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This thesis presents a model for the dynamical description of deconfined quark matter created in ultra-relativistic heavy ion collisions, treating quarks and antiquarks as classical point particles subject to a colour-dependent, Cornell-type potential interaction. The model provides a dynamical handle for hadronization via the recombination of quarks and antiquarks in colour neutral clusters. Gluons are not included explicitly in the model,but are described in an effective manner by the means of the potential interaction. The model includes four different quark flavours (up, down, strange and charm) and uses current masses for the quarks. The dynamical evolution of a system of colour charges subject to the Hamiltonian equations of motion of the model yields the formation of colour neutral clusters of quarks and antiquarks, which are subject only to a small remaining interaction, the strong interquark potential notwithstanding. These clusters can be mapped onto hadrons and hadronic resonances. Thus, the model allows a dynamical description of quarks degrees of freedom in heavy ion collisions, including a recombination scheme for hadronization. The thermal properties of the model turn pout to be very satisfying. The model shows a transition from a confining phase to a deconfined phase with rising temperature, going hand in hand with a softest point in the equation of state and a rise of energy density and pressure to the Stefan-Boltzmann limit of a gas of quarks and antiquarks. Moreover, the potential interaction is screened in the deconfined phase. For the dynamical description of ultra-relativistic heavy ion collision, the qMD model is coupled to UrQMD as a generator for its initial conditions. In this way, a fully dynamical description of the expansion and hadronization of the fireball created in such collisions can be achieved. Non-equilibrium aspects of the expansion dynamics and hadronization by recombination of quarks and antiquarks are discussed in detail, and a comparison with experimental data of collisions at the CERN-SPS is presented. The big advantage of the qMD model is the possibility to study cluster formation, including exotic clusters, and fluctuations in a dynamical manner. As an example, event-by-event fluctuations in electric charge are studied. Such fluctuations have been proposed as a clear criterion to distinguish a deconfined system from a hadrons gas. However, experimental data show hadron gas fluctuation measures even at RHIC, where deconfinement is taken for granted. We will see how the dynamics of quark recombination washes out the quark-gluon plasma signal in the fluctuation criterion. Moreover, we will discuss briefly the problem of entropy at recombination. In a second application, the formation of exotic hadronic clusters, larger than usual mesons and baryons, is studied. Such clusters could provide new measures for the thermalization and homogenization of a deconfined gas of colour charges. Moreover, number estimates for exotic clusters from recombination are considerably lower than corresponding predictions from thermal models, providing a clear difference between statistical hadronization and hadronization via quark recombination. A detailed analysis is provided for pentaquark candidates such as the Theta-Plus. It turns out that the distribution of exotic states over strangeness, isospin, and spin could provide a sensitive measure for thermalization and decorrelation in the deconfined quark phase, if it could be measured.
Nucleotide-binding domains (NBDs), roughly 27 kDa in size, are conservative components of the large family of ABC (ATP-binding cassette) transporters, which includes importers, exporters, and receptors. NBDs or ABC-ATPases supply energy for the translocation of a vast variety of substrates across biological membranes. Despite their hydrophilic sequence, many NBDs tend to aggregate and precipitate in solution upon isolation from the complete transporter. The conditions stabilizing an extremely labile NBD component of the E.coli HlyA transporter, HlyB-NBD, were developed. As a result, the pure highly concentrated enzyme was protected from precipitation for months that allowed screening of the unlimited crystallization conditions in the presence of different substrates and performance of the reproducible functional assays. HlyB-NBD was characterized in regard to its uncoupled ATPase activity, oligomeric state, and stability in solution. Comparative analysis of protein stability and ATPase activity in various buffers suggested an inverse relationship between the two. Kinetic analysis of ATPase activity revealed ATP-induced protein dimerization. Gel-filtration experiments with the wild type protein and H662A-mutant of HlyB-NBD provided further evidence of protein dimerization in the presence of ATP. The crystal structures in post- and pre-hydrolysis nucleotide-bound states of HlyB-NBD were determined at 1.6Å and 2.5Å resolution, respectively. While the hydrolytically deficient H662A mutant of HlyB-NBD was crystallized as a stable dimer in the presence of ATP or ATP-Mg2+, with two nucleotide molecules sandwiched between the two monomers, the same protein was shown to be a monomer in the ADP-loaded state. The wild type protein failed to develop crystals with bound ATP, yet formed ADP-bound crystals identical to those of the H662A-mutant. The X-ray structures of HlyB-NBD in various states of the hydrolytic cycle and the functional studies of the enzyme have provided an opportunity to characterize enzyme-substrate complexes and protein-protein interactions between the NBD subunits in great detail. Comparison of the nucleotide-free, the ADP-, and the ATP-loaded states revealed oligomeric and conformational changes of the protein upon substrate binding and resulted in a molecular picture of the catalytic cycle. The correlated results of the structural and functional investigations of HlyB-NBD are discussed with relation to the mechanism of action of ABC transporters.
The analysis of doxorubicin-loaded poly(butyl cyanoacrylate) nanoparticles in in vitro glioma models
(2005)
The use of doxorubicin for the treatment of glioma tumours would be an important approach in the chemotherapy treatment since doxorubicin is a very effective neoplastic agent. However, one problem faced by the use of doxorubicin for the treatment of brain tumours is the fact that doxorubicin is a substrate of an efflux pump protein, P-glycoprotein (P-gp), which is located on the luminal side of the brain capillary endothelium and in many tumour cells, which acts pumping out of the cell such substrate, and blocking its transport into the cell. A strategy to enhance the doxorubicin delivery into the brain would be the use of nanoparticles. This work showed, that the treatment of doxorubicin bound to poly(butyl cyanoacrylate) nanoparticles decreased the viability of the three glioma cell lines, the GS-9L, the RG-2, and the F-98 cell lines significantly in comparison to doxorubicin in solution, indicating an improvement of the nanoparticles-bound doxorubicin transport into the cells. The modification of the nanoparticles surface with different surfactants may even enhance the delivery of the drug into the cells. Searching for an improvement of the doxorubicin internalization, the nanoparticles surface was modified using polysorbate 80, poloxamer 188 and poloxamine 908 surfactants. The poloxamer 188 and polaxamine 908 surfactant modified nanoparticles did not show a significant enhancement of the doxorubicin internalization. Contrary, the treatment of polysorbate 80 surfactant modified nanoparticles led in some cases to a significant decrease of cancer cell viability. The use of doxorubicin in the three glioma cell lines allowed the measurement of different responses towards doxorubicin treatment. The different responses were due to the entry of various amounts of doxorubicin into the glioma cells, which express the P-glycoprotein in their cellular membrane. A higher level of the P-gp expression correlated with a weaker response towards the doxorubicin treatment. The GS-9L cell line showed a significant higher level of P-gp expression than the F-98, and RG-2 cell lines, and consequently, the GS-9L cell line presented the highest resistance to doxorubicin with the highest viability values after doxorubicin treatment. Due to the fact that the transport of doxorubicin is governed by the activity of the P-gp in the studied glioma cells, the use of poloxamer 185 as a P-gp inhibitor resulted in an enhancement of the uptake as well as of the accumulation of doxorubicin into the cells. The effect of poloxamer 185 on the doxorubicin uptake was significant marked in the case of doxorubicin-resistance cells, as the GS-9L cell line. In some cases, the presence of the nanoparticles formulation showed also an influence on such uptake improvement. The use of a P-gp inhibitor in combination with chemotherapeutic agents leads to encouraging results. Because of the wide spectrum of substances acting as P-gp inhibitors, the exact inhibitory mechanisms remain still unclear. For instance in our results the evaluation of a described P-gp inhibitor, polysorbate 80 did not show an important improvement in the doxorubicin uptake in the P-gp-expressing cell line, GS-9L. On the other hand, the Polysorbate 80-Dox-PBCA nanoparticles formulation decreased in greater extend the viability of the glioma cells than the poloxamer185-Dox-PBCA nanoparticles. Although, the P-gp inhibition was undoubtedly higher in the presence of poloxamer 185, polysorbate 80 showed a main effect on the disruption of the cellular membrane, resulting in an important cellular viability decrease. It seems that poloxamer 185 presents a direct effect on the functionality of the P-gp protein, which would be of great importance in the sensitization of resistant cancer cells. The range of concentration of poloxamer 185 is very important to yield an inhibitory effect on the P-gp-mediated transport mechanism. The accumulation of Rhodamine-123 (Rho-123), a known P-gp substrate, increased in a range of concentration from 0.001 % to 0.01, whereas at 0.1 % poloxamer 185 the accumulation significantly decreased. A maximal Rho-123 accumulation was reached at 0.01 % poloxamer 185.
Stem cells capable of self-renewal and differentiation into multiple tissues are important in medicine to reconstitute the hematopoietic system after myelo-ablative chemo- or radiotherapy. In the present situation, adult stem cells such as Mesenchymal stem cells (MSC) and Hematopoietic stem cells (HSC) are used for therapeutic purposes. For tissue regeneration and tissue constitution, engraftment of transplanted stem cells is a necessary feature. However, in many instances, the transplanted stem cells reach the tissues with low efficiency. Considering the three-step model of leukocyte extravasation by Springer et al, the rolling, adhesion and transmigration form the three major steps for the transplanted stem cells to enter the desired tissues. One of the molecular switches reported to be involved in these mechanisms are the Rho family GTPases. The present study investigates the role of Rho GTPases in adhesion and migration of stem and progenitor cells. Chemotactic and chemokinetic migration assays, transendothelial migration assays, migration of cells under shear stress, microinjection, retroviral and lentiviral gene transfer methods, oligonucleotide microarray analysis and pull down assays were employed in this study for the elucidation of Rho GTPase involvement in migration and adhesion of stem and progenitor cells. The transmigration assay used for the migration determination of the adherent cell type, MSC, was optimized for the efficient and effective assessment of the migrating cells. The involvement of Rho was found to be critical for stem and progenitor cell migration where inactivation of Rho by C2I-C3 transferase toxin and/or overexpression of C3 transferase cDNA increased the migration rate of Hematopoietic progenitor cells (HPC) and MSC. Moreover, modulation of Rho caused predictable cytoskeletal and morphological changes in MSC. Assessment of Rho GTPase involvement in the interacting partner, the endothelial cells during stem cell migration, revealed that active Rho expression induced E-selectin expression. The increased levels of E-selectin were functionally confirmed by the increased adhesion of progenitor cells (HPC) to the Human umbilical vein endothelial cell (HUVEC) layer. Moreover, inhibition of Rac in the migrating endothelial progenitor cells (eEPC) increased their adhesion to HUVEC correlating with the increased percentage expression of cell surface receptor, CD44 in Rac inactivated eEPC. In conclusion, this study shows that Rho GTPases control the adhesion and migration of stem and progenitor cells, HPC and MSC. Rho inhibition drives the cells to migrate in the blood vessels. The substantial increase in the level of active Rho in endothelial layer, manifested by the E-selectin surface expression assists the better adhesion of stem and progenitor cells to the endothelial layer. Serum factors and growth factors in the physiological system influence the Rho GTPase expression in both migrating stem cells and the barrier endothelial cells. Thus, specific modulation of Rho GTPases in the transplanted stem and progenitor cells could be an interesting tool to improve the migration and homing processes of stem cells for cellular therapy in future.
This work is dedicated to the investigation of nuclear matter at non-zero temperatures within an effective hadronic model based on the Walecka model. It includes fermions as well as a vector omega meson and a scalar sigma meson where for the latter a quartic self-interaction has been considered. The coupling constants have been adapted to the saturation properties of infinite nuclear matter. A set of self-consistent Schwinger-Dyson equations has been set up for all included particles within the Cornwall-Jackiw-Tomboulis formalism. This has been expanded to non-zero temperatures via the imaginary time formalism. Beside tree-level two different stages of approximations have been considered: the Hartree approximation which takes into account the double-bubble diagram for the scalar meson, and an improved approximation where in addition two-particle irreducible sunset diagrams for all fields were included. In the Hartree-approximation the Schwinger-Dyson equations can be solved by quasi-particle ansaetze, while in the improved approximation spectral functions with non-zero widths have to be introduced. The Schwinger-Dyson equations are solved by the fully dressed propagators. Comparing the two levels of approximation shows the influence of finite widths on the temperature dependence of the particle properties. The consideration of finite widths in fact has a significant influence on the transition from a phase of heavy nucleons to a transition of light nucleons, observed in the Walecka-model. The temperature dependence is weakend when finte widths are taken into account.
The present work was devised to address the systematic analysis of samples from a range of Roman non-ferrous metal artefacts from different archaeological contexts and sites in the Roman provinces of Germania Superior. One of the focal points of this study is the provenancing of different lead objects from five important Roman settlements between 15 BC and the beginning of fourth century AD. For this purpose, measurements were made on lead and copper ore samples from the Siegerland, Eifel, Hunsrück and Lahn-Dill area in Germany and supplemented with data from the literature to create a data bank of lead isotope ratios of European deposits. Compositional analysis of lead objects by Electron Microprobe analysis showed that Romans were able to purify lead from ore up to 99%. Multi-Collector Inductively Coupled Plasma Mass-Spectrometry was used to determine the source of lead, which played an important role in nearly all aspects of Roman life. Lead isotope ratios were measured for ore samples from German deposits from the eastern side of the Rhine (Siegerland, Lahn-Dill, Ems) and the western side of the Rhine (Eifel, Hunsrück), which contained enough ore reserves to answer the increasing local demand and are believed to have been mined during the Roman period. This data together with those from Mediterranean ore deposits from the literature was used to establish a data bank. The Mediterranean ore deposits range from Cambrian (high 207Pb/206Pb) to tertiary (lower 207Pb/206Pb) values. In particular, the Cypriot deposits are younger, while the Spanish deposits fall either with the younger Sardic ores or close to the older Cypriot ores. The lead isotope ratios of most German ore deposits fall in between the 208Pb/206Pb vs. 207Pb/206Pb ratios of Sardinia and Cyprus, where the lead isotope signature of ore deposits from France and Britain are also found. Over 240 lead objects were measured from Wallendorf (second century BC to first century AD) Dangstetten (15-8 BC), Waldgirmes (AD 1-10), Mainz (AD 1-300), Martberg (first to fourth centuries AD) & Trier (third to fourth centuries AD). Comparing the lead isotope ratios of lead objects and those from German ores shows that the source of over 85 percent of objects are Eifel ore deposits, but the Roman’s had also imported lead from the Southern Massif Central and from Great Britain. A further topic of this work was the systematic study of the variation of copper isotope ratios in different copper minerals and the mechanisms, which controls copper isotope fractionation in ores deposits. For this purpose, copper isotope analyses were made by Multi-Collector Inductively Coupled Plasma Mass-Spectrometry from a series of hydrothermal copper sulphides and their alteration products. Copper and lead isotope ratios were measured in coexisting phases of chalcopyrite and malachite and also coexisting malachite and azurite. No significant fractionation was observed in malachite-azurite phases, but in chalcopyrite-malachite coexisting phases, malachite always shows a positive fractionation to heavier isotope values. Zhu et al. and Larson et al. showed that isotopic variations in copper principally reflect mass fractionation in response to low temperature processes rather than source heterogeneity. The low temperature ore formation processes are mostly represented by weathering of primary sulphide ores to produce secondary carbonate phases and therefore are usually observed on the surface of ore deposits, which were probably removed during the early Bronze Age. Using this concept, copper isotope ratios were measured in some Early Bronze Age copper alloys and Roman copper alloys. However, no large copper isotope fractionation has been observed. Lead and copper isotope ratios were measured on samples from the Kupferschiefer. Two profiles were investigated; 1) Sangerhausen, which was not directly influenced by the oxidizing brines of Rote Fäule and 2) Oberkatz, where both Rote Fäule-controlled and structure-controlled mineralization were observed. Results from maturation studies of organic matter suggest the maximum temperature affecting the Kupferschiefer did not exceed 130°C. delta-65-Cu ranges between -0.78-+0.58‰, shows a positive correlation with copper concentration. Maximum temperature in the Kupferschiefer profile from Oberkatz is supposed to be around 150°C. delta-65Cu in this profile ranges between -0.71-+0.68‰. The pattern of copper isotope fractionation and copper concentration is same as the for profile of Sangerhausen. Origina lead isotope ratios are strongly overprinted by high concentrations of uranium in bottom of both profiles causing more radiogenic lead.
In order to investigate the role of neuronal synchronization in perceptual grouping, a new method was developed to record selectively from multiple cortical sites of known functional specificity as determined by optical imaging of intrinsic signals. To this end, a matrix of closely spaced guide tubes was developed in cooperation with a company providing the essential manufacturing technique RMPD® (Rapid Micro Product Development). The matrix was embedded into a framework of hard and software that allowed for the mapping of each guide tube onto the cortical site an electrode would be led to if inserted into that guide tube. With these developments, it was possible to determine the functional layout of the cortex by optical imaging and subsequently perform targeted recordings with multiple electrodes in parallel. The method was tested for its accuracy and found to target the electrodes with a precision of 100 µm to the desired cortical locations. Using the developed technique, neuronal activity was recorded from area 18 of anesthetized cats. For stimulation, Gabor-patches in different geometrical configurations were placed over the recorded receptive fields merging into visual objects appropriate for testing the hypothesis of feature binding by synchrony. Synchronization strength was measured by the height of the cross-correlation centre peaks. All pairwise synchronizations were summarized in a correlation index which determined the mean difference of the correlation strengths between conditions in which recording sites should or should not fire in synchrony according to the binding hypothesis. The correlation index deviated significantly from zero for several of these configurations, further supporting the hypothesis that synchronization plays an important role in the process of perceptual grouping. Furthermore, direct evidence was found for the independence of the synchronization strength from the neuronal firing rate and for neurons that change dynamically the ensemble they participate in. In parallel to the experimental approach, mechanisms of oscillatory long range synchronization were studied by network simulations. To this end, a biologically plausible model was implemented using pyramidal and basket cells with Hodgkin-Huxley like conductances. Several columns were built from these cells and intra- and inter-columnar connections were mimicked from physiological data. When activated by independent Poisson spike trains, the columns showed oscillatory activity in the gamma frequency range. Correlation analysis revealed the tendency to locally synchronize the oscillations among the columns, but a rapid phase transition occurred with increasing cortical distance. This finding suggests that the present view of the inter-columnar connectivity does not fully explain oscillatory long range synchronization and predicts that other processes such as top-down influences are necessary for long range synchronization phenomena.
Systematisch verabreichte Chemotherapeutika sind oft uneffektiv bei der Behandlung von Krankheiten des zentralen Nervensystems (ZNS). Eine der Ursachen hierfür ist der unzureichende Arzneistoff-Transport ins Gehirn aufgrund der Blut-Hirn-Schranke. Eine der Strategien für den nicht-invasiven Wirkstoff-Transport ins Gehirn ist die Verwendung von Nanopartikeln. Polybutylcyanoacrylat-Nanopartikel, die mit Polysorbat 80 (Tween® 80) überzogen wurden, können die Blut-Hirn-Schranke passieren und somit Wirkstoffe ins Gehirn transportieren. Wird die Blut-Hirn-Schranke durch einen Hirntumor partiell beschädigt und hierdurch ihre Permeabilität am Ort des Tumors erhöht, können Nanopartikel den Tumor zusätzlich durch den sogenannten EPR-Effekt erreichen. Im ersten Teil der vorliegenden Arbeit wurde die Beladung der Nanopartikel durch Variation der Formulierungparameter mit dem Ziel optimiert, eine Formulierung mit höherer Wirksamkeit für die Therapie von Glioblastom-tragenden Ratten zu entwickeln. Außerdem wurde das Potential von Doxorubicin, das an mit „Stealth Agents“ überzogenen Polybutylcyanoacrylat-Nanopartikel gebunden war, für die Chemotherapie von Hirntumoren untersucht. Im zweiten Teil dieser Studie wurden die Gehirn- und Körperverteilung in gesunden und in Glioblastom-101/8-tragenden Ratten nach i.v.-Gabe von Poly(butyl-2-cyano[3- 14C]acrylat)-Nanopartikeln, die mit Polysorbat 80 beschichtet wurden, und solchen, die noch zusätzlich mit Doxorubicin geladen waren (DOX-14C-PBCA + PS), untersucht. Die Standardformulierung von Doxubicin-Polybutylcyanoacrylat-Nanopartikeln (DOX-NP) wurde durch anionische Polymerisierung von Butylcyanoacrylat in Anwesenheit von DOX hergestellt. Zusätzlich wurden unterschiedliche DOX-NP Formulierungen durch Veränderung der Herstellung produziert. Das therapeutische Potential der Formulierungen wurde in Ratten mit ins Gehirn transplantieren Glioblastom 101/8 untersucht. Neben Polysorbat 80 wurden Poloxamer 188 und Poloxamin 908 als Überzugsmaterial verwendet. Die Resultate ergaben, dass die mit Polysorbat 80 überzogene Standardformulierung am effektivsten war. Die höhere Wirksamkeit von DOX-NP+PS 80 könnte durch die Fähigkeit dieser Träger erklärt werden, den Wirkstoff während eines frühen Stadiums der Tumorentwicklung durch einen Rezeptor-vermittelten Mechanismus, der durch den PS 80-Überzug aktiviert wurde über die intakte Blut-Hirn-Schranke, zu transportieren. Unsere Ergebnisse zeigen auch, dass Poloxamer 188 und Poloxamin 908 den antitumoralen Effekt von DOX-PBCA beträchtlich verbessern. Der anti-tumorale Effekt dieser Formulierungen könnte möglicherweise dem EPR-Effekt zugeschrieben werden. Es ist bekannt, dass die tumorale Arzneistoff-Aufnahme durch den EPR-Effektes für lang-zirkulierende Wirkstoffträger ausgeprägter ist und so mehr Wirkstoff durch die Tumor-geschädigte Blut-Hirn-Schranke gelangt. Unbeschichtete Nanopartikel, Polysorbat 80-beschichtete Nanopartikel oder mit Doxorubicin beladene und mit Polysorbat 80 beschichtete Nanopartikel wurden in gesunden und Tumor-tragenden Ratten injiziert. Diese Nanopartikel-Präparationen zeigten einer unterschiedliche Korpenverteilung in den Ratten. Unbeschichtete Nanopartikel sammelten sich in den RES-Organen an. Mit PS 80 beschichtete NP reduzierten die Aufnahme der NP in Leber und Milz, während sich die Konzentration der NP in der Lunge erhöhte. Diese Beobachtungen deuten darauf hin, dass die Änderung der Oberflächeneigenschaften der NP durch das Tensid, zu einer Interaktion mit unterschiedlichen Opsoninen führt, welches die Aufnahme der NP von verschiedenen phagozitierenden Zellen erleichtert. Hingegen war die Aufnahme der mit DOX beladenen, PS 80-beschichteten Nanopartikel den unbeschichteten Partikel ähnlich. Im Vergleich mit gesunden Ratten und mit Tumor-tragenden Ratten hingegen war die Konzentration der NP im Gehirn von Tumor tragenden Ratten 10 Tage nach der Tumor-implantation signifikant höher. In Anwesenheit des Glioblastoms ist der Transport von NP in das Gehirn das Resultat verschiedener Faktoren: zusätzlich zur Fähigkeit von PS 80-Nanopartikeln, die Blut-Hirn-Schranke zu passieren, extravasieren diese Träger wegen des EPR Effekts über das durch den Tumor undichte Endothelium. Die Konzentration von PS 80 [14C]-PBCA NP war im Glioblastom signifikant höher als mit DOX [14C]-PBCA NP. Dieses Phänomen kann durch die unterschiedliche Mikroumgebung von zerebralem intra-tumoralen und intaktem Gehirngewebe erklärt werde. Insbesondere können sich die positive Ladung der tumoralen Regionen und die positive Ladung der DOX [14C]-PBCA NP negativ beeinflussen. Dennoch waren die Doxorubicin-Konzentration in Glioblastom ausreichend, einen therapeutischen Effekt zu ermöglichen.
Group III presynaptic metabotropic glutamate receptors (mGluRs) play a central role in regulating presynaptic activity through G-protein effects on ion channels and signal transducing enzymes. Like all Class C G-protein coupled receptors, mGluR8 has an extended intracellular C-terminal domain (CTD) presumed to allow for modulation of downstream signaling. To elucidate the function and modulation of mGluR8, yeast two-hybrid screens of an adult rat brain cDNA library were performed with the CTDs of mGluR8a and 8b (mGluR8-C) as baits. Different components of the sumoylation cascade (ube2a, sumo-1, Pias1, Pias gamma and Pias xbeta) and some other proteins were identified as mGluR8 interacting proteins. Binding assays using recombinant GST-fusion proteins confirmed that Pias1 interacts not only with mGluR8-C, but all group III mGluR CTDs. Pias1 binding to mGluR8-C required a region N-terminally to a consensus sumoylation motif and was not affected by arginine substitution of the conserved lysine K882 within this motif. Co-transfection of fluorescently tagged mGluR8a-C, sumo-1 and enzymes of the sumoylation cascade into HEK 293 cells showed that mGluR8a-C can be sumoylated in cells. Arginine substitution of lysine K882 within the consensus sumoylation motif, but not of other conserved lysines within the CTD, abolished in vivo sumoylation. The results are consistent with post-translational sumoylation providing a novel mechanism of group III mGluR regulation.
Chemokines play a key role in the cellular infiltration of inflamed tissue. They are released by a wide variety of cell types during the initial phase of host response to injury, allergens, antigens, or invading microorganisms, and selectively attract leukocytes to inflammatory foci, inducing both migration and activation. Monocyte chemoattractant protein-1 (MCP-1), a member of the CC chemokine superfamily, functions in attracting monocytes, T lymphocytes, and basophils to sites of inflammation. MCP-1 is produced by monocytes, fibroblasts, vascular endothelial cells and smooth muscle cells in response to various stimuli such as tumour necrosis factor-a (TNF-a), interferon-g (IFN-g), and interleukin-1b (IL-1b). It also plays an important role in the pathogenesis of chronic inflammation, and overexpression of MCP-1 has been implicated in diseases including glomerulonephritis and rheumatoid arthritis. Oligonucleotide-directed triple helix formation offers a means to target specific sequences in DNA and interfere with gene expression at the transcriptional level. Triple helix-forming oligonucleotides (TFOs) bind to homopurine/homopyrimidine sequences, forming a stable, sequence-specific complex with the duplex DNA. Purine-rich sequences are frequent in gene regulatory regions and TFOs directed to promoter sequences have been shown to prevent binding of transcription factors and inhibit transcription initiation and elongation. Exogenous TFOs that bind homopurine/ homopyrimidine DNA sequences and form triple-helices can be rationally designed, while the intracellular delivery of single-stranded RNA TFOs has not been studied in detail before. In this study, expression vectors were constructed which directed transcription of either a 19 nt triplex-forming pyrimidine CU-TFO sequence targeting the human MCP-1 or two different 19 nt GU- or CA-control sequences, respectively, together with the vector encoded hygromycin resistance mRNA as one fusion transcript. HEK 293 cells were stable transfected with these vectors and several TFO and control cell lines were generated. Functional relevant triplex formation of a TFO with a corresponding 19 bp GC-rich AP-1/SP-1 site of the human MCP-1 promoter was shown. Binding of synthetic 19 nt CUTFO to the MCP-1 promoter duplex was verified by triplex blotting at pH 6.7. Underlining binding specificity, control sequences, including the GU- and CA-sequence, a TFO containing one single mismatch and a MCP-1 promoter duplex containing two mismatches, did not participate in triplex formation. Establishing a magnetic capture technique with streptavidin microbeads it was verified that at pH 7.0 the 19 nt TFO embedded in a 1.1 kb fusion transcript binds to a plasmid encoded MCP-1 promoter target duplex three times stronger than the controls. Finally, cell culture experiments revealed 76 ± 10.2% inhibition of MCP-1 protein secretion in TNF-a stimulated CU-TFO harboring cell lines and up to 88% after TNF-a and IFN-g costimulation in comparison to controls. Expression of interleukin-8 (IL-8) as one TNF-a inducible control gene was not affected by CU-TFO, demonstrating both highly specific and effective chemokine gene repression. Furthermore, another chemokine target, regulated upon activation normal T cell expressed and secreted (RANTES), which plays an essential role in inflammation by recruiting T lymphocytes, macrophages and eosinophils to inflammatory sites, was analysed using the triplex approach. A 28 nt TFO was designed targeting the murine RANTES gene promoter, and gel mobility shift assays demonstrated that the phosphodiester TFO formed a sequencespecific triplex with the double-stranded target DNA with a Kd of 2.5 x 10-7 M. It was analysed whether RANTES expression could be inhibited at the transcriptional level testing the TFO in two different cell lines, T helper-1 lymphocytes and brain microvascular endothelial cells (bend3 cells). Although there was a sequence-specific binding of the TFO detectable in the gel shift assays, there was no inhibitory effect of the exogenously added and phosphorothioate stabilised TFO on endogenous RANTES gene expression visible. Additionally, the small interfering RNA (siRNA) approach was tested as another strategy to inhibit expression of the pro-inflammatory chemokines MCP-1 and RANTES. Two different methods were pursuit, describing transient transfection with vector derived and synthetic siRNA. The vector pSUPER containing the siRNA coding sequence was used to suppress endogenous MCP-1 in HEK 293 cells. An empty vector without RNA sequence served as a control. Inhibition due to the siRNA was measured in stimulated and unstimulated cells. In TNF-a stimulated cells MCP-1 protein synthesis was decreased by 35 ± 11% after siRNA transfection. Using a synthetic double-stranded siRNA, the TNF-a induced MCP-1 protein secretion could be successfully inhibited about 62.3 ± 10.3% in HEK 293 cells, indicating that the siRNA is functional in these cells to suppress chemokine expression. The siRNA approach targeting murine RANTES in Th1 cells and b-end3 cells revealed no inhibition of endogenous gene expression. Gene therapy approaches rely on efficient transfer of genes to the desired target cells. A wide variety of viral and nonviral vectors have been developed and evaluated for their efficiency of transduction, sustained expression of the transgene, and safety. Among them, lentiviruses have been widely used for gene therapy applications. In order to improve the delivery of TFOs or siRNAs into the target cells, cloning of the lentiviral transfer vector SEW, the production of lentiviral particles by transient transfection were performed with the aim to generate lentiviral vector-derived TFOs in further experiments. Here, Th1 cells were transduced with infectious lentiviral particles and transduction efficacy was measured. Transduction efficacy higher than 82% could be achieved using the lentiviral vector SEW, opening optimal possibilities for the TFO or siRNA approach.
Lesion of the rat entorhinal cortex denervates the outer molecular layer of the fascia dentata followed by layer-specific axonal sprouting of uninjured fibers in the denervated zone. One of the candidate molecules regulating the laminar-specific sprouting response in the outer molecular layer is the transmembrane chondroitin sulfate proteoglycan NG2. NG2 is found in glial scars and has been suggested to impede axonal regeneration following injury of the spinal cord. The present study adressed the question whether NG2 could also regulate axonal growth in denervated areas of the brain. Therefore, (1) changes in NG2 mRNA and NG2 protein levels, (2) the cellular and the extracellular localisation of the molecule, (3) the identity of NG2 expressing cells, and (4) the generation of NG2-positive cells were studied in the rat fascia dentata before and following entorhinal deafferentation. Laser microdissection was employed to selectively harvest the denervated molecular layer and combined with quantitative reverse transcription-PCR to measure changes in NG2 mRNA amount (6h, 12h, 2d, 4d, 7d post lesion). The study revealed increases of NG2 mRNA at day 2 (2.5-fold) and day 4 (2-fold) post lesion. Immunocytochemistry was used to detect changes in NG2 protein distribution (1d, 4d, 7d, 10d, 14d, 30d, 6 months post lesion). NG2 staining was increased in the denervated outer molecular layer at 1 day post lesion, reached a maximum at 10 days post lesion, and returned to control levels within 6 month. Interestingly, the accumulation of NG2 protein was strongly restricted to the denervated outer molecular layer forming a border to the unaffected inner molecular layer. Using electron microscopy, NG2-immunoprecipitate was localized not only on glial surfaces and in the extracellular matrix but also in the vicinity of neuronal profiles indicating that NG2 is secreted following denervation. Double-labelings of NG2-immunopositive cells with markers for astrocytes, microglia/macrophages, and oligodendrocytes suggested that NG2-cells are a distinct glial subpopulation before and after entorhinal deafferentation. Bromodeoxyuridine-labeling revealed that some of the NG2-positive cells are postlesional generated. Taken together, the data revealed a layer-specific upregulation of NG2 in the denervated outer molecular layer of the fascia dentata that coincides with the sprouting response of uninjured fibers. This suggests that NG2 could regulate lesion-induced axonal growth in denervated areas of the brain.
In this dissertation a non-deterministic lambda-calculus with call-by-need evaluation is treated. Call-by-need means that subexpressions are evaluated at most once and only if their value must be known to compute the overall result. Also called "sharing", this technique is inevitable for an efficient implementation. In the lambda-ND calculus of chapter 3 sharing is represented explicitely by a let-construct. Above, the calculus has function application, lambda abstractions, sequential evaluation and pick for non-deterministic choice. Non-deterministic lambda calculi play a major role as a theoretical foundation for concurrent processes or side-effected input/output. In this work, non-determinism additionally makes visible when sharing is broken. Based on the bisimulation method this work develops a notion of equality which respects sharing. Using bisimulation to establish contextual equivalence requires substitutivity within contexts, i.e., the ability to "replace equals by equals" within every program or term. This property is called congruence or precongruence if it applies to a preorder. The open similarity of chapter 4 represents a new concept, insofar that the usual definition of a bisimulation is impossible in the lambda-ND calculus. So in section 3.2 a further calculus lambda-Approx has to be defined. Section 3.3 contains the proof of the so-called Approximation Theorem which states that the evaluation in lambda-ND and lambda-Approx agrees. The foundation for the non-trivial precongruence proof is set out in chapter 2 where the trailblazing method of Howe is extended to be capable with sharing. By the use of this (extended) method, the Precongruence Theorem proves open similarity to be a precongruence, involving the so-called precongruence candidate relation. Joining with the Approximation Theorem we obtain the Main Theorem which says that open similarity of the lambda-Approx calculus is contained within the contextual preorder of the lambda-ND calculus. However, this inclusion is strict, a property whose non-trivial proof involves the notion of syntactic continuity. Finally, chapter 6 discusses possible extensions of the base calculus such as recursive bindings or case and constructors. As a fundamental study the calculus lambda-ND provides neither of these concepts, since it was intentionally designed to keep the proofs as simple as possible. Section 6.1 illustrates that the addition case and constructors could be accomplished without big hurdles. However, recursive bindings cannot be represented simply by a fixed point combinator like Y, thus further investigations are necessary.
Jet physics in ALICE
(2005)
This work aims at the performance of the ALICE detector for the measurement of high-energy jets at mid-pseudo-rapidity in ultra-relativistic nucleus-nucleus collisions at LHC and their potential for the characterization of the partonic matter created in these collisions. In our approach, jets at high energy with E_{T}>50 GeV are reconstructed with a cone jet finder, as typically done for jet measurements in hadronic collisions. Within the ALICE framework we study its capabilities of measuring high-energy jets and quantify obtainable rates and the quality of reconstruction, both, in proton-proton and in lead-lead collisions at LHC conditions. In particular, we address whether modification of the jet fragmentation in the charged-particle sector can be detected within the high particle-multiplicity environment of the central lead-lead collisions. We comparatively treat these topics in view of an EMCAL proposed to complete the central ALICE tracking detectors. The main activities concerning the thesis are the following: a) Determination of the potential for exclusive jet measurements in ALICE. b) Determination of jet rates that can be acquired with the ALICE setup. c) Development of a parton-energy loss model. d) Simulation and study of the energy-loss effect on jet properties.
This thesis has explored how structural techniques can be applied to the problem of formal verification for sequential circuits. Algorithms for formal verification which operate on non-canonical gate netlist representations of digital circuits have certain advantages over the traditional techniques based on canonical representations as BDDs. They allow to exploit problem-specific knowledge because they can take into account structural properties of the designs being analyzed. This allows us to break the problem down into sub-problems which are (hopefully) easier to be solved. However, in the past, the main application of such structural techniques was in the field of combinational equivalence checking. One reason for this is that the behaviour of a sequential system does not only depend on its inputs but also on its internal states, and no concepts had been developed to-date allowing structural methods to deal with large sets of states. An important goal of this research was therefore to develop structural, non-canonical forms of representing the reachable states of a finite state machine and to develop methods for reachability analysis based on such representations. In order to reach this goal, two steps were taken. Firstly, a framework for manipulating Boolean functions represented as gate netlists has been established. Secondly, using this framework, a structural method for FSM traversal was developed serving as the basis for an equivalence checking algorithm for sequential circuits. The framework for manipulating Boolean functions represented as multi-level combinational networks is based on a new concept of an implicant in a multi-level network and on an AND/ORtype enumeration technique which allows us to derive such implicants. This concept extends the classical notion of an implicant in two-level circuits to the multi-level case. Using this notion, arbitrary transformations in multi-level combinational networks can be performed. The multi-level network implicants can be determined from AND/OR reasoning graphs, which are associated with an AND/OR reasoning technique operating directly on the gate netlist description of a multi-level circuit. This reasoning technique has the important property that it is complete, i.e. the associated AND/OR trees contain all prime implicants of a Boolean function at an arbitrary node in a combinational circuit. In other words, AND/OR graphs constructed for a network function serve as a representation of this function. A great advantage over BDDs is that AND/OR graphs, besides representing the logic function, also represent some structural properties of the analyzed circuitry. This permits to develop heuristics that are specially tailored for certain applications such as logic optimization or verification. Another advantage which is especially useful for logic optimization is the fact that the proposed AND/OR enumeration scheme is not restricted to the use of a specific logic alphabet such as B3 = {0, 1, X}. By using Roth’s D-calculus based on B5 = {0, 1, D, D-Komplement} permissible implicants can be determined. Transformations based on permissible implicants exploit observability don’t-care conditions in logic synthesis by creating permissible functions at internal network nodes. In order to evaluate the new structural framework for manipulating Boolean functions represented as gate netlists, several experiments with implicant-based optimization of multi-level circuits were performed. The results show that implicant-based circuit transformations lead to significantly better optimization results than traditional synthesis techniques. Next, based on the proposed structural methods for Boolean function manipulation, techniques for representing and manipulating the set of states of a sequential circuit have been developed. The concept of a “stub circuit” was introduced which implicitly represents a set of state vectors as the range of a multi-output function given as a gate netlist. The stub circuit is the result of an existential quantification operation which is obtained by functional decomposition using implicant-based netlist transformations and a network cutting procedure. Using this existential quantification operation, a new structural FSM traversal algorithm was formulated which performs a fixed point iteration on the set of reachable states represented by the stub circuit. The proposed approach performs a reachability analysis of the states of a sequential circuit. It operates on gate netlists and naturally allows to incorporate structural properties of a design under consideration into the reasoning. Therefore, structural FSM traversal is an interesting alternative to traditional symbolic FSM traversal, especially in those applications of formal verification, where structural properties can be exploited. Structural FSM traversal was applied to the problem of sequential equivalence checking. Here, structural similarities between the designs to be compared can effectively reduce the complexity of the verification task. The FSM to be traversed is a special product machine called sequential miter. The special structural properties of this product machine have made it possible to formulate an approximate algorithm for structural FSM traversal, called record and play(). This algorithm uses an approximation on the reachable state set represented by the stub circuit which is very beneficial for performance. Instead of calculating the stub circuit using the exact algorithm, implicant-based transformations directly using structural design similarities are performed. These transformations, together with existential quantification implemented by the cutting procedure, lead to an over-approximation of the reachable state set. By this overapproximation, only such unreachable product states are added to the set of states represented by the stub circuit which are unreachable at the current point in time but which are nevertheless equivalent. Therefore, more product states are added to the set of reachable states sometimes leading to drastic acceleration of the traversal, i.e. the fixed point is reached in much fewer steps. The algorithm record and play() was applied to the problem of checking the equivalence of a circuit with its optimized and retimed version. Retiming is a form of sequential circuit optimization which can radically alter the state encoding of a circuit. Traditional FSM traversal techniques often fail because the BDDs needed to represent the reachable state set and the transition relation of the product machine become too large. Experiments were conducted to evaluate the performance of record and play() on a standard set of sequential benchmark circuits. The algorithm was capable of proving the equivalence of optimized and retimed circuits with their original versions, some of which (to our knowledge) have never before been verified using traditional techniques like symbolic FSM traversal. The experimental results are very promising. Future research will therefore explore how structural FSM traversal can be applied to model checking.
The results presented here strongly indicate that ubiquitination of the recombinant human alpha1 GlyR at the plasma membrane of Xenopus oocytes is involved in receptor internalisation and degradation. Ubiquitination of the human alpha1 GlyR has been demonstrated by radio-iodination of plasma membrane-boundalpha1 GlyRs, whose subunits differed in molecular weight by additional 7, 14 or 21 kDa, corresponding to the molecular weights of one, two and three conjugated ubiquitin molecules, respectively, and by co-isolation of the non-tagged human alpha1 GlyR through hexahistidyl-tagged ubiquitin. Ubiquitin conjugated GlyRs where prominent at the plasma membrane, but could be hardly detected in total cell homogenates, indicating that ubiquitination takes place exclusively at the plasma membrane. Ubiquitination of the alpha1 GlyR at the plasma membrane was no longer detectable when the ten lysine residues of the cytoplasmic loop between transmembrane segments M3 and M4 were replaced by arginines. Despite this proteolytic cleavage continued to take place at the same extent as with the wild type alpha1 GlyR, suggesting that removal of GlyRs from the plasma membrane and routing to lysosomes for degradation were not dependent on ubiquitination. Also replacing a tyrosine in position 339, which was speculated to be part of an additional endocytosis motif, did not lead to a significant reduction of cleavage of the GlyR alpha1 subunits. However, a mutant lacking both, ubiquitination sites and 339Y, was significantly less processed. These results may suggest that the GlyR alpha1 subunit harbors at least two endocytosis motifs, which may act independently to regulate the density of alpha1 GlyR. Apparently, each of the two signals may be capable of compensating entirely the loss of the other. Part two of this Dissertation demonstrates that the correct topology of the glycine receptor alpha1 subunit depends critically on six positively charged residues within a basic cluster, RFRRKRR, located in the large cytoplasmic loop following the C-terminal end of M3. Neutralization of one or more charges of this cluster, but not of other charged residues in the M3-M4 loop, led to an aberrant translocation into the endoplasmic reticulum lumen of the M3-M4 loop. However, when two of the three basic charges located in the ectodomain linking M2 and M3 were neutralized, in addition to two charges of the basic cluster, endoplasmic reticulum disposition of the M3-M4 loop was prevented. We conclude that a high density of basic residues C-terminal to M3 is required to compensate for the presence of positively charged residues in the M2-M3 ectodomain, which otherwise impair correct membrane integration of the M3 segment. Part three of this Dissertation describes my contribution (blue native PAGE analysis of metabolically labeled alpha7 and 5HT3A receptors and the examination of the glycosylation state of metabolically labeled alpha7 subunits) to a work on the limited assembly capacity of Xenopus oocytes for nicotinic alpha7 subunits. While 5HT3A subunits combined efficiently to pentamers, alpha7 subunits existed in various assembly states including trimers, tetramers, pentamers, and aggregates. Only alpha7 subunits that completed the assembly process to homopentamers acquired complex-type carbohydrates and appeared at the cell surface. We conclude that Xenopus oocytes have a limited capacity to guide the assembly of alpha7 subunits, but not 5HT3A subunits to homopentamers. Accordingly, ER retention of imperfectly assembled alpha7 subunits rather than inefficient routing of fully assembled alpha7 receptors to the cell surface limits surface expression levels of alpha7 nicotinic acetylcholine receptors. Part four of this Dissertation describes my contribution (the biochemical analysis of the human P2X2 and P2X6 subtypes) to studies on the quaternary structure of P2X receptors. Armaz Aschrafi, the main author of the paper showed that subsequent to isolation under non-denaturing conditions from Xenopus oocytes the His-rP2X2 protein migrated on blue native PAGE predominantly in an aggregated form. The only discrete protein band detectable could be assigned to homotrimers of the His-rP2X2 subunit. Because of the exceptional assembly-behaviour of the rP2X2 protein compared to the rP2X1, rP2X3, rP2X4 and rP2X5 proteins, its human orthologue was investigated in the same manner. In contrast to rP2X2 subunits, hP2X2 subunits migrated under virtually identical conditions in a single defined assembly state, which could be clearly assigned to a trimer. P2X6 subunits represent the sole P2X subtype that is unable to form functional homomeric receptors in Xenopus oocytes. The blue native PAGE analysis of metabolically labeled hP2X6 receptors and the examination of the glycosylation state revealed that hP2X6 subunits form tetramers and aggregates that are not exported to the plasma membrane of Xenopus oocytes.
In the present work, the Heidelberg electron beam ion trap (EBIT) at the Max-Planck-Institute für Kernphysik (MPIK) has been used to produce, trap highly charged argon ions and study their magnetic dipole (M1) forbidden transitions. These transitions are of relativistic origin and, hence, provide unique possibilities to perform precise studies of relativistic effects in many electron systems. In this way, the transitions energies of the 1s22s22p for the 2P3/2 - 2P1/2 transition in Ar13+ and the 1s22s2p for the 3P1 - 3P2 transition in Ar14+, for 36Ar and 40Ar isotopes were compared. The observed isotopic effect has confirmed the relativistic nuclear recoil effect corrections due to the finite nuclear mass in a recent calculation made by Tupitsyn [TSC03], in which major inconsistencies of earlier theoretical methods have been corrected for the first time. The finite mass, or recoil effect, composed of the normal mass shift (NMS), and the specific mass shift (SMS) were corrected for relativistic contributions, RNMS and RSMS. The present experimental results have shown that the recoil effects on the Breit level are indeed very important, as well as the effects of the correlated relativistic dynamics in a many electron ion.
This thesis examines the spread and promotion of English on a global level, from a historical perspective in particular ‘Third World’ contexts. The globalization of English as an exclusive language of power is considered to be a trap, when accompanied by an ideology aiming to universalize monolingual and monocultural norms and standards. World-wide English diffusion is related - not to any mystical effects of some psycho-social mechanisms or transmuting alchemy - but to a global rise of military, political, economic, communicational and cultural Euro-American hegemony. The fact that the English language has become perhaps the primary medium of social control and power has not been given a prominent place in the analyses of established social scientists or political planners. On the contrary, the positively idealized dominance of English as a universal medium has become part of a collection of myths seeking to deny the global reality of multilingualism. Not allowing for the existence of any power besides itself, the perpetuation of this hegemony of English within a multilingual scenario has become a contradiction in terms. Centuries of colonialism, followed by neo-colonialism, are seen to have resulted in a world-wide consensus favouring centralization and homogenization of state and world economies, administrations, language, education and mass media systems, as prerequisites to local and global unity. The particular case of India as encountered by a colonizing Britain is used to illustrate the historical clash between differing language and educational traditions and cultures. It was on the strength of their own predominantly positive attitudes towards diversity - encoded in their promotion of complex social and religious philosophies, as well as varied economic and educational practices of pluralism and hierarchy-without-imposition, unity in diversity, etc. - that the people and their leaders finally achieved Indian independence from British colonialism. Contemporary Indian society, however, is still grappling with the legacy of a Eurocentric civilizational model - encoded in the neo-colonial system of English education - and in conflict with its own positively idealized and actively promoted traditions of pluralism. On national and international levels, the destabilization and destruction of diversity continues to threaten more than the linguistic and cultural uniqueness of numerous communities and individuals. For those majorities and minorities who refuse to give up their ‘differences’, political, economic and physical survival is at stake. A paradoxical reality, seldom acknowledged, is that while for the politically and economically already powerful language groups, the enormous resources spent on formal (language) education have become a means to maintain their material and political capital, whereas for the majority of modern societies' marginalized members, powerful linguistic barriers to full economic or political participation remain firmly in place. The justifications for perpetuating exclusionary policies and sustaining structural inequality have come from monocultural ideological assumptions in education and language policies as one of the key mechanisms for state control of labour. This thesis concludes that the trap of an ideologically exclusive status for English can be avoided by theoretically positivizing and institutionally promoting existing multilingual and multicultural peoples’ realities as an integral part of their human rights, in order to resist global Englishization.
Different numerical approaches and algorithms arising in the context of modelling of cellular tissue evolution are discussed in this thesis. Being suited in particular to off-lattice agent-based models, the numerical tool of three-dimensional weighted kinetic and dynamic Delaunay triangulations is introduced and discussed for its applicability to adjacency detection. As there exists no implementation of a code that incorporates all necessary features for tissue modelling, algorithms for incremental insertion or deletion of points in Delaunay triangulations and the restoration of the Delaunay property for triangulations of moving point sets are introduced. In addition, the numerical solution of reaction-diffusion equations and their connection to agent-based cell tissue simulations is discussed. In order to demonstrate the applicability of the numerical algorithms, biological problems are studied for different model systems: For multicellular tumour spheroids, the weighted Delaunay triangulation provides a great advantage for adjacency detection, but due to the large cell numbers the model used for the cell-cell interaction has to be simplified to allow for a numerical solution. The agent-based model reproduces macroscopic experimental signatures, but some parameters cannot be fixed with the data available. A much simpler, but in key properties analogous, continuum model based on reaction-diffusion equations is likewise capable of reproducing the experimental data. Both modelling approaches make differing predictions on non-quantified experimental signatures. In the case of the epidermis, a smaller system is considered which enables a more complete treatment of the equations of motion. In particular, a control mechanism of cell proliferation is analysed. Simple assumptions suffice to explain the flow equilibrium observed in the epidermis. In addition, the effect of adhesion on the survival chances of cancerous cells is studied. For some regions in parameter space, stochastic effects may completely alter the outcome. The findings stress the need of establishing a defined experimental model to fix the unknown model parameters and to rule out further models.
My graduate thesis is on the "Structural studies of membrane transport proteins". Transporters are membrane proteins that have multiple membrane-spanning a-helices. They are dynamic and diverse proteins, undergoing a large conformational change and transporting wide range of susbtrates. Based on their energy source they can be classified into primary and secondary transport systems. Primary transport systems are driven by the use of chemical (ATP) or light energy, while secondary transporters utilize ion gradients to transport substrates. I began my PhD dissertation on secondary transporters by two-dimensional crystallization and electron crystallographic analysis and recently my focus also has shifted towards 3D crystallization. The following projects constitute my PhD thesis: 1) 2D crystallization of MjNhaP1 and pH induced structural change: MjNhaP1, a Na+/H+ antiporter that is regulated by pH has been implicated in homeostasis of H+ and Na+ in Methanococcus jannaschii, a hyperthermophilic archaeon that grows optimally at 85°C. MjNhaP1 was cloned and expressed in E. coli. Two-dimensional crystals were obtained from purified protein at pH4. Electron cryo-microscopy yielded an 8Å projection map. The map of MjNhaP1 shows elongated densities in the centre of the dimer and a cluster of density peaks on either side of the dimer core, indicative of a bundle of 4-6 membrane-spanning helices. The effect of pH on the structure of MjNhaP1was studied in situ in 2D crystals revealing a major change in density within the helix bundle relative to the dimer interface. This change occurred at pH6 and above. The two conformations at low and high pH most likely represent the closed and open states of the antiporter, respectively. This is the first instance where a conformational change associated with the regulation of a secondary transporter appears to map structurally. Reconstruction of 3D map and high-resolution structure by x-ray crystallography would be necessary to understand the mechanism of ion transport and regulation by pH. 2) 2D crystallization of Proline transporter: Proline transporter (PutP) from E.coli belongs the sodium-solute symporter family that includes disease related sodium dependent glucose and iodide transporter in humans. Sodium and proline are co-transported with a stoichiometry of 1:1. Purified PutP was reconstituted to yield 2D crystals that were hexagonal in nature. The 2D crystals had tendency to stack indicating their willingness to form 3D crystals. A projection map of PutP from negatively stained crystals showed trimeric arrangement of protein. Other members of the SSF family have been shown to be monomers. My analysis of oligomeric state of PutP in detergent by blue native gel indicates a monomer in detergent solution. It is likely that PutP can function as a monomer but at higher concentration and in lipid bilayer it tends to form trimer. 3) Oligomeric state and crystallization of carnitine transporter from E.coli: E.coli carnitine transporter (CaiT) belongs to the BCCT (Betaine, Carnitine and Choline) superfamily that transports molecules with quaternary amine groups. CaiT is predicted to span the membrane 12 times and acts as a L-carnitine/g-butyrobetaine exchanger. Unlike other members in this transporter family, it does not require an ion gradient and does not respond to osmotic stress. Over-expression of the protein yielded ~2mg of protein/L of culture. The structure and oligomeric state of the protein were analyzed in detergent and lipid bilayers. Blue native gel electrophoresis indicated that CaiT was a trimer in detergent solution. Gel filtration and cross-linking studies further support this. Reconstitution of CaiT into lipid bilayers resulted in 2D crystals. Analysis of negatively stained 2D crystals confirmed that CaiT is a trimer in the membrane. Initial 3D crystallization trials have been successful and currently, the crystals diffract to 6Å and are being improved. 4) Monomeric porin OmpG: OmpG is a bacterial outer membrane b-barrel protein. It is monomeric and its size (33kDa) places it as a prime candidate for a structural solution, using the recently developed method of solid state NMR (work in collaboration with Prof.Hartmut Oskinat, FMP, Berlin). A long-term aim would be to study porins as templates for designing nanopores, for DNA sequencing and identification. I have expressed OmpG in inclusion bodies and refolded at an efficiency of >90% into a functional form using detergent. OmpG was then crystallized by 2D crystallization yielding an 8Å projection map whose structure was similar to native protein. In addition, these crystals were used for structure determination by solid state NMR. An initial spectrum of heavy isotopically labeled OmpG has allowed identification of specific amino acid residues including threonine and proline. Additionally, I obtained 3D crystals in detergent that diffract to 5.5Å and are being improved.
Protein-protein interactions within the plane of cellular membranes play a key role for many biological processes and in particular for transmembrane signaling. A prominent example is the ligand-induced crosslinking of cytokine receptors, where 3- dimensional cytokine binding followed by 2-dimensional interaction between the receptor subunits have been recognized to be important for regulating signaling specificity. The fundamental importance of such coupled interactions for cell-surface receptor activation has stimulated numerous theoretical studies, which have hardly been confirmed experimentally. An experimental approach to measure interactions and real time kinetics of type I interferon (IFN) induced assembly between interferon receptor subunits ifnar2 and ifnar1 on membrane was developed and determinants of the 2-dimensional interactions, such as dimensionality, size, valency, orientation, membrane fluidity and receptor density were quantitatively addressed The C-terminal decahistidine tagged extracellular domains (EC) of ifnar1 and ifnar2 were site- specifically tethered onto solid-supported fluid lipid membrane, which carried covalently attached chelator bis-nitrilotriacetic acid (bis-NTA) groups. Interactions on the lipid bilayer were detected with a novel solid phase detection technique, which allows simultaneous detection of ligand binding to a membrane anchored receptors and lateral interaction between them in the real time. This was achieved by combining two optical techniques: label-free reflectance interferometry (RIf) and total internal reflection fluorescence spectroscopy (TIRFS). Fluorescence signals, in the order of 10 fluorophores/µm2, were detected without substantial photobleaching. The sensitivity of the label-free interferometric detection was in the range of 10 pg/mm2. The crosstalk between the two signals was eliminated by means of spectral separation. Fluorescence was detected in the visible region and RIf was performed at 800 nm in the near infrared. Flow through conditions allowed to automate experiments and measure binding events as fast as ~ 5 s-1. Using this technique we have dissected the interactions involved in IFN-induced ifnar crosslinking. 2-dimensional association and dissociation rate constants were independently determined by tethering high stoichiometric excess of one of the receptor subunits and comparing dissociation of the labelled ligand away from the membrane in the absence and presence of the non-labelled high affinity competitor. Dissociation traces were fitted with the two-step dissociation model: the first step being the 2-dimensional separation of the ternary complex followed by the 3- dimensional ligand dissociation into solution. Label-free RIf detection allowed absolute parameterization of the 2-dimensional concentrations of the ifnar subunits on the membrane. The TIRFS signal provided high sensitivity of the ligand dissociation and was correlated against the RIf signal before fitting. These features of the detection system allowed us to parameterize the model, and the 2-dimensional association or dissociation rate constants were the only variables during the fitting. Another FRET based binding assay was developed to determine the 2- dimensional dissociation rate constant using a pulse-chase approach. The donor fluorescence from ifnar2-EC was quenched upon the ternary complex formation with the acceptor-labelled IFN and the nonlabelled ifnar1-EC. The equilibrium was perturbed by rapid tethering of substantial excess of the nonlabelled ifnar2-EC onto the membrane. The exchange of the labelled ifnar2-EC with the nonlabelled one was monitored as the decrease in the FRET signal with the 2-dimensional dissociation of ifnar2-EC from the ternary complex being the rate limiting step. Based on the several mutants and variants of the interacting proteins, the effect of different rate constants and receptor orientation on the 2-dimensional crosslinking dynamics was studied. We have identified several critical features of the 2- dimensional interactions on membranes, which cannot be readily concluded from the solution binding assays. The restricted rotation and the increased lifetime of the encounter complex due to high membrane viscosity are the main determinants of the 2-dimensional association. Tethering ifnar1-EC to the membrane via N-terminal decahistidine tag decreased the 2-dimensional association rate constant 4-5 fold. Electrostatic attraction and steering, the important mechanism to enhance association rate constant between the soluble proteins, are not pronounced for interactions on the membrane. Protein orientation due to membrane anchoring dominates over electrostatic effects and together with the increased lifetime of the encounter complex consequence that 2-dimensional association rate constants are quite similar and do not correlate with association rate constants in solution. The 2- dimensional dissociation rate constants were generally 2-5-fold lower compared to the corresponding 3-dimensional dissociation rate constants in solution. Possible explanations for this are that long lifetime of the encounter complex stabilizes the ternary complex or that membrane tethering affects the interaction diagram. In conclusion, combined TIRFS-RIf detection turn to be powerful and versatile technique to characterize protein-protein interactions on membranes.
Virtual screening of potential bioactive substances using the support vector machine approach
(2005)
Die vorliegende Dissertation stellt eine kumulative Arbeit dar, die in insgesamt acht wissenschaftlichen Publikationen (fünf publiziert, zwei eingerichtet und eine in Vorbereitung) dargelegt ist. In diesem Forschungsprojekt wurden Anwendungen von maschinellem Lernen für das virtuelle Screening von Moleküldatenbanken durchgeführt. Das Ziel war primär die Einführung und Überprüfung des Support-Vector-Machine (SVM) Ansatzes für das virtuelle Screening nach potentiellen Wirkstoffkandidaten. In der Einleitung der Arbeit ist die Rolle des virtuellen Screenings im Wirkstoffdesign beschrieben. Methoden des virtuellen Screenings können fast in jedem Bereich der gesamten pharmazeutischen Forschung angewendet werden. Maschinelles Lernen kann einen Einsatz finden von der Auswahl der ersten Moleküle, der Optimierung der Leitstrukturen bis hin zur Vorhersage von ADMET (Absorption, Distribution, Metabolism, Toxicity) Eigenschaften. In Abschnitt 4.2 werden möglichen Verfahren dargestellt, die zur Beschreibung von chemischen Strukturen eingesetzt werden können, um diese Strukturen in ein Format zu bringen (Deskriptoren), das man als Eingabe für maschinelle Lernverfahren wie Neuronale Netze oder SVM nutzen kann. Der Fokus ist dabei auf diejenigen Verfahren gerichtet, die in der vorliegenden Arbeit verwendet wurden. Die meisten Methoden berechnen Deskriptoren, die nur auf der zweidimensionalen (2D) Struktur basieren. Standard-Beispiele hierfür sind physikochemische Eigenschaften, Atom- und Bindungsanzahl etc. (Abschnitt 4.2.1). CATS Deskriptoren, ein topologisches Pharmakophorkonzept, sind ebenfalls 2D-basiert (Abschnitt 4.2.2). Ein anderer Typ von Deskriptoren beschreibt Eigenschaften, die aus einem dreidimensionalen (3D) Molekülmodell abgeleitet werden. Der Erfolg dieser Beschreibung hangt sehr stark davon ab, wie repräsentativ die 3D-Konformation ist, die für die Berechnung des Deskriptors angewendet wurde. Eine weitere Beschreibung, die wir in unserer Arbeit eingesetzt haben, waren Fingerprints. In unserem Fall waren die verwendeten Fingerprints ungeeignet zum Trainieren von Neuronale Netzen, da der Fingerprintvektor zu viele Dimensionen (~ 10 hoch 5) hatte. Im Gegensatz dazu hat das Training von SVM mit Fingerprints funktioniert. SVM hat den Vorteil im Vergleich zu anderen Methoden, dass sie in sehr hochdimensionalen Räumen gut klassifizieren kann. Dieser Zusammenhang zwischen SVM und Fingerprints war eine Neuheit, und wurde von uns erstmalig in die Chemieinformatik eingeführt. In Abschnitt 4.3 fokussiere ich mich auf die SVM-Methode. Für fast alle Klassifikationsaufgaben in dieser Arbeit wurde der SVM-Ansatz verwendet. Ein Schwerpunkt der Dissertation lag auf der SVM-Methode. Wegen Platzbeschränkungen wurde in den beigefügten Veröffentlichungen auf eine detaillierte Beschreibung der SVM verzichtet. Aus diesem Grund wird in Abschnitt 4.3 eine vollständige Einführung in SVM gegeben. Darin enthalten ist eine vollständige Diskussion der SVM Theorie: optimale Hyperfläche, Soft-Margin-Hyperfläche, quadratische Programmierung als Technik, um diese optimale Hyperfläche zu finden. Abschnitt 4.3 enthält auch eine Diskussion von Kernel-Funktionen, welche die genaue Form der optimalen Hyperfläche bestimmen. In Abschnitt 4.4 ist eine Einleitung in verschiede Methoden gegeben, die wir für die Auswahl von Deskriptoren genutzt haben. In diesem Abschnitt wird der Unterschied zwischen einer „Filter“- und der „Wrapper“-basierten Auswahl von Deskriptoren herausgearbeitet. In Veröffentlichung 3 (Abschnitt 7.3) haben wir die Vorteile und Nachteile von Filter- und Wrapper-basierten Methoden im virtuellen Screening vergleichend dargestellt. Abschnitt 7 besteht aus den Publikationen, die unsere Forschungsergebnisse enthalten. Unsere erste Publikation (Veröffentlichung 1) war ein Übersichtsartikel (Abschnitt 7.1). In diesem Artikel haben wir einen Gesamtüberblick der Anwendungen von SVM in der Bio- und Chemieinformatik gegeben. Wir diskutieren Anwendungen von SVM für die Gen-Chip-Analyse, die DNASequenzanalyse und die Vorhersage von Proteinstrukturen und Proteininteraktionen. Wir haben auch Beispiele beschrieben, wo SVM für die Vorhersage der Lokalisation von Proteinen in der Zelle genutzt wurden. Es wird dabei deutlich, dass SVM im Bereich des virtuellen Screenings noch nicht verbreitet war. Um den Einsatz von SVM als Hauptmethode unserer Forschung zu begründen, haben wir in unserer nächsten Publikation (Veröffentlichung 2) (Abschnitt 7.2) einen detaillierten Vergleich zwischen SVM und verschiedenen neuronalen Netzen, die sich als eine Standardmethode im virtuellen Screening etabliert haben, durchgeführt. Verglichen wurde die Trennung von wirstoffartigen und nicht-wirkstoffartigen Molekülen („Druglikeness“-Vorhersage). Die SVM konnte 82% aller Moleküle richtig klassifizieren. Die Klassifizierung war zudem robuster als mit dreilagigen feedforward-ANN bei der Verwendung verschiedener Anzahlen an Hidden-Neuronen. In diesem Projekt haben wir verschiedene Deskriptoren zur Beschreibung der Moleküle berechnet: Ghose-Crippen Fragmentdeskriptoren [86], physikochemische Eigenschaften [9] und topologische Pharmacophore (CATS) [10]. Die Entwicklung von weiteren Verfahren, die auf dem SVM-Konzept aufbauen, haben wir in den Publikationen in den Abschnitten 7.3 und 7.8 beschrieben. Veröffentlichung 3 stellt die Entwicklung einer neuen SVM-basierten Methode zur Auswahl von relevanten Deskriptoren für eine bestimmte Aktivität dar. Eingesetzt wurden die gleichen Deskriptoren wie in dem oben beschriebenen Projekt. Als charakteristische Molekülgruppen haben wir verschiedene Untermengen der COBRA Datenbank ausgewählt: 195 Thrombin Inhibitoren, 226 Kinase Inhibitoren und 227 Faktor Xa Inhibitoren. Es ist uns gelungen, die Anzahl der Deskriptoren von ursprünglich 407 auf ungefähr 50 zu verringern ohne signifikant an Klassifizierungsgenauigkeit zu verlieren. Unsere Methode haben wir mit einer Standardmethode für diese Anwendung verglichen, der Kolmogorov-Smirnov Statistik. Die SVM-basierte Methode erwies sich hierbei in jedem betrachteten Fall als besser als die Vergleichsmethoden hinsichtlich der Vorhersagegenauigkeit bei der gleichen Anzahl an Deskriptoren. Eine ausführliche Beschreibung ist in Abschnitt 4.4 gegeben. Dort sind auch verschiedene „Wrapper“ für die Deskriptoren-Auswahl beschrieben. Veröffentlichung 8 beschreibt die Anwendung von aktivem Lernen mit SVM. Die Idee des aktiven Lernens liegt in der Auswahl von Molekülen für das Lernverfahren aus dem Bereich an der Grenze der verschiedenen zu unterscheidenden Molekülklassen. Auf diese Weise kann die lokale Klassifikation verbessert werden. Die folgenden Gruppen von Moleküle wurden genutzt: ACE (Angiotensin converting enzyme), COX2 (Cyclooxygenase 2), CRF (Corticotropin releasing factor) Antagonisten, DPP (Dipeptidylpeptidase) IV, HIV (Human immunodeficiency virus) protease, Nuclear Receptors, NK (Neurokinin receptors), PPAR (peroxisome proliferator-activated receptor), Thrombin, GPCR und Matrix Metalloproteinasen. Aktives Lernen konnte die Leistungsfähigkeit des virtuellen Screenings verbessern, wie sich in dieser retrospektiven Studie zeigte. Es bleibt abzuwarten, ob sich das Verfahren durchsetzen wird, denn trotzt des Gewinns an Vorhersagegenauigkeit ist es aufgrund des mehrfachen SVMTrainings aufwändig. Die Publikationen aus den Abschnitten 7.5, 7.6 und 7.7 (Veröffentlichungen 5-7) zeigen praktische Anwendungen unserer SVM-Methoden im Wirkstoffdesign in Kombination mit anderen Verfahren, wie der Ähnlichkeitssuche und neuronalen Netzen zur Eigenschaftsvorhersage. In zwei Fällen haben wir mit dem Verfahren neuartige Liganden für COX-2 (cyclooxygenase 2) und dopamine D3/D2 Rezeptoren gefunden. Wir konnten somit klar zeigen, dass SVM-Methoden für das virtuelle Screening von Substanzdatensammlungen sinnvoll eingesetzt werden können. Es wurde im Rahmen der Arbeit auch ein schnelles Verfahren zur Erzeugung großer kombinatorischer Molekülbibliotheken entwickelt, welches auf der SMILES Notation aufbaut. Im frühen Stadium des Wirstoffdesigns ist es wichtig, eine möglichst „diverse“ Gruppe von Molekülen zu testen. Es gibt verschiedene etablierte Methoden, die eine solche Untermenge auswählen können. Wir haben eine neue Methode entwickelt, die genauer als die bekannte MaxMin-Methode sein sollte. Als erster Schritt wurde die „Probability Density Estimation“ (PDE) für die verfügbaren Moleküle berechnet. [78] Dafür haben wir jedes Molekül mit Deskriptoren beschrieben und die PDE im N-dimensionalen Deskriptorraum berechnet. Die Moleküle wurde mit dem Metropolis Algorithmus ausgewählt. [87] Die Idee liegt darin, wenige Moleküle aus den Bereichen mit hoher Dichte auszuwählen und mehr Moleküle aus den Bereichen mit niedriger Dichte. Die erhaltenen Ergebnisse wiesen jedoch auf zwei Nachteile hin. Erstens wurden Moleküle mit unrealistischen Deskriptorwerten ausgewählt und zweitens war unser Algorithmus zu langsam. Dieser Aspekt der Arbeit wurde daher nicht weiter verfolgt. In Veröffentlichung 6 (Abschnitt 7.6) haben wir in Zusammenarbeit mit der Molecular-Modeling Gruppe von Aventis-Pharma Deutschland (Frankfurt) einen SVM-basierten ADME Filter zur Früherkennung von CYP 2C9 Liganden entwickelt. Dieser nichtlineare SVM-Filter erreichte eine signifikant höhere Vorhersagegenauigkeit (q2 = 0.48) als ein auf den gleichen Daten entwickelten PLS-Modell (q2 = 0.34). Es wurden hierbei Dreipunkt-Pharmakophordeskriptoren eingesetzt, die auf einem dreidimensionalen Molekülmodell aufbauen. Eines der wichtigen Probleme im computerbasierten Wirkstoffdesign ist die Auswahl einer geeigneten Konformation für ein Molekül. Wir haben versucht, SVM auf dieses Problem anzuwenden. Der Trainingdatensatz wurde dazu mit jeweils mehreren Konformationen pro Molekül angereichert und ein SVM Modell gerechnet. Es wurden anschließend die Konformationen mit den am schlechtesten vorhergesagten IC50 Wert aussortiert. Die verbliebenen gemäß dem SVM-Modell bevorzugten Konformationen waren jedoch unrealistisch. Dieses Ergebnis zeigt Grenzen des SVM-Ansatzes auf. Wir glauben jedoch, dass weitere Forschung auf diesem Gebiet zu besseren Ergebnissen führen kann.
After a brief introduction on QCD and effective models in the first chapter, I analyze the dependence of the QCD transition temperature on the quark (or pion) mass in the second chapter. I found that a linear sigma model, which links the transition to chiral symmetry restoration, predicts a much stronger dependence of T_c on m_pi than seen in present lattice data for m_pi >~ 0.4 GeV. On the other hand, an effective Lagrangian for the Polyakov loop requires only small explicit symmetry breaking to describe T_c(m_pi) in the above mass range. In the third and fourth chapter, I study the linear sigma model with O(N) symmetry at nonzero temperature in the framework of the Cornwall-Jackiw-Tomboulis formalism. Extending the set of two-particle irreducible diagrams by adding sunset diagrams to the usual Hartree-Fock (or Hartree) contributions, I derive a new approximation scheme which extends the standard Hartree-Fock (or Hartree) approximation by the inclusion of nonzero decay widths.
In the present study possible sources and pathways of the gasoline additive methyl tertiary-butyl ether (MTBE) in the aquatic environment in Germany were investigated. The objective of the present study was to clarify some of the questions raised by a previous study on the MTBE situation in Germany. In the USA and Europe 12 million t and 3 million t of MTBE, respectively, are used as gasoline additive. The detection of MTBE in the aquatic environment and the potential risk for drinking water resources led to a phase-out of MTBE as gasoline additive in single states of the USA. Meanwhile there is also an ongoing discussion about the substitution of MTBE in Europe and Germany. The annual usage of MTBE in Germany is about 600,000 t. However, compared to the USA, significant less data exists on the occurrence of MTBE in the aquatic environment in Europe. Because of its physico-chemical properties, MTBE readily vaporizes from gasoline, is water soluble, adsorbs only weakly to the underground matrix and is largely persistent to biological degradation. The toxicity of MTBE remains to be completely investigated, but MTBE in drinking water has low taste- and odor thresholds of 20-40 microgram/L. The present study was conducted by collecting water samples and analyzing them for their MTBE concentrations through a combination of headspace-solid phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS). The detection limit was 10 ng/L. The method was successfully tested in the framework of an interlaboratory study and showed recoveries of reference values of 89% (74 ng/L) and 104% (256 ng/L). The relative standard deviations were 12% and 6%. The investigation of 83 water samples from 50 community water systems (CWSs) in Germany revealed a detection frequency of 40% and a concentration range of 17-712 ng/L. The detection of MTBE in the drinking water samples could be explained by a groundwater pollution and the pathway river - riverbank filtration - waterworks. Rivers are important drinking water sources. MTBE is emitted into rivers through a variety of sources. In the present study, potential point sources were investigated, i.e. MTBE production sites/refineries/tank farms and groundwater pollutions. For this purpose, the spatial distribution of MTBE in three German rivers with the named potential emission sources located close to the rivers was investigated by analyzing 49 corresponding river water samples. The influence of the potential emission sources groundwater pollution and refinery/tank farm was successfully demonstrated in certain parts of the River Saale and the River Rhine. Increasing MTBE concentrations from 24 ng/L to 379 ng/L and from 73 ng/L to 5 microgram/L, respectively, could be observed in the parts investigated in these two rivers. The identification of such emission sources is important for future modeling. Further sources of MTBE emission into surface water are industrial (non-petrochemical) and municipal sewage plant effluents. In the present study long-term monitoring of water from the River Main (n=67 samples), precipitation (n=89) and industrial (n=34) and municipal sewage plant effluents (n=66) was conducted. The comparison of the data sets revealed that maximum MTBE concentrations in the River Main of up to 1 microgram/L were most possibly due to single industrial effluents with MTBE concentrations of up to 28 microgram/L (measured in this study). The average MTBE content of 66 ng/L in the River Main most probably originated from municipal sewage plant effluents and further industrial effluents. Background concentrations of <30 ng/L could be related to the direct atmospheric input via precipitation. A certain aspect of the atmospheric MTBE input is represented by the input of MTBE into river water or groundwater through snow. In the present study 43 snow samples from 13 different locations were analyzed for their MTBE content. MTBE could be detected in 65% of the urban and rural samples. The concentrations ranged from 11-613 ng/L and were higher than the concentrations in rainwater samples formerly analyzed. Furthermore, a temperature dependency and wash-out effects could be observed. The atmospheric input of MTBE was in part also visible in the analyzed groundwater samples (n=170). The detection frequencies in non-urban and urban wells were 24% and 63%, respectively. The median concentrations were 177 ng/L and 57 ng/L. In wells located in the vicinity of sites with gasoline contaminated groundwater, MTBE concentrations of up to 42 mg/L could be observed. The MTBE emission sources and the different pathways of MTBE in the aquatic environment demonstrated in the present study and other works raise the question whether the use of MTBE in a bulk product like gasoline should be continued in the future. Currently, possible substitutes like ethyl tertiary-butyl ether (ETBE) or ethanol are being discussed.
Biophysical investigation of the ligand-induced assembling of the human type I interferon receptor
(2005)
Type I interferons (IFNs) elicit antiviral, antiproliferative and immunmodulatory responses through binding to a shared receptor consisting of the transmembrane proteins ifnar1 and ifnar2. Differential signaling by different interferons – in particular IFNalpha´s and IFNbeta – suggest different modes of receptor engagement. In this work either single ligand-receptor interactions or the formation of the extracellular part of a signaling complex were investigated referring to thermodynamics, kinetics, stoichiometry and structural organization. Initially an expression and purification strategy for the extracellular domain of ifnar1 (ifnar1-EC) using Sf9 insect cells yielding in mg amounts of glycosylated protein was established. Using reflectometric interference spectroscopy (RIfS) the interactions between IFNalpha2/beta and ifnar1-EC and ifnar2-EC was studied in order to understand the individual energetic contributions within the ternary complex. For IFNalpha2 a Kd of 5 µM for the interaction with ifnar1-EC was determined. Substantially tighter binding of IFNbeta with both ifnar2-EC and ifnar1-EC compared to IFNalpha2 was observed. For neither IFNalpha2 nor IFNbeta stabilization of the complex with ifnar1-EC in presence of soluble ifnar2-EC was detectable. In addition, no direct interaction between ifnar2 and ifnar1 was could be shown. Thus, stem-stem interactions between the extracellular domains of ifnar1 and ifnar2 do not seem to play a role for ternary complex formation. Furthermore, ligand-induced cross-talk between ifnar1-EC and ifnar2-EC being tethered onto solid-supported, fluid lipid bilayers was investigated by RIfS and total internal reflection fluorescence spectroscopy. A very stable binding of IFNalpha2 at high receptor surface concentrations was observed with an apparent kd approximately 200-times lower than for ifnar2-EC alone. This apparent kd was strongly dependent on the surface concentration of the receptor components, suggesting kinetic rather than static stabilization, which was corroborated by competition experiments. These results indicate that signaling is activated by transient cross-talk between ifnar1 and ifnar2, which is by several orders of magnitude more efficiently engaged by IFNbeta than by IFNalpha2. With respect to differential recognition of different IFNs ifnar1-EC was dissected into sub-fragments containing different of the four Ig-like domains. The appropriate folding and glycosylation of these proteins, also purified in mg amounts were confirmed by SDS-PAGE, size exclusion chromatography and CD-spectroscopy. Surprisingly, only one construct containing all three N-terminal Ig-like domains was active in terms of ligand binding, indicating that these domains were required. Competitive binding of IFNalpha2 and IFNbeta to both this fragment and ifnar1-EC was demonstrated. Cellular binding assays with different fragments, however, highlight the key role of the membrane-proximal Ig-like domain for the formation of an in situ IFN-receptor complex and the ensuing signal activation. Even substitution with Ig-like domains from homologous cytokine receptors did not restore high-affinity ligand binding. Receptor assembling analysis on supported lipid bilayer revealed that appropriate orientation of the receptor is required, which is controlled by the membrane-proximal Ig-domain. All results indicate that differential signalling is encoded by the efficiency of signalling complex formation, which is controlled by the binding affinity of IFNs to the extracellular domains of ifnar1 and 2.
Here I analyse 23 populations of D. galeata, a large-lake cladoceran, distributed mainly across the Palaearctic. I detected high levels of clonal diversity and population differentiation using variation at six microsatellite loci across Europe. Most populations were characterised by deviations from H-W equilibrium and significant heterozygote deficiencies. Observed heterozygote deficiencies might be a consequence of simultaneous hatching of individuals produced during different times of the year or of the coexistence of ecologically and genetically differentiated subpopulations. A significant isolation by distance was only found over large geographic distances (> 700 km). This pattern is mainly due to the high genetic differentiation among neighbouring populations. My results suggest that historic populations of Daphnia were once interconnected by gene flow but current populations are now largely isolated. Thus local ecological conditions which determine the level of biparental sexual reproduction and local adaptation are the main factors mediating population structure of D. galeata. The population genetic structure and diversity in D. galeata was investigated at a European scale using six microsatellite loci and 12S rDNA sequence data to infer and compare historical and contemporary patterns of gene flow. D. galeata has the potential for long-distance dispersal via ephippial resting eggs by wind and other dispersing vectors (waterfowl), but shows in general strong population differentiation even among neighbouring populations. A total of 427 individuals were analysed for microsatellite and 85 individuals for mitochondrial (mtDNA) sequence data from 12 populations across Europe. I detected genetic differentiation among populations across Europe and locations within sampling regions for both genetic marker systems (average values: mtDNA FST = 0.574; microsatellite FST = 0.389), resulting in a lack of isolation by distance. Furthermore, several microsatellite alleles and one haplotype were shared across populations. Partitioning of molecular variance was inconsistant for both marker systems. Microsatellite variation was higher within than among populations, whereas mtDNA data yielded an inverse pattern. Relative high levels of nuclear DNA diversity were found across Europe. The amount of mitochondrial diversity was low in Spain, Hungary and Denmark. Gene flow analysis at a European scale did not reveal typical pattern of population recolonization in the light of postglacial colonization hypotheses. Populations, which recently experienced an expansion or population-bottleneck were observed both in middle and northern Europe. Since these populations revealed high genetic diversity in both marker systems, I suggest these areas to represent postglacial zones of secondary contact among divergent lineages of D. galeata. In order to reveal the relationship between population genetic structure of D. galeata and the relative contribution of environmental factors, I used a statistical framework based on canonical correspondence analysis. Although I detected no single ecological gradient mediating the genetic differentiation in either lake regions, it is noteworthy that the same ecological factors were significantly correlated with intra- and interspecific genetic variation of D. galeata. For example, I found a relationship between genetic variation of D. galeata and differentiation with higher and lower trophic levels (phytoplankton, submerged macrophytes and fish) and a relationship between clonal variation and species diversity within Cladocera. Variance partitioning had only a minor contribution of each environmental category (abiotic, biomass/density and diversity) to genetic diversity of D. galeata, while the largest proportion of variation was explained by shared components. My work illustrates the important role of ecological differentiation and adaptation in structuring genetic variation, and it highlights the need for approaches incorporating a landscape context for population divergence.
Die vorliegende Arbeit beschäftigt sich mit der Charakterisierung des ALTRO Chips (ALICE TPC Readout), der ein integraler und wichtiger Bestandteil der Auslesekette des TPC (Time Projection Chamber) Detektors von ALICE (A Large Ion Collider Experiment) ist. ALICE ist ein Experiment am noch im Bau befindlichen LHC (Large Hadron Collider) am CERN mit der zentralen Ausrichtung, Schwerionenkollisionen zu untersuchen. Diese sind von besonderem Interesse, da durch sie ein experimenteller Zugriff zu dem QGP (Quark Gluon Plasma) existiert, dem einzigen vom Standardmodell vorhergesagten Phasenübergang, der unter Laborbedingungen erreichbar ist. Im Jahr 2004 wurden Messungen an einem Teststrahl am CERN PS (Proton Synchrotron) durchgeführt. Der Prototyp wurde voll mit FECs bestückt, was 5400 Kanälen entspricht und einer anderen Gasmixtur (Ne/N2/CO2 90%/5%/5%) befüllt. Für das optimale Leistungsverhalten der ALICE TPC muß der Digitalprozessor im ALTRO, bestehend aus vier Berechnungseinheiten, mit den passenden Werten konfiguriert werden. Der Datenfluss beginnt mit dem BCS1 (Baseline Correction and Subtraction 1) Modul, das systematische Störungen und die Grundlinie entfernt. Da der ALTRO kontinuierlich das anliegende Signal abtastet, entfernt es automatisch langsame Grundlinienveränderungen, die Beispielsweise durch Temperaturänderungen auftreten können. Gefolgt von dem TCF (Tail Cancellation Filter), der den Schweif des langsam fallenden, vom PASA generierten Signals entfernt. Um die nichtsystematischen Störungen der Grundlinie zu entfernen, folgt die BCS2 (Baseline Correction and Subtraction 2), die auf einer gleitenden Mittelwertsberechnung mit Ausschluß von Detektorsignalen über einen doppelten Schwellenwert basiert. Die finale Einheit für die Signalverarbeitung ist die ZSU (Zero Suppression Unit), die Meßpunkte unterhalb eines definierten Schwellwertes entfernt. Hier wird der weg beschrieben die TCF und BCS1 Parameter aus vorhandenen Detektordaten zu extrahieren. Während der Analyse der Daten von kosmischen Teilchen fiel bei Signalen mit hoher Amplitude (>700 ADC) eine zusätzliche Struktur in dem Schweif auf. Der Monitor wurde deswegen mit einem gleitenden Mittelwertfilter erweitert, worauf sich diese Struktur auch in kleineren Signalen (> 200 ADC) zeigte. Dieses Signal wird von Ionen erzeugt, die zur Kathode oder zu den Pads driften, bisher ist jedoch weder die Streuung der Elektronenlawine an der Anode, noch die Variationsbreite in den erzeugten Elektronlawinen verstanden oder gemessen worden. Eine erfolgreiche Messung, sowie Charakterisierung wird in dieser Arbeit beschrieben. Im Jahr 2005 im Sommer beginnt der Einbau der Gaskammern der TPC in ALICE, die Elektronik folgt am Ende dieses Jahres. Parallel hierzu wurde der Prototyp der TPC wieder in Betrieb genommen und im Frühling wird ein kompletter Sektor mit der Detektorelektronik ausgestattet. An diesen zwei Aufbauten wird die ALTRO Charakterisierung fortgeführt, verfeinert und komplettiert.
Mitochondial NADH:ubiquinone oxidoreductase (complex I) the largest multiprotein enzyme of the respiratory chain, catalyses the transfer of two electrons from NADH to ubiquinone, coupled to the translocation of four protons across the membrane. In addition to the 14 strictly conserved central subunits it contains a variable number of accessory subunits. At present, the best characterized enzyme is complex I from bovine heart with a molecular mass of about 980 kDa and 32 accessory proteins. In this study, the subunit composition of mitochondrial complex I from the aerobic yeast Y. lipolytica has been analysed by a combination of proteomic and genomic approaches. The sequences of 37 complex I subunits were identified. The sum of their individual molecular masses (about 930 kDa) was consistent with the native molecular weight of approximately 900 kDa for Y. lipolytica complex I obtained by BN-PAGE. A genomic analysis with Y. lipolytica and other eukaryotic databases to search for homologues of complex I subunits revealed 31 conserved proteins among the examined species. A novel protein named “X” was found in purified Y. lipolytica complex I by MALDI-MS. This protein exhibits homology to the thiosulfate sulfurtransferase enzyme referred to as rhodanese. The finding of a rhodanese-like protein in isolated complex I of Y. lipolytica allows to assume a special regulatory mechanism of complex I activity through control of the status of its iron-sulfur clusters. The second part of this study was aimed at investigating the possible role of one of these extra subunits, 39 kDa (NUEM) subunit which is related to the SDRs-enzyme family. The members of this family function in different redox and isomerization reactions and contain a conserved NAD(P)H-binding site. It was proposed that the 39 kDa subunit may be involved in a biosynthetic pathway, but the role of this subunit in complex I is unknown. In contrast to the situation in N. crassa, deletion of the 39 kDa encoding gene in Y. lipolytica led to the absence of fully assembled complex I. This result might indicate a different pathway of complex I assembly in both organisms. Several site-directed mutations were generated in the nucleotide binding motif. These had either no effect on enzyme activity and NADPH binding, or prevented complex I assembly. Mutations of arginine-65 that is located at the end of the second b-strand and responsible for selective interaction with the 2’-phosphate group of NADPH retained complex I activity in mitochondrial membranes but the affinity for the cofactor was markedly decreased. Purification of complex I from mutants resulted in decrease or loss of ubiquinone reductase activity. It is very likely that replacement of R65 not only led to a decrease in affinity for NADPH but also caused instability of the enzyme due to steric changes in the 39 kDa subunit. These data indicate that NADPH bound to the 39 kDa subunit (NUEM) is not essential for complex I activity, but probably involved in complex I assembly in Y. lipolytica.
The thesis entitled „Investigations on the significance of nucleo-cytoplasmic transport for the biological function of cellular proteins" aimed to unreveal molecular mechanisms in order to improve our understanding of the impact of nucleo-cytoplasmic transport on cellular functions. Within the scope of this work, it could be shown that regulated nucleo-cytoplasmic transport of a subfamily of homeobox transcription factors controlled their intra- and intercellular transport, and thereby influencing also their transcriptional activity. This study describes a novel regulatory mechanism, which could in general play an important role for the ordered differentiation of complex organisms. Besides cis-active transport Signals, also post-translational modifications can influence the localization and biological activity of proteins in trans. In addition to the known impact of phosphorylation on the transport and activity of STAT1, experimental evidence was provided demonstrating that acetylation affected the interaction of STAT1 with NF-kB p65, and subsequently modulated the expression of apoptosis-inducing NF-kB target genes. The impact of nucleo-cytoplasmic transport on the regulation of apoptosis was underlined by showing that the evolutionary conservation of a NES within the anti-apoptotic protein survivin plays an essential role for its dual function in the inhibition of apoptosis and ordered cell division. Since survivin is considered a bona fide cancer therapy target, these results strongly encourage future work to identify molecular decoys that specifically inhibit the nuclear export of survivin as novel therapeutics. In order to further dissect the regulation of nuclear transport and to efficiently identify transport inhibitors, cell-based assays are urgently required. Therefore, the cellular assay Systems developed in this work may not only serve to identify synthetic nuclear export and Import inhibitors but may also be applied in systematic RNAi-screening approaches to identify novel components of the transport machinery. In addition, the translocation based protease- and protein-interaction biosensors can be applied in various biological Systems, in particular to identify protein-protein interaction inhibitors of cancer relevant proteins. In summary, this work does not only underline the general significance of nucleo-cytoplasmic transport for cell biology, but also demonstrates its potential for the development of novel therapies against diseases like cancer and viral infections.
Calcium-activated potassium channels are fundamental regulators of neuron excitability. SK channels are activated by an intracellular increase of Ca++ (such as occurs during an action potential). They have a small single channel conductance (less than 20pS) and show no voltage dependence of activation. To date, there are only a few examples of high-resolution structures of eukaryotic membrane proteins. All of them were purified from natural sources. Since no abundant natural sources of eukaryotic K+ channels are available we overexpressed rSK2 in order to produce the quantities necessary for structural analysis. Unfortunately the Pichia pastoris expression system did not yield sufficient amount of pure protein, mainly because most of the protein was retained by in the ER and was only partially soluble. Subsequently, two constructs were expressed: SK2-FCYENE (containing a specific sequence that promotes surface expression), and SK2-q-CaM a concatamer of SK2 and calmodulin. Although these proved an improvement in terms of solubilisation, little improvement was found in terms of amounts of purified material obtained. For this reason we tested the Semliki Forest virus expression system, since the protein is expressed in a mammalian system where we hoped that it would be trafficked in the same way as in vivo. Using this system it was possible to express rSK2 and solubilise it with several detergents and to achieve much better purification. However, the levels were still not sufficient for high-resolution structural studies, although sufficient for single particle electron microscopy analysis.
Molecular dynamics (MD) simulation serves as an important and widely used computational tool to study molecular systems at an atomic resolution. No experimental technique is capable of generating a complete description of the dynamical structure of the biomolecules in their native solution environment. MD simulations allow us to study the dynamics and structure of the system and, moreover, helps in the interpretation of experimental observations. MD simulation was first introduced and applied by Alder and Wainwright in 1957 \cite{Alder57}. However, the first MD simulation of a macromolecule of biological interest was published 28 years ago \cite{McCammon77}. The simulation was concerned with the bovine pancreatic trypsin inhibitor (BPTI) protein, which has served as the hydrogen molecule'' of protein dynamics because of its small size, high stability, and relatively accurate X-ray structure available in 1977 \cite{Deisenhofer75}. This method is now widely used to tackle larger and more complex biological systems \cite{Groot01,Roux02} and has been facilitated by the development of fast and efficient methods for treating the long-range electrostatic interactions \cite{Essmann95}, the availability of faster parallel computers, and the continuous development of empirical molecular mechanical force fields \cite{Langley98,Cheatham99,Foloppe00}. It took several years until the first MD simulations of nucleic acid systems were performed \cite{Levitt83,Tidor83,Prabhakaran83,Nilsson86}. These investigations, which were also performed in vacuo, clearly demonstrated the importance of proper handling of electrostatics in a highly charged nucleic acid system, and different approaches, such as reduction of the phosphate charges and addition of hydrated counterions, have been applied to remedy this shortcoming and to maintain stable DNA structures. A few years later, the first MD simulation of a DNA molecule, including explicit water molecules and counterions was published \cite{Seibel85}. Various MD simulations on fully solvated RNA molecules with explicit inclusion of mobile ions indicated the importance of proper treatment of the environment of highly charged nucleic acids \cite{Lee95,Zichi95,Auffinger97,Auffinger99}. Given the central roles of RNA in the life of cells, it is important to understand the mechanism by which RNA forms three dimensional structures endowed with properties such as catalysis, ligand binding, and recognition of proteins. Furthermore, the increasing awareness of the essential role of RNA in controlling viral replication and in bacterial protein synthesis emphazises the potential of ribonucleicacids as targets for developing new antibacterial and new antiviral drugs. Driven by fruitful collaborations in the Sonderforschungsbereich RNA-Ligand interactions" the model RNA systems in this study include various RNA tetraloops and HIV-1 TAR RNA. For the latter system, the binding sites of heteroaromatic compounds have been studied employing automated docking calculations \cite{Goodsell90}. The results show that it is possible to use this tool to dock small rigid ligands to an RNA molecule, while large and flexible molecules are clearly problematic. The main part of this work is focused on MD simulations of RNA tetraloops.
The quinol:fumarate reductase (QFR) is the terminal reductase of anaerobic fumarate respiration, the most commonly occurring type of anaerobic respiration. This membrane protein complex couples the oxidation of menaquinol to menaquinone to the reduction of fumarate to succinate. The three-dimensional crystal structure of the QFR from Wolinella succinogenes has previoulsy been solved at 2.2 Å resolution. Although the diheme-containing QFR from W. succinogenes is known to catalyze an electroneutral process, structural and functional characterization of parental and variant enzymes has revealed active site locations which indicate electrogenic catalysis across the membrane. A solution to this apparent controversy was proposed with the so-called “Epathway hypothesis”. According to this, transmembrane electron transfer via the heme groups is strictly coupled to a parallel, compensatory transfer of protons via a transiently established pathway, which is inactive in the oxidized state of the enzyme. Proposed constituents of the E-pathway are the side chain of Glu C180, and the ring C propionate of the distal heme. Previous experimental evidence strongly supports such a role for the former constituent. One aim of this thesis is to investigate by a combination of specific 13C-heme propionate labeling and FTIR difference spectroscopy whether the ring C propionate of the distal heme is involved in redox-coupled proton transfer in the QFR from W. succinogenes. In addition to W. succinogenes, the primary structures of the QFR enzymes of two other e- proteobacteria are known. These are Campylobacter jejuni and Helicobacter pylori, which unlike W. succinogenes are human pathogens. The QFR from H. pylori has previously been established to be a potential drug target, and the same is likely for the QFR from C. jejuni. The two pathogenic species colonize mucosal surfaces causing several diseases. The possibility of studying these QFRs from these bacteria and creating more efficient drugs specifically active for this enzyme depends substantially on the availability of large amounts of high-quality protein. Further, biochemical and structural studies on QFR enzymes from e- proteobacteria species other than W. succinogenes can be valuable to enlighten new aspects or corroborate the current understanding of this class of membrane proteins.
A strong interest is currently going on in the physics of high intensity and high energy beams: intense proton or deuteron beams are required in various fields of science and industry, including sources of neutrons for research experiments and material processing, nuclear physics experiments, tritium production and nuclear waste transmutation. High current heavy ion beams are envisaged for power production facilities (inertial fusion). Several projects presently under study are based on rf linacs as driver, sometimes followed by accumulation and/or compressor rings [Acc98]. The critical issue for all of them is to be operated in a low loss regime, because of activation problems in the structure. For this reason careful investigations have to be performed in order to understand and control the beam behaviour, aiming at conserving the beam quality, reducing the emittance growth and filamentation and avoiding the formation of halo. The beam current to be accelerated is actually limited by the amount of beam losses, which depends upon the beam halo: in order to reduce induced radioactivity and to allow for hands-on maintenance, normally losses <1 W/m are considered as acceptable [Sto96]. One of the major facilities under study is the European Spallation Source (ESS), a project based on a H- linac accelerating a 107 mA peak current beam (360 ns pulse in the DTL) and on two compressor rings, producing 5 MW average beam power [ESS]. Also the USA are developing a proposal for a Spallation Neutron Source (SNS), providing a short pulse H- beam with average power of 1÷2 MW; a 30 mA linac is required [SNS]. The Accelerator for Production of Tritium (APT), studied at Los Alamos, requires a 100 mA proton beam current (cw) to produce a power of 130÷170 MW [APT]. A similar but smaller accelerator (40 mA, 40 MW beam power) would serve as driver for the Accelerator Driven Transmutation of Waste (ADTW) system [ATW]. The accelerator system for the International Fusion Material Irradiation Facility (IFMIF) will test the behaviour of materials to be used for magnetic fusion (e.g. ITER); it consists of two 125 mA deuteron beams in parallel, to generate a fusion-like neutron spectrum with 10 MW cw [IFM]. In the field of heavy ions, for about 20 years scientists have been working on inertial confinement fusion, as an alternative to magnetic confinement one, to find a practical and cleaner method for producing energy. Nuclear fusion occurs when the nuclei of lighter elements (in a state of matter called "plasma") merge to form heavier elements; the extremely high temperatures and densities needed to get the nuclei to collide in the proper way and release big amounts of energy are obtained in a small "pellet" of fusion fuel, which receives energy from laser or ion beams, implodes and its inertia compresses it hard enough to hold together the plasma until it reaches ignition. Both laser and accelerator facilities have been investigated as drivers, since a demonstration of ignition at low gains is more easily accessible by lasers, whereas the intrinsic properties of accelerators -efficiency and repetition rate- will be essential for a medium-gain power plant. One study for a fusion power system driven by heavy ion beams (HIBALL) was completed in Europe already in 1982 [Bad81]. When the USA declassified essential information on pellet design, "indirect drive" targets have been considered openly, where the pellet is hit by X-rays generated from laser or ion beams rather than directly from the beams. Main progress has been achieved during the latest years in the understanding of pellet dynamics after ignition, i.e. in plasma physics [Sym1][Sym2][Sym3][Bas97][Lut97], imposing also new requirements on the layout of the driver accelerator facilities. In 1994-95 Frankfurt University and several other European laboratories (leaded by GSI) started a new collaboration called HIDIF (Heavy Ion Driven Ignition Facility) in order to simplify the accelerator plant design owing to the new technique of indirectly driven targets and to some technological improvements. First studies were oriented towards the conceptual goal of a facility providing just enough beam energy for the ignition of fusion reactions at very low gain (a "proof of principle") [Hof98]. In a recent phase of the study, it was realized that the proposed concept would make this scheme a more appropriate choice for energy production rather than for ignition; the acronym HIDIF was therefore intended as Heavy Ion Driven Inertial Fusion, and the parameters are going to be modified accordingly [Hof96][Hof97][Hof98]. The scenario presently discussed by this group proposes the formation and acceleration of an intense beam (400 mA) of singly charged heavy ions of three different atomic species, with mass differences of about 10% (the reference one is 209Bi+) in a main rf linac; they are then injected into some storage rings at an energy of 50 MeV/u, bunched in induction linacs and finally transported to a target with different velocities in such a way that the three species merge on the pellet ("telescoping") at 500 TW peak power. In this thesis the main linac of the HIDIF proposal is extensively investigated as an example of a high intensity heavy ion linac. Results are presented from numerical simulations of multi-particle beam dynamics carried out for the first time in this context. After a short presentation of the HIDIF reference scenario (Ignition Facility), including a discussion of the motivations for a high current heavy ion linac, some elements of the theory of beam transport and acceleration are recalled [Con91][Hof82][Kap85] [Lap87][Law88][Mit78][Rei94][Str83]. Then the used simulation programs are described, and a particle dynamics layout of a conventional 200 MHz Alvarez DTL is discussed with respect to low emittance growth at high transmission, including large space-charge effects, taking into account the influence of different kinds of statistical errors and of input mismatch on the beam dynamics. The modifications needed for "telescoping" are investigated with simulations for the nominal mass difference (10%) and for a smaller one (5%); finally the transfer line between DTL and rings is discussed and studied both analytically and by numerical calculations. The large mass number (A= 209) helps to reduce the space-charge effects with respect to protons, therefore the behaviour of the beam is not space-charge dominated. Nevertheless the tune depression values (similar to those of the ESS linac e.g.) indicate that these effects cannot be neglected. For a linac with low duty cycle, as in the case of an ignition facility, the results from particle dynamics calculations can be considered as a reliable guideline for the DTL layout, since they indicate that such a high intensity linac can fulfill the requirements on smooth beam behaviour and low losses.
The challenging intricacies of strongly correlated electronic systems necessitate the use of a variety of complementary theoretical approaches. In this thesis, we analyze two distinct aspects of strong correlations and develop further or adapt suitable techniques. First, we discuss magnetization transport in insulating one-dimensional spin rings described by a Heisenberg model in an inhomogeneous magnetic field. Due to quantum mechanical interference of magnon wave functions, persistent magnetization currents are shown to exist in such a geometry in analogy to persistent charge currents in mesoscopic normal metal rings. The second, longer part is dedicated to a new aspect of the functional renormalization group technique for fermions. By decoupling the interaction via a Hubbard-Stratonovich transformation, we introduce collective bosonic variables from the beginning and analyze the hierarchy of flow equations for the coupled field theory. The possibility of a cutoff in the momentum transfer of the interaction leads to a new flow scheme, which we will refer to as the interaction cutoff scheme. Within this approach, Ward identities for forward scattering problems are conserved at every instant of the flow leading to an exact solution of a whole hierarchy of flow equations. This way the known exact result for the single-particle Green's function of the Tomonaga-Luttinger model is recovered.
Cancer has become one of the most fatal diseases. The Heidelberg Heavy Ion Cancer Therapy (HICAT) has the potential to become an important and efficient treatment method because of its excellent “Bragg peak” characteristics and on-line irradiation control by the PET diagnostics. The dedicated Heidelberg Heavy Ion Cancer Therapy Project includes two ECR ion sources, a RF linear injector, a synchrotron and three treatment rooms. It will deliver 4*10 high 10 protons, or 1*10 high 10 He, or 1*10 high 9 Carbons, or 5*10 high 8 Oxygens per synchrotron cycle with the beam energy 50-430AMeV for the treatments. The RF linear injector consists of a 400AkeV RFQ and of a very compact 7AMeV IH-DTL accelerator operated at 216.816MHz. The development of the IH-DTL within the HICAT project is a great challenge with respect to the present state of the DTL art because of the following reasons: • The highest operating frequency (216.816MHz) of all IH-DTL cavities; • Extremely large cavity length to diameter ratio of about 11; • IH-DTL with three internal triplets; • The highest effective voltage gain per meter (5.5MV/m); • Very short MEBT design for the beam matching. The following achievements have been reached during the development of the IH-DTL injector for HICAT : The KONUS beam dynamics design with LORASR code fulfills the beam requirement of the HICAT synchrotron at the injection point. The simulations for the IH-DTL injector have been performed not only with a homogeneous input beam, but also with the actual particle distribution from the exit of the HICAT RFQ accelerator as delivered by the PARMTEQ code. The output longitudinal normalized emittance for 95% of all particles is 2.00AkeVns, the emittance growth is less than 24%, while the X-X’ and Y-Y’ normalized emittance are 0.77mmmrad and 0.62mmmrad, respectively. The emittance growth in X-X’ is less than 18%, and the emittance growth in Y-Y’ is less than 5%. Based on the transverse envelopes of the transported particles, the redesign of the buncher drift tubes at the RFQ high energy end has been made to get a higher transit time factor for this novel RFQ internal buncher. An optimized effective buncher gap voltage of 45.4KV has been calculated to deliver a minimized longitudinal beam emittance, while the influence of the effective buncher voltage on the transverse emittance can be neglected. Six different tuning concepts were investigated in detail while tuning the 1:2 scaled HICAT IH model cavity. ‘Volume Tuning’ by a variation of the cavity cross sectional area can compensate the unbalanced capacitance distribution in case of an extreme beta-lambda-variation along an IH cavity. ‘Additional Capacitance Plates’ or copper sheets clamped on drift tube stems are a fast way for checking the tuning sensitivity, but they will be replaced by massive copper blocks mounted on the drift tube girders finally. ‘Lens Coupling’ is an important tuning to stabilize the operation mode and to increase or decrease the coupling between neighboring sections. ‘Tube Tuning’ is the fine tuning concept and also the standard tuning method to reach the needed field distributions as well as the gap voltage distributions. ‘Undercut Tuning’ is a very sensitive tuning for the end sections and with respect to the voltage distribution balance along the structure. The different types of ‘plungers’ in the 3rd and 4th sections have different effects on the resonance frequency and on the field distribution. The different triplet stems and the geometry of the cavity end have been also investigated to reach the design field and voltage distributions. Finally, the needed uniform field distribution along the IH-DTL cavity and the corresponding effective voltage distribution were realized, the remaining maximum gap voltage difference was less than 5% for the model cavity. The several important higher order modes were also measured. The RF tuning of the IH-DTL model cavity delivers the final geometry parameters of the IH-DTL power cavity. A rectangular cavity cross section was adopted for the first time for this IH-DTL cavity. This eases the realization of the volume tuning concept in the 1st and 2nd sections. Lens coupling determines the final distance between the triplet and the girder. The triplets are mounted on the lower cavity half shell. The Microwave Studio simulations have been carried out not only for the HICAT model cavity, but also for the final geometry of the IH-DTL power cavity. The field distribution for the operation mode H110 fits to the model cavity measurement as well as the Higher Order Modes. The simulations prove the IH-DTL geometrical design. On the other hand, the precision of one simulation with 2.3 million mesh points for full cross section area and the CPU time more than 15hours on a DELL PC with Intel Pentium 4 of 2.4GHz and 2.096GRAM were exploited to their limit when calculating the real parameters for the two final machining iterations during production. The shunt impedance of the IH-DTL power cavity is estimated by comparison with the existing tanks to about 195.8MOmega/m, which fits to the simulation result of 200.3MOmega/m with reducing the conductivity to the 5.0*10 high 7 Omega-1m-1. The effective shunt impedance is 153 MOmega/m. The needed RF power is 755kW. The expected quality factor of the IH-DTL cavity is about 15600. The IH-DTL power cavity tuning measurements before cavity copper plating have been performed. The results are within the specifications. There is no doubt that the needed accuracy of the voltage distribution will be reached with the foreseen fine tuning concepts in the last steps.
Prion diseases, also called transmissible spongiform encephalopathies, are a group of fatal neurodegenerative conditions that affect humans and a wide variety of animals. To date there is no therapeutic or prophylactic approach against prion diseases available. The causative infectious agent is the prion, also termed PrPSc, which is a pathological conformer of a cellular protein named prion protein PrPc. Prions are thought to multiply upon conversion of PrPc to PrPSc in a self-propagating manner. Immunotherapeutic strategies directed against PrPc represent a possible approach in preventing or curing prion diseases. Accordingly, it was already shown in animal models, that passive immunization delays the onset of prion diseases. The present thesis aimed at the development of a candidate vaccine towards the active immunization against prion diseases, an immune response, which has to be accompanied by the circumvention of host tolerance to the self-antigen PrPc. The vaccine development was approached using virus-like particles (retroparticles) derived from either the murine leukemia (MLV) or the human immunodeficiency virus (HIV). The display of PrP on the surface of such particles was addressed for both the cellular and the pathogenic form of PrP. The display of PrPc was achieved by either fusion to the transmembrane domain of the platelet derived growth factor receptor (PDGFR) or to the N-terminal part of the viral envelope protein (Env). In both cases, the corresponding PrPD- and PrPE-retroparticles were successfully produced and analyzed via immune fluorescence, Western Blot analysis, immunogold electron microscopy as well as by ELISA methods. Both, PrPD- and PrPE-retroparticles showed effective incorporation of N-terminally truncated forms of PrPc but not for the complete protein. PrPc at this revealed the typical glycosylation pattern, which was specifically removed by a glycosidase enzyme. Upon display of PrPc on retroparticles the protein remained detectable by PrP-specific antibodies under native conditions. Electron microscopy analysis of PrPc-variants revealed no alteration of the characteristic retroviral morphology of the generated particles. MLV-derived PrPD-retroparticles were successfully used in immunization studies. Contrary to approaches using bacterially expressed PrPc, the immunization of mice resulted in a specific antibody response. The display of the pathogenic isoform was aimed by two different strategies. The first one was directed at the conversion of the proteinase K (PK) sensitive from of PrP on the surface of PrPD-retroparticles into the PK resistant form. Albeit specific adaption of the PK digestion assay detecting resistant PrP, no PrP conversion was observed for PrPD-retroparticles. The second approach utilized a replication competent variant of the ecotropic MLV displaying PrPc on the viral Env protein. This MLV variant was stable in cell culture for six passages but did not replicate on scrapie-infected, PrPSc-propagating neuroblastoma cells. Thus, besides PrPc-displaying virus-like particles a replication competent MLV variant was obtained, which stably incorporated PrPc at the N-terminus of the viral Env protein. The incorporation of the cell-surface located PrPc into particles was expected from previously obtained data on protein display in the context of retrovirus-derived particles. Thus, the lack of incorporation observed for the complete PrPc sequence was rather unexpected and was found to be inhibited at both, fusion to PDGFR and the viral Env. In contrast to N-terminally truncated PrPc, the complete PrPc was shown to exhibit increased cell surface internalization rates and half-life times eventually contributing to the observed results. The PrP-vaccination approach described in this work represents the first successful system inducing PrP-specific antibody responses against the prion protein in wt mice. Explanations at this are based on the induction of specific T cell help or effects of the innate immunity, respectively. MLV-and HIV-derived particles bearing the PrP-coding sequence or being replication competent variants generated during this thesis might help to further improve the PrP-specific immune response.
This study analyses the labour market effects of fixed-term contracts (FTCs) in West Germany by microeconometric methods using individual and establishment level data. In the first part of the study the role of FTCs in firms’ labour demand is analysed. An econometric investigation of the firms’ reasons for using FTCs focussing on the identification of the link between dismissal protection for permanent contract workers and the firms’ use of FTCs is presented. Furthermore, a descriptive analysis of the role of FTCs in worker and job flows at the firm level is provided. The second part of the study evaluates the short-run effects of being employed on an FTC on working conditions and wages using a large cross-sectional dataset of employees. The final part of the study analyses whether taking up an FTC increases the (permanent contract) employment opportunities in the long-run (stepping stone effect) and whether FTCs affect job finding behaviour of unemployed job searchers. Firstly, an econometric unemployment duration analysis distinguishing between both types of contracts as destination states is performed. Secondly, the effects of entering into FTCs from unemployment on future (permanent contract) employment opportunities are evaluated attempting to account for the sequential decision problem of job searchers.
Drug target 5-lipoxygenase : a link between cellular enzyme regulation and molecular pharmacology
(2005)
Leukotriene (LT) sind bioaktive Lipidmediatoren, die in einer Vielzahl von Entzündungskrankheiten wie z.B. Asthma, Psoriasis, Arthritis oder allergische Rhinitis involviert sind. Des Weiteren spielen LT in der Pathogenese von Erkrankungen wie Krebs, Osteoarthritis oder Atherosklerose eine Rolle. Die 5-Lipoxygenase (5-LO) ist das Enzym, das für die Bildung von LT verantwortlich ist. Aufgrund der physiologischen Eigenschaften der LT, ist die Entwicklung von potentiellen Arzneistoffen, welche die 5-LO als Zielstruktur besitzen, von erheblichem Interesse. Die Aktivität der 5-LO wird in vitro durch Ca2+, ATP, Phosphatidylcholin und Lipidhydroperoxide (LOOH) und durch die p38-abhängige MK-2/3 5-LO bestimmt. Inhibitorstudien weisen darauf hin, dass der MEK1/2-Signalweg ebenfalls in vivo an der 5-LO Aktivierung beteiligt ist. Hauptziel dieser Arbeit war es zu untersuchen, welche Rolle der MEK1/2-Signalweg bei der Aktivierung der 5-LO besitzt und welchen Einfluss der 5-LO Aktivierungsweg auf die Wirksamkeit potentieller Inhibitoren hat. „In gel kinase“ und „In vitro kinase“ Untersuchungen zeigten, dass die 5-LO ein Substrat für die Extracellular signal-regulated kinase (ERK) und MK-2/3 darstellt. Der Zusatz von mehrfach ungesättigten Fettsäuren (UFA), wie AA oder Ölsäure, verstärkte den Phosphorylierungsgrad der 5-LO sowohl durch ERK1/2 als auch durch MK-2/3. Die genannten Kinasen sind demnach auch für die 5-LO Aktivierung durch natürliche Stimuli verantwortlich, die den zellulären Ca2+-Spiegel kaum beeinflussen. Daraus ist ersichtlich, dass die Phosphorylierung der 5-LO durch ERK1/2 und/oder MK-2/3 einen alternativen Aktivierungsmechanismus neben Ca2+ darstellt. Ursprünglich wurden Nonredox-5-LO-Inhibitoren als kompetitive Wirkstoffe entwickelt, die mit AA um die Bindung an die katalytische Domäne der 5-LO konkurrieren. Vertreter dieser Inhibitoren, wie ZM230487 und L-739,010, zeigen eine potente Hemmung der LT-Biosynthese in verschiedenen Testsystemen. Sie scheiterten jedoch in klinischen Studien. In dieser Arbeit konnten wir zeigen, dass die Wirksamkeit dieser Inhibitoren vom Aktivierungsweg der 5-LO abhängig ist. Verglichen mit 5-LO Aktivität, die durch den unphysiologischen Stimulus Ca2+-Ionophor induziert wird, erfordert die Hemmung zellstress-induzierter Aktivität eine 10- bis 100-fach höhere Konzentration der Nonredox-5-LO-Inhibitoren. Die nicht-phosphorylierbare 5-LO Mutante (Ser271Ala/Ser663Ala) war wesentlich sensitiver gegenüber Nonredox-Inhibitoren als der Wildtyp, wenn das Enzym durch 5-LO Kinasen aktiviert wurde. Somit zeigen diese Ergebnisse, dass, im Gegensatz zu Ca2+, die 5-LO Aktivierung mittels Phosphorylierung die Wirksamkeit der Nonredox-Inhibitoren deutlich verringert. Des Weiteren wurde das pharmakologische Profil des neuen 5-LO Inhibitors CJ-13,610 mittels verschiedener in vitro-Testsysteme charakterisiert. In intakten PMNL, die durch Ca2+-Ionophor stimuliert wurden, hemmte die Substanz die 5-LO Produktbildung mit einem IC50 von 70 nM. Durch Zugabe von exogener AA, wird die Wirkung vermindert und der IC50 des Inhibitors steigt an. Dies deutet auf eine kompetitive Wirkweise hin. Wie die bekannten Nonredox-Inhibitoren, verliert auch CJ-13,610 seine Wirkung bei erhöhtem zellulärem Peroxidspiegel. Der Inhibitor CJ-13,610 zeigt jedoch keine Abhängigkeit vom Aktivierungsweg der 5-LO. Grundsätzlich ist es also von fundamentaler Bedeutung bei der Entwicklung von neuen Arzneistoffen, die zellulären Zusammenhänge, insbesondere die Regulierung der Aktivität von Enzymen, zu kennen. Wie in dieser Arbeit gezeigt, hat die Phosphorylierung der 5-LO einen starken Einfluss auf die Regulation der 5-LO Aktivität und eine elementare Wirkung auf die Hemmung des Enzyms durch verschiedene Wirkstoffe.
A fundamental work on THz measurement techniques for application to steel manufacturing processes
(2004)
The terahertz (THz) waves had not been obtained except by a huge system, such as a free electron laser, until an invention of a photo-mixing technique at Bell laboratory in 1984 [1]. The first method using the Auston switch could generate up to 1 THz [2]. After then, as a result of some efforts for extending the frequency limit, a combination of antennas for the generation and the detection reached several THz [3, 4]. This technique has developed, so far, with taking a form of filling up the so-called THz gap . At the same time, a lot of researches have been trying to increase the output power as well [5-7]. In the 1990s, a big advantage in the frequency band was brought by non-linear optical methods [8-11]. The technique led to drastically expand the frequency region and recently to realize a measurement up to 41 THz [12]. On the other hand, some efforts have yielded new generation and detection methods from other approaches, a CW-THz as well as the pulse generation [13-19]. Especially, a THz luminescence and a laser, originated in a research on the Bloch oscillator, are recently generated from a quantum cascade structure, even at an only low temperature of 60 K [20-22]. This research attracts a lot of attention, because it would be a breakthrough for the THz technique to become widespread into industrial area as well as research, in a point of low costs and easier operations. It is naturally thought that a technology of short pulse lasers has helped the THz field to be developed. As a background of an appearance of a stable Ti:sapphire laser and a high power chirped pulse amplification (CPA) laser, instead of a dye laser, a lot of concentration on the techniques of a pulse compression and amplification have been done. [23] Viewed from an application side, the THz technique has come into the limelight as a promising measurement method. A discovery of absorption peaks of a protein and a DNA in the THz region is promoting to put the technique into practice in the field of medicine and pharmaceutical science from several years ago [24-27]. It is also known that some absorption of light polar-molecules exist in the region, therefore, some ideas of gas and water content monitoring in the chemical and the food industries are proposed [28-32]. Furthermore, a lot of reports, such as measurements of carrier distribution in semiconductors, refractive index of a thin film and an object shape as radar, indicate that this technique would have a wide range of application [33-37]. I believe that it is worth challenging to apply it into the steel-making industry, due to its unique advantages. The THz wavelength of 30-300 ¼m can cope with both independence of a surface roughness of steel products and a detection with a sub-millimeter precision, for a remote surface inspection. There is also a possibility that it can measure thickness or dielectric constants of relatively high conductive materials, because of a high permeability against non-polar dielectric materials, short pulse detection and with a high signal-to-noise ratio of 103-5. Furthermore, there is a possibility that it could be applicable to a measurement at high temperature, for less influence by a thermal radiation, compared with the visible and infrared light. These ideas have motivated me to start this THz work.
Das Ziel der Untersuchung von ultra-relativistischen Schwerionenkollisionen ist die Suche nach dem Quark Gluon Plasma (QGP), einem Zustand hochdichter stark wechselwirkender Materie in dem der Einschluss von Quarks und Gluonen in Hadronen aufgehoben ist. Die bisher gewonnenen experimentellen Hinweise deuten daraufhin,daß in Schwerionenkollisionen bei den derzeit höchsten zur Verfügung stehenden Energien von 158 GeV/Nukleon in Pb+Pb Reaktionen am CERN-SPS die Rahmenbedingungen für einen Phasenübergang von hadronischer Materie zu einer partonischen Phaseerfüllt sind. Die exakte Phasenstruktur stark wechselwirkender Materie hingegen ist derzeit noch nicht vollständig verstanden. Da inklusive hadronische Observablen und "penetrierende Proben" nicht direkt sensitiv auf die Existenz und Natur des Phasenübergangs sind, wurde die Analyse von Einzelereignis-"event-by-event"-Fluktuationenvorgeschlagen. Das Fluktuationsverhalten von Einzelereignis-Observablen sollte direkt sensitiv auf die Natur des zu beobachtenden Phasenübergangssein. In dieser Arbeit wurden Fluktuationen in der "chemischen" Zusammensetzung der Teilchenquelle untersucht und erste Ergebnisse werden präsentiert.
The mammalian retina contains around 30 morphological varieties of amacrine cell types. These interneurons receive excitatory glutamatergic input from bipolar cells and provide GABA- and glycinergic inhibition to other cells in the retina. Amacrine cells exhibit widely varying light evoked responses, in large part defined by their presynaptic partners. We wondered whether amacrine functional diversity is based on a differential expression of glutamate receptors among cell populations and types. In whole cell patch-clamp experiments on mouse retinal slices, we used selective agonists and antagonists to discriminate responses mediated by NMDA/ non-NMDA (NBQX) and AMPA/ KA receptors (cyclothiazide, GYKI 52466, GYKI 53655, SYM 2081). We sampled a large variety of individual cell types, which were classified by their dendritic field size into either narrow-field or wide-field cells after filling with Lucifer yellow or neurobiotin. In addition, we used transgenic GlyT2-EGFP mice, whose glycinergic neurons express EGFP. This allowed us to classify amacrines on basis of their neurotransmitter into either glycinergic or GABAergic cells. All cells (n = 300) had good responses to non-NMDA agonists. Specific AMPA receptor responses could be obtained from almost all cells recorded: 94% of the AII (n = 17), 87% of the narrow-field (n = 45), 81% of the wide-field (n = 21), 85% of the glycinergic (n = 20) and 78% of the GABAergic cells (n = 9). KA receptor selective drugs were also effective on the majority of the AII (79%, n = 14), narrow-field (93%, n = 43), wide-field (85%, n = 26), glycinergic (94%, n = 16) and GABAergic amacrine cells (100%, n = 6). Among the cells tested for the two receptors (n = 65), we encountered both exclusive expression of AMPA or KA receptors and co-expression of the two types. Most narrow-field (70%, n = 27), glycinergic (81%, n = 16) and GABAergic cells (67%, n = 6) were found to have both AMPA and KA receptors. In contrast, only less than half of the wide-field cells (43%, n = 14) were found to co-express AMPA and KA receptors, most of them expressing exclusively AMPA (36%) or KA receptors (21%). We could elicit small NMDA responses from most of the wide-field (75%, n = 13) and GABAergic cells (67%, n = 3), whereas only 47% of the narrow-field (n = 15), 14% of the AII (n = 22) and no glycinergic cell (n = 2) reacted to NMDA. Abstract 83 Our data suggest that AMPA, KA and NMDA receptors are differentially expressed among different types of amacrine cells rather than among populations with different neurotransmitters or different dendritic coverage of the retina. Selective expression of kinetically different glutamate receptors among amacrine types may be involved in generating transient and sustained inhibitory pathways in the retina. Since AMPA and KA receptors are not generally clustered at the same postsynaptic sites, a single amacrine cell expressing both AMPA and KA receptors may provide inhibition with different temporal characteristics to individual synaptic partners.
Life of Varroa destructor, Anderson and Trueman, an ectoparasitic mite of honeybees, is divided into a reproductive phase in the bee brood and a phoretic phase during which the mite is attached to the adult bee. Phoretic mites leave the colony with workers involved in foraging tasks. Little information is available on the mortality of mites outside the colony. Mites may or not return to the colony as a result of death of the infested foragers, host change by drifting of foragers, or removal of mites outside the colony. That mites do not return to the colony was indicated by substantially higher infestation of outflying workers compared to the infestation of returning workers (Kutschker, 1999). The main objective of the study was to provide information whether V. destructor influences flight behaviour of foragers and consequently returning frequency of foragers to the colony. I first repeated the experiment of Kutschker (1999) examining the infestation of outflying and returning workers. Further, I registered flight duration of foragers using a video method. In this experiment I compared also the infestation and flight duration of bees of different genetic origin, Carnica from Oberursel and bees from Primorsky region. I investigated returning time of workers, returning frequency until evening, drifting to other colonies and orientation toward the nest entrance in the experiments in which workers were released in close vicinity of the colony. At last, I measured the loss of foragers in relation to colony infestation using a Bee Scan. Results from this study, listed below, showed considerable influence of V. destructor on flight behavior of foragers translating into loss of mites. Loss of mites with foragers add substantial component to mite mortality and was underestimated in previous studies. Such loss might be viewed as a mechanism of resistance against V. destructor. a) The mean infestation of outflying workers (0.019±0.018) was twice as the mean infestation of returning workers (0.009±0.018). The difference in the infestation between outflying and returning workers was more marked in highly infested colonies. b) Investigation of individually tagged workers by use of a two camera video recording device showed significantly higher infestation of outflying workers compared to returning workers. Mites were lost by the non returning of infested foragers (22%) and by loss of mites from foragers that returned to the colony without the mite (20%). A small portion of mites (1.8%) was gained. Loss of mites significantly exceeded mite gain. c) The flight duration of infested workers determined by using the same two camera video system was significantly higher in infested compared to uninfested workers of the same age that flew closest at time. The median flight duration of infested workers was 1.7 higher (214s) than the median duration of unifested workers (128s). d) Infested workers took 2.3 times longer to return to the colony than uninfested workers of the same age when released from the same locations, closest at time. The returning time increased with the distance of release. In a group of bees released simultaneously the infestation was higher in bees returning later and in those that did not return in the observation period of 15 min. e) Released workers did not return to the colony 1.5 more frequently than uninfested workers in evening. The difference in returning was significant for locations of 20 and 50m from the colony. No difference in returning between infested and uninfested workers were observed for the most distant location of 400m. f) No significant difference was found in returning time and/or in the returning frequency until evening between workers artificially infested overnight and naturally infested workers. Artificially infested workers returned later and less frequently than a control group indicating rapid influence of V. destructor on flight behavior of foragers. g) The orientation ability of infested workers toward the nest entrance was impaired. Infested workers compared to uninfested workers twice as often approached a dummy entrance before finding the nest entrance. h) No significant differences were found in drifting between infested and uninfested workers. Drifting in the neighboring nucleus colony occurred in about 1% occasions after release of marked workers. Similarly, more infested, but not significantly more infested workers (2.6%) entered a different colored hive than the same colored hive (1.9%). However, the number of drifting bees were to low to make results conclusive. i) The comparison between Carnica and Primorsky workers revealed higher infestation in Carnica compared to Primorsky. Further, Primorsky workers lost more mites during foraging due to mite loss from foragers and non returning of infested workers. No significant differences in flight duration were observed between the two bee stocks. j) Loss of foragers, as determined by the Bee Scan counts of outflying and returning foragers, and the infestation of outflying bees increased significantly over a period of 70 days. A colony with 7.7. higher infestation of outflying foragers lost 2.2. time more bees per flight per day compared to a low infested colony. k) The estimates of mite loss with foragers from mite population per day up to 3.1% exceeds approximately mite mortality of 1% within the colony as represented by counting dead mites on bottom board inserts.
Cold target recoil ion momentum spectroscopy (COLTRIM) has been employed to image the momentum distributions of continuum electrons liberated in the impact of slow He2+ on He and H2. The distributions were measured for fully determined motion of the nuclei that is as a function of the impact parameter and in a well de ned scattering plane The single ionization (SI) of H2 leading to H2+ recoil ions in nondissociative states (He2+ + H+ -> He2+ + H+ + e-) and the transfer ionization (TI) of H2 leading to H2 dissociation into two free protons (He2+ H2 -> He+ + H+ + H+ + e-) were investigated. Similar measurements have been carried out for He target, the corresponding atomic two electron system, i.e. the single ionization (SI) (He2+ + He -> He+ + He2+ e- and the transfer ionization (TI) (He2+ + He -> He+ + He2+ + e-). These measurements have been exploited to understand the results obtained for H target. In comparing the continuum electron momentum distributions for H2 with that for He, a high degree of similarity is observed. In the case of transfer ionization of H2, the electron momentum distributions generated for parallel and perpendicular molecular orientations revealed no orientation dependence. The in scattering plane electron momentum distributions for the transfer ionization of H2 by He2+ and for the transfer ionization of He by He2e showed that the salient feature of these distributions for both collisions systems consists in the appearance of two groups of electrons with difeerent structures. In addition to the group of the saddle electrons forming two jets separated by a valley along the projectile axis we nd a new group of electrons moving with a velocity higher than the projectile velocity These new fast forward electrons result from a narrow range of impact parameters and appear as image saddle in the projectile frame. In contrast to the transfer ionization of He, the fast forward electrons group disappears in the in scattering plane electron momentum distribution generated for the single ionization of He. Instead of this group another new group of electrons appear These electrons exhibit an amount of backscattering These backward elec trons appear as image saddle in the target frame The structures that the saddle electrons show are owing to the quasi molecular nature of the collision process For the TI of H2, the TI of He and the SI of He, a pi-orbital shape of the electron momentum distribution is observed This indicates the importance of the rotational coupling 2-p-theta -> 2p-pi in the initial promotion of the ground state followed by further promotions to the continuum The backward electrons as well as the fast forward electrons are not discussed in the theoretical literature at all. However, a number of obvious indications of the existence of the backward and fast forward electrons could be seen in the experimental works of Abdallah et al. as well as in the theoretical calculations of Sidky et al One might speculate that electrons which are promoted on the saddle for some time during the collision could finally swing around the He+ ion in the way out of the collision, i.e. either around the projectile in the forward direction as in the TI case forming the fast forward electrons or around the recoil ion in the backward direction as in the SI case forming the backward electrons. This might be a result of the strong gradient, and hence the large acceleration of the screened He+ potential.
Alzheimer’s disease (AD) is the most common neurodegenerative disorder world wide, causing presenile dementia and death of millions of people. During AD damage and massive loss of brain cells occur. Alzheimer’s disease is genetically heterogeneous and may therefore represent a common phenotype that results from various genetic and environmental influences and risk factors. In approximately 10% of patients, changes of the genetic information were detected (gene mutations). In these cases, Alzheimer’s disease is inherited as an autosomal dominant trait (familial Alzheimer’s disease, FAD). In rare cases of familial Alzheimer’s disease (about 1-3%), mutations have been detected in genes on chromosomes 14 and 1 (encoding for Presenilin 1 and 2, respectively), and on chromosome 21 encoding for the amyloid precursor protein (APP), which is responsible for the release of the cell-damaging protein amyloid-beta (ß-amyloid, Aß). Familial forms of early-onset Alzheimer’s disease are rare; however, their importance extends far beyond their frequency, because they allow to identify some of the critical pathogenetic pathways of the disease. All familial Alzheimer mutations share a common feature: they lead to an enhanced production of the Aß, which is the major constituent of senile plaques in brains of AD patients. New data indicates that Aß promotes neuronal degeneration. Therefore, one aim of these thesis was to elucidate the neurotoxic biochemical pathways induced by Aß, investigating the effect of the FAD Swedish APP double mutation (APPsw) on oxidative stress-induced cell death mechanisms. This mutation results in a three- to sixfold increased Aß production compared to wild-type APP (APPwt). As cell models, the neuronal PC12 (rat pheochromocytoma) and the HEK (human embryonic kidney 293) cell lines were used, which have been transfected with human wiltyp APP or human APP containing the Swedish double mutation. The used cell models offer two important advantages. First, compared to experiments using high concentrations of Aß at micromolar levels applied extracellularly to cells, PC12 APPsw cells secret low Aß levels similar to the situation in FAD brains. Thus, this cell model represents a very suitable approach to elucidate the AD-specific cell death pathways mimicking physiological conditions. Second, these two cell lines (PC12 and HEK APPwt and APPsw) with different production levels of Aß may additionally allow to study dose-dependent effects of Aß. The here obtained results provide evidence for the enhanced cell vulnerability caused by the Swedish APP mutation and elucidate the cell death mechanism probably initiated by intracellulary produced Aß. Here it seems likely that increased production of Aß at physiological levels primes APPsw PC12 cells to undergo cell death only after additional stress, while chronic high levels in HEK cells already lead to enhanced basal apoptotic levels. Crucial effects of the Swedish APP mutation include the impairments of cellular energy metabolism affecting mitochondrial membrane potential and ATP levels as well as the additional activation of caspase 2, caspase 8 and JNK in response to oxidative stress. Thereby ,the following model can be proposed: PC12 cells harboring the Swedish APP mutation have a reduced energy metabolism compared to APPwt or control cells. However, this effect does not leads to enhanced basal apoptotic levels of cultured cells. An exposure of PC12 cells to oxidative stress leads to mitochondrial dysfunction, e.g., decrease in mitochondrial membrane potential and depletion in ATP. The consequence is the activation of the intrinsic apoptotic pathway releasing cytochrome c and Smac resulting in the activation of caspase 9. This effect is amplified by the overexpression of APP, since both APPsw and APPwt PC12 cells show enhanced cytochrome c and Smac release as well as enhanced caspase 9 activity as vector transfected control. In APPsw PC12 cells a parallel pathway is additionally emphased. Due to reduced ATP levels or enhanced Aß production JNK is activated. Furthermore, the extrinsic apoptotic pathway is enhanced, since caspase 8 and caspase 2 activation was clearly enhanced by the Swedish APP mutation. Both pathways may then converge by activating the effector enzyme, caspase 3, and the execution of cell death. In addition, caspase independent effects also needs to be considered. One possibility could be the implication of AIF since AIF expression was found to be induced by the Swedish APP mutation. In APPsw HEK cells high chronic Aß levels leads to enhanced apoptotic levels, reduce mitochondrial membrane potential and ATP levels even under basal conditions. Summarizing, a hypothetical sequence of events is proposed linking FAD, Aß production, JNK-activation, mitochondrial dysfunction with caspase pathway and neuronal loss for our cell model. The brain has a high metabolic rate and is exposured to gradually rising levels of oxidative stress during life. In Swedish FAD patients the levels of oxidative stress are increased in the temporal inferior cortex. This study using a cell model mimicking the in vivo situation in AD brains indicates that probably both, increased Aß production and the gradual rise of oxidative stress throughout life converge at a final common pathway of an increased vulnerability of neurons to apoptotic cell death from FAD patients. Presenilin (PS) 1 is an aspartyl protease, involved in the gamma-secretase mediated proteolysis of Amyloid-ß-protein (Aß), the major constituent of senile plaques in brains of Alzheimer’s disease (AD) patients. Recent studies have suggested an additional role for presenilin proteins in apoptotic cell death observed in AD. Since PS 1 is proteolytic cleaved by caspase 3, it has been prosposed that the resulting C-terminal fragment of PS1 (PSCas) could play a role in signal transduction during apoptosis. Moreover, it was shown that mutant presenilins causing early-onset of familial Alzheimer's disease (FAD) may render cells vulnerable to apoptosis. The mechanism by which PS1 regulates apoptotic cell death is yet not understood. Therefore one aim of our present study was to clarify the involvement of PS1 in the proteolytic cascade of apoptosis and if the cleavage of PS1 by caspase 3 has an regulatory function. Here it is demonstrated that both, PS1 and PS1Cas lead to a reduced vulnerability of PC12 and Jurkat cells to different apoptotic stimuli. However a mutation at the caspase 3 recognition site (D345A/ PSmut), which inhibits cleavage of PS1 by caspase 3, show no differences in the effect of PS1 or PSCas towards apoptotic stimuli. This suggest that proteolysis of PS1 by caspase 3 is not a determinant, but only a secondary effect during apoptosis. Since several FAD mutation distributed through the whole PS1 gene lead to enhanced apoptosis, an abolishment of the antiapoptotic effect of PS1 might contribute to the massive neurodegeneration in early age of FAD patients. Here, the regulate properties of PS1 in apoptosis may not be through an caspase 3 dependent cleavage and generation of PSCas, but rather through interaction of PS1 with other proteins involved in apoptosis.
In contrast to the class A heat stress transcription factors (Hsfs) of plants, a considerable number of Hsfs assigned to classes B and C have no evident function as transcription activators on their own. In the course of my PhD work I showed that tomato HsfB1, a heat stress induced member of class B Hsf family, is a novel type of transcriptional coactivator in plants. Together with class A Hsfs, e.g. tomato HsfA1, it plays an important role in efficient transcrition initiation during heat stress by forming a type of enhanceosome on fragments of Hsp promoter. Characterization of promoter architecture of hsp promoters led to the identification of novel, complex heat stress element (HSE) clusters, which are required for optimal synergistic interactions of HsfA1 and HsfB1. In addition, HsfB1 showed synergistic activation of the expression of a subset of viral and house keeping promoters. CaMV35S promoter, the most widely expressed constitutive promoter turned out to be the the most interesting candidate to study this effect in detail. Because, for most house-keeping promoters tested during this study, the activators responsible for constitutive expression are not known, but in case of CaMV35S promoter they are quite well known (the bZip proteins, TGA1/2). These proteins belong to the acidic activators, similar to class A Hsfs. Actually, on heat stress inducible promoters HsfA1 or other class A Hsfs are the synergistic partners of HsfB1, whereas on house-keeping or viral promoters, HsfB1 shows synergistic transcriptional activation in cooperation with the promoter specific acidic activators, e.g. with TGA proteins on 35S promoter. In agreement with this the binding sites for HsfB1 were identified in both house-keeping and 35S promoter. It has been suggested during this study that HsfB1 acts in the maintenance of transcription of a sub-set of house-keeping and viral genes during heat stress. The coactivator function of HsfB1 depends on a single lysine residue in the GRGK motif in its CTD. Since, this motif is highly conserved among histones as the acetylation motif, especially in histones H2A and H4,. It was suggested that the GRGK motif acts as a recruitment motif, and together with the other acidic activator is responsible for corecruitment of a histone acetyl transferase (HAT). So, the effect of mammalian CBP (a well known HAT) and its plant orthologs (HAC1) was tested on the stimulation of synergistic reporter gene activation obtained with HsfA1 and HsfB1. Both in plant and mammalian cells, CBP/HAC1 further stimulated the HsfA1/B1 synergistic effect. Corecruitment of HAC1 was proven by in vitro pull down assays, where the NTD of HAC1 interacted specifically both with HsfA1 and HsfB1. Formation of a ternary complex between HsfA1, HsfB1 and CBP/HAC1 was shown via coimmunoprecipitation and electrophoretic mobility shift assays (EMSA). In conclusion, the work presented in my thesis presents a new model for transcriptional regulation during an ongoing heat stress.
In an attempt to search for potential candidate molecules involved in the pathogenesis of endometriosis, a novel 2910 bp cDNA encoding a putative 411 amino acid protein, shrew-1 was discovered. By computational analysis it was predicted to be an integral membrane protein with an outside-in transmembrane domain but no homology with any known protein or domain could be identified. Antibodies raised against the putative open-reading frame peptide of shrew-1 labelled a protein of ca. 48 kDa in extracts of shrew-1 mRNA positive tissues and also detected ectopically expressed shrew-1. In the course of my PhD work, I confirmed the prediction that shrew-1 is indeed a transmembrane protein, by expressing epitope-tagged shrew-1 in epithelial cells and analysing the transfected cells by surface biotinylation and immunoblots. Additionally, I could show that shrew-1 is able to target to E-cadherin-mediated adherens junctions and interacts with the E-cadherin-catenin complex in polarised MCF7 and MDCK cells, but not with the N-cadherin-catenin complex in non-polarised epithelial cells. A direct interaction of shrew-1 with beta-catenin could be shown in an in vitro pull-down assay. From this data, it could be assumed that shrew-1 might play a role in the function and/or regulation of the dynamics of E-cadherin-mediated junctional complexes. In the next part of my thesis, I showed that stable overexpression of shrew-1 in normal MDCK cells. causes changes in morphology of the cells and turns them invasive. Furthermore, transcription by ²-catenin was activated in these MDCK cells stably overexpressing shrew-1. It was probably the imbalance of shrew-1 protein at the adherens junctions that led to the misregulation of adherens junctions associated proteins, i.e. E-cadherin and beta-catenin. Caveolin-1 is another integral membrane protein that forms complexes with Ecadherin- beta-catenin complexes and also plays a role in the endocytosis of E-cadherin during junctional disruption. By immunofluorescence and biochemical studies, caveolin-1 was identified as another interacting partner of shrew-1. However, the functional relevance of this interaction is still not clear. In conclusion, it can be said that shrew-1 interacts with the key players of invasion and metastasis, E-cadherin and caveolin-1, suggesting its possible role in these processes and making it an interesting candidate to unravel other unknown mechanisms involved in the complex process of invasion.
In dieser Arbeit werden Untersuchungen über die Anwendbarkeit von vier Methoden zur selektiven Einführung von Radikalen in DNA vorgestellt. Hierzu wurde die EPR-Spektroskopie (Elektronen-paramagnetische Resonanz) benutzt. Die selektive Einführung und Erzeugung von Radikalen in DNA ist nötig, um J-Kopplungen in DNA zu untersuchen. Vor dem Fernziel der Bestimmung der Austauschkopplungskonstanten J in biradikalischer DNA und deren Korrelation mit der charge-transfer-Geschwindigkeitskonstanten kCT stellen diese Untersuchungen einen wichtigen Ausgangspunkt dar. Stabile aromatische Nitroxide. Simulationen von Raumtemperatur-CW-X-Band-EPRSpektren fünf verschiedener aromatischer Nitroxide, welche potentielle DNA-Interkalatoren sind, wurden durchgeführt. Die aromatischen Nitroxide zeigen aufgelöste Hyperfeinkopplungen, welche zu dem Schluss führen, dass die Spindichte in hohem Maße delokalisiert ist, was die Verwendung dieser Verbindungen zur Messung von J-Kopplungen in biradikalischer DNA erlaubt. Transiente Guanin-Radikale. Transiente Guanin-Radikale werden in DNA selektiv durch die Flash-Quench-Technik erzeugt, bei der optisch anregbare Ruthenium-Interkalatoren verwendet werden. Transiente Thymyl-Radikale aus UV-bestrahltem 4'-Pivaloyl-Thymidin. Es werden photoinduzierte Prozesse untersucht, welche durch Bestrahlung von Thymin-Nukleosiden, die an der 4’-Position die optisch spaltbare Pivaloyl-Gruppe tragen, erzeugt werden. Dieses Nukleosid wurde speziell dafür entworfen, um Elektronenlöcher in DNA zu injizieren. In dieser Arbeit wird gezeigt, dass diese Verbindung benutzt werden kann, um selektiv eine Thymin-Base zu reduzieren. Transiente Thymyl-Radikale erzeugt durch ein neuartig modifiziertes Thymin nach UV-Bestrahlung. Photoinduzierte Prozesse, welche durch Bestrahlung eines ähnlichen Thymidin-Nukleosids erzeugt wurden, werden hier untersucht. Dieses Thymidin- Nukleosid wurde modifiziert, indem die optisch spaltbare Pivaloyl-Gruppe an eine Seitenkette angehängt wurde, welche an der C6-Position der Thymin-Base sitzt. Die Thymin-Base wurde speziell dafür entworfen, um Elektronen in DNA zu injizieren. In dieser Arbeit wurde bestätigt, dass ein Überschuss-Elektron selektiv auf eine Thymin-Base transferiert werden kann.
Die in Englisch verfasste Dissertation, die unter der Betreuung von Herrn Prof. Dr. H. F. de Groote, Fachbereich Mathematik, entstand, ist der Mathematischen Physik zuzuordnen. Sie behandelt Stonesche Spektren von Neumannscher Algebren, observable Funktionen sowie einige Anwendungen in der Physik. Das abschließende Kapitel liefert eine Verallgemeinerung des Kochen-Specker-Theorems. Stonesche Spektren und observable Funktionen wurden von de Groote eingeführt. Das Stonesche Spektrum einer von Neumann-Algebra ist eine Verallgemeinerung des Gelfand-Spektrums, die observablen Funktionen verallgemeinern die Gelfand-Transformierten. Da de Grootes Ergebnisse zum großen Teil unveröffentlicht sind, folgt nach dem Einleitungskapitel im zweiten Kapitel eine Übersichtsdarstellung dieser Ergebnisse. Das dritte Kapitel behandelt die Stoneschen Spektren endlicher von Neumann-Algebren. Für Algebren vom Typ In wird eine vollständige Charakterisierung des Stoneschen Spektrums entwickelt. Zu Typ-II1-Algebren werden einige Resultate vorgestellt. Das vierte Kapitel liefert. einige einfache Anwendungen des Formalismus auf die Physik. Das fünfte Kapitel gibt erstmals einen funktionalanalytischen Beweis des Kochen-Specker-Theorems und liefert die Verallgemeinerung dieses Satzes, wobei die Situation für alle von Neumann-Algebren geklärt wird.
Die Ermittlung von Proteinstukturen mittels NMR-Spektroskopie ist ein komplexer Prozess, wobei die Resonanzfrequenzen und die Signalintensitäten den Atomen des Proteins zugeordnet werden. Zur Bestimmung der räumlichen Proteinstruktur sind folgende Schritte erforderlich: die Präparation der Probe und 15N/13C Isotopenanreicherung, Durchführung der NMR Experimente, Prozessierung der Spektren, Bestimmung der Signalresonanzen ('Peak-picking'), Zuordnung der chemischen Verschiebungen, Zuordnung der NOESY-Spektren und das Sammeln von konformationellen Strukturparametern, Strukturrechnung und Strukturverfeinerung. Aktuelle Methoden zur automatischen Strukturrechnung nutzen eine Reihe von Computeralgorithmen, welche Zuordnungen der NOESY-Spektren und die Strukturrechnung durch einen iterativen Prozess verbinden. Obwohl neue Arten von Strukturparametern wie dipolare Kopplungen, Orientierungsinformationen aus kreuzkorrelierten Relaxationsraten oder Strukturinformationen, die sich in Gegenwart paramagnetischer Zentren in Proteinen ergeben, wichtige Neuerungen für die Proteinstrukturrechnung darstellen, sind die Abstandsinformationen aus NOESY-Spektren weiterhin die wichtigste Basis für die NMR-Strukturbestimmung. Der hohe zeitliche Aufwand des 'peak-picking' in NOESY-Spektren ist hauptsächlich bedingt durch spektrale Überlagerung, Rauschsignale und Artefakte in NOESY-Spektren. Daher werden für das effizientere automatische 'Peak-picking' zuverlässige Filter benötigt, um die relevanten Signale auszuwählen. In der vorliegenden Arbeit wird ein neuer Algorithmus für die automatische Proteinstrukturrechnung beschrieben, der automatisches 'Peak-picking' von NOESY-Spektren beinhaltet, die mit Hilfe von Wavelets entrauscht wurden. Der kritische Punkt dieses Algorithmus ist die Erzeugung inkrementeller Peaklisten aus NOESY-Spektren, die mit verschiedenen auf Wavelets basierenden Entrauschungsprozeduren prozessiert wurden. Mit Hilfe entrauschter NOESY-Spektren erhält man Signallisten mit verschiedenen Konfidenzbereichen, die in unterschiedlichen Schritten der kombinierten NOE-Zuordnung/Strukturrechnung eingesetzt werden. Das erste Strukturmodell beruht auf stark entrauschten Spektren, die die konservativste Signalliste mit als weitgehend sicher anzunehmenden Signalen ergeben. In späteren Stadien werden Signallisten aus weniger stark entrauschten Spektren mit einer größeren Anzahl von Signalen verwendet. Die Auswirkung der verschiedenen Entrauschungsprozeduren auf Vollständigkeit und Richtigkeit der NOESY Peaklisten wurde im Detail untersucht. Durch die Kombination von Wavelet-Entrauschung mit einem neuen Algorithmus zur Integration der Signale in Verbindung mit zusätzlichen Filtern, die die Konsistenz der Peakliste prüfen ('Network-anchoring' der Spinsysteme und Symmetrisierung der Peakliste), wird eine schnelle Konvergenz der automatischen Strukturrechnung erreicht. Der neue Algorithmus wurde in ARIA integriert, einem weit verbreiteten Computerprogramm für die automatische NOE-Zuordnung und Strukturrechnung. Der Algorithmus wurde an der Monomereinheit der Polysulfid-Schwefel-Transferase (Sud) aus Wolinella succinogenes verifiziert, deren hochaufgelöste Lösungsstruktur vorher auf konventionelle Weise bestimmt wurde. Neben der Möglichkeit zur Bestimmung von Proteinlösungsstrukturen bietet sich die NMR-Spektroskopie auch als wirkungsvolles Werkzeug zur Untersuchung von Protein-Ligand- und Protein-Protein-Wechselwirkungen an. Sowohl NMR Spektren von isotopenmarkierten Proteinen, als auch die Spektren von Liganden können für das 'Screening' nach Inhibitoren benutzt werden. Im ersten Fall wird die Sensitivität der 1H- und 15N-chemischen Verschiebungen des Proteinrückgrats auf kleine geometrische oder elektrostatische Veränderungen bei der Ligandbindung als Indikator benutzt. Als 'Screening'-Verfahren, bei denen Ligandensignale beobachtet werden, stehen verschiedene Methoden zur Verfügung: Transfer-NOEs, Sättigungstransferdifferenzexperimente (STD, 'saturation transfer difference'), ePHOGSY, diffusionseditierte und NOE-basierende Methoden. Die meisten dieser Techniken können zum rationalen Design von inhibitorischen Verbindungen verwendet werden. Für die Evaluierung von Untersuchungen mit einer großen Anzahl von Inhibitoren werden effiziente Verfahren zur Mustererkennung wie etwa die PCA ('Principal Component Analysis') verwendet. Sie eignet sich zur Visualisierung von Ähnlichkeiten bzw. Unterschieden von Spektren, die mit verschiedenen Inhibitoren aufgenommen wurden. Die experimentellen Daten werden zuvor mit einer Serie von Filtern bearbeitet, die u.a. Artefakte reduzieren, die auf nur kleinen Änderungen der chemischen Verschiebungen beruhen. Der am weitesten verbreitete Filter ist das sogenannte 'bucketing', bei welchem benachbarte Punkte zu einen 'bucket' aufsummiert werden. Um typische Nachteile der 'bucketing'-Prozedur zu vermeiden, wurde in der vorliegenden Arbeit der Effekt der Wavelet-Entrauschung zur Vorbereitung der NMR-Daten für PCA am Beispiel vorhandener Serien von HSQC-Spektren von Proteinen mit verschiedenen Liganden untersucht. Die Kombination von Wavelet-Entrauschung und PCA ist am effizientesten, wenn PCA direkt auf die Wavelet-Koeffizienten angewandt wird. Durch die Abgrenzung ('thresholding') der Wavelet-Koeffizienten in einer Multiskalenanalyse wird eine komprimierte Darstellung der Daten erreicht, welche Rauschartefakte minimiert. Die Kompression ist anders als beim 'bucketing' keine 'blinde' Kompression, sondern an die Eigenschaften der Daten angepasst. Der neue Algorithmus kombiniert die Vorteile einer Datenrepresentation im Wavelet-Raum mit einer Datenvisualisierung durch PCA. In der vorliegenden Arbeit wird gezeigt, dass PCA im Wavelet- Raum ein optimiertes 'clustering' erlaubt und dabei typische Artefakte eliminiert werden. Darüberhinaus beschreibt die vorliegende Arbeit eine de novo Strukturbestimmung der periplasmatischen Polysulfid-Schwefel-Transferase (Sud) aus dem anaeroben gram-negativen Bakterium Wolinella succinogenes. Das Sud-Protein ist ein polysulfidbindendes und transferierendes Enzym, das bei niedriger Polysulfidkonzentration eine schnelle Polysulfid-Schwefel-Reduktion katalysiert. Sud ist ein 30 kDa schweres Homodimer, welches keine prosthetischen Gruppen oder schwere Metallionen enthält. Jedes Monomer enhält ein Cystein, welches kovalent bis zu zehn Polysulfid-Schwefel (Sn 2-) Ionen bindet. Es wird vermutet, dass Sud die Polysulfidkette auf ein katalytischen Molybdän-Ion transferiert, welches sich im aktiven Zentrum des membranständigen Enzyms Polysulfid-Reduktase (Psr) auf dessen dem Periplasma zugewandten Seite befindet. Dabei wird eine reduktive Spaltung der Kette katalysiert. Die Lösungsstruktur des Homodimeres Sud wurde mit Hilfe heteronuklearer, mehrdimensionaler NMR-Techniken bestimmt. Die Struktur beruht auf von NOESY-Spektren abgeleiteten Distanzbeschränkungen, Rückgratwasserstoffbindungen und Torsionswinkeln, sowie auf residuellen dipolaren Kopplungen, die für die Verfeinerung der Struktur und für die relative Orientierung der Monomereinheiten wichtig waren. In den NMR Spektren der Homodimere haben alle symmetrieverwandte Kerne äquivalente magnetische Umgebungen, weshalb ihre chemischen Verschiebungen entartet sind. Die symmetrische Entartung vereinfacht das Problem der Resonanzzuordnung, da nur die Hälfte der Kerne zugeordnet werden müssen. Die NOESY-Zuordnung und die Strukturrechnung werden dadurch erschwert, dass es nicht möglich ist, zwischen den Intra-Monomer-, Inter-Monomer- und Co-Monomer- (gemischten) NOESY-Signalen zu unterscheiden. Um das Problem der Symmetrie-Entartung der NOESY-Daten zu lösen, stehen zwei Möglichkeiten zur Verfügung: (I) asymmetrische Markierungs-Experimente, um die intra- von den intermolekularen NOESY-Signalen zu unterscheiden, (II) spezielle Methoden der Strukturrechnung, die mit mehrdeutigen Distanzbeschränkungen arbeiten können. Die in dieser Arbeit vorgestellte Struktur wurde mit Hilfe der Symmetrie-ADR- ('Ambigous Distance Restraints') Methode in Kombination mit Daten von asymetrisch isotopenmarkierten Dimeren berechnet. Die Koordinaten des Sud-Dimers zusammen mit den NMR-basierten Strukturdaten wur- den in der RCSB-Proteindatenbank unter der PDB-Nummer 1QXN abgelegt. Das Sud-Protein zeigt nur wenig Homologie zur Primärsequenz anderer Proteine mit ähnlicher Funktion und bekannter dreidimensionaler Struktur. Bekannte Proteine sind die Schwefeltransferase oder das Rhodanese-Enzym, welche beide den Transfer von einem Schwefelatom eines passenden Donors auf den nukleophilen Akzeptor (z.B von Thiosulfat auf Cyanid) katalysieren. Die dreidimensionalen Strukturen dieser Proteine zeigen eine typische a=b Topologie und haben eine ähnliche Umgebung im aktiven Zentrum bezüglich der Konformation des Proteinrückgrades. Die Schleife im aktiven Zentrum umgibt das katalytische Cystein, welches in allen Rhodanese-Enzymen vorhanden ist, und scheint im Sud-Protein flexibel zu sein (fehlende Resonanzzuordnung der Aminosäuren 89-94). Das Polysulfidende ragt aus einer positiv geladenen Bindungstasche heraus (Reste: R46, R67, K90, R94), wo Sud wahrscheinlich in Kontakt mit der Polysulfidreduktase tritt. Das strukturelle Ergebnis wurde durch Mutageneseexperimente bestätigt. In diesen Experimenten konnte gezeigt werden, dass alle Aminosäurereste im aktiven Zentrum essentiell für die Schwefeltransferase-Aktivität des Sud-Proteins sind. Die Substratbindung wurde früher durch den Vergleich von [15N,1H]-TROSY-HSQC-Spektren des Sud-Proteins in An- und Abwesenheit des Polysulfidliganden untersucht. Bei der Substratbindung scheint sich die lokale Geometrie der Polysulfidbindungsstelle und der Dimerschnittstelle zu verändern. Die konformationellen Änderungen und die langsame Dynamik, hervorgerufen durch die Ligandbindung können die weitere Polysulfid-Schwefel-Aktivität auslösen. Ein zweites Polysulfid-Schwefeltransferaseprotein (Str, 40 kDa) mit einer fünffach höheren nativen Konzentration im Vergleich zu Sud wurde im Bakterienperiplasma von Wolinella succinogenes entdeckt. Es wird angenommen, dass beide Protein einen Polysulfid-Schwefel-Komplex bilden, wobei Str wässriges Polysulfid sammelt und an Sud abgibt, welches den Schwefeltransfer zum katalytischen Molybdän-Ion auf das aktive Zentrum der dem Periplasma zugewandten Seite der Polysulfidreduktase durchführt. Änderungen chemischer Verschiebungen in [15N,1H]-TROSY-HSQC-Spektren zeigen, dass ein Polysulfid-Schwefeltransfer zwischen Str und Sud stattfindet. Eine mögliche Protein-Protein-Wechselwirkungsfläche konnte bestimmt werden. In der Abwesenheit des Polysulfidsubstrates wurden keine Wechselwirkungen zwischen Sud und Str beobachtet, was die Vermutung bestätigt, dass beide Proteine nur dann miteinander wechselwirken und den Polysulfid-Schwefeltransfer ermöglichen, wenn als treibende Kraft Polysulfid präsent ist.
Im Rahmen dieser Dissertation wurde die Photophysik und die elektronische Struktur einer Klasse neuartiger Donator-Akzeptor-Ladungstransfer-Komplexe untersucht. Im Wesentlichen bestehen diese Verbindungen aus einem Ferrocen-Donator (Fc) und organischen Akzeptoren, die über B-N-Bindungen verbrückt sind, welche sich bei dieser Art von makromolekularen Systemen spontan bilden. Zentraler Gegenstand dieser Arbeit war die spektroskopische Untersuchung des Metall-zu-Ligand-Ladungstransfers (engl. Abkürzung: MLCT) im elektronischen Anregungszustand dieser kationischen Komplexverbindungen, die im Weiteren als „Fc-B-bpy“-Verbindungen bezeichnet werden. Die vorliegende Arbeit analysiert eine Vielzahl miteinander verwandter Fc-B-bpy-Derivate. Die Arbeit ist gegliedert in 1.) die Analyse der Absorptionsspektren vom UV- bis zum nahen Infrarot-Spektralbereich (250-1000 nm) von Lösungen, dotierten Polymer-Dünnfilmen und Einkristallen, 2.) die zeitaufgelöste optische Spektroskopie des angeregten Zustands auf der Pikosekunden-Zeitskala, 3.) die Analyse elektrochemischer Messungen an Lösungen, und 4.) die Auswertung quantenchemischer Berechnungen. Für die zeitaufgelösten Messungen wurde ein komplexes optisches Spektroskopie-System mit breitbandigen Femtosekunden-Pulsen sowie den entsprechenden zeitaufgelösten Detektionsmethoden (spektral gefilterte Weißlicht-Detektion) aufgebaut. Die Ergebnisse dieser Arbeit beweisen die Existenz eines MLCT-Übergangs mit fast vollständigem Übergang eines Fc-Donator-Elektrons zum B-bpy-Akzeptor bei optischer Anregung. Die vergleichenden Untersuchungen der spektroskopischen Eigenschaften verschiedener Derivate liefern wichtige Information für die Entwicklung neuartiger Derivate, einschließlich verwandter Polymere, mit verbesserten spektroskopischen Eigenschaften. Es wurden transiente Absorptionsmessungen bestimmter Fc-B-bpy-Derivate in Lösung nach gepulster Anregung der MLCT-Bande (bei 500 nm) über einen Zeitbereich von 0,1-1000 ps und einen Wellenlängenbereich von 460-760 nm vorgenommen. Aus den Messergebnissen geht hervor, dass die Relaxation aus dem angeregten MLCT-Zustand in den Grundzustand auf verschiedenen Zeitskalen geschehen kann, welche im Bereich zwischen ~18 und 900 ps liegen. Ein Vergleich verschiedener Derivate mit unterschiedlicher Flexibilität in der Konformation zeigt, dass die Starrheit der Bindungen zwischen Donatoren und Akzeptoren ein wesentlicher Faktor für die Lebensdauer des angeregten Zustands ist. Wenn die Akzeptorgruppen relativ frei rotieren können, ist es der Verbindung möglich, eine Geometrie einzunehmen, von der aus ein effizienter, strahlungsfreier Übergang in den Grundzustand erfolgen kann. Dieser Befund zeigt einen Weg auf, wie neuartige, verwandte Verbindungen mit größerer Lebensdauer das angeregten Zustands synthetisiert werden können, indem darauf geachtet wird, daß eine starre molekulare Architektur zwischen Donator und Akzeptor verwirklicht wird.
The hypothesis that oxidative stress plays a role in the pathogenesis of Alzheimer’s disease (AD) was tested by studying oxidative damage, acitvities of antioxidant enzymes and levels of reactive oxygen species (ROS) in several models. To this end, mouse models transgenic for mutant presenilin (PS1M146L) as well as mutant amyloid precursor protein (APP) and human post mortem brain tissue from sporadic AD patients and age-matched controls were studied. Aging leads to an upregulation of antioxidant enzyme activities of Cu/Zn-superoxide dismutase (Cu/Zn-SOD), glutathione peroxidase (GPx) and glutathione reductase (GR) in brains from C57BL/6J mice. Simultaneously, levels of lipid peroxidation products malondialdehyde MDA and 4-hydroxynonenal HNE were reduced. Additionally, pronounced gender effects were observed, as female mice display better protection against oxidative damage due to higher activity of GPx. Hence, antioxidant enzymes provide an important contribution to the protection against oxidative damage. In PS1M146L transgenic mice oxidative damage was only detectable in 19-22 months old mice, arguing for an additive effect of aging and the PS1 mutation. Both HNE levels in brain tissue as well as mitochondrial and cytosolic levels of ROS in splenic lymphocytes were increased in PS1M146L mice. Antioxidant defences were unaltered. In PDGF-APP and PDGF-APP/PS1 trangenic mice no changes in any of the parameters studied were observed in any age group. In contrast, Thy1-APP transgenic mice display oxidative damage as assessed by increased HNE levels. Reduced activity of Cu/Zn-SOD may explain this observation. Additionally, gender modified this effect, as female APP transgenic mice display higher b-secretase cleavage of APP and simultaneously increased HNE levels and reduced Cu/Zn-SOD activity earlier than male mice, i.e. from an age of 3 months and before the formation of Ab plaques. Reduced Cu/Zn-SOD activity was also found in another APP transgenic mouse model, in APP23 mice. In post mortem brain tissue from sporadic AD patients activities of Cu/Zn-SOD and GPx were however increased, and changes were most pronounced in temporal cortex. Simultaneously, levels of HNE but not MDA were elevated. Additionally, in vitro stimulation of lipid peroxidation led to increased MDA formation in samples from AD patients, indicating that increased activity of Cu/Zn-SOD and GPx are insufficient to protect against oxidative damage. Furthermore, the observed changes were subject to a gender effect, as samples from female AD patients showed increased activities of Cu/Zn-SOD and GPx as well as increased HNE levels, indicating that brain tissue from females is more sensitive towards oxidative damage. Levels of soluble Ab1-40 were positively correlated with with MDA levels and activities of Cu/Zn-SOD and GPx. Additionally, levels of lipid peroxidation products MDA and HNE are gene-dose-dependently modulated by the Apolipoprotein E4 allele, the most important genetic risk factor for AD known so far. While MDA levels were negatively correlated with MMSE scores, a measure for cognitive function, HNE levels were highest in AD patients with moderate cognitive impairment. Hence, increased HNE levels may play an important role in neurodegenerative events at an early disease stage. In summary, oxidative damage, as assessed by increased HNE levels, could be detected in sporadic AD patients and in different transgenic mouse models. The results of this thesis therefore support the further research of pharmacological targets aiming at augmentation of antioxidant defences for therapy or prophylaxis of Alzheimer’s disease.
The cytochrome bc1 complex is a cornerstone in bioenergetic electron transfer chains, where it carries out tasks as diverse as respiration, photosynthesis, and nitrogen fixation. This homodimeric multisubunit membrane protein has been studied extensively for several decades and the enzyme mechanism is described with the modified protonmotive Q cycle. Still, the molecular and kinetic description of the catalytic cycle is not complete and questions remain regarding the bifurcation of electron transfer at the quinol oxidation (Qo) site, substrate occupancy, pathways of proton conduction, and the nature of the Rieske protein domain movement. We used competitive inhibitors to study the molecular architecture at the Qo site with X-ray crystallography. The structure of the enzyme with the substrate analog 5-n-heptyl-6-hydroxy-4,7-dioxobenzothiazole (HHDBT) bound at the Qo site was determined at 2.5 Å resolution. Spectroscopic studies showed that HHDBT is negatively charged when bound at the active site. Mechanistic interpretations from inhibitor binding are in line with single occupancy model for quinol oxidation and structural analysis supports the proposed proton transfer pathway. For functional insight into the enzyme mechanism, redox-sensitive protonation changes were studied by Fourier transform infrared spectroscopy. The protein purification procedure was optimized for less delipidation and the isolated enzyme was more active. Furthermore, two new phospholipids were identified in the X-ray structures, including a cardiolipin. Strikingly, conserved lipid binding cavities were observed in structural comparison with homologous enzymes. The functional role of tightly bound phospholipids will be discussed. Finally, the Qo site is a target for various compounds of agricultural and pharmaceutical importance. Importantly, the X-ray structures permit detailed analysis of the molecular reasons for acquired resistance to and treatment failure of Qo site inhibitors, such as atovaquone, that is used to treat malaria and pneumonia, as discussed herein.
The cytochrome bc1 complex or ubiquinol:cytochrome c oxidoreductase (QCR) catalyses electron transfer from ubiquinol to cytochrome c in respiration and photosynthesis coupled to a vectorial proton transport across the membrane, in which the enzyme resides. In both bacteria and eukaryotic organisms, QCR participates in supramolecular assembly of membrane proteins that comprise the respiratory or photosynthetic chain. In the present work, proton transfer pathways, substrate binding and the supramolecular assembly of the respiratory chain in yeast were probed by structure-based site-directed mutagenesis and characterization of the variants. Both active sites centre P, the place of quinol oxidation, and centre N, where quinone reduction takes place, lack direct access to the bulk solvent necessary for proton release and uptake. Based on the X-ray structure, proton transfer pathways were postulated. Analysis at centre P showed, that E272 and Y132 of cytochrome b are important for QCR catalysis as indicated by increased superoxide production and lowered Cyc1p reductase activity in these variants. Pre-steady state heme reduction kinetics in combination with stigmatellin resistance indicated that charge and length of the side chain at position 272 are crucial for efficient docking of the ISP to form the enzyme substrate complex and for electron bifurcation at centre P. Variants of Y312 and F129, both residues of cytochrome b, showed an increased Km indicating participation of these residues in coordination of ubiquinol or the possible intermediate semiquinone anion radical. F129 proved to be crucial for a functional Q-cycle as indicated by respiratory negative growth phenotype and a lowered H+/e- stoichiometry of F129 variants. At centre N, the postulated CL/K and E/R proton transfer pathways are located at opposite sites of the bound ubiquinone. Variants in the surface residues R218 (cytochrome b) and E52 (Qcr7) of the E/R pathway and E82 (Qcr7) of the CL/K pathway showed instability upon purification indicating an important role of these residues for QCR integrity. The slowed down centre N reduction kinetics in H85 (CL/K), R218 and N208 (both E/R) variant was attributed to a destabilised semiquinone anion consistent with the observed decreased sensitivity towards the site-specific inhibitor antimycin and an increased Km. Variants of residues of both pathway, E82Q and R218M, exhibited a decreased H+/e- stoichiometry indicating a crucial role of both residue for maintaining a working Q-cycle and supporting the proposed protonation of the substrate via the Cl/K and the E/R pathway. Long-range interaction between centre N and centre P were observed by altered reduction kinetics of the high potential chain and increased superoxide production in the centre N variants. The role of the cation-pi-interaction between F230 of Cyt1p and R19 of cytochrome c in binding of the redox carrier to QCR was analysed. In F230L hydrophobic interaction were partially lost as was deduced from the ionic strength dependence of Cyc1p reductase activity and Cycp1 binding, as detected by ionic strength sensitive Kd and Km for Cyc1p. The decreased enzymatic rate of F230W could be explained by a disturbed binding of Cyc1p to the variant enzyme. F230 may influence the heme mid point potential and thereby the electron transfer rate to Cyc1p. Reduction of Cobp via both centre P and centre N was disturbed suggesting an interaction between high and low potential chain. Supramolecular association between QCR and cytochrome c oxidase (COX) in yeast mitochondria was probed by affinity chromatography of a his-tagged QCR in the presence of the mild detergent digitonin. In comparison to purification with laurylmaltoside, the presence of both QCR and COX subunits was detected in the elution fractions by SDS-PAGE, Cyc1p reductase and TMPD oxidase activity assays and immunoblot analysis. The CL-dependent formation of the supercomplex between QCR and COX was analysed by replacement variants in the CL-binding site of QCR in CL containing and CL free environment. With an increasing number of replacements of the three lysines the CL-binding pocket supercomplex formation was not abolished, when CL is present as shown by BN-PAGE analysis. This was supported by the synergetic decrease in enzyme activity for both enzymes upon increased number of replacements. In the CL-free environment, no supracomplex formation was observed for a wildtype CL binding site. By replacements of two lysines in the CL-binding pocket, supercomplex formation could be recovered as revealed by BN-PAGE. This indicates, that CL may serve as a charge neutralizer for the lysines near the presumed interaction domain between complex III and complex IV. The obtained results for centre P provide new information of residues critical for stabilisation of ubiquinol and controlling electron short circuit reactions. The observations for centre N variants clearly support the proposed two proton transfer pathways and the role of the bound phospholipids in centre N kinetics. Variants in the Cyc1p binding site suggest a role for F230 both in Cyc1p binding and electron transfer. Clear interaction between the high and low potential chain in both Cyt1p and centre N variants strongly support long-range interactions in the complex. Studies on the supramolecular association of complex III and complex IV indicate a new role of Cl in stabilising a supracomplex.
The enzyme quinol:fumarate reductase (QFR) from the anaerobic e-proteobacterium Wolinella succinogenes is part of the anaerobic respiratory system of this organism. It couples the reduction of fumarate to succinate to the oxidation of menaquinol to menaquinone. W. succinogenes uses fumarate as terminal electron acceptor and can use various substrates (e.g., formate or molecular hydrogen) as electron donors. The concerted catalytic substrate turnover of either a hydrogenase or a formate dehydrogenase in conjunction with QFR contributes to the generation of an electrochemical potential gradient across the bacterial plasma membrane, which is used for the phosphorylation of ADP with inorganic phosphate, Pi, to ATP. In addition to an FAD (in subunit A) and three iron-sulfur clusters (in subunit B), QFR binds a low- and a high-potential heme b group in its transmembrane subunit C, as was ultimately shown in the crystal structure at 2.2 Å resolution (Lancaster et al., 1999, Nature 402, 377– 385). Both hemes are part of the electron transport chain between the two catalytic sites of this redox enzyme. The midpoint potentials of the hemes are well established but their assignment to the distal and proximal positions in the structure had not yet been determined. Furthermore, QFR from W. succinogenes has been proposed to exhibit a novel coupling mechanism of transmembrane electron and proton transfer, which has been described in the so-called “E-pathway” hypothesis (Lancaster, 2002, Biochim. Biophys. Acta 1565, 215–231). The aim of this project was to characterize the relationship between structure and function of QFR and to investigate the details of the proposed coupling mechanism (“Epathway”) with the help of computer-based electrostatic calculations on the QFR wild-type (WT) coordinates, and electrochemically induced FTIR and VIS difference spectroscopy on the QFR WT and available variant enzymes (in particular enzyme variant E180Q, in which the glutamic acid at position C180 has been replaced by a glutamine). 1.) It was demonstrated in this study that the diheme-containing QFR exhibits stable and reproducible electrochemically induced FTIR difference bands in the midinfrared range from 1800 cm-1 to 1000 cm-1 that reflect transitions from the reduced to the oxidized state of the enzyme. The spectral features that were observed in the FTIR difference spectra are fully reversible when changing from a reductive to an oxidative reference potential at the working electrode and vice versa. This indicates that the underlying redox reactions of the enzyme at the gold grid working electrode are also fully reversible under the applied experimental conditions. The same reversible spectral redox behavior in the visible range could also be ascertained for the Soret- and a-band of the two heme b groups of QFR. This behavior allowed to reliably determine the heme b midpoint potentials of QFR at various pH values. Analysis of the FTIR difference spectra in the amide I range yields evidence for structural reorganizations of the polypeptide backbone upon the electrochemically induced redox reaction. 2.) The redox titrations of the high- and low-potential heme b of QFR as simulated by multiconformation continuum electrostatics (MCCE) calculations showed a very high level of agreement with respect to the experimentally observed midpoint potentials of the heme b groups at pH 7. As determined with the help of the theoretical calculations, prominent features governing the differences in redox potential between the two hemes are the higher loss of reaction field energy for the proximal heme and the stronger destabilization of the oxidized form of the proximal heme due to several buried and ionized Arg and Lys residues. The explicit incorporation of crystallographically identified water molecules in the calculations had a noticeable effect on the absolute values of the determined midpoint potentials, although the relative difference of the two obtained midpoints did not change significantly. The results of the electrostatic calculations clearly showed that the lowpotential heme corresponds to the distal position bD in the structure, and that the high-potential heme is identical to the proximal heme bP. This assignment could previously not be achieved unequivocally with experimental methods. 3.) In addition, the currently discussed mechanism of coupled electron and proton transfer in the QFR of W. succinogenes (i.e., the “E-pathway” hypothesis) is further supported by the results of this study. The simulations of intermediate states of electron transfer via the heme b groups show that the protonation state of the key amino acid residue Glu C180 depends on the redox states of the heme groups as suggested in the “E-pathway” hypothesis. This result yields a possible mechanism for the coupling of transient transmembrane proton transfer via Glu C180 to the electron transfer via the heme b groups, since Glu C180 could be part of a “proton wire” and its redox-dependent protonation state could serve as the regulatory element of the “E-pathway”. Furthermore, the results of simulated heme reduction indicate that the side chain of Glu C180 also changes its conformation with respect to the redox state of the hemes. Both major results concerning the role of Glu C180, the change of protonation as well as the reorientation of the side chain upon reduction of the heme groups, are consistent with the results from electrochemically induced FTIR difference spectroscopy: Of particular interest was the spectral range above 1710 cm-1, where C=O stretching vibrations of protonated COOH carboxyl groups absorb, because those groups can act as proton donors, respectively acceptors, and can be involved in intra-protein proton transfer reactions. It was possible to observe signals of such protonated carboxyl groups originating from QFR enzyme, which either change their protonation state and/or experience an environmental change in the course of the induced redox reaction. This finding was supported by the fact that the relevant FTIR difference signals are sensitive to an isotopic hydrogen/deuterium (1H/2H) exchange via the buffer solution, since they were shifted towards lower wavenumbers in D2O. Furthermore, it could be shown with the help of site-directed mutagenesis that the acidic residue Glu C180, which is located in the membranespanning, diheme-containing subunit C of QFR, is contributing to the redox dependent signal of protonated carboxyl groups. The observed residual signal in the FTIR double-difference spectrum of QFR wild-type and enzyme variant E180Q (Glu C180 has been replaced with a Gln residue) could be interpreted as a protonation/deprotonation event that is superimposed by an environmental effect on the specific C=O vibration. This result strongly supports the proposed “E-pathway” of coupled transmembrane electron and proton transfer in the QFR enzyme, which states that residue Glu C180 is an essential constituent of a transient redox-controlled transmembrane proton transfer pathway. 4.) As a second possible constituent of the suggested “E-pathway”, the ring C propionate of the distal heme was found to be unusually fully protonated in all simulated redox states, indicating a possible role as a transient proton donor/acceptor in the “E-pathway”. Similarly to Glu C180, experimental evidence from FTIR difference spectroscopy on a modified QFR with 13C-labeled heme propionates was obtained, which indicates an involvement of at least one of the two propionates of heme bD in proton transfer. The observed signals can tentatively be interpreted as a redox-coupled (de)protonation of the ring C propionate of bD, which is possibly xiii superimposed by a conformational or environmental change of the specific propionate. 5.) Also the observation of a strong redox Bohr effect for both heme b groups in QFR is in line with the proposed “E-pathway” hypothesis, as this effect yields a possible and well-established mechanism for the coupling of proton transfer and redox changes of the heme groups. The comparison of the observed effect in QFR WT and E180Q together with the results from FTIR spectroscopy and MCCE calculation indicate that the ring C propionate of the distal heme is dominating the pHdependence of the midpoint potential of bD, and that the corresponding group for bP is Glu C180. The origin of the redox Bohr effect for bP in the enzyme variant E180Q (which is dramatically changed with respect to the WT) could not be identified unequivocally, but the observation of this redox Bohr effect in the variant implies the presence of other protolytic groups, which interact with heme bP and which may be necessary for a functional “E-pathway”.
Die vorliegende Arbeit soll einen Beitrag zur Erforschung der Verarbeitungsmechanismen des Gehirns leisten. Die Erregung des komplexen Systems "Hirn" liefert Antworten, deren Analyse zu einem besseren Verständnis dieser Informationsverarbeitung führt. Zu diesem Zweck wurde das Gehirn mit unterschiedlichen visuellen Stimuli angeregt und die hirnelektrischen Signale gemessen, die von Nervenzellgruppen (Multiunits) im visuellen Kortex der Katze ausgesandt wurden.Die verwendeten Stimuli waren ein Streifenmuster sowie eine Zufallspunktverteilung, deren Kohärenz beliebig geändert werden konnte. Darüber hinaus wurden die Antworten auf eine Vielzahl von Stimuli analysiert, die nur aufgrund des Bewegungskontrastes zwischen punktdefiniertem Objekt und Hintergrund zu erkennen sind (Shape-from-Motion- (SFM-) Stimuli). Die aufgenommenen Daten wurden mit Hilfe einer umfangreichen Signalanalyse untersucht. So wurden in Abhängigkeit von der Stimulusbedingung die Anzahl der Nervenimpulse pro Zeiteinheit (Feuerraten), Synchronisation, Frequenzverteilung sowie Kopplung von Aktionspotenzialen und LFPDaten analysiert. Die Experimente im ersten Teil dieser Arbeit untersuchten den Einfluss von Kohärenz auf die Verarbeitung von Bewegungsinformation im primären visuellen Areal (A17) und im posteromedialen lateralen suprasylvischen Sulcus (Area PMLS) der Katze. Es konnte gezeigt werden, dass Multiunits in A17 und PMLS sowohl auf Streifenmuster als auch auf Zufallspunktverteilungen antworten und dass die Stärke der Antwort als eine Funktion der Stimulusrichtung variiert. Die Vorzugsrichtung ist in beiden Arealen weitgehend unabhängig von der Art des verwendeten Stimulus, was darauf hindeutet, dass die Stimulusrichtung für Streifenmuster und Zufallspunktmuster in diesen Arealen durch einen einheitlichen Mechanismus bestimmt wird. Bei einer Abnahme der Stimuluskohärenz zeigen die Multiunits eine Abnahme der Feuerrate, wobei im Vergleich zu PMLS in A17 eine stärkere Abnahme der Kohärenz nötig ist, um die gleiche Abnahme der Feuerrate zu erreichen. Dieses Ergebnis konnte durch die unterschiedlichen Größen der rezeptiven Felder der beiden Areale erklärt werden und ist ein weiterer Hinweis darauf, dass eine wichtige Funktion von PMLS in der Analyse von Bewegung und räumlich verteilter Information liegt. Da beide Areale keine signifikante Änderungen der Feuerrate bei Inkohärenzniveaus von mehr als 50% zeigten, scheinen sie nicht in der Lage zu sein, die Bewegungsrichtung eines inkohärenten Zufallspunktmusters nahe der psychophysischen Detektionsschwelle von 95% auf der Basis von Feuerraten zu erkennen. Die Korrelation der Aktionspotenziale unterschiedlicher Multiunits zeigte bereits bei einer geringen Abnahme der Stimuluskohärenz eine monotone Verbreiterung des zentralen Maximums in den Korrelogrammen beider Areale. Die Stärke der Synchronisation hingegen war kaum beeinflusst. Darüberhinaus kam es zu einer Verschiebung der Leistung im lokalen Feldpotential (LFP) von hohen hin zu niedrigen Frequenzbereichen. Diese Verschiebung wurde auch für die Kopplung zwischen LFP und Akvi tionspotenzialen nachgewiesen. Diese Resultate unterstützen die Theorie, dass präzise Synchronisation und hochfrequente Oszillationen ein Mechanismus für die Bindung kohärenter Objekte sind. Sie zeigen darüber hinaus, dass Synchronisation auch nicht kohärente Stimuli binden kann und dass die Verschiebung im LFP hin zu niedrigeren Frequenzen wichtig für die Integration verteilter Information über einen größeren visuellen Raum sein kann. Da bei hohen Inkohärenzniveaus keine präzise Synchronisation mehr nachgewiesen werden konnte, kann jedoch auch die Synchronisation nicht als alleiniger Mechanismus zum Erkennen einer Bewegungsrichtung eines inkohärenten Zufallspunktmusters herangezogen werden. In den Experimenten im zweiten Teil dieser Arbeit wurde untersucht, wie das Gehirn SFM-Stimuli verarbeitet. Die Auswertungen der Feuerraten haben gezeigt, dass Multiunits in PMLS sowohl auf helligkeitsdefinierte Kontrastbalken als auch auf SFM-Balken reagieren. Die Stärke der Antwort hängt von der Kombination von Stimulus und Hintergrund und von der relativen Bewegungsrichtung zueinander ab. Während ähnliche Feuerraten für Balken mit hohem Kontrast relativ zum Hintergrund und für punktdefinierte Balken gefunden wurde, die sich über einen dunklen Hintergrund bewegten, führte ein statischer Zufallspunkthintergrund zu einer starken Abnahme der von dem SFM-Balken hervorgerufenen Antwort. Ein in die Gegenrichtung bewegter Hintergrund sowie ein reduziertes Kohärenzniveau des Zufallspunkthintergrundes führten dazu, dass die Multiunits auf den SFM- Balken nicht mehr mit einer Zunahme der Feuerraten reagierten. Um die hemmende Wirkung des Hintergrundes aufzuheben, musste der Hintergrund auf einer Fläche des visuellen Feldes, die der Größe des rezeptiven Feldes entsprach, abgedeckt werden. Dieses Ergebnis zeigt, dass die Feuerraten für diese Art Stimulus nicht wesentlich von Arealen außerhalb des rezeptiven Feldes beeinflusst werden. Zur weiteren Analyse der Fähigkeit von PMLS, SFM-Balken nur aufgrund des Bewegungskontrastes zwischen punktdefiniertem Objekt und Hintergrund zu erkennen, wurde mit Hilfe von zwei Tuningkurven-Stimuli, bei denen sich die Bewegungsrichtung der Punkte innerhalb des Balkens um 90° unterschied, die Vorzugsrichtung der Multiunits bestimmt. Die Auswertung ergab, dass sich die gemessene Vorzugsrichtung der Multiunit um 45° drehte, obwohl sich die Bewegungsrichtung des Balkens selbst nicht änderte. Darüber hinaus wurden verschiedene SFM-Stimuli untersucht, die alle dieselbe Bewegungsrichtung des Balkens, jedoch unterschiedliche Bewegungsrichtungen der Punkte innerhalb des Balkens aufwiesen. Wenn PMLS die Bewegung des SFM-Objekts statt der Bewegung der einzelnen Punkte verarbeitet, sollte die Feuerrate für alle diese Bedingungen identisch sein. Die Ergebnisse zeigen jedoch, dass sich die durch die verschiedenen SFM-Stimuli hervorgerufenen Feuerraten verringerten, je weiter sich die Punkte, die den Balken bildeten, von der Bewegungsrichtung des Balkens – und damit von der Vorzugsrichtung der Multiunit – weg bewegten. Durch dieses Ergebnis konnte gezeigt werden, dass Multiunits in PMLS nicht in der Lage sind, die Richtung von kinetisch definierten Balken zu analysieren und statt dessen nur die Bewegung der einzelnen Komponenten erfassen.
Proton-translocating NADH:ubiquinone oxidoreductase (complex I) transports two electrons from NADH to membranal ubiquinone: in this process protons are translocated across the membrane, producing 40% of the total proton gradient between matrix side and intermembrane space. Mitochondrial complex I contains at least 46 subunits in mammals, and has a molecular weight of around 1000 kDa. Electronic microscopy analysis showed that complex I has an L-form, which consists of two domains: a peripheral “arm” (hydrophilic domain) and a membrane “arm” (hydrophobic domain). The peripheral domain, which protrudes into the matrix, contains one non-covalently bound flavin mononucleotide (FMN) and the iron-sulfur clusters N1a, N1b, N2, N3, N4 and N5 as redox active groups. They transport electrons from NADH to ubiquinone. Cluster N2 is supposed to be the immediate electron donor to ubiquinone by virtue of its highest and pH dependent redox midpoint potential (Em,7 –150 mV). The exact location of the tetra-nuclear cluster N2 is still object of discussion. The TYKY and the PSST subunits contain three binding motifs for tetranuclear clusters which are formed by twelve cysteins. In an effort to investigate the “ubiquinone reduction module” of complex I, in the first part of this work site directed mutagenesis of the TYKY and PSST subunits has been carried out. Mutant strains were characterised in terms of complex I content, catalytic activity and EPR signature of cluster N2. The second part of this work was aimed at developing a substrate inducible version of the internal alternative NADH:ubiquinone oxidoreductase (NDH2i). A substrate inducible NDH2i is expected to offer a “switch” between complex I activity dependent (no NDH2i activity) and independent (NDH2i activity) cell growth, by changing between activating and non-activating substrates. This strategy would allow the screening for two types of complex I mutants, which is a prerequisite for realising a random PCR mutagenesis of single subunits of complex I, that allows the production of a high number of point mutations in relatively short time. Y. lipolytica complex I deficiency mutant strains could be easily identified, by virtue of their inability to survive under complex I dependent growth conditions (no NDH2i activity). By this way, amino acids that have an important role for complex I structure or function could be identified by subsequent sequence analysis. Each of the twelve cysteines that form the above mentioned three binding motifs for iron-sulfur cluster have been mutagenised. In mutant mitochondrial membranes, no assembled complex I could be detected. From these data one may conclude that the mutagenised 6 SUMMARY 92 cysteines play an important role for complex I stability, or that are a prerequisite for complex I assembly in Y. lipolytica, but there is not direct evidence indicating that any of the four mutagenised residues acts as a ligand. Two aspartates in the PSST subunit, Asp-99 and Asp-115, were found to be essential for complex I catalytic activity. EPR spectroscopic analysis indicated that the electron transfer to N2 cluster was not blocked and implied that this was not the reason for the loss of catalytic activity. From these data it can be concluded that D99 and D115 play a vital role for complex I NADH:ubiquinone reductase activity, but are not ligands for cluster N2 and that their position is not close enough to the cluster to influence directly its electromagnetic environment. Three mutations, identified in the PSST and TYKY homologous subunits of patients affected with Leigh syndrome (V119M in PSST, P78L and R101H in TYKY) were reconstructed in the obligate aerobic yeast Y. lipolytica. This approach may help to understand the aetiology of the Leigh syndrome, in terms of the ability of complex I to oxidize NADH and to transport electrons. In fact, all three mutations showed effects on electron transport, reducing the VMax by about 50%. Mutant V119M in the PSST subunit, which had a lethal effect in two patients that were homozygous for this mutation, affects a fully conserved residue. Overall, the results from site directed mutagenesis carried out so far support the theory that the “catalytic core ” (N2 cluster and quinone binding site) of complex I has been evolved from the electron transfer module of the [Ni-Fe] hydrogenases. In fact, mutagenesis of residues that are fully conserved between complex I and [Ni-Fe] hydrogenases, showed dramatic effects on complex I in terms of assembly (cysteine mutants) or catalytic activity (D99-D115). Differently, changing aspartate 174 and glutamic acid 185 (not fully conserved, Fig 4.1A) had little or no effect on the Michaelis-Menten parameters and N2 EPR signal. In recent years Y. lipolytica has been developed as a yeast genetic system to study mitochondrial complex I. The present work introduced the promoter for the isocitrate lyase (pICL1) as a useful tool for the substrate selective expression of the internal version of the alternative NADH:ubiquinone oxidoreductase (pICL1-NDH2i). This allows to rescue complex I deficiencies “in vivo” selectively by growth on acetate (or ethanol) medium. The integration of the pICL1-NDH2i construct into the genome of Y. lipolytica and subsequent deletion of nuclear-coded subunits like PSST, TYKY and 49 kDa, would contribute to further develop this organism as a useful genetic model for studying subunits of mitochondrial complex I by site directed mutagenesis.
Stability, unfolding and refolding of the outer membrane protein porin from Paracoccus denitrificans was investigated using genetic and spectroscopic methods. Structural and functional activity studies on wild type and mutant porins: The site-directed mutants were constructed based on conserved residues and evidences on the role of certain amino acids from previous studies with OmpF. Secondary structure analysis of wild type and mutants E81Q, W74C, E81Q/D148N, E81Q/D148N/W74C by FTIR and CD spectroscopy are in line with the fact that porins are predominantly ß-sheet structure. The functional activity studies by black lipid bilayer techniques showed that the wild type and mutants W74C, E81Q/D148N, E81Q/D148N/W74C have a conductance of 3.25 nS. For mutant E81Q conductance of 1.25nS was more predominant over 3.25 nS. The activity of the mutants was observed to be far less than the wild type. This indicates that structural similarities does not implies similar functional activity. Thermal stability analysis of porin in detergent micelles and reconstituted into liposomes: Thermal stability analysis of wild type and mutants in detergent micelles showed changes in secondary and quaternary structure. It was found that wild type porin unfolds into aggregated structure with a high transition temperature of 86.2 °C. For mutants E81Q, W74C, E81Q/D148N the transition temperature was found to be 84.2 °C, 80.3 °C and 80.2 °C respectively. Functional activity assays at high temperatures revealed that the protein tends to loose its activity on heating up to 50 °C. This shows that structural stability does not imply functionality in the case of porins. Thermal stability analysis of porin reconstituted into liposomes showed that there was no change in the secondary and quaternary structure of the protein up to 100 °C, revealing that the protein becomes more thermostable when it is reconstituted into liposomes. Refolding of aggregated porin: This study shows that disaggregation of ß-sheet membrane protein porin is possible by changing its chemical and thermodynamic parameters. An increase of the solution pH to 12 or above results in opening up of the aggregated protein into unordered structure, as observed by FTIR and CD spectroscopy. This unordered structure could be refolded into native-like structure forming trimers. The secondary structure of the refolded protein deviated slightly from the native one. The thermal stability analysis of the native-like refolded proteins showed that the unfolding pattern is entirely different when compared to the native porins. pH dependent unfolding of porin: Thermal stability of porin at different pH values showed that the protein is stable in a pH range of 1-11. At pH 12 and above the protein unfolds into unordered structure instead of aggregating. The high pH unfolding of porin is a reversible process. The secondary structure of the refolded protein varied slightly from the native-one. Whereas thermal stability was entirely different. This shows that even though the unfolding of porin at high pH is reversible, it results in changes in local interaction between the amino acids resulting in a difference in stability. Unfolding in presence of urea and guanidinium hydrochloride (GuHCl): Denaturation of porin in the presence of chemical denaturants like urea and GuHCl showed that porin unfold into unordered structure. The unfolding is a reversible process. Unfolded protein was refolded into detergent micelles and liposomes. Refolding into detergent micelles was faster compared to refolding into liposomes, as seen by kinetic gel shift assays. The refolding into liposomes showed the presence of intermediates similar to those reported for OmpF. This study shows the difference in thermal stability of the outer membrane protein porin from Paracoccus denitrificans in detergent micelles and native-like liposomes. It suggests various unfolding pathways, which can be further investigated for unfolding and refolding kinetics. This report also suggests that it is possible to refold a heat-aggregated protein.
Results were presented from Brownian dynamics simulations for cyt c molecules approximated as spherical particles with diameter 2R ' 3.3 nm interacting with a charged planar membrane surface. Using the well-known Ermak-McCammon algorithm of ref. [36, 37] for solving the Langevin equations (see Chapter 2), a new computer program in C++ was developed. An overview of the way it is implemented is given in Chapter 3. The program in its current state is able to compute the trajectories (translation and rotation) of hundreds of spherical particles in systems with typical dimensions of 103 − 1003 nm3 . As explained in the introductory Chapter 1 the motivation for studying the dynamics of cyt c molecules in such systems came from the progress in the research of photosynthetic bacteria, e.g. While the internal processes of energy transduction (light harvesting, channelling to RC, charge separation) are quite well understood, the dynamics of soluble cyt c as an electron transporter in this context is not yet clear. In many textbooks one can find illustrations where a single cyt c is responsible for the electron transport between two integral membrane proteins (the reaction centre RC and the bc1 complex). But as pointed out in publications like refs. [49], [59], [60], [61] or [62] biological cells are crowded with different molecules. Consequently, one can assume that the electron transport between two integral membrane proteins is not simply taken on by one single cyt c molecule. Instead it is likely that many of these particles are located in a cyt c pool above the membrane and that they perform the electron transport in turns. Thus, it is desirable to have a simulation package that is able to compute the trajectories of many proteins. Note that the detailed processes of electron transfer and binding to membrane proteins are not modelled here. The details of these processes are quite complicated so that we refrained from including them in the coarse-grained simulations. Here, the actual binding is simply defined by a particle distance zb from the membrane which marks the beginning of the attractive potential. ...
Hinreichend kalte und dichte Quarkmaterie ist ein Farbsupraleiter. Ähnlich wie Elektronen in einem gewöhnlichen Supraleiter bilden Quarks Cooper-Paare. Während bei Elektronen der Austausch von Phononen zu einer Anziehung führt, ist im Falle von Quarks der Antitriplett-Kanal der starken Wechselwirkung attraktiv. Arbeiten in den letzten Jahren haben verschiedene Phasen von farbsupraleitender Quarkmaterie untersucht und sich dabei vor allem auf Phasen konzentriert, m denen der Gesamtspin eines Cooper-Paares verschwindet. In der vorliegenden Dissertation habe ich hauptsächlich Farbsupraleiter diskutiert, deren Cooper-Paare im Spin-Triplett-Kanal kondensieren, d.h. die Cooper-Paare haben den Gesamtspin 1. Diese Art von Supraleiter ist möglicherweise relevant für Systeme in der Natur, wie z.B. das Innere von Neutronensternen. Denn bei der Spin-0-Farbsupraleitung wird vorausgesetzt, dass die Fermi-Impulse zweier Quark-Flavor gleich ist oder zumindest hinreichend klein, was für realistische Systeme, also für nicht zu große Dichten, fragwürdig ist. Diese Einschränkung gibt es im Falle von Spin-1-Farbsupraleitern nicht, da hier Quarks des gleichen Flavors Cooper-Paare bilden. Ich habe in meiner Dissertation die verschiedenen möglichen Phasen eines Spin-1-Farbsupraleiters systematisch klassifiziert. Dies wurde mit Hilfe von gruppen-theoretischen Methoden durchgeführt, basierend auf der Tatsache, dass die Farbsupraleitung durch das theoretische Konzept der spontanen Symmetriebrechung beschrieben werden kann. Ähnlich wie bei supraflüssigem Helium-3 gibt es eine Vielzahl theoretisch möglicher Phasen. Ich habe die physikalischen Eigenschaften von vier dieser Phasen untersucht, nämlich der polaren und planaren Phasen sowie der A- und CSL-(color-spin-locked)Phasen. Mit Hilfe der QCD-Lückengleichung wurde die Energielücke sowie die kritische Temperatur bestimmt. Es stellt sich heraus, dass die Energielücke eines Spin-1-Farbsupraleiters um 2-3 Größenordnungen kleiner ist als die eines Spin-0-Farbsupraleiters, d.h. sie liegt im Bereich von 10 - 100 keV. Zwei besondere Eigenschaften der Energielücke werden diskutiert, nämlich eine 2-Lücken-Struktur, die in zwei der untersuchten Fälle auftritt, sowie mögliche Anisotropien, insbesondere Nullstellen der Lückenfunktion. Die Berechnung der kritischen Temperatur zeigt, dass es durchaus farbsupraleitende Materie in einer Spin-1-Phase im Innern von Neutronensternen geben kann, da die Temperatur von alten Neutronensternen im Bereich von einigen keV oder sogar darunter liegt. Darüber hinaus wurde die Frage untersucht, ob ein Farbsupraleiter auch ein gewöhnlicher Supraleiter ist. In diesem Zusammenhang ist die Frage von Interesse, ob ein Spin-1-Farbsupraleiter gewöhnliche Magnetfelder aus seinem Innern verdrängt, was sicherlich Auswirkungen auf die Observablen eines Neutronensterns hätte. Tatsächlich stellt sich heraus, dass ein Spin-1-Farbsupraleiter, im Gegensatz zu einem Spin-0-Farbsupraleiter, einen elektronmagnetischen Meissner-Effekt aufweist. Dieses Ergebnis wurde mit Hilfe von gruppentheoretischen Überlegungen vorausgesagt und mit Hilfe einer detaillierten Berechnung der Photon-Meissner-Massen bestätigt.
A new experimental setup, for pump-probe fs DFWM measurements, which is based on a femtosecond laser system, has been constructed. It allows for the investigation of molecular species in the gas phase at different temperatures, from ~30 K in a seeded supersonic jet up to ~500 K in a heat-pipe oven. In comparison to other RCS methods the employed fs DFWM technique is less complicated and gives much higher signal-to-noise ratio [BFZ86, FeZ95a, CKS89, CCH90, HCF91, WRM02, Rie02]. A general computer code for the simulation of fs DFWM spectra of nonrigid asymmetric top molecules has been developed. This new DFWM code in combination with a non-linear fitting routine allows one to determine rotational and centrifugal distortion constants and obtain information on the polarizability tensor components from the experimental spectra. Fs DFWM spectroscopy was successfully applied to the medium-sized molecules benzene and benzene-d6 in a gas cell and in a supersonic jet. The spectrum from a seeded expansion has been measured up to delay time of 3.9 ns (restricted by the length of the delay stage) with excellent signal-to-noise ratio (102-103). In that way 87 and 72 J-type transients have been recorded for benzene and benzene-d6, correspondingly. A relative accuracy on the order of 10-5 has been achieved for the rotational constant. From the room temperature experiments, precise values of centrifugal distortion constants DJ and DJK have been extracted. The literature data for cyclohexane have been revised and a new precise rotational constant B0 has been obtained, which is (+5.5 MHz) shifted from the one reported in the former Raman investigation by Peters et al. [PWW73]. Additionally, high-level ab initio calculations of cyclohexane have been carried out using a large number of basis sets at several levels of theory. In particular, the vibrational averaging effects have been examined in order to critically compare the experimentally determined and theoretically evaluated rotational constants. The contribution of highly symmetric vibrational modes to vibrational averaging effects was clarified. More structural information could be obtained from fs DFWM measurements of asymmetric top species, since different type of rotational recurrences can appear, and all three rotational constants (A, B, C) can be extracted. On the other hand the analysis of the asymmetric top spectra is no longer trivial. In fact the simple formula for rotational recurrence periods of symmetric top species (Tab. 2.1) can not be applied to asymmetric top molecules. Thus, in order to extract high-resolution data for asymmetric species, a complete fitting of the experimental spectra is necessary. The fs DFWM and (1+2') PPI method have been applied to the asymmetric top molecules pyridine in the ground (S0) and pDFB in the S0 and electronically excited (S1) states. By fitting the measured fs DFWM spectra the rotational and centrifugal distortion constants have been extracted with good precision and the value of the parametrized polarizability angle of pDFB was obtained. In this work, the first application of fs DFWM spectroscopy to a molecular cluster has been reported. Also, the chemical equilibrium between monomeric and dimeric species was studied. In particular formic and acetic acid have been investigated in a gas cell and in a supersonic expansion. Many spectral features have been observed and analized in the fs DFWM spectrum of formic acid vapor in a gas cell at room temperature. Most of them were attributed to rotational recurrences of the formic acid monomer, but also spectral feature originating from the formic acid dimer of O-H×××O/O×××H-O type have been detected and analyzed. From the fitted simulation, the rotational and centrifugal distortion constants, and parametrized polarizability angle were extracted for the dimeric structure of O-H×××O/O×××HO type. With the assumption of unperturbed monomers a center-of-mass distance of R = 2.990 ± 0.001 Å for the monomers within the dimer has been calculated from the spectroscopic results. This distance is 0.028 Å smaller than that reported from electron diffraction [ABM69]. Thus, the centers-of-mass distance was assigned as the main point of disagreement between results of fs DFWM and electron diffraction experiments. In contrast to formic acid, acetic acid shows strong recurrences from dimeric species even in the fs DFWM spectra at room temperature. This is explained in terms of different symmetry of the moments-of-inertia tensor, which modulates the intensity of RRs (the fs DFWM signal is in general stronger from symmetric species). Due to the symmetric nature of the acetic acid dimer, only the sum (B+C) of the rotational constants has been extracted. The changes of geometrical parameters upon dimer formation have been analyzed for, both, formic and acetic acid. A heat-pipe oven has been used in order to overcome the main drawback of fs DFWM spectroscopy – the square dependence of the signal intensity on the sample number density. Two-ring molecules (cyclohexylbenzene, para-cyclohexylaniline and nicotine) with low vapor pressure (<0.1 mbar) at room temperature have been investigated. From the analysis of the experimental and ab-initio results for CHB and pCHA a nearly perpendicular conformation of the aromatic vs. cyclohexane ring for both system is inferred. The enlargement of the benzene ring of CHB in the electronically excited state (S1) has been found to cause the smaller rotational constants in S1. This conclusion has been drawn from the comparison of the ground and electronically excited state experimental rotational constants in combination with ab-initio calculations. The extraction of precise structural information for nicotine was not possible due to it weak fs DFWM signal. However, the fact that fs DFWM technique can be applied to conformational analysis of molecular species in an equilibrium mixture opens other applications for this kind of spectroscopy. In general the results obtained in this work show that the fs DFWM technique, being an experimental implementation of RCS, provides one with an important tool for structural analysis of molecular species in the gas phase in particular for the species to which microwave spectroscopy can not be applied. It gives spectra with excellent signal-to-noise ratio even at low number density samples expanded in a seeded supersonic jet. It provides an alternative and innovative approach towards rotational Raman spectroscopy of large polyatomic molecules applicable under various experimental conditions (broad temperature and pressure range). With the introduction of femtosecond (10-15s) laser pulses (usually picosecond (10-12s) laser pulses were used in RCS) an improvement in time-resolution and therefore in precision for the rotational constants by more than one order of magnitude has been achieved. Molecular systems in the ground electronic state without permanent dipole moment and chromophore can be studied with high precision, providing thereby molecular benchmark systems for the electronic structure theory. As has been shown, the study of molecular clusters by fs DFWM spectroscopy is possible, but its potential are restricted by the square dependence of the fs DFWM signal from the sample number density, which is even more important for supersonic jet expansions. Here, the application of near-resonant and resonant FWM schemes should help in order to compensate for the low sample concentration. With the introduction of the heat pipe oven for fs DFWM experiments, the investigation of large nonvolatile molecules under equilibrium conditions is possible now. In our laboratory the first results on the structural analysis of different conformers of pyrrolidine in the gas phase have been obtained [MaR04]. This method can have even more prospects for the structural investigations of large molecular species in combination with new non-thermal gas phase sources for nonvolatile molecules, like laser desorption [CTL89], laser oblation [MHL83], electrospray [FMM90], laser induced liquid beam ion desorption [KAB96, Sob00] etc. A very recent application of the fs DFWM technique is the investigation of the influence of strong laser fields on molecular gas phase sample, which could range from active alignment [PPB03] over molecular deformation to field ionization [CSD03]. In regards to future development in fs DFWM spectroscopy for more complex molecules one has to take into account, how large amplitude motions such as the van der Waals vibrations or internal rotation (see section 6.4.2) affect the rotational coherences. In any case, femtosecond Degenerate Four-Wave Mixing as experimental implementation of Rotational Coherence Spectroscopy can be considered as an innovative, developing, and powerful method for the structural investigation of the molecular species, which are hard to study by classical frequency-resolved spectroscopy [FeZ95a, Dan01, Rie02].
Nitric oxide (NO) represents a short-lived mediator that pivotally drives keratinocyte movements during cutaneous wound healing. In this study, we have identified p68 DEAD box RNA helicase (p68) from a NO-induced differential keratinocyte cDNA library. Subsequently, we have analyzed regulation of p68 by wound-associated mediators in the human keratinocyte cell line HaCaT. NO, serum, growth factors and pro-inflammatory cytokines were potent inducers of p68 expression in the cells. p68 was constitutively expressed in murine skin, but rapidly down-regulated upon injury. The down-regulation appeared to be transient, as p68 protein expression increased again after the inflammatory phase of repair. However, p68 protein expression did not completely disappear during wound inflammation, as immunohistochemistry and cell fractiona tion analysis revealed a restricted localization of p68 in keratinocyte nuclei of the developing epithelium. In line, cultured human (HaCaT) and murine (PAM 212) keratinocyte cell lines showed a nuclear localization of the helicase. Moreover, confocal microscopy revealed a strong localization of p68 protein within the nucleoli of the keratinocytes. Functional analyses demonstrated that p68 strongly participates in keratinocyte proliferation and gene expression. Keratinocytes that constitutively overexpressed p68 protein were characterized by a marked increase in serum-induced proliferation and vascular endothelial growth factor (VEGF) expression, whereas down-regulation of endogenous p68 using small interfering RNA (siRNA) markedly attenuated serum-induced proliferation and VEGF expression. Altogether, our results suggest a tightly controlled expression and nucleolar localization of p68 in keratinocytes in vitro and during skin repair in vivo that functionally contributes to keratinocyte proliferation and gene expression.
Reliable communication in the central nervous system requires the precise control of the duration and the intensity of neurotransmitter action at specific molecular targets. After their release at the synapse, neurotransmitters activate pre- and/or postsynaptic receptors. To terminate synaptic transmission, neurotransmitters are in turn inactivated by either enzymatic degradation or active uptake into neuronal and/or glial cells by neurotransmitter transporters. In the present study, two types of membrane proteins involved in transcellular signal transduction were investigated, the P2X receptors, which are ATP-gated ion channels and the glutamate transporters of the EAAT family. The first part of this study is concerned with the targeting and anchoring of P2X receptors at specific locations. P2X receptors play a role of fast excitatory neurotransmission to extracellular ATP in both the peripheral and central nervous system. For several ligand-gated ion channel, like glycine receptors or nicotinic acetylcholine receptors, it is known that specific binding proteins exist, which are involved in receptor trafficking and anchoring of the receptors at appropriate sites on the synapse. Within the P2X family, amino acid homology is scattered over the protein sequence excepted of the cytoplasmic C-terminal tails, which do not share significant sequence similarity, indicating that they might provide peculiar properties to the respective receptor isoforms. Using GST fusion proteins containing the C terminal end of the P2X2A, P2X5 and P2X7 subunits as baits, ßIII tubulin was identified by MALDI-TOF mass spectrometry as a direct interacting partner of P2X2A. ßIII tubulin did not interact with P2X5 nor with P2X7. The tubulin binding motif of P2X2A could be confined to a 42 amino acid long region ranging from amino acid 371 to 412 of the complete P2X2A subunit. This domain, which includes a total of six serine residues and twelve proline residues, interestingly overlaps to a significant extent with a 69 amino acid long sequence, which is lacking in P2X2B, a splice variant of P2X2A. P2X2B receptors are known to desensitize - significantly faster than P2X2A receptors. The interaction of the P2X2A receptor with ßIII tubulin may contribute to receptor desensitization as well as tethering of the P2X2A receptor at specialized regions of the cell. In a second part of this work, the oligomeric state of two distantly related glutamate transporters, the human glial glutamate transporter hEAAT2, and the glutamate transporter ecgltP of E.coli was determined. Excitatory amino acid transporters (EAATs) buffer and remove synaptically released L-glutamate and maintain its concentration below neurotoxic levels. Mammalian glutamate transporter subunits are known to form homomultimers, but controversial numbers of subunits per transporter complex have been reported, ranging from 2-5. Both hEAAT2 and ecgltP proteins expressed at high levels in Xenopus laevis oocytes, from which they were purified in a [35S]methionine-labeled form under nondenaturing conditions by metal affinity chromatography. Blue native PAGE analysis revealed that both the hEAAT2 and ecgltP transporters exist exclusively as homogenous populations of homotrimers in Xenopus oocytes. The trimeric structure was corroborated by chemical crosslinking. Also, ecgltP purified as a recombinant protein from its natural host E.coli migrated as a trimeric protein on blue native PAGE gels. The conservation of the quaternary structure from prokaryotes to mammals assigns an important functional role to the trimeric structure. Glutamate transporters are known to exhibit a dual mode of operation by functioning both as glutamate Na+/K+/H+ co-transporters and as anion channels. It is intriguing to speculate that the EAAT monomer is responsible for the secondary active transport of glutamate, whereas a barrel-like arrangement of the three subunits forms a central anion pore mediating anion conductivity.
The detailed mechanism of the 20 S proteasome from Thermoplasma acidophilum is unknown. Substrates are degraded processively to small fragments without the release of intermediates, but the basis for this unique degradation mode remains obscure. The proteasome is a molecular machine, but how the different nanocompartments interplay and whether more than one substrate can be treated simultaneously has not been elucidated yet. To address these questions we had to disable the functionality of one aperture in order to dissect whether the other pore can compensate for the loss. As it is challenging to introduce mutations solely around one pore aperture of the highly symmetrical construct, we chose a novel approach by unique orientation of the proteasome at interfaces. For this purpose we purified recombinant 20 S proteasomes, where hexahistidine tags were fused either around the entrances or at the sides. According to electron microscopic studies we immobilized these constructs uniformly either end-on or side-on at metal-chelating interfaces (lipid vesicles, lipid monolayers and self-assembled thiol monolayers). Degradation of small fluorogenic peptides and large proteins like casein was analyzed. Small substrates were degraded with comparable activity by free and immobilized proteasomes, irrespective of their orientation. Thus it can be assumed that peptides can pass the sealed entrance of the 'dead-end' proteasome. However, larger substrates like fluorescently labeled casein were processed near the temperature optimum by side-on immobilized and soluble proteasomes with threefold activity compared to end-on immobilized proteasomes. Hence it can be concluded that one pore is sufficient for substrate entry and product release. In other words, the pore and antechamber can fulfil a triple function in the import and unwinding of substrates and the egress of products. With means of surface plasmon resonance the exact substrate/proteasome stoichiometry could be determined to ~1 for 'dead-end' proteasomes and ~2 for side-on immobilized (active and inactive) proteasomes. Most importantly, a fit with the Hill equation revealed positive cooperativity for side-on immobilized (Hill coefficient ~2) in contrast to end-on immobilized proteasomes (Hill coefficient ~1). Thus in case of soluble proteasomes two substrates bind presumably in opposite antechambers with positive cooperativity. The off-rate of casein as substrate is twofold for the active side-on immobilized proteasome in comparison to the end-on immobilized proteasome. The exact 2:1 stoichiometry of the off-rates equals the ratio of exit pathways amenable in case of side-on orientated versus 'dead-end' immobilized proteasomes. Thus crevices along the cylindrical body of the 20 S proteasome seem not to participate in the egress of small products. An inactive proteasome mutant displays a concentration-dependent off-kinetic against casein. Accordingly, the off-rate of the bisubstrate:proteasome complex can be attributed around half the value of the monosubstrate:proteasome complex. Consequently, substrates exit the inactive proteasome via the route of access due to obstruction of the trans side with an entering substrate. Hence the active proteasomes have to chop substrates down to small fragments prior to release through both pores. Thus the processive degradation mode might result from positive binding cooperativity. The on-rate constants for casein suggested that substrate association represents a two-step process comprising a rate-limiting translocation step and a fast binding step. As fluorescence cross-correlation revealed that two substrates can be co-localized in the proteasome and bind successively with increasing affinity (KD,1 = 8 µM versus KD,2 = 700 nM), an allosteric transition in the proteasome can be assumed. Combining our results with the data from other research groups led to a mechanistic model for the 20 S proteasome. Accordingly, the first substrate undergoes a slow translocation step, binds in the antechamber and diffuses subsequently to the catalytic centers, where it is degraded. By switching on the catalytic activity, the pores at both termini are dilated via conformational changes. Hence entry of the second substrate into the proteasome is facilitated due to omission of the rate-determining translocation step. The second substrate is either accommodated in the antechamber before it is processed (alternating degradation) or, most probably, is directly threaded into the central cavity (simultaneous degradation). As effusing peptides compete with entering proteins for binding in the antechamber, the pores are kept in an open state. After finishing digestion the pores are closed and a new degradation cycle can be reinitiated. In summary, substrate association with the proteasome underlies an ordered alternating binding mechanism in contrast to the random mode of degradation. Thus the two-stroke engine offers the advantage of speeding up degradation without enhancing complexity.
Transmembrane proteins play crucial roles in biological systems as active or passive channels and receptors. Experimentally only few structures could be determined so far. Gaining structural insights enables besides a general understanding of biological mechanisms also further processing such as in drug design. Due to the lack of experimental data, reliable theoretical predictions would be of high value. However, for the same reason, missing data, the knowledge-based class of prediction methods that is well established for soluble proteins can not be applied. The goal of predicting transmembrane protein structures with ab initio methods demands locating the free energy minimum. Main difficulties here are, first, the computational costs of explicitly calculating all involved interactions and, second, providing an algorithm that is capable of finding the minimum within an extremely complex and rugged energy landscape. We have developed promising energy functions that describe the interactions of amino acids on a residue level, reducing computational costs while still containing most information on the atomistic level. We have also found a way to describe the interaction of the residues with its surrounding in a realistic manner by distinguishing residues exposed to the environment from those buried within helices using a sphere algorithm. The sphere algorithm can also be applied for a different purpose: one can measure how densely sidechains are packed for certain helical conformations, and thereby get an estimate of the sidechain entropy. In addition, overcrowding effects can be identified which are not well-described by the energy functions due to the pairwise calculation. To determine the absolute free energy minimum, we assume the helices to be located on an equidistance grid with slightly larger distances than to be expected. Optimizing the helices on the grid provides a starting point that should enable common minimizing algorithms, gradient-based or not, to find the absolute minimum beyond the grid. To simulate the dynamics of the helices on large time scales, we split them into rigid body dynamics and internal dynamics in terms of the dihedrals. The former one is well-known with its inherent problem of numerical drift and plenty of approaches to it, among which we have chosen the quaternions to represent the rotation of the rigid bodies. The latter one requires a detailed analysis of the torque size exerted on the dihedrals caused by the forces acting on the residues.
Die 5 Lipoxygenase (5 LO) ist das Schlüsselenzym in der Synthese von Leukotrienen. Sie wird auf transkriptioneller und posttranskriptioneller Ebene reguliert. Die Differenzierung myeloider Zelllinien mit 1,25-Dihydroxyvitamin D3 (1,25(OH)2D3) und transformierendem Wachstumsfaktor beta (TGFbeta) führt zu einer Erhöhung der 5 LO mRNA-, Protein-Bildung und der zellulären Enzymaktivität. Hier wurde gezeigt, dass dabei reife, nicht jedoch prä-mRNA der 5 LO im Zytosol und im Zellkern stark angereichert wird und dass beide Agentien in die mRNA-Prozessierung eigreifen. Obwohl die Bindung von VDR-Retinoid-X-Rezeptor (RXR)-Heterodimeren an Bindungsstellen im 5 LO-Promotor mittels DNAseI-Footprinting und EMSAs nachgewiesen wurde, konnten Reportergene unter der Kontrolle des 5 LO-Promotors in transienten und stabilen Transfektionen durch 1,25(OH)2D3/TGFbeta nicht stimuliert werden. Offensichtlich wird die Induktion der Expression der 5 LO durch 1,25(OH)2D3/TGFbeta durch Elemente außerhalb des Promotors vermittelt. In transienten Transfektionen führte der Einbau der kodierenden Sequenz der 5 LO in Luziferase-Plasmide bei Cotransfektion von VDR/RXR zu einer 5 fachen Induktion der Reportergen-Aktivität durch 1,25(OH)2D3/TGFbeta, was durch zusätzlichen Einbau der letzten vier Introns auf eine 13-fache Erhöhung gesteigert wurde. Der VDR zeigte einen Ligand-unabhängigen Effekt. Diese Reportergen-Effekte waren promotorunabhängig und von der kodierenden Sequenz gesteuert. RT-PCR-Analyse wies auf eine Deletion von Teilen der kodierenden Sequenz im Laufe der mRNA-Prozessierung hin, was durch 1,25(OH)2D3/TGFbeta verhindert wird. Auch Cotransfektion der TGFbeta-Effektoren Smads 3/4 führte in Abhängigkeit von der kodierenden Sequenz und in geringerem Maße von der 3'-UTR und den Introns J M, aber unabhängig vom Promotor, zu einer starken Erhöhung der Reportergenaktivität. Die 5 LO-Expression wird in den untersuchten Zellen vermutlich durch posttranskriptionelle Prozesse (Splicing, mRNA-Reifung) herunterreguliert, während 1,25(OH)2D3/TGFbeta die Expression der 5 LO durch eine Gegenregulation zu erhöhen, an der Komplexe beteiligt sind, die vermutlich Smads, VDR-RXR-Dimere, andere Transkriptionsfaktoren, Coaktivatoren, RNA-Polymerase II und Splicing-Faktoren enthalten. Hyperacetylierung des 5 LO-Promoters durch Inkubation mit mit dem Histondeacetylase-Inhibitor TsA führte zu einer transkriptionellen Aktivierung. Die kodierende Sequenz (und die Introns) wirkt diesem Effekt vermutlich durch die Rekrutierung von HDACs an VDR oder Smads, die direkt oder indirekt an die kodierende Region binden, entgegen.
The transporter associated with antigen processing (TAP) plays a pivotal role in the adaptive immune response against virus-infected or malignantly transformed cells. As member of the ABC transporter family, TAP hydrolyzes ATP to energize the transport of antigenic peptides from the cytosol into the lumen of the endoplasmic reticulum. TAP forms a heterodimeric complex composed of TAP1 and TAP2 (ABCB2/3). Both subunits contain a hydrophobic transmembrane domain and a hydrophilic nucleotide-binding domain. The aim of this work was to study the ATP hydrolysis event of the TAP complex and gain further insights into the mechanism of peptide transport process. To analyze ATP hydrolysis of each subunit I developed a method of trapping 8- azido-nucleotides to TAP in the presence of phosphate transition state analogs followed by photocross-linking, immunoprecipitation, and high-resolution SDS-PAGE. Strikingly, trapping of both TAP subunits by beryllium fluoride is peptide-specific. The peptide concentration required for half-maximal trapping is identical for TAP1 and TAP2 and directly correlates with the peptide-binding affinity. Only background levels of trapping were observed for low affinity peptides or in the presence of the herpes simplex viral protein ICP47, which specifically blocks peptide binding to TAP. Importantly, the peptideinduced trapped state is reached after ATP hydrolysis and not in a backward reaction of ADP binding and trapping. In the trapped state, TAP can neither bind nor exchange nucleotides, whereas peptide binding is not affected. In summary, these data support the model that peptide binding induces a conformation that triggers ATP hydrolysis in both subunits of the TAP complex within the catalytic cycle. The role of the ABC signature motif (C-loop) on the functional non-equivalence of the NBDs was investigated. The C-loops of TAP transporter contain a canonical C-loop (LSGGQ) for TAP1 and a degenerated ABC signature motif (LAAGQ) for TAP2. Mutation of the leucine or glycine (LSGGQ) in TAP1 fully abolished peptide transport. TAP complexes with equivalent mutations in TAP2 showed however still residual peptide transport activity. To elucidate the origin of the asymmetry of the NBDs of TAP, we further examined TAP complexes with exchanged C-loops. Strikingly, the chimera with two canonical C-loops showed the highest transport rate whereas the chimera with two degenerated C-loops had the lowest transport rate, demonstrating that the ABC signature motifs control the peptide transport efficiency. All single-site mutants and chimeras showed similar activities in peptide or ATP binding, implying that these mutations affect the ATPase activity of TAP. In addition, these results prove that the serine of the C-loop is not essential for TAP function, but rather coordinates, together with other residues of the C-loop, the ATP hydrolysis in both nucleotide-binding sites. To study the coupling between the ATP binding/hydrolysis and the peptide binding, the putative catalytic bases of the TAP complex were mutated to generate the so-called EQ mutants. The mutations did not influence the peptide-binding ability. Dimerization of the NBDs of EQ mutants upon ATP binding does not alter the peptide binding property. At 27°C, both ATP and ADP could induce the loss of peptide-binding ability (Bmax) only in the variants bearing a mutated TAP2. Further studies are required to deduce at which stage in the catalytic cycle the peptide-binding site is affected. In addition, mutation of the putative catalytic base of both subunits showed a magnesium-dependent peptide transport activity, demonstrating these mutants did not abolish the ATP hydrolysis. Thus, the function of this acidic residue as the catalytic base is not likely to be universe for all ABC transporters.
Ligands of Iron-Sulphur Cluster N2: In this work the ubiquinone reducing catalytic core of NADH:ubiquinone oxidoreductase (complex I) from Y. lipolytica was studied by a series of point mutations replacing conserved histidines or arginines in the 49-kDa subunit. Although the missing 4th ligand of cluster N2 could not be found in the 49-kDa subunit of complex I, it was clearly demonstrated that iron-sulphur cluster N2 resides directly on the interface between the PSST and 49-kDa subunits. The results presented in this work show that residues in the 49-kDa subunit have strong influence on this redox centre and also on catalytic activity. The strong influence of Arg-141 and His-226 residues in 49-kDa subunit on this cluster can be deducted from complete loss of N2 signals in EPR spectra such as in case of mutants H226A and R141A. In the case of mutant H226M the EPR signal from cluster N2 was shifted and cluster N2 even lost the pH dependence of its redox midpoint potential and became more similar to the other so called 'isopotential' clusters. Specifically in the case of mutants R141M and R141K the characteristic signature of cluster N2 became undetectable in EPR spectra. However, specific dNADH:DBQ oxidoreductase activity that could be inhibited with the specific complex I inhibitors DQA and rotenone was not absolutely abolished but rather reduced. These reductions in complex I activity did not correspond to similar reductions in the specific EPR signal of cluster N2 as it was observed in the His-226 mutant series. No indications could be found that these mutations had modified the magnetic properties of cluster N2, resulting in different EPR spectra. From these observations it could be concluded that both mutants R141K and R141M virtually or entirely lack iron-sulphur cluster N2. The rates in complex I activity could be reconciled with electron transfer theory: After removal of a single redox centre in a chain, electron transfer rates are predicted to be still much faster than steady-state turnover of complex I. These results from mutants R141K, R141M and also the result from mutant H226M that protons are being pumped even if the redox midpoint potential of cluster N2 is not pH dependent questions the prominent role in the catalytic mechanism of complex I that has been ascribed to cluster N2. Histidine 91 and 95 were found to be absolutely essential for activity of complex I since in both mutants complex I was fully assembled and artificial NADH:HAR activity was parental whereas complex I specific dNADH:DBQ activity was abolished. The signal from cluster N2 in EPR spectra was parental for all His-91 and -95 mutants. Mutations at the C-terminal arginine 466 affected ubiquinone affinity and inhibitor sensitivity but also destabilised complex I. All these results provide further support for a high degree of structural conservation between the 49-kDa subunit of complex I and the large subunit of water soluble [NiFe] hydrogenases. Remodelling of Human Pathogenic 49-kDa Mutations in Y. lipolytica: Y. lipolytica has been proven a good system for studying complex I properties and thus also for studying defects that occur in humans. In this work pathogenic mutations in the 49-kDa subunit of complex I were recreated and studied. The P232Q mutant showed non-assembly of complex I and this is probably the cause why this mutation was lethal in patients. The mutants R231Q and S416P were parental for the content, artificial and also specific complex I activity, Km for DBQ and IC50 for DQA. From these results we can conclude that these two residues Arg-228 and Ser-413 in mammalian cells have specific structural importance for the 49-kDa subunit even if they are not directly involved in catalytic process.
Removal of apoptotic cells by macrophages or resident semi-professional phagocytes is a prominent principle with important implications for the pathophysiology of chronic inflammatory diseases, viral infections, or cancer. To characterize mechanisms which may determine the fate of apoptotic cells, I investigated chemokine expression in apoptotic promonocytic U-937 cells or PBMC. Exposure of U-937 cells to the anti-cancer drug etoposide (VP-16), an inducer of apoptosis in these cells, was associated with increased expression of the chemokines IL-8 and macrophage inflammatory protein 1alpha (MIP-1alpha). Upregulation of IL-8 mRNA expression by VP-16 was observed as early as 4 h after onset of treatment and was still detectable after 19h of exposure. A serine protease inhibitor prevented both VP-16-induced apoptosis and release of IL-8, whereas inhibition of p38 MAP-kinases reduced IL-8 secretion only. Moreover, I observed that incubation with 2-chlorodeoxyadenosine (CdA) upregulated release of IL-8 from adherent PBMC in parallel to induction of apoptosis. In these cells a modest but significant induction of TNF-alpha release by CdA was also detected. In addition, CdA augmented release of IL-8 from whole blood cultures. By facilitating adequate recruitment of phagocytes to sites of cell death, stress-induced upregulation of chemokines associated with apoptosis may contribute to mechanisms aiming at efficient removal of apoptotic cells.
This dissertation study argues that 'policy advice formation', as a discourse development, is a differentiated hybrid resultant from merger between comparative education and policy studies disciplines. Through discourse analysis based on John Creswell's format, this study identifies revisions, restatements and shifts in emphasis of theories, methodological models and challenge topics of comparative education and policy studies. Findings which display the development of policy advice formation' discourse. In conclusion, this study found differential patterns seemingly formed because of collaborative affects of standardization in education science knowledge expressed within discourse.
Remodeling of extracellular matrix (ECM) is an important physiologic feature of normal growth and development. In addition to this critical function in physiology many diseases have been associated with an imbalance of ECM synthesis and degradation. In the kidney, dysregulation of ECM turnover can lead to interstitial fibrosis, and glomerulosclerosis. The major physiologic regulators of ECM degradation in the glomerulus are the large family of zinc-dependent proteases, collectively refered to matrix metalloproteinases (MMPs). The tight regulation of most of these proteases is accomplished by different mechanisms, including the regulation of MMP gene expression, the processing and conversion of the inactive zymogen by other proteases such as serine proteases and finally the inhibition of active MMPs by endogenous inhibitors of MMPs, denoted as tissue inhibitors of metalloproteinases (TIMPs). Namely, the MMP-9 has been shown to be critically involved in the dysregulation of ECM turnover associated with severe pathologic conditions such as rheumatoid arthritis or fibrosis of lung, skin and kidney. In the present work I searched for a possible modulation of MMP-9 expression and/or activity in glomerular mesangial cells which are thought as key players of many inflammatory and non-inflammatory glomerular diseases. I found that various structurally different PPARalpha agonists such as WY-14,643, LY-171883 and fibrates potently suppress the cytokine-induced MMP-9 expression in renal MC. Furthermore, I demonstrate that the inhibition of MMP-9 expression by PPARalpha agonists was paralleled by a strong increase of cytokine-induced iNOS expression and subsequent NO formation, suggesting that PPARalpha-dependent effects on MMP-9 expression level primarily result from alterations in NO production which in turn reduces the MMP-9 mRNA half-life. Searching for the detailed mechanism of NO-dependent effects on MMP-9 mRNA stability, I found that NO either given from exogenous sources or endogenously produced increases the MMP-9 mRNA degradation by decreasing the expression of the mRNA stabilizing factor HuR. Furthermore, I demonstrate a reduction in the RNA-binding capacity of HuR containing complexes to MMP-9 ARE motifs in cells treated with NO. Since the reduction of HuR expression can be mimicked by the cGMP analog 8-Bromo-cGMP, I suggest that NO reduces in a cGMP-dependent manner the expression of HuR. Finally, I elucidated the modulatory effect of extracellular nucleotides, mainly ATP, on cytokine-triggered MMP-9 expression. Interestingly, I found that in contrast to NO, gamma-S-ATP the stable analog of ATP potently amplifies the IL-beta mediated MMP-9 expression. The increase in mRNA stability was paralleled by an increase in the nuclear-cytosolic shuttling of the mRNA stabilizing factor HuR. Furthermore, I demonstrate an increase in the RNA-binding capacity of HuR containing complexes to the 3'-UTR of MMP-9 by ATP. In summary, the data presented here may help to find new targets (posttranscriptional regulation) that could be used to manipulate or modulate the expression of not only MMP-9 but also other genes regulated on the level of mRNA stability.
In this thesis the anti-proton to proton ratio in 197Au + 197Au collisions, measured at mid-rapidity, at a center of mass energy of psNN = 200GeV is reported. The value was measured to be ¹p/p = 0.81+-0.002stat +- 0.05syst: in the 5% most central collisions. The ratio shows no dependence on rapidity in the range jyj < 0:5. Furthermore, a dependence on transverse momentum within 0:4< p? < 1:0 GeV/c is not observed. At higher p?, a slight drop in the ratio is observed. In the present analysis, the highest momentum considered is p? = 4:5 GeV/c yielding ¹p=p = 0:645§0:005stat: §0:10syst:. However, the systematic error is higher in this momentum range. A slight centrality dependence was observed, where a decrease from ¹p=p = 0:83§0:002stat:§0:05syst: for most peripheral collisions (less than 80% central) to ¹p=p = 0:78§0:002stat:§0:05syst: for the 5% most central collisions was measured. An estimate of the feed-down contributions fromthe decay of heavier strange baryons results in ¹p=p = 0:77 § 0:05syst:. The measured ratio indicates a » 12:5 times higher value compared to the highest SPS energy of psNN = 17:3 and an \almost net-baryon free" region, at mid- rapidity. The asymmetry of protons and anti-protons may be explained by the contribution ofvalence quarks in a nucleus break-up picture. In such a scenario, the absolute value of the ratio and the fact that the ratio does not depend on rapidity (at mid-rapidity) is well reproduced. Fragmentation of quarks and anti- quarks into protons and anti-protons is assumed. An estimate of the ratio, when feed-down correction is taken into consideration, agrees well with the prediction of a statistical model analysis at a temperature of T = 177 § 7 MeV and a baryon chemical potential of ¹B = 29 § 8 MeV. The temperature achieved is only slightly higher when compared to the top SPS energy, while the baryochemical potential is factor »10 lower. As in the case of the SPS results, these parameters are close to the phase boundary of Figure 1.6. The measurement of the ratio at high transverse momentum was of special in- terest in this analysis, since at RHIC energies, the cross section for hadrons at high transverse momentum is increased with respect to SPS energies. The weak dependence of the ratio on the transverse momentum is well described by the non- perturbative quenched and baryon junction scenario (i.e. Soft+Quench model), where baryon creation is enhanced by baryon junctions. In comparison the ratio does not decrease within the considered momentum range as predicted by pQCD.
Der Produktion von Interleukin-8 (IL-8), Hämoxygenase-1 (HO-1), und dem vaskulären endothelialen Wachstumsfaktor (VEGF) wird zunehmend größere Bedeutung im Rahmen der Regulation der Immunantwort bei Entzündung, Infektion und Tumorwachstum zugemessen. Ziel dieser Arbeit war die Untersuchung der Regulation dieser Botenstoffe in vitro durch Verwendung der humanen Dickdarmkarzinomzellinie DLD-1. Die Substanz Pyrrolidinedithiocarbamate (PDTC) verstärkt nicht nur die durch Tumornekrosefaktor-a (TNF-a) vermittelte Ausschüttung von IL-8, sondern induziert auch als alleiniger Stimulus die IL-8-Sekretion. Mutationsanalysen des IL-8-Promotors und "Electrophoretic Mobility Shift" Untersuchungen (EMSA) zeigten, daß die Aktivierung des Transkriptionsfaktors AP-1 (Aktivator Protein-1) und die Bindungsaktivität von konstitutiv aktiviertem NF-KB in DLD-1 Zellen für die PDTC induzierte IL-8 Expression zwingend erforderlich waren. Weiterhin war PDTC in der Lage in DLD-1 Zellen neben IL-8 auch die Expression von HO-1 und VEGF zu verstärken. Die Induktion von IL-8 durch PDTC war nicht nur auf DLD-1 Zellen beschränkt, sondern wurde auch in Caco-2 Zellen (ebenfalls Dickdarmkrebszellen) und in humanen mononukleären Blutzellen beobachtet. Die Verwendung von PDTC wird seit kurzem als Kombinationspräparat für Zytostatia zur Behandlung von verschiedenen bösartigen Tumoren, unter ihnen auch Darmkrebs, vorgeschlagen. Aus unseren Versuchen läßt sich ableiten, daß die Induktion von IL-8, HO-1 und VEGF die therapeutische Anwendung dieser Substanz nachteilig beeinflussen könnte. Dies ergibt sich daraus, daß alle drei genannten Faktoren durch proangiogene Wirkungen das Tumorwachstum fördern. Die Expression der induzierbaren Stickoxidsynthase und die Produktion von Stickoxid (NO) korreliert mit der Angiogenese bei verschiedenen Krebserkrankungen darunter Melanome, Tumore im Hals- und Kopfbereich und Darmkrebs. Da tumorbegünstigende Funktionen von NO mit vermehrter Angiogenese in Verbindung gebracht werden, wurden die Effekte von NO hinsichtlich der Produktion von ausgesuchten Chemokinen, die an der Steuerung des Tumorwachstums beteiligt sind, untersucht. Zu diesen Chemokinen gehören das proangiogene IL-8 sowie das tumorsuppressiv durch Interferon induzierbare Protein-10 (IP-10) und das Monokin induziert durch Interferon-y (MIG). Diese Chemokine werden, nach Stimulation mit IL- 1ß und lnterferon-? (IFN-?) von DLD-1 Zellen, ausgeschüttet. Unter diesen Bedingungen wird die IL-8 Freisetzung alleine durch IL-1ß vermittelt, aber nicht durch INFy. Im Gegensatz zu IL-8 hängt die Sekretion von IP-10 und MIG von der Aktivierung durch IFNy ab. Die Effekte von NO wurden analysiert indem DLD-1 Zellen mit dem NO-Donor DETA-NO inkubiert wurden. DETA-NO besitzt eine Halbwertzeit von 16,5h und simuliert damit die Effekte der endogenen NO-Synthase. Synthese und Freisetzung von IL-8 wurden durch die Behandlung mit NO stark gesteigert. Außerdem wurde in Zellen die dem NO-Donor ausgesetzt wurden die basale Sekretion des VEGF signifikant verstärkt. Dies steht im Gegensatz zur IL-Iß/IFNy-induzierten Produktion von IP-10 und MIG, beide wurden durch Koinkubation mit NO unterdrückt. Ebenso wurde die Regulation der IFNy abhängigen induzierbaren Stickoxidsynthase in DLD-1 Zellen von NO unterdrückt. Die vorliegenden Daten ergänzen vorherige Studien, in denen NO mit Tumorangiogenese und verstärkten Tumorwachstum in Verbindung gebracht wird. Die NO vermittelte Induktion von IL-8 und VEGF, ebenso wie die Verminderung der IP-10 and MIG Expression, könnte zu diesem Phänomen beitragen. Unsere Studien stützen die Hypothese, daß spezifische lnhibitoren der iNOS therapeutischen Nutzen bei humanen Neoplasien haben könnten.
Cytochrome c oxidase is the terminal enzyme in the respiratory chain of mitochondria and aerobic bacteria. This enzyme ultimately couples electron transfer from cytochrome c to an oxygen molecule with proton translocation across the inner mitochondrial and bacterial membrane. This reaction requires complicated chemical processes to occur at the catalytic site of the enzyme in coordination with proton translocation, the exact mechanism of which is not known at present. The mechanisms underlying oxygen activation, electron transfer and coupling of electron transfer to proton translocation are the main questions in the field of bioenergetics. The major goal of this work was to investigate the coupling of electron transfer and proton translocation in cytochrome c oxidase from Paracoccus denitrificans. Different theoretical approaches have been used to investigate the coupling of electron and proton transfer. This thesis presents an internal water prediction scheme in the enzyme and a molecular dynamics study of cytochrome c oxidase from Paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. Two parallel molecular dynamics simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water molecules and their corresponding hydrogen-bonded networks inside cytochrome c oxidase. The average number of solvent sites in the proton conducting K- and D- pathways was determined. The highly fluctuating hydrogen-bonded networks, combined with the significant diffusion of individual water molecules provide a basis for the transfer of protons in cytochrome c oxidase, therefore leading to a better understanding of the mechanism of proton pumping. The importance of the hydrogen bonding network and the possible coupling of local structural changes to larger scale changes in the cytochrome c oxidase during the catalytic cycle have been shown.
Obwohl Böden unzweifelhaft ein signifikanter Pool von organischem Kohlenstoff sind, ist ihre Bedeutung als potenzielle langfristige Senke für atmosphärischen Kohlenstoff keineswegs klar. Trotz bedeutender wissenschaftlicher Forschritte aus den letzten Jahren zur Klärung der Kohlenstoffdynamik in Böden gibt es nach wie vor offene Fragen insbesondere hinsichtlich der spezifischen geochemischen Mechanismen, die für die Stabilisierung organischen Kohlenstoffs in Böden verantwortlich sind. Vor diesem Hintergrund besteht ein wesentliches Ziel der vorliegenden Dissertation darin, in unterschiedlichen Bodentypen die Konzentration von organischem Kohlenstoff und Stickstoff sowie die mineralogische Zusammensetzung zu untersuchen, um Hinweise auf einen möglichen Einfluss der Tonmineralogie, der spezifischen Oberfläche und der Oxidkonzentration auf die Stabilisierung organischen Materials zu ermitteln. Die Ergebnisse sollen einen Beitrag dazu liefern, die Mechanismen der Fixierung organischer Substanz in Böden besser zu verstehen und das vorhandene Wissen hierüber zu erweitern. Hierzu wurden fünf verschiedene Bodenprofile aus Hessen mit unterschiedlicher mineralogischer Zusammensetzung untersucht. Um die Auswirkungen verschiedener physikalischer und geochemischer Faktoren auf den Gehalt organischer Substanz in den untersuchten Böden festzustellen, wurden folgende Parameter untersucht: -Tonmineralogie, -organische Kohlenstoff- und Stickstoff-Konzentrationen, -%-Kationensättigung, -spezifische Oberfläche, -dithionit- und oxalatlösliche Gehalte an Fe, Al und Mn. Anhand dieser Parameter wurden weiterführende statistische Analysen unter Verwendung der Statistiksoftware SPSS für Windows durchgeführt, um mögliche statistische Zusammenhänge aufzudecken, die für die Stabilisierung von organischem Kohlenstoff in den betrachteten Böden verantwortlich sind. Die im Rahmen der vorliegenden Dissertation ermittelten Ergebnisse zeigen, dass der Tonanteil und die Tonmineralogie der untersuchten Böden nur einen begrenzten Einfluss auf die Stabilisierung organischer Substanz haben. Weiterhin wird gezeigt, dass die in der Literatur propagierte Beziehung zwischen spezifischer Oberfläche und der Konzentration organischen Kohlenstoffs nicht auf alle Böden anwendbar ist. Die Ergebnisse deuten darauf hin, dass die Präsenz von amorphen Eisen- und Aluminiumoxiden der wichtigste Einflussfaktor für die Fixierung von organischem Material in den untersuchten Böden ist. Die größeren Konzentrationen von organischem Kohlenstoff in den kleinsten Fraktionen (Feinschluff und Ton) der Profile sind vor allem darauf zurückzuführen, dass Oxide ebenfalls in diesen Fraktionen aufzufinden sind. Tonminerale haben demnach eine sekundäre Bedeutung, indem sie Komplexe mit den Oxiden bilden, die zur Stabilisierung von organischer Substanz führen können. Insgesamt deuten die Ergebnisse daraufhin, dass Böden keine geeignete Senke für die langfristige Speicherung von organischem Kohlenstoff sind. Obwohl Mechanismen wie die Adsorption von organischer Substanz an Oxide die Stabilisierung organischen Materials unterstützen, scheinen diese nicht stark genug zu sein, um eine permanente Speicherung von organischem Kohlenstoff zu bewirken.
A gene trap strategy was used to identify genes induced in hematopoietic cells undergoing apoptosis by growth factor withdrawal. IL-3 dependent survival of hematopoietic cells relies on a delicate balance between proliferation and apoptosis that is controlled by the availability of cytokines (Thompson, 1995; Iijima et al., 2002). From our previous results of gene trap assay, we postulated that transcriptionally activated antagonistic genes against apoptosis might actually block or delay cell death (Wempe et al., 2001) causing cells to have carcinogenic behavior. The analysis attempted to better understand the outcome of a death program following IL-3 deprivation and to identify those survival genes whose expression is affected by time dependent manner. As described in the chapter 4, there would be two major conclusions evident from the three separate experiments (Genetrap, Atlas cDNA array and Affymetrix chips): Firstly 56% of trapped genes, that are up-regulated by IL-3 withdrawal (28 of 50), are directly related to cell death or survival. Secondly, unlike most array technologies, gene trapping only selects for the transiently induced genes that is independent of pre-existing steady state mRNA levels. In regarding correlations of the genes with potential carcinogenesis, the pre-existing mRNA makes difficult to describe the unique characteristics of deregulated tumor tissue genes. For a joint project with Schering (Schering AG, Berlin), the genes of our GTSTs were examined. The first screen with custom array was used to look for whether the survival genes of our GTSTs are involved in various cancer cell lines, whilst the second screen with Matched Tumor/Normal Array was used to characterize if the selected seven genes (ERK3, Plekha2, KIAA1140, PI4P5Ka/g, KIAA0740, KIAA1036 and PEST domains) are transformation-related genes or not in different tumor tissues. Twenty-six genes were identified as either induced or repressed in one or more cell lines. Genetic information is expressed in complex and ever changing patterns throughout a life span of cells. A description of these patterns and how they relate to the tissue specific cancer is crucial for our understanding of the network of genetic interactions that underlie the processes of normal development, disease and evolution. The development of cancer and its progression is clearly a multiplex phenotype, as a function of time, involving dozens of primary genes and hundreds of secondary modifier genes. There would be a major conclusion evident from the three separate experiments (Genetrap, Affymetrix mouse chip and Matched Tumor/Normal Array): ERK3 could play a significant role in breast, stomach and uterus carcinogenesis with tissue specific regulations. It is clear that ERK3 is obvious putative survival gene in these tumor tissues. Especially, in breast tumors, seven times up-regulation was considerable and the activation of ERK3 could be a feature of breast tumors. My results imply that the unique deregulation of ERK3 is perhaps the major consequence of possible transformation of normal cells into malignant cancer cells, even though further analysis remains to be determined whether an alterated activity of associated survival genes is primarily responsible for a carcinogenesis. However unlike all the other known MAP Kinases, no stimuli and no nuclear substrates of ERK3 is reported. Therefore, it will be necessary first to determine the spectrum of substrates and to identify the proximal effectors for the ERK3 in breast carcinoma cells.
Zahnwale sind die einzige Säugetiergruppe, die umfassend an ein Leben im Wasser angepasst ist und dabei ein aktives Sonarsystem zur Orientierung nutzt. Wahrscheinlich produzieren alle Zahnwalarten sonische oder ultrasonische Klicklaute, deren Echos die Tiere zu einem drei-dimensionalen "akustischen Bild" zusammensetzen. Im Gegensatz zu den meisten anderen Säugetieren produzieren Zahnwale diese Laute im Nasen-Komplex durch einen pneumatisch betriebenen Mechanismus. Jedoch spielt auch der Kehlkopf dabei eine wichtige Rolle, indem er den nötigen Luftdruck in der Nase erzeugt. Die Ergebnisse werden in Bezug auf die physikalischen Voraussetzungen eines Bio-Sonars in einer aquatischen Umwelt interpretiert. Um die morphologischen Eigenschaften (Struktur, Form, Topographie) der Organe im Kopf verschiedener Zahnwalarten vollständig zu erfassen, wurden diese mittels Computertomographie und Magnetresonanztomographie gescannt. Daraufhin wurden die Köpfe makroskopisch präpariert und histologische Schnitte von Gewebeproben angefertigt. Schließlich wurden die Ergebnisse durch digitale dreidimensionale Rekonstruktionen vervollständigt. Diese Studie basiert zum größten Teil auf der Untersuchung von Schweinswalen (Phocoena phocoena) und Pottwalen (Physeter macrocephalus). Zum Vergleich wurden fetale und postnatale Individuen anderer Zahnwalarten herangezogen wie Delphinartige (Delphinus delphis, Stenella attenuata, Tursiops truncatus), Flussdelphinartige (Pontoporia blainvillei, Inia geoffrensis) und der Zwergpottwal (Kogia breviceps). Im Allgemeinen konnte durch die morphologischen Daten dieser Studie die einheitliche "phonic lips-Hypothese der Schallproduktion bei Zahnwalen, wie sie von Cranford, Amundin und Norris [J. Morphol. 228 (1996): 223-285] aufgestellt wurde, bestätigt werden. Diese Hypothese beschreibt eine ventilartige Struktur in der Nasenpassage, den sogenannten "monkey lips/dorsal bursae complex" (MLDB) als Schallgenerator. Der pneumatische Mechanismus lässt die beiden Hälften des MLDB aufeinanderschlagen und erzeugt damit die initiale Schallschwingung im Gewebe ("phonic lips"). Diese Vibration wird über die Melone, einen großen Fettkörper in der vorderen Nasenregion der Zahnwale, fokussiert und in das umgebende Wasser übertragen. Die akzessorischen Nasensäcke und spezielle Schädel- und Bindegewebestrukturen können zu der Fokussierung beitragen. Obwohl die Echolotsignale der Schweinswale sehr spezialisiert zu sein scheinen, weisen die Übereinstimmungen in der Topographie und in der Form der Nasenstrukturen im Vergleich zu Delphinen und Flussdelphinartigen (Pontoporia und Inia) auf eine ganz ähnliche Funktion der Nase bezüglich der Produktion und Emission von Echolotschall hin. Allerdings gibt es einige anatomische Besonderheiten im Nasenkomplex des Schweinswals, welche die besondere Pulsstruktur der Sonarsignale erklären könnte. Diese werden in der Dissertation diskutiert. Bei einem Vergleich der Nasenmorphologie der Pottwale einerseits und der nicht-pottwalartigen Zahnwale andererseits fällt vor allem der Grad der Asymmetrie ins Auge. Im Gegensatz zu dem oben für Delphine und Schweinswale beschrieben Mechanismus betreiben Pottwale die Schallproduktion an den "monkey lips" mit Luft, die im rechten Nasengang unter Druck gesetzt wird (und nicht im nasopharyngealen Raum). Zudem könnte durch Änderung des Luftvolumens im rechten Nasengang die Schalltransmission zwischen den Fettkörpern, und somit die Schallemission, kontrolliert werden. In diesem theoretischen Szenario fungiert der breite rechte Nasengang als eine Art "akustische Schranke", welche zwischen zwei verschiedenen Modi der Klickproduktion wechselt: Der erste Modus mit luftgefülltem Nasengang führt zur Produktion der Kommunikationsklicks ("coda clicks") und der zweite Modus zur Aussendung von Echolotklicks, wenn der Nasengang kollabiert ist. Somit scheinen die zentrale Position und die nahezu horizontale Orientierung des rechten Nasengangs im Kopf der Pottwale als Schnittstelle (Schranke) zwischen den beiden großen Fettkörpern mit dem Mechanismus der Schallproduktion bei veränderten Luftvolumina korreliert zu sein. Die hier beschriebenen und andere Ergebnisse dieser Dissertation deuten darauf hin, dass die Gestalt und das Ausmaß der Nasenasymmetrie nicht mit der systematischen Zugehörigkeit der jeweiligen Art korrelieren, sondern durch den jeweiligen Typus des Sonarsystems als Ausdruck einer bestimmten ökologischen Anpassung bedingt sind. Bei Zahnwalen ist der Kehlkopf charakterisiert durch eine rostrale Verlängerung des Kehldeckels und der beiden Stellknorpel, die ein gänseschnabelartiges Rohr bilden, das von einem starken Sphinktermuskel umrundet und dabei in Position gehalten wird. Auf diese Weise ist das Atemrohr vollständig vom Digestionstrakt getrennt. Aus anatomischer Sicht ist es wahrscheinlich, dass die Schallerzeugung bei Zahnwalen durch eine Kolbenbewegung des Kehlkopfes in Richtung der Choanen zustande kommt, wodurch der Luftdruck im Nasenbereich erzeugt wird. Die Kontraktion des Sphinktermuskels als einem muskulösen Schlauch erzeugt wahrscheinlich die größte Kraft für diese Kolbenbewegung. Jedoch dürften die Muskelgruppen, die den Kehlkopf und das Zungenbein am Unterkiefer und an der Schädelbasis aufhängen, signifikant zur Druckerhöhung beitragen.
The endothelin B receptor belongs to the rhodopsin-like G-protein coupled receptors family. It plays an important role in vasodilatation and is found in the membranes of the endothelial cells enveloping blood vessels. During the course of this work, the production of recombinant human ETB receptor in yeast, insect and mammalian cells was evaluated. A number of different receptor constructs for production in the yeast P. pastoris was prepared. Various affinity tags were appended to the receptor N-and C-termini to enable receptor detection and purification. The clone pPIC9KFlagHisETBBio, with an expression level of 60 pmol/mg, yielded the highest amount of active receptor (1.2 mg of receptor per liter of shaking culture). The expression level of the same clone in fermentor culture was 17 pmol/mg, and from a 10L fermentor it was possible to obtain 3 kg of cells that contained 20-39 mg of the receptor. For receptor production in insect cells, Sf9 (S. frugiperda) suspension cells were infected with the recombinant baculovirus pVlMelFlagHisETBBio. The peak of receptor production was reached at 66 h post infection, and radioligand binding assays on insect cell membranes showed 30 pmoL of active receptor /mg of membrane protein. Subsequently, the efficiency of different detergents in solubilizing the active receptor was evaluated. N-dodecyl-beta-D-maltoside (LM), lauryl-sucrose and digitonine/cholate performed best, and LM was chosen for further work. The ETB receptor was produced in mammalian cells using the Semliki Forest Virus expression system. Radioligand binding assays on membranes from CHO cells infected with the recombinant virus pSFV3CAPETBHis showed 7 pmol of active receptor /mg of membrane protein. Since the receptor yield from mammalian cells was much lower than in yeast and insect cells, this system was not used for further large-scale receptor production. After production in yeast and insect cells, the ETB receptor was saturated with its ligand, endothelin-1, in order to stabilize its native form. The receptor was subsequently solubilized with n-dodecyl-beta-D-maltoside and subjected to purification on various affinity matrices. Two-step affinity purification via Ni2+-NTA and monomeric avidin proved the most efficient way to purify milligram amounts of the receptor. The purity of the receptor preparation after this procedure was over 95%, as judged from silver stained gels. However, the tendency of the ETB receptor produced in yeast to form aggregates was a constant problem. Attempts were made to stabilize the active, monomeric form of the receptor by testing a variety of different buffer conditions, but further efforts in this direction will be necessary in order to solve the aggregation problem. In contrast to preparations from yeast, the purification of the ETB receptor produced in insect cells yielded homogeneous receptor preparations, as shown by gel filtration analysis. This work has demonstrated that the amounts of receptor expressed in yeast and insect cells and the final yield of receptor, isolated by purification, represent a good basis for beginning 3D and continuing 2D crystallization trials.
Hepatitis E virus (HEV) is a positive-stranded RNA virus with a 7.2 kb genome that is capped and polyadenylated. The virus is currently unclassified : the organisation of the genome resembles that of the Caliciviridae but sequence analyses suggest that it is more closely related to the Togaviridae. HEV is an enterically transmitted virus that causes both epidemics and sporadic cases of acute hepatitis in many countries of Asia and Africa but only rarely causes disease in more industrialised countries. Initially the virus was believed to have a limited geographical distribution. However, serological studies suggest that that HEV may be endemic also in the United states and Europe even though it infrequently causes overt disease in these countries. Many different animal species worldwide recently have been shown to have antibodies to HEV suggesting that hepatitis E may be zoonotic. Although two related strains have been experimentally transmitted between species, direct transmission from animal to a human has not been documented. Our main objective in this study is to evaluate the suitability of current available HEV antibody assays for use in low-endemicity areas such as in Germany. Methods: We selected sera on the basis of at least borderline reactivity in the routinely used Abbot EIA. Most were tested as part of routine screening of long-term expatriates in endemic countries. The following assays (recombinant antigens : ORF2 and ORF3) were used: Abbot EIA, Genelabs ELISA, Mikrogen recomBlot and a 'Prototype' DSL-ELISA. We observed a wide range of sensitivity ( average of 56.8%) and specificity ( an average of 61.4%) in these used assays. These results implies that , these assays might be unreliable for detection of HEV infection in areas where hepatitis E is not endemic. However, most anti- HEV assays have not been correlated with the HEV RNA determined by reverse transcription. Many of these unexpected results and discrepancies can be alluded to the following reasons: I. The choice and the size of the HEV antigen. II. Duration of the antibody persistence III. A cross reactivity with different agent IV. Due to geographic species V. A low sensitivity of the available assays. VI. And infection with non-pathogenic HEV strain. (zoonotic strain?). We therefore suggest that, further studies will be required to improve the sensitivity and specificity of the available commercial assays on the market.
In the present study the cryo-immunogold technique was used and optimized for investigating the ultrastructure and immunolabeling of synaptic proteins. It is evidently a suitable method for the localization of membrane proteins since the antigens are not treated with any chemical denaturation before immunolabeling except for the fixation and since the antigens are directly exposed to the surface of the cryo-ultrasections. The v-SNARE VAMP II and the vesicle-associated proteins SV2 and Rab3A were detected extensively at small vesicles in the mossy fiber terminals. The t-SNARE SNAP-25, and N-type and P/Q type Ca2+ channels were allocated to the plasma membrane both at the active zone and outside the active zone. SNAP-25 and N-type Ca2+ channels appeared also at synaptic vesicles. A significantly increased immunolabeling of VAMP II, SV2, Rab3A, SNAP-25 and N-type Ca2+ channels was found at the active zones of fast synapses, indicating a concentration of these proteins at sites of exocytosis. The widespread distribution of the t-SNARE SNAP-25 at the axonal plasma membrane reveals that membrane-targeting specificity cannot be determined solely by v/t-SNARE interactions. Additional control components are required to assure the docking and exocytosis of the synaptic vesicles at active zones. The novel protein Bassoon was only found at active zones of central synapses and showed the highest specific labeling among all proteins investigated. Its labeling pattern implies an association of Bassoon with the presynaptic dense projections, the structural guide for vesicle exocytosis. The involvement of Bassoon in the organization of the neurotransmitter release site suggests that Bassoon may play an important role in determining the specificity of vesicle docking and fusion. In the neurosecretory endings of neurohypophysis the synaptic proteins VAMP II, SNAP- 25, SV2, Rab3A, and the N-type Ca2+ channels showed a preferential labeling over microvesicles. Moreover, the immunolabeling intensity of these proteins over microvesicles corresponded closely to that over synaptic vesicles. This suggests that these synaptic proteins share an identical association with synaptic vesicle and microvesicles. A significant labeling of SNAP-25, the N-type Ca2+ channels and VAMP II was also detected at the plasma membrane near the clustered microvesicles, indicating the competence of microvesicles for docking and exocytosis along the plasma membrane in the absence of active zones. No significant labeling of VAMP II, SNAP-25, SV2 and N-type Ca2+ channel was observed at the membrane of neurosecretory granules. This is in agreement with the notion that synaptic vesicles and microvesicles possess regulatory mechanisms for exocytosis different from those of granules. In contrast, a/ß-SNAP and NSF were found on the granules, and Rab3A and the P/Q-type Ca2+ channels on granules in a subset of terminals. Rab3A is associated specifically with the oxytocin-containing granule population. Interestingly, some plasma membrane proteins, such as SNAP-25 and even N-type Ca2+ channels and P/Q-type Ca2+ channels, were observed not only at the plasma membrane but also at the vesicular organelles. This suggests that these vesicular organelles may be involved in transporting newly synthesized proteins from the soma to the plasma membrane of the terminal. Furthermore, the vesicular pool of the Ca2+ channels may serve in the stimulationinduced translocation into the plasma membrane when required. Using the conventional preembedding method with Epon and the post-embedding method with LR Gold, VAMP II was localized at vesicular organelles of varying size and on horseradish peroxidase filled endocytic organelles in cultured astrocytes, with and without stimulation in the presence of the horseradish peroxidase. This indicates that VAMP II is involved in the cycle of vesicular exocytosis and endocytosis in astrocytes. U373 cells are capable of expressing all three members of the synaptic SNARE complex (v-SNARE VAMP II, t-SNARE syntaxin I and SNAP25). This indicates the competence of U373 to carry out regulated exocytosis by means of the classical SNARE mechanism. In addition, the ubiquitous v-SNARE cellubrevin and the endosome-associated small GTPbinding protein Rab5 could be expressed in U373 cells. All recombinant synaptic proteins investigated in U373 cells revealed a punctuate cellular distribution under the fluorescence microscope, suggesting that they are mainly associated with intracellular compartments. The cryo-electron microscopy provided direct evidence for the association of all expressed proteins with electron-lucent vesicular organelles. It further supports the potential of U373 MG cells to release low molecular weight messengers by a regulated exocytosis mechanism. In addition, myc-VAMP II was found on dispersed granules. Probably, VAMP II also participates in the exocytosis event of granules in U373 cells. Gold labeling for the two presumptive t-SNAREs syntaxin I and SNAP-25 in U373 cells was confined to the vesicular organelles. At the ultrastructural level no significant labeling was identified at the plasma membrane. The high level of colocalization of the two SNARE proteins VAMP II and syntaxin I in the cell body and in cell processes suggests that the two proteins are mostly sorted into identical vesicular organelles. A partial colocalization of VAMP II and cellubrevin as well as of VAMP II and Rab5 was observed under the fluorescence microscope. At the ultrastructural level, a colocalization of VAMP II and cellubrevin as well as of VAMP II and Rab5 was found on some clustered vesicles. The partial colocalization of VAMP II and cellubrevin implies that they similarly function as v-SNAREs. The partial colocalization of Rab5 with VAMP II in U373 cells suggests that the endosomal protein Rab5 is associated with VAMP II-containing organelles during some stages of their life cycle.
The focus of this study were Celtic gold coins excavated from the Martberg, a Celtic oppidium and sanctuary, occupied in the first century B.C. by a Celtic tribe known as the Treveri. These coins and a number of associated coinages, were characterised in terms of their alloy compositions and their geochemical and isotopic signatures so as to answer archaeological and numismatic questions of coinage development and metal sources. This required the development of analytical methods involving; Electron Microprobe (EPMA), Laser Ablation-ICP-MS, solution Multicollector-ICPMS and LA-MC-ICP-MS. The alloy compositions (Au-Ag-Cu-Sn) were determined by EPMA on a small polished area on the edge of the coins. A large beam size, 50µm (diameter), was used to overcome the extreme heterogeneity of these alloys. These analyses were shown to be representative of the bulk composition of the coins. The metallurgical development of the coinages was defined and showed that the earlier coinages followed a debasement trend, which was superceded by a trend of increasing copper at the expense of sliver while gold compositions remained stable. This change occurred with the appearance of the inscribed "POTTINA" coinage, Scheers 30/V. Two typologically different coinages, Scheers 16 and 18 ("Armorican Types") were found to have markedly different compositions which do not fit into the trends described above. A Flan for a gold coin, which may indicate the presence of a mint at the Martberg, was found to have an identicle weight and composition as the Scheers 30/I coins, which preceeded the majority of the coins found at the Martberg in the coin development chronology. The trace element anaylses were made by Laser Ablation-ICPMS using an AridusTM desolvating nebuliser to introduce matrix matched solution standards to calibrate the measurements, which were then normalised to 100%. Quantitative results were obtained for the following elements: Sc, Ti, Cr, Mn, Co, Ni, Cu, Zn, Se, Ru, Rh, Pd, Ag, Sb, Te, W, Ir, Pt, Pb, Bi. The remaining elements remain problematic as they produced incorrect standardisations mainly due to chemical effects in solution such as adsorption onto the beaker walls or oxidation : V, Fe, Ga, Ge, As, Mo, Sn, Re, Os, Hg. Changes in the sources of Au, Ag and Cu were observed during the development of the coinages through the variation of trace elements, which correlate positively with the major components of the coin alloys. Changes in the Pt/Au ratios show that the Scheers 23 coins contain distinctly different gold from the later coinages and that the Scheers 18 gold source was also different. Te/Ag was used to show that the Sch.23 coins also contained different silver and some subgroups were observed in the Sch. 30/V coins. A major change in copper source is indicated by the sudden increase of Sb and Ni with the introduction of the Sch. 30/V coins (POTTINA), which can be linked to a similar change in copper observed in the contemporary silver coinage, Sch. 55 (with a ring). Lead isotopic analyses were made by solution- and Laser Ablation - MC-ICP-MS, The laser technique proved to be in good agreement with the solution analyses with precisions between 1 and 0.1%o (per mil). The development of the laser method opens the way for easy and virtually non-destructive Pb isotopic determinations of ancient gold coins. The results showed that Sch. 23 is very different from the following coinages, Sch. 16 and 18 are also different, forming their own group, and all the later "Eye" staters (Sch. 30/I-VI) lie on a mixing line controlled by the addition of copper from a Mediterranean source, probably Sardinia or Spain. An indication of gold and silver sources should be possible with further analyses of the Sch. 23 and Rainbow Cup gold coins and the Sch. 54 and 55 silver coinages. Copper Isotopic analyses were made by solution- and Laser Ablation - MC-ICP-MS. Both techniques require further development to produce more reproducible results. The results show that there appears to be a trend to more positive d Cu65 values for the later coinages and that the link between the copper used in the Sch. 30/V (POTTINA) coins and the silver Sch. 55 (with a ring) coins is also shown by similarly postive d Cu65 values. The full suite of analyses were also made on samples of gold from the region. They were mostly composed of "placer gold", alluvial gold found in rivers. It was found that when a study is restricted to a limited number of deposits or areas then it is possible to distinguish between deposits based on the concentration of those elements which are least affected by transport related alteration processes. These elements include; the PGE's, due to their refractory nature, and those elements which are usually present in high enough concentrations to remain relatively unaffected, eg: Cu, Pb and Sb. Due to the nature of the coin alloy it is not possible to link the gold used in the coins studied here with gold deposits, as the large amounts of Ag and Cu, added to the coin alloys, have masked the Au signature. However, further Pb isotopic analyses of gold deposits should prove useful in determining from which regions Celtic gold was derived.
Role in routing to the plasma membrane of the L 0 domain of the multidrug resistance protein MRP1
(2003)
Die mehrfache Chemotherapieresistenz (Multidrug Resistance) beruht auf vermehrtem Transport von Xenobiotika aus der Zelle, was zu einer dramatischen Verringerung der intrazellulären Konzentration von chemotherapeutischen Substanzen führt. Dieser Effekt wird von transmembranen Transporter-Proteinen der ABC-Familie verursacht. Zu dieser Familie gehört MRP1, die eine große Vielfalt an Substraten transportieren kann. MRP1 ist ein 190 kDa Glykoprotein mit einer vermuteten Topologie, die zusätzlich zum typischen P-gp ähnlichen Kern (Delta MRP1) eine amino-proximale transmembrane Domäne aufweist, die aus fünf transmembranen Alpha-Helices besteht. Sie ist durch einen cytoplasmatischen Verbindungs-Loop (L0) mit Delta MRP1 verbunden. Wenn MRP1 in polarisierten Zellen exprimiert wird, wird es zu der basolateralen Membran geleitet. In der vorliegenden Arbeit sollte nun die Funktion des amino-terminalen Bereichs von MRP1, der aus der ersten transmembranen Domäne TMD0 und dem cytoplasmischen Verbindungs-Loop L0 besteht, durch Expression und Koexpression von diversen MRP1 Mutanten in polarisierten MDCKII Zellen untersucht werden. Es wurde gezeigt, dass in der L0 Region eine amphipathische Helix vorhanden ist, die für die Funktionalität der MRP1 notwendig ist; dass das isolierte L0-Peptid in der Lage ist, sich mit Delta MRPI zu assoziieren (dadurch erlangt das Protein wieder seine Funktion und lokalisiert sich in der basolateralen Membrane); dass TMD0L0 sich teilweise in der basolaterale Membrane befindet und dass seine Anwesenheit genügt, um die Glycosilierung (Fig. 4.17 in der Dissertation) und die Lokalisierung in der basolateralen Membrane des Delta MRP1 zu ermöglichen (Fig. 4.18 in der Dissertation); dass die Koexpression der zwei komplementären Fragmente eine wild-type-ähnliche Transportaktivität ergibt (Fig. 4.19 in der Dissertation) und dass die beiden Fragmente interagieren (Fig. 4.21 in der Dissertation). Es wurde ausserdem ein chimerisches Protein hergestellt, welches aus TMD0 von MRP1 und L0 von MRP2 besteht und in MDCKII und MDCKII-Delta MRP1 Zellen exprimiert. Es wurde festgestellt, dass das unvollständig glycosiliert ist (Fig. 4.24 in der Dissertation) und dass es sich im endoplasmatischen Reticulum lokalisiert (Fig. 425 in der Dissertation).
In dieser Arbeit wurde der chemische Ozonverlust in der arktischen Stratosphäre über elf Jahre hinweg, zwischen 1991 und 2002, mit Hilfe der so genannten "Ozon-Tracer Korrelationstechnik" (TRAC), untersucht. Bei dieser Methode werden Korrelationen zwischen Ozon und langlebigen Spurenstoffen im Verlauf des Winters im Polarwirbels beobachtet und so der jährliche akkumulierte Ozonverlust berechnet. Die Ergebnisse dieser Arbeit basieren im wesentlichen auf Messdaten der Satelliteninstrumente: HALOE (Halogen Occultation Experiment) auf UARS (Upper Atmosphere Research Satellite) und ILAS (Improved Limb Atmospheric Spectrometer) Instrument auf ADEOS (Advanced Earth Observing Satellite). Das HALOE Instrument misst seit Oktober 1991 kontinuierlich alle zwei bis drei Monate für einige Tage in höheren nördlichen Breiten. ILAS lieferte ausschließlich für den Winter 1996-97 Messungen, die über sieben Monate hinweg in hohen Breiten aufgenommen wurden. Aufgrund der eingeführten Erweiterungen und Verbesserungen der Methode in dieser Arbeit, konnte die Methode anhand einer detaillierten Studie für den Winter 1996-97 validiert werden. Die ILAS Messreihe wurde dazu verwendet, erstmals die Untersuchung der zeitlichen Entwicklung von Ozon-Tracer Korrelationen kontinuierlich für die gesamte Lebensdauer des Polarwirbels durchzuführen. Dabei wurden auch Korrelationen während der Bildung des Wirbels untersucht und im Besonderen mögliche Mischungsvorgänge zwischen Wirbelluft und Luftmassen außerhalb des Wirbels. Ausserdem wurde ein Vergleich der Ergebnisse von ILAS und HALOE Messdaten durchgeführt und Unterschiede in den Ergebnissen tiefgreifend analysiert. Basierend auf HALOE Messungen konnte die erweiterte TRAC Methode über elf Jahren hinweg angewendet werden. Damit war erstmals eine konsistente Analyse von Ozonverlust und Chloraktivierung über diesen Zeitraum möglich. Die Erweiterungen führten zu einer Verringerung und genauen Quantifizierung von Unsicherheiten der Ergebnisse. Ein deutlicher Zusammenhang zwischen meteorologischen Bedingungen, Chloraktivierung und dem chemischen Ozonverlust wurde deutlich. Weiterhin zeigte sich eine Abhängigkeit zwischen den meteorologischen Bedingungen und der Homogenität des Ozonverlustes innerhalb eines Winters, sowie der mögliche Einfluss von horizontaler Mischung auf Luftmassen in einem schwach ausgeprägten Polarwirbel. In dieser Arbeit wurde eine positive Korrelation zwischen den über die gesamte Lebensdauer des Wirbels auftretenden möglichen PSC-Flächen und den akkumulierten Ozonverlusten für die elf untersuchten Jahre deutlich. Es konnte darüber hinaus gezeigt werden, dass der Ozonverlust von deutlich mehr Einflüssen als nur von der Fläche möglichen PSC Auftretens bestimmt wird, sondern zum Beispiel von der Stärke der Sonneneinstrahlung abhängt. Außerdem lassen sich Auswirkungen von Vulkanausbrüchen, wie zum Beispiel im Jahr 1991 der des Mount Pinatubo, identifizieren.
Die Infrarotspektroskopie in Verbindung mit photoaktivierbaren Substraten wurde zur Untersuchung von Substrat-Protein-Wechselwirkungen eingesetzt. Dabei wurden Konformationsänderungen der Ca2+-ATPase des Sarkoplasmatischen Retikulums bei Bindung des Nukleotids, der Phosphorylierung der ATPase und der Hydrolyse des Phosphoenzyms beobachtet. Verwender wurden das native Substrat ATP und seine Analoga ADP, AMPPNP, 2'-deoxyATP, 3'-deoxyATP, ITP, AMP, Pyrophosphat, Ribosetriphosphat und TNP-AMP beobachtet. Diese Analoga waren an spezifischen funktionellen Gruppen des Substrats ATP modifiziert. Modifikation der 2'- und 3'-OH Gruppe des Ribosetriphosphats, der beta- und gamma-Phosphatgruppe und der Aminogruppe des Adenins reduzieren das Ausmaß an bindungsinduzierten Konformationsänderungen. Ein besonders starker Effekt wird für die 3'-OH Gruppe und die Aminogruppe des Adenins beobachtet. Dies zeigt die strukturelle Empfindlichkeit des Nukleotid-ATPase Komplexes auf einzelne Wechselwirkungen zwischen dem Nukleotid und der ATPase. Die Wechselwirkungen einer bestimmten Ligandengruppe mit der ATPase hängen von Wechselwirkungen anderer Ligandengruppen mit die ATPase ab. Die TNP-AMP Bindung verursacht teilweise gegenläufige und kleinere Konformationsänderungen verglichen mit ATP. Die Bindungweise von TNP-AMP ist unterschiedlich zu der von ATP, AMPPNP und anderen Tri- und Diphosphat Nucleotiden. Die Phosphorylierung der ATPase wurde mit ITP und 2'-deoxyATP beobachtet. Ca2E1P wurde in gleichem Ausmaß mit ITP und 2'-deoxyATP wie mit ATP akkumuliert, obwohl das Ausmaß der Konformationsänderungen bei Ca2E1P-Bildung geringer ist. Änderungen der 2'- und 3'-OH des Ribosetriphosphats und der Aminogruppe des Adenins beeinflussen die Reaktionsgeschwindigkeit der Phosphorylierung der ATPase. Es gibt keine direkte Verbindung zwischen dem Ausmaß der Konformationsänderung bei Nukleotid- Bindung und der Rate der Phosphorylierung. Das volle Ausmaß der ATP-induzierten Konformationsänderung ist nicht zwingend für die Phosphorylierung. Die Konformationen von Ca2E1N und Ca2E1P hängen vom Nukleotid ab. Dies weist darauf hin, dass die Struktur von ATPase Zuständen heterogener ist, als bisher erwartet. Die Aussagekraft und der Reichtum an Informationen in den Infrarotspektren zeigen, dass hiermit eine leistungsfähige Methode für die Untersuchung von Enzym-Substrat-Wechsel-Wirkungen und das räumliche Abtasten von Bindungstaschen zur Verfügung steht.
In this study we investigated the regulation of IL-18BPa by IFN-y in the context of colon cancer and human autoimmune diseases. IL-18BPa is a naturally occuring inhibitor that counteracts IL-18 bioactivity. By enhancing IFN-y production IL-18 has been introduced as pivotal mediator of TH1 immune responses. Indeed, many IL-18 effects are mediated by IFN-y. IL-18 bioactivity is connected with the pathogenesis of different inflammatory diseases, for instance, septic shock, colitis, Crohn's disease, myasthenia gravis, multiple sclerosis, rheumatoid arthritis, atherosclerosis, and organ transplant rejection. In addition, IL-18 has tumor-suppressive properties. IFN-y induced IL-18BPa expression was shown on protein and mRNA level in different colon carcinoma cell lines, organ cultures of colonic intestinal biopsy specimens, HaCaT keratinocytes as well as rheumatoid arthritis fibroblastlike synoviocytes (RA-FLS). The IFN-y-mediated induction of IL-18BPa appears to be a more general phenomenom. The capability of IFN-y to induce IL-18BPa also has been confirmed on the promoter level by performing luciferase reporter gene studies with two IL- 18BP promoter fragments. A GAS-site proximal to the transcription start site has been identified to be relevant for IFN-y-mediated induction of these two IL18BP promoter fragments. The induction of IL-18BPa is most likely mediated by STAT-1 in DLD-1 colon carcinoma cells. Sodium butyrate inhibited IFN-y-induced IL-18BPa expression in these cells. On the basis of our observations, we postulate a negative feedback mechanism, by which IFN-y-dependent and -independent IL-18 action might be counterregulated. In this model sodium butyrate is an additional player, that may interrupt the postulated negative feedback loop. A coculture system was performed to simulate an inflammatory TH1 response. This model which is more close to the in vivo situation, confirmed upregulation of IL-18BPa by endogenously produced IFN-y. The role of IL-18BPa is manifold and depends on IL-18 function in each particular case. In autoimmune diseases, for instance, which are often characterized by a TH1 polarized immune response, IL-18BPa might counterregulate IL-18 and/or IL-18-induced IFN-y bioactivity. Important examples are Crohn's disease and rheumatoid arthritis. In CD therapeutic use of IL-18BPa may therefore restore a hypothetically disturbed IL-18/IL-18BP balance. Concerning RA, IL-18BPa expression might contribute to protective functions of IFN-y, observed in different murine models for arthritis and in rheumatoid arthritis patients. Moreover, IL-18BPa might inhibit IL-18-mediated induction of subsequent cardinal inflammatory cytokines responsible for the pathogenesis of these diseases. Indeed, the pharmaceutical industry successfully used IL-18BP as therapeutic agent in a murine model of RA and in phase I clinical trials. On the contrary, in the context of carcinogenesis IFN-y- mediated IL-18BPa expression might be disadvantageous. By counterregulating the IL-18 arm of immune defenses against tumors, IL-18BP may have the potential to promote carcinogenesis. Our hypothesis is underlined by the observation that sodium butyrate, known to be protective in colon cancer, inhibited IFN-y-induced IL-18BPa expression. In parallel, IL-18-induced IFN-y is also responsible for iNOS induction. iNOS-derived NO provides a second possible way for inhibition of IFN-y-dependent and -independent tumor suppressive effects of IL-18. Finally, IFN-y-induced IL-18BPa expression was confirmed on the promoter level. This induction on the promoter level was associated with STAT-1 binding to the GAS element proximal to the start of transcription. It is tempting to speculate that blockage of the cytokine cascade upstream of IL-1 and TNF- a on the level of IL-18 may be of therapeutic benefit. Our data reflect the relationship between inflammation and cancer, in that inflammatory cells and cytokines found in tumors are likely to contribute to tumor growth, progression, and immunosuppression than they are to mount an effective host antitumour response.
In the recent years, high-resolution conditions have been established in solid-state NMR by the combination of magic angle spinning, state-of-the-art r.f. pulse schemes and the introduction of ultra-high magnetic fields. Similar to what is now routine in solution-state NMR, this has opened the way for structure determination by HR-SSNMR methods. Complete structural or dynamical characterization of the biomolecule of interest is most easily achieved if multiple or even uniformly [13C, 15N]-labeled versions are studied. In a first step, experiments that allow the complete assignment of the 13C and 15N resonances have been recently designed. To date, nearly complete chemical shift assignments were reported for two well-ordered proteins, the ±-spectrin SH3 domain and the Crh protein. The SSNMR analysis of the later protein has been presented in Section 4.1. For SSNMR applications, not the molecular size or solubility, but the spectral resolution can be of crucial importance. Experimental parameters and sample inherent conditions such molecular disorder may reduce the overall spectral dispersion. In these circumstances, techniques that allow for spectral simplification without the need of elaborated biochemical procedures (of isotopelabeling) are of special importance. In Section 2, several spectral editing methods have been proposed. These methods not only select resonances due to changesin the physical and chemical environment of the nucleus but they can also directly probe molecular properties such as dynamics and conformational heterogeneity. Once the chemical shifts are available for the biomolecule of interest, methods that permit to obtain structural restraints can be applied. In the case of multiply isotope labeled proteins, such techniques can in principle result in multiple structural parameters. In Section 3.1, we have shown that, similar to solution-state NMR, secondary chemical shifts can be readily employed to study the local backbone conformation. Inaddition, distance constraints between protons may be encoded in high-resolution on rare spins like 13C and 15N and measured. Finally, carbon-carbon constraints may be probed by employing frequency selective r.f. pulse schemes. These dihedral and distance constraints may subsequently lead to the determination of protein secondary to tertiary structure from a single protein sample. In Section 4.2,we have shown that high-affinity ligand binding to membrane proteins can be investigated with solid-state NMR. Here, the neuropeptide neurotensin which binds to the Gprotein coupled receptor NTS1 in sub-nanomolar affinity was investigated.Except for the case of rhodopsin, there is currently no information on the high-resolution structure of any other GPCR or a corresponding high-affinity ligand.Our SSNMR results identify, for the first time, a distinct binding mode of neurotensin that could be of considerable relevance for further pharmacological studies. As exemplified in section 4.3, HR-SSNMR based structural studies can also assist in refining existing (X-ray or solution-state NMR) membrane-protein structures. The presented results provide, for the first time, direct experimental evidence for a double occupancy of the Q0 binding site in the ubiquinone-bc1 complex and may provide the basis for the complete 3D structural determination of the ubiquinone binding pocket. Advancements regarding sample preparation (for example, including modular labeling, in vitro expression and intein technology) and improvements in NMR hardware instrumentation could open up new areas of solid-state NMR research such as the investigation of large protein-protein complexes or the complete 3D characterization of larger membrane proteins. Solid-state NMR studies of multiply-labeled biomolecules will furthermore profit from improved procedures for calculating 3D structures, in particular in the presence of ambiguousor a limited number of structural constraints. Unlike X-ray crystallography, protein motion does not hinder solid-state NMR methods. In fact, complementary to solution-state NMR, it may provide a very efficient means to study protein folding, flexibility and function under biologically relevant conditions. Hand in hand with solution-state techniques and crystallographic methods, solid-state NMR could provide insight into protein function and the chemistry of life with unprecedented accuracy and flexibility.
Im ersten Teil dieser Arbeit sind Protein-Protein Docking-Studien dokumentiert. Bis heute konnten die meisten Protein-Komplex-Strukturen nicht experimentell aufgeklärt werden, so auch die beiden oben genannten Elektrontransfer-Komplexe. Nach einem erfolgreichen Test wurden verschiedene Cytochrom c Oxidase:Cytochrom c Paare mit der gleichen Methode gedockt: COX aus Paracoccus denitrificans mit Pferdeherz Cytochrom c und COX mit dem löslichen Fragment des membrangebundenen Cytochrom C552 (beide aus P. denitrificans). Im zweiten Teil dieser Arbeit wurde die diffusive Annäherung des Cytochrom c an die Cytochrom c Qxidase mit der Brownschen Dynamik Methode simuliert. Die Diffusionsbewegung eines Brownschen Teilchens in wässriger Lösung wird durch die Langevin-Gleichung bestimmt. Der auf dieser Gleichung fußende Ermak-McCammon-Algorithmus ist Grundlage der Simulationsmethode. Die so ermittelten Raten für COX und Pferdeherz, sowie für COX und Cytochrom C552, wurden dann mit experimentell gewonnenen Raten verglichen. Da die Elektrostatik für den Annäherungsprozeß dieser Proteine eine so gewichtige Rolle spielt, wirken sich Mutationen, die mit einer Ladungsänderung einhergehen, merklich aus. Dies ist vor allem dann der Fall, wenn sich die Mutation in der Nähe der Bindungsstelle befindet. Aus dem gleichen Grund ist die Assoziationsrate auch stark von der Ionenstärke der umgebenden Lösung abhängig. Steigt die Ionenkonzentration wird die elektrostatische Komplementarität der Bindingsstellen der beiden Makromoleküle stärker abgeschirmt, und die Rate sinkt. Diese beiden relativen Trends konnten durch die Simulationen gut reproduziert und bestätigt werden. Allerdings liegen die absoluten Resultate merklich über den experimentell gemessenen Raten. Es ist sehr gut möglich, daß post-diffusive Effekte, die nicht in einer Brownschen Dynamik Simulation von starren Körpern berücksichtigt werden können, die Raten erniedrigen. Um den Einfluß der Membranumgebung auf die Wechselwirkung des Elektrontransportsystems zu untersuchen. wurde eine DPPC Doppelschicht um die Oxidase modelliert und energieminimiert. Mit Poisson-Boltzmann Rechnungen wurde das elektrostatische Potential dieses Nanosystems untersucht und mit dem der einzelnen Oxidase verglichen. Durch einen modifizierten Set-up konnten dann auch für dieses Membransystem Brownsche Dynamik Simulationen durchgeführt werden. Der Vergleich mit den vorhergehenden Simulationen ohne Membran erbrachte bemerkenswerte Ergebnisse. Während die Assoziationsraten für Pferdeherz Cytochrom c durch den Membraneinfluß erniedrigt wurden, stiegen sie im Fall des physiologischen Transferpartners c552. Pferdeherz Cytochrom c weist eine positive Nettoladung und einen ausgeprägten bipolaren Charakter auf. Eine große Zahl positiv geladener Seitenketten befindet sich auf der gleichen Hemisphäre wie die Bindungsstelle. Obwohl die DPPC Lipidmoleküle neutral sind, zeigten die Elektrostatikrechnungen, daß die Membranoberfläche abstoßend auf positive Ladungen wirkt. Da sich nun die Bindungsstelle der Oxidase für Cytochrom c nur etwa 10 Å oberhalb der Membran befindet, verringert sich die Wahrscheinlichkeit der Assoziation.
Mitogen activated protein kinases (MAPKs) are found in all eukaryotic cells and represent crucial elements in the signal transduction from the plasma membrane to the nucleus. Although a broad variety of extracellular stimuli activate MAPKs, they evoke very distinct cellular responses. The amplitude and duration of MAPK activation determine signal identity and ultimately cell fate. A tight and finely tuned regulation is therefore critical for a specific cellular response. The role and the regulation of extracellular signal-regulated kinase 5 (ERK5), a MAPK with a large and unique C-terminal tail, were studied in different cellular systems. The study highlights two aspects of ERK5 regulation: control of the phosphorylation state and regulated protein stability. In analogy to other MAPKs ERK5 is activated by dual phosphorylation of threonine and tyrosine residues in its activation motif. A first part of the study concentrates on whether and how the protein tyrosine phosphatase PTP-SL is involved in the downregulation of the ERK5 signal. The direct interaction of both proteins is shown to result in mutual modulation of their enzymatic activities. PTP-SL is a substrate of ERK5 and, independent of its phosphorylation, binding to the kinase enhances its catalytic phosphatase activity. On the other hand, interaction with PTP-SL does not only downregulate enzymatic ERK5 activity but also effectively impedes its translocation to the nucleus. The second part of this study focuses on the interaction of ERK5 with c-Abl and its oncogenic variants Bcr/Abl and v-Abl. In this study these tyrosine kinases are demonstrated to regulate ERK5 by two mechanisms: first, by induction of kinase activity and secondly, by stabilisation of the ERK5 protein. Stabilisation involves the direct interaction of unique ERK5 domains with Abl kinases and is independent of MAPK cascade activation. The level of ERK5 and its intrinsic basal activity – rather than its activation – are essential for v-Abl-induced transformation as well as for survival of Bcr/Abl-positive leukaemia cells. Stabilisation of ERK5 thus contributes to cell survival and should therefore be considered as an additional aspect in therapy of chronic myeloid leukaemia. Taken together, the results obtained in this study demonstrate that diverse pathways regulate ERK5 signalling by affecting kinase activity, localisation and protein stability. While the phosphatase PTP-SL is involved in negative regulation of ERK5, Abl kinases potently activate ERK5 and increase its half-life. Protein stabilisation thus is presented as a novel mechanism in the regulation of MAPKs.
Gegenstand dieser Arbeit sind Eigenschaften angeregter hadronischer Materie sowie physikalische Systeme, in denen diese Materie auftritt bzw. produziert wird. Die Beschreibung der stark wechselwirkenden Materie erfolgt in einem hadronischen, chiral-symmetrischen SU(3)L x SU(3)R Modell, welches die Saturierungseigenschaften von Kernmaterie und die Eigenschaften von Atomkernen reproduziert. Die Untersuchung heißer und dichter unendlicher hadronischor Materie zeigt, dass das vom Modell vorhergesagte Phasendiagramm stark von den Kopplungen der Baryonenresonanzen abhängt. Für kalte hadronische Materie ergibt die Einbeziehung des Baryonendekupletts und die Freiheit in deren Vektorkopplungen eine sehr große Bandbreite an verschiedenen Zustandsgleichungen. Für heiße hadronische Materie mit verschwindendem baryochemischen Potential zeigt sich ebenfalls eine starke Abhängigkeit der Eigenschaften hadronischer Materie von der Ankopplung der baryonischen Resonanzen. Es werden drei verschiedene Parametrisierungen betrachtet. Das resultierende Phasenübergangsverhalten variiert von einem "Crossover" über einen schwachen, zu einem doppelten Phasenübergang erster Ordnung. Es zeigt sich jedoch, dass die beobachteten Eigenschaften von Neutronensternen die Unbestimmtheit bzgl. der Vektorkopplung dieser Freiheitsgrade und damit der Zustandsgleichung deutlich verringern. Das Raum-Zeit Verhalten relativistischer Schwerionenkollisionen bei SPS- und RHIC-Energien wird mittels einer hydrodynamischen Simulation unter Benutzung der chiralen Zustandsgleichungen untersucht. Dabei spiegelt sich das unterschiedliche Phasenübergangsverhalten deutlich im Ausfrierverhalten der hadronischen Materie wider. Die im chiralen Modell berechneten Teilchenzahlverhältnisse werden mit den aus Schwerionenkollisionen von AGS- bis RHIC-Energien erhaltenen experimentellen Daten verglichen. Dabei zeigt sich, dass die verschiedenen Parametersätze des chiralen Modells und die Rechnungen für ein nichtwechselwirkendes, ideales Hadronengas eine ähnlich gute Beschreibung der gemessenen Weite liefern. Die deduzierten Ausfrierwerte für die Temperatur sind sensitiv auf das Phasenübergangsverhalten und liegen unterhalb der jeweiligen kritischen Temperatur. Die vorhergesagten Ausfriermassen sind in allen Parametrisierungen sehr ähnlich mit Abweichungen bis zu 15% von den entsprechenden Vakuumwerten. Die Untersuchung der Eigenschaften von Vektormesonen in dichter Materie erfolgt in der Mittleren-Feld- und in der HartreeNäherung. Hierbei zeigt sich eine signifikante Reduzierung der Teilchenmassen durch Vakuumpolarisationseffekte.
We consider the long-time behaviour of spatially extended random populations with locally dependent branching. We treat two classes of models: 1) Systems of continuous-time random walks on the d-dimensional grid with state dependent branching rate. While there are k particles at a given site, a branching event occurs there at rate s(k), and one of the particles is replaced by a random number of offspring (according to a fixed distribution with mean 1 and finite variance). 2) Discrete-time systems of branching random walks in random environment. Given a space-time i.i.d. field of random offspring distributions, all particles act independently, the offspring law of a given particle depending on its position and generation. The mean number of children per individual, averaged over the random environment, equals one The long-time behaviour is determined by the interplay of the motion and the branching mechanism: In the case of recurrent symmetrised individual motion, systems of the second type become locally extinct. We prove a comparison theorem for convex functionals of systems of type one which implies that these systems also become locally extinct in this case, provided that the branching rate function grows at least linearly. Furthermore, the analysis of a caricature model leads to the conjecture that local extinction prevails generically in this case. In the case of transient symmetrised individual motion the picture is more complex: Branching random walks with state dependent branching rate converge towards a non-trivial equilibrium, which preserves the initial intensity, whenever the branching rate function grows subquadratically. Systems of type 1) and systems of type 2) with quadratic branching rate function show very similar behaviour. They converge towards a non-trivial equilibrium if a conditional exponential moment of the collision time of two random walks of an order that reflects the variability in the branching mechanism is finite almost surely. The equilibrium population has finite variance of the local particle number if the corresponding unconditional exponential moment is finite. These results are proved by means of genealogical representations of the locally size-biased population. Furthermore, we compute the threshold values for existence of conditional exponential moments of the collision time of two random walks in terms of the entropy of the transition functions, using tools from large deviations theory. Our results prove in particular that - in contrast to the classical case of independent branching - there is a regime of equilibria with variance of the local number of particles.
One of the known apoptotic pathways in mammalian cells involves release of mitochondrial Cytochrome c into the cytosol. Cyt c then together with ATP or dATP induces a conformational change in the adaptator protein Apaf-1 (a homologue of the C. elegans CED4 protein) (Zou, Henzel et al. 1997), leading to its oligomerization and the recruitment of several pro-Casp-9 molecules. This protein complex assembly called "apoptosome" leads to the activation of Casp-9 which then initiates or amplifies the caspase cascade. The cell death program can be stalled at several points and we were interested in identifying new proteins inhibiting cell death downstream of Cyt c release. This thesis describes how I have screened a cDNA library derived from a pool of human breast carcinomas in a yeast-based survival screen, using the S. pombe yeast strain HC4 containing an inducible CED4 construct(James, Gschmeissner et al. 1997). The screen resulted in the identification of six proteins displaying cell death-inhibiting activity in S. pombe as well as anti-apoptotic potential in mammalian cells. Those six molecules were RoRet (Ruddy, Kronmal et al. 1997), Aven (Chau, Cheng et al. 2000), Fte-1/S3a (Kho, Wang et al. 1996), PGC2 (Padilla, Kaur et al. 2000; Goetze, Eilers et al. 2002), SAA1-2ß (Moriguchi, Terai et al. 2001) and FBP (Brockstedt, Rickers et al. 1998) of which I selected RoRet, Aven and Fte-1/S3a for further analysis. RoRet is a new anti-apoptotic molecule that can inhibit the mitochondrial pathway via its PRY-SPRY domain. RoRet does not seem to bind to Apaf-1, and does not co-localize with the activated Apaf-1/Caspase-9 complex. Aven was published to act as an anti-apoptotic protein and suggested to function via the recruitment of Bcl-XL to Apaf-1. This work shows that its C-terminal domain can bind to Apaf-1 and has a strong anti-apoptotic activity by itself. Moreover, Aven co-localizes with the activated Apaf-1/Caspase-9 complex suggesting that it is a component of the apoptosome. Furthermore, the expression of Aven is regulated in mammary glands during the pregnancy cycle. Fte-1/S3a has been already implicated in increased transformation capacity of v-Fos in fibroblasts (Kho and Zarbl 1992; Kho, Wang et al. 1996). This work shows that it has anti-apoptotic activity and can protect against Bak- and Apaf-1-induced apoptosis. It can bind directly to activated Apaf-1 at the linker domain between the WD40 repeats and the CED4-like domain, suggesting that it may protect by sequestering the activated Apaf-1 to some organelles whose nature remains to be determined. Moreover, expression studies on mRNA and protein level showed upregulation of Fte-1/S3a in colon, lung and kidney carcinoma. Hmgb1 (Flohr, Rogalla et al. 2001; Pasheva, Ugrinova et al. 2002; Stros, Ozaki et al. 2002) was identified during a survival screen performed with a NIH 3T3 mouse fibroblast cDNA library in a Bak-expressing yeast S. pombe strain. HMGB1 can protect against Bak-, UV-, FasL- and TRAIL-induced apoptosis. Significant overexpression of HMGB1 was found in breast and colon carcinoma, and elevated mRNA amounts were detected in uterus, colon and stomach carcinoma, suggesting that it may be a tumour marker (Brezniceanu et al., 2003).
Resistive Plate Chambers (RPCs) are gaseous parallel plate avalanche detectors that implement electrodes made from a material with a high volume resistivity between 10 high 7 and 10 high 12 omega cm. Large area RPCs with 2mm single gaps operated in avalanche mode provide above 98% efficiency and a time resolution of around 1 ns up to a flux of several kHz/cm high 2. These Trigger RPCs will, as an example, equip the muon detector system of the ATLAS experiment at CERN on an area of 3650 m high 2 and with 355.000 independent read out channels. Timing RPCs with a gas gap of 0.2 to 0.3mm are widely used in multi gap configurations and provide 99% efficiency and time resolution down to 50 ps. While their performance is comparable to existing scintillator-based Time-Of-Flight (TOF) technology, Timing RPCs feature a significantly, up to an order of magnitude, lower price per channel. They will for example equip the 176 m high 2 TOF barrel of the ALICE experiment at CERN with 160.000 independent read out cells. RPCs were originally operated in streamer mode providing large signals which simplifies readout electronics and gap uniformity requirements. However, high rate applications and detector aging issues made the operation in avalanche mode popular. This was also facilitated by the development of new highly quenching C2F4H2-based gas mixtures with small contents of SF6. While the physics of streamers is difficult to study, the avalanche mode opened the possibility for a detailed simulation of the detector physics processes in RPCs. Even though RPCs were introduced in the early eighties and have been (will be) used in experiments, there are still disagreements about the explanation of several aspects of the RPC performance. The high efficiency of single gap RPCs would require a large ionization density of the used gases, which according to some authors contradicts measurements. Even in the case of a large ionization density the gas gain has to be extremely large, in order to arrive at the observed RPC efficiency. This raises other questions: A very strong space charge effect is required to explain the observed small avalanche charges around 1 pC. Doubts have been raised whether an avalanche can progress under such extreme conditions without developing into a streamer. To overcome these difficulties, other processes, like the emission of an electron from the cathode, were suggested. Moreover, the shape of measured charge spectra of single gap RPCs differs largely from what is expected from the statistics of the primary ionization and the avalanche multiplication. In this thesis we discuss the detector physics processes of RPCs, from the primary ionization and the avalanche statistics to the signal induction and the read out electronics. We present Monte-Carlo simulation procedures that implement the described processes. While the fundament of the described model and some results were already published elsewhere [1], the subject of this thesis is the implementation of the space charge effect. We present analytic formulas for the electrostatic potential of a point charge in the gas gap of an RPC. These formulas were developed in collaboration with the University of Graz [2] and were published in [3, 4]. The simulation model presented in [1] is completed by the dynamic calculation of the space charge field using these formulas. Since the gas parameters like drift velocity and the Townsend and attachment coefficients depend on the electric field, they are calculated dynamically as well. The functional dependence of these parameters on the field is obtained with the simulation programs MAGBOLTZ and IMONTE. For the primary ionization parameters, we use the values that are predicted by the program HEED. While the described procedure only simulates the longitudinal avalanche development towards the anode of the RPC, we also present more dimensional models that allow a careful study of the transverse repulsive and attractive forces of the space charge fields, and of the consequences for the avalanche propagation. We shall show that the efficiencies of single gap Timing RPCs is indeed explained by the high primary ionization density (about 9.5 /cm as predicted by HEED) and a large effective Townsend coefficient (around 113 /mm as predicted by IMONTE). We show that the space charge field reaches the same magnitude as the applied electric field in avalanches at large gas gain. This strong space charge effect effectively suppresses large values for the avalanche charges. The shape of the simulated charge spectra is very similar to the measurements. Also the simulated average charges are close to the experimental results. RPCs are operated in a strong space charge regime over a large range of applied voltage, contrary to wire chambers. We apply only standard detector physics simulations to RPCs. The performance of Timing and Trigger RPCs is well reproduced by our simulations. The results concerning the space charge effect were presented and discussed at the 'RPC 2001' workshop [5] and on the '2002 NSS/MIC' conference [6].
In summary, the cooled heavy-ion beams of the ESR storage ring offer excellent experimental conditions for a precise study of the effects of QED in the groundstate of high-Z one- and two-electron ions. This has been demonstrated within the series of experiments conducted at the electron cooler device as well as at the gasjet target. In this work we have used a recently developed experimental approach to obtain the first direct measurement of the two-electron contributions to the ground state binding energy of helium-like uranium. By employing our method, all one-electron contributions to the binding energy such as finite-nuclear size corrections and the one-electron self energy cancel out completely. Note, this is a distinctive feature of this particular kind of QED test and is in contrast to all other tests of bound state QED for high-Z ions such as 1s Lamb shift (in one-electron systems), g-factor of bound electrons, or hyperfine splitting. Compared to former investigations conducted at the superEBIT in Livermore we could already substantially improve the statistical accuracy and extend studies to the higher-Z regime. Moreover, our result has reached a sensitivity on specific two-electron QED contributions. Our value agrees with the theoretical predictions within the experimental uncertainty. Similar to the superEBIT experiment possible sources of systematic errors are essentially eliminated and the final result is limited only by counting statistics. For the case of the 1s Lamb shift in hydrogen-like uranium, the achieved accuracy of +- 4.2 eV is a substantial improvement by a factor of 3 compared to the most precise value up to now [44] (see Fig. 5.6). Our result already provides a test of the first-order QED contributions at the 1.5% level and only a slight improvement is required in order to achieve a sensitivity to QED contributions beyond first-order SE and VP.
The mechanism of peptide transport has been studied on two different ABC transporters of S. cerevisiae. Thereby, the aim of this PhD thesis was to characterise the transporter function on molecular level and shed light on the physiological role of these transporters. The ABC gene YLL048 encodes a novel intracellular transporter translocating peptides from the cytosol to the lumen of the ER. Deletion of the gene resulted in loss of peptide transport activity. The transport activity was fully restored after transformation of the deletion mutant by plasmid-encoded YLL048. Studying the substrate specificity using randomized peptide libraries it was demonstrated that peptides of the size from 6 to 56 amino acids are recognized. So far, no upper limit of the substrate size was obtained. Introduction of D-amino acids in various positions of a nonamer peptide did not impair transport activity. The physiological function of YLL048p is not well understood. The gene product is not essential for cell viability as the deletion mutant did not show any growth phenotype. To examine the possibility that YLL048 encoded protein is part of a quality control of yeast cells involved in the unfolded protein response (UPR), upregulation of YLL048 transcription by heat shock and stress conditions were investigated. We could not observe an influence of stress factors on YLL048 mRNA level. Upregulation of gene expression by the transcription factors Pdr1p and Pdr3p was excluded. The ABC transporter Mdl1p has been identified as peptide transporter of the inner mitochondrial membrane. This protein is required for the export of peptides with the size of 6 to 21 amino acids from the matrix into the intermembrane space. These peptides are generated by m-AAA proteases degrading non-assembled or missfolded membrane proteins. In order to understand the transport mechanism in detail, Mdl1p was expressed in S. cerevisiae and E. coli. Partially enriched protein was reconstituted into liposomes and was active in ATP binding. The association of the NBDs has been described as a central step of the ATPase cycle of ABC transporters, but it is still controversial how both motor domains cooperate and coordinate ATP hydrolysis. To address this question, the Mdl1p-NBD was overexpressed in E. coli and purified to homogeneity. The isolated NBD was active in ATP binding and hydrolysis with a turnover of 0.5 ATP per min and a Km value of 0.2 mM. Isolated NBDs did not show cooperativity in ATPase activity. However, the ATPase activity was observed to be non-linearly dependent on protein concentration suggesting the active form of this enzyme is not a monomer. Very importantly, for the first time an ATP-induced dimer was observed after trapping the NBD by ortho-vanadate or BeFx. The nucleotide composition of the trapped intermediate state was determined and two ADP molecules were simultaneously bound per dimer. An ATP-induced dimer of the ATPase inactive mutant (E559Q) was observed already in the absence of ATPase inhibitor. The E599Q dimer contained two ATP molecules in the absence of Mg2+ at 4°C. Prolonged incubation at 30°C in the presence of Mg2+ induced a stable dimer in which one ATP and ADP molecule were trapped at the same time. Based on these experiments, a new cycle for ATPase activity of ABC transporters was proposed. Binding of ATP to two NBD monomers induces dimerization. Both nucleotides are hydrolysed sequentially. During the hydrolysis cycle the nucleotides cannot be released from the dimer. After hydrolysis of two ATP molecules the domains dissociate and start a new cycle.
Die Entwicklung der Renormierungsgruppen-Technik, die in ihrer feldtheoretischen Version auf Ideen von Stückelberg und Petermann und in der Festkörperphysik auf K.G. Wilson zurückgeht, hat wesentliche Einsichten in die Natur physikalischer Systeme geliefert. Insbesondere das Konzept der so genannten Universalitätsklassen erhellt, warum Systeme, die durch scheinbar sehr verschiedene Hamilton-Operatoren beschrieben werden, doch im Wesentlichen die selbe (Niederenergie-)Physik zeigen. Ein weiterer Grund für den Erfolg dieser Methode liegt darin begründet, dass sie in systematischer Weise unendlich viele Feynman-Diagramme aufsummiert und somit über konventionelle Störungstheorie hinaus geht. Dies spielt in der Festkörperphysik vor allem dann eine wichtige Rolle, wenn das vorliegende physikalische System stark korreliert ist. Entsprechend der Vielzahl von Anwendungsmöglichkeiten hat sich in den vergangenen Jahrzehnten eine große Bandbreite verschiedener Formulierungen der Renormierungsgruppen-Technik ergeben. Eine davon ist die sogenannte funktionale Renormierungsgruppe, die auf Wegner und Houghton zurück geht und die auch in der vorliegenden Arbeit benutzt und weiter entwickelt wurde. Wir haben hier insbesondere auf die Einbeziehung der wichtigen Reskalierungsschritte wertgelegt. Als erstes Anwendungsgebiet des neu entwickelten Formalismus wurden stark korrelierte Elektronen in einer Raumdimension ausgewählt und hier insbesondere ein Modell, das als Tomonaga-Luttinger-Modell (TLM) bezeichnet wird. Im TLM wechselwirken Elektronen mit einer strikt linearen Energiedispersion ausschließlich über so genannte Vorwärtsstreu-Prozesse. Aufgrund der Linearisierung der Energiedispersion nahe der Fermipunkte ergibt sich ein Modell, das z.B. mit Hilfe der so genannten Bosonisierungs-Technik exakt gelöst werden kann. Hauptziel der vorliegenden Arbeit ist es, die bekannte Spektralfunktion dieses Modells unter Verwendung des Renormierungsgruppen-Formalismus zu reproduzieren. Gegenüber der bisherigen Implementierung der Renormierungsgruppe, bei der lediglich der Fluss einer endlichen Anzahl von Kopplungskonstanten betrachtet wird, stellt die Berechnung des Flusses ganzer Korrelationsfunktionen eine enorme Erweiterung dar. Der Erfolg dieser Herangehensweise im TLM bestärkt die Hoffnung, dass es in Zukunft auch möglich sein wird, die Spektralfunktionen anderer Modelle mit dieser Methode zu berechnen, bei denen herkömmliche Techniken versagen.