.
According to Nicholas Wolterstorff, there are a large number of distinct truth-relevant merits in beliefs, and that neither “Justification” nor “rationality”513 picks out single such merit, both are highly ambiguous terms, each picking out a number of distinct merits. Religious beliefs are formed or evoked by experience of some sort, or by believing what is said in some discourse, or by reflection on the implications of some complex of beliefs that one has previously acquired. Here, we notice that there are no rational activities to understand or justify the experience.
Richard Swinburne considered the nature of actual belief. He saw how in a sense all beliefs given rise to action and must be based on evidence. But he knows that not all beliefs are rational beliefs. For him a beliefs will fail to be rational if it is based on evidence in the wrong way or if it is based on the wrong sort of evidence. According to Swinburne beliefs are rational in so far as they are based on investigation which was, in the believer’s view, adequate, and if the believer believes it to be rational. Swinburne understand by religious beliefs as about transcendent reality, including his belief about whether or not there is a God, and his beliefs about what properties God has (what God is like) and what actions he has performed.514
According to John Hick, the issue is not whether it can be established as an item of indubitable public knowledge that God (or the divine or the Transcendent) exists, or most probably exists, but whether it is rational for those who experience some of life’s moments theistically to believe that God exists, and to proceed to conduct their lives on that basis. Hick looks at a rational belief in general way. For him “belief” can mean a proposition believed or it can be defined as an act or state of believing. The idea of evidence normally presupposes a gap between an observed fact, or body of facts, and an inferred conclusion. Therefore, our ordinary moment - to moment perceptual beliefs contradict the principle that all rational believing must be based upon adequate evidence. It is not that they are based upon inadequate evidence, but rather that the model of evidence-inference-belief does not apply here. Ordinary perceptual beliefs arise directly out of our experience, and it is entirely appropriate, proper, and rational to form these beliefs in this way. The relationship between experience and belief has been much debated in recent work in the philosophy of religion. This discussion has focused upon specifically theistic belief and Hick discusses also in these terms and his argument is that it is rational to believe in the reality of God.
Alvin Plantinga argues on these manifestation-experiences that they are properly basic.515 That is to say, it is as rational for religious persons to hold these basic religious beliefs as it is for all of us to hold our basic perceptual beliefs. But, more basically, it is the biblical assumption translated into philosophical terms. According to Plantinga this experience is what justifies me in holding (the belief) that is the ground of my justification, and by extension, the ground of the belief itself. He then applies this principle to religious beliefs.
In philosophy, experience is generally what we perceive by the senses what we learn from others, or whatever comes from external sources or from inner reflection. In the sense, experience is associated with observation and experiment. Empiricism stresses that our knowledge must be based on experience, but rationalism claims that experience is a potential source of error and prefers rational certainty to mere empirical generalization. In ordinary usage, for every experience there must be something experienced that is independent of the subject of experience. But in philosophy, the relation between experience as a state of consciousness and independent objects of experience becomes a focus of debate. There are many different kinds of experiences, but it is religious experiences that interest me here.
From the point of view of epistemology the modifications of consciousness consisting our apparently perceptual experience are of importantly different kinds. In addition to true perceptions there are misperceptions, illusions, and hallucinations. Therefore, if anyone misled by any of these forms of perceptual error, he or she is then deluded. In each case the delusion consists in a mistaken implicit belief about the cause of the experience: Applying this concept of delusion to the realm of religious experience, we have to ask whether those who assume that their experience of living in God’s presence is caused by their being in God’s presence are believing truly or are, on the contrary, under a delusion.
In modern philosophy of mind a major theme which bears on many theoretical issues, concerns the alleged privacy of an experience as an event knowable only to its possessor and the possibility of public access to that experience. There is much philosophical debate concerning precisely how perception is to be analyzed. In particular, questions are raised concerning the status of the phenomenon. But there is general agreement that in perception, objects present themselves to us in ways that enable us to know them. Similarly, in religious experience God presents himself in ways that enable us to know him and his actions. For Alston there are, it seems, important differences between ordinary perceptual or sense experience and religious experience. Sense perception is a common experience, whereas religious experience is less common, perhaps, even rare, sense perception yields a great deal of information about the world, whereas religious experience yields apparently little information about God, all humans have the capacity for sense perception, but many seem not to have the capacity for religious experience. These differences, however, do not show that religious experience has a structure unlike perception. For one thing, neither the frequency of an experience nor the amount of information it yields tells us anything about its structure.
On the other hand, the limitation of the rationalist way is that the only truths capable of being strictly proved are analytic and ultimately tautological. But we cannot by logic alone demonstrate any matter of fact and existence; these must be known through experience. For sure if nothing were given through experience in its various modes, we should never have anything to reason about. This is as true in religion as in other fields. If God exists, God is not an idea but a reality outside us, in order to be known to men and women, God must therefore become manifest in some way within their experience. This conclusion is in line with the contemporary revolt against the rationalist assumptions which have dominated much of western philosophy since the time of Descartes.516 Descartes held that we can properly be said to know only truths that are self-evident or that can be reached by logical inferences from self-evident premises.
Therefore, those who stress faith and attack reason often place a great deal of emphasis on religious experience. However, religious experience is by no means a purely emotional “happening”; rather, it involves concepts and beliefs about the being that is experienced. If we tried to separate religious experiences from such concepts and beliefs - from the religious belief-system, as we shall call it - then there would be no way saying who or what is that is experienced, or of explaining what sort of difference the experience ought to make to the person who has it. However, such a religious belief system needs to be understood; at least to some degree - it is hard to see how understanding it is not going to involve the use of reason.
For Rationalisms, in order for a religious belief-system to be properly and rationally accepted, it must be possible to prove that the belief-system is true. Rationalism in this sense implies a reliance on reason, or intelligence, in deciding our beliefs and actions. The central idea of strong rationalism was stated forcefully by W. K. Clifford. According to his opinion, no religious belief-system is capable of meeting the high standard of proof that should govern all of our believing, and so a reasonable (and moral) person must do without religious beliefs. Among the objections to Christian belief, as well as to Judaic and Muslim, Characteristic of the modern intelligentsia is the objection that it is no longer rational, if ever it was, to believe that God exists. Therefore, the rational person will have to make his way in the world without supposing that there exists any God in whom he could trust.517
However, according to Nicholas Wolterstorff, to believe in God is our fundamental human obligation. Central to Christianity, Judaism, and Islam alike is the conviction that we as human beings are called to believe in God to trust in him, to rely on him, to place our confidence in him. Central also is the conviction that only by believing in God can the deepest stirrings of the human heart be satisfied. Duty and fulfillment here coalesce. The rationality of trusting someone presupposes the rationality of believing that person exists.
John Locke was among the first to formulate articulately the evidentialist challenge to theistic belief. Reason is reasoning for Locke, and clearly he thinks of it as one among others of our belief-forming processes. Faith is another belief-forming process. It, by contrast, consists in accepting something “as coming from God.”518 However, for Locke it still belongs to reason to judge of the truth of its being a revelation, and of the signification of the words wherein it is delivered.
For evidentialist, one’s belief that God exists is rational only if it is formed or sustained by good inference by inferring it from others of one’s beliefs, which in fact provide adequate evidence for it. But, Wolterstorff, see no reason what so ever to suppose that by the criterion offered the evidentialist challenge is tenable. He see no reason to suppose that people who hold as one of their immediate beliefs that God exists always have adequate reason to surrender that belief or ought to believe that they do. However, for him those abstract and highly general theses of evidentialism no longer look very interesting, once we regard them in the light of the criterion offered. Therefore, for him the fact that it is not rational for some person to believe that God exists does not follow that he ought to give up that belief.
But can we accept the Principle of Credulity? One problem is that whereas there is a fundamental uniformity about the way we report both ordinary perceptual experiences and the beliefs about objects of those experiences, there is quite a diversity of reports about religious experiences and the claim based on them. Person give incompatible descriptions of the Reality experienced. Therefore, where perceptions yield conflicting testimony, we must turn to other experiences and rational arguments to determine the truth of the various claims. That is, where there are different accounts, additional considerations must be introduced to help decide which, if any, of the religious experiences are veridical. Although the reports provide a prima facie ground for their acceptance, not all beliefs based on such experiences are true. Just as we at times doubt perceptual claims for good reason, we might do the same for claims based on religious experience.
According to Hick, religion constitutes our varied human response to transcendent reality. Religious experience then is structured by religious beliefs which are implicit within religious experience. But the question is if this complex of experience and beliefs that takes place in different shapes within the different traditions, is to be regarded simply as a human creation or as our response to a transcendent reality, even if a response whose particular forms always involve the creative activity of the human imagination. Of course the problem of terminology is obvious as we see in many parts of philosophy, and without explanatory gloss none of the available descriptive labels for these two possibilities is entirely adequate.
Much of the philosophical discussion of religious diversity continues to centre on the work of John Hick.519 He is not interested in the question of what can justifiably be affirmed in the face of such diversity, rather, he is primarily concerned with the question of which justified response is most reasonable. Moreover, on this question, he leaves no doubt as to his opinion:
519 See John Hick, An Interpretation of Religion: Human response to the Transcendent, (New Haven: Yale University and London: Macmillan press, 1989), 172.
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religious pluralism is by far the most plausible explanation for the pervasive religious diversity we encounter.
Many Westerners will best understand the emergence of inclusivism and pluralism in terms of the history of Christianity. For most of its history, Christianity has been resolutely exclusivist. In late antiquity, it was a new religion, struggling to establish itself in the face of criticism and persecution. It is not surprising to find it making exclusive claims on behalf of its charismatic founder, Jesus of Nazareth. Of course, Christianity is not the only religion to have fostered exclusivist attitudes. In their more militant movements, Muslims have done the same. Some Jews cherish an ethnically exclusive identity as God’s chosen people, and some Hindus revere the Vedas as a source of absolute truth, Buddhists often see in the teachings of Gautama the only dharma that can liberate humans from illusion and suffering.
Hick has set forth a philosophically sophisticated pluralistic hypothesis that may avoid problems of this sort.520 As he sees it, each of the major religious traditions offers a path to salvation or liberation that involves a transformation of human existence from self-centeredness to reality- centeredness.
Religious plurality is simply a fact. There are religious traditions that differ deeply in terms of their doctrines, practices, institutions, scriptures, experiences, and hope. According to pluralism, a single ultimate religious reality is being differently experienced and understood in all the major religious traditions; they all, as far as the philosophers can tell, offer equally effective paths to salvation or liberation.
According to Harold Coward, Judaism is an appropriate tradition in which to begin the stay of religious pluralism and the world religions. The experience of being a minority group in other cultures, which becoming more common place for all the world religions as religious pluralism spreads, has been the norm for Judaism for countless generations. From the biblical period to the present, Judaism has had to formulate its beliefs and practices in the face of challenges from other cultures and religions. The viewpoint of the modern Jew opens the way for relations with Christianity, Islam, and perhaps Hinduism; however, Buddhism - especially Mahayana Buddhism may prove to be in a separate category. The Buddhist consciousness in which no transcendent God is recognized and the Mahayana awareness of the Divine in the
520 Ibid.
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secular may be judged by the Jewish philosopher as a modern idolatry. Therefore, perhaps the most serious challenge for Judaism comes in its response to Buddhism. As long as a religion is founded on the experience of a transcendent God, Judaism seems to be able to enter into spiritual partnership with it. But if that experience does not hold true for the Buddhist - if it is not a transcendent God that is being experienced - can the Jew still embrace the Buddhist as a spiritual partner? This question has yet to be faced by Judaism.521
The relationship between Christianity and the other religions is one of the key issues in Christian self-understanding. Perhaps pluralism is so pressing a challenge because of the exclusivist missionary approaches adopted by Christianity over the past several hundred years.
In the rapidly expanding body of literature resulting from the encounter with other religions, many Christian theologians are concluding that Christian theology cannot continue to be formulated in isolation from the other religions, and that in fact future developments in Christian theology will be the direct result of serious dialogue with the other religions. Although the Churches are altering their ecclesiology so as to open the way for serious dialogue with other religions, the fundamental Christology that underlies traditional ecclesiology has not yet changed.
Through out the centuries the basic Islamic approach to other religions was to search for some fundamental structures that were harmonious with Islam but which lay hidden beneath the other religion’s deviations from true Islam: A major obstacle for understanding other religions was the lack of accurate information. However, Islam has essentially reached the truth toward which all other religions are evolving. Christianity, it seems, has also virtually reached this goal. It is possible that various nations or cultures will reach the truth in their own way. The Qur’an itself teaches that every community in every age has had its prophet. However, modern education will offer Muslims an opportunity to understand each religion in terms of its own culture, history, world view, and claims to truth. This will have an effect on Islamic self-perception.
Therefore, the religious pluralism of the modern world will force Islam, finding itself in much the same position as the other traditions, to come to grips with them rather provincial
521 See Harold Coward, Pluralism: Challenge to World Religions, Harold Coward, 1-12.
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character of some of its past views of other religions.
According to Hinduism, there is one divine reality that manifests itself in many forms. The various religions are simply different revelations of the one divine reality. Hinduism sees itself as being a very open and tolerant religion. But because it asserts that the Vedas are the most perfect revelation of divine truth, Hinduism also sees itself as providing the criteria against which the revelations of all other religions must be tested. Nevertheless, the Hindu view that there is one Divine, which may be reached by many paths, has proven through out the centuries to be a powerful influence upon Hinduism’s interaction with the other religions.522 Therefore, the Hindu contribution to the modern challenge of religious pluralism is to encourage the inquiring spirit and devotion to truth that is larger than any individual tradition.
The Buddhist attitude to other religions has been described as “critical tolerance”523 combined with a missionary goal. Buddhism has demonstrated a remarkable degree of tolerance and flexibility throughout the course of its expansion. Unlike some other religious expansions, the spread of Buddhism has been accomplished more through the dissemination of ideas than by migration of peoples.
Buddhism rejects the worship of God or gods and the performance of religious rituals as a means to release. It also rejects speculations about ultimate beginnings, especially about whether the self and the world were eternal, and a number of speculations about the ultimate state of the self in the future. The tolerant but critical attitude of the Buddha toward the plurality of religious views is shaped into a rigorous philosophic approach by the Madhyamika Buddhists. If, as the Buddha discovered, the goal of religion is compassion, then, say the Madhyamika, the biggest obstacle to realizing that goal is attachment to our own religious beliefs in such a way as to make them absolute. Based on this understanding, the Madhyamika Buddhist’s attitude towards other religions is one of openness and indeed a “missionary desire”524 to enter into dialogue.
The inherent desire to conceptualize and share religious experience is too deeply ingrained in
522 Ibid., 63-80.
523 See K. N. Jayatilleke, The Buddhist Attitude to Other Religions (Kandy, Sri Lanka: Buddhist Publication Society, 1975). And see also Harold Coward Pluralism: Challenge to World Religions, 81.
524 See Harold Coward, Pluralism: Challenge to World Religions, 88.
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human nature to render silence an acceptable answer. In fact the Madhyamika himself has been far from silent. His prescription of silence was only intended to apply to claims of absolute knowledge. As long as the limitation is honored, then discussion, including theological discussion, could take place.
The dialogical approach opens the way for the meeting of Christians with Jews, Muslims, and Hindus. However, the theocentric premise could become an obstacle to meaningful encounters with Buddhists and Advaita Vedantists. Therefore, an unresolved problem for all of these approaches is the Buddhist and even those with considerable exposure to Buddhism and Hinduism seem almost willfully to turn a blind eye to this problem. One possible exception might be found in Tillich’s formulation of the “god above gods” as the “ground of being.”525
Dialogue starts from the assumption that each religion has its absolute claims which cannot be relativized. No amount of reformulation will do away with the difference. But, by letting our theologizing be influenced by others we will be forced to greater honesty and deeper spirituality. The prerequisite for dialogue is not the harmonizing of all beliefs but the recognition that each spiritual person has a committed and absolute conviction, and that these convictions are different.
Therefore, the expected outcome is not the homogenization of particular religions but the mutual deepening of spiritual experience within each particular religion, which may lead to glimpses of a common transcendent reality. This shift in perspective had the effect of drawing attention to the universal nature of religious experience in its many different traditions. In addition to turning attention away from metaphysics, rationalism, or revelation, the focus on the humanity of religion has had the effect of highlighting some of the limitations in human nature that must be taken seriously in all future religion.
The brain is characterized by its immune privileged state. However, recent studies suggest an extended contribution of hematopoietic cells to the brain. After transplantation of genetically labeled bone marrow into bone marrow depleted mice, not only labeled blood cells but also labeled neurons and other non-hematopoietic cells can be observed. Initially interpreted as transdifferentiated hematopoietic stem cells, this contribution later was identified as cell fusion of hematopoietic cells and neurons. Our lab previously addressed the question whether these fusion events also occur under non-invasive conditions. A Cre-LoxP based transgenic mouse line was used to irreversibly label all hematopoietic cells. In these mice, Cre expression is controlled by a hematopoietic promoter, thus causing recombination and subsequent marker gene expression restricted to blood cells. Interestingly, contribution of these hematopoietic cells to non-hematopoietic tissues was observed, but fusion could be excluded as the underlying mechanism. The Cre mRNA or protein seems to reach the non-hematopoietic cells from an external source. Extracellular vesicles, specifically exosomes, are increasingly recognized as a vehicle for the intercellular transfer of cellular components such as proteins or mRNAs. However, if they contribute to signaling between tissues in vivo is completely unknown and would represent a major paradigm shift for intercellular communication. Therefore, the aim of this PhD study is to investigate whether an exosomal transfer between the hematopoietic system and the brain exists. To confirm the previous results, a second Cre-LoxP mouse line that expresses the Cre recombinase under a different hematopoietic promoter is used additionally. Both mouse lines are screened for recombination and show comparable numbers and types of different non-hematopoietic cells. Besides hepatocytes and cells in lung and intestine, recombined Purkinje neurons in the cerebellum are detectable. To assess the influence of inflammation on these recombination events, different lesions such as peripheral tumors or peritonitis are applied to the mice. Inflammatory stimuli strongly increase the numbers of recombined Purkinje neurons. These neurons remain mononuclear, indicating that fusion does not occur. Also in human cerebellar material, no evidence for inflammation induced cell fusion is detectable. To screen for Cre recombinase containing exosomes, exosome purification protocols such as differential ultracentrifugation and sucrose gradient fractioning, are applied. The exosomal content is analyzed with nested PCR and western blot. Hematopoietically expressed Cre mRNA is detectable in blood plasma and hematopoietic cell culture conditioned medium. Further analysis reveals that this Cre mRNA but no Cre protein is contained in exosomes. The exosomal ability to induce recombination is investigated by injections into Cre reporter mice. After direct cerebellar injection, exosomes are sufficient to induce recombination of Purkinje neurons. Brain tissue of mice that received an inflammation is analyzed further to reveal other recombined cell types. The main immune cells of the brain, microglia, are not recombined. Mainly neuronal cell types are recombined in different areas of the brain. The observations made in this study are consistent with the hypothesis that a previously unrecognized way to communicate RNA based signals between the immune system and the brain exists. Specifically neurons are target cells for the uptake of hematopoietic exosomes and seem able to translate exosomal mRNA into functional protein. Microglial cells are neither involved as target cells, nor do they release Cre containing exosomes. By using the Cre-LoxP system, in vivo tracing of exosomes could be achieved for the first time. With this knowledge, other exosomal routes can be uncovered in future. The discovery of the exosomal transfer between the blood and the brain enables further research about the relevance of this signaling pathway. It will be important to investigate its role especially in the context of neural malfunctions and further studies might help to find new therapeutical approaches.
The adaptive immune system protects against daily infections and malignant transformation. In this, the translocation of antigenic peptides by the transporter associated with antigen processing (TAP) into the ER lumen is an essential step in the antigen presentation by MHC I molecules. The heterodimeric ATP-binding cassette transporter (ABC) TAP consist of the two halftransporters TAP1 and TAP2. Each monomer contains an N-terminal transmembrane domain (TMD) and a conserved C-terminal nucleotide-binding domain (NBD). Together, the TMDs build the translocation core and the NBDs bind and hydrolyze ATP, energizing the peptide transport. TAP features an asymmetry in the two ATP-binding sites that are built of several conserved motifs. One motif is the D-loop with the consensus sequence SALD. The highly conserved aspartate of the D-loop of TAP1 reaches into the canonic ATP-binding site and contacts the Walker A motif and the H-loop of the opposite NBD, while the Asp of D-loop of TAP2 is part of the non-canonic ATP-binding site.
To examine this ABC transport complex in mechanistic detail, a purification and reconstitution procedure was established with the function of TAP being preserved. The heterodimeric TAP complex was purified via a His10-tag at TAP1 in a 1:1 ratio of the subunits. Nucleotide binding to the purified transporter was elucidated by tryptophan quenching assays and the affinity constants for MgADP and MgATP were determined to be 1.0 μM and 0.7 μM, respectevely. In addition, the TAP complex shows strict coupling between peptide binding and ATP hydrolysis, revealing no basal ATPase activity in the absence of peptides. Furthermore, TAP was reconstituted into proteoliposomes and the activity was tested by peptide transport and ATP hydrolysis. Interestingly, the kinetic parameters of the transporter in the reconstituted state are comparable to the data gained for TAP in microsomes.
To characterize the functional importance of the D-loop, D-loop mutants of either TAP1 or TAP2 were analyzed. Strikingly, TAP containing a mutated D-loop in TAP1 (D674A) shows an ATP-hydrolysis independent peptide translocation. Accordingly, the MHC I surface expression is similar to the wildtype situation. However, the same mutation in TAP2 (D638A) results in an ATPase dependent peptide transport similar to wildtype, whereas TAP containing mutations in both subunits leads to an inactive transporter. Although all D-loop mutants showed no altered peptide binding activity, the TAP1 mutant is inactive in peptide-stimulated ATPase activity. Strikingly, ATP or ADP binding is strictly required for the peptide translocation. Experiments carried out in proteoliposomes demonstrate that wildtype TAP can export peptides against their gradient when low peptide concentrations are offered. In contrast, the D674A mutant can facilitate peptide translocation along their concentration gradient in the two directions. At high peptide concentrations, TAP is trapped in a transport incompetent state induced by trans-inhibition. In conclusion, a TAP mutant that uncouples solute translocation from ATP hydrolysis was created. Since this passive substrate movement is strictly dependent on binding of ATP or ADP, an active transporter was turned into a “nucleotide-gated facilitator”.
In a cysteine cross-linking approach the conformational changes of TAP during peptide transport and the flexibility of the nucleotide binding domains were examined. Single cysteines were introduced in the D-loops of TAP1 and TAP2. Cross-linking by copper-phenantroline (CuPhe) was possible for all combinations. However, by adding ATP, ADP or peptide to the TAP complex no differences in the cross-linking efficiency were detected. By CuPhe cross-linking TAP was trapped in a conformation, in which the peptide binding site was not accessible. To complete a transport cycle, a flexibility of at least 17.8 Å of the NBDs is needed, since TAP cross-linked by CuPhe (2.0 Å) or bismaleimidoethane (BMOE, 8.0 Å) was transport inactive but when TAP was cross-linked by 1,11-bismaleimido-triethyleneglycol (BM[PEG]3, 17.8 Å) transport activity was preserved.
5-Lipoxygenase (5-LO) catalyzes the two initial steps in the biosynthesis of leukotrienes, a group of inflammatory lipid mediators derived from arachidonic acid. Here, the regulation of 5-LO mRNA expression by alternative splicing and nonsense-mediated mRNA decay (NMD) was investigated. In the present study, the identification of two truncated transcripts and four novel 5-LO splice variants containing premature termination codons (PTC) was reported. The characterization of one of the splice variants, 5-LOΔ3, revealed that it is a target for NMD since knockdown of the NMD factors UPF1, UPF2 and UPF3b in the human monocytic cell line Mono Mac 6 (MM6) altered the expression of 5-LOΔ3 mRNA up to 2-fold in a cell differentiation-dependent manner suggesting that cell differentiation alters the composition or function of the NMD complex. In contrast, the mature 5-LO mRNA transcript was not affected by UPF knockdown. Thus, the data suggest that the coupling of alternative splicing and NMD is involved in the regulation of 5-LO gene expression.
RT-PCR analysis of different cell types revealed the existence of a large number of 5-LO splice variants. The most interesting splice variants were observed in BL41-E95A cells, which give a raise to novel 5-LO protein isoforms. This leads to the hypothesis of a novel regulatory mechanism in which the dimerization of 5-LO with 5-LO isoforms might regulate the 5-LO activity.
The 5-LO protein expression was reduced on translational level in UPF1 knock down cells, suggesting that UPF1 has a positive influence on 5-LO translation. Therefore, a mass spectrometry based proteomics study was started to identify compartment specific protein expression changes upon UPF1 knockdown in differentiated and undifferentiated MM6 cells. The proteomics analysis demonstrated that the knockdown of UPF1 results in numerous protein changes in the microsomal fraction (~ 21%) but not in the soluble fraction (< 1%). Western blot data confirmed the trend of the proteomics analysis. This data suggest that UPF1 is a critical gene expression regulator in a compartment specific way. During differentiation by TGFβ and calcitriol the majority of UPF1 regulated proteins was adjusted to normal level. It appears that that not only the NMD mechanism alters its composition during differentiation. Also the gene expression regulation on translational level by UPF1 seems to be also cell differentiation dependent. An interesting group of UPF1 target genes represent the downregulated proteins. qRT-PCR analysis of randomly chosen genes revealed no effect on mRNA expression upon UPF1 knockdown, suggesting that UPF1 positively influences the translation of these genes. Computational sequence analysis identified a conserved C-rich sequence which might be a hnRNP E2-binding site. hnRNP E2 has been characterized as a translational repressor in myeloid cells. Western blot analysis revealed a differentiation independent up regulation of hnRNP E2 by UPF1 knockdown. Additionally, microRNA-328 (miR-328) has been described as an RNA decoy modulating hnRNP E2 regulation. Due to this, stem loop qRT-PCR showed an up regulation of miR-328 in TGFβ and calcitriol differentiated MM6 cells. Based on this data we suggest a model in which downregulation of UPF1 increases hnRNP E2 expression, leading to translation inhibition. During differentiation, miRNA-328 is upregulated thereby competing with hnRNP E2 leading to an efficient translation