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This work presents a contribution to the literature on methods in search of lowdimensional models that yield insight into the equilibrium and kinetic behavior of peptides and small proteins. A deep understanding of various methods for projecting the sampled configurations of molecular dynamics simulations to obtain a low-dimensional free energy landscape is acquired. Furthermore low-dimensional dynamic models for the conformational dynamics of biomolecules in reduced dimensionality are presented. As exemplary systems, mainly short alanine chains are studied. Due to their size they allow for performing long simulations. They are simple, yet nontrivial systems, as due to their flexibility they are rapidly interconverting conformers. Understanding these polypeptide chains in great detail is of considerable interest for getting insight in the process of protein folding. For example, K. Dill et al. conclude in their review [28] about the protein folding problem that "the once intractable Levinthal puzzle now seems to have a very simple answer: a protein can fold quickly and solve its large global optimization puzzle simply through piecewise solutions of smaller component puzzles".
The reggie protein family consists of two homologous members, reggie-1 and reggie-2, also termed flotillin-2 and flotillin-1, respectively, that are ubiquitously expressed and evolutionarily well conserved, suggesting an important but so far ill-defined function. In various cell types, both reggies have been found to be constitutively associated with lipid rafts by means of acylation modifications and oligomerization. Lipid rafts are glycosphingolipid- and cholesterol-rich membrane microdomains which have been implicated in several cellular processes including membrane transport and signal transduction through growth factor receptors. However, the molecular details of these processes are still poorly understood. With the observation that reggies colocalize with activated glycosylphosphatidylinositolanchored proteins (GPI-APs) and Fyn kinase in rafts, a role for these proteins in signaling events has been suggested. In agreement with that, we have previously shown that reggie-1 becomes multiply tyrosine phosphorylated by Src kinases in response to epidermal growth factor (EGF) stimulation, pointing to a function for reggie-1 in growth factor signaling. Furthermore, overexpression of reggie-1 enhances spreading on fibronectin substrate in a tyrosine-dependent manner, thus revealing a role for reggie-1 in regulation of actin cytoskeleton through growth factor receptors. Due to the similarity shared by reggie proteins at amino acid level and to their ability to form hetero-oligomeric complexes, the first aim of this study was to analyze the putative tyrosine phosphorylation of reggie-2 in growth factor stimulated cells. Similarly to reggie-1, reggie-2 was found to be multiply tyrosine phosphorylated by Src kinase and to exist in a molecular complex with Src, with the degree of co-immunoprecipitation dependent on the activity of Src. Recent studies from us have also shown that administration of EGF results in the endocytosis of reggie-1 from the plasma membrane into endosomes, which is in line with a proposed role for reggies in membrane trafficking processes. In order to characterize in detail the endocytic mechanism that mediates the uptake of reggie-1, the dependency of reggie-1 endocytosis on clathrin and dynamin was investigated by means of overexpressing a variant form of Eps15 or a dominant negative form of dynamin-2. In either case the translocation of reggie-1 into endosomes in response to EGF was not affected, and this, together with the results that reggie-1 colocalized with cholera toxin (CTX) but not with transferrin receptor (TfnR) during EGF signaling, indicates that reggie-1 is taken up by means of a dynaminindependent, raft-mediated pathway. These findings are very well in line with recent data showing the pathway of entry into cells of reggie-2 as a raft-mediated endocytic pathway. The endocytosis of reggie-2 in response to EGF was also analyzed in this study. Similarly to reggie-1, in growth factor stimulated cells reggie-2 underwent a translocation from the plasma membrane to endosomes where the two reggies were found to colocalize with each other, suggesting that epidermal growth factor signaling might trigger the endocytosis of reggie oligomers. In addition, colocalization with both the late endosomal marker LAMP3/CD63 and epidermal growth factor receptor (EGFR) was detected, again indicating a function for reggies in signal transduction through growth factor receptors. EGFR has been reported to localize in rafts but, although this association is thought to be functional during EGF stimulation, how segregation of EGFR into rafts modulates its endocytosis and signaling is still under debate. Since reggie oligomers have recently been suggested to define a raft subtype, a further aim of this study was to investigate whether the depletion of reggies by means of small interfering RNA could interfere with the signaling and the trafficking through EGFR. Knockdown of reggie-2 resulted in an altered tyrosine phosphorylation of EGFR in response to EGF, while the degree of ubiquitination was not affected. Less efficient phosphorylation of tyrosine residues, especially of those which are docking sites for Grb2 and Shc, led in turn to an impaired activation of p38 and ERK1/2 MAPKs. Depletion of reggie-2 did not affect the early trafficking of activated EGFRs, with receptors being endocytosed and delivered to late endosomes as efficiently as in control cells. This would be in line with the normal degree of ubiquitination observed for EGFR, as ubiquitin moieties have been proposed to represent sorting tags that ensure receptor endocytosis into early endosomes and its proper intracellular trafficking. On the contrary, after prolonged EGF stimulation, depletion of reggie-2 resulted in a decreased downregulation of both receptor-bound ligand and EGFR, and in their accumulation in intracellular vesicles, thus pointing to a role for reggie-2 in the degradative pathway. Taken all together, these data ndicate that the association of EGFR with reggie-microdomains is likely to be important for proper receptor trafficking and signaling.
In the present work, the photo-protection mechanisms in plants and purple bacteria were investigated experimentally at the molecular level. For this purpose, several spectroscopic methods were combined and applied to elucidate the function of carotenoids, pigments of the photosynthetic apparatus, in photo-protection. The experiments were focused on the mechanisms involved in quenching of singlet and triplet states of the electronically excited (bacterio)chlorophylls. This photosynthetic reaction events occur on an ultrafast time-scale. Measuring such short-lived events, and understanding the underlying principles, demand some of the most precise experiments and exact measurement technologies currently available. This implies certain requirements for the light source used: a suitable wavelength within the absorption band of the sample, sufficient power, and, most importantly, a pulse duration short compared to the studied reaction. Nowadays, we can achieve all this requirements using femtosecond-spectroscopic systems, which produce laser pulses shorter than 100 femtoseconds (fs). Transient absorption spectroscopy provides important information on molecular dynamics interrogating electronic transitions. The technique is based on photochemical generation of transient species with femtoseconds pump pulses and measuring transient absorption changes of the sample using a second, time delayed probe pulse which in this case is a spectrally broad white-light pulse.
Cytochrome c oxidase (CcO), also called Complex IV of the aerobic respiratory chain, is located in the plasma membrane of prokaryotes and in the inner mitochondrial membrane of eukaryotes. The redox energy of dioxygen reduction is used to translocate protons across the membrane resulting in an electrochemical proton gradient. The generated proton gradient is exploited by the adenosine-5’-triphosphate synthase. In this work, bacterial four-subunit aa3-Type CcO from Paracoccus denitrificans (ATCC 13543, 4 SU-wt ATCC CcO) was used for analyses. 1) The recombinant homologously produced 4 SU-wt CcO (4 SU-wt rec CcO) was functionally compared with the native 4 SU-wt ATCC CcO. The 4 SU-wt rec CcO showed functional deficiencies as determined by UV-vis spectroscopy and electron paramagnetic resonance (EPR) studies. Total X-ray Reflection Fluorescence measurements show in both wild type CcOs the same ratio of the redoxactive Fe and Cu (2 Fe : 3 Cu) indicating full complement of the functional metals. If CcO contains only subunit I and II, it loses its functional integrity during continuous turnover activity. The importance of subunit III for integrity of CcO was demonstrated using 2 SU-wt rec CcO. Crystallisation trials of suicide inactivated 2 SU-wt rec CcOs have been ineffective using standard crystallisation conditions. Crystals of active 2 SU-wt rec CcO (positive control) have been obtained under these conditions and this result indicates possible structural changes in suicide inactivated 2 SU-wt rec CcO. The structure of active 2 SU-wt rec CcO was determined to 2.25 Å resolution. 2) Terminal oxidases require four electrons for the cleavage of the dioxygen bond (O=O). In general, the catalytic cycle of CcO is described by the electron input and thus by the different redox states of the metal centres: the O, E, R, P and F state. The two-electron reduced R intermediate is able to donate four electrons for dioxygen reduction forming the P state. The P intermediate is an oxoferryl state implying the lack of an electron for the R -> P transition, because the metal centres can only provide three electrons (Fe+II forms Fe+IV and Cu+II forms Cu+I). The P state, where the dioxygen bond is already broken, shows an oxoferryl state (FeIV=O2-) and a nearby tyrosine is proposed to form a tyrosyl radical representing the donor of the missing electron. H2O2-induced artificial intermediates provide the opportunity to investigated different catalytic intermediates in detail. Mixing equimolar amounts of H2O2 to CcO in the O state induces the "two-electron" reduced PH state at high pH and the electronically equal "two-electron" reduced F• H state at low pH. The addition of an excess amount of H2O2 leads to the three-electron reduced FH state. Functional studies using the 4 SU-wt ATCC CcO have demonstrated a bound peroxide (O- - O-) intermediate during the catalytic cycle. Using EPR it was previously shown that Y167 hosts a radical species in PH/F• H state which suggests that Y167 could provide this "missing electron". While X-ray structural models of CcO and Fourier-transformed infrared (FTIR) measurements of oxygenated ("pulsed") 4 SU-wt ATCC CcO suggest a bound peroxide in the O state, UV-vis and EPR spectroscopic studies indicate that other intermediates may also contain such peroxide species. Equimolar and excess amounts of H2O2 induce the PH/F• H and FH states, respectively and catalase treatment of the FH state leads, contrary to the natural direction of the catalytic cycle, to the apparent transition of the FH -> PH/F• H states, which is accompanied by reappearance of an EPR signal from the Y167• radical. The novel PFH/F• FH states are presented here and we postulate that the FH state hosts a superoxide (or peroxide) adduct at CuB in the binuclear site. In addition, the novel P10 state is also introduced having a maximum at lambda = 612 nm in the difference absorption spectrum (minus the O state). The P10 state is induced by mixing CcO in the O state with a pH 10 buffer. This pH 10 induced state resembles standard P states such as PCO, PH and PR. However, the P10 state evolves out of the O state without addition of reduction equivalents. Using EPR spectroscopy it was shown that Y167 hosts a radical species in the P10 state such as in the PH state. In summary, all functional data presented here provide evidence for a peroxide bound during the O state. Finally, a new model for the natural catalytic cycle is proposed. If the O state contains a peroxide, it is also likely that the E and R state contain this species. Even the oxoferryl intermediates P and F states may complex a peroxide at CuB in the binuclear site. 3) The amino acid residue Y167, which hosts the radical in the PH/F•H states, is not directly part of the binuclear site of CcO. For identification of the primary electron donor, two tryptophan variants of CcO, W272F and W164F, which are located nearby the binuclear site, were produced. Evidence is provided that W272 is a kinetically fast electron donor for the O2 molecule. The electron is replenished by Y167, or probably by Y280 in the natural cycle. The Y167 radical is detectable by EPR spectroscopy after treatment with equimolar amounts of H2O2 in the active variant W164F, but is absent in the inactive variant W272F. 4) CcO contains two proton conducting pathways, the D- and the K-pathway. Proteoliposomes of the variants H28A and D30N, mutations located at the entrance of the D-pathway, both show the identical proton pumping activity as the 4 SU-wt rec CcO (pumped H+/e- = 1). The variant N113D shows abolished proton pumping (pumped H+/e- = 0), but a relative high cytochrome c oxidation activity (63 %). G196D displays no cytochrome c oxidation and proton pumping activity. Overall, the addition or removal of a negative charge within the D-pathway such as in D124N, N131D, N113D and G196D leads to a decoupled phenotype indicating the high degree of electrostatic coupling in CcO.
Reggie-1 (flotillin-2) and reggie-2 (flotillin-1) are membrane microdomain proteins which are associated with the membrane by means of acylation. They influence different cellular signaling processes, such as neuronal, T-cell and insulin signaling. Upon stimulation of the EGF receptor, reggie-1 becomes phosphorylated and undergoes tyrosine 163 dependent translocation from the plasma membrane to endosomal compartments. In addition, reggie-1 was shown to influence actindependent processes. Reggie-2 has been demonstrated to affect caveolin- and clathrin-independent endocytosis. Both proteins form homo- and hetero-oligomers, but the function of these oligomers has remained elusive. Moreover, it has not been clarified if functions of reggie-1 are also influenced by reggie-2 and vice versa. The first aim of the study was to further investigate the interplay and the heterooligomerization of reggie proteins and their functional effects. Both reggie proteins were individually depleted by means of siRNA. In different siRNA systems and various cell lines, reggie-1 depleted cells showed reduced protein amounts of reggie-1 and reggie-2, but reggie-2 knock down cells still expressed reggie-1 protein. The decrease of reggie-2 in reggie-1 depleted cells was only detected at protein but not at mRNA level. Furthermore, reggie-2 expression could be rescued by expression of siRNA resistant wild type reggie-1-EGFP constructs, but not by the soluble myristoylation mutant G2A. This mutant was also not able to associate with endogenous reggie-1 or reggie-2, which demonstrates that membrane association of reggie-1 is necessary for hetero-oligomerization. In addition, fluorescence microscopy studies and membrane fractionations showed that correct localization of overexpressed reggie-2 was dependent on co-overexpressed reggie-1. Thus, hetero-oligomerization is crucial for membrane association of reggie-2 and for its protein stability or protein expression. Moreover, the binding of reggie-2 to reggie-1 required tyrosine 163 of reggie-1 which was previously shown to be important for endosomal translocation of reggie-1. Since reggie-2 was implicated to function in clathrin- and caveolin-independent endocytosis pathways, the effect of reggie-2 depletion on reggie-1 endocytosis was investigated. Indeed, reggie-1 was dependent on reggie-2 for endosomal localization and EGF-induced endocytosis. By FRET-FLIM analysis it could be shown that reggie heterooligomers are dynamic in size or conformation upon EGF stimulation. Thus, it can be concluded that reggie proteins are interdependent in different aspects, such as protein stability or expression, membrane association and subcellular localization. In addition, these results demonstrate that the hetero-oligomers are dynamic and reggie proteins influence each other in terms of function. A further aim was the characterization of reggie-1 and reggie-2 function in actindependent processes, where so far only reggie-1 was known to play a role. Depletion of either of the proteins reduced cell migration, cell spreading and the number of focal adhesions in steady state cells. Thus, also reggie-2 affects actin-dependent processes. Further investigation of the focal adhesions during cell spreading revealed that depletion of reggie-1 displayed different effects as compared to reggie-2 knock down. Reggie-1 depleted cells had elongated cell-matrix-adhesions and showed reduced activation of FAK and ERK2. On the other hand, depletion of reggie-2 resulted in a restricted localization of focal adhesion at the periphery of the cell and decreased ERK2 phosphorylation, but it did not affect FAK autophosphorylation. Hence, reggie proteins influence the regulation of cell-matrix-adhesions differently. A link between reggie proteins and focal adhesions is the actin cross-linking protein -actinin. The interaction of -actinin with reggie-1 could be verified by means of co-immunoprecipitations and FRET-FLIM analysis. Reggie-1 binds -actinin especially in membrane ruffles and in other locations where actin remodeling takes place. Moreover, -actinin showed a different localization pattern during cell spreading in reggie-1 depleted cells, as compared to the control cells. These results provide further insights into the function of both reggie proteins. Their interplay and hetero-oligomerization was shown to be crucial for their role in endocytosis. In addition, both reggie proteins influence actin-dependent processes and differentially affect focal adhesion regulation.
Driving can be dangerous. Humans become inattentive when performing a monotonous task like driving. Also the risk implied while multi-tasking, like using the cellular phone while driving, can break the concentration of the driver and increase the risk of accidents. Others factors like exhaustion, nervousness and excitement affect the performance of the driver and the response time. Consequently, car manufacturers have developed systems in the last decades which assist the driver under various circumstances. These systems are called driver assistance systems. Driver assistance systems are meant to support the task of driving, and the field of action varies from alerting the driver, with acoustical or optical warnings, to taking control of the car, such as keeping the vehicle in the traffic lane until the driver resumes control. For such a purpose, the vehicle is equipped with on-board sensors which allow the perception of the environment and/or the state of the vehicle. Cameras are sensors which extract useful information about the visual appearance of the environment. Additionally, a binocular system allows the extraction of 3D information. One of the main requirements for most camera-based driver assistance systems is the accurate knowledge of the motion of the vehicle. Some sources of information, like velocimeters and GPS, are of common use in vehicles today. Nevertheless, the resolution and accuracy usually achieved with these systems are not enough for many real-time applications. The computation of ego-motion from sequences of stereo images for the implementation of driving intelligent systems, like autonomous navigation or collision avoidance, constitutes the core of this thesis. This dissertation proposes a framework for the simultaneous computation of the 6 degrees of freedom of ego-motion (rotation and translation in 3D Euclidean space), the estimation of the scene structure and the detection and estimation of independently moving objects. The input is exclusively provided by a binocular system and the framework does not call for any data acquisition strategy, i.e. the stereo images are just processed as they are provided. Stereo allows one to establish correspondences between left and right images, estimating 3D points of the environment via triangulation. Likewise, feature tracking establishes correspondences between the images acquired at different time instances. When both are used together for a large number of points, the result is a set of clouds of 3D points with point-to-point correspondences between clouds. The apparent motion of the 3D points between consecutive frames is caused by a variety of reasons. The most dominant motion for most of the points in the clouds is caused by the ego-motion of the vehicle; as the vehicle moves and images are acquired, the relative position of the world points with respect to the vehicle changes. Motion is also caused by objects moving in the environment. They move independently of the vehicle motion, so the observed motion for these points is the sum of the ego-vehicle motion and the independent motion of the object. A third reason, and of paramount importance in vision applications, is caused by correspondence problems, i.e. the incorrect spatial or temporal assignment of the point-to-point correspondence. Furthermore, all the points in the clouds are actually noisy measurements of the real unknown 3D points of the environment. Solving ego-motion and scene structure from the clouds of points requires some previous analysis of the noise involved in the imaging process, and how it propagates as the data is processed. Therefore, this dissertation analyzes the noise properties of the 3D points obtained through stereo triangulation. This leads to the detection of a bias in the estimation of 3D position, which is corrected with a reformulation of the projection equation. Ego-motion is obtained by finding the rotation and translation between the two clouds of points. This problem is known as absolute orientation, and many solutions based on least squares have been proposed in the literature. This thesis reviews the available closed form solutions to the problem. The proposed framework is divided in three main blocks: 1) stereo and feature tracking computation, 2) ego-motion estimation and 3) estimation of 3D point position and 3D velocity. The first block solves the correspondence problem providing the clouds of points as output. No special implementation of this block is required in this thesis. The ego-motion block computes the motion of the cameras by finding the absolute orientation between the clouds of static points in the environment. Since the cloud of points might contain independently moving objects and outliers generated by false correspondences, the direct computation of the least squares might lead to an erroneous solution. The first contribution of this thesis is an effective rejection rule that detects outliers based on the distance between predicted and measured quantities, and reduces the effects of noisy measurement by assigning appropriate weights to the data. This method is called Smoothness Motion Constraint (SMC). The ego-motion of the camera between two frames is obtained finding the absolute orientation between consecutive clouds of weighted 3D points. The complete ego-motion since initialization is achieved concatenating the individual motion estimates. This leads to a super-linear propagation of the error, since noise is integrated. A second contribution of this dissertation is a predictor/corrector iterative method, which integrates the clouds of 3D points of multiple time instances for the computation of ego-motion. The presented method considerably reduces the accumulation of errors in the estimated ego-position of the camera. Another contribution of this dissertation is a method which recursively estimates the 3D world position of a point and its velocity; by fusing stereo, feature tracking and the estimated ego-motion in a Kalman Filter system. An improved estimation of point position is obtained this way, which is used in the subsequent system cycle resulting in an improved computation of ego-motion. The general contribution of this dissertation is a single framework for the real time computation of scene structure, independently moving objects and ego-motion for automotive applications.
Prion diseases or transmissible spongiform encephalopathies (TSEs) are rare neurological disorders that may be of genetic or infectious origin, but most frequently occur sporadically in humans. Their outcome is invariably fatal. The infectious agent has been defined as prion (from proteinaceous infectious only) in 1992 by Stanley B. Prusiner and represent mainly, if not solely, an abnormal, protease-resistant isoform (PrPSc) of a cellular protein, the prion protein or PrPC. According to the “protein only” hypothesis, the prion is devoid of informational nucleic acids and consists of an “infectious” protein that is capable of converting the normal host protein PrPC into a likeness of itself. TSEs can be distinguished from other neurodegenerative diseases because of their infectivity and transmission capability. The only organ system in which severe histopathological damage can be demonstrated as a consequence of infection with prions is the nervous system. The communal lesions are neuronal loss, spongiosis and astrogliosis, accompanied by an intra- and extracellular accumulation of PrPSc, occasionally in form of amyloid plaques. Even if a strong activation of microglia and astrocytes occurs, no immunological response is usually detectable as consequence of prion infection. Despite the considerable attention for its involvement in TSEs, the physiological role of the cellular, nonpathogenic isoform of PrPC, has not yet been determined. In the last years, several putative cellular functions have been attributed to PrPC: its localization in “lipid rafts” is consistent with a possible role in cell adhesion, transmembrane signalling or as a recognition molecule. Furthermore, PrPC has been implicated in protection against oxidative stress, copper metabolism, apoptosis, cell proliferation and in the regeneration of blood precursors stem cells in the adult. It has also been shown that PrPC interacts with the neuronal cell adhesion molecule NCAM, promoting neurite outgrowth. However, both the PrPC-mediated effects and the role of PrPC-dependent pathways on neuronal differentiation are still not elucidated. First objective of this Ph.D thesis was the establishment of a novel in vitro cellular model for the study of the role of PrPC in neuronal differentiation and neurite outgrowth. Furthermore, an additional goal of this project was the indentification of the PrPC domains responsible for the induction of neuronal differentiation. A novel PrPC-depleted cell line (PrP0/0 ML) was derived from murine primary PrP-knockout neuronal cells by SV40 large T antigen-mediated immortalization. A temperature sensitive form of this oncogenic protein was used, allowing a temperature-mediated regulation of its expression. This cell line was then characterised for its growth potential, for the expression of specific cellular markers and for its ability to differentiate. It was found that, under culture conditions promoting the expression of the temperature-sensitive SV40 large T antigen, the cells expressed nestin, a specific marker of neuronal precursor cells. Therefore, the PrP0/0 ML cell line was identified as a potential neuronal stem cell line. In fact, under nonpermissive culture conditions when the expression of the temperature-sensitive SV40 large T antigen is downregulated, the PrP0/0 ML cells differentiated into neurons. Noteworthy, maintenance of the cells in conditions that promote cell differentiation induced a progressive reduction in the expression levels of nestin, an event that strongly correlated with the appearance of the specific neuronal markers MAP-2b and NeuN. In order to investigate the role of PrPC in the process of neuronal differentiation, the PrP0/0 ML cells were then reconstituted for the expression of either the full-length PrP or a N-terminal truncated PrPC form (PrPdel32-134). The differentiation potential of both reconstituted cell lines under nonpermissive culture conditions was then compared with that of the parenteral PrP0/0 ML cells. This in vitro study clearly highlights that PrPC expression in the PrP0/0 ML cell line accelerates neuronal differentiation and that the N-terminal domain of the prion protein is not necessary for this PrP-mediated function. Prion diseases like BSE, vCJK, Kuru and the majority of iatrogenic cases of CJK are caused by a peripheral infection. Infectious prions accumulate in the central and peripheral nervous system as well as in extracerebral tissues, such as the secondary lymphoid organs and muscles. The prion pathogenesis is a dynamic process which can be defined temporary and spatially in different phases: i) infection and peripheral replication, ii) neuroinvasion, transport of prions from the periphery to the central nervous system (CNS), and iii) neurodegeneration. In the last years, progresses in the elucidation of the peripheral prion pathogenesis were achieved. The identification of the cell types involved in the lymphoreticular prion replication phase and the recognition of the role of the peripheral nervous system in the process of prion spread from the periphery to the CNS have elucidated some of the cellular mechanisms that are involved in prion uptake, replication and propagation. However, relatively little information is available about the mechanism(s) underlying intercellular prion transfer and tissue-to tissue prion spread. Microvesicles (MVs) are submicron vesicles (0,03-1 microm.) with a single membrane and are shed from most eukaryotic cells undergoing activation or apoptosis. The segregation of specific proteins is followed by blebbing of the membrane surface, leading to the formation of MVs and their release in the extracellular environment. MVs can be also secreted upon fusion of multivesicular endosomes with the plasma membrane (exosomes). The secretion of MVs is the result of a complex cellular process involving changes in the metabolism of lipids and proteins. The functional role of MVs is still largely unknown. However, there is evidence showing that they are important modulators of cell-to-cell communication, participate in a variety of intracellular adhesion processes and are able to induce cellular response(s). The release of PrPC and infectious PrPSc by prion infected epithelial, neuroglial and neuronal cells in association with exosomes has recently been highlighted. Furthermore, it has been shown that exosomes can propagate prion infectivity both in vitro and in vivo, suggesting that PrPSc-bearing exosomes may provide a mechanism for intercellular transmission of infectious prions in addition to cell-to-cell contact. Second objective of this Ph.D thesis was to determine the possible role of plasma membrane-derived microvesicles in the propagation and transmission of prions. The release of MVs was first studied in different murine neuronal cell lines. Here it is shown for the first time that neurons also shed plasma membrane derived MVs, in addition to exosomes. Immunoelectron microscopy and immunoblot analyses clearly demonstrated the presence of PrPC on the membrane of MVs released from PrPC-expressing cells. Characterization of lipid rafts components in MVs highlighted the presence of the ganglioside GM2, the tyrosine kinase p59Fyn, flotillin-2 and the neuronal protein GAP-43. In order to investigate whether MVs are involved in the intercellular transmission of prions, MVs were first isolated from two prion infected murine neuronal cell lines, namely the Neuro-2a PK1 and the N2a58 cells, and then used for in vitro and in vivo infection assays. Immunoblot analyses after proteinase K treatment demonstrated the association of PrPSc with the secreted MVs. The PrPSc-bearing MVs were then used to perform infection experiments on noninfected cells. By the use of cell blot assay, a method that allows the detection of PrPSc-amplification and -accumulation in cultured cells, the kinetic of prion infection in the de novo infected cells was followed. Noteworthy, it was found that PrPSc-bearing MVs were capable to transmit prions in vitro and to stably infect the recipient cells. In order to investigate the role of MVs in the transmission of infectivity in vivo, PrPSc-bearing MVs as well as MVs isolated from noninfected cells (as negative control) were injected intracerebrally in PrPC-overexpressing indicator mice (tga20). The development of clinical disease was followed in a time-dependent manner. Clinical symptoms could be observed only in the group of indicator mice inoculated with the PrPSc-bearing MVs, which then succumbed to desease. These findings clearly demonstrated that MVs are biological carriers of both PrPSc and prion infectivity. MVs could therefore participate in vivo in the processes of intercellular prion transmission and propagation.
Antibiotic resistance of pathogenic bacteria is a major worldwide problem. Bacteria can resist antibiotics by active efflux due to multidrug efflux pumps. The focus of this study has been the mycobacterial multidrug transporter TBsmr because it belongs to the small multidrug resistance (SMR) family whose members are a paradigm to study multidrug efflux due to their small size. SMR proteins are typically 11-12 kDa in size and have a four-transmembrane helix topology. They bind cationic, lipophilic antibiotics such as ethidium bromide (EtBr) and TPP+, and transport them across the membrane in exchange for protons. To understand the molecular mechanism of multidrug resistance, we have to gain information about the structure and function of these proteins. The research described in this thesis aimed to deduce details about the topology, transport cycle and key residues of TBsmr using biophysical techniques. Solid-state NMR (ssNMR) can provide detailed insight into structural organization and dynamical properties of these systems. However, a major bottleneck is the preparation of mg amounts of isotope labeled protein. In case of proteoliposomes, the problem is compounded by the presence of lipids which have to fit into the small active volume of the ssNMR rotor. In Chapter 3, an enhanced protein preparation is described which yields large amounts of TBsmr reconstituted in a native lipid environment suitable for further functional and structual studies. The achieved high protein-to-lipid ratios made a further characterization by ssNMR feasible. The transport activity and oligomeric state of the reconstituted protein in different types of lipid was studied as shown in Chapter 4. The exact oligomeric state of native SMR proteins is still uncertain but a number of biochemical and biophysical studies in detergent suggest that the minimal functional unit capable of binding substrate is a dimer. However, binding assays are not ideal since a protein may bind substrate without completing the transport cycle which can only be shown for reconstituted protein in transport assays.By combining functional data of a TPP+ transport assay with information about theoligomeric state of reconstituted TBsmr obtained by freeze-fracture electron microscopy, it could be shown that lipids affect the function and the oligomeric state of the protein, and that the TBsmr dimer is the minimal functional unit necessary for transport. The transport cycle must involve various conformational states of the protein needed for substrate binding, translocation and release. A fluorescent substrate will therefore experience a significant change of environment while being transported, which influences its fluorescence properties. Thus the substrate itself can report intermediate states that form during the transport cycle. In Chapter 5, the existence of such a substrate-transporter complex for the TBsmr and its substrate EtBr could be shown. The pH gradient needed for antiport has been generated by co-reconstituting TBsmr with bacteriorhodopsin. The measurements have shown the formation of a pH-dependant, transient substrate-protein complex between binding and release of EtBr. This state was further characterized by determining the Kd, by inhibiting EtBr transport through titration with non-fluorescent substrate and by fluorescence anisotropy measurements. The findings support a model with a single occluded intermediate state in which the substrate is highly immobile. Liquid-state NMR is a useful tool to monitor protein-ligand interactions by chemical shift mapping and thus identify and characterize important residues in the protein which are involved in substrate binding. In agreement with previous studies (Krueger-Koplin et al., 2004), the detergent LPPG was found to be highly suitable for liquid-state NMR studies of the membrane protein TBsmr and 42% of the residues could be assigned, as reported in Chapter 6. However, no specific interactions with EtBr were found. This observation was confirmed by LILBID mass spectrometry which showed that TBsmr was predominantly in the non-functional monomeric state. Functional protein was prepared in proteoliposomes which can be investigated by solidstate NMR (Chapter 7). Besides the essential E13, the aromatic residues W63, Y40, and Y60 have been shown to be directly involved in drug binding and transport. Different isotope labeling strategies were evaluated to improve the quality of the NMR spectra to identify and characterize these key residues. In a single tryptophan mutant of reconstituted TBsmr W30A, the binding of ethidium bromide could be detected by 13C solid-state NMR. The measurements have revealed two populations of the conserved W63 residue with distinct backbone structures in the presence of substrate. There is a controversy about the parallel or anti-parallel arrangement of the protomers in the EmrE dimer (Schuldiner, 2007) but this structural asymmetry is consistent with both a parallel and anti-parallel topology.
Background and objectives: Constrictive pericarditis (CP) is the result of a spectrum of primary cardiac and non-cardiac conditions. Little data exists on the cause-specific survival after pericardiectomy in the modern era. The impact of pericardial calcification (CA) on survival is unclear. We sought to determine the association of etiology of CP, CA and other clinical variables with long-term survival after pericardiectomy. Methods: We analyzed the records of 163 patients who underwent pericardiectomy for CP over a 24-year period at a single center. The diagnosis of CP was established by surgical report. Vital status was obtained by the Social Security Death Index. The Kaplan Meier method was used to estimate overall survival and survival by etiology group. Cox proportional hazards regression analysis was performed to assess the effect of various causes for CP on longterm survival while adjusting for age. Results: The etiology of CP was idiopathic in 75 patients (46%), prior cardiac surgery in 60 (37%), radiation treatment in 15 (9%) and miscellaneous in 13 patients (8%). Vital status was obtained in 160 patients (98%). Median follow-up was 6.9 years (range: 0.8 to 24.5 years). Perioperative mortality for all patients was 6%. Idiopathic CP had the best prognosis (7 year survival: 88%, 95% confidence interval [CI] 76% to 94%) followed by postsurgical (66%, 95% CI 52% to 78%) and postradiation CP (27%, 95% CI 9% to 58%). In bootstrap-validated proportional hazards analyses, predictors of poor survival were prior radiation, worse renal function, higher pulmonary artery pressure (PAP), abnormal left ventricular (LV) systolic function, lower serum sodium level, and older age. Pericardial calcification had no impact on survival. Conclusion: Long-term survival after pericardiectomy for CP is determined by the underlying etiology of constriction, LV systolic function, renal function, serum sodium, and PAP. Patients with postsurgical as well as postradiation CP have a survival inferior to patients with idiopathic CP. Perioperative Mortality is low. The relatively good survival after pericardiectomy in patients with idiopathic CP emphasizes the safety of pericardiectomy in this group.
The dissertation, ”Coping with emergent hearing loss”, is written in English and is based on the diversity of problems connected to hearing loss and the adaptation of hearing aids. The research was carried out in Denmark and involves adults with an emergent hearing loss, who have decided to become hearing aid users. The data is analyzed through methods of cultural anthropology with focus on the following topics: How do the new users cope with the status passage towards being hearing aid users, how do they integrate the hearing aids into their lives, and what are the involved learning processes. What are the consequences of the provision by the state of free hearing aids, their free adaptation as well as free batteries, and does the state take part in the construction of the social group of new hearing aid users? The method is based on qualitative field work. Two public hospitals were helpful in identifying 24 new users, who acquired a free hearing aid through the hearing health care system. Through ENTs and private dispensers 17 further respondents joined the study – these acquired their hearing aids with a considerable state subsidy but mostly they themselves contributed financially as well. The 41 respondents between the ages of 42 to 92 years of age came from a wide range of professions and were followed throughout 2003 und 2004. After an in-depth qualitative interview, the contact to the respondents was maintained in order to follow the process of integration into their lives. When possible, the respondents were accompanied to their appointments in the private or public clinics. Moreover, interviews with experts from the public hearing health care system, politicians and user organisations were carried out, and the general public debate on the hard of hearing and hearing loss was followed and recorded. The second chapter gives an overview of the position of audiology in Denmark, of epidemiological information on hearing loss in the Danish society and statistics to the use of hearing aids. Moreover, basic information is given about the functioning of the human ear, the auditive perception and diagnosis and classification of hearing loss as well as a short introduction to the hearing aid technology. The structure of the further thesis divides the material into three pillars that make the discussion of the interaction processes possible. (1) The user’s interaction with the lifeworld concerns the meaning of hearing in relation to social participation. For some of the users, a good sense of hearing was essential to communicate freely and uphold their position in relation to others, whereas other respondents paid less attention to the information they acquired through their sense of hearing. A number of the respondents were selective and only used their hearing aids in specific situations, whereas another group discontinued the use of their hearing aids for various reasons. Status passages that hold specific challenges like a new work place or a new marriage motivate the continued everyday use. On the whole, the thesis illustrates that hearing loss is a socially dividing factor that complicates the interaction with others. In comparison to other bodily impairments or diseases, the hearing loss is rarely used as occasion to unite with fellow sufferers, join patient organisations or form self help groups. (2) The users’ interaction with the institutions The medical anthropologist Arthur Kleinman conceptualises health care as a moral process in which essential issues are at stake for the users. Different factors interact in the process: the training of the experts, allocation of funds, the quality of the technology, the dispensing procedures and the motivation and individual characteristics of the new users. The integration of the hearing aid into the lifeworld can be compared to a learning process, for which reason the learning theory of the anthropologist Gregory Bateson is outlined. Susanne Bisgaard’s own theory lists the meaning creating elements that serve as motivation for the users to counteract contingency (occurrences that influence the adaptation negatively). In the interaction between individual and society, the individual can apply strategies in order to eliminate stumbling blocks. (3) The users’ interaction with the technology A number of theorists from Anthropology as well as Science and Technology Studies are discussed in order to question their validity with regard to human action autonomy vs. technological determination and test the theoretical models with regard to their usability for the thesis. Hearing aids have a supporting function in everyday life and have the capability of moderating the user’s perception of sound. The alienating experience of hearing one’s own voice amplified, of wearing a foreign body in the ear and the different strategies that emerge from the more or less successful handling of the technology is reported by way of case stories and quotes from the interviews.
Pulsed electron-electron double resonance (PELDOR) is a well established method concerning nanometer distance measurements involving two nitroxide spin-labels. In this thesis the applicability of this method to count the number of spins is tested. Furthermore, this work explored the limits, up to which PELDOR data obtained on copper(II)-nitroxide complexes can be quantitatively interpreted. Spin counting provides access to oligomerization studies – monitoring the assembly of homo- or hetero-oligomers from singly labeled compounds. The experimental calibration was performed using model systems, which contain one to four nitroxide radicals. The results show that monomers, dimers, trimers, and tetramers can be distinguished within an error of 5% in the number of spins. Moreover, a detailed analysis of the distance distributions in model complexes revealed that more than one distance can be extracted from complexes bearing several spins, as for example three different distances were resolved in a model tetramer – the other three possible distances being symmetry related. Furthermore, systems exhibiting mixtures of oligomeric states complicate the analysis of the data, because the average number of spin centers contributes nonlinearly to the signal and different relaxation behavior of the oligomers has to be treated explicitly. Experiments solving these problems are proposed in the thesis. Thus, for the first time spin counting has been experimentally calibrated using fully characterized test systems bearing up to four spins. Moreover, the behavior of mixtures was quantitatively interpreted. In addition, it has been shown that several spin-spin distances within a molecule can be extracted from a single dataset. In the second part of the thesis PELDOR experiments on a spin-labeled copper(II)-porphyrin have been quantitatively analyzed. Metal-nitroxide distance measurements are a valuable tool for the triangulation of paramagnetic metal ions. Therefore, X-band PELDOR experiments at different frequencies have been performed. The data exhibits only weak orientation selection, but a fast damping of the oscillation. The experimental data has been interpreted based upon quantitative simulations. The influence of orientation selection, conformational flexibility, spin-density distribution, exchange interaction J, as well as anisotropy and strains of the g-tensor has been examined. An estimate of the spin-density delocalization has been obtained by density functional theory calculations. The dipolar interaction tensor was calculated from the point-charge model, the extension of the point-dipole approximation to several spin bearing centers. Even assuming asymmetric spin distributions induced by an ensemble of asymmetrically distorted porphyrins the effect of delocalization on the PELDOR time trace is weak. The observed damping of dipolar oscillations has been only reproduced by simulations, if a small distribution in J was assumed. It has been shown that the experimental damping of dipolar modulations is not solely due to conformational heterogeneity. In conclusion the quantitative interpretation of PELDOR data is extended to copper-nitroxide- and multi-spin-systems. The influence of the mean distance, of the number of coupled spins, of the conformational flexibility, of spin-density distribution and of the electronic structure of the spin centers has been analyzed using model systems. The insights on model compounds mimicking spin-labeled biomacromolecules – in oligomeric or metal bound states – calibrate the method with respect to the information that can be deduced from the experimental data. The resulting in-depth understanding allows correlating experimental results (from for example biological systems) with models of structure and dynamics. It also opens new fields for PELDOR as for example triangulation of metal centers and oligomerization studies. In general, this thesis has demonstrated that modern pulsed electron paramagnetic resonance techniques in combination with quantitative data analysis can contribute to a detailed insight into molecular structure and dynamics.
Dicer and Drosha are the major enzymes involved in microRNA processing. Using siRNA targeting Dicer and Drosha, thereby downregulating a substantial number of microRNAs in EC, we demonstrate a crucial role of both enzymes in angiogenic processes. Interestingly, Dicer inhibition exerts more profound effects on processes like migration and viability of EC in comparison to Drosha inhibition. Moreover, Dicer effects in vivo angiogenesis, a process which is unaffected by Drosha. This discrepancy might be partially due to the involvement of Dicer in other cellular processes like heterochromatin formation and to the fact that Dicer and Drosha target mainly different subsets of microRNAs. In addition, we identified miR-92a as a novel endogenous repressor of the angiogenic program in EC, which impairs their angiogenic functions in vitro and in vivo. Consistent with these data, blocking miR-92a by systemic infusion of antagomirs enhances neovascularization and functional recovery after ischemia in vivo. At first sight, the anti-angiogenic function of miR-92a in EC appears to contradict the previously identified anti-apoptotic and pro-angiogenic activities of the miR-17~92 cluster in tumor cells. However, this apparent discrepancy might be well rationalized by a predominant function of miR-18a and miR-19a in tumor cells, which are responsible for the tumorigenic and non-cell autonomous pro-angiogenic functions of the miR-17~92 cluster. Instead, miR-92a expression is specifically upregulated in ischemic tissues and appears to cell-autonomously repress the angiogenic potential of EC. Among the various targets and verified regulated genes identified by microarray, we confirmed the downregulation of Integrin a5 in vitro and in vivo. The relevance of this miR-92a target is evidenced by severe vascular defects in the absence of Integrin a5. In addition, endothelial miR-92a interferes with the expression pattern of genes controlling key EC functions at various levels, some of which, e.g. eNOS, might be secondarily affected by directly targeted genes. Obviously, our data do not formally exclude effects of antagomir-92a on perivascular and other cell types, but surely include effects on EC. Regardless of this, the capacity of miR-92a to target various downstream effectors might be an advantage of miRNA-based therapeutic strategies and may overcome the limited therapeutic capacity of single growth factor or single gene therapies in ischemic diseases, since the highly organized process of vessel growth, maturation and functional maintenance is well known to require the fine-tuned regulation of a set of genes.
In this study I analysed past and recent Daphnia populations from Lake Constance and Greifensee. Herefore, I first established a set of microsatellite markers applicable to European Hyalodaphnia species (chapter 1). Primers were also identified for species specific fragment lengths. 32 markers were then available to characterize the resting egg banks of Daphnia galeata and D. hyalina. Chapter 2 presents the reconstruction of the taxonomic composition in these two ecologically different lakes. This part of my work shows that the eutrophication that occurred in both lakes in the mid of the last century has strongly influenced the Daphnia populations. In both lakes Daphnia galeata established and hybridized with the indigenous D. hyalina. Interspecific hybridization resulted in introgression on the mitochondrial and nuclear level. In chapter 3 resting eggs from the sediments of the 1960s, 1970s, 1980s, 1990s and 2000s were characterized with microsatellite markers. The aim was to specify the extent of interspecific hybridization and nuclear introgression assuming that the genetic exchange between both species has an impact on their adaptation to their habitat. In life history experiments D. galeata and D. galeata x hyalina clones hatched from different time periods showed significant differential responses to food quality. Therefore, the question had to be answered how the Daphnia resting egg bank and the planktonic population are connected. In chapter 4 hatching experiments were conducted to bridge this gap of scientific knowledge in the life cycle of cyclic parthenogenetic waterfleas. Only D. galeata individuals were able to establish a clonal lineage after maturity. All observed recombinant individuals did not reproduce at all or firstly went through another sexual phase of reproduction i.e. produced resting eggs. In order to compare the findings of chapter 4 with the taxon composition of the recent planktonic population of Daphnia in Lake Constance, samples were taken over one season (between May 2005 and September 2006). During the season, the taxonomic composition of Daphnia changes severely with D. galeata being most abundant during the warm season and D. hyalina in the cold season. Moreover, some individuals were detected, that did not follow this pattern. With mitochondrial analysis those individuals were identified as mitochondrial introgressants and processed to life history experiments. Significant differences in the somatic growth rate under different temperatures (5°C, 12.5°C and 20°C) were related to the origin of the mitochondrial genome rather than the nuclear taxonomic assignment of the individual.
The findings of this study show that all organisms exposed to rapid ecological changes and their microevolutionary reaction to those.
The growth of blood vessels is crucial for organ growth in the embryo and repair of wounded tissues in the adult. An imbalance in this process contributes to numerous malignant, inflammatory, ischemic, infectious and immune disorders (Ferrara et al., 2003). Postnatal neovascularization occurs through the recruitment of progenitor cells and angiogenesis. Integrins are heterodimeric cell surface molecules and are the main receptors for extracellular matrix proteins. Regulation of integrin activation is crucial during embryonic development and during adult life. Dysregulation of integrin activity leads to severe diseases. In this study, we have demonstrated that Rap1, a small GTPase regulating integrin activity, and its GEF Epac1 are expressed in both EPC and endothelial cells. Moreover, the pharmacological activator of Epac activates the small GTPase Rap1 in progenitor cells. In parallel the angiogenic growth factors VEGF and bFGF activate Rap1 in endothelial cells. In addition, the regulation of Rap1 activity in EPC and in endothelial cells plays an important role in the regulation of migration and adhesion to matrix proteins, by regulating the activity of different integrins, a mechanism known as integrin inside‐out signaling. Furthermore, regulation of Rap1 activity affects probably indirectly through outside‐in signaling of integrins the activity of several and crucial proteins such PKB/Akt and focal adhesion kinase in endothelial cells. In line with these results, we have demonstrated that Rap1 activity affect angiogenesis, homing of EPC to ischemic tissues and thereby postnatal neovascularization. The understanding how Rap1 regulates integrin activity in endothelial cells is still not completely clear, for example we have demonstrated that the known effectors of Rap1 mediating the increase of integrin activity in T and B cells, such as RAPL and RIAM are, respectively, either not increasing integrin activity or not expressed in endothelial cells. We aim to find the effector of Rap1 promoting integrin activity in endothelial cells and how RAPL regulates integrin functions and angiogenesis. Moreover data from us and others using genetic models and generation of Rap1a or Rap1b deficient mice or deficient for Rap1a and Rap1b led to embryonic lethality suggesting that Rap1 is a key node protein during embryonic development. The development of conditionnal Rap1a/b endothelial/pericytes restricted deficient mice will help us to decipher more precisely the role of Rap1 during vascular development and angiogenesis.
The research presented in this thesis characterizes U2AF homology motifs (UHM) and their interactions with UHM ligand motifs (ULM) in the context of splicing regulation. UHM domains are a subgroup of RNA recognition motifs (RRM) originally discovered in the proteins U2AF65 and U2AF35. Whereas canonical RRMs are usually involved in binding of RNA, UHM domains bind tryptophan containing linear protein motifs (ULM) instead. In the first article, we analyze the complex network of interactions between splicing factors and RNA that initiate the assembly of the spliceosome at the 3´ splice site of an intron. The protein U2AF65 binds a pyrimidine-rich element in introns and recruits U2snRNP by binding its protein component SF3b155. My contribution was to define the binding site of the protein U2AF65 to the intrinsically unstructured N-terminus of the scaffolding protein SF3b155. I could show that the UHM domain of U2AF65 recognizes a ULM in SF3b155, and that this binding site is not overlapping with the binding sites of other splicing factors, like p14, to SF3b155. As the U2AF65-UHM:SF3b155-ULM interaction is mutually exclusive with an interaction between U2AF65-UHM and a ULM in the splicing factor SF1, which was reported to initially recognize the branch point sequence, my results provide the molecular details on how SF3b155 replaces SF1 during spliceosomal reorganizations. In the second article, we show that overexpression of the UHM domain of the splicing factor SPF45 induces exon 6 skipping in the pre-mRNA of Fas (CD95/APO-1). I provide evidence for in vitro binding of SPF45-UHM to ULM sequences in the splicing factors U2AF65, SF1, and SF3b155. I crystallized free and SF3b155-bound SPF45 UHM and solved both structures by X-ray crystallography. The analysis of the complex interface and sequence differences in the ULMs allowed me to design mutations of SPF45-UHM, which selectively inhibit binding to distinct ULMs. After assessing the ULM binding properties in vitro, we could show that the activity of SPF45-UHM in influencing the splicing pattern of Fas relies on interactions with SF3b155 and/or SF1, but that an interaction with U2AF65 is dispensable. A mechanism for the activity of SPF45-UHM could thus be engaging in ULM interactions and thus interfering with the network of interactions that initiate the assembly of the spliceosome at the 3´splice site, as described above. In the third article, we describe an unusual flexible homodimerization mode of the UHM in the splicing factor Puf60, which enables simultaneous interactions with ULM sequences on other splicing factors. I could show that the NMR relaxation properties of Puf60-UHM are inconsistent with a model of a rigid dimer, but rather indicate a dimerization via a flexible linker. I identified a flexible loop in the peptide backbone of Puf60-UHM, and showed that mutiation of acidic residues in this loop impairs the dimerization. To analyze the dimerization interface in further detail, I solved the structure of Puf60-UHM by X-ray crystallography. The acidic residues in the flexible loop of one UHM dimer subunit mediate the dimerization by contacting basic residues on the β-sheet surface of the other dimer subunit. Differences in the four dimer interfaces observed for the eight molecules in the asymmetric unit of the crystal support the model of an undescribed, flexible mode of dimerization, and thus complement the NMR relaxation data. Furthermore, I could show that the Puf60-UHM dimer and U2AF65-UHM contact different ULM sequences on the SF3b155 N-terminus in vitro, thus providing a possible explanation for the mutual cooperative activation of Puf60 and U2AF65 in splicing assays described in the literature. The fourth article is a review about recent research on the recognition of DNA double strand breaks (DSB) by covalent histone modifications. The p53 binding protein 1 (53BP1) is a DSB sensor and a checkpoint protein for mitosis. Recent crystallographic evidence indicates that 53BP1 recognizes DSB sites by binding histone H4 dimetylated at lysine 20 (H4-K20). We provide a comprehensive overview of the atomic resolution structures that revealed how proteins can specifically recognize histone tail modifications, especially methylated lysines, to read the information stored in what is called the histone code.
Crohn´s disease (CD) and Ulcerative colitis (UC) are idiopathic inflammatory disorders. Environmental factors, infectious microbes, ethnic origin, genetic susceptibility, and a dysregulated immune system can result in mucosal inflammation. However, the etiology of both CD and UC still remains largely unclear. Inflammatory bowel diseaserelated animal models suggest that a combination of genetic susceptibility factors and altered immune response driven by microbial factors in the enteric environment may contribute to the initiation and chronification of the disease. The intestinal immune system represents a complex network of different lymphoid and non-lymphoid cell populations as well as humoral factors. In inflammatory bowel disease, the controlled balance of the intestinal immune system is disturbed at all levels. In CD, naïve T cells preferably differentiate into Th1 or Th17 producing cells, while in UC, these cells differentiate into aberrant Th2 cells. Overall, in active inflammatory bowel disease effector T cell activity (Th1, Th17, Th2) predominates over regulatory T cells. Animal models of intestinal inflammation are indispensable for our understanding of the pathogenesis of CD and UC. When chosen appropriately, these models proved to be a helpful tool to investigate pathophysiological mechanisms, as well as to test emerging therapeutic options in the preclinical phase. 2,4,6-Trinitrobenzene sulfonic acid (TNBS) and oxazolone are the two major chemicals applied to induce Th1- and Th2-skewed intestinal inflammation, respectively. Colitis can be induced in susceptible strains of mice by intrarectal instillation of the haptenating substances TNBS or oxazolone in ethanol, which is necessary for an initial desintegration of the epithelial barrier. TNBS or oxazolone are believed to haptenize colonic autologous or microbiotic proteins rendering them immunogenic to the host immune system. While TNBS administration in the presence of ethanol results in a transmural infiltrative disease in the entire colon based on an IL-12/IL-23 driven, Th1-or Th17 mediated response, oxazolone instillation finally leads to a colitis caused by a polarized Th2 IL-13-dominated lymphocyte response. Rectal oxazolone instillation in ethanol produces a more superficial inflammation that affects the distal half of the colon rather than the whole colon. Therapeutic modulation of the disturbed immune response in patients with inflammatory bowel disease still represents a complex challenge in the clinic. Currently, none of the therapeutic measure are disease specific and they generally target the pathophysiology downstream of the driving immunpathology. So, there is still the need to develop a tailored approach to prevention of the initiation and perpetuation of the inflammatory cascade before tissue injury occurs. One important aspect of this approach might involve the induction or re-establishment of immunological tolerance. FTY720 following rapid phosphorylation to FTY-P by endogenous sphingosine kinases acts as a sphingosine-1-phosphate (S1P) receptor agonist and represents the prototype of a new generation of S1P receptor modulators. While changing currently its proposed mode of action still focus on the fact, that FTY720 effectively inhibits the egress of T-cells from lymph nodes, thereby reducing the number of antigen-primed/restimulated cells that re-circulate to peripheral inflammatory tissues. However, recent studies indicate, that its immunomodulatory properties might be more complex and exerted not only via interactions with other S1P receptor subtypes but also via a direct modulation of the inflammatory capacity of dendritic cells (DC) resulting in a modified regulation of T cell effector functions as well as in an induction of regulatory T cells and function. 1,25(OH)2D3, the active form of vitamin D, is a secosteroid hormone that has in addition to its central function in calcium and bone metabolism pronounced immune regulatory properties. The biological effects of calcitriol are mediated by the vitamin D receptor (VDR), a member of the superfamily of nuclear hormone receptors. A number of studies identified calcitriol/VDR as prominent negative regulators of Th1-type immune responses, whereas Th2 responses are not affected or even augmented. These effects have been mainly explained by direct activities on lymphocytes, subsequent studies clearly supported a role of calcitriol in modulating monocyte differentiation or DC maturation. However, to translate the immunosuppressive capacities of calcitriol into an effective immunointervention, a great challenge was the design of structural analogs of calcitriol that are devoid of adverse effects related to hypercalcemic activity. The intense study of the 25-oxa series generated a large number of calcitriol analogs exhibiting substantial dissociation between possible immunomodulatory capacities and undesired hypercalcemia. Especially, the combination of the 22-ene modification with the 25-oxa element as realized in ZK156979 yielded a very promising set of new analogs for further characterization in animal models resembling human autoimmune diseases. So, the overall aim of the studies presented here was to evaluate strategies of enhancing regulatory immunity in mouse models of Th1- and Th2-mediated colitis as a new therapeutic approach. To this end we used FTY720, 22-ene-25-oxa vitamin D (ZK156979), as well as the combination of calcitriol and dexamethasone to evaluate the respective pro-tolerogenic potential in intestinal inflammation models in mice. First, to induce Th1-mediated colitis a rectal enema of TNBS was given to Balb/c mice. FTY720 was administered i.p. from day 0-3 or 3-5. FTY720 substantially reduced all clinical, histopathologic, macroscopic, and microscopic parameters of colitis analyzed. The therapeutic effects of FTY720 were associated with a down-regulation of IL-12p70 and subsequent Th1 cytokines. Importantly, FTY720 treatment resulted in a prominent up-regulation of FoxP3, IL-10, TGFβ and CTLA4. Moreover, we observed a significant increase of CD25 and FoxP3 expression in isolated lamina propria CD4+ T cells of FTY720-treated mice. The impact of FTY720 on regulatory T cell induction was further confirmed by concomitant in vivo blockade of CTLA4 or IL-10R which significantly abrogated its therapeutic activity. Thus, our data provide new and strong evidence that besides its well-established migratory properties FTY720 down-regulates proinflammatory signals while simultaneously inducing the functional activity of CD4+CD25+ regulatory T cells. In a second approach, the rectal instillation of oxazolone yielded a Th2-mediated colitis. Treatment with FTY720 prominently reduced the clinical and histopathologic severity of oxazolone-induced colitis, abrogating body weight loss, diarrhea, and macroscopic and microscopic intestinal inflammation. The therapeutic effects of FTY720 were associated with a prominent reduction of the key Th2 effector cytokines IL-13, IL-4 and IL-5. Moreover, FTY720 inhibited GATA3 and T1/ST2 expression, which represent distinct markers for Th2 differentiation and Th2 effector function. Thus, our data are supportive for the view that FTY720 exhibits beneficial prophylactic as well as therapeutic effects in Th2-mediated experimental colitis by directly affecting Th2 cytokine profiles, probably by reducing GATA3 and T1/ST2. Recently, we described 22-ene-25-oxa-vitamin D (ZK156979) as a representative of a novel class of low calcemic vitamin D analogs showing prominent immunomodulative capacities. Here, we used the Th1-mediated TNBS colitis to test its anti-inflammatory properties in vivo. We found that treatment with ZK156979 clearly inhibited the severity of TNBS-induced colitis without exhibiting calcemic effects. Both early and late treatment abrogated all the clinical macroscopic and microscopic parameters of colitis severity; in addition we observed a clear down-regulation of the relevant Th1 cytokine pattern including the T-box transcription factor, T-bet. On the other hand, application of ZK156979 increased local tissue IL-10 and IL-4. Finally, as a new approach we evaluated the pro-tolerogenic potential of calcitriol and dexamethasone in acute Th1-mediated colitis. Calcitriol and/or dexamethasone were administered i.p. from day 0-3 or from day 3-5 following the instillation of the haptenating agent. The combination of these steroids most effectively reduced the clinical and histopathologic severity of TNBS colitis. Th1-related parameters were down- while Th2 markers like IL-4 and GATA3 were up-regulated. Clearly distinguishable from known steroid effects calcitriol in particular promoted regulatory T cell profiles as indicated by a marked increase of IL-10, TGFß, FoxP3 and CTLA4. Furthermore, analysis of DC mediators responsible for a pro-inflammatory differentiation of T cells revealed a clear reduction of IL-12p70, and IL23p19 as well as IL-6 and IL-17. Thus, our data suggest the concept of a steroid-sparing application of calcitriol derivatives in inflammatory bowel disease. Furthermore, the data presented suggest that early markers of inflammatory DC and Th17 differentiation might qualify as new target molecules for both calcitriol as well as for selective immune modulating vitamin D analogs. In conclusion the data of these published investigations added to the substantial progress in understanding the biology of tolerogenic DC and regulatory T cells with respect to their roles in health and disease achieved in the past years. This has led to an increasing interest in the possibility of using DC and regulatory T cells as biological therapeutics to preserve and restore tolerance to self antigens and alloantigens. Especially DC may be helpful to exert their important roles in directing tolerance and immunity by modulation of subpopulations of effector T cells and regulatory T cells. The data demonstrated in the present studies may assist to define the divergent implications of new therapeutic concepts for the treatment of inflammatory bowel disease, especially with regard to a possible auspicious impact on pro-tolerogenic DC and regulatory T cell functions. However, further studies are needed to fulfil our understanding of the complex immunomodulatory profiles of FTY720 as well as of calcitriol and its low calcemic analog ZK156979, thus accelerating their entry into the clinic as new therapeutic options for the cure of inflammatory bowel disease.
Flexibility and constraints in migration and breeding of the barnacle goose Maximising fitness means, to a large extent, optimising management of time and energy. This thesis investigates aspects of timing and resource acquisition and utilisation in the barnacle goose Branta leucopsis during spring migration and reproduction. The barnacle goose population wintering along the Wadden Sea coast, and traditionally migrating via a stopover in the Baltic to its breeding sites in northern Russia, has shown some remarkable developments, among them, a geometric growth rate since the 1950s and a notable change in the timing of departure from the wintering grounds. Furthermore, long being regarded as an obligate Arctic breeder, within the past three decades this species has successfully colonised a wide variety of habitats at temperate latitudes, thereby shortening the migratory distances considerably or refraining from migration altogether. These remarkable changes raise questions about the flexibility of migratory and reproductive schedules. What are the costs and benefits of different migration strategies? And, given the context of global change, to what extent are animals capable of adapting to rapidly changing environments? In order to answer these questions we tracked migratory geese by satellite and with the help of data loggers and, furthermore, explored possible relationships of migratory behaviour and breeding performance. Another central thesis topic represents a within-species comparison of major life-history traits in populations breeding along a large ecological gradient from arctic to temperate environments. Fieldwork was conducted in arctic Russia, Sweden and The Netherlands.
Deformation quantization on symplectic stacks and applications to the moduli of flat connections
(2008)
It is a common problem in mathematical physics to describe and quantize the Poisson algebra on a symplectic quotient [...] given in terms of some moment map [...] on a symplectic manifold [...] with a hamiltonian action by a Lie group G. Among others, problems may arise in two parts of the process: c might be a singular value of the moment map and the quotient might not be well-behaving; in the interesting cases the quotient often is singular. By the famous result of Sjamaar and Lerman ([102]) X is a symplectic stratified space. We are interested in cases for which we can give a deformation quantization of the possibly singular Poisson algebra of X. To that purpose we introduce a Poisson algebra on the associated stack [...] for special cases and consider its deformations and their classification. We dedicate ourselves to use the rather geometric methods introduced by Fedosov for symplectic manifolds in [37]. That leads to the question how to perform differential geometry on a smooth stack. The Lie groupoid atlas of a smooth stack is a nice model for the same space (Tu, Xu and Laurent-Gengoux in [107] and Behrend and Xu in [16]), but both have different topoi. We give a morphism (P,R) that compares the topologies of a smooth stack and its atlas. This yields a method to transport sheaves and their sections between a smooth stack and its Lie groupoid atlas. A symplectic stack is a smooth separated Deligne-Mumford stack with a 2-form which is closed and non-degenerate in an atlas. Via (P,R) a deformation quantization on a symplectic stack can be performed in terms of an atlas. We also give a classification functor for the quantizations in the spirit of Deligne ([35]) based on the geometric interpretation given by Gutt and Rawnsely in [49]. As an application we give a deformation quantization for the moduli stack of flat connections in particular configurations. We use Darboux charts provided by Huebschmann (e.g. in [54]) to construct the corresponding Lie groupoid. This captures the symplectic form arising in the reduction process and differs from other approaches using gerbes of bundles (e.g. Teleman [105]).
The crude oil constituents benzene, toluene, ethylbenzene, and the three xylene isomers (BTEX) are the dominating groundwater contaminants originating from surface spill accidents by oil production facilities and with gasoline and jet fuel. Thereby BTEX posing a threat to the world´s scarce drinking water resources due to their water solubility and toxicity. An active remediation cleanup involving a BTEX event proves not only to be very expensive but almost impossible when it comes to the complete removal of contaminants from the subsurface. A favoured and common practice is combining an active remediation process focussing on the source of contamination coupled together with the monitoring of the residual contamination in the subsurface (monitored natural attenuation; MNA). MNA include all naturally occuring biological, chemical and physical processes in the subsurface. The general goal of this work was to improve the knowledge of biodegradation of aromatic hydrocarbons under anaerobic conditions in groundwater. For this groundwater and soil at the former military underground storage tank (UST) site Schäferhof – Süd near Nienburg/Weser (Niedersachsen, Germany) were sampled and analysed. The investigations were done in collaboration of the Umweltbundesamt, the universitys of Frankfurt and Bremen and the alphacon GmbH Ganderkesee. To investigate the extent of groundwater contamination, the terminal electron acceptor processes (TEAPs) and the metabolites of BTEX degradation in groundwater, six observation wells were sampled at regular intervals between January 2002 and September 2004. The wells were positioned in order to cover the upstream, the source area and the downstream of the presumed contamination source. Additionally, vertical sediment profiles were sampled and investigated with respect to spreading and concentration of BTEX in the subsurface. A large residual contamination involving BTEX is present in soil and groundwater at the studied locality. Maximum BTEX concentration values of 17 mg/kg were recorded in analysing sediment in the unsaturated zone. In the capillary fringe, values of 450 mg/kg were recorded (October 2004) and in the saturated zone maximum values of 6.7 mg/kg BTEX were detected. The groundwater samples indicate increasing BTEX concentrations in the groundwater flow direction (from 532 µg/l up to 3300 µg/l (mean values)). Biodegradation of aromatic hydrocarbons under anaerobic conditions in the sub surface at contaminated sites is characterised by generation of metabolites. From the monoaromatic hydrocarbons BTEX metabolites such as benzoic acid (BA) and the methylated homologs and C1-and C2-benzyl-succinic acids (BSA) are generated as intermediates. A solid-phase extraction method based on octadecyl-bonded silica sorbent has been developed to concentrate such metabolite compounds from water samples followed by derivatization and gas chromatography/mass spectrometry (GC/MS) of the extracts. The recovery rate range between 75 and 97%. The method detection limit was 0.8 µg/l. Organic acids were identified as metabolic by-products of biodegradation. Benzoic acid, C1-, C2- and C3-benzoic acid were determined in all contaminated wells with considerable concentrations. Furthermore, the depletion of the dominant terminal electron acceptors (TEAs) oxygen, nitrate, and sulphate and the production of dissolved ferrous iron and methane in groundwater indicate biological mediated processes in the plume evidently proving the occurrence of NA. A large overlap of different redox zones at the studied part of the plume has been observed. A important finding in this study is the strong influence of groundwater level fluctuations on the BTEX concentration in groundwater. A very dry summer in 2003 was recorded during the monitoring period, resulting on site in a drop of the groundwater level to 1.7 m and a concomitant increase of BTEX concentrations from 240 µg/l to 1300 µg/l. The groundwater level fluctuations, natural degradation and retention processes essentially influence BTEX concentrations in the groundwater. Groundwater level fluctuations have by far a stronger influence than the influence of biological degradation. Increasing BTEX concentrations are hence not a consequence of limited biological degradation. Another part of the study was to observe the isotopic fractionation of the electron acceptor Fe(III), due to biologically mediated reduction of Fe(III) to the watersoluble Fe(II) at the site and first field data are presented. Both groundwater and sediment samples were analysed with respect to their Fe isotopic compositions using high mass resolution Multi Collector-Inductively Coupled Plasma-Mass Spectrometry (MC-ICP-MS). The delta56Fe -values of groundwater samples taken from observation wells located downstream of the source area were isotopically lighter than delta56Fe -values obtained from groundwater in the uncontaminated well. The Fe isotopic composition of most parts of the sediment profile was similar to the Fe isotopic composition of uncontaminated groundwater. Thus, a significant iron isotope fractionation can be observed between sediment and groundwater downstream of the BTEX contamination.
The Na+,K+-ATPase was discovered more than 50 years ago, but even today the pumpcycle and its partial reactions are still not completely understood. In this thesis, Voltage Clamp Fluorometry was used to monitor the conformational changes that are associated with several electrogenic partial reactions of the Na+,K+-ATPase. The conformational dynamics of the ion pump were analyzed at different concentrations of internal Na+ or of external K+ and the influences on the conformational equilibrium were determined. To probe the effect of the internal Na+ concentration on the Na+ branch of the ion pump, oocytes were first depleted of internal Na+ and then loaded with Na+ using the epithelial sodium channel which can be blocked by amiloride. The conformational dynamics of the K+ branch were studied using different external K+ concentrations in the presence and in the absence of external Na+ to yield additional information on the apparent affinity of K+. The results of our Voltage Clamp Fluorometry experiments demonstrate that lowering the intracellular concentration of Na+ has a comparable effect on the conformational equilibrium as increasing the amount of K+ in the external solution. Both of these changes shift the equilibrium towards the E1/E1(P) conformation. Furthermore, it can be shown that the ratio between external Na+ and K+ ions is also a determinant for the position of the conformational equilibrium: in the absence of external Na+, the K+ dependent shift of the equilibrium towards E1 was observed at a much lower K+ concentration than in the presence of Na+. In addition, indications were found that both external K+ and internal Na+ bind within an ion well. Finally, the crucial role of negatively charged glutamate residues in the 2nd extracellular loop for the control of ion-access to the binding sites could be verified.