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Capoeta damascina (Teleostei: Cyprinidae) is one of the most common freshwater fish species, found throughout the Levant, Mesopotamia, Turkey and Iran. According to the state of knowledge prior to this study, C. damascina, which is distributed over a wide range of isolated water bodies, was not a well-defined species. It was questionable whether it represents a single species or a complex of closely related species with high intraspecific and comparatively low interspecific variability. The goal of this study was to investigate the taxonomy, systematic position of the C. damascina species complex and the phylogenetic relationships among its members, based on morphological features as well as molecular phylogeny. Samples obtained from throughout the geographic range of this species complex were subjected to comparative morphological analyses in order to define, properly diagnose and separate species within the C. damascina complex. To elucidate phylogenetic relationships among members of the C. damascina species complex, samples were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (COI, n = 103) and the two adjacent divergence regions (D1-D2) of the nuclear 28S rRNA genes (LSU, n = 65). Based on morphological and molecular genetic data, six closely related species were recognized within the C. damascina complex: C. buhsei, C. caelestis, C. damascina, C. saadii, C. umbla and an undescribed species, Capoeta sp.1. Analyses of the morphometric and meristic data obtained in this study revealed phenotypic variability among the various populations within a species and among the different species. Such differences in morphological characters reflect genetic differences, environmentally induced phenotypic variation or both, as the meristic phenotype of fish is sometimes a consequence of environmental parameters acting on the genotype. Based on phylogenetic analyses, two main lineages were identified within the C. damascina species complex: a western lineage represented by C. caelestis, C. damascina and C. umbla and an eastern lineage represented by C. buhsei, C. saadii and Capoeta sp.1. The close phylogenetic relationships between C. damascina and C. umbla and the sharing of same haplotypes between one specimen of C. damascina from Euphrates and another of C. umbla from Tigris reflect one of three possibilites: recent speciation, mitochondrial introgression or a combination of both. The results obtained in this study indicate that speciation of the above-mentioned six taxa is quite recent and that their dispersal and present-day distribution can be related to Pleistocene events. The drying out of the Persian Gulf, probably during one of the first glacials of the Pleistocene, led the ancestor of the C. damascina species complex in Mesopotamia to reach the rivers of the Gulf and of Hormuz basins and differentiate there, giving rise to the eastern lineage (ancestor of C. buhsei, C. saadii and Capoeta sp.1). As connections presumably existed among the different river drainages and basins in Iran during the wet periods of the Pleistocene, the ancestor of C. buhsei, C. saadii and Capoeta sp.1 was subsequently able to colonize the various Iranian drainages and differentiate there, giving rise to C. buhsei, C. saadii and Capoeta sp.1. After the separation from the eastern lineage, the western lineage, represented by the ancestor of C. damascina, C. umbla and C. caelestis, most likely reached the Levant from the Tigris-Euphrates system during the Pleistocene glacials, when river connections existed in the regions of the upper courses of Ceyhan Nehri (southern Turkey) and some western affluents to the Euphrates. From Ceyhan Nehri, it dispersed into other rivers in southern Turkey during Pleistocene periods of low sea levels until it reached Göksu Nehri and evolved into C. caelestis. The sister population differentiated into C. damascina and C. umbla. Based on the results obtained in this study, it is likely that C. damascina colonized the Levant and southern Turkey during the Pleistocene glacials. This is well supported by the low genetic variability among the C. damascina populations. Direct connections existed among the river drainages in the Levant during the Pleistocene periods of low sea level, thus serving as a pathway for the dispersal of C. damascina. The results of this study provide a coherent picture of the taxonomic position, phylogenetic relationships and evolutionary history of the C. damascina species complex and explain present patterns of distribution considering paleogeographic events.
The current work investigated the association of trait anxiety and the neural efficiency of cognitive processing for affectively neutral (not threat-related) information. In a sample of 46 healthy volunteers, three fMRI experiments were conducted to test the prediction derived from attentional control theory (Eysenck et al., 2007) that high as compared to low trait-anxious individuals expend more neural effort on tasks requiring the top-down control of attention to reach a given level of performance. In a colour-word Stroop task requiring the inhibition of irrelevant stimulus information and associated responses as well as in a working-memorymanipulation task requiring the shifting of attention between items in working memory, trait anxiety (as measured with the State-Trait Anxiety Inventory; Spielberger et al., 1970) was positively associated with task-related increases in the activation of two adjacent regions in the right dorsolateral prefrontal cortex (DLPFC). The finding that along with a stronger activation of this brain region commonly implicated in top-down control processes, the high-anxious subjects showed equal (working memory manipulation) or worse (Stroop) performance when compared to low-anxious subjects, does support the assumption that processing is less efficient in the high anxious. However, in contrast to the predictions, trait anxiety did not show a significant association with task-related brain activation in a task-switching paradigm requiring shifting between task sets. It is discussed how different attentional control demands of the task may account for differences in the effects of trait anxiety on overt behavioural performance and underlying neural processes. In addition to DLPFC activation, trait anxiety modulated the functional connectivity of distributed regions involved in processing of the Stroop and the working-memory-manipulation task. It is discussed how the observed differences in regional DLPFC activation and network connectivity relate to each other. A possible interpretation suggests that activation increases in the DLPFC reflect an attempt to compensate for suboptimal connectivity by investing more effort in prefrontally supported control processes. Overall, the current work shows an association of trait anxiety with the neural efficiency of cognitive processing in affectively neutral tasks involving attentional control. Furthermore, it suggests that investigations of neural efficiency should take into account difference in functional integration in addition to regional activation.
This thesis is based on the following publications (in chronological order): 1. Biegel, E., S. Schmidt & V. Müller (2009) Genetic, immunological and biochemical evidence for a Rnf complex in the acetogen Acetobacterium woodii. Environ. Microbiol. 11: 1438-1443. My contribution: Amplification, sequence determination and analysis of Rnf homologues, enrichment of the Rnf complex 2. Biegel, E. & V. Müller (2010) Bacterial Na+-translocating ferredoxin:NAD+ oxidoreductase. Proc. Nat. Acad. Sci. U. S. A. 107: 18138-18142. My contribution: I designed and performed all experiments shown and interpreted the data. 3. Biegel, E., S. Schmidt, J. Gonzáles & V. Müller (2010) Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes. Cell. Mol. Life Sci., in press. DOI: 10.1007/s00018-010-0555-8. My contribution: I was involved in writing all chapters except chapters: „phylogenetic analyses of rnf genes“ and „distribution of rnf genes“. 4. Biegel, E. & V. Müller (2010) A Na+-translocating pyrophosphatase in the acetogenic bacterium Acetobacterium woodii. J. Biol. Chem., in press. DOI: 10.1074/jbc.M110.192823. My contribution: I designed and performed all experiments shown and interpreted the data.
Effort estimates are of utmost economic importance in software development projects. Estimates bridge the gap between managers and the invisible and almost artistic domain of developers. They give a means to managers to track and control projects. Consequently, numerous estimation approaches have been developed over the past decades, starting with Allan Albrecht's Function Point Analysis in the late 1970s. However, this work neither tries to develop just another estimation approach, nor focuses on improving accuracy of existing techniques. Instead of characterizing software development as a technological problem, this work understands software development as a sociological challenge. Consequently, this work focuses on the question, what happens when developers are confronted with estimates representing the major instrument of management control? Do estimates influence developers, or are they unaffected? Is it irrational to expect that developers start to communicate and discuss estimates, conform to them, work strategically, hide progress or delay? This study shows that it is inappropriate to assume an independency of estimated and actual development effort. A theory is developed and tested, that explains how developers and managers influence the relationship between estimated and actual development effort. The theory therefore elaborates the phenomenon of estimation fulfillment.
This thesis consist of three chapters of which each investigates a topic from financial and monetary economics. In the first chapter a novel method to analyze the monetary policy of central banks is presented. In the second chapter (joint work with Professor Michael Binder, Goethe-University Frankfurt) the effects of conditional loan programs of the International Monetary Fund (IMF) on participating countries' output growth are investigated. In the third chapter (joint work with Professor Jan Pieter Krahnen, Goethe-University Frankfurt) a network model of interconnected bank balance sheets which gives rise to systemic risk is developed and used to analyze the implications of a bank levy related to banks' contribution to systemic risk. All three chapters give important insights to the policy design of macroeconomic institutions such as central banks, the IMF, and agencies charged with macroprudential supervision.
Conclusion: Proteins containing a Jumonji C (JmjC) domain appear in almost all living organisms and catalyze a variety of oxidation reactions. Therefore, they are important regulators in many biological processes such as proliferation and differentiation. They act either as protein hydroxylases, histone demethylases or by regulate mRNA splicing. Given the fact that some of the JmjC domain-containing proteins are shown to be upregulated in response to hypoxia as well as the dependency of JmjC domain catalytic activity on oxygen led to the assumption of an involvement in angiogenesis. For Jmjd6, a member of the JmjC domain-containing protein family, a regulatory involvement in mRNA splicing has been shown. The Jmjd6-/- mouse dies perinatally due to several severe organ malformations, especially in the heart. Despite the pale appearance, the growth retardation and the cardiac defects, it is unclear whether these mice exhibit defects of cells comprising the vasculature. Therefore, the involvement of Jmjd6 in angiogenesis was examined in vitro using angiogenesis assays as well as in vivo using the Jmjd6+/- mouse. An siRNA-mediated knockdown of Jmjd6 in ECs significantly impaired the formation of capillary-like networks in the tube formation assay as well as sprouting in the spheroid assay. Moreover, after siRNA-mediated knockdown of Jmjd6 in ECs cell migration was significantly reduced. These findings were confirmed in the matrigel plug assay in vivo. Implanted matrigel plugs of Jmjd6+/- mice exhibited significantly less perfused vessels compared to wildtype littermates. Furthermore, cultured lung ECs from Jmjd6+/- mice exhibited impaired network forming activity ex vivo compared to cells isolated from wildtype littermates. To elucidate the mechanisms underlying the requirement of Jmjd6 in angiogenesis, an Affymetrix exon-array was performed, which allows detection of changes in gene expression as well as splicing. The siRNA-mediated knockdown of Jmjd6 altered the expression of genes known to play a role in vascular biology. The bioinformatic assessment of alternative splice variants revealed that Jmjd6 silencing affects the splicing of the VEGF receptor 1 (Flt1). Differential splicing of Flt1 was shown to generate a short and soluble form of Flt1 (sFlt1), which sequestrates VEGF and PlGF, and thereby inhibits angiogenesis. In particular, a significant increase in sFlt1 expression was observed. Jmjd6 was recently reported to hydroxylate the splicing factor U2AF65. Therefore, we investigated whether U2AF65 might mediate Flt1 splicing and binds to Flt1 mRNA. Indeed, U2AF65 co-immunoprecipitated with Jmjd6 in ECs, while an interaction of U2AF65 with sFlt1 was demonstrated. Moreover, inhibition of Jmjd6 catalytic function by reduced oxygen concentration altered splicing of Flt1 resulted in an increase of the sFlt1 splice variant. Finally, saturating concentrations of VEGF or PlGF or neutralizing antibodies against sFlt1 significantly reduced the inhibition of sprouting caused by Jmjd6 knockdown in vitro.
Collectively, our results indicate that Jmjd6 has an essential role in the oxygen-dependent regulation of angiogenesis by controlling the splicing of Flt1 mRNA, thereby adjusting the generation of the anti-angiogenic short splice variant sFlt1. Several publications demonstrated a major importance for sFlt1 as a biomarker for many severe human diseases such as preeclampsia, sepsis, cancer, myocardial infarction as well as chronic heart failure. Therefore, the identification of the molecular mechanism behind the generation of sFlt1 might enable the development of new or more precise clinical markers for the diagnosis of the corresponding diseases. Furthermore, the discovery of the enzymes involved in the generation of sFlt1 provides further possibilities to modulate sFlt1 levels and thereby may potentially gives rise to the development of new therapies.
According to the World Health Organization (WHO) bacterial resistance to antibiotic drug therapy is emerging as a major public health problem around the world. Infectious diseases seriously threaten the health and economy of all countries. Hence, the preservation of the effectiveness of antibiotics is a world wide priority. The key to preserving the power of antibiotics lies in maintaining their diversity. Many microorganisms are capable of producing these bioactive products, the so called antibiotics. Specifically in microorganisms, polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS) produce these natural bioactive compounds. Besides being used as antibiotics these non-ribosomal peptides and polyketides display an even broader spectrum of biological activities, e.g. as antivirals, immunosuppressants or in antitumor therapy. The wide functional spectrum of the peptides and ketides is due to their structural diversity. Mostly they are cyclic or branched cyclic compounds, containing non-proteinogenic amino acids, small heterocyclic rings and other unusual modifications such as epimerization, methylation, N‐formylation or heterocyclization. It is has been shown that these modifications are important for biological activity, but little is known about their biosynthetic origin.
PKS and NRPS are multidomain protein assembly lines which function by sequentially elongating a growing polyketide or peptide chain by incorporating acyl units or amino acids, respectively. The growing product is attached via a thioester linkage to the 4’-phosphopantetheine (4’-Ppant) arm of a holo acyl carrier protein (ACP) in PKSs or holo peptidyl carrier protein (PCP) in NRPSs and is passed from one module to another along the chain of reaction centers. The modular arrangement makes PKS and NRPS systems an interesting target for protein engineering. More than 200 novel polyketide compounds have already been created by module swapping, gene deletion or other specific manipulations. Unfortunately, however, engineered PKS often fail to produce significant amounts of the desired products. Structural studies may faciliate yield improvement from engineered systems by providing a more complete understanding of the interface between the different domains. While some information about domain-domain interactions, involving the most common enzymatic modules, ketosynthase and acyltransferase, is starting to emerge, little is known about the interaction of ACP domains with other modifying enzymes such as methyltransferases, epimerases or halogenases.
To further improve the understanding of domain-domain interactions this work focuses on the curacin A assembly line. Curacin A, which exhibits anti-mitotic activity, is from the marine cyanobacterium Lyngbya majuscula. This outstanding natural product contains a cyclopropane ring, a thiazoline ring, an internal cis double bond and a terminal alkene. The biosynthesis of curacin A is performed by a 2.2 Mega Dalton (MDa) hybrid PKS-NRPS cluster. A 10-enzyme assembly catalyzes the formation of the cyclopropane moiety as the first building block of the final product. Interestingly, for these enzymes the substrate is presented by an unusual cluster of three consecutive ACPs (ACPI,II,III). Little is known about the function of multiple ACPs which are supposed to increase the overall flux for enhanced production of secondary metabolites.
The first task in this work was to elucidate the structural effect of the triplet ACP repetition by nuclear magnetic resonance (NMR). The initial data show that the excised ACPI, ACPII or ACPIII proteins resulted in [15N, 1H]-TROSY spectra with strong chemical shift perturbations (CSPs), suggesting an effect on the structure. The triplet ACP domains display a high sequence identity (93- 100%) making structural investigation using usual NMR techniques due to high peak overlap impossible. To enable the investigation of the triplet ACP in its native composition we developed a powerful method, the three fragment ligation. Segmental labeling allows incorporating isotopes into one single domain in its multidomain context. As a result we could prepare the triplet ACP with only one domain isotopically labeled and therefore assign the full length protein. In this way our method paved the way to study the structural effects of the triplet ACP repetition. We could show unexpectedly, that, despite the fact that the triplet repeat of CurA ACPI,II,III has a synergistic effect in the biosynthesis of CurA, the domains are structurally independent.
In the second part of this work, we studied the structure of the isolated ACPI domain. Our results show that the CurA ACPI undergoes no major conformational changes upon activation via phosphopantetheinylation and therefore contradicts the conformational switching model which has been proposed for PCPs. Further we report the NMR solution structures of holo-ACPI and 3-hydroxyl-3-methylglutaryl (HMG)-ACPI. Data obtained from filtered nuclear overhauser effect (NOE) experiments indicate that the substrate HMG is not sequestered but presented on the ACP surface.
In the third part of this work we focussed on the protein-protein interactions of the isolated ACPI with its cognate interaction partners. We were especially interested in the interaction with the halogenase (Cur Hal), the first enzyme within the curacin A sub-cluster, acting on the initial hydroxyl-methyl-glutaryl (HMG) attached to ACPI. Primarily we studied the interaction using NMR titration and fluorescence anisotropy measurements. Surprisingly no complex between ACPI and Cur Hal could be detected. The combination of an activity assay using matrix-assisted laser desorption/ionization (MALDI) mass spectroscopy and mutational analysis revealed several amino acids of ACPI that strongly decrease the activity of CurA Hal. Mapping these mutations according to their effect on the Cur Hal activity onto the structure of HMG-ACPI displays that these amino acids surround the substrate and form a consecutive surface. These results suggest that this surface is important for Cur Hal recognition and selectivity. Our research presented herein is an excellent example for protein-protein interactions in PKS systems underlying a specific recognition process.
The ubiquinol:cytochrome c oxidoreductase is a key component of several aerobic respiratory chains in different organisms. It is an integral membrane protein complex, made up of three catalytic subunits (cytochrome b, cytochrome c1 and Rieske iron sulphur protein) and up to eight additional subunits in mitochondria. The complex oxidizes one quinol molecules and reduces two cytochrome c during the Q cycle, originally described by Peter Mitchell. Electrons are split between the low and the high potential chain and protons are released on the positive side of the membrane, increasing the protonmotive force needed by the ATP-synthase for energy transduction. The cytochrome bc1 complex from P. denitrificans is a perfect model for structural and functional studies. Bacteria are easy to grow and the genetic material is readily accessible for genetic manipulation. Moreover, the P. denitrificans aerobic respiratory chain is very close to the mitochondrial one: the complexes involved in electron transfer resemble the ones found in mitochondria, but lack most of the additional subunits. As a unique feature, P. denitrificans has a strongly acidic domain at the N-terminal region of the cytochrome c1, a sequence of 150 aminoacids which does not correlate with any known protein. An analogous composition can be found in the eukaryotic cytochrome bc1 complex as a part of an accessory subunit, proposed to be involved in facilitating electron transfer between the complex and the electron acceptor cytochrome c. In order to study the function of this domain in the P. denitrificans cytochrome bc1 complex, a deletion mutant has been previously cloned and modified with an affinity tag as a C-terminal extension of cytochrome b. The complex is purified by affinity chromatography and characterized by steady-state kinetics using not only horse heart cytochrome c but also the endogenous electron acceptor, the membrane bound cytochrome c552, employed here as a soluble fragment. Steady–state kinetics indicate that the deletion of the long acidic domain had effects neither on the turnover rate nor on the apparent affinity for the substrate. To understand wether the deletion affects the reaction between the cytochrome bc1 complex and the substrate, laser flash photolysis experiments are performed, showing that the interaction observed was not changed in the complex missing the acidic domain. The results presented in this work confirm the ones previously obtained by Julia Janzon using soluble fragments of the same interaction partners. The deletion, however, affected the oligomerization state of the complex, as shown by LILBID (Laser Induced Liquid Bead Ion Desorption) analysis. The wild type complex has a tetrameric structure, better described as a “dimer of dimers”. The deletion of the acidic domain on the cytochrome c1 results in the separation of the two dimers, yielding the canonical dimer. Therefore, the complex deleted in the acidic domain is used for cloning and expression of a heterodimeric complex, containing an inactivating mutation in the quinol oxidation site in only one monomer, thus allowing a selective switch-off for half the complex. Such a complex is needed for the verification of an internal regulation mechanism, the half-of-the-sites reactivity. According to it, the dimeric structure of the cytochrome bc1 complex has functional implications, since the two monomers can communicate and work in a coordinated manner. This approach confirms that substrate oxidation does effectively take place only in one of the two monomers constituting the dimer, and that the binding of substrate at the Qo and Qi site regulates the switch between active and inactive monomer. Moreover, this mechanism works also as an effective protection against the reaction of quinone intermediates with oxygen and the formation of reactive oxygen species (ROS), responsable for cellular aging. The motion of the ISP head domain is also addressed in this work; in particular the mechanism which regulates the movements towards the cytochrome c1 and the electron bifurcation at the quinol oxidation site. Laser flash kinetics in presence of several inhibitors and the substrate allow studying the response of the ISP to the binding of different species at the quinol oxidation site. The binding of ligand at the Qo site in the complex triggers the conformational switch in the ISP head domain, supporting the mechanism proposed in the literature according to which the Qo site is able to “sense” the presence of substrate and transfer the information to the ISP, regulating its mobility. The internal electron pathway between the ISP and the cytochrome c1 has been analyzed also by stopped-flow kinetics, in presence and absence of inhibitors. The results indicate that two kinetic phases describe the reduction of cytochrome c1 by the ISP, and a model for the simulation of the data is proposed.
Nanotechnology is a rapidly developing branch of science, which is focused on the study of phenomena at the nanometer scale, in particular related to the possibilities of matter manipulation. One of the main goals of nanotechnology is the development of controlled, reproducible, and industrially transposable nanostructured materials.
The conventional technique of thin-film growth by deposition of atoms, small atomic clusters and molecules on surfaces is the general method, which is often used in nanotechnology for production of new materials. Recent experiments show, that patterns with different morphology can be formed in the course of nanoparticles deposition process on a surface. In this context, predicting of the final architecture of the growing materials is a fundamental problem worth studying.
Another factor, which plays an important role in industrial applications of new materials, is the question of post-growth stability of deposited structures. The understanding of the post-growth relaxation processes would give a possibility to estimate the lifetime of the deposited material depending on the conditions at which the material was fabricated. Controllable post-growth manipulations with the architecture of deposited structures opens new path for engineering of nanostructured materials.
The task of this thesis is to advance understanding mechanisms of formation and post-growth evolution of nanostructured materials fabricated by atomic clusters deposition on a surface. In order to achieve this goal the following main problems were addressed:
1. The properties of isolated clusters can significantly differ from those of analogous clusters occurring on a solid surface. The difference is caused by the interaction between the cluster and the solid. Therefore, the understanding of structural and dynamical properties of an atomic cluster on a surface is a topic of intense interest from the scientific and technological point of view. In the thesis, stability, energy, and geometry of an atomic cluster on a solid surface were studied using a liquid drop approach which takes into account the cluster-solid interaction. Geometries of the deposited clusters are compared with those of isolated clusters and the differences are discussed.
2. The formation scenarios of patterns on a surface in the course of the process of cluster deposition depend strongly on the dynamics of deposited clusters. Therefore, an important step towards predicting pattern morphology is to study dynamics of a single cluster on a surface. The process of cluster diffusion on a surface was modeled with the use of classical molecular dynamics technique, and the diffusion coefficients for the silver nanoclusters were obtained from the analysis of trajectories of the clusters. The dependence of the diffusion coefficient on the system’s temperature and cluster-surface interaction was established. The results of the calculations are compared with the available experimental results for the diffusion coefficient of silver clusters on graphite surface.
3. The methods of classical molecular dynamics cannot be used for modeling the self-assembly processes of atomic clusters on a surface, because these processes occur on the minutes timescale, what would require an unachievable computer resource for the simulation. Based on the results of molecular dynamics simulations for a single cluster on a surface a Monte-Carlo based approach has been developed to describe the dynamics of the self-assembly of nanoparticles on a surface. This method accounts for the free particle diffusion on a surface, aggregation into islands and detachment from these islands. The developed method is allowed to study pattern formation of structures up to thousands nm, as well as the stability of these structures. Developed method was implemented in MBN Explorer computer package.
4. The process of the pattern formation on a surface was modeled for several different scenarios. Based on the analysis of results of simulations was suggested a criterion, which can be used to distinguish between different patterns formed on a surface, for example: between fractals or compact islands.This criteria can be used to predict the final morphology of a growing structure.
5. The post-growth evolution of patterns on a surface was also analyzed. In particular, attention in the thesis is payed to a systematical theoretical analysis of the post-growth processes occurring in nanofractals on a surface. The time evolution of fractal morphology in the course of the post-growth relaxation was analyzed, the results of these calculations were compared with experimental data available for the post-growth relaxation of silver cluster fractals on graphite substrate.
All the aforementioned problems are discussed in details in the thesis.
Almost two decades ago, microRNAs were discovered as novel posttranscriptional regulators of gene expression. Since then, research efforts have uncovered their involvement in the control of various cellular processes including migration, proliferation and cell survival. Even more complex events, such as the formation of new blood vessels or organ development, have been shown to be tightly regulated and orchestrated by microRNAs. Due to their crucial regulatory role in tissue homeostasis in vertebrates, it does not come as a big surprise that dysregulated microRNA ex-pression is associated with pathology of diverse diseases. In this regard, the miR-17-92 cluster is a prime example since it has become famous for its amplified expression in tumours and its on-cogenic potential. Our lab demonstrated the expression of the members of the miR-17-92 cluster, namely miR-17, -18a, -19a, -20a, -19b and -92a, in endothelial cells and provided evidence for the anti-angiogenic activity of miR-92a in ECs as well as its important regulatory role in tissue re-covery after ischemia. In this work we addressed the function of the remaining members of the miR-17-92 cluster, i.e. miR-17, miR-18a, miR-19a and miR-20a, in endothelial cells and angiogenesis. Surprisingly, the individual members all displayed anti-angiogenic properties in endothelial cells in vitro, although overexpression of the whole cluster in transformed colonocytes was shown to promote tumour angiogenesis in a mouse model. In this context, we provide evidence that the individual miRs differentially affect the paracrine angiogenic activity of endothelial and tumour cells. Moreover, Antagomir-mediated inhibition of miR-17/20 in a mouse tumour model did not affect tumour angi-ogenesis, although miR-17/20 inhibition profoundly increased vascularization of Matrigel plugs. Thus, our research efforts suggest a differential involvement of the members of the miR-17-92 cluster in physiological and tumour angiogenesis. Additionally, we identified Janus kinase (JAK) 1 as a novel miR-17 target in endothelial cells and demonstrated the involvement of JAK1 in angio-genesis and in the phosphorylation of STAT3 in response to different cytokines in vitro. Overall, inhibition of specific members of the miR-17-92 cluster might represent an attractive therapeutic strategy to enhance angiogenesis in ischemic diseases. In the second part of the present work we investigated the therapeutic value of Antagomir-mediated microRNA inhibition in animal models of pulmonary arterial hypertension. Collectively, inhibition of miR-17 by the respective Antagomir revealed a significant improvement of pulmonary hemodynamics and cardiac function in both the chronic hypoxia mouse model and the mono-crotaline-induced lung injury rat model. Histomorphometric analysis of the lungs of the pulmonary hypertensive mice and rats uncovered a significant reduction of disease associated musculariza-tion of pulmonary arteries in Antagomir-17 treated animals compared to the control animals indicating interference with smooth muscle cell proliferation or survival. Probing of lung tissue of the pulmonary hypertensive rats for selected miR-17 targets uncovered a profound increase in the expression of the cyclin dependent kinase inhibitor p21 in the Antagomir-17 treated rats suggest-ing that inhibition of miR-17 impairs proliferation by impeding cell cycle progression. Analysis of miR-17 function in human smooth muscle cells in vitro corroborated the results from the animal experiments by demonstrating pro-proliferative activity of miR-17 and decreased levels of p21 in these cells. Collectively, our results indicate that Antagomir-17 improves pulmonary hemodyna-mics and cardiac function by interfering with vascular remodelling within the lung. Hence, inhibi-tion of miR-17 might be of therapeutic value to ameliorate the disease pattern in pulmonary arte-rial hypertension. In summary, the present work provides insights into the regulatory functions of members of the miR-17-92 cluster, especially miR-17, in blood vessels and suggests that specific inhibition of members of the miR-17-92 cluster might be a novel option to treat vascular diseases.
Purpose: The aim of this retrospective study is to evaluate the long term implant survival at 5 years, periimplantary conditions and prosthetic maintenance requirements for implant supported mandibular removable dentures retained on only 2 Ankylos® implants placed interforaminally in the mandible and using only conical double crown attachments. Materials and methods: Using the database at the Faculty of Dentistry, University of Frankfurt a selection process was performed to choose patients receiving only 2 Ankylos® implants placed interforaminally in the mandible and using only conical double crown attachments. Implant survival, periimplant condition (periodontal bleeding, plaque index and probing depth), bone loss (from panoramic radiographs) and mobility (using Periotest®) were monitored annually following implant loading. In addition a detailed prosthetic maintenance list was created for each patient based on their yearly checkups and emergency appointments. 37 patients with edentulous mandibles (34 with complete dentures in the upper jaw and 3 with tissue-tooth borne coverdentures) received 2 interforaminal Ankylos® implants (67 in the canine region, 7 in 2nd incisor region). Results: Mean Periotest® values at 5 years (-1.97 ±2.24) were lower than at loading (-1.47 ±2.33). A drop was seen in the Periotest® readings after the first year of loading. The decrease in mean Periotest® values between PTV5 and PTV 1 were not statistically significant (Tukey-Kramer test: p>0.05)
14 patients (37.8%) displayed no resorption at all with an average of 0.801 mm mesially and 0.807mm distally after 5 years. The most increase in bone loss was seen after the first year of loading. There was a gradual increase in bone resorption after the first year of loading. The differences between both distal and mesial bone resorption level at five years and at one year after loading are not significant (Tukey-Kramer test: p<0.05) Plaque and bleeding index values were low at a mean of 0.97 ±0.86 and 0.59 ±0.77 respectively after 5 years of loading. The increase from the first year of loading till the 5th year of loading was significantly higher for plaque measurements but not for bleeding measurements (Tukey-Kramer Test: p<0.05 and p>0.05 respectively). Mean probing depth values were higher after 5 years (2.61 ±0.92 mm) in comparison to the values at loading (2.15 ±0.75 mm). The difference between average values at year 5 and year 1 was statistically significant (Tukey-Kramer test: p<0.05). The most occurring form of maintenance was minor adjustments such as pressure point (15 patient or 40,5%) and relining 11 patients or 29.7%). Teeth breaking off the denture were less common (4 patients or 10.8%). 5 decementations of primary crowns occurred in 4 patients (10.8%) within the 5 year observation time. Other major complications were 4 loose abutments in 3 patients (8.1%), 3 decementations of secondary copings in 3 patients (8.1%) and 1 case (2.7%) in which the prosthetic metal framework fractured. No fracture of abutments or primary crowns occurred during the investigation. Implant survival was 100% percent after 5 years ,1 implants did not fulfil Albrektsson’s success criteria and showed more than 0.2 mm of bone loss per year after the first year of loading with the first year giving a success rate of 98.8%. Conclusion: In conclusion this study has demonstrated that patients have a wider variety of options when it comes to choosing a reliable prosthesis in the lower jaw. Patients with financial limitations can be provided with a reliable prosthetic option using removable dentures retained by conical double crown attachments on 2 implants. The requirements for such a construction are a mechanically stable implant system and a mechanically stable framework. When these prerequirments are fulfilled, the patient can be satisfied with a prosthesis of superior quality to other attachment types and the dentist can rely on the fact that frequent maintenance which costs time and money can be eliminated or at least reduced. Through further innovation this type of construction can also reach patients who are lower down on the economic scale such as elderly patients and retirees.
Protein translocation across the chloroplast membrane is mediated by molecular machinery composed of protein complexes termed the TOC/TIC (the outer/inner envelope chloroplasts translocases). This translocation process is regulated by metabolic energy in form of GTP and ATP and is influenced by the lipid composition of the membrane. The ability to study the function of a single complex “TOC” in vitro using purified protein or purified chloroplast outer envelope vesicles has been instrumental for our understanding of the mechanism underlying this process.
Indeed, the TOC complex has been purified by previously established procedures. However its functional and structural analyses are impaired by the limited yield of purified protein. Therefore, protocols for native TOC complex purification are described here. The complex isolation is achieved by direct biochemical treatment of biological membrane hosting this complex or by tandem affinity purification of modified protein complex components from generated transgenic plants.
Furthermore, in this thesis, radioactive based in vitro import assays are described, namely those that allow monitoring translocation activity across the outer envelope of chloroplast. Based on the analysis of knock-out plants and isolated complexes it was previously suggested that lipid dependence of protein translocation might exist. Thus, the question was raised whether the lipid composition of the membrane has a direct influence on the behavior and functionality of the TOC translocon, or whether additional components of the chloroplast membrane account for the observed effect in vivo. To answer this question, a technique for vesicle fusion was developed. The principal aim was to explore the effect of an exchange of the lipid environment surrounding the complex translocon. This method helped to demonstrate that the SQDG and PI act stimulatory on the translocation across the outer envelope of chloroplast, whereas DGDG exhibits an inhibitory effect on TOC complex functionality.
Within the present work, photodissociation reactions on 100Mo, 93Mo and 92Mo isotopes were studied by means of the Coulomb dissociation method at the LAND setup at GSI. Experimental data on these isotopes are important to explain the problem of the underproduction of the lighter p-nuclei - 92; 94Mo - within the models of the p-process nucleosynthesis. The reaction rates used in the nucleosynthesis calculations are usually obtained within the framework of the statistical model. In order to verify the model predictions and reduce the uncertainties, experimental measurements of the reaction cross sections are required. In particular, the data on (γ,n) reactions are of interest, since these reactions were shown to dominate the p-process flow in the molybdenum mass region.
As a result of the analysis of the present experiment, integrated Coulomb excitation cross sections of the 100Mo(γ,n), 100Mo(γ,2n), 93Mo(γ,n) and 92Mo(γ,n) reactions were determined. The measurement of the 93Mo isotope is particularly important, since this nucleus is unstable, and the corresponding cross section has not been measured before.
It should be emphasized that Coulomb dissociation is a unique tool to study photoninduced reactions on unstable nuclei, which is especially relevant in the context of nucleosynthesis network calculations. However, because of to the complexity of the data analysis procedure and a number of model assumptions that are required in order to extract the Coulomb excitation cross section from the data, one of the main aspects of this thesis was to verify the method by comparing the results with the previously published data obtained with real photon beams. Integrated cross sections of the 100Mo(γ,n) and 100Mo(γ,2n) reactions were directly compared to the data by Beil et al., obtained at Saclay with photons from positron annihilation, while an indirect comparison could be performed with a recent photoactivation measurement by Erhard and co-workers. A reasonable agreement was observed for the 1n channel: a scaling factor of 0.8 ± 0.1 between our result and Beil et al. data is consistent with the scaling factor of 0.89±0.09 reported by Erhard et al. between their data and Beil et al. data. Both results are in agreement with the scaling factor of 0.85 ± 0.03 recommended by Berman et al. for the data measured at Saclay on nuclei in the respective mass region. A somewhat lower factor of 0.61 ± 0.09 between the present data and Beil et al. data was obtained for the 2n channel. The discrepancy might be explained by both the substantial efficiency correction that has to be applied to the LAND data in the two-neutron case, as well as by an insufficiently accurate assumption that the Saclay neutron detector efficiency is energy- and multiplicity- independent.
A second important topic of the present thesis is the investigation of the efficiency of the CsI gamma detector. The calorimetric information that it delivers is essential to reconstruct the energy-differential cross section from the present measurement. The data taken with the gamma calibration sources shortly after the experiment were used for the investigation. In addition, a test experiment in refined conditions was conducted within the framework of this thesis. Numerous GEANT3 simulations of the detector were performed in order to understand various aspects of its performance. As a result, the efficiency of the detector was determined to be approximately a factor of 2 lower than the efficiency expected from the simulation. This result is consistent with several independent investigations, which were performed using different methods. At the same time, a remarkable agreement between the simulated and experimental data was achieved under assumption that the inefficiency of the detector is explained by the loss of data from a number of crystals, which are randomly chosen in each event according to their averaged performance ratio (the ”on-off” effect). The reasons for the observed malfunction are yet not fully clear. Regardless of the exact reason, in the present conditions a deconvolution of the measured data from the CsI response is not possible. Consequently, within the framework of this thesis, the results are presented in terms of integrated cross sections. A search for alternative methods of data interpretation, allowing to extract energy-differential information out of the available data, in currently ongoing.
In the more recent experiments at the LAND setup, where the Crystal Ball gamma detector was used as a calorimeter, the reconstruction of the energy-differential cross section with a reasonable resolution was already shown to be feasible. It means that, even considering the uncertainties of the present experiment of the order of 10%, the uncertainties of the statistical model predictions, which are on average estimated to be within a factor of 1.5-2, can already be constrained.
The analysis of the present experiment is still in progress. As a next step, Coulomb excitation cross section for 94Mo will be obtained. The 94Mo(γ,n) reaction cannot be studied by photoactivation, since the life time of the daughter nucleus is too long (4000 y). At the same time, this reaction plays a key role in the p-process nucleosynthesis.
The future of the LAND setup - the R3B setup1 at FAIR2 - will take advantage of a three orders of magnitude higher intensity of the radioactive beams [85], as well as of a completely new detector system. High-resolution measurements of the energy-differential cross sections will be possible for exotic nuclei, which were never accessible in the laboratory before. Such measurements will open great opportunities for nuclear astrophysics, allowing to obtain high-quality experimental data even for regions of the nuclear chart where the statistical model calculations are not applicable.
Stem cells are often referred to as potential candidates for the treatment of different pathologies. Their ability to differentiate into various tissue specific cell types offers the possibility to engineer cell systems or organs for replacement. One of the main questions in stem cell biology is how stemness properties are regulated and to what extend this regulation is intrinsic or conveyed by the direct microenvironment (‘niche’). In order to elucidate such regulatory processes, it is informative to analyze processes or molecules that are shared between different stem cell populations.
One such molecule that is expressed on a wide range of different embryonic and adult as well as tumor stem cells is the ABC transporter Abcg2. ABC transporters in general are transmembrane proteins that actively extrude endo- and exotoxins as well as xenobiotics, thereby protecting cells and organs. Additionally, ABC transporters are responsible for drug resistance in many cancers. A well-described characteristic of stem cells expressing Abcg2 is the formation of the ‘side population’ (SP) phenotype: An active Abcg2 transporter mediates the efflux of a particular fluorescent dye that is taken up by all cells, thus leading to a less brightly stained population. This phenomenon is widely used to characterize and isolate the most primitive stem cell subpopulation from embryonic and adult tissues, including tumors. Besides its role as toxin transporter little is known about the function of Abcg2 in stem cells. This is mainly due to the fact that its physiological substrate in stem cells remains unknown. The identification of such substrates is therefore of high interest because it would directly link the activity of ABC transporters to regulatory mechanisms in stem cell biology.
In the present study we wanted to test the hypothesis that the sphingolipid ceramide is a physiological substrate of the ABC transporter Abcg2. Sphingolipids are potent second messengers and are known to have regulatory functions in stem cells. In particular, the sphingolipid ceramide is described as a mediator of controlled cell death and inducer of differentiation. It is suggested that stem cells need to keep their intracellular ceramide content at low levels in order to prevent apoptosis or differentiation. We propose that Abcg2 and ceramide interact and that this interaction leads to changes in the absolute or relative amounts of ceramide. This in turn influences basic stem cell functions such as self renewal and differentiation.
We show that Abcg2 prevents cells from accumulating fluorescence labeled ceramide. Furthermore, exogenously applied ceramides inhibit the transport activity of Abcg2, measured by a decrease of the side population phenotype. This inhibitory effect is consistent with a competitive inhibition mechanism. Additionally, we show that active Abcg2 can increase the ceramide concentration in cell culture supernatant. Finally we demonstrate that Abcg2 protects from ceramide induced cytotoxicity in human cell lines. In summary, these in vitro results strongly suggest that Abcg2 has the ability to regulate ceramide levels.
Murine hematopoietic stem cells (HSCs) are the best characterized adult stem cell system so far. By using 7-colour fluorescence-activated cell sorting (FACS) we established the purification of the most primitive HSCs, reflected by their high engraftment capability when transplanted to lethally irradiated mice. By using this sorted cell populations it was in addition possible to establish a system to reproducibly manipulate HSCs ex vivo. This experimental system will serve in further elucidating the physiological consequences of Abcg2 mediated changes in ceramide levels on stem cells in vivo.
Taken together, this study shows that Abcg2 has the ability to regulate ceramide levels in cells. This in turn can lead to cellular protection from ceramide induced apoptosis. Additionally, the experimental techniques to further analyze the role of Abcg2 and ceramide in the most primitive hematopoietic stem cells were successfully established, enabling more detailed analysis in the future.
In the work presented herein the microscopic transport model BAMPS (Boltzmann Approach to Multi-Parton Scatterings) is applied to simulate the time evolution of the hot partonic medium that is created in Au+Au collisions at the Relativistic Heavy Ion Collider (RHIC) and in Pb+Pb collisions at the recently started Large Hadron Collider (LHC). The study is especially focused on the investigation of the nuclear modification factor R_{AA}, that quantifies the suppression of particle yields at large transverse momentum with respect to a scaled proton+proton reference, and the simultaneous description of the collective properties of the medium in terms of the elliptic flow v_{2} within a common framework.
In this thesis, laboratory investigations have been conducted to investigate several processes occurring during the melt segregation (crystal settling and compaction processes), as well as during emplacement of plutons. With the help of three different sets of centrifuge experiments rates of these three magmatic processes have been evaluated. In the first series of the centrifuge experiments, the diapiric ascent of buoyant material from two source layers at different depths was studied. Through five models, the hypothesis of ascending diapirs was tested and it was demonstrated whether a rising diapir ascends straight upward or if its ascent might be deviated by another buoyant, softer – and consequently easier to travel through – layer which is located within the overburden strata. We were interested under which conditions they can be formed. For this purpose we placed perturbations on top of both the buoyant layers; either with a set-off of both the protrusions (for three of these experiments), or with both protrusion sitting directly on top of each other (for one of the experiments). In the first experiment, we omitted the perturbations, to test which pathways diapirs take which grow from natural Rayleigh-Taylor instabilities. Three others experiments differed in the viscosity contrast between the overburden and the buoyant material. Through the experimental runs, the effects of different overburden viscosities and perturbation positions on the number of the diapirs were observed. The modeling results show that two diapirs rising from the offset perturbations do not take the same pathway through the overburden layer. Rather, each diapir takes a different pathway, with the deeper diapir piercing through its overburden while rising, regardless if it was a buoyant layer or denser overburden layers. However, when the two perturbations were situated directly above each other in the different PDMS layers, this resulted in the formation of one big diapir rather than several smaller ones, and the overburden layer was less deformed than with offset perturbations. Diapiric structures as those derived from the models without perturbation and where the perturbation are offset occur within Great Kavir Basin (Iran), where numerous salt diapirs grew from several salt horizons, which show a similar spatial distribution. The resulting structure observed in the model where the two perturbations situated directly above each other, is close to what is observed in composite batholiths such as the Flasergranitoid Zone within the Bergsträßer Odenwald Crystalline Complex (Germany). The second series of models were aimed to study crystal settling within a magma. For this purpose experiments with an artificial magma of 30 vol% olivine in 70 vol% basaltic melt were conducted to elucidate the formation mechanisms and time scales of gravitational cumulates. Through the experiments, two physical processes have been observed: (i) purely mechanical compaction, and (ii) chemical compaction induced by dissolution and re-precipitation of settled crystals. The results reveals that the mechanical settling of the dense olivine suspension occurs at about 1/6 the speed of simple Stokes settling, and a sedimentation exponent n of 4.1 is found. Evidences of chemical compaction induced by dissolution and re-precipitation of settled crystals have been highlighted by a detailed analysis of the fine structure of olivine grain boundaries. This last has revealed (1) the presence of Ca, which is characteristic only for MORB-melt, at the interface of two adjacent Ol-grains even when no melt is present; (2) a not fully crystallized boundary layer between two adjacent olivine grains. The crystal size distribution curves and the grain size growth exponent n ~3.6 indicate that diffusion controlled Ostwald ripening is the dominant crystal growth mechanism in concentrated magmatic suspensions. Finally, the formation times in natural olivine adcumulates have been calculated. The last series of centrifuge experiments deals with the crystal-melt settling-floating mechanism in a system composed of natural two pyroxene gabbro. The results have revealed a vertical evolution of the major and trace elements in the melt phase. Then, a numerical modelling of the sedimentation process of the crystals has been made in order to describe the compaction evolution with time. In comparing the numerical simulation with the centrifuge modelling, the stratification of the compacted layer in the runs is reproduced in numerical models. Moreover, on the base of the numerical and centrifuge modelling, a sedimentation exponent describing a deviation of settling in concentrated suspensions from Stokes sedimentation has been evaluated. Finally, the numerical simulation is applied to the Muskox intrusion to estimate the formation time and the melt fraction evolution in using the hindered sedimentation model calculations.
A pattern is a word that consists of variables and terminal symbols. The pattern language that is generated by a pattern A is the set of all terminal words that can be obtained from A by uniform replacement of variables with terminal words. For example, the pattern A = a x y a x (where x and y are variables, and the letter a is a terminal symbol) generates the set of all words that have some word a x both as prefix and suffix (where these two occurrences of a x do not overlap). Due to their simple definition, pattern languages have various connections to a wide range of other areas in theoretical computer science and mathematics. Among these areas are combinatorics on words, logic, and the theory of free semigroups. On the other hand, many of the canonical questions in formal language theory are surprisingly difficult. The present thesis discusses various aspects of the inclusion problem of pattern languages. It can be divide in two parts. The first one examines the decidability of pattern languages with a limited number of variables and fixed terminal alphabets. In addition to this, the minimizability of regular expressions with repetition operators is studied. The second part deals with descriptive patterns, the smallest generalizations of arbitrary languages through pattern languages ("smallest" with respect to the inclusion relation). Main questions are the existence and the discoverability of descriptive patterns for arbitrary languages.
Visual perception has increasingly grown important during the last decades in the robotics domain. Mobile robots have to localize themselves in known environments and carry out complex navigation tasks. This thesis presents an appearance-based or view-based approach to robot self-localization and robot navigation using holistic, spherical views obtained by cameras with large fields of view. For view-based methods, it is crucial to have a compressed image representation where different views can be stored and compared efficiently. Our approach relies on the spherical Fourier transform, which transforms a signal defined on the sphere to a small set of coefficients, approximating the original signal by a weighted sum of orthonormal basis functions, the so-called spherical harmonics. The truncated low order expansion of the image signal allows to compare input images efficiently, and the mathematical properties of spherical harmonics also allow for estimating rotation between two views, even in 3D. Since no geometrical measurements need to be done, modest quality of the vision system is sufficient. All experiments shown in this thesis are purely based on visual information to show the applicability of the approach. The research presented on robot self localization was focused on demonstrating the usability of the compressed spherical harmonics representation to solve the well-known kidnapped robot problem. To address this problem, the basic idea is to compare the current view to a set of images from a known environment to obtain a likelihood of robot positions. To localize the robot, one could choose the most probable position from the likelihood map; however, it is more beneficial to apply standard methods to integrate information over time while the robot moves, that is, particle or Kalman filters. The first step was to design a fast expansion method to obtain coefficient vectors directly in image space. This was achieved by back-projecting basis functions on the input image. The next steps were to develop a dissimilarity measure, an estimator for rotations between coefficient vectors, and a rotation-invariant dissimilarity measure, all of them purely based on the compact signal representation. With all these techniques at hand, generating likelihood maps is straightforward, but first experiments indicated strong dependence on illumination conditions. This is obviously a challenge for all holistic methods, in particular for a spherical harmonics approach, since local changes usually affect each single element of the coefficient vector. To cope with illumination changes, we investigated preprocessing steps leading to feature images (e.g. edge images, depth images), which bring together our holistic approach and classical feature-based methods. Furthermore, we concentrated on building a statistical model for typical changes of the coefficient vectors in presence of changes in illumination. This task is more demanding but leads to even better results. The second major topic of this thesis is appearance-based robot navigation. I present a view-based approach called Optical Rails (ORails), which leads a robot along a prerecorded track. The robot navigates in a network of known locations which are denoted as waypoints. At each waypoint, we store a compressed view representation. A visual servoing method is used to reach a current target waypoint based on the appearance and the current camera image. Navigating in a network of views is achieved by reaching a sequence of stopover locations, one after another. The main contribution of this work is a model which allows to deduce the best driving direction of the robot based purely on the coefficient vectors of the current and the target image. It is based on image registration as the classical method by Lucas-Kanade, but has been transferred to the spectral domain, which allows for great speedup. ORails also includes a waypoint selection strategy and a module for steering our nonholonomic robot. As for our self-localization algorithm, dependance on illumination changes is also problematic in ORails. Furthermore, occlusions have to be handled for ORails to work properly. I present a solution based on the optimal expansion, which is able to deal with incomplete image signals. To handle dynamic occlusions, i.e. objects appearing in an arbitrary region of the image, we use the linearity of the expansion process and cut the image into segments. These segments can be treated separately, and finally we merge the results. At this point, we can decide to disregard certain segments. Slicing the view allows for local illumination compensation, which is inherently non-robust if applied to the whole view. In conclusion, this approach allows to handle the most important criticism to holistic view-based approaches, that is, occlusions and illumination changes, and consequently improves the performance of Optical Rails.
Clathrin-mediated endocytosis (CME) involves spatially and temporally restricted molecular dynamics.
Although protein kinases and the actin cytoskeleton contribute to the process, whether and how
functions of kinases and actin are integrated remains unknown. Here, we demonstrate that neural
Wiskott-Aldrich syndrome protein (N-WASP) and protein kinase CK2 form a complex and localize on
clathrin-coated vesicles (CCVs). N-WASP binds to and is phosphorylated by CK2, thereby reducing the
kinase activity of CK2. By contrast, N-WASP-promoted actin polymerization is decreased upon both
phosphorylation and binding of CK2. Knockdown of N-WASP and CK2, alone or in combination, results
in impaired endocytosis of epidermal growth factor (EGF) and increased cell-surface levels of EGF
receptor (EGFR). In order to rescue the phenotype of N-WASP-CK2 knockdown cells, both N-WASP and
CK2 activities and abilities to assemble in a complex are required. In summary, this study shows that the
N-WASP-CK2 complex integrates in a single circuit different activities contributing to CME of EGFR and
that the interplay between the two proteins optimizes this process.
Time-resolved spectroscopic analysis of fucoxanthin-chlorophyll proteins and isolated carotenoids
(2011)
The aim of this thesis was to elucidate the excitation energy transfer in the fucoxanthin-chlorophyll proteins (FCPs) isolated from the diatom Cyclotella meneghiniana in detail and to clarify the role of the different pigments contained. In a first step the excited state dynamics of the free pigments were studied by means of time-resolved absorption spectroscopy. The FCPs contain three different carotenoid species. Besides the main light-harvesting carotenoid fucoxanthin (fx) the xanthophyll cycle pigments diadinoxanthin (ddx) and diatoxanthin (dtx) are found in substoichiometric amounts. Fx is contained in an unusual carotenoid-to-chlorophyll ratio of about one. In case of ddx and dtx, changing the solvent polarity showed no significant effects on the absorption spectrum and the excited state dynamics were hardly influenced. In contrast, a solvent dependence is observed in the absorption spectrum and excited state dynamics of fx. The S1 lifetime depends strongly on the solvent polarity and an additional broad excited state absorption band red shifted compared to the S1 excited state absorption appears. The occurrence of the described features can be explained with an intramolecular charge transfer state, which is stabilized in a polar environment and appears only in carotenoids with a conjugated carbonyl group. Despite its rather short excited state lifetimes of less than 200 fs (S2) and 30-60 ps (S1), fx acts as a very efficient energy donor in the FCPs. The ultrafast energy transfer dynamics of the isolated proteins FCPa and FCPb were investigated in a comprehensive study using transient absorption in the visible and NIR spectral region complemented with polarized transient absorption spectroscopy. The excitation energy transfer was not influenced significantly by changing the light conditions during the growth, which yields an altered amount of ddx and dtx. It can be concluded that the contribution of the xanthophyll cycle pigments to the energy transfer is not significant. The altered oligomerization state results in a more efficient energy transfer for the trimeric FCPa, which is also reflected in different Chl a fluorescence quantum yields. Thus, an increased quenching in the higher oligomers of FCPb can be assumed. The observed dynamics change drastically for two different excitation wavelengths λ = 500 nm and λ = 550 nm, which both lead to the population of the S2 excited state of individual carotenoids, namely blue and red absorbing fx molecules. The differing absorption maxima result from distinct microenvironments within the protein. For FCPa an additional slow time constant of 25 ps was found after excitation at 500 nm. By means of polarized transient absorption spectroscopy applied to FCPa different transition dipole moments for the S1 and the ICT state of fx could be identified. Based on the presented studies a detailed model explaining the excitation energy transfer pathways could be developed. In agreement with the faster overall transfer rate which is also evident in the anisotropy data in case of 550 nm excitation, upon excitation at 500 nm one slow transfer channel is active. It can be attributed to a blue absorbing fx not strongly associated with a Chl a molecule. Most likely excitation energy transfer takes place between the S1/ICT states of two different fx molecules before the energy is transferred to Chl a. Additional transient absorption experiments with an improved time resolution were performed to investigate the oscillations observed. These coherent effects superimposed the kinetics of isolated carotenoids as well as FCPs within the first 500 fs. The oscillations showed a very unusual damping behavior and vanished already after two oscillation periods. In case of fx, the solvent environment as well as the excitation wavelengths had an influence on the oscillations. The frequencies of the oscillations were 70-100 cm^-1 for fx in solvents with varying polarity and 50-80 cm^-1 for the FCPs. These results could further confirm the assumption that the red absorbing fx molecules are located in a more polar environment within the protein compared to the blue absorbing fx. To clarify the origin of the oscillations in more detail, further experiments with a controlled chirp of the applied pulses and comparison between different carotenoids in various solvents are required. This approach promises to give further insight in the excited state dynamics and to answer the question whether dark states are involved. Right now, the coherent excitation of the strongly coupled excited states 1Bu+ (S2) and 1Bu- resulting in electronic quantum beats and the existence of an additional short lived excited state absorption (S2-SN2) in the visible spectral region are the most reasonable explanations for the occurrence of the coherent effects in the transient absorption spectra of carotenoids.
Occurrence and sources of 2,4,7,9-tetramethyl-5-decyne-4,7-diol (TMDD) in the aquatic environment
(2011)
The aim of the present study was to identify the sources of 2,4,7,9-tetramethyl-5-decyne-4,7-diol (TMDD) into the aquatic environment and to investigate its occurrence in rivers and wastewater treatment plants (WWTPs). Therefore, TMDD was analyzed in 441 wastewater samples from influents and effluents of 27 municipal WWTPs, in 6 sludge samples, in 52 wastewater samples from 3 sewage systems of municipal WWTPs, in 489 surface samples from 24 rivers, in 9 wastewater samples of 3 paper-recycling industries and in 65 groundwater samples. TMDD was also analyzed in household paper products, in 23 samples of toilet
papers, in 5 types of paper towels and in 12 types of paper tissues. The samples were collected between 2007 and 2011. The water samples were extracted with solid phase extraction (SPE) and the household paper samples with Soxhlet extraction. Gas chromatography-mass spectrometry (GC-MS) was used for quantification purposes. Between November 2007 and January 2008, TMDD was detected in the river Rhine at Worms with permanent high concentrations (up to 1330 ng/L). The results showed that TMDD is uniformly distributed across the river at Worms. An increase of the mean TMDD concentration from approximately 500 ng/L to 1000 ng/L was registered in January 2008. Due to the minor fluctuations of the TMDD concentration during the sampling period it is expected that the input of TMDD into the river is continuous. Therefore, TMDD might rather originate from effluents of municipal WWTPs than from temporal sources. The mean TMDD load based on the analysis of 147 water samples collected in the River Rhine was 62.8 kg/d which is equivalent to 23 t/a suggesting that TMDD must be used and/or produced in high quantities in order to be found in those high concentrations. To determine if TMDD is discharged by effluents of municipal WWTPs into the rivers, 24 hours influent and effluent samples of four municipal WWTPs in the Frankfurt/Rhine-Main metropolitan region were collected during November 2008 and February 2010 and analyzed for TMDD. The TMDD influent concentrations varied between 134 ng/L and 5846 ng/L and the effluent concentrations between <LOQ (limit of quantitation) and 3539 ng/L. The TMDD elimination rates in the four WWTPs varied between 33% and 68%. The results showed that effluents of municipal WWTPs are an important source of TMDD in the aquatic environment because TMDD is not completely removed from the sewage during the wastewater treatment. Weekly and daily variations of the TMDD concentration in the influents of two municipal WWTPs indicated that both private households and indirect industrial dischargers contribute to the introduction of TMDD into the municipal sewage systems. A more detailed study of the TMDD elimination rate in the different wastewater treatment stages was carried out in the WWTP Niederrad/Griesheim in Frankfurt am Main. The results showed that the removal of TMDD is mainly carried out during the aerobic biological treatments, where the elimination rate was 46%. In contrast, during the anoxic treatment the removal efficiency was only 1.4% and during the mechanical treatment the elimination rate was 19%. To determine the sources of TMDD in the sewage, household paper products (paper tissues, toilet papers and paper towels) were analyzed for TMDD using Soxhlet extraction. TMDD was detected in 83% of the samples (n=40). The highest mean TMDD concentrations were found in recycled toilet paper (0.20 μg/g) and in paper towels (0.11 μg/g). In paper tissues and non-recycled toilet paper the mean TMDD concentrations were lower 0.080 μg/g and 0.025 μg/g respectively. According to these results the high TMDD influent concentrations found previously in municipal WWTPs (mean 1.20 μg/L) cannot be explained due to migration of TMDD from the household paper products into the sewage. Thus indirect industrial dischargers are the cause of the high influent TMDD concentrations. Effluents of municipal WWTPs with different indirect industrial dischargers (textile-, metal processing-, food processing-, electroplating-, paper-recycling- and printing ink factories) were analyzed. The highest mean TMDD concentrations were found in the effluents of municipal WWTPs that have paper-recycling (71.3 μg/L) and printing ink factories (138 μg/L) as indirect industrial dischargers. These results were confirmed by analyzing process wastewater of three paper-recycling factories located in Germany. High TMDD concentrations were detected and fluctuated between 1.83 μg/L and 113 μg/L. TMDD was also analyzed in the wastewater of a non-recycling-paper factory but its concentration was much lower (0.066 μg/L) indicating that TMDD is introduced into the processing water during the papermaking process due to the use of waste paper. Analyses of wastewater samples from different parts of the sewage pipes of a municipal WWTP in Hesse, which receives the wastewater from a printing ink factory, were carried out. The TMDD concentration in the wastewater sample from the sewage pipe of the printing ink factory was much higher (3,300 μg/L) than the TMDD concentration detected in the other wastewater samples from the sewage system (0.030 μg/L – 0.89 g/L). These results confirm the printing ink production as one of the principal sources of TMDD in the sewage. Analysis of surface water samples of the River Modau downstream from the effluent of the WWTP Nieder-Ramstadt showed TMDD concentrations of up to 28.0 μg/L. These high TMDD concentrations might be caused by the indirect wastewater discharges of a paint factory connected to the municipal sewage system. These results indicate that TMDD is introduced into the municipal WWTPs principally by indirect industrial dischargers and they are mainly paint and printing ink factories. The paper-recycling factories also represent an important source of TMDD in municipal WWTPs but indirectly. According to statements given by the representatives of two paper recycling factories neither TMDD or any other TMDD containing product is used or added during the papermaking process. Therefore, TMDD is washed out from the printing inks of the coloured waste paper and concentrated in the process wastewater in the closed water circuits of paper-recycling factories reaching rivers and municipal WWTPs. The occurrence and distribution of TMDD in surface waters in Germany was also studied. The results showed that TMDD is widely distributed across different rivers systems in the federal states of Hesse, North-Rhine-Westphalia, Bavaria, Baden-Wuerttemberg and Rhineland-Palatinate. In Hesse, TMDD was detected in the some of main rivers with mean concentrations of 812 ng/L (Schwarzbach, Hessian Ried), 374 ng/L (Kinzig), 393 ng/L (Main, at Frankfurt), 539 ng/L (Werra), 326 ng/L (Fulda), 151 ng/L (Emsbach) and 161 ng/L (Nidda). In small rivers (creeks) the mean TMDD concentrations varied between <LOQ (Diemel, Urselbach) and 1890 ng/L (Darmbach). The results showed that the TMDD concentrations in creeks are highly influenced by both effluents of WWTPs and by the distance between the sampling point and the nearest WWTP. Surface samples from sampling locations downstream from WWTPs dischargers showed higher TMDD concentrations (mean 518 ng/L) than sampling locations upstream from WWTPs dischargers (mean 35.1 ng/L). The behavior of TMDD during bank filtration was investigated at two locations, at a water utility company at the Lower River Rhine (urban area) and at the Oderbruch polder (rural area). The results indicated that TMDD is removed from the surface water by bank filtration at both sampling locations. The removal process is probably carried out in the first meters of the aquifer (hyporheic zone) by biodegradation processes, since TMDD does not tend to be absorbed by sediments and it was not found in the groundwater of monitoring wells. In groundwater samples from the Hessian Ried (n=23) TMDD was found only in five samples and the highest TMDD concentration was 135 ng/L. According to these results, TMDD does not represent a concern for drinking water in Germany, since it does not reach the groundwater with high concentrations and it has a low toxicity potential. The input of TMDD into the North Sea was estimated to be 60.7 t/a by considering the mean transported loads of TMDD by the River Rhine at Wesel (58.3 t/a) and Meuse in the Netherlands (2.40 t/a). The estimated discharge of TMDD by German municipal WWTPs (8.19 t/a) and paper-recycling factories (9.24 t/a) into rivers seems to be too low considering that the mean TMDD load in the River Rhine downstream from Wesel is 58.3 t/a. However, due to the high density of population and industries at the Lower Rhine it is expected that more relevant sources of TMDD are located along the Rhine River increasing the transported load. According to the results of this PhD project TMDD is a non-ionic surfactant contained in products, which are applied on surfaces (printing inks and paints) and has the potential to reach the aquatic environment. Therefore, TMDD should fulfill the requirement of a biodegradability of 80% established by the “Law on the Environmental Impact of Detergents and Cleaning Products” in Germany. However, due to the partial elimination rates of TMDD obtained in municipal WWTPs (between 33% and 68%) and to the absence of information about the execution of the biodegradation test on TMDD, it is unknown if TMDD is in accordance with this law. Otherwise, its use as surfactant in such products is questionable.
Sponges are one of the major components of benthic communities and are considered to be a
key role organism in marine ecosystems. In addition to their importance in terms of
biodiversity, sponges are becoming increasingly attractive to the industry, as they themselves
or associated symbionts, produce various kinds of secondary metabolites of pharmaceutical
properties. Some of them have already been clinically applied.
The taxonomic characters of Porifera are limited to only a few morphological and
histological characters. In addition, sponges of the same species often show a wide
morphological variability, whereas the latter depends on different ecological parameters such
as water depth and current conditions. Thus, the taxonomic classification of sponges often
becomes a scientific challenge.
The fauna of the Yellow Sea rates among the least studied worldwide. At the same time,
according to the UN Atlas of the Ocean, the Yellow Sea is one of the most intensively
exploited marine areas in the world. This is not least due to the dense human population living
in the entire catchment area of the Yellow Sea region. In order to compile medium- and longterm
conclusions about the anthropogenic impact on biota of the Yellow Sea, the knowledge
of species and their distribution is of crucial importance, as these data form the baseline for all
future conservation efforts.
Until now the sponge fauna of the Chinese Yellow Sea is insufficiently investigated.
Thus, there is only one publication on sponges from this region that has been released
hitherto. This paper is dealing with only a view species. However, there is no reference
concerning the present location of the voucher material, on which this publication is based on.
Consequently, no scientific collection on Porifera from the Chinese part of the Yellow Sea
exists to date.
In order to compile a documentation of the recent sponge community of the Chinese
Yellow Sea, 12 study sites along the coast of the Liaoning Peninsula, China, Northeast
Yellow Sea, were investigated with focus on sponge distribution. The corresponding habitats
were characterized in regard to their topographical features, abiotic parameters, and common
composition of benthic megafaunal and macroalgal assemblages.
Due to the lack of comparable studies, a comprehensive literature research on sponges of the
shallow Northwest Pacific Ocean was required. As a result the first compilation of
publications is presented, dealing with sponges from shallow depths of the northwestern
Pacific Ocean.
Abstract
2
In the course of this study, 31 sponge species in total were recorded, which are scientifically
processed. With the exception of four all specimens were determined to species- level.
Twelve out of the total number of species are new to science and are described and classified
according to the recent taxonomic system of the phylum Porifera.
The results of this study indicate considerable differences in species composition between
investigated sites. It is shown that physical factors (particularly current regime, sedimentation,
seasonally related variations in temperatures), as well the availability of suitable substrates are
directly related to the diversity and abundance of investigated sponge communities. In this
context possible adaptation strategies of the corresponding sponges were discussed in detail.
Two sponge species, Clathria (Clathria) asodes and Antho (Acarnia) lithophoenix, formerly
known exclusively from the northeastern Pacific Ocean, are now recorded from the Northwest
Pacific Ocean for the first time. Furthermore, Penares hongdoensis, Clathria (Clathria)
hongdoensis and Celtodoryx girardae were synonymized with Penares cortius, Clathria
(Clathria) acanthostyli, and Celtodoryx ciocalyptoides respectively. Moreover, the occurrence
of eight sponge species, which were known from previous records from the Yellow Sea, could
be confirmed.
As a result of this study the Asian origin of a sponge species that is invasive to the French and
Dutch coasts of the Northeast Atlantic Ocean since the 1990s could be established. Moreover,
it is demonstrated that Celtodoryx girardae from the northeastern Atlantic is in fact
conspecific with Cornulum ciocalyptoides described by Burton (1935) from the Posiet Bay,
Sea of Japan. Apart from taxonomic remarks, variations between populations from both
oceans are examined and discussed thoroughly in regard to possible ecological implications.
The community of documented sponges shows overlapping with the one from the Sea of
Japan. According to the results it is assumed that the endemic degree of the sponges from the
Chinese Yellow Sea is rather low to moderate.
The material obtained in the course of this study was integrated in the collection of the
Senckenbergischen Naturforschenden Sammlungen. Therefore, it is the first scientific
collection of sponges from the Chinese Yellow Sea that can be consulted as a basis for all
further studies on sponges of this region.
The present study is the only investigation of sponges from Dalian and adjacent waters before
the spill occurred in the Dalian harbour in July 2010. Therefore, it provides an essential
baseline needed to assess the impact of the oil spill on benthic communities.
Statistical machine translation (SMT) should benefit from linguistic information to improve performance but current state-of-the-art models rely purely on data-driven models. There are several reasons why prior efforts to build linguistically annotated models have failed or not even been attempted. Firstly, the practical implementation often requires too much work to be cost effective. Where ad-hoc implementations have been created, they impose too strict constraints to be of general use. Lastly, many linguistically-motivated approaches are language dependent, tackling peculiarities in certain languages that do not apply to other languages. This thesis successfully integrates linguistic information about part-of-speech tags, lemmas and phrase structure to improve MT quality. The major contributions of this thesis are: 1. We enhance the phrase-based model to incorporate linguistic information as additional factors in the word representation. The factored phrase-based model allows us to make use of different types of linguistic information in a systematic way within the predefined framework. We show how this model improves translation by as much as 0.9 BLEU for small German-English training corpora, and 0.2 BLEU for larger corpora. 2. We extend the factored model to the factored template model to focus on improving reordering. We show that by generalising translation with part-of-speech tags, we can improve performance by as much as 1.1 BLEU on a small French- English system. 3. Finally, we switch from the phrase-based model to a syntax-based model with the mixed syntax model. This allows us to transition from the word-level approaches using factors to multiword linguistic information such as syntactic labels and shallow tags. The mixed syntax model uses source language syntactic information to inform translation. We show that the model is able to explain translation better, leading to a 0.8 BLEU improvement over the baseline hierarchical phrase-based model for a small German-English task. Also, the model requires only labels on continuous source spans, it is not dependent on a tree structure, therefore, other types of syntactic information can be integrated into the model. We experimented with a shallow parser and see a gain of 0.5 BLEU for the same dataset. Training with more training data, we improve translation by 0.6 BLEU (1.3 BLEU out-of-domain) over the hierarchical baseline. During the development of these three models, we discover that attempting to rigidly model translation as linguistic transfer process results in degraded performance. However, by combining the advantages of standard SMT models with linguistically-motivated models, we are able to achieve better translation performance. Our work shows the importance of balancing the specificity of linguistic information with the robustness of simpler models.
This thesis combines behavioral and cognitive approaches regarding the Web for analyzing users' behavior and supposed interests.
The work is placed in a new field of research called Web Science, which includes, but is not restricted to, the analysis of the World Wide Web. The term Web Science is affected by Tim Berners-Lee et al., who invited the researchers to "create a science of the web" [BLHH+06a]. The thesis is structured in two parts, reflecting the intersection of disciplines that is required for Web Science.
The first part is related to computer science and information systems. This part defines the Gugubarra concepts and algorithms for web user profiling and builds upon the results by Mushtaq et al. [MWTZ04]. This profiling aims at understanding the behavior and supposed interests of users. Based on these concepts, a framework was implemented to support the needs of web site owners. The core technologies used are Java, Spring, Hibernate, and content management systems. The design principles, architecture, implementation, and tests of the prototype are reported.
The second part is directly related to behavioral economics and is connected to the areas of economics, mathematics, and psychology. This part contributes to behavior models, as was claimed by Tim Berners-Lee et al.: "Though individual users may or may not be rational, it has long been noted that en masse people behave as utility maximisers. In that case, understanding the incentives that are available to web users should provide methods for generating models of behaviour..."[BLHH+06b]. The focus here is on studies that investigate the user's choice of online information services in a multi-attribute context. The introduced research framework takes into account background and local context effects and builds upon theoretical foundations by Tversky and Kahneman [TK86]. The findings provide useful insights to behavioral scientists and to practitioners on how to use framing strategies to alter the user's choice.
The translocation of nuclear-encoded precursor proteins into chloroplasts is a highly ordered process involving the action of several components to regulate this molecular ensemble. Not only GTP hydrolysis and GDP release but also the phosphorylation of TOC GTPases is a widely discussed mechanism to regulate protein import. The receptor component (Toc34) and its isoform of A. thaliana (atToc33) were found to be regulated by phosphorylation. Although the phosphorylation of Toc33 is already known for several years, several questions regarding the molecular components involved in the regulation of the phosphorylation process, precisely what is the protein kinase and where this kinase is initially localized, so far remained unclear.
This thesis aimed at the defining of the phosphorylation status of TOC GTPases in monomeric and/or dimeric states, the identification of the nature of Toc33-PK (protein kinase), and in the same context it aimed at gaining first insights into the physiological significance of Toc33 phosphorylation. To this end, (I) An in vitro and in vivo system for investigating of TOC GTPases Phosphorylation (in monomeric or dimeric state) was developed. Since no information is available about the phosphorylation status of the Toc159 isoforms, the second receptor of the TOC complex, it was interesting to investigate whether these isoforms undergo phosphorylation or not. The results indicated that atToc159 isoforms are able to be phosphorylated by the kinase activity in purified outer envelope membranes (OEMs) of pea, but not atToc132. Moreover, an artificial dimer of psToc34 based on the interaction of a C-terminally fused leucine zipper was not phosphorylated. This result reflected the inability of the OEM kinase to phosphorylate the dimers of TOC GTPases. Also, In vivo labeling of atToc33 was developed and occurred in a dose-dependent manner. Therefore, this results evidenced that in vitro phosphorylation of atToc33 (both endogenous wild type and recombinant expressed proteins) is not artificial labeling but represents a physiological relevance. CD (circular dichroism) measurements revealed that recombinant GTPase domain of atToc33 is preferentially phosphorylated in its folded state. Therefore, it could be suggested that folding of atToc33rec is a prerequisite for its phosphorylation and the phosphorylation event occurs as a posttranslational modification most likely after insertion of Toc33 (Toc34) into the OE of chloroplasts.
Secondly, (II) Isolation and identification of Toc33-PK from OEMs of chloroplasts was performed. Four independent strategies were developed to identify the Toc33-protein kinase: UV-induced and chemically-based crosslinking, different applied chromatographic techniques, identification of PK-Toc33 interaction by means of HDN-PAGE (histidine- and deoxycholate-based native PAGE), and finally mass spectrometric approaches were performed on fractions including the potential kinase activity. UV-induced crosslinking procedure was developed and resulted in covalent bonding of nine proteins to [a-32P] ATP, while chemically-based one was not significant. The applied chromatographic and HDN-PAGE approaches, including mass spectrometry, have revealed the identification of 13 protein kinases. Of these identified kinases, phototropin2 (Phot2, AT5G58140), leucine-rich repeat PK (LRR-PK, AT4G28650.1), and receptor-like transmembrane PK (RLK, AT5G56040.2) were selected as the most promising candidates (ca. kinase type and one transmembrane helix for membrane localization).
(III) The physiological significance of Toc33 phosphoryation was shown to link this process with the environmental changes (especially, the light conditions). Identification of chloroplast OE-located PKs performed by nLC-MALDI-MS/MS resulted in the detection of Phot2. Furthermore, the subcellular localization of Phot2 in OEM of chloroplasts was confirmed by immunoblotting experiments using a-Phot2 antibody. The kinase activity of Phot2 towards TOC GTPases was characterized and revealed that fused GST-KD (kinase domain) protein able to specifically phosphorylate atToc33rec, but not atToc159rec. Also, endogenous atPhot2 was upregulated and heavily detected in the ppi1-S181A plant line (where serine to alanine exchange was performed to abolish the phosphorylation of atToc33). Hence, we suggested that certain signal cascades may directly or indirectly link Toc33 receptor phosphorylation, protein levels of Phot2 (as promising PK candidate), and irradiation conditions (as an inducing signal of the subsequent phosphorylation events). Light-dependent phosphorylation of Toc33 was shown either after de-etiolation conditions or after high light intensities of blue light was performed. Therefore, phosphorylation of Toc33 might be identified as an external regulatory signal to regulate preproteins import into chloroplasts in response to environmental conditions (e.g. light changes) or as a signal of chloroplast biogenesis.
In der vorliegenden Arbeit konzentrierte ich mich auf mediterrane wirbellose Tierarten, welche sich als Konsequenz ihrer Lebensweise nur schlecht ausbreiten können. Nichtsdestotrotz haben es Süßwasserkrabben der Gattung Potamon und Landschnecken der Gattung Tudorella geschafft, große Gebiete zu besiedeln, die heute durch das Mittelmeer getrennt sind. Für beide Gruppen wurde spekuliert, dass Menschen an ihrer Ausbreitung beteiligt waren. Es war mein Ziel die biogeographischen Muster dieser beiden Gattungen zu analysieren und abzuschätzen, ob Menschen tatsächlich Vektoren ihrer Ausbreitung waren. Meine Analysen fanden auf drei Ebenen statt: Taxonomie, Gattung und Art.
5-lipoxygenase (5-LO) catalyzes the first two steps in leukotriene (LT) biosynthesis. In a two step reaction the enzyme oxygenates arachidonic acid (AA) to form the highly unstable epoxide leukotriene A4 (LTA4) in dehydrating a hydroperoxide intermediate (20). LTA4 can then be further metabolized by two terminal synthases yielding either the potent chemoattractant leukotriene B4 (LTB4) or the cysteinyl leukotrienes (CysLTs). 5-LO enzyme expression is primarily found in mature leukocytes (22) where it can either reside in the cytoplasm or in the nucleus associated with euchromatin (29). Its enzymatic activity is embedded in a complicated network in intact cells regulating LT synthesis by various factors dependent on the cell type and nature of stimulus. Factors such as the amount of free AA released by phospholipase A2 enzymes, levels of enzymes involved, catalytic activity per enzyme molecule and availability of different small molecules influence 5-LO activity (36).
The 5-LO derived LTs are lipid mediators which were shown to primarily mediate inflammatory and allergic reactions and their role in the pathogenesis of asthma is well defined. CysLTs are among the most potent bronchoconstrictors yet studied in man and play an important role in airway remodeling. LTB4 has no bronchoconstrictory effects in healthy and asthmatic humans but displays potent chemoattractant properties on neutrophils and increases leukocyte adhesion to the vessel wall endothelium (22). Therefore, LTB4 enhances the capacity of macrophages and neutrophils to ingest and kill microbes. In concert with LTB4, histamine and prostaglandin E2 (PGE2) CysLTs are thought to maintain the tone of the human airways (82).
Besides their well studied role in asthma, 5-LO derived LTs have also been implicated to play a role in cardiovascular diseases and cancer. In contrast to healthy tissues, LT pathway enzymes and receptors were found to be abundantly expressed in cancer tissues, atherosclerotic lesions in the aorta, heart and carotid artery (86). Pharmacological inhibition of 5-LO potently suppressed tumour cell growth by inducing cell cycle arrest and triggering cell death via the intrinsic apoptotic pathway (92, 93). In several studies LTs were found to exhibit cardiovascular actions by promotion of plasma leakage in postcapillary venules, coronary artery vasoconstriction and impaired ventricular contraction leading to reduced coronary blood flow and cardiac output (24). Unfortunately, the precise molecular mechanisms through which LTs influence carcinogenesis and cardiovascular diseases are still incompletely understood.
In contrast, an increasing number of studies questions the correlation between 5-LO and cancer (95-97) since extreme LT concentrations were applied to induce proliferative effects in the majority of the publications. A few studies exist which show susceptibility towards 5-LO products in physiological concentrations or achieve anti-proliferation by applying low concentrations of 5-LO inhibitors (98) ...
NK cells are part of the innate immune system, and are important players in the body’s first defence line against virus-infected and malignantly transformed cells. While T cells recognize neoplastic cells in an MHC-restricted fashion, NK cells do not require prior sensitization and education about the target. In leukemia and lymphoma patients undergoing allogeneic hematopoietic stem cell transplantation not only T cells but also NK cells have been found to mediate potent graft-versus-tumor effects. Hence, autologous or donor-derived NK cells hold great promise for cancer immunotherapy. Since the generation of highly purified NK cell products for clinical applications is labor-intensive and time consuming, established human NK cell lines such as NK-92 are also being considered for clinical protocols. NK-92 cells display phenotypic and functional characteristics similar to activated primary NK cells. While NK-92 cells are highly cytotoxic towards malignant cells of hematologic origin, they do not affect healthy human tissues. NK-92 cells can be expanded under GMP-compliant conditions, and can therefore be provided in sufficient numbers with defined phenotypic characteristics for clinical applications. Safety of NK-92 cells for adoptive immunotherapy was already shown in two phase I/II clinical trials...
The aim of this study is a better understanding of radiation processes in regional climate models (RCMs) in order to quantify their impact and to reduce possible errors. A first important task in finding an answer to this question was to examine the accuracy of the components of the radiation budget in regional climate simulations. To this end, the simulated radiation budgets of two regional climate simulations for Europe were compared with a satellite-based reference. In the simulations with the RCM COSMO-CLM there were some serious under- and overestimations of short- and long-wave net radiation in Europe. However, taking into account the differences in the reference datasets, the results of the COSMO-CLM were quite satisfactory.
Using statistical methods, the influence of potential sources of uncertainties was estimated. Uncertainties in the cloud cover and surface albedo had a significant impact on uncertainties in short-wave net radiation, the explained variance of uncertainties in cloud cover was two to three times higher than that of uncertainties in surface albedo. Uncertainties in the cloud cover resulted in significant errors in the net long-wave radiation. However, the influence of uncertainties in soil temperature on errors in the long-wave radiation budget was low or even negligible. These results were confirmed in a comparison with simulations of the REMO and ALADIN regional climate models. It is reasonable to expect that a better parameterization of relatively simple parameters such as cloud cover and surface albedo is a means of significantly improving the simulation of radiation budget components in the COSMO-CLM.
An important question for the application of RCMs is to examine whether the results of radiation uncertainties and their impact factors are comparable if the model is applied in a region that is not the one for which it was originally created. Comparisons of the simulated radiation budgets of different RCMs for West Africa showed that problems in the simulation of short- and long-wave radiation fluxes were a widespread problem. Most of the tested models showed some considerable under- or overestimation of the short- and long-wave radiation fluxes.
Similar to Europe uncertainties in cloud cover were also in the simulations for Africa a significant factor affecting uncertainties in the simulated radiation fluxes. However, for the African simulations uncertainties in the parameterization of surface albedo were much more important than in Europe. On average, overland uncertainties in the cloud cover and surface albedo were of similar importance. Uncertainties in soil temperature simulations were of higher importance in Africa, and reached overland similar values of the mean explained variance (R2 ≈ 0.2) such as uncertainties in the cloud cover. This indicates a geographical dependence of the model error. This study confirmed the assumption that an improved parameterization of relatively simple parameters such as the surface albedo in RCMs leads to a significant improvement in the modeled radiation budget, particularly in Africa.
The influence of errors in the simulated radiation budget components on the simulation of climate processes, such as the West-African monsoon (WAM), was investigated in a next step. The evaluation of ERA-Interim and ECHAM5 driven COSMO-CLM simulations for Africa showed that the main features of the WAM were well reproduced by the model, but there were only slight improvements compared to the driving data. The index of convective activity in the model simulations was much too high and precipitation was underestimated in large parts of tropical Africa. The partly considerable differences between the ERA-Interim and ECHAM5 driven simulations demonstrated the sensitivity of the RCM to the boundary conditions and in particular to the sea surface temperature. An excessive northwards shift of the monsoon in the model was influenced by the land-sea temperature gradient and the strength of the Saharan heat low. Consequently, a part of the error was due to the driving data and the model itself produced another part.
By modifying the parameterization of the bare soil albedo the errors in the radiation budget and 2 m temperature in the Sahara region were significantly reduced. Similarly, the overesti-mation of precipitation and convection has been reduced in the Sahel. The effect of this modifi-cation on the examined WAM area was low. This confirmed that especially in desert regions, errors in the surface albedo were a driving factor for errors in the radiation budget. However, there are other important factors not yet sufficiently understood that have a strong influence on the quality of the simulation of the WAM.
The analysis of the actual state, the quantification of error sources and the highlighting of connections made it possible to find means to reduce uncertainties in the simulated radiation in RCMs and to have a better understanding of radiation processes. However, the magnitude of the errors found, the number of possible influencing factors, and the complexity of interactions, indicate that there is still a need for further research in this area.
Owing to long-term similarities with regard to orbital climate forcing (i.e., low eccentricity and a dampened influence of precession), Marine Isotope Stage (MIS) 11 represents one of the closest astronomical analogues for present and future climate. Hence, insights into the climate variability of MIS 11 can contribute to a better understanding of the climatic evolution of the present (Holocene) interglacial as it would occur without human interference. In order to elucidate the natural climate variability during MIS 11, this study examines predominantly annually laminated lake sediments of Holsteinian age from Dethlingen, northern Germany. The Holsteinian interglacial is widely accepted to be the terrestrial equivalent of MIS 11c in central Europe and can be biostratigraphically correlated with the Hoxnian, Mazovian and Praclaux interglacials on the British Isles, in Poland and in France, respectively. These correlations yield the potential to cross-check the results from individual sites on a regional scale. This study is based on a multi-proxy approach including palynological, micropaleontological, sedimentological, geochemical and time series analyses within a wellconstrained chronological framework that has been established through varve counting and regional bio-stratigraphic correlations with other annually laminated archives of Holsteinian age. In particular, the here-presented study aims at (i) fingerprinting the long-term (centennial- to millennial-scale) and short-term (sub-decadal- to decadal-scale) climate variability during the Holsteinian interglacial, (ii) deciphering the nature, tempo and trigger mechanisms of abrupt climate change under interglacial boundary conditions, and (iii) assessing its impact on terrestrial ecosystems. With regard to long-term climate variability, the vegetation succession at Dethlingen as inferred from pollen data provides insights into the mesocratic to telocratic forest phases of a glacial-interglacial cycle spanning ~11500 (± 1000) years of the 15-16-ka-long Holsteinian interglacial. The development of temperate mixed forests suggests a general prevalence of mild climatic conditions during the Holsteinian. The older parts of the interglacial are characterised by the strong presence of boreal tree taxa (e.g., Picea), whereas the younger parts of the interglacial are marked by the expansion of sub-Atlantic to Atlantic forest elements (e.g., Abies, Buxus, Ilex, Quercus) and the decline of boreal tree taxa. This vegetation succession suggests a general warming trend and decreasing seasonality over the course of the Holsteinian interglacial. Based on the maximum pollen abundances of indicator tree taxa (e.g., Buxus and Quercus), peak warmth was reached during the later stages of the interglacial; it was accompanied by high humidity. The forest succession of the Holsteinian interglacial was punctuated by abrupt and gradual changes in the abundances of temperate plant taxa. These vegetation changes indicate considerable intra-interglacial climate variability. In particular, two marked declines of temperate taxa leading to the transient development of boreal and sub-boreal forests were triggered by centennial-scale climate oscillations, here termed Older and Younger Holsteinian Oscillations (OHO and YHO). These oscillations occurred ~6000 and ~9000 years after the onset of the interglacial pioneer forestation in central Europe, respectively. To assess the impact of abrupt climate change on terrestrial ecosystems during the Holsteinian and to investigate the underlying driving mechanisms, the intervals spanning the OHO and the YHO at Dethlingen were subjected to decadal-scale palynological and sedimentological analyses. Based on these data, the OHO comprises a 90-year-long decline of temperate taxa associated with expansion of Pinus and non-arboreal pollen, and a subsequent 130-year-long recovery of temperate taxa marked by the pioneer expansion of Betula and Alnus. Owing to its highly characteristic imprint on vegetation dynamics, the OHO can be identified in pollen records from the central European lowlands north of 50º latitude, from the British Isles to Poland. A close inspection of individual pollen records from that region reveals the prevalence of colder winters during the OHO, with a gradient of decreasing temperature and moisture availability, and increased continentality towards eastern Europe. This climate pattern points to a weakened influence of the westerlies and/or stronger influence of the Siberian High connected to the OHO. The vegetation dynamics during the YHO are characterised by a decline of temperate taxa (particularly of Carpinus) and the expansion of pioneer trees (mainly Betula). In contrast to the OHO, frost-sensitive taxa (e.g., Ilex, Buxus and Hedera) continued to thrive. This suggests that mean winter temperatures remained relatively high (>0 ºC) during the YHO pointing to a decrease of summer warmth related to the climatic deterioration. The YHO, which has a duration on the order of 300 years, is centered within a long-term (~1500-year) decline and subsequent, millennial-scale recovery of temperate taxa. Because the impact of the OHO and the YHO on the vegetation at Dethlingen was markedly different, both short-term climate oscillations may have been caused by different trigger mechanisms. For the OHO, the inferred regional-scale winter cooling over central Europe lasting for several decades points to a decrease in ocean heat transport, most likely related to a transient slowdown in North Atlantic Deep Water formation. This view is supported by the strong resemblance of the OHO to the 8.2 ka event of the Holocene with regard to the duration, imprint on terrestrial ecosystems, spatial pattern of the climatic impact, timing within the respective interglacial, and prevailing interglacial boundary conditions. In contrast, the presence of frost-sensitive taxa during the YHO appears to exclude a reduction in oceanic heat transport as postulated for the OHO. Instead, the long-lasting, gradual changes in the abundances of temperate taxa suggest a connection to orbital forcing, with the triggering mechanism causing the centennial-scale vegetation setback itself remaining unclear. The characteristics of short-term climate variability were investigated based on microfacies and time series analyses of a ~3200-year-long, annually laminated window of the Dethlingen record. The annual laminations at Dethlingen comprise biogenic varves consisting of two discrete sub-layers. The light layers, which are controlled by the intensity of diatoms blooms during spring/summer, reflect changes in the productivity of the Dethlingen palaeolake. In contrast, the dark layers, which consist predominantly of amorphous organic matter and fragmented diatom frustules, represent sediment deposition during autumn/winter. Spectral analyses of the thicknesses of the light and dark layers have revealed several peaks exceeding the 95% and 99% confidence levels that are near-identical to those known from modern instrumental data and Holocene records. Decadal-scale signals at periods of 90, 25, and 10.5 years are likely associated with the 88-, 22- and 11-year solar cycles; hence, solar activity appears to have been a forcing agent in productivity changes of the Dethlingen palaeolake. Sub-decadal-scale signals at periods between 3 and 5 years and ~6 years may reflect an influence of the El Niño-Southern Oscillation (ENSO) and the North Atlantic Oscillation (NAO) on varve formation during winter.
NOSTRIN belongs to the recently defined F-BAR protein family. F-BAR proteins are
multi-domain proteins, which serve as adaptors between plasma membrane and
cytoskeleton components in processes such as membrane protrusion formation,
endocytosis and migration. NOSTRIN encompasses a F-BAR domain at the N-terminus,
which mediates membrane association, followed by a HR1 motif and an intermediate
domain (ID) domain in the middle, and a SH3 domain at the C-terminus. The domain
architecture and ability to form oligomers enable NOSTRIN to coordinate several
interaction partners namely dynamin, caveolin, N-WASP and endothelial nitric oxide
synthase (eNOS) in the process of eNOS trafficking. In this context NOSTRIN was
originally identified and hence termed eNOS traffick inducer. NOSTRIN is expressed in
vascularized tissues (e.g. liver and lung) and in primary endothelial cells.
Aims of the present work were (1) to investigate if NOSTRIN is involved in other
processes besides eNOS trafficking, (2) to analyse the function of NOSTRIN in vivo
through knockdown of NOSTRIN in developing zebrafish and (3) to study the
consequences of the loss of NOSTRIN on signal transduction in a primary cell culture
model derived from NOSTRIN knockout mice.
To study the possible involvement of NOSTRIN in other processes besides eNOS
trafficking a yeast two-hybrid screen was performed in which fibroblast growth factor
receptor 1 (FGFR1) was identified as a putative novel interaction partner of NOSTRIN. In
a series of yeast two-hybrid, pulldown and co-immunoprecipitation experiments the
interaction between NOSTRIN and FGFR1 was confirmed to occur between
endogenously expressed proteins and determined to be direct and to depend on the ID
domain of NOSTRIN and the 130 C-terminal amino acid residues of FGFR1. FGFR1 is
activated by binding of fibroblast growth factors (FGFs) and induces several different
signal transduction pathways (e.g. MAPK and Akt pathway). Overexpression of
NOSTRIN in HeLa cells specifically enhanced FGF2-dependent MAPK activation.
Accordingly, depletion of NOSTRIN attenuated FGF2-dependent MAPK activation and
did not affect FGF2-induced Akt activation.
In summary, NOSTRIN has been identified as a novel interaction partner of FGFR1
involved in FGF2-dependent signal transduction.
The morpholino oligonucleotide-mediated knockdown of NOSTRIN in developing
zebrafish caused vascular leakage and irregular vascular patterning e.g. a loss of the
proper trajectory of intersegmental vessel and interruptions of the dorsal longitudinal
anastomotic vessel. The vascular phenotype was consistent upon use of two different
morpholinos and could be rescued in a dose dependent manner by the injection of
zebrafish NOSTRIN mRNA. Detailed analysis involving confocal and time lapse
microscopy in zebrafish with endothelial specific expression of EGFP revealed that the
knockdown of NOSTRIN impacts in vivo on the migration and morphology of endothelial
tip cells and leads to a reduction of filopodia number and length.
Additionally a NOSTRIN knockout mouse was generated. The analysis of FGFR1 signal
transduction in primary mouse lung endothelial cells (MLECs) from NOSTRIN knockout
and wild type mice revealed that FGF2-dependent MAPK activation was attenuated in
MLECs isolated from NOSTRIN knockout mice when compared to MLECs isolated from
wild type mice. The effect of NOSTRIN on FGF2-dependent signal transduction seems to
be specific, since VEGF-induced MAPK activation was not affected in NOSTRIN
knockout MLECs. The importance of NOSTRIN for FGF2 signal transduction in vivo is
demonstrated by the greatly impaired angiogenic response to FGF2 in NOSTRIN
knockout mice in matrigel plug assay. In a detailed biochemical analysis it was
discovered that NOSTRIN interacts with the activated small GTPase Rac1 and that
overexpression of NOSTRIN enhances Rac1 activation. Furthermore, the interactions of
NOSTRIN with both Rac1 and its GEF Sos1 are required for NOSTRIN-mediated
activation of Rac1. In accordance, activation of Rac1 was not detected upon FGF2
stimulation in NOSTRIN knockout MLECs.
In conclusion, the present work describes a novel function of the F-BAR protein
NOSTRIN in FGFR1 signal transduction. Data presented in this work demonstrate that
NOSTRIN is required for the assembly of a complex consisting of FGFR1, Sos1 and
Rac1 and subsequently for the FGF2-dependent activation of Rac1 in endothelial cells.
The phenomenon of magnetism is a pure quantum effect and has been studied since the beginning of civilization. The practical use of magnetic materials for technical purposes was well established in the 19th century; still nowadays there is no lack of new high-tech applications based on magnetism for example in information technology to store and process data. This thesis does not focus on the development of new applications of magnetism in technology, nor enhancement of known fields of application. Instead, the intention is to use a quantum theory of magnetism for obtaining new insights on physical effects that accompany the phenomenon of magnetism. Therefore three different model systems, each of which are believed to describe a class of real compounds, are considered. Starting from the idea that magnetism can be understood by use of the so-called Heisenberg model that microscopically characterizes the interaction between localized magnetic moments, we restrict ourselves to the case where a long-range magnetic order is present. In order to deduce consequences resulting from this microscopic picture we use the spin-wave theory that is introduced in the first chapter. Central objects of this theory are the magnons which are elementary quantum excitations in ordered magnets. An application of these mathematical techniques to a model that describes an antiferromagnet in an external magnetic field is presented in the second chapter. Quantities like the spin-wave velocity and the damping of magnons are calculated using a Hermitian operator approach in the framework of spin-wave theory. A strong renormalization of the magnetic excitations arises because the symmetry of the system is reduced due to the external magnetic field. In the second model system, that describes thin films of a ferromagnet, concepts of classical physics meet quantum physics: The magnetic dipole-dipole interaction that is also known in everyday life from the magnetic forces between magnets and was initially formulated in the theory of electromagnetism, is included in the microscopic model. Having a special compound in mind where the magnetic excitations are directly accessible in experiments, the energy dispersions of magnon modes in thin-film ferromagnets are deduced. Our approach is essentially a basis for further investigations beyond this thesis to describe strong correlations and condensation of magnons. A recent realization of data processing devices with spin waves puts the understanding of physical processes in these ferromagnetic films in the focus of upcoming research. The third model system brings in the so-called frustration where the interactions between the spins are such that the total energy cannot be minimized by an appropriate alignment of the magnetic moments in the classical picture. In the simplest case this appears because the antiferromagnetically coupled spins are located on a triangular lattice. This situation will lead to strong quantum fluctuations which make this model system interesting. Finally the overall symmetry is reduced by inclusion of spin anisotropies and an external magnetic field. Instead of focusing on the properties of the magnetic excitations, the effect of the magnetic field on the properties of the lattice vibrations is subject to the investigation. This is interesting because the characteristics of lattice vibrations can be measured experimentally using the supersonic technique.
Pulsed electron-electron double resonance (PELDOR) is a pulsed EPR method that can reliably and precisely provide structural information regarding duplex RNAs and DNAs by measuring long-range distances (1.5-7 nm) utilizing distance-dependent magnetic dipole-dipole interaction between two nitroxide spin labels. In this thesis the application field of PELDOR spectroscopy has been expanded. For the first time the global architecture of tertiary folded RNA has been mapped in vitro. Moreover, the first application of PELDOR for determining structural aspects of RNA and DNA molecules inside cells has been presented. RNA has the central role in cellular processes and gene regulation. It can adopt complex three dimensional structures, which in combination with its conformational dynamics is essential for its function as biological catalyst, structural scaffold and regulator of gene expression. Riboswitches are cis-acting RNA segments that modulate gene expression by direct binding of small molecules with high affinity and specificity. Neomycin-responsive riboswitch is an engineered riboswitch developed by combination of in vitro selection and in vivo screening. Upon insertion into the 5‟ untranslated region of mRNA and binding the cognate ligand it is able to inhibit translational initiation in yeast. Using enzymatic probing the secondary structure had been postulated comprising global stem-loop architecture with a terminal and an internal loop. In the first part of this thesis, the global conformational arrangement of this 27 nucleotides long RNA element has been studied by means of site-directed spin labeling and PELDOR spectroscopy. Spin-labeled neomycin-responsive riboswitch mutants were synthesized via a Sonogashira cross-coupling reaction between 5-membered pyrroline ring based nitroxide radical (TPA) and 5-iodo-uridine. The labeling positions were chosen outside of the binding pocket and UV melting curves revealed that spin-labeling neither disturbs the secondary structure nor interferes with ligand binding. Efficient ligand binding was proven by thermal stabilization of 20.3±3.3 oC upon addition of neomycin, as well as by cw EPR spectra. PELDOR time traces with long observation time windows and with good signal to noise ratio and modulation depth were recorded for all double-labeled samples allowing a reliable data analysis. The fact that there were no shifts in the measured distances upon addition of neomycin implied the existence of a prearranged tertiary structure of the neomycin-sensing riboswitch without a significant global conformational change induced by ligand binding. Measured distances were in very good agreement with the NMR structure of the ligand-bound state of the riboswitch indicating the intrinsic propensity of the global RNA architecture toward its energetically favored ligand-bound form at low temperature. The results harvested in this work represent the first application of PELDOR for mapping the global structure of a tertiary folded RNA. In the second part of this thesis the possibility of applying PELDOR on nucleic acids (NAs) in cellular environment has been investigated. It was shown before that global NA structure depends on matrix conditions, such as concentration of ions and small molecules, molecular crowding, viscosity and interactions with proteins. Therefore, PELDOR spectroscopy on a double-labeled 12-base pair DNA duplex, the 14-mer cUUCGg tetraloop hairpin RNA and the 27-mer neomycin-sensing riboswitch has been used to obtain long-range distance constraints on such systems in Xenopus laevis oocytes and to compare them with in vitro measurements. The reduced lifetime of nitroxide spin labels under cellular conditions has been a major challenge in these measurements. Investigation of nitroxide reduction kinetics in-cell has revealed that the 5-membered pyrrolidine and pyrroline rings are significantly slower reduced compared to 6-membered piperidine ring based nitroxides. Due to prolonged lifetime of the TPA nitroxides covalently attached to NA molecules PELDOR signals could be measured with good signal-to-noise ratios up to 70 minutes of incubation time. The partial loss of coupled spin labels due to nitroxide reduction only led to a decrease in the modulation depth upon increasing the incubation time. No alterations in the measured distances between in vitro and in-cell experiments implies the existence of stable overall conformations of the 14-mer cUUCGg tetraloop hairpin RNA and the 27-mer neomycin-sensing riboswitch, whereas the 12-bp duplex DNA experiences stacking in-cell but retaining the secondary structure. Thus, for the first time nanometer distance measurements were performed inside cells, clearly laying a foundation for the application of PELDOR spectroscopy to study biological processes in cells, such as diffusion, interaction with proteins and other factors or chemical reactions.
The role of small leucine-rich proteoglycans, biglycan and decorin, in podocytopathy and albuminuria
(2011)
Biglycan is a member of the small leucine-rich proteoglycan (SLRP) family and is involved in the assembly of extracellular matrix components. In macrophages soluble biglycan acts as an endogenous ligand of the innate immunity receptors TLR2 and TLR4. Data addressing the role of biglycan in renal pathology are surprisingly limited. In a normal kidney, biglycan is expressed mainly in the tubulointerstitium; however, in the course of various renal diseases its expression may be altered. The biological role and mechanisms of biglycan action in the pathology of renal diseases, especially those affecting glomeruli, remain poorly understood.
Albuminuria is the first detectable clinical abnormality in diabetic nephropathy. In this study we detected increased biglycan mRNA expression in glomeruli of renal biopsies of patients with incipient diabetic nephropathy, with predominant localization in podocytes. This novel finding raised the question about the role and mechanisms of biglycan action in diabetic podocyte injury and whether the mechanisms of biglycan signaling causing podocyte injury and albuminuria could be extrapolated to other glomerular diseases.
To investigate the role of biglycan in the cause of diabetic podocyte injury and albuminuria we used the murine model of STZ-induced diabetic nephropathy and wild type (Bgn+/0) and biglycan deficient (Bgn-/0) mice. We observed that biglycan was expressed on mRNA and protein levels in podocytes of diabetic Bgn+/0 mice and that diabetic Bgn+/0 mice also had significantly higher albuminuria compared to non-diabetic mice 6 and 12 weeks after disease induction. Biglycan deficiency was shown to be an important factor in albuminuria development. Namely, we observed that diabetic Bgn-/0 mice had significantly lower levels of urinary albumin compared to diabetic Bgn+/0 mice. We showed that less severe podocyte loss in the urine of diabetic Bgn-/0 mice was associated with significantly higher nephrin and podocin glomerular expression compared to diabetic Bgn+/0 mice. Our data suggested that biglycan deficiency was protective against podocyte loss into urine and might be beneficial against development of albuminuria in diabetes.
Biglycan contributed to podocyte actin rearrangement due to increased phosphorylation of Rac1 in vitro. Furthermore, biglycan induced caspase-3 activity and production of reactive oxygen species (ROS), thus enhancing apoptosis in cultured podocytes. Biglycan-induced ROS generation was TLR2/TLR4-dependent. Overexpression of soluble biglycan in wild type mice induced albuminuria under normal conditions and significantly increased albuminuria under pathological conditions (murine model of LPS-induced albuminuria). Inhibition of Rac1 activity in vivo decreased the albuminuria induced by biglycan overexpression. In patients with glomerular diseases, biglycan was detected in urine and was associated with nephrin appearance in the urine of these patients and with increased albuminuria. Collectively, our results elucidate a novel mechanism for biglycan-induced TLR2- and TLR4-dependent, Rac1- and ROS-mediated podocytopathy leading to podocyturia, albuminuria development and progression of glomerular diseases. Interfering with biglycan actions and blocking its signaling via TLR2 and TLR4 might be a potential therapeutic strategy against these diseases. To achieve this goal, the specific mechanisms for binding of biglycan to TLR2 and TLR4 must be elucidated and effective ways of preventing this binding must be developed. Nevertheless, biglycan remains the “danger signal” that activates innate immune receptors in non-immune cells and triggers the deleterious mechanisms leading to aggravation of renal injury.
Recent data indicate that reactive oxygen species (ROS) are produced in the nociceptive system during persistent pain and contribute to pain sensitization. Aim of this study was to investigate potential antinociceptive effects of ROS scavengers in different animal models of pain. Intrathecal injection of ROS scavengers 1-Oxyl-2,2,6,6-tetramethyl -4-hydroxypiperidine (TEMPOL) or Phenyl-N-tert-butylnitrone (PBN) significantly inhibited formalin-induced nociceptive behavior in mice, suggesting that ROS released in the spinal cord are involved in nociceptive processing. Formalin-induced nociceptive behavior was also inhibited by intraperitoneal injection of a combination of vitamin C and vitamin E, but not of vitamin C or vitamin E alone. Moreover, the combination of vitamin C and E dose-dependently attenuated mechanical allodynia in the spared nerve injury (SNI) model of neuropathic pain. The SNI-induced mechanical allodynia was also reduced after intrathecal injection of the combination of vitamin C and E, and western blot analyses revealed that vitamin C and E treatment can ameliorate the activation of p38 MAPK in the spinal cord and in DRGs. These data suggest that a combination of vitamin C and E can inhibit the nociceptive behavior in animal models of pain, and points to a role of the spinal cord as an important area of ROS production during nociceptive processing.
This study comprises a survey on ecology, morphology and taxonomy of parasitic fungi infecting Pteridophytes and Orchidaceae found by the author on several field trips to Western Panama as part of the project plant parasitic micro-fungi of Western Panama (ppMP). In Panama, approximately 9500 species of vascular plants are found. Of these, Orchidaceae are with ca. 1150 (ca. 12%) species by far the most speciose family. The Pteridophytes in Panama comprise ca. 940 species in 31 families. Most fungal pathogens on Orchidaceae in tropical regions were described from plants in culture or from material intercepted at borders by plant quarantine services and not from their natural habitats. Therefore, little is known about distribution and ecology of these pathogens in their natural range. The author determined and classified several hundred Orchidaceae-species and Pteridophytes at the sites selected in the context of the project. This work facilitated the identification of many host plants (at least to genus-level) even in sterile condition in the field. About 65 species of Pucciniales are known to infest Orchidaceae and ca. 38% of them are described from tropical America. All available types of Pucciniales on Orchidaceae in tropical America were studied and compared with 91 specimens of rust fungi on orchids collected by the author in Panama. Several hundred additional specimens housed in the BPI, almost all intercepted from plant quarantine services, were used for comparison. As result of this work, it is suggested to combine Uromyces stenorrhynchi Henn. to Sphenospora and, as this is the oldest epithet, to synonymize S. kevorkianii Linder, S. mera Cumm. and S. saphena Cumm. with it. Further, it could be demonstrated that Uredo aurantiaca Montemartini, U. cyrtopodii Syd. & P. Syd., U. epidendri Henn., U. guacae Mayor, U. gynandrearum Corda, U. lynchii (Berk.) Plowr., U. neopustulata Cumm. (≡U. pustulata Henn.), U. nigropuncta Henn., U. oncidii Henn., U. ornithidii F. Kern., Cif. & Thurst., and presumably U. scabies Cke., are anamorphs of this variable species. U. gynandrearum is the oldest anamorph-name for all these taxa. Therefore, it can be established that this rust infects more than 80 species of Orchidaceae in three subfamilies. In total, the anamorph of this species was collected by the author on 17 different species of Orchidaceae in Panama which, apart from one species, are all new hosts to science. The molecular data obtained by the author confirm this view, although more data, especially from material from the whole range of distribution of U. gynandrearum, are necessary. Puccinia spiranthicola Cumm. was found to be a synonym of P. cinnamomea Diet. & Holw. and was found by the author on three different Orchidaceae in two subfamilies. Uredo pleurothallidis Keissl. is now considered a synonym of U. wittmackiana Henn. and the latter as the anamorph of Puccinia oncidii Cumm. In the anamorph genus Uredo, a new species was found infecting at least five different species of Sobralia and Elleanthus (Sobraliinae) at different localities. Molecular data indicate it to be related to the currently polyphyletic Phakopsoraceae. For the rusts with suprastomatal sori on Orchidaceae, now separated from Hemileia and placed in the genus Desmosorus (nom. inval.), the current concept with only one taxon is rejected and the establishment of three subspecies is suggested. The complicated taxonomy is discussed and makes it necessary to validate the genus-name and make a new combination. Another Hemileia-anamorph species was found by the author and is considered to be new to science. This is the first species of this alliance in America on Orchidaceae. Molecular data obtained by the author confirm the separation of Desmosorus from Hemileia and the position of the new species. For rusts on Pteridophytes, a new species of Milesia, (teleomorph: Milesina) and a new anamorphic species of Uredinopsis was found, both on hosts hitherto not known. In Calidion, the presumable anamorph-genus of Uncol, the species C. cf. cenicafeae Salazar & Buriticá was found on several new hosts. Further, the teleomorph was found. Morphologically, this teleomorph did not agree with the description of Uncol by the author of the genus, although the anamorph characteristics left no doubt that it is Calidion. Apparently, the description of Uncol is inadequate, but cannot be improved, as the type is unavailable. Molecular data obtained by the author show this species to be closest to Desmosorus. For Uredo superficialis Speg., the anamorph of Desmella, nine new hosts in eight different fern families were found by the author and the collaborators of the ppMP-project. Ecological data indicate that this species includes different host specific races, which, however could not be distinguished morphologically. For all these rusts, a thorough discussion of the ecology in their habitats is given. In total, 21 LSU rDNA sequences from 6 different rust species on Orchidaceae and Pteridophytes were obtained and analyzed with the Maximum Parsimony and Minimum Evolution method. Here, the position of several groups could be confirmed, and some anamorphs could be assigned to different teleomorphic relationships. Within the Ascomycota and their anamorphs, several hitherto unknown species and species not known from these hosts or not known from Panama were found and analyzed. On Orchidaceae, the following fungi belonging to the Ascomycota are described, illustrated and discussed: In the Phyllachorales, a hitherto not known Phyllachora sp. was found on Oncidium warszewiczii Rchb. f. and was compared with the other species of this order currently known from Orchidaceae. In the Asterinaceae s. l. Lembosia cf. epidendri Meir. Silva & O. R. Pereia was found on Maxillaria crassifolia (Lindl.) Rchb. f., which is a new host and new host alliance for this fungus hitherto only known from Brazil. The fungus is described and compared with all species of Asterinaceae currently known on Orchidaceae. In the Meliolaceae, Meliola orchidacearum Cif. was found on Camaridium biolleyi (Schltr.) Schltr. and an Epidendrum sp. which are new hosts and new host alliances of this fungus which was hitherto only known from the Caribbean Islands. It is described, illustrated and compared with the type. In the Glomerellaceae, Glomerella cingulata and its anamorph Colletotrichum gloeosporioides were found on several hosts. The species is illustrated, described and compared with data from literature. In the anamorphic Mycosphaerellaceae, Pseudocercospora odontoglossii (Prill. & Delacr.) U. Braun, a species currently only known from culture, was found on the new host Pleurothallis imraei Lindl. It is illustrated, described and compared with data from literature. On ferns, the following other fungi are described, illustrated and discussed: A conspicuous undescribed form of Polycyclus was found by the author on Elaphoglossum ciliatum (C. Presl.) T. Moore (Dryopteridaceae) and Serpocaulon loriceum (L.) A. R. Sm. (Polypodiaceae). A conspectus of Parmulariaceae infecting ferns is given and demonstrated that Polycyclina should be synonymized under Polycyclus. Summing up, it can be assessed, especially for the Pucciniales, that the most speciose plant family in Panama carries remarkable few species of specific parasites, and that many of them seem to be distributed over a wide range of species which often are not closely related. One reason amongst others seems to be that parasites need a minimum density of host plants in a habitat to survive. As orchid species often occur with only few (and often small) individual plants at a given locality, the probability for a specific pathogen to infect a plant gets too low, hence high diversity by low abundance of hosts might be an impediment for specific pathogens. In this case, unspecific parasites, or such which are infecting larger alliances, are in advantage. Other reasons could be specific traits of orchids, like succulence and mycotrophy which might hamper fungal infections.
The NS5B protein of the hepatitis C virus (HCV) is a RNA-dependent RNA polymerase, which is the key enzyme for viral replication. It is recognized as one of the promising targets for antiviral intervention within the new HCV treatment approach of direct-acting antivirals (DAA). However, several of the known non-nucleoside HCV polymerase inhibitors (NNIs) identified by screening approaches show limitations in the coverage of all six major HCV genotypes (GT). Genotypic profiling therefore has to be implemented early in the screening cascade to discover new broadly active NNIs. This implies knowledge of the specific individual biochemical properties of polymerases from all GTs which is to date limited to GT 1 only. The work submitted here gives a comprehensive overview of the biochemical properties of HCV polymerases derived from all major GTs 1 - 6. Biochemical analysis of polymerases from 38 individual sequences revealed that the optima for monovalent cations, pH and temperature were similar between the GTs, whereas significant differences concerning concentration of the preferred cofactor Mg2+ were identified. Implementing the optimal requirements for the polymerases from each individual GT led to significant improvements in their enzymatic activities. However, the specific activity was distributed unequally across the GTs and could be ranked in the following descending order: 1b, 6a > 2a, 3a, 4a, 5a > 1a. Furthermore, the optimized assay conditions for GT profiling were confirmed by testing the inhibitory activity of four known prototype NNIs, each addressing one of the four NNI binding sites. Additionally, a novel NNI chemotype - identified by screening - is described, the substituted N-phenyl-benzenesulphonamides (SPBS). This inhibitor class showed reversible inhibition of NS5B from HCV 1b Con1 with IC50 values up to 39 nM. Based on the decreased inhibitory activity against a recombinant NS5B protein carrying the mutation L419M, it was assumed that the SPBS inhibitors bound to the thumb site II as it has been described for the carboxy thiophene inhibitors. The postulated binding site was consequently confirmed by analysing a provided co-crystal structure of NS5B in complex with a SPBS analogue. Notably, the two SPBS analogues SPBS-1 and SPBS-2 reported here revealed significant differences in addressing the NH-group of the main chain Y477 by hydrogen-bonds, watermediated or directly, which provoked a shift of the carboxyphenyl group of the inhibitors towards the H475 position for the water-mediated binding mode. Interestingly, the differences observed in the binding mode led to a different cross resistance profile at positions M423 and I482. Using the previously optimized biochemical primer-dependent transcription assay, inhibitory activity of the SPBS could be demonstrated against polymerases from HCV GTs 1a and 1b whereas the inhibitor class failed to inhibit any of the non-GT 1 polymerases. Furthermore, initial antiviral activity for SPBS was demonstrated against the subgenomic replicons of HCV GTs 1a and 1b, respectively, and no considerable cytotoxic potential against a panel of ten different cell types. Finally, concerning a possible future treatment without PEG-IFN α or ribavirin, the SPBS analogues were found to display additive to synergistic effects in combination with the benzothiadiazine, the benzofuran and the indole - representative inhibitors for the binding sites palm I, palm II and thumb I, repectively - in the biochemical assay. Within the same binding site as the SPBS, the reference compound hydroxydihydropyranone displayed additive interactions only with the benzothiadiazine (palm I) in the biochemical assay as well as in cell culture. Hence it could be concluded that, having characterized one individual NNI, no universal predication is possible concerning the combinatory behaviour of NNIs binding to the same binding site. As synergistic, antagonistic or additive interactions are inhibitor-dependent (not binding sitedependent) each novel NNI has to be characterized individually in one-to-one combinations.
Decorin, a small leucine rich proteoglycan (SLRP) of the extracellular matrix (ECM) is a biologically active molecule with signaling capabilities modulating diverse cellular functions 1. In this report, we explore the role of the matrix proteoglycan decorin in the regulation of inflammation and apoptosis and the resultant biological significance in cancer and diabetic nephropathy. The mechanisms linking immunity and inflammation with tumor development are not well defined. Here we report a novel finding that the soluble form of decorin could autonomously trigger the synthesis of TNFα and IL-12 in macrophages through TLR2 and TLR4 in a p44/42- and p38-dependent manner. In the presence of LPS, decorin enhanced the effects of LPS by signaling additionally via TLR2. Further, decorin could enhance PDCD4 protein expression with subsequent inhibition of LPS-mediated IL-10 protein synthesis by two mechanisms: i) by TLR2/TLR4-dependent stimulation of PDCD4 synthesis and ii) by inhibition of the TGFβ1-induced increase of miR-21, a posttranscriptional suppressor of PDCD4 protein synthesis. Enhanced PDCD4, a translational inhibitor of IL-10, downregulated this anti-inflammatory cytokine, thereby further driving the cytokine profile towards a proinflammatory phenotype.
Importantly, these mechanisms appear to operate in a broad biological context linking pathogen-mediated with sterile inflammation as shown here for sepsis and growth retardation of established tumor xenografts. In sepsis, decorin is an early response gene evoked by inflammation and is markedly elevated in plasma of septic human patients and in plasma and tissues of septic mice. Our findings suggested that in vivo decorin alone mimics the effects of LPS by enhancing the plasma and tissue levels of pro-inflammatory TNFα, IL-12 and PDCD4 but when administered together with LPS, it potentiated the proinflammatory response of this PAMP by inhibiting active TGFβ1, miR-21 and hence the LPS mediated IL-10 production. In vivo, overexpression of decorin in tumor xenografts resulted in decorin/TLR2/4-driven synthesis of PDCD4, TNFα, IL-12 and decorin/TGFβ1/miR-21-mediated inhibition of PDCD4 suppression shifting the immune response to a pro-apoptotic and proinflammatory axis with strong anti-tumorigenic effects resulting in increased apoptosis and growth retardation of solid tumor. Thus, decorin signaling boosts inflammatory activity in sepsis and tumor. In contrast to the proinflammatory and proapoptotic role of decorin in tumor, decorin deficiency in diabetic kidneys led to enhanced apoptosis and increased mononuclear cell infiltration indicating that decorin might give rise to distinct biological outcomes depending on the cell type and biological context. Accordingly, in this study, we used a model of streptozotocin-induced diabetes type 1 in wild-type (Dcn+/+) and decorin-deficient- (Dcn-/-) mice to further elucidate the role of decorin in diabetic nephropathy. In this model, decorin was overexpressed in the mesangial matrix of the glomerulus and in the tubulointerstitium both at the mRNA and protein level in early stages of diabetic nephropathy which declined as the disease further progressed supporting the concept that decorin might act as a part of a natural response to hyperglycemia and to damage caused there from. These observations correlate with the data obtained in renal biopsies from patients at various stages of diabetic nephropathy 15, suggesting clinical relevance of our findings for the human disease. In the diabetic kidney, decorin deficiency was associated with: i) glomerular and tubular overexpression of p27Kip1 and enhanced proteinuria, ii) enhanced expression of TGFβ1 and CTGF resulting in increased accumulation of ECM, iii) overexpression of biglycan and elevated infiltration of mononuclear cells, iv) enhanced apoptosis of tubular epithelial cells despite overexpression of tubular IGF-IR. We further discovered that decorin binds to the IGF-IR in tubular epithelial cells and conveys protection against high glucose-mediated apoptosis providing evidence for a protective role of decorin during diabetic nephropathy development.
Thus, future therapeutic approaches that would either enhance the endogenous production of decorin or deliver exogenous decorin to the diseased solid tumors and/or diabetic kidney might improve the prognosis of these chronic diseases.
Nonequilibrium phase transitions in chiral fluid dynamics including dissipation and fluctuation
(2011)
Chiral fluid dynamics combines the fluid dynamic expansion of a hot and dense plasma created in a heavy-ion collision with the explicit propagation of fluctuations at the chiral phase transition of quantum chromodynamics. From systems in equilibrium long-range fluctuations are expected at a conjectured critical point. Heavy-ion collisions are, however, finite in size and time and very dynamic. It is thus likely that nonequilibrium effects diminish the signal of a critical point. They can, however, stimulate phenomena at a first order phase transitions, like nucleation and spinodal decomposition. Both of phase transition scenarios are investigated in this work. Based on the linear sigma model with constituent quarks a consistent quantum field theoretical approach using the two-particle irreducible effective action is developed to derive both, the local equilibrium properties of the expanding quark fluid and the damping and noise terms in the Langevin equation of the order parameter of the phase transition, the sigma field. Within this formalism it is possible to obtain a conserved energy-momentum tensor of the coupled system. It describes the energy dissipation from the sigma field to the heat bath during relaxation. Within this model we investigate nonequilibrium phenomena in a scenario with a critical point and a first order phase transition. We observe long relaxation times at the phase transition, phase coexistence at the first order phase transition and critical slowing down at the critical point. We find a substantial supercooling in a first order phase transition in our model and due to the energy-momentum exchange also reheating is present. While at the critical point the correlation length increases slightly we find an enhanced intensity of nonequilibrium fluctuations at the first order phase transition, which leads to an increased production of sigma mesons.
In total, this dissertation comprises three research papers. Objective of all of these papers are to detect mistakes of private investors when conducting mutual funds investments and to analyze the implications. Moreover, the question is addressed whether financial advisors help private investors to avoid these investment mistakes. All three research papers use the same data base which has been provided by a German online brokerage house. The detailed data set allows contributing to existing literature on mutual fund investments, smart decision making, household finance as well as financial advice on an investor- and transaction-specific level. The first paper addresses the question which particular decision criteria private investors use when purchasing mutual funds. It can be shown that funds volume is the dominating decision criterion, whereas historical performance is only of minor importance. As performance persistence exists in the underlying data set, it can be concluded that the majority of investors make investment mistakes. In the second paper it is shown that smart investors, i.e. investors who purchase mutual funds by chasing historical performance, are older, wealthier, more experienced and less likely to be overconfident. In addition, it can be verified that there exists a positive impact of the ability to select mutual funds by chasing historical performance on the overall investment success. Hence, the quality of mutual fund selection ability is an ex-ante measure for investment success. Finally, the third paper analyzes the influence of financial advice on mutual fund decision making of private investments. Evidence can be provided that financial advisors do not help their customers to purchase mutual funds by chasing historical performance. In fact, advisors recommend high-volume mutual funds from well-known fund families. Apparently, financial advisors are much more salesmen than real advisors. These results hold when controlling for potential endogeneity issues.
Blood vessel formation is a well orchestrated process where multiple components including different cells types, growth factors as well as extracellular matrix proteins act in synergistic and highly regulated manner to support the growth of new blood vessels. During embryonic development this process is marked as vasculogenesis and entails the differentiation of mesodermal cells into angioblasts and their subsequent fusion into a primitive vascular plexus. Angiogenesis, in contrast, describes the formation of new vessels from the pre-existing vasculature and it occurs in the embryo during remodeling of the primitive plexus into a mature vascular network. Furthermore, in the adult, angiogenic processes play a role in various physiological and pathological conditions. Angiogenesis is governed by a set of factors and molecular mechanisms whose identification has been a major focus of cardiovascular research for the past several decades. Most recently, Epidermal growth factor-like domain 7 (EGFL7) has been described as a novel molecular player in this context. This secreted protein is produced by endothelial cells and has been implicated in vessel development. Studies performed in zebrafish revealed an important role for EGFL7 in lumen formation during vasculogenesis although the underlying molecular mechanism has not been elucidated yet. In contrast, the investigation of EGFL7’s functions during angiogenic sprouting has faced several challenges and the role of EGFL7 in angiogenesis remained elusive. The purpose of this thesis was to identify the functions of EGFL7 during angiogenic mode of vessel formation in a systematic fashion using numerous in vitro as well as in vivo approaches.
Previously it has been suggested that EGFL7 might associate with the extracellular matrix from where it could exert its effects. Indeed, we could show that EGFL7 accumulates on the outer surface of endothelial cells in vivo by demonstrating its co-localization with collagen IV, a major constituent of the basal lamina. Furthermore, after its secretion to the extracellular matrix (ECM), EGFL7 seemed to interact with some components of the extracellular matrix including fibronectin and vitronectin, but not collagens and laminin.
A major group of receptors that mediate the interaction between the cells and the ECM are integrin receptors. Our co-immunoprecipitation studies revealed that EGFL7 associated with integrin αvβ3 which is highly expressed in endothelial cells and known to be important for vessel growth. Importantly, this EGFL7-αvβ3 integrin interaction was dependent on Arg-Gly-Asp (RGD) motif present within the second EGF-like domain of EGFL7 protein. Adhesion assays performed with human umbilical vein endothelial cells (HUVEC) revealed that EGFL7 promoted endothelial cell adhesion compared to BSA used as a negative control, however, adhesion seemed to be less efficient as compared to bona fide ECM proteins such as fibronectin and vitronectin. In addition, cultivation of endothelial cells on EGFL7 was characterized by the absence of mature focal adhesions and stress fibers, but was paralleled by increased phosphorylation of kinases typical for integrin activation signaling cascade such as FAK, Src and Akt. This led us to the hypothesis that EGFL7 creates an environment that supports a motile phenotype of endothelial cells by serving as a modulator of existing interactions between the cells and the surrounding matrix. Indeed, EGFL7 increased random migration of HUVEC on fibronectin in an αvβ3 integrin dependent manner as shown using a live cell imaging platform. Most importantly, this was paralleled by a decrease in endothelial cell adhesion to fibronectin which is consistent with previous reports on secreted proteins that support a medium strength of adhesion and such promote cellular migration. To assess the overall effect of EGFL7 on the process of blood formation several in vitro and in vivo approaches were employed. First, the addition of EGFL7 to Matrigel injected subcutaneously into mice significantly increased the invasion of endothelial cells into the plugs. Second, a spheroid-based sprouting assay in three-dimensional collagen matrix clearly demonstrated the ability of EGFL7 to support angiogenic sprouting in an integrin dependent manner. This is consistent with the observed effects of EGFL7 on endothelial cell migration. Third, using in vivo assays such as the chick chorioallantoic membrane (CAM) assay as well as a zebrafish model system we were able to validate the importance of the EGFL7-integrin interaction for the process of angiogenesis in vivo. Taken together, I identified some of the major cellular functions EGFL7 modulates during angiogenesis. In addition, with integrin αvβ3 I unraveled a novel interaction partner of EGFL7 that delivers a mechanistical explanation for EGFL7’s effects on blood vessel formation. Most importantly, data presented in this PhD thesis contribute substantially to the existing literature on EGFL7 unambiguously assigning a role for this protein in the process of angiogenesis.
Proteomic analysis is the large-scale identification and characterization of proteins including post translational modifications. Proteomics encompasses a number of approaches including bottom-up and top-down workflows which are widely used independently and complementary as tools for the successful study of protein species. However, up to the present day these techniques have not been able to overcome every analytical limitation. Mass spectrometry has played a vital role alongside proteomics in providing the required analytical means of detecting protein amounts down to the atomole range. Soft ionization methods such as matrix assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) have permitted the transfer of peptides and intact proteins into the gas phase without extensive degradation. The introduction of recent developments in MALDI technology such as the highly sensitive 4-chloro-alpha-cyanocinnamic acid matrix (Cl-CCA) as well as the commercial availability of a MALDI-LTQ-Orbitrap which boosts peptide mass accuracy below 3 parts per million (ppm), have offered new prospective in protein analysis. The aim of the current study is to incorporate these new aspects and provide further advancements in gel-based as well as gel-free proteomic workflows.
Peptides of proteolytically digested proteins are routinely analyzed by means of peptide mass fingerprinting (PMF) often combined with MS/MS analyses to complement and substantiate PMF results by peptide sequence information. The most widely used protease for enzymatic digestion is trypsin, since it exhibits a very specific cleavage behavior limited to C-terminal hydrolyses after basic amino acids. However, less specific enzymes such as chymotrypsin, elastase and pepsin have emerged as useful tools in the analysis of particular protein classes e.g. membrane, cereal, and phosphorylated proteins. In this work a comprehensive bottom-up proteomic investigation including in-solution and in-gel protein digestions of analytes covering small to large, acidic to basic, and hydrophobic to hydrophilic proteins in combination with a series of less specific enzymes are presented in order to show the superiority of the novel MALDI matrix Cl-CCA. The Cl-CCA matrix proved to be highly superior compared to standard α-cyano-4-hydroxycinnamic acid (CHCA) since an average detection of more than 2- to 3-fold peptide amount was possible depending on the used protease and, therefore, resulting in strongly increased sequence coverage. Additionally, protein identification of chymotrypsin and elastase in-gel digested protein standards was evaluated. The MALDI-LTQ-Orbitrap providing peptide mass accuracy below and up to 3 ppm in combination with Cl-CCA as matrix and newly optimized digestion conditions led to unambiguous protein identifications of all chymotryptic digests outperforming its tryptic counterparts in the case of hydrophobic bacteriorhodopsin and α-globin from hemoglobin A (α-HgbA). In addition, significantly higher sequence coverage and increased number of detected peptides was acquired. Moreover, a proposed workaround for elastase digestions was capable of providing a solution for successful identification results.
Apart from digestions of singly separated proteins, solution isoelectic focusing (sIEF) was evaluated. OFFGEL fractionation is an efficient means of fractionating peptides and proteins according to their isoelectric point (pI) values through immobilized pH gel (IPG) strips after which samples are recovered in solution. Consequently, an issue of peptide recovery arises as a category of peptides relatively insoluble to the recovery solution should be present. A method was developed including the scraping of gel matrix from the IPG strips and peptide extraction using acetonitrile as organic solvent in combination with analytical techniques such as nLC-MALDI-MS/MS for peptide identification. The nature of the peptide species remaining in-gel was analysed and attributed to peptide solubility. A general trend in which a high percentage of neutral and hydrophobic peptides remaining entrapped in the IPG gel strip was observed.
The present work also examines a new top-down proteomic workflow involving protein elution from cleavable gels containing the labile crosslinker ethylene-glycol-diacrylate (EDA). Protein amounts of as low as 100 ng loaded onto EDA gels were detected using MALDI-TOF MS in the linear acquisition mode. Proteins from 8.5 up to 78 kDa were successfully measured including a hydrophobic 15 kDa core protein attaining a GRAVY score of +0.079. Additionally, the method was compatible with one dimensional protein separation as well as for 2-D IEF/SDS-PAGE. Lastly, two methods for protein identification were tested and found to be compatible to the proposed technique.
This thesis has light mesons and their vacuum interactions as its topic. In particular, the work examines the question where the scalar antiquark-quark states are found in the physical spectrum -- in the energy region below or above 1 GeV. Contrary to the naive expectation, the mentioned states are found in the region above 1 GeV. This has consequences for the building of order parameters for the chiral symmetry breaking of Quantum Chromodynamics (QCD).
It has been estimated that about 1% of live births carry severe congenital heart defects and 20-30% among them have valve malformations. Despite its medical importance the underlying cause of many valvular diseases remains undiscovered. Thus, it is important to identify genes that play a crucial role in cardiac valve formation and maturation.
A temporal RNA expression analysis of heart development suggested that the extracellular matrix protein Nephronectin might be a novel regulator of valve development and/or trabeculation. Nephronectin is transiently expressed during rat heart development at the time of heart valve morphogenesis and trabeculation. Moreover, the extracellular matrix is known to be crucial for organogenesis. It is a complex, dynamic and critical component that regulates cell behavior by modulating the activity, bioavailability, or presentation of growth factors to cell surface receptors.
In order to verify the hypothesis that Nephronectin is a novel regulator of valve formation and/or trabeculation the zebrafish was chosen as model system. Females are able to spawn at intervals of 5 days laying hundreds of eggs in each clutch. Development progresses rapidly with precursors to all major organs appearing within 36 hours post fertilization. Zebrafish embryos develop externally, are translucent and continue to grow for several days despite developing severely malformed, non functional hearts. In addition, gene expression can be easily modulated. During the present study it has been shown that Nephronectin expression is correlated to valve development and trabeculation. Morpholinomediated knockdown of Nephronectin in zebrafish caused failure of valve formation and trabeculation resulting in > 85% lethality at 7 days post fertilization.
Cardiac valve formation is initiated at the junction of atrium and ventricle and is characterized by extracellular matrix deposition and endocardial cell differentiation. In accordance with the above-described phenotype the earliest observed abnormality in Nephronectin morphants was an extended tube like structure at the atrio-ventricular boundary. In addition, the expression of myocardial genes involved in cardiac valve formation (cspg2, fibulin1, tbx2b, bmp4) was expanded and endocardial cells along the extended tube like structure exhibited characteristics of atrio-ventricular cells (has2, notch1b and Alcam expression, cuboidal cell shape). Inhibition of has2 in Nephronectin morphants rescued the endocardial but not the myocardial expansion. In contrast, diminishment of BMP signaling in npnt morphants resulted in reduced ectopic expression of myocardial and endocardial atrio-ventricular markers. Taken together, these results identify Nephronectin as a novel upstream regulator of BMP4-HAS2 signaling playing a crucial role in atrio-ventricular canal differentiation.
The enzyme quinol:fumarate reductase (QFR) from the anaerobic epsilon-proteobacterium Wolinella succinogenes is a membrane protein complex that couples the catalysis of the oxidation of menaquinol to menaquinone to that of the reduction of fumarate to succinate. This is the terminal step in fumarate respiration, a form of anaerobic respiration in which oxygen is replaced by fumarate as the terminal electron acceptor in many anaerobic microorganisms. In QFR, both the heme groups (low-potential distal and high-potential proximal heme b group in transmembrane subunit C) are part of the electron transport chain between the two catalytic sites of the redox enzyme. Although the reduction of fumarate by menaquinol is exergonic, it is not exergonic enough to support the generation of a transmembrane electrochemical proton potential delta p. Evidence has previously shown that this reaction is catalysed by a novel mechanism, involving the facilitation of transmembrane electron transfer by transmembrane proton transfer via an essential compensatory transmembrane proton transfer pathway ("E-pathway") which is inactive in the oxidized state of the enzyme. The two key constitutents of the the pathway are the amino acid residue Glu C180 of the transmembrane helix V (located in subunit C) and the ring C propionate of the distal heme bD. The aim of the project was to obtain, by employing a combination of time-resolved as well as static spectroscopic approaches, a detailed insight of the transmembrane electron coupled proton transfer mechanism. Minute changes in both the oxidized and reduced states of a redox protein system can be selectively and sensitively monitored by static Fourier Transformed Infrared (FTIR) difference spectroscopy. The technique employed in this context, electrochemically induced FTIR difference spectroscopy, is complemented by computer-based electrostatic calculations. In order to elucidate the catalytic mechanism of the important reactions in QFR, it is necessary to investigate these in a time-resolved manner. Rapid scan FTIR difference spectroscopy is a suitable technique that allows the course of the reaction to be monitored in a time dependent fashion. The techniques employed in this context are time-resolved (tr-FTIR) and transient absorption spectroscopy. In the following, the details of individual sub-projects are discussed in brief. ...
Since combinatorial chemistry and high throughput screening have become a common technique in the drug discovery phase the number of compounds being considered has increased frequently. These structures are often characterized by high molecular weight, high lipophilicity and low solubility in aqueous and physiological media. Due to the generally poor bioavailability, new in vitro techniques were needed for screening of pharmacokinetic properties. An important parameter for these screening methods is the implementation at an early state of drug discovery phase, to find potential lead structures, before investment costs become significant. The established in vitro methods for the prediction of membrane interaction are not reliable especially for poorly soluble compounds. A new method that is fast and easy to use, requires only small amounts of NCE and which can provide more reliable predictions is needed. In this study, a new screening technique based on surface activity profiling for the prediction of oral drug absorption was evaluated with special emphasis on the predictability of biological membrane interaction of poorly soluble drug compounds. It was demonstrated that drug absorption through a bilayer membrane can be modeled by the orientation of compounds at the air/water interface. Thus amphilicity of a drug is generally related to both oral absorption and blood brain barrier penetration. In turn, amphiphilicity is influenced by the lipophilicity, size and charge distribution of a drug. Surface activity profiling was determined by analysis of surface pressure profiles using the Gibbs adsorption isotherm. The surface activity measurements were carried out using a multichannel tensiometer Delta 8, which was developed by Kibron to be utilized in conjugation high throughput screening in early drug discovery processes. For this study two test sets were analyzed, one for the prediction of gastrointestinal wall interaction and the second for the prediction of the penetration behavior at the blood brain barrier. Both test sets consist of drug compounds with a wide range of absorption properties and consist mainly of compounds with poor water solubility. Since the drugs characteristics varied, they were classified according to water solubility and surface activity and a sample preparation method for each group was established. For the prediction of oral drug absorption, three different methods were established to model the interaction of compound and gastrointestinal wall. For drug compounds with solubility above 1mmol/L the traditional shake-flask method enabled the determination of the amphiphilic properties of drug compounds in pure aqueous media. Compounds with solubility below 1mmol/L tend to not to exhibit any increase in surface activity. Thus surface tension measurements of compounds, which exhibited a limited surface activity due to poor aqueous solubility, were conducted from stock solutions prepared with various organic solvents. Mainly polar organic solvents were used. A mixture of DMSO and DMF resulted in the best combination of properties: the intensive solubility enhancing effect of DMF and the lower intrinsic surface activity of DMSO. The polar solvent ruptured the water clusters, so that highly lipophilic structures had a higher affinity to the solvent and higher concentrations could be obtained. For these compounds higher maximum surface pressure were generated than was possible in pure aqueous media. The surface pressure data were correlated with the fraction absorbed values in vivo. However it was found that poor water solubility is not the only limiting step to exhibiting any surface activity. Some compounds were showed no surface activity in either solvent system. Therefore a micelle vehicle method was established using short chain phospholipids to mimic the gastrointestinal wall. It could be concluded from the results, that non surface active drugs can interact with the phospholipids micelle vehicle in a way analogous to their interaction with the membrane bilayer. The relative critical micelle concentration was correlated with the fraction absorbed of this test set. A sample preparation schema based on the three types of drugs was established. This schema enabled us to predict the absorbance of slightly soluble and poorly soluble drugs with acceptable reliability for early compound screening. For the prediction of blood brain barrier penetration using surface activity profiling as analyzing method, a test set with very poorly soluble characteristics was chosen. The sample preparation method was based on a strictly aqueous approach using the ‘shake flask’ method. The surface tension measurements enabled correlation of the amphiphilic properties of the very poorly soluble drug compounds with BBB uptake. From the aqueous surface pressure profiles and the determination of physicochemical parameters, it was found that blood brain barrier is more likely when a drug provides a small cross-sectional area, As, at the interface. The cross-sectional area is the only parameter which is independent from the maximal concentration in aqueous media and it is particularly suitable for lower solubility compounds. In summary, it was shown that amphilicity is related to biological membrane interaction in the human body and that surface activity profiling with appropriate sample preparation can be used as a reliable screening tool for the prediction of oral drug absorption of poorly soluble drugs. Furthermore an in vitro screening method of blood-brain-barrier penetration was established.
Die Familie der Proteorhodopsine (PR) besteht aus Hunderten von PR Molekülen, die unter Lichteinwirkung Protonen pumpen und somit eine bedeutende Rolle für die Energiegewinnung spielen könnten. Da der pKa Wert des Proton Akzeptors der Schiff‘schen Base (SB) (~7.2) dem pH Wertes der Ozeane (~7.9) ähnelt, wird auch über eine regulatorische Funktion spekuliert. Wird in Erwägung gezogen, dass 24 000 PR Moleküle pro SAR86 Zelle vorhanden sind (Beja et al. 2001) und dass 13% der Bakterien der Meeresoberfläche PR besitzen (Sabehi et al. 2005) liefert dieses Protein wahrscheinlich einen bedeutenden Energiebeitrag neben der Photosynthese. Einblicke in den Mechanismus der Energieumwandlung erfordern sowohl die Untersuchung des Chromophores, welches die Lichtenergie absorbiert als auch der Struktur des Apoproteins, das durch die Generierung eines Protonengradienten zur Energiegewinnung beiträgt. Der Fokus der Doktorarbeit liegt auf dem Chromophor und seiner Umgebung. Eine erste Charakterisierung der SB und des Retinals erfolgt durch UV/VIS und NMR Messungen (Pfleger et al. 2008). Die 13C chemische Verschiebungen von 10,11-13C2 Retinal und die 15N chemische Verschiebung der protonierten SB, gebildet durch K231, zeigt eindeutig, dass im Grundzustand nur eine Konformation der Retinals, all-trans, vorliegt. Die 15N chemische Verschiebung weist außerdem auf eine starke Wechselwirkung der SB mit ihren Gegenionen hin. Desweiteren kann durch Messungen der 15N chemischen Verschiebung der SB bei verschiedenen pH Werten der pKa Wert der SB abgeschätzt werden, auf ~12. Diese Stabilisierung der positiv geladenen protonierten Form der SB weist auf die Existenz eines Wasserclusters hin, das durch die hohe Dielektrizitätskonstante die protonierte Form der SB stabilisieren könnte. Um zu überprüfen, ob Wasser an der SB gebunden ist, wird ein sogenanntes 15N-1H HETCOR Experiment durchgeführt. Der Bereich der 15N chemischen Verschiebung der SB korreliert mit einer Protonenresonanz bei ~5 ppm, welche im Bereich einer Wasserresonanz liegt und die durch D2O austauschbar ist. Dies indiziert eine wichtige Bedeutung von Wasser in der Nähe der SB für die Funktion von PR. Der Einfluss von Mutationen des Histidins H75 und des Aspartats D97 auf die 15N chemische Verschiebung der SB sowie die Auswirkung von Histidinmutationen auf das Chromophor deuten eine direkte Wechselwirkung von Aspartat 97 und der SB an, nicht aber eine direkte Wechselwirkung von H75 und der SB. Neben dem Chromophor ist außerdem das Signalpeptid Gegenstand der Untersuchung der Doktorarbeit. Motivation für die Untersuchung war die Inhomogenität der Proben, die im Zusammenhang mit ungleich prozessiertem PR stehen könnten. Ein zweiter Teil beschäftigt sich mit neuen Konzepten der Datenaufnahme, da das S/R in der Festkörper NMR ein limitierender Faktor darstellt. Diese beinhalten Verstärkung der Relaxation (RELOAD) sowie die Refokussierung von T2 bei Verwendung eines Prozessierungsschrittes, der „half echo alternating transformation“ (HEAT).
Agriculture of crops provides more than 85% of the energy in human diet, while also securing income of more than 2.6 billion people. To investigate past, present and future changes in the domain of food security, water resources and water use, nutrient cycles, and land management it is required to know the agricultural land use, in particular which crop grows where and when. The current global land use or land cover data sets are based on remote sensing and agricultural census statistics. In general, these only contain one or very few classes of agricultural land use. When crop-specific areas are given, no distinction of irrigated and rainfed areas is made, whereas it is necessary to distinguish rainfed and irrigated crops, because crop productivity and water use differ significantly between them.
To support global-scale assessments that are sensitive to agricultural land use, the global data set of Monthly Irrigated and Rainfed Crop Areas around the year 2000 (MIRCA2000) was developed by the author. With a spatial resolution of 5 arc-minutes (approximately 9.2 km at the equator), MIRCA2000 provides for the first time, spatially explicit irrigated and rainfed crop areas separately for each of the 26 crop classes for each month of the year, and includes multi-cropping. The data set covers all major food crops as well as cotton, while the remaining crops are grouped into three categories (perennial, annual and fodder grasses). Also for the first time, crop calendars on national or sub-national level were consistently linked to annual values of harvested area at the 5 arc-minutes grid cell level, such that monthly growing areas could be computed that are representative for the time period 1998 to 2002.
The downscaling algorithm maximizes the consistency to the grid-based input data of cropland extent [Ramankutty et al., 2008], crop-specific total annual harvested area [Monfreda et al., 2008], and area equipped for irrigation [Siebert et al., 2007]. In addition to the methodology, this dissertation describes differences to other datasets and standard scaling methods, as well as some applications. For quality assessment independent datasets and newly developed quality parameters are used, and scale effects are discussed.
Supplementary Appendices document crop calendars for irrigated and rainfed crops for each of the 402 spatial units (Appendix I), data sources of harvested area and of cropping periods for irrigated crops, country by country (Appendix K), as well as data quality parameters (Appendix L, including spreadsheet files).