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The incidence matrices of many combinatorial structures satisfy the so called rectangular rule, i.e., the scalar product of any two lines of the matrix is at most 1. We study a class of matrices with rectangular rule, the regular block matrices. Some regular block matrices are submatrices of incidence matrices of finite projective planes. Necessary and sufficient conditions are given for regular block matrices, to be submatrices of projective planes. Moreover, regular block matrices are related to another combinatorial structure, the symmetric configurations. In particular, it turns out, that we may conclude the existence of several symmetric configurations from the existence of a projective plane, using this relationship.
ZnO-based semiconductors were studied by Raman spectroscopy and complementary methods (e.g. XRD, EPS) with focus on semimagnetic alloying with transition metal ions, doping (especially p-type doping with nitrogen as acceptor), and nanostructures (especially wet-chemically synthesized nanoparticles).
Why is our universe so fine-tuned? In this preprint we discuss that this is not a strange accident but that fine-tuned universes can be considered to be exceedingly large if one counts the number of observable different states (i.e. one aspect of the more general preprint http://www.opus-bayern.de/uni-wuerzburg/volltexte/2009/3353/). Looking at parameter variation for the same set of physical laws simple and complex processes (including life) and worlds in a multiverse are compared in simple examples. Next the anthropocentric principle is extended as many conditions which are generally interpreted anthropocentric only ensure a large space of different system states. In particular, the observed over-tuning beyond the level for our existence is explainable by these system considerations. More formally, the state space for different systems becomes measurable and comparable looking at their output behaviour. We show that highly interacting processes are more complex then Chaitin complexity, the latter denotes processes not compressible by shorter descriptions (Kolomogorov complexity). The complexity considerations help to better study and compare different processes (programs, living cells, environments and worlds) including dynamic behaviour and can be used for model selection in theoretical physics. Moreover, the large size (in terms of different states) of a world allowing complex processes including life can in a model calculation be determined applying discrete histories from quantum spin-loop theory. Nevertheless there remains a lot to be done - hopefully the preprint stimulates further efforts in this area.
Abstract: Intensification of land-use in agricultural landscapes is responsible for a decline of biodiversity which provide important ecosystem services like pest-control. Changes in landscape composition may also induce behavioural changes of predators in response to variation in the biotic or abiotic environment. By controlling for environmentally confounding factors, we here demonstrate that the orb web spider Araneus diadematus alters its web building behaviour in response to changes in the composition of agricultural landscapes. Thereby, the species increases its foraging efficiency (i.e. investments in silk and web asymmetry) with an increase of agricultural land-use at intermediate spatial scales. This intensification is also related to a decrease in the abundance of larger prey. A negative effect of landscape properties at similar spatial scales on spider fitness was recorded when controlling for relative investments in capture thread length. This study consequently documents the web building flexibility in response to changes in landscape composition, possibly due to changes in prey availability.
1. Species assemblages of naturally disturbed habitats are governed by the prevailing disturbance regime. Consequently, stochastic flood events affect river banks and the inhabiting biota. Predatory arthropods occupy predominantly river banks in relation to specific habitat conditions. Therefore, species sorting and stochastic processes as induced by flooding are supposed to play important roles in structuring riparian arthropod assemblages in relation to their habitat preference and dispersal ability. 2. To ascertain whether assemblages of spiders and carabid beetles from disturbed river banks are structured by stochastic or sorting mechanisms, diversity patterns and assemblage-wide trait-displacements were assessed based on pitfall sampling data. We tested if flooding disturbance within a lowland river reach affects diversity patterns and trait distribution in both groups. 3. Whereas the number of riparian spider species decreased considerably with increased flooding, carabid beetle diversity benefited from intermediate degrees of flooding. Moreover, regression analyses revealed trait-displacements, reflecting sorting mechanisms particularly for spiders. Increased flooding disturbance was associated with assemblage-wide increases of niche breadth, shading and hygrophilic preference and ballooning propensity for spider (sub)families. Trait patterns were comparable for Bembidiini carabids, but were less univocal for Pterostichini species. Body size decreased for lycosid spiders and Bembidiini carabids with increased flooding, but increased in linyphiid spiders and Pterostichini carabids. 4. Our results indicate that mainly riparian species are disfavoured by either too high or too low degrees of disturbance, whereas eurytopic species benefit from increased flooding. Anthropogenic alterations of flooding disturbance constrain the distribution of common hygrophilous species and/or species with high dispersal ability, inducing shifts towards less specialized arthropod assemblages. River banks with divergent degrees of flooding impact should be maintained throughout dynamic lowland river reaches in order to preserve typical riparian arthropod assemblages.
Abstract: From a conservation point of view, species- tolerances towards disturbance are often generalised and lack reference to spatial scales and underlying processes. In order to investigate how average typical species react to habitat fragmentation and disturbance, we adopted a multi-species approach to address occupancy patterns of five specialised dune arthropods (butterflies Hipparchia semele, Issoria lathonia; grasshopper Oedipoda caerulescens; spiders Alopecosa fabrilis, Xysticus sabulosus) in recently fragmented coastal dune habitats which are subjected to varying levels and modes of local disturbance, i.e. trampling by cattle or people. Occupancy patterns were assessed during two successive years in 133 grey dune fragments of the Flemish coastal dunes (Belgium, France). By treating species as a random factor in our models, emphasis was placed on generalisations rather than documenting species-specific patterns. Our study demonstrates that deteriorating effects of local disturbance on arthropod incidence cannot be interpreted independent of its landscape context, and appear to be more severe when patch area and connectivity decrease. When controlled for patch area and trampling intensity, the probability of species occupancy in poorly connected patches is higher under cattle trampling than under recreation. Incidences additionally decrease with increasing intensity of cattle trampling, but increases with trampling by tourists. This study provides evidence of mode- and landscape-dependent effects of local disturbance on species occupancy patterns. Most importantly, it demonstrates that trampling of sensitive dune fragments will lead to local and metapopulation extinction in landscapes where trampling occurs in a spatially autocorrelated way, but that the outcome (spatial patterns) varies in relation to disturbance mode, indicating that effects of disturbance cannot be generalised.
In patients suffering from end-stage renal disease who are treated by hemodialysis genomic damage as well as cancer incidence is elevated. One possible cause for the increased genomic damage could be the accumulation of genotoxic substances in the blood of patients. Two possible sources for those toxins have to be considered. The first possibility is that substances from dialysers, the blood tubing system or even contaminated dialysis solutions may leach into the blood of the patients during dialysis. Secondly, the loss of renal filtration leads to an accumulation of substances which are normally excreted by the kidney. If those substances possess toxic potential, they are called uremic toxins. Several of these uremic toxins are potentially genotoxic. Within this thesis several exemplary uremic toxins have been tested for genotoxic effects (homocysteine, homocysteine-thiolactone,leptine, advanced glycated end-products). Additionally, it was analysed whether substances are leaching from dialysers or blood tubing and whether they cause effects in in vitrotoxicity testing. The focus of chemical analytisis was on bisphenol A (BPA), the main component of plastics used in dialysers and dialyser membranes.
Towards localizing the Synapsin-dependent olfactory memory trace in the brain of larval Drosophila
(2008)
Animals need to adapt and modify their behaviour according to a changing environment. In particular, the ability to learn about rewarding or punishing events is crucial for survival. One key process that underlies such learning are modifications of the synaptic connection between nerve cells. This Thesis is concerned with the genetic determinants of such plasticity, and with the site of these modifications along the sensory-to-motor loops in Drosophila olfactory learning. I contributed to the development and detailed parametric description of an olfactory associative learning paradigm in larval fruit flies (Chapter I.1.). The robustness of this learning assay, together with a set of transgenic Drosophila strains established during this Thesis, enabled me to study the role for Synapsin, a presynaptic phosphoprotein likely involved in synaptic plasticity, in this form of learning (Chapter I.2.), and to investigate the cellular site of the corresponding Synapsin-dependent memory trace (Chapter I.3.). These data provide the first comprehensive account to-date of the neurogenetic bases of learning in larval Drosophila. The role for Synapsin was also analyzed with regard to pain-relief learning in adult fruit flies (Chapter II.1.); that is, if an odour precedes an electric shock during training, flies subsequently avoid that odour (‘punishment learning’), whereas presentation of the odour upon the cessation of shock subsequently leads to approach towards the odour (‘relief larning’). Such pain-relief learning was also the central topic of a study concerning the white gene (Chapter II.2.), which as we report does affect pain-relief as well as punishment learning in adult flies, but leaves larval odour-food learning unaffected. These studies regarding pain-relief learning provide the very first hints, in any experimental system, concerning the genetic determinants of this form of learning.
This thesis deals with the economics of innovation. In a general introduction we illustrate how several aspects of competition policy are linked to firms' innovation incentives. In three individual essays we analyze more specific issues. The first essay deals with interdependencies of mergers and innovation incentives. This is particularly relevant as both topics are central elements of a firm's competitive strategy. The essay focuses on the impact of mergers on innovative activity and competition in the product market. Possible inefficiencies due to organizational problems of mergers are accounted for. We show that optimal investment strategies depend on the resulting market structure and differ significantly from insider to outsider. In our linear model mergers turn out to increase social surplus. The second essay analyzes the different competitive advantages of large and small firms in innovation competition. While large firms typically have a better access to product markets, small firms often have a superior research efficiency. These distinct advantages immediately lead to the question of cooperations between firms. In our model we allow large firms to acquire small firms. In a pre-contest acquisition game large firms bid sequentially for small firms in order to combine respective advantages. Innovation competition is modeled as a patent contest. Sequential bidding allows the first large firms to bid strategically to induce a reaction of its competitor. For high efficiencies large firms prefer to acquire immediately, leading to a symmetric market structure. For low efficiencies strategic waiting of the first large firm leads to an asymmetric market structure even though the initial situation is symmetric. Furthermore, acquisitions increase the chances for successful innovation. The third essay deals with government subsidies to innovation. Government subsidies for research and development are intended to promote projects with high returns to society but too little private returns to be beneficial for private investors. Apart from the direct funding of these projects, government grants may serve as a signal of good investments for private investors. We use a simple signaling model to capture this phenomenon and allow for two types of risk classes. The agency has a preference for high risk projects as they promise high expected social returns, whereas banks prefer low risk projects with high private returns. In a setup where the subsidy can only be used to distinguish between high and low risk projects, government agency's signal is not very helpful for banks' investment decision. However, if the subsidy is accompanied by a quality signal, it may lead to increased or better selected private investments. The last chapter summarizes the main findings and presents some concluding remarks on the results of the essays.
Abstract: Understanding the causes and consequences of dispersal is a prerequisite for the effective management of natural populations. Rather than treating dispersal as a fixed trait, it should be considered a plastic process that responds to both genetic and environmental conditions. Here, we consider how the ambient temperature experienced by juvenile Erigone atra, a spider inhabiting crop habitat, influences adult dispersal. This species exhibits 2 distinct forms of dispersal, ballooning (long distance) and rappelling (short distance). Using a half-sib design we raised individuals under 4 different temperature regimes and quantified the spiders' propensity to balloon and to rappel. Additionally, as an indicator of investment in settlement, we determined the size of the webs build by the spiders following dispersal. The optimal temperature regimes for reproduction and overall dispersal investment were 20 °C and 25 °C. Propensity to perform short-distance movements was lowest at 15 °C, whereas for long-distance dispersal it was lowest at 30 °C. Plasticity in dispersal was in the direction predicted on the basis of the risks associated with seasonal changes in habitat availability; long-distance ballooning occurred more frequently under cooler, spring-like conditions and short-distance rappelling under warmer, summer-like conditions. Based on these findings, we conclude that thermal conditions during development provide juvenile spiders with information about the environmental conditions they are likely to encounter as adults and that this information influences the spider's dispersal strategy. Climate change may result in suboptimal adult dispersal behavior, with potentially deleterious population level consequences.
Parametric weighted finite automata (PWFA) are a multi-dimensional generalization of weighted finite automata. The expressiveness of PWFA contains the expressiveness of weighted finite automata as well as the expressiveness of affine iterated function system. The thesis discusses theory and applications of PWFA. The properties of PWFA definable sets are studied and it is shown that some fractal generator systems can be simulated using PWFA and that various real and complex functions can be represented by PWFA. Furthermore, the decoding of PWFA and the interpretation of PWFA definable sets is discussed.
Although known about and investigated since the late 1970’s, the picture of the basic principles governing inhibitor strengths and the structure-activity relationships of the cysteine protease inhibition mechanism is still very incomplete. Computational approaches can be a very useful tool for investigating such questions, as they allow the inspection of single, specific effects in isolation from all others, in a manner very difficult to achieve experimentally. The ab initio treatments of such large systems like proteins are still not feasible. However, there is a vast number of computational approaches capable of dealing with protein structures with reasonable accuracy. This work presents a summary of theoretical investigations into cysteine protease cathepsin B using a range of methods. We have concentrated on the investigation of cysteine protease inhibition by epoxide- and aziridine-based inhibitors in order to obtain better insight into these important topics. Various model systems are simulated by means of pure quantum mechanical methods and by hybrid (QM/MM) methods. Both approaches provide a static picture. Dynamical effects are then accounted for by additional molecular dynamics (MD) simulations, using both classical and QM/MM MD approaches. The quantum mechanical approach was used to study very small model systems consisting only of the electrophilic warhead of the inhibitor (both substitituted and not) and molecular moieties simulating a very simplified protein active site (methylthiolate instead of Cys29 and methylimidazolium instead of His199 residue) and solvent surroundings (two waters or two ammonium ions, in combination with a continuum solvent model). Although simple, such a system provides a good description of the most important interactions involved in the inhibition reaction. It also allows investigation of the influence of the properties of the electrophilic warhead on the reaction rate. Beside the properties of the electrophilic warhead, the protein and solvent environment is also an important factor in the irreversible deactivation of the enzyme active site by the inhibitor. The non-covalent interactions of the inhibitor with the oxyanion hole and other subsites of the enzyme, as well as its interaction with the solvent molecules, need to be explicitly taken into account in the calculations, because of their possible impact on the reaction profile. As molecular modeling methods allow the treatment of such large systems, but lack the possibility of describing covalent interactions, our method of choice was the combined quantum mechanics/molecular modeling approach. By splitting the system into a smaller part that undergoes the bond cleavage/formation process and must be treated quantum mechanically, and a larger part, comprised of the rest of the protein, which could be treated using force fields, we managed to simulate the system at the desired precision. Our investigations concentrated on the role of His199 in the inhibition mechanism as well as on the structure-reactivity relationships between cysteine protease and various inhibitors, yielding new insight into the kinetics, regio- and stereospecificity of the inhibition. In particular, our calculations provide the following insights: i.) an explanation for the regioselectivity of the reaction, and original insight into which interactions affect the stereoselectivity; ii.) a clear model which explains the known structure-activity relationships and connects these effects with the pH-dependency of the inhibition; iii.) our computations question the generally accepted two-step model by showing that substituent effects accelerate the irreversible step to such an extent that the achievement of an equilibrium in the first step is doubtful; iv.) by way of theoretical characterizations of aziridine models, the reasons for similarities and differences in the mode of action of epoxide- and aziridine-based inhibitors are elucidated; and finally, v.) combining our results with experimental knowledge will allow rational design of new inhibitors. To account for dynamical effects as well, molecular dynamics (MD) computations were also performed. In these calculations the potential energy was computed at the force field level. The results not only supported and clarified the QM/MM results, but comparison with previous X-ray structures helped correct existing errors in the available geometrical models and resolved inconsistencies in the weighting of various factors governing the inhibition. In the work the first QM/MM MD calculations on the active site of the cysteine proteases are presented. In contrast to the MD simulations, these calculations used potential energies computed at the QM/MM-level. With the help of these computations we sought to address strongly disputed questions about the reasons for the existence of the active site ion pair and its role in the high activity of the enzyme.
LINC, the human homologue of an evolutionary conserved complex, regulates the transcription of a set of genes essential during the G2/M transition (Osterloh et al., 2007; Schmit et al., 2007). One component of the LINC core module is LIN-9. LIN-9 is essential for the transcriptional activation of LINC target genes and also promotes differentiation in association with pRB (Gagrica et al., 2004). However, nothing is known about its function in vivo. Histological and molecular analysis revealed that Lin9 is ubiquitously expressed throughout embryonic development and in all examined adult organs. Additionally, Lin9 mRNA is expressed in ES cells and blastocysts. Moreover the analogous distribution of the other LINC components suggested that they all function in the same cells and most likely in the same pathway. To deeper investigate the role of LIN9 in cell cycle and differentiation in vivo, a Lin9 gene trap mouse model (GT) was successfully generated and examined. Heterozygouse Lin9GT/+ mice were inconspicuous and develop normally. However, homozygouse knockout embryos were never obtained. The Lin9GT/GT embryos die at peri-implantation, probably due to a defect in the development of the epiblast, which could be shown with in situ hybridization with specific lineage markers. In vitro, the ICM of Lin9-deficient blastocysts did not develop properly. These data suggest that the loss of Lin9 leads to embryonic lethality at peri-implantation, and indicates that LIN9 is required for proper formation of the epiblast. In parallel, the first conditional Lin9 mouse model based on the Cre-loxP technology was generated. The Lin9fl/fl allele can be deleted by Cre-recombinase, in vivo and in vitro. Therefore an inducible system with Lin9fl/fl mice harboring Cre-ERT2 was established. The MEFs generated from these transgenic mice carried a nearly complete knockout upon induction with tamoxifen. Deletion of LIN9 in MEFs had a major impact upon the cell cycle and growth rates. Specifically, they arrested in G2/M phase and stopped to proliferate. Taken together, I was able to generate a lin9 gene trap and a lin9 conditional knockout mouse model. All results obtained so far demonstrate, that Lin9 is an essential gene for embryonic development and cell cycle control. It will be of great interest to further investigate Lin9-deficiency to gain insights into the mechanism of cell cycle control in early embryonic development and cell differentiation.
In the present study a knockout mouse model of the Popeye domain containing gene 2 (Popdc2) was generated and functionally characterized. The Popdc2 null mutants were viable with an apparent normal life span. ß-galactosidase staining to visualize the expression of the Popdc2-LacZ transgene revealed the presence of the Popdc2 in heart, bladder, smooth and skeletal muscles. In the heart LacZ was found to be present in cardiac myocytes with elevated levels in the myocytes of the cardiac conduction system. Holter ECGs records of the heart function of the 8 months (but not in 3 and 6 months) old mutant and WT littermates revealed a pronounced sinus bradycardia in the mutant mice in response to three different stress regimens: isoproterenol infusion, mental stress and a physical exercise. Histological examination of the Popdc2 null mutants SAN revealed structural alterations as was detected by HCN4 staining. Moreover, volume measurements using 3-D reconstructions of serial sections stained with HCN4 antibody revealed a volume reduction of about 30% in the mutant SAN. Taken together data presented in this study suggest that the Popdc2 KO mouse line may serve as an animal model of human sick sinus syndrome. In the second part of this thesis the Popdc2 gene promoter was analyzed. Three transcription factors binding sites were predicted in the promoter region and characterized.
In order to test the effects of environmental factors on different characteristics of plant leaf waxes, barley plants (Hordeum vulgare) were abiotically stress treated (exposure to darkness, heavy metal, high salt concentrations and drought), and biotically stressed by the infection with powdery mildew (Blumeria graminis f.sp. hordei; Bgh). Different wax parameters like amount, chemical composition, and micromorphology of epicuticular wax crystals, were investigated. Etiolated leaves of barley showed distinctly reduced wax amounts and modifications in their relative composition. The alterations of these wax parameters might be a result of a developmental delay, which could have been caused by a decreased availability of energy for cellular processes, due to lack of light. Cadmium exposure led to a 1.5-fold increase of wax amount, while chemical composition was unaffected. In drought- and salt-stressed plants, all investigated leaf wax parameters remained unaltered. In each of the abiotic treatments, the microstructure of epicuticular wax crystals, formed as typical platelets, was not modified. Even after 6d infection with powdery mildew (Bgh), neither locally nor systemically enforced modifications of wax features were revealed.
The analyzed leave surfaces, resulting from these four abiotic and the biotic treatment (phenotypic approach), were compared to altered leaf surfaces’ characteristics of 18 analyzed eceriferum (cer-) wax mutants (genotypic approach). Within the screening, 5 mutants were selected which distinctly differed from the wild-type in wax amount, portions of epi- and intracuticular wax fraction, relative chemical composition, crystal morphology, and surface wettability (hydrophobicity).
Apart from quantitative and qualitative effects on the leaf waxes, environmentally enforced modifications in cuticular waxes might be reflected in molecular processes of wax biogenesis. Therefore, a barley wax-microarray was established. 254 genes were selected, which are putatively involved in processes of de novo fatty acid biosynthesis, fatty acid elongation, and modification, and which are supposed to take part in lipid-trafficking between cell compartments, and transport of wax components to the outer cell surface. The regulations within the expression pattern evoked by the respective treatments were correlated with the corresponding analytical wax data, and the observed molecular effects of a 3d powdery mildew infection were compared with succeeding fungal morphogenesis. Etiolation and cadmium exposition pointed to transcriptional modifications in the de novo fatty acid synthesis, and in the screened, transport-related mechanisms, which correlate with respective alterations in surface wax characteristics. Moderate changes in the gene expression pattern, evoked by drought- and salinity-stress, might give hints for evolved adaptations in barley to such common habitat stresses. Theinvasion of powdery mildew into the epidermal host cells was reflected in the regulation of several genes. Beside other functions, these genes take part in pathogen defense, and intracellular component transport, or they encode transcription factors. The different modifications within the molecular responses evoked by the investigated abiotic treatments, and the effects of powdery mildew infection representing a biotic stressor, were compared between the different treatments.
In order to test the potential impact of different wax parameters on Bgh, conidia germination and differentiation was comparably investigated on leaf surfaces of abiotically stressed wild-type and cer-mutants, isolated cuticles, and further artificial surfaces. The rates of conidial development were similar on each of the leaf surfaces resulting from the abiotic treatments, while a significant reduction of the germination and differentiation success was revealed for the wax mutant cer-yp.949. Compared to the wild-type, developmental rates on isolated cuticles and extracted leaf waxes of the mutant cer-yp.949 indicated a modified embedding of cuticular waxes, and a possibly changed three-dimensional structure of the cer-yp.949 cuticle, which might explain the reduced conidial developmental rates on leaf surfaces of this particular mutant.
Experiments with Bgh conidia on mechanically de-waxed leaf surfaces (selective mechanical removal of the epicuticular leaf waxes with glue-like gum arabic, followed by an extraction of the intracuticular wax portion with chloroform) demonstrated the importance of the wax coverage for the germination and differentiation of the fungal conidia. On all dewaxed leaf surfaces, except those of cer-yp.949, the differentiation success of the germlings was significantly reduced, by about 20% (“wax-effect”). This result was verified through an artificial system with increased conidia developmental rates on glass slides covered with extracted leaf waxes. Further comparative tests with the major components of barley leaf wax, hexacosanol and hexacosanal, showed that the germination and differentiation of powdery mildew conidia not only depends on the different chemistry, but is also influenced by the respective surface hydrophobicity. Compared to hexacosanol, on hexacosanal coated glass surfaces, higher germination and differentiation rates were achieved, which correlated with increased levels of surface hydrophobicity. Developmental rates of conidia on hydrophobic foils demonstrated that hydrophobicity, as a sole surface factor, may stimulate the conidial germination and differentiation processes. Moreover, the survival of conidia on artificial surfaces is determined by additional surface derived factors, e.g. the availability of water, and a pervadable matrix.
The human genome has been sequenced since 2001. Most proteins have been characterized now and with everyday more bioinformatical predictions are experimentally verified. A project is underway to sequence thousand humans. But still, little is known about the evolution of the human proteome itself. Domains and their combinations are analysed in detail but not all of the human domain architectures at once. Like no one before, we have large datasets of high quality human protein-protein-protein interactions and complexes available which allow us to characterize the human proteome with unmatched accuracy. Advanced clustering algorithms and computing power enable us to gain new information about protein interactions without touching a pipette. In this work, the human proteome is analysed at three different levels. First, the origin of the different types of proteins was analysed based on their domain architectures. The second part focuses on the protein-protein interactions. Finally, in the third part, proteins are clustered based on their interactions and non-interactions. Most proteins are built of domains and their function is the sum of their domain functions. Proteins that share the same domain architecture, the linear order of domains are homologues and should have originated from one common ancestral protein. This ancestor was calculated for roughly 750 000 proteins from 1313 species. The relations between the species are based on the NCBI Taxonomy and additional molecular data. The resulting data set of 5817 domains and 32868 domain architectures was used to estimate the origin of these proteins based on their architectures. It could be observed, that new domain architectures are only in a small fraction composed of domains arisen at the same taxon. It was also found that domain architectures increase in length and complexity in the course of evolution and that different organisms like worm, and human share nearly the same amount of proteins but differ in their number of distinct domain architectures. The second part of this thesis focuses on protein-protein interactions. This chapter addresses the question how new evolved proteins form connections within the existing network. The network built of protein-protein interactions was shown to be scale free. Scale free networks, like the internet, consist of few hubs with many connections and many nodes with few connections. They are thought to arise by two mechanisms. First, newly emerged proteins interact with proteins of the network. Second, according to the theory of preferential attachment, new proteins have a higher chance to interact with already interaction rich proteins. The Human Protein Reference Database provides an on in-vivo interaction data based network for human. With the data obtained from chapter one, proteins were marked with their taxon of origin based on their domain architectures. The interaction ratio of proteins of the same taxa compared to all interactions was calculated and higher values than the random model showed for nearly every taxa. On the other hand, there was no enrichment of proteins originated at the taxon of cellular organisms for the node degree found. The node degree is the number of links for this node. According to the theorie of preferential attachment the oldest nodes should have the most interactions and newly arisen proteins should be preferably attached to them not together. Both could not be shown in this analysis, preferential attachment could therefore not be the only explanation for the forming of the human protein interaction network. Finally in part three, proteins and all their interactions in the network are analysed. Protein networks can be divided into smaller highly interacting parts carrying out specific functions. This can be done with high statistical significance but still, it does not reflect the biological significance. Proteins were clustered based on their interactions and non-interactions with other proteins. A version with eleven clusters showed high gene ontology based ratings and clusters related to specific cell parts. One cluster consists of proteins having very few interactions together but many to proteins of two other clusters. This first cluster is significantly enriched with transport proteins and the two others are enriched with extracellular and cytoplasm/membrane located proteins. The algorithm seems therefore well suited to reflect the biological importance behind functional modules. Although we are still far from understanding the origin of species, this work has significantly contributed to a better understanding of evolution at the protein level and has, in particular, shown the relation of protein domains and protein architectures and their preferences for binding partners within interaction networks.
Objective: The objective of this study was to study recurrence in patients with differentiated thyroid carcinoma who after initial therapy consisting of total thyroidectomy and I-131 ablation, were cured defined as a negative TSH-stimulated Tg-levels and a negative I-131 whole body scan (WBS) at the first follow-up after ablation. Methods: Retrospective data for differentiated thyroid carcinoma patients from three university hospitals were pooled. Out of 1993 patients, 526 cured patients were included. All patients received at least one more TSH-stimulated WBS and Tg-measurement within 5 years after initial treatment. Results: 12 patients (2.1%) developed a recurrence after an average interval of 35 months (range: 12-59 months) following administration I-131 ablation. Overall disease-free survival according to the method of Kaplan-Meier was 96.6%. There was no difference in disease-free survival between high- and low-risk patients (p=0.61). Recurrence was first discovered by Tg-measurement during levothyroxin therapy in 7 patients, and by TSH-stimulated Tg-measurement in 5 patients. I-131 WBS did not contribute to the detection of recurrences. Multivariate analysis showed that age TNM-stage (p=0.015) and histology (p=0.032) were independent predictors of disease-free survival. Conclusion: Recurrence is a rare event in patients with DTC who received total thyroidectomy with subsequent I-131 ablation, and who had a negative first follow-up TSH-stimulated I-131 WBS and negative concurrent Tg. In the study population there were no recurrences after more than 5 years of follow-up.
One of the major challenges today is the global shortage of managerial staff. Globalization and opening up of new markets lead to a steadily rising demand, but the supply of Western talent is decreasing. Now enterprises tend to seek skilled personnel in rapidly developing economies such as China. China as a fast growing economy is usually assumed to have a vast number of low-cost workers and a bountiful supply of talent. This perception is likely to turn out to be a miscalculation endangering efficiency, growth or even the existence of enterprises that are willing to enter the Chinese market. However, not only foreign enterprises located in China suffer from talent shortage. State enterprises are also affected by competition for managerial staff. The remains of the socialist era are not yet completely overcome, especially with respect to human resource management (HRM renli ziyuan guanli). Combined with the demographic shift towards an ageing society caused by the Cultural Revolution, the One-Child Policy and a higher life expectancy, the upcoming shortage could impede economic growth. It is the cause of an increase in wages and competition, as well as rapidly changing enterprise and HRM strategies. This thesis basically concentrates on the development of the HRM sector with regard to recruitment, retention, motivation and performance appraisal of managerial staff. The current situation of staff shortage also requires a closer look on the recruitment strategies for the future generation of leaders, which are today’s young graduates. The thesis will not deal with the shortage of chief executive officers (CEO) as their turnover is closely related to shareholders and enterprise performance. Explaining this aspect would go beyond the scope of this thesis. Consequently, this thesis focuses on the central aspects of HRM under three main angles. First, HRM practice in China originated in the Mao era and in the shift from state control to reform and market liberalization. The Party planned every aspect of HRM and created a soft budget constraint. These factors prevented the development of efficient and profitable HRM strategies. Market liberalization and the state’s retreat from labor market control led to the initiation of competition. In order to adapt to these changing conditions, enterprises had to rationalize production, financing and human resources. The responsibility was gradually handed over to the enterprises, which now have to cope with market mechanisms and emerging challenges. Then, the current challenge to HRM is subject to the second part of this thesis. Managerial staff shortage is influenced by policies adopted a long time ago, but also by long distances immobility of staff. This narrows down the number of suitable personnel despite the national supply and leads to a high competition between enterprises. Competition related problems are increasing wages, which trigger a high turnover rate. Companies in China need to find a solution to all these problems as to not endanger their economic achievements. Finally, the third part analyzes the development and new approaches of the HRM sector towards recruitment, retention, motivation and assessment. The future developments are uncertain and depend on the pace of adaptation to new challenges. In spite of that, the fourth part not only summarizes the main aspects of this thesis, but also tries to give an outlook. Concerning actuality and reliability of sources it has to be stressed, that the Chinese labor market has not been subject to studies on HRM for many years. Therefore, most of the references used in this thesis are newspaper articles and internet sources. They are most suitable to represent the current conditions on the labor market. In this respect the Hudson Reports and the study by Diana Farrell were important, as they are reliable sources for numerical data. The interview with Madelaine Pfau was essential for this thesis, since her experiences with the Chinese market offered insight into the subject. Several of her ideas and opinions were the basis for further research, such as the suggestion to take a look at the HRM of Haier. The minutes of this interview are attached to my thesis. The Chinese sources consist of two research studies, an internet newspaper article and a publication from BriTay. One of the research studies deals with the adaptation of the Behavioral Event Interview to the Chinese HRM. The other gives an introduction to the HRM strategies of Haier. The newspaper article covers the use of competency models in China and tries to give further suggestions to the topic in form of an interview. The last suitable Chinese source is also an internet source from BriTay. BriTay is a consulting and management service company that was acquired by the international consultancy MRI worldwide in 2002. Therefore, BriTay was considered to be another reliable source for this thesis.
This work deals with teams in teleoperation scenarios, where one human team partner (supervisor) guides and controls multiple remote entities (either robotic or human) and coordinates their tasks. Such a team needs an appropriate infrastructure for sharing information and commands. The robots need to have a level of autonomy, which matches the assigned task. The humans in the team have to be provided with autonomous support, e.g. for information integration. Design and capabilities of the human-robot interfaces will strongly influence the performance of the team as well as the subjective feeling of the human team partners. Here, it is important to elaborate the information demand as well as how information is presented. Such human-robot systems need to allow the supervisor to gain an understanding of what is going on in the remote environment (situation awareness) by providing the necessary information. This includes achieving fast assessment of the robot´s or remote human´s state. Processing, integration and organization of data as well as suitable autonomous functions support decision making and task allocation and help to decrease the workload in this multi-entity teleoperation task. Interaction between humans and robots is improved by a common world model and a responsive system and robots. The remote human profits from a simplified user interface providing exactly the information needed for the actual task at hand. The topic of this thesis is the investigation of such teleoperation interfaces in human-robot teams, especially for high-risk, time-critical, and dangerous tasks. The aim is to provide a suitable human-robot team structure as well as analyze the demands on the user interfaces. On one side, it will be looked on the theoretical background (model, interactions, and information demand). On the other side, real implementations for system, robots, and user interfaces are presented and evaluated as testbeds for the claimed requirements. Rescue operations, more precisely fire-fighting, was chosen as an exemplary application scenario for this work. The challenges in such scenarios are high (highly dynamic environments, high risk, time criticality etc.) and it can be expected that results can be transferred to other applications, which have less strict requirements. The present work contributes to the introduction of human-robot teams in task-oriented scenarios, such as working in high risk domains, e.g. fire-fighting. It covers the theoretical background of the required system, the analysis of related human factors concepts, as well as discussions on implementation. An emphasis is placed on user interfaces, their design, requirements and user testing, as well as on the used techniques (three-dimensional sensor data representation, mixed reality, and user interface design guidelines). Further, the potential integration of 3D sensor data as well as the visualization on stereo visualization systems is introduced.
Echinococcus multilocularis is the causative agent of alveolar echinococcosis (AE), a life-threatening disease with limited options of chemotherapeutic treatment. Anti-AE chemotherapy is currently based on a single class of drugs, the benzimidazoles. Although acting parasitocidic in vitro, benzimidazoles are merely parasitostatic during in vivo treatment of AE and cause severe site effects. In the case of operable lesions, the resection of parasite tissue needs to be supported by a prolonged chemotherapy. Thus, the current treatment options for AE are inadequate and require alternatives. In the present work, the flatworm signaling pathways were analyzed to establish potential targets for novel therapeutic approaches. I focused on factors that are involved in development and proliferation of E. multilocularis using molecular, biochemical and cell biological methods. Among the analysed factors were three MAP kinases of the parasite, EmMPK1, an Erk-1/2 orthologue, EmMPK2, a p38 orthologue and EmMPK3, an Erk7/8 orthologue. Further, I identified and characterized EmMKK2, a MEK1/2 orthologue of the parasite, which, together with the known kinases EmRaf and EmMPK1, forms an Erk1/2-like MAPK module. Moreover, I was able to demonstrate several influences of host growth factors such as EGF (epidermal growth factor) and insulin on worm signaling mechanisms and larval growth, including the phosphorylation of Elp, an ezrin-radixin-moesin like protein, EmMPK1, EmMPK3 and increased mitotic activity of Echinococcus cells. In addition, several substances were examined for their efficacy against the parasite including (i) general tyrosine kinase inhibitors (PP2, leflunamide), (ii) compounds designed to inhibit the activity of receptor tyrosine kinases, (iii) anti-neoplastic agents (miltefosine, perifosine), (iv) serine/threonine kinase inhibitors that have been designed to block the Erk1/2 MAPK cascade and (v) inhibitors of p38 MAPKs. In these studies, EmMPK2 proved to be a promising drug target for the following reasons. Amino acid sequence analysis disclosed several differences to human p38 MAPKs, which is likely to be the reason for the observed enhanced basal activity of recombinant EmMPK2 towards myelin basic protein in comparison to human recombinant p38 MAPK-α. In addition, the prominent auto-phosphorylation activity of the recombinant EmMPK2 protein together with the absence of an interaction with the Echinococcus MKKs suggest a different mechanism of regulation compared to the human enzyme. EmMPK2 activity could be effectively inhibited in vitro and in cultivated metacestode vesicles by treatment with SB202190 and ML3403, two ATP-competitive pyridinyl imidazole inhibitors of p38 MAPKs, in a concentration-dependent manner. Moreover, both compounds, in particular ML3403, caused parasite vesicle inactivation at concentrations which did not affect cultured mammalian cells. Likewise, during the cultivation of Echinococcus primary cells, the presence of ML3403 prevented the generation of new vesicles. Targeting members of the EGF signaling pathway, particulary of the Erk1/2-like MAPK cascade, with Raf and MEK inhibitors prevented the phosphorylation of EmMPK1 in metacestodes cultivated in vitro. However, although parasite growth was prevented under these conditions, the structural integrity of the metacestode vesicles maintained during long-term cultivation in the presence of the MAPK cascade inhibitors. Similar results were obtained when studying the effects of other drugs mentioned above. Taken together, several targets could be identified that reacted with high sensitivity to the presence of inhibitory substances, but did not cause the parasite’s death with one exception, the pyridinyl imidazoles. Based on the presented data, I suggest pyridinyl imidazoles as a novel class of anti-Echinococcus drugs and imply EmMPK2 as survival signal mediating factor, the inhibition of which could be used for the treatment of AE.
The role of elastic interactions, particularly for the self-organized formation of periodically faceted interfaces, was investigated in this thesis for archetype organic-metal interfaces. The cantilever bending technique was applied to study the change of surface stress upon formation of the interface between 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) and Ag(111). This system is known to form a chemisorptive bonding. Indeed, the sign and the coverage-dependence of the surface stress change are in agreement to models and previous measurements of chemisorptive systems in literature. While the adsorption of molecules into the large domains is associated with a negative, i.e. compressive stress change, the formation of domain boundaries in the molecular layer induces a stress change of opposite sign, increasing the surface stress. The magnitude of the surface stress change of (-0.30 +- 0.10} N/m reflects a relatively weak binding of a PTCDA molecule to each individual single silver atom. It is emphasized, however, that if normalized to the surface stress change per molecule, this value corresponds to a stress change of (-2.2 +- 0.2) eV per molecule which is in the order of the suspected binding energy of this system. Therefore, these experiments reveal elastic interactions to be of significant order of magnitude for this system class. Thereby, they add a new point of view to the understanding of these interfaces. Besides, since the results are in agreement with the well-known properties of this interface, they establish the cantilever bending technique in the field of organic-metal interfaces. The mere existence of a bending of the sample implies an interesting detail for the PTCDA/Ag(111) interface in particular. It is the first experimental evidence for a structural change in the topmost substrate layers upon adsorption of PTCDA on Ag(111). Since such a modification has significant implications for the interpretation of other experimental results, a further investigation with more quantitative structural methods appears necessary. The main focus of this work, however, was on the investigation of the formation of the long-range ordered, self-organized faceted PTCDA/Ag(10 8 7) interface. Reciprocal space maps of this interface were recorded both by spot profile analysis low energy electron diffraction (SPA-LEED) and low energy electron microscopy (LEEM) in selected area LEED mode. Complementary to the reciprocal data, also microscopic real-space LEEM data were used to characterize the morphology of this interface. Six different facet faces ((111), (532), (743), (954), (13 9 5), and (542)) were observed for the preparation path of molecular adsorption on the substrate kept at 550 K. Facet-sensitive dark-field LEEM localized these facets to grow in homogeneous areas of microscopic extensions. If the pristine mesoscopic orientation locally deviates from the average orientation, e.g. in pristine step density, locally different facet types are formed, distorting the otherwise regular mesoscopic pattern. Hence, the original mesoscopic orientation of the substrate strongly determines the degree of order of the faceted surface and the facet species formed. The temperature-dependence of the interface formation was studied in a range between 418 K and 612 K in order to learn more about the kinetics of the process. Additional steeper facets of 27° inclination with respect to the (111) surface were observed in the low temperature regime. Furthermore, using facet-sensitive dark-field LEEM, spatial and size distributions of specific facets were studied for the different temperatures. The nucleation density of the facets did not depend on temperature and can therefore be concluded not to be limited by diffusion. Moreover, the facet dimensions were statistically analyzed. The total island size of the facets follows an exponential distribution, indicating a random growth mode in absence of any mutual facet interactions. While the length distribution of the facets also follows an exponential distribution, the width distribution is peaked, reflecting the high degree of lateral order. This anisotropy is temperature-dependent and occurs starting above 478 K substrate temperature during growth. The peaked distribution indicates the presence of a long-range interaction which leads to the structural order of the self-organized grating. The origin of this long-range interaction was investigated combining three complementary in-situ methods, all providing new insights into the formation of faceted organic-metal interfaces: the cantilever bending technique, high-resolution low energy electron diffraction (SPA-LEED), and microscopy (LEEM). The cantilever bending technique was applied for the first time to a faceting system at all. Below the faceting transition temperature the surface stress change associated with the formation of the PTCDA/Ag(10 8 7) interface resembles in shape and magnitude the one observed for the reference interface PTCDA/Ag(111). But above the transition temperature the absolute surface stress change of (-0.67 +- 0.10) N/m observed for the faceted PTCDA/Ag(10 8 7) interface is considerably larger than for the previous cases. Moreover, the stress change happens in distinguishable stages with a clearly resolvable fine structure of regimes of positive and negative stress changes. These different regimes of surface stress change can be correlated to different stages of the structural phase transition observed by the structural in-situ methods. Thereby, morphological objects (i.e. the facets) are assigned to a specific stress character. Thus, domains of different stress character can be identified on the surface. These stress domains are the prerequisite to apply continuum descriptions of the self-ordering process based on elastic interactions. Hence, the results are the first experimental verification that these continuum descriptions are indeed also applicable to the whole system class of faceting organic-metal interfaces. In conclusion, the results provide strong evidence for elastic interactions being the physical origin of long-range order for this system. In addition, the clear correlation of structural phase transition and surface stress change regimes suggests surface stress to play also an important role for the kinetics of the system. Indeed, the system seems to try to limit the overall stress change during the interface formation by forming facets of positive and negative stress character. Hence, the selection of specific facets could depend on the corresponding stress character. Furthermore, the system seems willing to re-facet at high coverages in order to prevent imperfect domain boundaries which are associated with an increase of surface stress. Finally, template-assisted growth of lateral, heterorganic nanostructures has been explored. Therefore, self-assembled monolayers as a second archetype class of molecules were grown on partially covered PTCDA/Ag(10 8 7) interfaces. Indeed, using standard surface science techniques, the basic principle of this growth scheme was confirmed to be successful.
Study of the properties of channel-forming proteins of the cell walls of different Corynebacteriae
(2008)
The genus Corynebacterium belongs, together with Mycobacterium, Nocardia, Rhodococcus and further closely related genera, to the distinctive suprageneric taxon mycolata. Many species within this diverse group of mycolic acid containing actinomycetes are known either because of their medical or biotechnological relevance. For instance, Mycobacterium tuberculosis, Mycobacterium leprae, Corynebacterium diphtheriae and Nocardia farcinica, causer of most dangerous bacterial infectious diseases world-wide, are among this exceptional group of Gram-positive bacteria. Likewise of importance are some harmless mycolata species which find use in industrial settings. Corynebacterium glutamicum and Corynebacterium efficiens are, e.g., potent producers of the flavour enhancer glutamate and the animal feed additive lysine, while several Rhodococcus species are applied in the production of acrylic acids. The cell wall of mycolata species, compared with that of Gram-positive bacteria, exhibits an unusual composition and organization. Besides an arabinogalactan-peptidoglycan complex, the cell walls of most actinomycetes contain large amounts of mycolic acids. Comparable to the outer membrane of Gram-negative bacteria, these long-chained branched fatty acids form a highly impermeable hydrophobic outer layer which provides the basis of the exceptional drug resistance of mycolata species. Like the outer membrane of Gram-negative bacteria, the cell wall of mycolata contains channel-forming proteins that allow the passage of hydrophilic solutes. By permitting and controlling the exchange and communication between the interior of the cell and the environment in which the bacterium lives, the channels play an important role for the function of the bacterial cell envelope. This thesis aimed to extend our knowledge about cell wall channels in corynebacteria. For this purpose, we examined PorA and PorH proteins that have been associated by previous studies with cell wall pores in C. glutamicum, C. efficiens and Corynebacterium callunae in order to resolve unanswered questions and to gain structural knowledge. We also investigated cell walls of pathogenic corynebacteria, in particular of Corynebacterium diphtheriae and Corynebacterium jeikeium, to investigate if these species possessed channels as is the case with their harmless relatives. In this work we provided evidence for the existence of large and water-filled cell wall channels in C. diphtheriae and C. jeikeium. Moreover, we demonstrated that the major cell wall channels of C. glutamicum, C. efficiens and C. diphtheriae consist of two distinctive polypeptides; one of whom belongs to the class of PorH proteins and the other to the class of PorA proteins. This heteromeric structure of channels of corynebacteria represents a novelty for channels of the mycolata. In contrast, the C. jeikeium channel is solely constituted by a single protein, CjPorA, arranged as an oligomer. Although the molecular mass of this protein (4kDa) is comparable to those of PorH and PorA proteins (5-7 kDa), it shares no distinctive homology in its primary sequence with them. However, there is evidence for relationship between CjPorA and PorH/PorA proteins because the gene jk0268, coding for CjPorA, is localized in a chromosomal region of C. jeikeium that corresponds to the genomic region containing the porH/porA genes in the other corynebacteria. This suggests that jk0268 (coding for the homomeric cell wall channel in C. jeikeium) and the porH/porA genes of C. glutamicum, C. efficiens and C. diphtheriae (coding for heteromeric cell wall channels) are presumably descendants of a common ancestor gene. This assumption gets support from data on phylogenetic analysis of the genus Corynebacterium. Moreover, these data suggest that the here investigated cell wall channels are presumably widespread within this genus. A profound knowledge of cell wall channels, building the main passage of solutes through the outer mycolate membrane in corynebacteria and other members of the mycolata, can be of great economical and medical value.
In neurons the Ras signaling pathway is activated by a large number of various stimuli, including trophic factors, neurotransmitters and modulatory peptides. Guanine nucleotide exchange factors (GEFs) mediate the activation of Ras GTPases, by catalyzing the exchange of GDP for GTP, and facilitate signaling networks crosstalk. In this work, very-KIND (VKIND), a new brain specific RasGEF was structurally and functionally characterized. VKIND belongs to the KIND protein family along with the non-receptor tyrosine phosphatases type 13 and Spir actin nucleation factors. The kinase non-catalytic C-lobe domain (KIND) is similar to the C-terminal protein kinase catalytic fold (C-lobe) of the p21-activated kinase (PAK). The open reading frame (ORF) of the VKIND gene of 5229 base pairs was cloned. The VKIND ORF translates into a protein of 1742 amino acids residues with a size of 191 kD. The VKIND protein structure is highly conserved among species and at present the protein is found only in Vertebratae and Echinodermatae. The arrangement of two KIND domains at its amino-terminal region, KIND1 and KIND2, is depicted in its name. The KIND module functions as a molecular interaction structure that is deprived of any enzymatic activity. While the precise occupation of the KIND1 domain remains elusive, the KIND2 domain binds to the microtubules-associated protein 2 (MAP2). The protein central portion features two clusters of high conservation of yet unknown function as well as a coiled-coil motif with a putative multiple protein-protein interaction activity. At the carboxy-terminal region VKIND features a guanine nucleotide exchange factor for Ras-like small GTPases (RasGEF) with a structural RasGEFN motif attached at its N-terminal site. The VKIND RasGEF motif is structurally related to the yeast catalytic domain CDC25. The closest relation of the VKIND RasGEF domain with an average sequence identity of 23% is assigned to the RasGEF domains of exchange factors specific for Rap GTPases with two unique insertions: the first one of 24 amino acids in the N-terminal end of the domain (between helixes αA and αB of the SOS1 RasGEF module) and the second one of 11 amino acids in the C-terminal part (between, helixes αJ and αK of the Sos1 RasGEF module). The RasGEFN domain plays a critical role in sustaining the structural and catalytical integrity of the guanidine exchange factor. VKIND is specifically and highly expressed in the murine nervous system during embryonic development and adulthood. During embryogenesis VKIND expression is present in the murine neural tube, telencephalon, retinal ganglion cells, and rhombencephalon. In the adult murine brain VKIND expression is most prominent in the cerebellum, however exclusively restricted to the granular and Purkinje cell layers. Subcellular distribution studies and time-lapse analysis revealed the gradual accumulation of VKIND into highly motile circular particles which featured estimated maximum velocity of 12 μm/min. By merging the nascent structures progressively grew to estimated 2 μm in size suggesting a role for VKIND in the vesicular transport process. Furthermore, the KIND1/KIND2 region of the VKIND protein was found to be phosphorylated by the p38 mitogen-activated protein kinase (MAPK), recently discovered to induce neurite outgrowth in response to hyperosmotic shock. In the light of VKIND negatively controlling neurite outgrowth, further elucidation of the complex Ras pathways may provide rewarding insights in the neuronal physiology.
We have established the novel interaction between mCHL2, Tsg and BMP-2 for the first time. Tsg binds to VWC1 and VWC3 of mCHL2 in a cooperative waz and plazs a role in strengthening the binding affinity. Furthermore, Tsg/mCHL2/BMP-2 termary complex and Tsg/mCHL2 binary complex have been isolated by gel-filtration chromatography. Therefore mCHL2 can form a ternary complex with Tsg and BMP-2 and this complex makes mCHL2 a better BMP-2 antagnonist.
This thesis deals with the management and analysis of source code, which is represented in XML. Using the elementary methods of the XML repository, the XML source code representation is accessed, changed, updated, and saved. We reason about the source code, refactor source code and we visualize dependency graphs for call analysis. The visualized dependencies between files, modules, or packages are used to structure the source code in order to get a system, which is easily to comprehend, to modify and to complete. Sophisticated methods have been developed to slice the source code in order to obtain a working package of a large system, containing only a specific functionality. The basic methods, on which the visualizations and analyses are built on can be changed like changing a plug-in. The visualization methods can be reused in order to handle arbitrary source code representations, e.g., JAML, PHPML, PROLOGML. Dependencies of other context can be visualized, too, e.g., ER diagrams, or website references. The tool SCAV supports source code visualization and analyzing methods.
In this PhD thesis, the effect of strain on heteroepitaxial growth is investigated by means of Kinetic Monte Carlo simulations. In this context the lattice misfit, arising from the different lattice constants of the adsorbate and the substrate material, is of particular interest. As a consequence, this lattice misfit leads to long-range elastic strain effects having strong influence on the entire growing crystal and its resulting surface morphology. The main focus of this work is the investigation of different strain relaxation mechanisms and their controlling parameters, revealing interesting consequences on the subsequent growth. Since epitaxial growth is carried out under conditions far away from thermodynamic equilibrium, it is strongly determined by surface kinetics. At this point the relevant kinetic microscopic processes are described, followed by theoretical considerations of heteroepitaxial growth disclosing an overview over several independent methodological streams, used to model epitaxy in different time and length scales, as well as the characterization of misfit dislocations and the classification of epitaxial growth modes based on thermodynamic considerations. The epitaxial growth is performed by means of Kinetic Monte Carlo simulations which allows for the consideration of long range effects in systems with lateral extension of few hundred atoms. By using an off-lattice simulation model the particles are able to leave their predefined lattice sites, which is an indispensable condition for simulating strain relaxation mechanisms. The main idea of our used model is calculating the activation energy of all relevant thermally activated processes by using simple pair potentials and then realizing the dynamics by performing each event according to its probability by means of a rejection-free algorithm method. In addition, the crystal relaxation procedure, the grid-based particle access method, which accelerates the simulation enormously, and the efficient implementation of the algorithm are discussed. To study the influence of long range elastic strain effects, the main part of this work was realized on the two dimensional triangular lattice, which can be treated as a cross section of the real three dimensional case. Chapter 4 deals with the formation of misfit dislocations as a strain relaxation mechanism and the resulting consequences on the subsequent heteroepitaxial growth. We can distinguish between two principally different dislocation formation mechanisms, depending strongly on the sign as well as on the magnitude of the misfit, but also the surface kinetics need to be taken into account. Additionally, the dislocations affect the lattice spacings of the crystal whose observed progression is in qualitative good agreement with experimental results. Furthermore, the dislocations influence the subsequent growth of the adsorbate film, since the potential energy of an adatom is modulated by buried dislocations. A clear correlation between the lateral positions of buried dislocations and the positions of mounds grown on the surface can be observed. In chapter 5, an alternative strain relaxation mechanism is studied: the formation of three dimensional islands enables the particles to approach their preferred lattice spacing. We demonstrate that it is possible to adjust within our simulation model each of the three epitaxial growth modes: Volmer–Weber, Frank–van der Merve or layer-by-layer, and Stranski–Krastanov growth mode. Moreover, we can show that the emerging growth mode depends in principle on two parameters: on the one hand the interaction strength of adsorbate particles with each other, compared to the interaction of adsorbate with substrate particles, and on the other hand the lattice misfit between adsorbate and substrate particles. A sensible choice of these two parameters allows the realization of each growth mode within the simulations. In conclusion, the formation of nanostructures controlled by an underlying dislocation network can be applied in the concept of self-organized pattern formation as well as by the tendency to form ordered arrays of strain-induced three dimensional grown islands. In chapter 6, we extend our model to three dimensions and investigate the effect of strain on growth on bcc(100) surfaces. We introduce an anisotropic potential yielding a stable bcc lattice structure within the off-lattice representation. We can show that the strain built up in submonolayer islands is mainly released at the island edges and the lattice misfit has strong influence on the diffusion process on the plane surface as well as on the situation at island edges with eminent consequences on the appearance of submonolayer islands.
In this PhD thesis, we study the heteroepitaxial crystal growth by means of Monte Carlo simulations. Of particular interest in this work is the influence of the lattice mismatch of the adsorbates relative to the substrate on surface structures. In the framework of an off-lattice model, we consider one monolayer of adsorbate and investigate the emerging nanopatterns in equilibrium and their formation during growth. In chapter 1, a brief introduction is given, which describes the role of computer simulations in the field of the physics of condensed matter. Chapter 2 is devoted to some technical basics of experimental methods of molecular beam epitaxy and the theoretical description. Before a model for the simulation can be designed, it is necessary to make some considerations of the single processes which occur during epitaxial growth. For that purpose we look at an experimental setup and extract the main microscopic processes. Afterwards a brief overview of different theoretical concepts describing that physical procedures is given. In chapter 3, the model used in the simulations is presented. The aim is to investigate the growth of an fcc crystal in the [111] direction. In order to keep the simulation times within a feasible limit a simple pair potential, the Lennard-Jones potential, with continuous particle positions is used, which are necessary to describe effects resulting from the atomic mismatch in the crystal. Furthermore the detailed algorithm is introduced which is based on the idea to calculate the barrier of each diffusion event and to use the barriers in a rejection-free method. Chapter 4 is attended to the simulation of equilibrium. The influence of different parameters on the emerging structures in the first monolayer upon the surface, which is completely covered with two adsorbate materials, is studied. Especially the competition between binding energy and strain leads to very interesting pattern formations like islands or stripes. In chapter 5 the results of growth simulations are presented. At first, we introduce a model in order to realize off-lattice Kinetic Monte Carlo simulations. Since the costs in simulation time are enormous, some simplifications in the calculation of diffusion barriers are necessary and therefore the previous model is supplemented with some elements from the so-called ball and spring model. The next point is devoted to the calculation of energy barriers followed by the presentation of the growth simulations. Binary systems with only one sort of adsorbate are investigated as well as ternary systems with two different adsorbates. Finally, a comparison to the equilibrium simulations is drawn. Chapter 6 contains some concluding remarks and gives an outlook to possible further investigations.
We model Milky Way like isolated disk galaxies in high resolution three-dimensional hydrodynamical simulations with the adaptive mesh refinement code Enzo. The model galaxies include a dark matter halo and a disk of gas and stars. We use a simple implementation of sink particles to measure and follow collapsing gas, and simulate star formation as well as stellar feedback in some cases. We investigate two largely different realizations of star formation. Firstly, we follow the classical approach to transform cold, dense gas into stars with an fixed efficiency. These kind of simulations are known to suffer from an overestimation of star formation and we observe this behavior as well. Secondly, we use our newly developed FEARLESS approach to combine hydrodynamical simulations with a semi-analytic modeling of unresolved turbulence and use this technique to dynamically determine the star formation rate. The subgrid-scale turbulence regulated star formation simulations point towards largely smaller star formation efficiencies and henceforth more realistic overall star formation rates. More work is necessary to extend this method to account for the observed highly supersonic turbulence in molecular clouds and ultimately use the turbulence regulated algorithm to simulate observed star formation relations.
The present thesis demonstrates the potential of dipolar aggregation of merocyanine dyes as novel directional and specific supramolecular binding motif for the creation of more elaborate supramolecular architectures beyond simple dimers. Furthermore, the self-assembly studies into bis(merocyanine) nanorods gave new insights into the kinetics of morphogenesis in supramolecular aggregates.
The subject of this thesis is the synthesis and characterization of PBI-based fluorescent metallosupramolecular polymers and cyclic arrays. Terpyridine receptor functionalized PBIs of predesigned geometry have been used as building blocks to construct desired macromolecular structures through metal-ion-directed self-assembly. These metallosupramolecular architectures have been investigated by NMR, UV/Vis and fluorescence spectroscopy, mass spectrometry, and atomic force microscopy.
Insects living in temperate latitudes need to adjust their life-history to a seasonally variable environment. Reproduction, growth, and development have to be completed within the limited period where environmental conditions are favourable while climatically adverse conditions have to be spent in a state of diapause. Consequently, questions how individuals adapt their life-history to seasonality and which mechanisms underlie the responses to seasonal cues, like photoperiod, are important issues in the study of life-history strategies. This thesis focuses on the life-history adaptation to seasonality in the wing-dimorphic common pond skater Gerris lacustris L. (Heteroptera: Gerridae). Using a combination of field and laboratory studies as well as mathematical modelling, it is adressed how variation in the availability of thermal energy impacts on various aspects of larval development such as accumulated thermal energy (i.e. physiological development time), developmental pathway (direct reproduction vs. diapause) and wing dimorphism.
Streptococcus pneumoniae (pneumococci) are Gram-positive bacteria and commensals of the nasopharyngeal cavity. Besides colonization, pneumococci are responsible for severe local infections such as otitis media, sinusitis and life-threatening invasive diseases, including pneumonia, sepsis and meningitis. The surface of pneumococci is decorated with proteins that are covalently or non-covalently anchored to the cell wall. The most unique group of cell wall associated proteins in pneumococci are the choline-binding proteins (CBPs). PspC, also known as SpsA or CbpA, is a multifunctional choline-binding protein that plays an essential role in pneumococcal pathogenesis by functioning as an adhesin. PspC promotes adherence of pneumococci to mucosal epithelial cells by interacting in a human specific manner with the free secretory component (SC) or to SC as part of the secretory IgA (SIgA) or polymeric immunoglobulin receptor (pIgR). PspC also interacts specifically with the soluble complement Factor H. Apparently, PspC uses two different epitopes for binding the soluble host protein Factor H and SC of pIgR. However, the mechanism by which these independent interactions facilitate pneumococcal infections under physiological and host specific conditions have not yet been completely elucidated. This study aims to explore the impact of the PspC interaction with human pIgR (hpIgR) or complement regulator Factor H on pneumococcal virulence. Here the cellular and molecular basis of PspC-mediated adherence to and invasion of host epithelial and endothelial cells was demonstrated. The genetic approach, specific pharmacological inhibitors and immunoblot analysis demonstrated the complexity of the induced signal transduction pathways during PspC-hpIgR mediated pneumococcal uptake by host cells. Inhibition studies with specific inhibitors of actin cytoskeleton and microtubules demonstrated that the dynamics of host cell cytoskeleton are essential for pneumococcal uptake by mucosal epithelial cells. Moreover, this study reports for the first time that the small GTPase Cdc42 is essential for pneumococcal internalization into epithelial cells via the PspC-hpIgR mechanism. In addition, in infection experiments performed in presence of specific inhibitors of PI3-kinase/Akt and protein tyrosine kinase (PTKs), hpIgR-mediated pneumococcal uptake by host cells was significantly blocked. Amongst PTKs the Src kinase pathway, ERK1/2 and JNK pathways were implicated during pneumococcal ingestion by hpIgR expressing cells. In addition, inhibition experiments performed in the presence of individual inhibitors or with a combination of inhibitors suggested the independent activation of PI3-kinase/Akt and Src kinase pathways during pneumococcal infections of hpIgR expressing cells. By employing specific inhibitors and siRNA in cell culture infection experiments it was further demonstrated that pneumococcal endocytosis by host epithelial cells via the PspC-hpIgR mechanism depends on clathrin and dynamin. PspC recruits also Factor H to the pneumococcal cell surface. Consequently, the impact of pneumococcal cell surface bound Factor H on adherence to host cells and the molecular mechanism facilitating the uptake of Factor H bound pneumococci by epithelial cells was investigated. Flow cytometry and immunoblots revealed that S. pneumoniae has evolved the ability to recruit both purified Factor H as well as Factor H from human plasma or serum. Moreover, it was demonstrated that the recruitment of Factor H is independent of the PspC-subtypes and that capsular polysaccharide (CPS) interferes with its recruitment. Factor H bound to pneumococci significantly increased bacterial attachment to and invasion of host epithelial cells including nasopharyngeal cells (Detroit562), lung epithelial cells (A549), and human brain-derived endothelial cells (HBMEC). Blocking experiments demonstrated that bacteria bound Factor H interacts via the heparin binding sites on Factor H with eukaryotic cell surface glycosaminoglycans and that this interaction promotes pneumococcal adherence to host cells. In addition, inhibition studies with mAbs recognizing specifically different short consensus repeats (SCR) of Factor H suggested that SCR 19-20 of Factor H are essential for the pneumococcal interaction with host epithelial cells via Factor H. In the presence of Factor H, attachment of pneumococci to human polymorphonuclear leukocytes (PMNs) is enhanced. The integrin CD11b/CD18 was identified as the cellular receptor on PMNs. By using pharmacological inhibitors the impact of host cell cytoskeleton and signalling molecules, such as PTKs and PI3-kinase, for Factor H-mediated pneumococcal internalization into eukaryotic cells was shown. Taken together, the results revealed that Factor-H mediated pneumococcal infection requires a concerted role of host epithelial cell surface glycosaminoglycans, integrins and host cell signalling pathways.
Myelinmutationen des zentralen und peripheren Nervensystems verursachen erheblich behindernde und bislang nicht heilbare Erkrankungen. In dieser Arbeit verwendeten wir transgene PLP überexprimierende Mäuse (PLPtg) als Modell für zentrale Myelinopathien und heterozygot P0 defiziente (P0+/-) Mäuse als Modell für hereditäre Neuropathien des peripheren Nervensystems. Beide Modelle zeigen eine niedriggradige Inflammation des Nervengewebes. Durch Verpaarung mit immundefizienten Mausstämmen konnten wir die Relevanz von Makrophagen und T- Lymphozyten in der Entstehung der Myelinpathologie zeigen. Nachdem wir beweisen konnten, dass CD8+ T- Lymphozyten maßgeblich zur Pathologie in PLPtg Mäusen beitragen untersuchten wir den Einfluss eines wichtigen zytotoxischen Moleküls, Granzym B, auf den neuralen Schaden. Durch Generierung von Granzym B defizienten PLPtg Knochenmarkschimären konnten wir eine deutliche Reduktion des glialen Schadens und der Oligodendrozytenapoptose nachweisen. Granzym B ist also zumindest teilweise verantwortlich für die Schädigung, die durch T- Lymphozyten hervorgerufen wird. Um die zusätzliche Informationen über die Rolle der Immunmodulation in unseren Modellen zu gewinnen, untersuchten wir das koinhibitorische Molekül PD-1, einen CD-28 verwandten Rezeptor, der auf B- und T- Lymphozyten exprimiert wird. Bei der Untersuchung von Myelinmutanten des ZNS und PNS (PLPtg und P0+/-), die zusätzlich PD-1 defizient waren, konnten wir einen signifikanten Anstieg von CD8+ T- Lymphozyten und eine deutliche Verschlechterung des glialen Schadens beobachten. In PLPtg Mäusen induzierte die Abwesenheit von PD-1 verstärkte Oligodendrozytenapoptose und klonale Expansion. Außerdem neigen ZNS- Lymphozyten aber nicht periphere CD8+ T- Zellen zur verstärkten Sekretion von proinflammatorischen Zytokinen. In P0+/- Mäusen führt Abwesenheit von PD-1 zu moderaten motorischen und sensorischen Störungen, was die wichtige Rolle von PD-1 in immunologischen Regulationsmechanismen unterstreicht. Zusammenfassend kann man festhalten, daß Granzym B ein wichtiges Effektormolekül zytotoxischer T- Zellen in PLPtg Mäusen ist. PD-1 spielt eine wichtige Rolle in der Regulation von Effektorzellen in unseren Modellen für zentrale und periphere Myelinopathien. Veränderungen dieser Regulation können deutliche Neuroinflammation mit starker Myelinpathologie hervorrufen. Diese Ergebnisse können dazu beitragen, die starke klinische Variabilität von polygenen und sogar monogenen neurologischen Erkrankungen zu erklären.
The prototyical tumor suppressor p53 is able to arrest cells after DNA damage or as a response to oncogene expression. The transactivation-competent (TA) isoforms of the more recently discovered p53 family member p73 also prevent tumors, but the underlying mechanisms are less well understood. The work presented here addressed this issue by using a cell culture model of tumorigenesis in which normal human diploid fibroblasts are stepwise transduced with oncogenes. Cells in pretransformed stages were shown to harbour high levels of TAp73 mRNA and protein. This positive regulation was probably a result of pRB inactivation and derepression of E2F1, a key activator of TAp73. Consequences for such cells included an increased sensitivity to the cytostatic drug adriamycin, slower proliferation and reduced survival at high cell density, as demonstrated by rescue experiments using siRNA-mediated knockdown of TAp73. In order to identify potential effector pathways, the gene expression profile of siRNA treated, matched fibroblast cell lines with high and low TAp73 levels were compared in DNA microarrays. These findings support the notion of TAp73 up-regulation as an anti-proliferative defense mechanism, blocking the progress towards full transformation. This barrier could be overcome by the introduction of a constitutively active form of Ras which caused a switch from TAp73 to oncogenic DeltaNp73 expression, presumably through the phosphatidylinositol 3-kinase (PI3K) pathway. In summary, the results presented emphasize the tumor-suppressive function of TAp73 and indicate that its downregulation is a decisive event during the transformation of human cells by oncogenic Ras mutants.
Abstract: Background Group formation and food sharing in animals may reduce variance in resource supply to breeding individuals. For some species it has thus been interpreted as a mechanism of risk avoidance. However, in many groups reproduction is extremely skewed. In such groups resources are not shared equally among the members and inter-individual variance in resource supply may be extreme. The potential consequences of this aspect of group living have not attained much attention in the context of risk sensitive foraging. Results We develop a model of individually foraging animals that share resources for reproduction. The model allows analyzing how mean foraging success, inter-individual variance of foraging success, and the cost of reproduction and offspring raising influence the benefit of group formation and resource sharing. Our model shows that the effects are diametrically opposed in egalitarian groups versus groups with high reproductive skew. For individuals in egalitarian groups the relative benefit of group formation increases under conditions of increasing variance in foraging success and decreasing cost of reproduction. On the other hand individuals in groups with high skew will profit from group formation under conditions of decreasing variance in individual foraging success and increasing cost of reproduction. Conclusion The model clearly demonstrates that reproductive skew qualitatively changes the influence of food sharing on the reproductive output of groups. It shows that the individual benefits of variance reduction in egalitarian groups and variance enhancement in groups with reproductive skew depend critically on ecological and life-history parameters. Our model of risk-sensitive foraging thus allows comparing animal societies as different as spiders and birds in a single framework.
The Internet sees an ongoing transformation process from a single best-effort service network into a multi-service network. In addition to traditional applications like e-mail,WWW-traffic, or file transfer, future generation networks (FGNs) will carry services with real-time constraints and stringent availability and reliability requirements like Voice over IP (VoIP), video conferencing, virtual private networks (VPNs) for finance, other real-time business applications, tele-medicine, or tele-robotics. Hence, quality of service (QoS) guarantees and resilience to failures are crucial characteristics of an FGN architecture. At the same time, network operations must be efficient. This necessitates sophisticated mechanisms for the provisioning and the control of future communication infrastructures. In this work we investigate such echanisms for resilient FGNs. There are many aspects of the provisioning and control of resilient FGNs such as traffic matrix estimation, traffic characterization, traffic forecasting, mechanisms for QoS enforcement also during failure cases, resilient routing, or calability concerns for future routing and addressing mechanisms. In this work we focus on three important aspects for which performance analysis can deliver substantial insights: load balancing for multipath Internet routing, fast resilience concepts, and advanced dimensioning techniques for resilient networks. Routing in modern communication networks is often based on multipath structures, e.g., equal-cost multipath routing (ECMP) in IP networks, to facilitate traffic engineering and resiliency. When multipath routing is applied, load balancing algorithms distribute the traffic over available paths towards the destination according to pre-configured distribution values. State-of-the-art load balancing algorithms operate either on the packet or the flow level. Packet level mechanisms achieve highly accurate traffic distributions, but are known to have negative effects on the performance of transport protocols and should not be applied. Flow level mechanisms avoid performance degradations, but at the expense of reduced accuracy. These inaccuracies may have unpredictable effects on link capacity requirements and complicate resource management. Thus, it is important to exactly understand the accuracy and dynamics of load balancing algorithms in order to be able to exercise better network control. Knowing about their weaknesses, it is also important to look for alternatives and to assess their applicability in different networking scenarios. This is the first aspect of this work. Component failures are inevitable during the operation of communication networks and lead to routing disruptions if no special precautions are taken. In case of a failure, the robust shortest-path routing of the Internet reconverges after some time to a state where all nodes are again reachable – provided physical connectivity still exists. But stringent availability and reliability criteria of new services make a fast reaction to failures obligatory for resilient FGNs. This led to the development of fast reroute (FRR) concepts for MPLS and IP routing. The operations of MPLS-FRR have already been standardized. Still, the standards leave some degrees of freedom for the resilient path layout and it is important to understand the tradeoffs between different options for the path layout to efficiently provision resilient FGNs. In contrast, the standardization for IP-FRR is an ongoing process. The applicability and possible combinations of different concepts still are open issues. IP-FRR also facilitates a comprehensive resilience framework for IP routing covering all steps of the failure recovery cycle. These points constitute another aspect of this work. Finally, communication networks are usually over-provisioned, i.e., they have much more capacity installed than actually required during normal operation. This is a precaution for various challenges such as network element failures. An alternative to this capacity overprovisioning (CO) approach is admission control (AC). AC blocks new flows in case of imminent overload due to unanticipated events to protect the QoS for already admitted flows. On the one hand, CO is generally viewed as a simple mechanism, AC as a more complex mechanism that complicates the network control plane and raises interoperability issues. On the other hand, AC appears more cost-efficient than CO. To obtain advanced provisioning methods for resilient FGNs, it is important to find suitable models for irregular events, such as failures and different sources of overload, and to incorporate them into capacity dimensioning methods. This allows for a fair comparison between CO and AC in various situations and yields a better understanding of the strengths and weaknesses of both concepts. Such an advanced capacity dimensioning method for resilient FGNs represents the third aspect of this work.
In this thesis, the low-temperature regime of replica symmetry breaking in the SK-model has been thoroughly investigated. In order to access this regime and to perform self-consistence calculations with high accuracy at high orders of replica symmetry breaking, a formalism has been developed which reduces the numerical effort to the absolute minimum. The central idea of its derivation is the identification of asymptotic regions in which the recursion relations can be solved analytically. The new object in the numerical treatment is then the correction to this asymptotic regime, represented by a sequence of so-called kernel correction functions. This method increased the effciency of the numerics considerably so that up to 200 orders of RSB could be calculated at zero temperature and zero external field, and up to 60 (65) orders of RSB for finite temperature (external field). The remarkable high precision of these calculations allowed the extraction of several quantities with accuracy exceeding the literature values by several orders of magnitude. The results of the numerical calculations have been analyzed in great detail. Especially the convergence behavior of various observables and of the order function with respect to the RSB order has been investigated since the high but finite RSB regime has been addressed in the present work for the first time. Several unexpected features of finite order replica symmetry breaking have been observed.
Charcot-Marie-Tooth 1B (CMT1B) is a progressive inherited demyelinating disease of human peripheral nervous system leading to sensory and/or motor function disability and is caused by mutations in the P0 gene. Mice heterozygously deficient for P0 (P0+/-) are an adequate model of this human disorder showing myelin degeneration, formation of onion bulbs, remyelination and a reduced motor conduction velocity of around 30m/s similar to patients. Previously, it had been shown that T-lymphocytes and macrophages play a crucial role during pathogenesis in peripheral nerves of P0+/- mice. Both, T-lymphocytes and macrophages increase in number in the endoneurium and deletion of T-lymphocytes or deletion of a macrophage-directed cytokine ameliorates the disease. In this study the monocyte chemoattractant protein-1 (MCP-1) was identified as an early regulated cytokine before onset of disease is visible at the age of six months. MCP-1 mRNA and protein expression could be detected in femoral quadriceps and sciatic nerves of P0+/- mice already at the age of one month but not in cutaneous saphenous nerves which are never affected by the disease. MCP-1 was shown to be expressed by Schwann cells and to mediate the immigration of immune cells into peripheral nerves. Deletion of MCP-1 in P0+/- mice accomplished by crossbreeding P0 and MCP-1 deficient mice revealed a substantial reduction of immune cells in peripheral nerves of P0+/-/MCP-1+/- and P0+/-/MCP-1-/- mice at the age of six months. In twelve months old mice reduction of immune cells in peripheral nerves is accompanied by amelioration of demyelinating disease in P0+/-/MCP-1+/- and aggravation of demyelinating disease in lumbar ventral roots of P0+/ /MCP-1-/- mice in comparison to P0+/ /MCP 1+/+ mice. Furthermore, activation of the MEK1/2-ERK1/2 signalling cascade could be demonstrated to take place in Schwann cells of affected peripheral nerves of P0+/- mice overlapping temporarily and spatially with MCP-1 expression. An animal experiment using a MEK1/2-inhibitor in vivo, CI-1040, revealed that upon reduction of ERK1/2 phosphorylation MCP-1 mRNA expression is diminished suggesting that the activation of the MEK1/2-ERK1/2 signalling cascade is necessary for MCP-1 expression. Additionally, peripheral nerves of P0+/- mice showing reduced ERK1/2 phosphorylation and MCP-1 mRNA expression also show reduced numbers of macrophages in the endoneurium. This study shows a molecular link between a Schwann cell based mutation and immune cell function. Inhibition of the identified signalling cascade might be a putative target for therapeutic approaches.
We investigate iterative numerical algorithms with shifts as nonlinear discrete-time control systems. Our approach is based on the interpretation of reachable sets as orbits of the system semigroup. In the first part we develop tools for the systematic analysis of the structure of reachable sets of general invertible discrete-time control systems. Therefore we merge classical concepts, such as geometric control theory, semigroup actions and semialgebraic geometry. Moreover, we introduce new concepts such as right divisible systems and the repelling phenomenon. In the second part we apply the semigroup approach to the investigation of concrete numerical iteration schemes. We extend the known results about the reachable sets of classical inverse iteration. Moreover, we investigate the structure of reachable sets and systemgroup orbits of inverse iteration on flag manifolds and Hessenberg varieties, rational iteration schemes, Richardson's method and linear control schemes. In particular we obtain necessary and sufficient conditions for controllability and the appearance of repelling phenomena. Furthermore, a new algorithm for solving linear equations (LQRES) is derived.
Rat organic cation transporter 1 (rOCT1): investigation of conformational changes and ligand binding
(2008)
Polyspecific organic cation transporters (OCTs) of the SLC22 family mediate downhill transport of organic cations and play an essential role in excretion and distribution of endogenous organic cations and for the uptake, elimination and distribution of cationic drugs and toxins. Although physiological and pharmacological significance of OCTs is widely accepted, many questions concerning structure and transport mechanism still remain open. To investigate conformational changes of the rat OCT1 during transport cycle, voltage-clamp fluorometry was performed with a cysteine-deprived mutant in which phenylalanine 483 in transmembrane helix (TMH) 11 close to the extracellular surface was replaced by cysteine and covalently labeled with tetramethylrhodamine-6-maleimide. Potential-dependent fluorescence changes were observed that were sensitive to the presence of substrates choline, tetraethylammonium (TEA), 1-methyl-4-phenylpyridinium (MPP), and of the contransported inhibitor tetrabutylammonium (TBuA). The data suggest that the transporter undergoes conformational changes in voltage- and substrate-dependent manner which are compatible with alternating access mechanism. Using potential-dependent fluorescence changes as readout, one high-affinity binding site per substrate and two highaffinity binding sites for TBuA were identified in addition to the previously described single interaction sites. Coexisting high-affinity cation binding sites in organic cation transporters may collect xenobiotics and drugs; however, translocation of organic cations across the membrane may only be induced when a low-affinity cation binding site is loaded. Whereas high-affinity binding of TBuA has no effect on cation uptake by wildtype rat OCT1, replacement by cysteine or serine of amino acids W147, F483, and F486 located in a modeled contact region between TMH2 and TMH11 outside the binding pocket leads to inhibition of MPP or TEA uptake. Thus, mutations of amino acids in transport relevant key positions, which can be distinct from the cation binding region, may transform noninhibitory highaffinity binding sites of high-affinity inhibition sites and thereby cause adverse drug reactions in patients.
The control of quantum mechanical processes, especially the selective manipulation of photochemical reactions by shaped fs laser pulses was successfully demonstrated in many experiments in the fields of physics, chemistry and biology. In this work, attention is directed to the control of two systems that mark a bridge to real synthetic chemistry. In a liquid phase environment the outcome of the photo-induced Wolff rearrangement of an industrially relevant diazonaphthoquinone compound, normally used in photoresists (e.g. Novolak) was optimized using shaped fs laser pulses. In the second series of experiments chemical reactions on a catalyst metal surface which comprise laser induced molecular bond formation channels were selectively manipulated for the first time. The control of liquid phase reactions necessitates adequate spectroscopic signals that are characteristic for the formed product species. Therefore, a pump-probe setup for transient absorption spectroscopy in the mid-infrared for the purpose of investigating ultrafast structural changes of molecules during photoreactions was constructed. This versatile setup enables to monitor structural changes of molecules in the liquid phase and to find appropriate feedback signals for the control of these processes. Prior to quantum control experiments, the photoinduced Wolff-rearrangement reaction of 2-diazo-1-naphthoquinone (DNQ) dissolved in water and methanol was thoroughly investigated. Steady state absorption measurements in the mid-infrared in combination with quantum chemical density functional theory (DFT) calculations revealed the characteristic vibrational bands of DNQ and of possible products. A mid-infrared transient absorption study was performed, to illuminate the structural dynamics of the ultrafast rearrangement reaction of DNQ. The experimental observations indicate, that the Wolff rearrangement reaction of DNQ proceeds within 300 fs. A model for the relaxation dynamics of the ketene photoproduct and DNQ after photoexcitation can be deduced that fits the measured data very well. The object of the quantum control experiments on DNQ was the improvement of the ketene yield. It was shown that the ketene formation after Wolff rearrangement of DNQ is very sensitive to the shape of the applied excitation laser pulses. The variation of single parameters, like the linear chirp as well as the pulse separation of colored double pulses lead to the conclusion that the well known intrapulse dumping mechanism is responsible for the impact of the frequency ordering within the excitation pulse on the photoproduct yield. Adaptive optimizations using a closed learning loop basically lead to the same result. Adaptive fs quantum control was also applied to surface reactions on a catalyst metal surface for the first time. Therefore, the laser-induced catalytic reactions of carbon monoxide (CO) and hydrogen (H2) on a Pd(100) single crystal surface were studied. This photochemical reaction initiated with fs laser pulses has not been observed before. Several product molecules could be synthesized, among them also species (e.g. CH^3+) for whose formation three particles are involved. The systematic variation of different parameters showed that the reactions are sensitive to the catalyst surface, the composition of the adsorbate and to the laser properties. A pump-probe study revealed that they occur on an ultrafast time scale. These catalytic surface reactions were then investigated and improved with phaseshaped fs laser pulses. By applying a feedback optimal control scheme, the reaction outcome could be successfully manipulated and the ratio of different reaction channels could be selectively controlled. Evidence has been found that the underlying control mechanism is nontrivial and sensitive to the specific conditions on the surface. The experiments shown here represent the first successful experiment on adaptive fs quantum control of a chemical reaction between adsorbate molecules on a surface. In contrast to previous quantum control experiments, reaction channels comprising the formation of new molecular bonds rather than the cleavage of already existing bonds are controlled. This work successfully showed that quantum control can be extended to systems closer to situations encountered in synthetic chemistry as was demonstrated in the two examples of the optimization of a complicated rearrangement reaction and the selective formation of chemical bonds with shaped fs laser pulses.
VACV GLV-1h68 was reported as a diagnostic/therapeutic vector which enters, replicates in, and reveals the locations of tumors in mice. Furthermore, the effect on tumor colonization, on tumor growth, regression and eradication by VACV GLV-1h68 without the need of any known genes with anti-tumoral activities was determined. To investigate differential protein expression between infected tumor cells and corresponding tumors, as well as between infected tumor cells, between infected tumors, proteomics is particularly used, possibly contributing to the understanding oncolytic ability on the protein level of VACV GLV-1h68. The given effects of VACV GLV-1h68 infection on cellular protein expression support tumor cell killing. In this study, differential protein expression was analyzed at different time points with two-dimensional gel electrophoresis (2DE) followed by MALDI-TOF/TOF identification. Comparative analysis of multiple 2-DE gels revealed that the majority of protein expression changes appeared at 48 hours post infection in cell cultivation and at 42 days post infection in tumors. Mass spectrometry identified 68, 75, 159 altered cellular proteins in the GI-101A, HT-29, PC-3 infected cells, respectively, including 30, 23, 49 up-regulated proteins and 38, 52, 110 down-regulated proteins 12 to 48 hours after infection. For xenografts, mass spectrometry identified 270, 101, 91 altered cellular proteins in the infected GI-101A, HT-29, PC-3 tumors, respectively, including 89, 70, 40 up-regulated proteins and 181, 31, 51 down-regulated proteins 7 to 42 days after infection. In general, in the cell lines, the proteins found to be differentially regulated are most often associated with metabolic processes, in particular with primary energy metabolism (glucose catabolism, TCA and lactate production). VAVC GLV 1h68 infection results in hijacking of the host translation apparatus, alteration of cytoskeleton networks, induce ubiqitin proteasome pathway (UPP) disorders. Particularly in tumors, the responses cover a much broader panel of cellular processes, including signalling (e.g., cell death), transport (in particular of iron ions) and migration. A common pathway to be up-regulated in both tumors and cell lines is the "unfolded protein response". Notably, VACV GLV-1h68 affected the anti-apoptosis pathways in GI-101A and PC-3 cancer cells but not in HT-29 xenografts. For example, GI-101A xenografts in mice appear 12 proteins associated with anti-apoptosis function. They were found down-regulated, including tumor protein-translationally-controlled (H-TPT1), rho-GDP-dissociation inhibitor alpha (H-GDIa), ywhaq protein (M-1433T), H-PRDX4, serine/threonine-protein phosphatase-2A-catalytic subunit beta isoform PP2A (M-Ppp2cb), eukaryotic translation initiation factor 2-subunit 1 alpha-35kDa (H-eIF2), H-actinin-α1 (ACTN1 ), Annexin A1 (H-A1), annexin A5 (H-A5), Mouse albumin 1 (M-Alb1), dimethylarginine dimethylaminohydrolase 2 (H-DDAH2). In PC-3 xenografts, anti-apoptosis expression is lesser than those in GI-101A cells, however 3 anti-apoptosis associated proteins were down-regulated such as ARP3 actin-related protein-3-homolog (H-ARP3), Human FLNA protein, Rho GDP dissociation inhibitor (GDI) alpha (H-GDIa). In contrast, in HT-29 xenografts, there are several anti-apoptosis-associated proteins that show even to be up-regulated; they mostly belong to peroxiredoxin proteins. Lesson from HT-29 had been given what various means the HT-29 cells use to escape their apoptosis fate. This suggests that VAVC GLV1h68 infection may induce unbalance of unfolded protein response (UPR) but tending to anti-apoptosis-mediated proteins and promote the destructive elements of UPR, including caspase-12 cleavage and apoptosis. Taken together in this thesis research I have tried to compare protein profiles obtained from responder cell line and from regressing solid tumors colonized by VAVC GLV-1h68 with that of non-responding tumors. I also compared these data with PC-3 prostate cell line and tumor data on intermediate responder which alter mouse protein profiling in tumors similarly to the highly efficacious GI-101A breast tumor cell line. From these comparisons I have deduced exciting protein pattern signature characteristic for a responder or distinctly different from non-responder system. Combining these few crucial genes involved with the transcriptional test data obtained by fellow graduate student at NIH a novel national designed VACV GLV-1h68 strains with enhanced efficacy in many today non-responder cancer cell lines will be available to be tested into ongoing clinical trials.
In the course of this study, several endogenous compounds and model substances were used to mimic the conditions in patients suffering from hypertension. As endogenous compounds, angiotensin II and aldosterone were chosen. As model substances, 4-nitroquinoline-1-oxide (NQO), hydrogen peroxide and phorbol 12-myristate 13-acetate (PMA) were selected. Benfotiamine as well as α-tocopherol proved in the course of the experiments to be able to prevent angiotensin II-induced formation of oxidative DNA strand breaks and micronuclei. This could be due to a prior inhibition of the release of reactive oxygen species and is in contrast to results which were achieved using thiamine. Furthermore, experiments in which cells were pre-incubated with benfotiamine followed by incubation with NQO showed that benfotiamine was not able to prevent the induction of oxidative stress. The hypothesis that benfotiamine has, like α-tocopherol, direct antioxidative capacity was fortified by measurements in cell free systems. In brief, a new working mechanism for benfotiamine in addition to the ones already known could be provided. In the second part of the study, angiotensin II was shown to be dose-dependently genotoxic. This effect is mediated via the angiotensin II type 1 receptor (AT1R) which. Further experiments were extended from in vitro settings to the isolated perfused kidney. Here it could be shown that angiotensin II caused vasoconstriction and DNA strand breaks. Co-perfusion of kidneys with angiotensin II and candesartan prevented vasoconstriction and formation of strand breaks. DNA strand break formation due to mechanical stress or hypoxia could be ruled out after additional experiments with the thromboxane mimetic U 46619. Detailed investigation of the DNA damage in vitro revealed that angiotensin II induces single strand breaks, double strand breaks and 8-hydroxydeoxyguanosine (8-oxodG)-adducts as well as abasic sites. Investigations of the effects of aldosterone-treatment in kidney cells showed an increase of oxidative stress, DNA strand breaks and micronuclei which could be prevented by the steroidal mineralocorticoid receptor antagonist eplerenone. Additional experiments with the non-steroidal mineralocorticoid receptor antagonist (S)-BR-4628 revealed that this substance was also able to prevent oxidative stress and genomic damage and proved to be more potent than eplerenone. In vivo, hyperaldosteronism was imitated in rats by aid of the deoxycorticosteroneacetate (DOCA) salt model. After this treatment, levels of DNA strand breaks and chromosomal aberrations in the kidney could be observed. Furthermore, an increase in the release of ROS could be measured. Treatment of these animals with spironolactone , BR-4628 and enalaprile revealed that all antagonists were effective BR-4628 was the most potent drug. Finally, rosuvastatin was investigated. In HL-60 cells phorbol 12-myristate 13-acetate caused oxidative stress. Rosuvastatin was able to prevent the release of ROS and subsequent oxidative DNA damage when co-incubated with PMA. Furthermore, not only an inhibition of PMA-induced oxidative stress but also inhibition of the unspecific release of ROS induced by hydrogen peroxide was observable. Addition of farnesyl pyrophosphate (FPP), geranylgeranyl pyrophosphate (GGPP), and mevalonate, intermediates of the cholesterol pathway, caused only a marginal increase of oxidative stress in cells treated simultaneously with PMA and rosuvastatin, thus indicating the effect of rosuvastatin to be HMG-CoA-reductase-independent. Investigation of the gene expression of subunits of NAD(P)H oxidase revealed a down-regulation of p67phox following rosuvastatin-treatment. Furthermore, it could be shown that rosuvastatin treatment alone or in combination with PMA increased total glutathione levels probably due to an induction of the gene expression and enzyme activity of γ-glutamylcysteine synthetase (γ-GCS).
Supersymmetry is currently the best motivated extension of the Standard Model and will be subject to extensive studies in the upcoming generation of colliders. The e-e- mode would be a straight forward extension to the currently planed International Linear Collider, planned to operate in e+e- mode. The low background in this mode may prove advantageous in the study of CP- and Lepton Flavour Violtation. In this work a CP sensitive observable based on transverse beam polarisation is introduced and the impact of neutralino mixing on the total cross section in cas of non-vanishing CP-violtating phases is studied in representative scenarios including non-GUT scenarios. Additionally, the mixing of sleptons is studied in the context of LFV, an analytical approximation is developed, and possible background free measurements of these effects are investigated.
Cognitive views of the psychopathology of anxiety propose that attentional biases toward threatening information play a substantial role in the disorders’ etiology and maintenance. For healthy subjects, converging evidence show that threatening stimuli attract attention and lead to enhanced activation in visual processing areas. It is assumed that this preferential processing of threat occurs at a preattentive level and is followed by fast attentional engagement. High-anxious individuals show augmented tendencies to selectively attend toward fear-relevant cues (Mathews, 1990) and exhibit elevated neural processing of threatening cues compared to non-anxious individuals (Dilger et al., 2003). Regarding attentional biases in high-anxious subjects, it remains unanswered up to now whether initial engagement of attention toward threat or difficulties to disengage from threat is an underlying mechanism. Furthermore, little is known whether the preferential (attentive) processing of threatening cues does influence perceptional outcomes of anxious subjects. In order to directly study separate components of attentional bias the first study of this dissertation was a combined reaction time and eye-tracking experiment. Twenty one spider phobic patients and 21 control participants were instructed to search for a neutral target while ignoring task-irrelevant abrupt-onset distractor circles which contained either a small picture of a spider (phobic), a flower (non-phobic, but similar to spiders in shape), a mushroom (non-phobic, and not similar to spiders in shape), or small circles with no picture. As expected, patients’ reaction times to targets were longer on trials with spider distractors. However, analyses of eye movements revealed that this was not due to attentional capture by spider distractors; patients more often fixated on all distractors with pictures. Instead, reaction times were delayed by longer fixation durations on spider distractors. This result does not support automatic capture of attention by phobic cues but suggests that phobic patients fail to disengage attention from spiders. To assess whether preferential processing of phobic cues differentially affects visual perception in phobic patients compared to healthy controls, the second study of this dissertation used a binocular rivalry paradigm, where two incompatible pictures were presented to each eye. These pictures cannot be merged to a meaningful percept and temporarily, one picture predominates in conscious perception whereas the other is suppressed. 23 spider phobic patients and 20 non-anxious control participants were shown standardized pictures of spiders or flowers, each paired with a neutral pattern under conditions of binocular rivalry. Their task was to continuously indicate the predominant percept by key presses. Analyses show that spider phobic patients perceived the spider picture more often and longer as dominant compared to non-anxious control participants. Thus, predominance of phobic cues in binocular rivalry provides evidence that preferential processing of fear-relevant cues in the visual system actually leads to superior perception. In combination both studies support the notion that phobic patients process phobic cues preferentially within the visual system resulting in enhanced attention and perception. At early stages of visual processing, this is mainly reflected by delayed attentional disengagement and across time, preferential processing leads to improved perception of threat cues.
The plant surface is the substrate upon which herbivorous insects and natural enemies meet and thus represents the stage for interactions between the three trophic levels. Plant surfaces are covered by an epicuticular wax layer which is highly variable depending on species, cultivar or plant part. Differences in wax chemistry may modulate ecological interactions. We explored whether caterpillars of Spodoptera frugiperda, when walking over a plant surface, leave a chemical trail (kairomones) that can be detected by the parasitoid Cotesia marginiventris. Chemistry and micromorphology of cuticular waxes of two barley eceriferum wax mutants (cer-za.126, cer-yp.949) and wild type cv. Bonus (wt) were assessed. The plants were then used to investigate potential surface effects on the detectability of caterpillar kairomones. Here we provide evidence that C. marginiventris responds to chemical footprints of its host. Parasitoids were able to detect the kairomone on wild type plants and on both cer mutants but the response to cer-yp.949 (reduced wax, high aldehyde fraction) was less pronounced. Experiments with caterpillar-treated wt and mutant leaves offered simultaneously, confirmed this observation: no difference in wasp response was found when wt was tested against cer-za.126 (reduced wax, wt-like chemical composition) but wt was significantly more attractive than cer-yp.949. This demonstrates for the first time that the wax layer can modulate the detectability of host kairomones.
This thesis deals with the synthesis of improved organic semiconductors, the detailed investigation of the molecular properties and the solid state arrangements revealed by single crystal X-ray diffraction and finally the development of structureperformance dependencies by measuring of the charge carrier mobilities of the derivatives in thin film transistors. The two main-goals of this thesis were achieved. Well soluble acene derivatives for spin-coated TFTs were obtained, showing charge carrier mobilities in the range of polymer p-type materials. Novel core-fluorinated perylene bisimide dyes were synthesized particularly and the use of electron deficient substituents lead to PBIs with outstanding air-stable mobilities in thin film transistors prepared by vacuum deposition techniques. The relationship between performance, air stability and solid state packing was elucidated in detail by single crystal X-ray diffraction analysis.
Mobile telecommunication systems of the 3.5th generation (3.5G) constitute a first step towards the requirements of an all-IP world. As the denotation suggests, 3.5G systems are not completely new designed from scratch. Instead, they are evolved from existing 3G systems like UMTS or cdma2000. 3.5G systems are primarily designed and optimized for packet-switched best-effort traffic, but they are also intended to increase system capacity by exploiting available radio resources more efficiently. Systems based on cdma2000 are enhanced with 1xEV-DO (EV-DO: evolution, data-optimized). In the UMTS domain, the 3G partnership project (3GPP) specified the High Speed Packet Access (HSPA) family, consisting of High Speed Downlink Packet Access (HSDPA) and its counterpart High Speed Uplink Packet Access (HSUPA) or Enhanced Uplink. The focus of this monograph is on HSPA systems, although the operation principles of other 3.5G systems are similar. One of the main contributions of our work are performance models which allow a holistic view on the system. The models consider user traffic on flow-level, such that only on significant changes of the system state a recalculation of parameters like bandwidth is necessary. The impact of lower layers is captured by stochastic models. This approach combines accurate modeling and the ability to cope with computational complexity. Adopting this approach to HSDPA, we develop a new physical layer abstraction model that takes radio resources, scheduling discipline, radio propagation and mobile device capabilities into account. Together with models for the calculation of network-wide interference and transmit powers, a discrete-event simulation and an analytical model based on a queuing-theoretical approach are proposed. For the Enhanced Uplink, we develop analytical models considering independent and correlated other-cell interference.
Eine der größten Herausforderungen in der Neurobiologie ist es, die neuronalen Prozesse zu verstehen, die Lernen und Gedächtnis zugrundeliegen. Welche biochemischen Pfade liegen z.B. der Koinzidenzdetektion von Reizen (klassische Konditionierung) oder einer Handlung und ihren Konsequenzen (operante Konditionierung) zugrunde? In welchen neuronalen Unterstrukturen werden diese Informationen gespeichert? Wie ähnlich sind die Stoffwechselwege, die diese beiden Arten des assoziativen Lernens vermitteln und auf welchem Niveau divergieren sie? Drosophila melanogaster ist wegen der Verfügbarkeit von Lern-Paradigmen und neurogenetischen Werkzeugen ein geeigneter Modell-Organismus, zum diese Fragen zu adressieren. Er ermöglicht eine umfangreiche Studie der Funktion des Gens S6KII, das in der Taufliege in klassischer und operanter Konditionierung unterschiedlich involviert ist (Bertolucci, 2002; Putz et al., 2004). Rettungsexperimenten zeigen, dass die olfaktorische Konditionierung in der Tully Maschine (ein klassisches, Pawlow’sches Konditionierungsparadigma) von dem Vorhandensein eines intakten S6KII Gens abhängt. Die Rettung war sowohl mit einer vollständigen, als auch einer partiellen Deletion erfolgreich und dies zeigt, dass der Verlust der phosphorylierenden Untereinheit der Kinase die Hauptursache des Funktionsdefektes war. Das GAL4/UAS System wurde benutzt, um die S6KII Expression zeitlich und räumlich zu steuern. Es wurde gezeigt, dass die Expression der Kinase während des adulten Stadiums für die Rettung hinreichend war. Dieser Befund schließt eine Entwicklungsstörung als Ursache für den mutanten Phänotyp aus. Außerdem zeigte die gezielte räumliche Rettung von S6KII die Notwendigkeit der Pilzkörper und schloss Strukturen wie das mediane Bündel, die Antennalloben und den Zentralkomplex aus. Dieses Muster ist dem vorher mit der rutabaga Mutation identifizierten sehr ähnlich (Zars et al., 2000). Experimente mit der Doppelmutante rut, ign58-1 deuten an, dass rutabaga und S6KII im gleichen Signalweg aktiv sind. Vorhergehende Studien hatten bereits gezeigt, dass die unterschiedlichen Ergebnisse bei operanter und klassischer Konditionierung auf verschiedenen Rollen für S6KII in den zwei Arten des Lernens hindeuten (Bertolucci, 2002; Putz, 2002). Diese Schlussfolgerung wurde durch den mutanten Phänotyp der transgenen Linien in der Positionskonditionierung und ihr wildtypisches Verhalten in der klassischen Konditionierung zusätzlich bekräftigt. Eine neue Art von Lern-Experiment, genannt „Idle Experiment“, wurde entworfen. Es basiert auf der Konditionierung der Laufaktivität, stellt eine operante Aufgabenstellung dar und überwindet einige der Limitationen des „Standard“ Heat-Box Experimentes. Die neue Art des Idle Experimentes erlaubt es, „gelernte Hilflosigkeit“ in Fliegen zu erforschen, dabei zeigte sich eine erstaunliche Ähnlichkeit zu den Vorgängen in komplizierteren Organismen wie Ratten, Mäusen oder Menschen. Gelernte Hilflosigkeit in der Taufliege wurde nur in den Weibchen beobachtet und wird von Antidepressiva beeinflusst.