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Spin waves in yttrium-iron garnet has been the subject of research for decades. Recently the report of Bose-Einstein condensation at room temperature has brought these experiments back into focus. Due to the small mass of quasiparticles compared to atoms for example, the condensation temperature can be much higher. With spin-wave quasiparticles, so-called magnons, even room temperature can be reached by externally injecting magnons. But also possible applications in information technologies are of interest. Using excitations as carriers for information instead of charges delivers a much more efficient way of processing data. Basic logical operations have already been realized. Finally the wavelength of spin waves which can be decreased to nanoscale, gives the opportunity to further miniaturize devices for receiving signals for example in smartphones.
For all of these purposes the magnon system is driven far out of equilibrium. In order to get a better fundamental understanding, we concentrate in the main part of this thesis on the nonequilibrium aspect of magnon experiments and investigate their thermalization process. In this context we develop formalisms which are of general interest and which can be adopted to many different kinds of systems.
A milestone in describing gases out of equilibrium was the Boltzmann equation discovered by Ludwig Boltzmann in 1872. In this thesis extensions to the Boltzmann equation with improved approximations are derived. For the application to yttrium-iron garnet we describe the thermalization process after magnons were excited by an external microwave field.
First we consider the Bose-Einstein condensation phenomena. A special property of thin films of yttrium-iron garnet is that the dispersion of magnons has its minimum at finite wave vectors which leads to an interesting behavior of the condensate. We investigate the spatial structure of the condensate using the Gross-Pitaevskii equation and find that the magnons can not condensate only at the energy minimum but that also higher Fourier modes have to be occupied macroscopically. In principle this can lead to a localization on a lattice in real space.
Next we use functional renormalization group methods to go beyond the perturbation theory expressions in the Boltzmann equation. It is a difficult task to find a suitable cutoff scheme which fits to the constraints of nonequilibrium, namely causality and the fluctuation-dissipation theorem when approaching equilibrium. Therefore the cutoff scheme we developed for bosons in the context of our considerations is of general interest for the functional renormalization group. In certain approximations we obtain a system of differential equations which have a similar transition rate structure to the Boltzmann equation. We consider a model of two kinds of free bosons of which one type of boson acts as a thermal bath to the other one. Taking a suitable initial state we can use our formalism to describe the dynamics of magnons such that an enhanced occupation of the ground state is achieved. Numerical results are in good agreement with experimental data.
Finally we extend our model to consider also the pumping process and the decrease of the magnon particle number till thermal equilibrium is reached again. Additional terms which explicitly break the U(1)-symmetry make it necessary to also extend the theory from which a kinetic equation can be deduced. These extensions are complicated and we therefore restrict ourselves to perturbation theory only. Because of the weak interactions in yttrium-iron garnet this provides already good results.
A stochastic model for the joint evaluation of burstiness and regularity in oscillatory spike trains
(2013)
The thesis provides a stochastic model to quantify and classify neuronal firing patterns of oscillatory spike trains. A spike train is a finite sequence of time points at which a neuron has an electric discharge (spike) which is recorded over a finite time interval. In this work, these spike times are analyzed regarding special firing patterns like the presence or absence of oscillatory activity and clusters (so called bursts). These bursts do not have a clear and unique definition in the literature. They are often fired in response to behaviorally relevant stimuli, e.g., an unexpected reward or a novel stimulus, but may also appear spontaneously. Oscillatory activity has been found to be related to complex information processing such as feature binding or figure ground segregation in the visual cortex. Thus, in the context of neurophysiology, it is important to quantify and classify these firing patterns and their change under certain experimental conditions like pharmacological treatment or genetical manipulation. In neuroscientific practice, the classification is often done by visual inspection criteria without giving reproducible results. Furthermore, descriptive methods are used for the quantification of spike trains without relating the extracted measures to properties of the underlying processes.
For that reason, a doubly stochastic point process model is proposed and termed 'Gaussian Locking to a free Oscillator' - GLO. The model has been developed on the basis of empirical observations in dopaminergic neurons and in cooperation with neurophysiologists. The GLO model uses as a first stage an unobservable oscillatory background rhythm which is represented by a stationary random walk whose increments are normally distributed. Two different model types are used to describe single spike firing or clusters of spikes. For both model types, the distribution of the random number of spikes per beat has different probability distributions (Bernoulli in the single spike case or Poisson in the cluster case). In the second stage, the random spike times are placed around their birth beat according to a normal distribution. These spike times represent the observed point process which has five easily interpretable parameters to describe the regularity and the burstiness of the firing patterns.
It turns out that the point process is stationary, simple and ergodic. It can be characterized as a cluster process and for the bursty firing mode as a Cox process. Furthermore, the distribution of the waiting times between spikes can be derived for some parameter combination. The conditional intensity function of the point process is derived which is also called autocorrelation function (ACF) in the neuroscience literature. This function arises by conditioning on a spike at time zero and measures the intensity of spikes x time units later. The autocorrelation histogram (ACH) is an estimate for the ACF. The parameters of the GLO are estimated by fitting the ACF to the ACH with a nonlinear least squares algorithm. This is a common procedure in neuroscientific practice and has the advantage that the GLO ACF can be computed for all parameter combinations and that its properties are closely related to the burstiness and regularity of the process. The precision of estimation is investigated for different scenarios using Monte-Carlo simulations and bootstrap methods.
The GLO provides the neuroscientist with objective and reproducible classification rules for the firing patterns on the basis of the model ACF. These rules are inspired by visual inspection criteria often used in neuroscientific practice and thus support and complement usual analysis of empirical spike trains. When applied to a sample data set, the model is able to detect significant changes in the regularity and burst behavior of the cells and provides confidence intervals for the parameter estimates.
Das Gehirn ist die wohl komplexeste Struktur auf Erden, die der Mensch erforscht. Es besteht aus einem riesigen Netzwerk von Nervenzellen, welches in der Lage ist eingehende sensorische Informationen zu verarbeiten um daraus eine sinnvolle Repräsentation der Umgebung zu erstellen. Außerdem koordiniert es die Aktionen des Organismus um mit der Umgebung zu interagieren. Das Gehirn hat die bemerkenswerte Fähigkeit sowohl Informationen zu speichern als auch sich ständig an ändernde Bedingungen anzupassen, und zwar über die gesamte Lebensdauer. Dies ist essentiell für Mensch oder Tier um sich zu entwickeln und zu lernen. Die Grundlage für diesen lebenslangen Lernprozess ist die Plastizität des Gehirns, welche das riesige Netzwerk von Neuronen ständig anpasst und neu verbindet. Die Veränderungen an den synaptischen Verbindungen und der intrinsischen Erregbarkeit jedes Neurons finden durch selbstorganisierte Mechanismen statt und optimieren das Verhalten des Organismus als Ganzes. Das Phänomen der neuronalen Plastizität beschäftigt die Neurowissenschaften und anderen Disziplinen bereits über mehrere Jahrzehnte. Dabei beschreibt die intrinsische Plastizität die ständige Anpassung der Erregbarkeit eines Neurons um einen ausbalancierten, homöostatischen Arbeitsbereich zu gewährleisten. Aber besonders die synaptische Plastizität, welche die Änderungen in der Stärke bestehender Verbindungen bezeichnet, wurde unter vielen verschiedenen Bedingungen erforscht und erwies sich mit jeder neuen Studie als immer komplexer. Sie wird durch ein komplexes Zusammenspiel von biophysikalischen Mechanismen induziert und hängt von verschiedenen Faktoren wie der Frequenz der Aktionspotentiale, deren Timing und dem Membranpotential ab und zeigt außerdem eine metaplastische Abhängigkeit von vergangenen Ereignissen. Letztlich beeinflusst die synaptische Plastizität die Signalverarbeitung und Berechnung einzelner Neuronen und der neuronalen Netzwerke.
Der Schwerpunkt dieser Arbeit ist es das Verständnis der biologischen Mechanismen und deren Folgen, die zu den beobachteten Plastizitätsphänomene führen, durch eine stärker vereinheitlichte Theorie voranzutreiben.Dazu stelle ich zwei funktionale Ziele für neuronale Plastizität auf, leite Lernregeln aus diesen ab und analysiere deren Konsequenzen und Vorhersagen.
Kapitel 3 untersucht die Unterscheidbarkeit der Populationsaktivität in Netzwerken als funktionales Ziel für neuronale Plastizität. Die Hypothese ist dabei, dass gerade in rekurrenten aber auch in vorwärtsgekoppelten Netzwerken die Populationsaktivität als Repräsentation der Eingangssignale optimiert werden kann, wenn ähnliche Eingangssignale eine möglichst unterschiedliche Repräsentation haben und dadurch für die nachfolgende Verarbeitung besser unterscheidbar sind. Das funktionale Ziel ist daher diese Unterscheidbarkeit durch Veränderungen an den Verbindungsstärke und der Erregbarkeit der Neuronen mithilfe von lokalen selbst-organisierten Lernregeln zu maximieren. Aus diesem funktionale Ziel lassen sich eine Reihe von Standard-Lernenregeln für künstliche neuronale Netze gemeinsam abzuleiten.
Kapitel 4 wendet einen ähnlichen funktionalen Ansatz auf ein komplexeres, biophysikalisches Neuronenmodell an. Das Ziel ist eine spärliche, stark asymmetrische Verteilung der synaptischen Stärke, wie sie auch bereits mehrfach experimentell gefunden wurde, durch lokale, synaptische Lernregeln zu maximieren. Aus diesem funktionalen Ansatz können alle wichtigen Phänomene der synaptischen Plastizität erklärt werden. Simulationen der Lernregel in einem realistischen Neuronmodell mit voller Morphologie erklären die Daten von timing-, raten- und spannungsabhängigen Plastizitätsprotokollen. Die Lernregel hat auch eine intrinsische Abhängigkeit von der Position der Synapse, welche mit den experimentellen Ergebnissen übereinstimmt. Darüber hinaus kann die Lernregel ohne zusätzliche Annahmen metaplastische Phänomene erklären. Dabei sagt der Ansatz eine neue Form der Metaplastizität voraus, welche die timing-abhängige Plastizität beeinflusst. Die formulierte Lernregel führt zu zwei neuartigen Vereinheitlichungen für synaptische Plastizität: Erstens zeigt sie, dass die verschiedenen Phänomene der synaptischen Plastizität als Folge eines einzigen funktionalen Ziels verstanden werden können. Und zweitens überbrückt der Ansatz die Lücke zwischen der funktionalen und mechanistische Beschreibungsweise. Das vorgeschlagene funktionale Ziel führt zu einer Lernregel mit biophysikalischer Formulierung, welche mit etablierten Theorien der biologischen Mechanismen in Verbindung gebracht werden kann. Außerdem kann das Ziel einer spärlichen Verteilung der synaptischen Stärke als Beitrag zu einer energieeffizienten synaptischen Signalübertragung und optimierten Codierung interpretiert werden.
Der Begriff psychologische Akkulturation beschreibt jene Veränderungen, die infolge des dauerhaften Aufeinandertreffens verschiedener kultureller Gruppen auf individueller Ebene zu beobachten sind (Berry, 1997). Die vorliegende Arbeit umfasst drei Publikationen, die sich mit Akkulturationsprozessen von Kindern und Jugendlichen mit Migrationshintergrund in Deutschland befassen. Zunächst wird ein Überblick über den aktuellen Stand der Forschung zur Situation junger Migranten in Deutschland vorgelegt. An zentraler Stelle steht dabei die Frage, wie die Migrationsgeschichte und Immigrationspolitik Deutschlands sowie die öffentliche Einstellung gegenüber Migranten die transkulturelle Adaptation von Kindern und Jugendlichen nicht-deutscher ethno-kultureller Herkunft beeinflussen. Bereits bestehende wissenschaftliche Erkenntnisse werden verknüpft mit den Ergebnissen neuerer empirischer Studien um zu einem tieferen Verständnis der Ursachen für die vielfach berichteten problematischen Verläufe psychologischer und soziokultureller Adaptation von Migranten beizutragen. Neben anderen Risiken und protektiven Faktoren wird diskutiert, wie sich Besonderheiten Deutschlands als Aufnahmeland, wie z.B. die Eigenarten des Schulsystems, auf Adaptationsverläufe auswirken können. Unsere eigenen Studien tragen zum Verständnis der Anpassungsprozesse junger Migranten bei, indem sie aufzeigen, dass nicht die Akkulturationsstrategie der Integration, sondern speziell die Orientierung an der deutschen Kultur bei Individuen zu den günstigsten psychologischen und soziokulturellen Ergebnissen zu führen scheint. Im Rahmen dieser Arbeit wird weiterhin ein empirischer und methodologischer Beitrag zur Akkulturationsforschung geleistet, indem ein Messinstrument zur Erfassung psychologischer Akkulturation bei Kindern im deutschen Sprachraum – die Frankfurter Akkulturationsskala für Kinder (FRAKK-K)– entwickelt, validiert und schließlich anhand einer Fragestellung praktisch angewandt wird. Die Skalenentwicklung und –optimierung erfolgte auf der Grundlage von zwei Studien, welche Daten von 387 Grundschülern aus zwei städtischen Regionen in Deutschland umfassen (Frankenberg & Bongard, 2013). Die Ergebnisse konfirmatorischer Faktorenanalysen sprechen für zwei Faktoren, Orientierung an der Aufnahmekultur und Orientierung an der Herkunftskultur, die jeweils mittels 6 Items erfasst werden. Beide Subskalen weisen eine zufriedenstellende interne Reliabilität und Kriteriumsvalidität auf und lassen sich zwecks Erfassung der Akkulturationsstrategie kombinieren (i.e. Assimilation, Integration, Separation und Marginalisierung). In einer ersten praktischen Anwendung der Skala wird der Frage nachgegangen, inwiefern erweiterter Musikunterricht und Orchesterspiel in der Grundschule über verstärkte Gruppenkohäsion zur Förderung kultureller Integration beitragen können.
Grundschüler, die in einem Orchester gespielt haben, zeigen über einen Zeitraum von 1,5 Jahren einen stärkeren Anstieg der Orientierung an der deutschen Kultur als Schüler, die keinen erweiterten Musikunterricht erhielten. Musikschüler fühlen sich außerdem stärker in die Klassengemeinschaft integriert. Dies deutet darauf hin, dass die Erfahrung der Zusammenarbeit und des Musizierens innerhalb einer Gruppengemeinschaft zu einer stärkeren Orientierung an der deutschen Kultur geführt hat. Die Orientierung an der Herkunftskultur blieb unbeeinflusst. Somit können Programme, die jungen Migranten die Gelegenheit bieten Musik innerhalb einer größeren, kulturell heterogenen Gruppe aufzuführen, als eine effektive Intervention zur Förderung der kulturellen Anpassung an die Mehrheitskultur und der Integration innerhalb – und außerhalb – des Klassenzimmers führen.
Abschließend werden die Ergebnisse der empirischen Untersuchungen vor dem Hintergrund des aktuellen Forschungsstandes zu neueren Akkulturationsmodellen sowie zu der Terminologie und den methodischen Herausforderungen des Forschungsfeldes in Beziehung gesetzt und kritisch reflektiert. Daraus abgeleitet werden Implikationen für zukünftige Interventionen und Forschung diskutiert.
Die Adoleszenz, d.h. die Reifungsphase des Jugendlichen zum Erwachsenen, stellt einen zentralen Abschnitt in der menschlichen Entwicklung dar, der mit tief greifenden emotionalen und kognitiven Veränderungen verbunden ist. Neure Studien (Bunge et al., 2002; Durston et al., 2002; Casey et al., 2005; Crone et al., 2006; Bunge and Wright, 2007) machen deutlich, dass sich die funktionelle Architektur des Gehirns während der Adoleszenz grundlegend verändert und dass diese Veränderungen mit der Reifung höherer kognitiven Funktionen in der Adoleszenz assoziiert sein könnten. Messungen des Gehirn-Volumens mit Hilfe der Magnet-Resonanz-Tomographie (MRT) zum Beispiel zeigen eine nicht-lineare Reduktion der grauen und eine Zunahme der weißen Substanz während der Adoleszenz (Giedd et al., 1999; Sowell et al., 1999, 2003). Des weiteren treten in dieser Zeit Veränderungen in exzitatorischen und inhibitorischen Neurotransmitter-Systemen auf (Tseng and O’Donnell, 2005; Hashimoto et al., 2009). Zusammen deuten diese Ergebnisse darauf hin, dass während der Adoleszenz ein Umbau der kortikalen Netzwerke stattfindet, der wichtige Konsequenzen für die Reifung neuronaler Oszillationen haben könnte. Im Anschluss an eine Einführung im Kapitel 2, fasst Kapitel 3 der vorliegenden Dissertation die Vorbefunde bezüglich entwicklungsbedingter Veränderungen in der Amplitude, Frequenz und Synchronisation neuronaler Oszillationen zusammen und diskutiert den Zusammenhang zwischen der Entwicklung neuronaler Oszillationen und der Reifung höhere kognitiver Funktionen während der Adoleszenz. Ebenso werden die anatomischen und physiologischen Mechanismen, die diesen Veränderungen möglicherweise zu Grunde liegen könnten, theoretisch vorgestellt. Die in Kapitel 4-6 vorgestellten eigenen empirischen Arbeiten untersuchen neuronale Oszillationen mit Hilfe der Magnetoencephalographie (MEG), um die Frequenzbänder und die funktionellen Netzwerke zu charakterisieren, die mit höheren kognitiven Prozessen und deren Entwicklung in der Adoleszenz assoziiert sind. Hierzu wurden drei Experimente durchgeführt, bei denen MEG-Aktivität während der Bearbeitung einer Arbeitsgedächtnisaufgabe und im Ruhezustand aufgezeichnet wurde. Die Ergebnisse dieser Experimente zeigen, dass Alpha Oszillationen und Gamma-Band Aktivität sowohl task-abhängig als auch im Ruhezustand gemeinsam auftreten. Darüber hinaus ergänzen die vorliegenden Untersuchungen Vorarbeiten, indem sie eine Wechselwirkung zwischen beiden Frequenzbändern aufgezeigt wird, die als ein Mechanismus für das gezielte Weiterleiten von Informationen dienen könnte. Die in Kapitel 6 vorgestellten Entwicklungsdaten weisen weiterhin darauf, dass in der Adoleszenz späte Veränderungen im Alpha und Gamma-Band stattfinden und dass diese Veränderungen involviert sind in die Entwicklung der Arbeitsgedächtnis-Kapazität und die Entwicklung der Fähigkeit, Distraktoren zu inhibieren. Abschliessend werden in Kapitel 7, die in dieser Dissertation vorgestellten Arbeiten, aus einer übergeordneten Perspektive im Gesamtzusammenhang diskutiert.
Driven by rapid technological advancements, the amount of data that is created, captured, communicated, and stored worldwide has grown exponentially over the past decades. Along with this development it has become critical for many disciplines of science and business to being able to gather and analyze large amounts of data. The sheer volume of the data often exceeds the capabilities of classical storage systems, with the result that current large-scale storage systems are highly distributed and are comprised of a high number of individual storage components. As with any other electronic device, the reliability of storage hardware is governed by certain probability distributions, which in turn are influenced by the physical processes utilized to store the information. The traditional way to deal with the inherent unreliability of combined storage systems is to replicate the data several times. Another popular approach to achieve failure tolerance is to calculate the block-wise parity in one or more dimensions. With better understanding of the different failure modes of storage components, it has become evident that sophisticated high-level error detection and correction techniques are indispensable for the ever-growing distributed systems. The utilization of powerful cyclic error-correcting codes, however, comes with a high computational penalty, since the required operations over finite fields do not map very well onto current commodity processors. This thesis introduces a versatile coding scheme with fully adjustable fault-tolerance that is tailored specifically to modern processor architectures. To reduce stress on the memory subsystem the conventional table-based algorithm for multiplication over finite fields has been replaced with a polynomial version. This arithmetically intense algorithm is better suited to the wide SIMD units of the currently available general purpose processors, but also displays significant benefits when used with modern many-core accelerator devices (for instance the popular general purpose graphics processing units). A CPU implementation using SSE and a GPU version using CUDA are presented. The performance of the multiplication depends on the distribution of the polynomial coefficients in the finite field elements. This property has been used to create suitable matrices that generate a linear systematic erasure-correcting code which shows a significantly increased multiplication performance for the relevant matrix elements. Several approaches to obtain the optimized generator matrices are elaborated and their implications are discussed. A Monte-Carlo-based construction method allows it to influence the specific shape of the generator matrices and thus to adapt them to special storage and archiving workloads. Extensive benchmarks on CPU and GPU demonstrate the superior performance and the future application scenarios of this novel erasure-resilient coding scheme.
Ribosome biogenesis is best understood in the yeast Saccharomyces cerevisiae. In human or mammalian ribosome biogenesis, it has been shown that basic principles are conserved to yeast, but additional features have been reported. Our understanding about the interplay between proteins and RNA in human ribosome biogenesis is far from complete.
The present study focused on the analysis of the human ribosome biogenesis co-factors PWP2, EMG1 and Exportin 5 (XPO5) to understand the degree of conservation of ribosome biogenesis. The proteins were characterized in respect to their localization and interaction partners. For the early 90S co-factor, PWP2, it was possible to pull down and identify the human UTP-B complex with MALDI mass spectrometry. Besides the orthologues of the members of this complex known in yeast (TBL3, WDR3, WDR36, UTP6, UTP18), the human UTP-B complex is not only conserved from yeast to humans, but contains also additional components, like the DEAD-box RNA helicase DDX21, which lacks a yeast orthologue. DDX21 was localized to the nucleus, assembled to the native UTP-B complex and co-precipitated also with other UTP-B complex members, presumably extending the functions of this complex in ribosome biogenesis.
This phenomenon was also observed for the 90S co-factor EMG1, an RNA methyltransferase, whose mutant form causes the Bowen-Conradi syndrome, if aspartic acid is mutated to glycine at position 86. This study revealed that the mutant, EMG1-D86G, clearly lost its nucleolar localization and co-precipitated to histones for unknown reasons.
A participation of the nuclear export receptor XPO5 in human ribosome biogenesis was shown in this study. Pulldown analysis, sucrose density gradients and UV crosslinking and analysis of cDNAs of XPO5 revealed the involvement of XPO5 in pre-60S subunit maturation. Moreover, besides the known pre-miRNAs and tRNAs as substrates for nuclear export, XPO5 crosslinked to snoRNAs. XPO5 was further demonstrated to interact with the miRNA Let-7a, which has an important regulatory function for MYC, a transcription factor required for ribosome biogenesis.
All results support a role of these proteins in human ribosome biogenesis and therefore it seems that the biogenesis of ribosomes in human cells requires additional components, like DDX21 and XPO5.
Due to recent technical developments, it became evident that the mammalian transcriptome is much more complex than originally expected. Alternative splicing(AS) and the transcription of long non-coding RNAs (lncRNAs) are two phenomenas which have been greatly underestimated in their frequency. Nowadays it is accepted that almost every gene has at least one alternative isoform and the number of lncRNAs exceeds the one of protein-coding genes.
We built user-friendly web interfaces which can process Affymetrix GeneChip Exon 1.0 ST Arrays (exon arrays) and GeneChip Gene 1.0 ST Arrays (gene arrays)for the analysis of alternative splicing events. Results are presented with detailed annotation information and graphics to identify splice events and to facilitate biological validations. Based on two studies using exon arrays, we show how our tools were used to profile genome-wide splicing changes under silencing of Jmjd6 and under hypoxic conditions. Since gene arrays are not intended for AS analysis originally, we demonstrated their applicability by profiling alternative splicing events during embryonic heart development.
To measure lncRNAs expressions with exon arrays, we completely re-annotation all probes and built a lncRNA specific annotation. To demonstrate the applicability of exon arrays in combination with our annotation, we profiled the expression of tens of thousands of lncRNAs. Further, our custom annotation allows for a detailed inspection of lncRNAs and to distinguish between isoforms, as we validated by RTPCR.
To allow for a general usage to the research community, we integrated the annotation in an easy-to-use web interface, which provides various helpful features for the analysis of lncRNAs.
The economic success of the World Wide Web makes it a highly competitive environment for web businesses. For this reason, it is crucial for web business owners to learn what their customers want. This thesis provides a conceptual framework and an implementation of a system that helps to better understand the behavior and potential interests of web site visitors by accounting for both explicit and implicit feedback. This thesis is divided into two parts.
The first part is rooted in computer science and information systems and uses graph theory and an extended click-stream analysis to define a framework and a system tool that is useful for analyzing web user behavior by calculating the interests of the users.
The second part is rooted in behavioral economics, mathematics, and psychology and is investigating influencing factors on different types of web user choices. In detail, a model for the cognitive process of rating products on the Web is defined and an importance hierarchy of the influencing factors is discovered.
Both parts make use of techniques from a variety of research fields and, therefore, contribute to the area of Web Science.
Calcium-deficiency rickets (CDR) is a metabolic bone disease in children that is characterized by impaired mineralization and severe bone deformities. As CDR is often an endemic phenomenon that is almost exclusively restricted to tropical areas, environmental conditions are currently considered to be a possible predisposing factor for the CDR. Apart from a lack of macronutrients and micronutrients, an oversupply of potentially toxic elements (PTEs) in the soil-plant pathway of the CDR areas is thought to be involved in the aetiology of CDR. This study is the first to comprehensively analyze the impact of the environment on Ca deficiency and the resulting CDR.
To analyze the impact of the environment on CDR in developing countries, a rural region near Kaduna City, northern Nigeria, was chosen as a study area. From this area, cases of CDR have been reported since the early 2000s with a prevalence rate of 5%. Within this study area, 11 study sites, including areas with a high CDR prevalence (HR), a low CDR prevalence (LR) and no CDR prevalence (NR), were visited. In these HR, LR and NR study sites, the bedrock was investigated and the types of parent materials were identified. Local farmers were interviewed to determine the type and intensity of the land use. The soil types were determined along toposequences. The soil textures as well as the clay mineral fractions were determined. The pH values were measured, and the contents of organic carbon (OC) were determined. The potential cation-exchange capacity (CECpot) and the base saturation (BS) were analyzed. Furthermore, the total and plant-available macronutrient, micronutrient and PTE concentrations were measured in the soils. The drinking water was analyzed for pH values and the concentrations of Ca, Se and F were measured. The maize was analyzed for the Ca, Mg, K and P, Se and phytic acid (PA) contents.
The field and laboratory analyses on the bedrock showed that the HR, LR and NR study sites near Kaduna City, northern Nigeria, were underlain by Older Granites. A direct link between the distribution of the bedrock, the parent materials and the prevalence of CDR was not found. Interviews with the local farmers showed that the land use in the Kaduna study area is dominated by the cultivation of cash crops and food crops. Field analyzes on the soil types in the Kaduna study area showed that the distribution of the soil types is highly dependent on the topography and the distribution of the parent materials. In near vicinity to the inselbergs, Lixisols had developed on grus slope deposits. In the lower pediment and plain positions, Acrisols had developed on grus slope deposits and pisolite slope deposits. In the upper plains, Plinthosols had developed on pisolite slope deposits and in the river valleys, Fluvisols had developed on river deposits. Such soil types and soil type distributions are typical for granite-underlain areas in the northern guinea savanna of West Africa. Similarly, the physical soil conditions were representative for the soils of the northern guinea savanna: sandy topsoils, clayey subsoils and relatively high contents of kaolinite clay minerals in the clay fractions. With regard to the geochemical composition, no significant difference was found between the soils of the Kaduna study area and the soils of other granite-underlain areas in West Africa. Only the concentrations of P were considerably low in the soils of the Kaduna study area. However, P deficiency is a typical phenomenon in West African savanna soils and is not restricted to CDR areas. The micronutrient concentrations in the soils were low, but not critically low. Laboratory analyses on the amounts of PTEs showed that compared to worldwide background levels and international critical limits the PTE concentrations were very low in the soils of the Kaduna study area. In the drinking water, neither a significant lack of macronutrients and micronutrients, nor a noticeable oversupply of PTEs was found. The maize in the HR, LR and NR study sites contained normal contents of Mg, K and P, low contents of Ca and Se as well as slightly elevated concentrations of PA compared to West African food composition tables. Comparisons between the mineral contents of traditional and modern maize cultivars showed that the traditional maize cultivars contained significantly higher contents of Ca and noticeably lower concentrations of PA than the modern maize cultivars.
A direct link between the environmental conditions and the CDR in the Kaduna study area was considered unlikely, as neither a statistically significant lack of macronutrients and micronutrients, nor a statistically significant oversupply of PTEs was found in the environment of this area. Instead, the results indicated that the nutrition rather than the environmental conditions that impacts the prevalence of CDR.
Im Zentralen Nervensystem (ZNS) kommunizieren neuronale Synapsen über eine Kombination von chemischen und elektrischen Signalen, die in ihrer Umgebung eine spezifische Komposition von Ionen benötigen. Um eine strenge Kontrolle des ZNS-Milieus zu gewährleisten, hat sich in Säugetieren eine endotheliale Blut-Hirn-Schranke (BHS) entwickelt. Die BHS limitiert den parazellulären Molekül Transport und wird von den Kapillargefässen des Gehirns gebildet, wobei die physische Barrier von den Tight Junctions (TJs) des vaskulären Endothels generiert wird. Das Gehirnendothel ist Teil einer neurovaskulären Einheit (NVE), zu der auch Perizyten (PZ), Astrozyten (AZ), Mikroglia und Interneurone zählen. Fehlkommunikation oder defekte zelluläre Komponenten in der NVE führen in der Regel zu Störungen in der BHS Funktion und können schwerwiegende neuronale Erkrankungen zur Folge haben.
Vor einigen Jahren haben wir und andere Forschungsgruppen herausgefunden, dass der Wnt/β-Catenin Signalweg essentiell für die Vaskularisierung des Gehirns während der Embryonalentwicklung ist und darüber hinaus auch eine bedeutende Rolle in der Induktion der BHS spielt. Des Weiteren konnte im Zebrafischmodell eine Aktivierung des kanonischen Wnt Signalweges auch im adulten Organismus nachgewiesen werden. Allerdings ist die Quelle der Wnt Wachstumsfaktoren bis dato unbekannt. Der Wnt Signalweg ist eine hoch konservierte und komplexe zelluläre Signalkaskade, die in allen mehrzelligen Organismen vorkommt. Wnt Wachstumsfaktoren sind sekretierte, hydrophobe Signalmoleküle, die sowohl über lange als auch kurze Strecken entweder den β-Catenin-abhängingen („kanonischen“) oder β-Catenin-unabhängingen („nicht-kanonischen“) Wnt Signalweg aktivieren können.
Da die meisten ZNS Erkrankungen mit einem Zusammenbruch der BHS-Funktion assoziiert sind, ist die Forschung bestrebt die Mechanismen, die der Entstehung und Aufrechterhaltung der BHS zugrunde liegen, zu ermitteln und zu verstehen. Das Ziel meiner Doktorarbeit war es herauszufinden, ob AZ Wnts produzieren und ob deren Wirkung auf das Gehirnendothel an der Aufrechterhaltung der BHS beteiligt ist. Zu diesem Zweck, habe ich ein in vitro BHS Kokultivierungs-Modellsystem etabliert das erstmalig ausschliesslich auf der Verwendung von murinen AZ und Gehirnendothelzellen basiert. Zu Beginn der Studie wurden sowohl primäre AZ als auch eine murine Gehirnendothel-zelllinie (MBE) bezüglich ihrer zell-spezifischen Eigenschaften charakterisiert. Dabei konnte belegt werden, dass sowohl die primären AZ als auch die MBE Zelllinie, aufgrund ihrer Proteinexpressionsprofile als repräsentative Vertreter ihres Zelltyps eingestuft werden können. Die darauffolgenden Untersuchungen konnten zeigen, dass primäre AZ über mehrere Passagen hinweg fast alle 19 Wnt Liganden auf mRNA Ebene exprimierten. Ferner konnte in primären Gehirnendothelzellen und zwei Gehirnendothelzelllinien die korrespondierenden Frizzled (FZD) Rezeptoren und low density lipoprotein receptor-related protein (LRP) Korezeptoren nachgewiesen werden. Dieser Befund legte Nahe, dass AZ und Gehirnendothelzellen die basalen Eigenschaften besitzen, um über den Wnt Signalweg miteinander zu kommunizieren. Die Stimulation von pMBEs mit Astrozyten konditioniertem Medium (AKM) induzierte die Hochregulation von Claudin-3 einem bekannten kanonischen Wnt Zielgens. Interessanterweise konnte diese Regulation teilweise durch die Zugabe von dickkopf 1 (Dkk1), einem Wnt/β-Catenin Antagonisten, inhibiert werden.
Um die physiologische Rolle der Wnt Liganden zu bestimmen, habe ich mir die Eigenschaft des universellen Sekretionsmechanismus der Wachstumsfaktoren, welcher von dem Transmembranprotein evenness interrupted (Evi) abhängig ist, zu Nutze gemacht. Die Verpaarung von Evifl/fl mit hGFAP-Cre Mäusen erlaubt die AZ-spezifische Deletion des Evi Proteins (Evi KO), was zur Folge hat, dass die Astrozyten der Nachkommen keine Wnt Wachstumsfaktoren sekretieren können.
In vitro führte der Verlust von Wnts in AKM zu einer teilweisen Delokalisierung von Junction Proteinen. Während die Kokultivierung mit Evi WT AZ einen straken Anstieg im TEER und reduzierte Permeabilitätsmesswerte induzierten, konnten diese pro-BHS Eigenschaften bei Evi KO AZ nicht beobachtet werden. Diese Ergebnisse zeigten deutlich, dass Wnts sekretiert von AZ den BHS Phenotyp positive beeinflussen, indem sie die Zell-Zell-Verbindung verstärken, was wiederum zu erhöhtem Zellwiderstand und reduzierter transzellulärer Permeabilität führt. Die Analyse des in vivo Phänotyps von Evi KO Mäusen ergab, dass mit fortschreitendem, postnatalem Alter makroskopisch erkennbare zerebrale Blutungen auftraten. Ausserdem konnte ich zeigen, dass eine Subpopulation von Blutgefässen Malformationen aufwies, die mit reduzierter Astrozytenendfuss-Assoziierung einhergingen.
Das Wissen um die Beteiligung des Wnt Signalweges an der Regulation der BHS auch im adulten Organismus kann in Zukunft von wichtiger Bedeutung sein, da es potentielle therapeutische Anwendungen ermöglicht.
Protein quality control systems (PQC), i.e. UPS and aggresome-autophagy pathway, have been suggested to be a promising target in cancer therapy. Simultaneous pharmacological inhibition of both pathways have shown increase efficacy in various tumors, such as ovarian and colon carcinoma. Here, we investigate the effect of concomitant inhibition of 26S proteasome by FDA-approved inhibitor Bortezomib, and HDAC6, as key mediator of the aggresome-autophagy system, by the highly specific inhibitor ST80 in rhabdomyosarcoma (RMS) cell lines. We demonstrated that simultaneous inhibition of 26S proteasome and selective aggresome-autophagy pathway significantly increases apoptosis in all tested RMS cell lines. Interestingly, we observed that a subpopulation of RMS cells was able to survive the co-treatment and, upon drug removal, to recover similarly to untreated cells. In this study, we identified co-chaperone BAG3 as the key mediator of this recovery: BAG3 is transcriptionally up-regulated specifically in the ST80/Bortezomib surviving cells and mediates clearance of cytotoxic protein aggregates by selective autophagy. Impairment of the autophagic pathway during the recovery phase, both by conditional knock-down of ATG7 or by inhibition of lysosomal degradation by BafylomicinA1, triggers accumulation of insoluble protein aggregates, loss of cell recovery and cell death similarly to stable short harpin RNA (shRNA) BAG3 knock-down. Our results are the first demonstration that BAG3 mediated selective autophagy is engaged to cope with proteotoxicity induced by simultaneous inhibition of constitutive PQC systems in cancer cell lines during cell recovery. Moreover, our data give new insights in the regulation of constitutive and on demand PQC mechanisms pointing to BAG3 as a promising target in RMS therapy.
ATP synthases are multi-subunit membrane enzymes, which utilize the energy stored in a transmembrane electrochemical ion gradient to produce adenosine-5´-triphosphate (ATP), the universal energy carrier in biological systems. Research on these important enzymes goes back more than 50 years and has produced innumerable studies. The F-type ATP synthase consists of two functionally distinct, but tightly coupled subcomplexes, the water-soluble F1 and the membrane-embedded Fo complex. In its simplest form, F1 consists of five different subunits with a stoichiometry of α 3β3γδε, and harbors three catalytic centers in the α 3β3-headpiece, while Fo consists of three different subunits in a stoichiometry of ab2cn, where n varies between 8 to 15 depending on the species. From a mechanistic standpoint, the complex can also be divided into two different units, namely a stator, α3β3δ-ab2, and a rotor, γε-cn. The enzyme utilizes the energy stored in a transmembrane electrochemical gradient of protons, or in some cases Na+, to drive ATP synthesis. In particular, the downhill translocation of these ions across the Fo complex drives rotation of the γε-cn unit, which is then transduced to the active centers, catalyzing the phosphorylation of adenosine-5`-diphosphate (ADP) with inorganic phosphate (Pi), and the release of ATP....
Biological membranes separate the cell interior from the outside and have diverse functions from signal transduction, apoptosis to transportations of ions and small molecules in and out of the cell. Most of these functions are fulfilled by proteins incorporated in the membrane. However, lipids as the main component of membrane not only serve as structural element for bilayer formation but they are also directly involved e.g. signalling processes and bilayer properties are important to mediate protein interactions. To fully understand the role of lipids, it is necessary to develop a molecular understanding of how certain membrane components modify bulk bilayer structure and dynamics. Membranes are known to have many different motions in different conditions and time scales. Temperature, pH, water content and many other conditions change membrane dynamics in a high degree. In addition to this, time scales of motions in membranes vary from ns to ms range corresponding to fast motion and slow motion, respectively. Therefore, membranes are needed to be studied systematically by varying the conditions and using methods to investigate motions in various time scales separately. The aim of this study was therefore perform a combined solid-state NMR / molecular dynamics study on model membranes. Different substrates, such as potential drugs, polarizing agents and signaling lipids were incorporated into bilayers and their location within the membrane and their effect onto the membrane was probed. NSAIDs (non-steroidal anti-inflammatory drugs), pirinixic acid derivatives, ceramides and polarizing agents were the substrates for membranes in this study. There were several experimental methods that were applied in order to investigate effects of these substrates on membrane dynamics. Different kind of phospholipids including POPC, DMPC and DPPC were used. In addition to experimental work, with the information gathered from solid state NMR experiments molecular dynamics simulations were performed to obtain more information about the membranes at the molecular level. As a result, combination of solid-state NMR with molecular dynamics simulations provides very systematic way of investigating membrane dynamics in a large range of time scales.
Pirinixic acid derivatives were special interest of this study because of their activity on peroxisome proliferator-activated receptor (PPAR) as an agonist as well as on enzymes of microsomal prostaglandin E2 synthase-1 (PGE2s) -1 and 5-lipoxygenase (5-LO) as dual inhibitor. Two potent pirinixic acid derivatives, 2-(4-chloro-6-(quinolin-6-ylamino)pyrimidin-2-ylthio)octanoic acid (compound 2) and 2-(4-chloro-6-(quinolin-6-ylamino)pyrimidin-2-ylthio)octanoate (compound 3), have been worked and their insertion depts were investigated by combining of solid state NMR and molecular dynamics simulations. Both experimental and theoretical results pointed out that compound 3 was inserted the phospholipid bilayer more deeply than 2. NSAIDs – lipid mixtures have been also studied here. It is known that consumption of NSAIDs as in mixture with lipids results much fewer side effects than consumption of the drugs alone. Thus, it is crucial to understand interactions of NSAIDs with lipids and investigate the possible complex formation of drugs with lipids. In this study, interactions of three widely used NSAIDs, ibuprofen, diclofenac and piroxicam, with DPPC were investigated by solid-state NMR. 1H and 31P NMR results depicted that ibuprofen and diclofenac had interactions with lipids, which is an indication of drug-lipid complex formation whereas piroxicam didn’t show any interactions with lipids suggesting that no complex formation occurred in the case of piroxicam. Ceramides are known to play key roles in many cell processes and many studies showed that the functions of ceramides are related with the ceramide effects on biological membranes. Therefore, in this study, influences of ceramides on biophysics of lipid bilayers were investigated by using various solid state NMR techniques and molecular dynamics simulations. Results from molecular dynamics simulations clearly showed that ceramide and lipids have strong interactions. More evidences about ceramide-lipid interactions were provided from 1H and 14N NMR results. In addition, it was indicated by both simulation and experimental methods that ceramide increased the rigidity of DMPC by increasing chain order parameters. BTbk is a biradical, which is used as polarizing agent for dynamic nuclear polarization (DNP) experiments and found to be more efficient than other widely used polarizing agents such as TOTAPOL. Since it is a hydrophobic compound, which prefers to stay inside lipid bilayer it is important to investigate the location and orientation of bTbk along the bilayer in order to understand its enhancement profile in DNP measurements. In this study, both NMR relaxation time measurements and molecular dynamics simulations revealed that bTbk tends to stay more close to hydrophobic chain of lipids than the interfacial part of lipids at bilayer surface.
In the first part of this work, a brief introduction on lipid membranes as well as a theoretical summary on both methods of solid-state NMR and molecular dynamics simulations is given. Then, in the second part methodology is introduced for both solid-state NMR spectrometer and theoretical calculations. Afterwards, results of different membrane systems are discussed in the following parts for both solid state NMR and MD. Finally, in the last part, a summary and the conclusion of the overall results together with some future plans are explained.
ß1-integrins are essential for angiogenesis but the mechanisms regulating integrin function in endothelial cells (EC) and their contribution to angiogenesis remain elusive. BRAG2 is a guanine nucleotide exchange factor for the small Arf-GTPases Arf5 and Arf6. The role of BRAG2 in EC and angiogenesis and the underlying molecular mechanisms remains unclear. siRNA-mediated BRAG2-silencing reduced EC angiogenic sprouting and migration. BRAG2-siRNA-transfection differentially affected a5ß1- and aVß3-integrin function: specifically, BRAG2-silencing increased focal/fibrillar adhesions and EC adhesion on ß1-integrin-ligands (fibronectin and collagen), while reducing the adhesion on the aVß3-integrin-ligand, vitronectin. Consistent with these results, BRAG2-silencing enhanced surface expression of a5ß1-integrin, while reducing surface expression of aVß3-integrin. Mechanistically, BRAG2 mediated recycling of aVß3-integrins and endocytosis of ß1-integrins and specifically of the active/matrix bound a5ß1-integrin present in fibrillar/focal adhesions (FA), suggesting that BRAG2 contributes to the disassembly of FA via ß1-integrin-endocytosis. Arf5 and Arf6 are promoting downstream of BRAG2 angiogenic sprouting, ß1-integrin-endocytosis and the regulation of FA. In vivo silencing of the BRAG2-orthologues in zebrafish embryos using morpholinos perturbed vascular development. Furthermore, in vivo intravitral injection of plasmids containing BRAG2-shRNA reduced pathological ischemia-induced retinal and choroidal neovascularization. These data reveals that BRAG2 is essential for developmental and pathological angiogenesis by promoting EC sprouting through regulation of adhesion by mediating ß1-integrin internalization and associates for the first time the process of ß1-integrin endocytosis with angiogenesis.
Alzheimer’s disease (AD), which was first reported more than a century ago by Alhzeimer, is one of the commonest forms of dementia which affects >30 million people globally (>8 million in Europe). The origin and pathogenesis of AD is poorly understood and there is no cure available for the disease. AD is characterized by the accumulation of senile plaques composed of amyloid beta peptides (Ab 37-43) which is formed by the gamma secretase (GS) complex by cleaving amyloid precursor protein. Therefore GS can be an attractive drug target. Since GS processes several other substrates like Notch, CD44 and Cadherins, nonspecific inhibition of GS has many side effects. Due to the lack of crystal structure of GS, which is attributed to the extreme difficulties in purifying it, molecular modeling can be useful to understand its architecture. So far only low resolution cryoEM structures of the complex has been solved which only provides a rough structure of the complex at low 12-15 A resolution Furthermore the activity of GS in vitro can be achieved by means of cell-free (CF) expression.
GS comprises catalytic subunits namely presenilins and supporting elements containing Pen-2, Aph-1 and Nicastrin. The origin of AD is hidden in the regulated intramembrnae proteolysis (RIP) which is involved in various physiological processes and also in leukemia. So far growth factors, cytokines, receptors, viral proteins, cell adhesion proteins, signal peptides and GS has been shown to undergo RIP. During RIP, the target proteins undergo extracellular shredding and intramembrane proteolysis.
This thesis is based on molecular modeling, molecular dynamics (MD) simulations, cell-free (CF) expression, mass spectrometry, NMR, crystallization, activity assay etc of the components of GS complex and G-protein coupled receptors (GPCRs).
First I validated the NMR structure of PS1 CTF in detergent micelles and lipid bilayers using coarse-grained MD simulations using MARTINI forcefield implemented in Gromacs. CTF was simulated in DPC micelles, DPPC and DLPC lipid bilayer. Starting from random configuration of detergent and lipids, micelle and lipid bilyer were formed respectively in presence of CTF and it was oriented properly to the micelle and bilyer during the simulation. Around DPC molecules formed micelle around CTF in agreement of the experimental results in which 80-85 DPC molecules are required to form micelles. The structure obtained in DPC was similar to that of NMR structure but differed in bilayer simulations showed the possibility of substrate docking in the conserved PAL motif. Simulations of CTF in implicit membrane (IMM1) in CHAMM yielded similar structure to that from coarse grained MD.
I performed cell-free expression optimization, crystallization and NMR spectroscopy of Pen-2 in various detergent micelles. Additionally Pen-2 was modeled by a combination of rosetta membrane ab-initio method, HHPred distant homology modeling and incorporating NMR constraints. The models were validated by all atom and coarse grained MD simulations both in detergent micelles and POPC/DPPC lipid bilayers using MARTINI forcefield.
GS operon consisting of all four subunits was co-expressed in CF and purified. The presence of of GS subunits after pull-down with Aph-1 was determined by western blotting (Pen-2) and mass spectrometry (Presenilin-1 and Aph-1). I also studied interactions of especially PS1 CTF, APP and NTF by docking and MD.
I also made models and interfaces of Pen-2 with PS1 NTF and checked their stability by MD simulations and compared with experimental results. The goal is to model the interfaces between GS subunits using molecular modeling approaches based on available experimental data like cross-linking, mutations and NMR structure of C-terminal fragment of PS1 and transmembrane part of APP. The obtained interfaces of GS subunits may explain its catalysis mechanism which can be exploited for novel lead design. Due to lack of crystal/NMR structure of the GS subunits except the PS1 CTF, it is not possible to predict the effect of mutations in terms of APP cleavage. So I also developed a sequence based approach based on machine learning using support vector machine to predict the effect of PS1 CTF L383 mutations in terms of Aβ40/Aβ42 ratio with 88% accuracy. Mutational data derived from the Molgen database of Presenilin 1 mutations was using for training.
GPCRs (also called 7TM receptors) form a large superfamily of membrane proteins, which can be activated by small molecules, lipids, hormones, peptides, light, pain, taste and smell etc. Although 50% of the drugs in market target GPCRs , only few are targeted therapeutically. Such wide range of targets is due to involvement of GPCRs in signaling pathways related to many diseases i.e. dementia (like Alzheimer's disease), metabolic (like diabetes) including endocrinological disorders, immunological including viral infections, cardiovascular, inflammatory, senses disorders, pain and cancer.
Cannabinoid and adrenergic receptors belong to the class A (similar to rhodopsin) GPCRs. Docking of agonists and antagonists to CB1 and CB2 cannabinoid receptors revealed the importance of a centrally located rotamer toggle switch, and its possible role in the mechanism of agonist/antagonist recognition. The switch is composed of two residues, F3.36 and W6.48, located on opposite transmembrane helices TM3 and TM6 in the central part of the membranous domain of cannabinoid receptors. The CB1 and CB2 receptor models were constructed based on the adenosine A2A receptor template. The two best scored conformations of each receptor were used for the docking procedure. In all poses (ligand-receptor conformations) characterized by the lowest ligand-receptor intermolecular energy and free energy of binding the ligand type matched the state of the rotamer toggle switch: antagonists maintained an inactive state of the switch, whereas agonists changed it. In case of agonists of β2AR, the (R,R) and (S,S) stereoisomers of fenoterol, the molecular dynamics simulations provided evidence of different binding modes while preserving the same average position of ligands in the binding site. The (S,S) isomer was much more labile in the binding site and only one stable hydrogen bond was created. Such dynamical binding modes may also be valid for ligands of cannabinoid receptors because of the hydrophobic nature of their ligand-receptor interactions. However, only very long molecular dynamics simulations could verify the validity of such binding modes and how they affect the process of activation.
Human N-formyl peptide receptors (FPRs) are G protein-coupled receptors (GPCRs) involved in many physiological processes, including host defense against bacterial infection and resolving inflammation. The three human FPRs (FPR1, FPR2 and FPR3) share significant sequence homology and perform their action via coupling to Gi protein. Activation of FPRs induces a variety of responses, which are dependent on the agonist, cell type, receptor subtype, and also species involved. FPRs are expressed mainly by phagocytic leukocytes. Together, these receptors bind a large number of structurally diverse groups of agonistic ligands, including N-formyl and nonformyl peptides of different composition, that chemoattract and activate phagocytes. For example, N-formyl-Met-Leu-Phe (fMLF), an FPR1 agonist, activates human phagocyte inflammatory responses, such as intracellular calcium mobilization, production of cytokines, generation of reactive oxygen species, and chemotaxis. This ligand can efficiently activate the major bactericidal neutrophil functions and it was one of the first characterized bacterial chemotactic peptides. Whereas fMLF is by far the most frequently used chemotactic peptide in studies of neutrophil functions, atomistic descriptions for fMLF-FPR1 binding mode are still scarce mainly because of the absence of a crystal structure of this receptor. Elucidating the binding modes may contribute to designing novel and more efficient non-peptide FPR1 drug candidates. Molecular modeling of FPR1, on the other hand, can provide an efficient way to reveal details of ligand binding and activation of the receptor. However, recent modelings of FPRs were confined only to bovine rhodopsin as a template.
To locate specific ligand-receptor interactions based on a more appropriate template than rhodopsin we generated the homology models of FPR1 using the crystal structure of the chemokine receptor CXCR4, which shares over 30% sequence identity with FPR1 and is located in the same γ branch of phylogenetic tree of GPCRs (rhodopsin is located in α branch). Docking and model refinement procedures were pursued afterward. Finally, 40 ns full-atom MD simulations were conducted for the Apo form as well as for complexes of fMLF (agonist) and tBocMLF (antagonist) with FPR1 in the membrane. Based on locations of the N- and C-termini of the ligand the FPR1 extracellular pocket can be divided into two zones, namely, the anchor and activation regions. The formylated M1 residue of fMLF bound to the activation region led to a series of conformational changes of conserved residues. Internal water molecules participating in extended hydrogen bond networks were found to play a crucial role in transmitting the agonist-receptor interactions. A mechanism of initial steps of the activation concurrent with ligand binding is proposed.
I accurately predicted the structure and ligand binding pose of dopamine receptor 3 (RMSD to the crystal structure: 2.13 Å) and chemokine receptor 4 (CXCR4, RMSD to the crystal structure 3.21 Å) in GPCR-Dock 2010 competition. The homology model of the dopamine receptor 3 was 8 th best overall in the competition.
Introduction: Postural control is a prerequisite to many everyday and sporting activities which requires the interaction of multiple sensorimotor processes. As long as we have no balance disorders, the maintenance of an erect standing position is taken for granted with automatic running control processes. It is well known that with increasing age or disease balance problems occur which often cause fall-related injuries. To assess balance performance, posturography is widely applied in which body sway is traditionally viewed as a manifestation of random fluctuations. Thus, the amount of sway is solely used as an index of postural stability, that is, less sway is an indication of better control. But, traditional measures of variability fail to account for the temporal organisation of postural sway. The concept of nonlinear dynamics suggests that variability in the motor output is not random but structured. It provides the stimulus to reveal the functionality of postural sway. This thesis evaluates nonlinear analysis tools in addition to classic linear methods in terms of age-related modifications of postural control and under different standing conditions in order to broaden the existing knowledge of postural control processes.
Methods: Static posturographic analyses were conducted which included the recording of centre of pressure (COP) time series by means of a force plate. Linear and nonlinear methods were used to quantify postural sway variability in order to evaluate both the amount and structure of sway. Classic time and frequency domain COP parameters were computed. In addition, wavelet transform (WT), multiscale entropy, detrended fluctuation analysis, and scaled windowed variance method were applied to COP signals in order to derive structural COP parameters. Two experiments were performed. 1) 16 young (26.1 ± 6.7 years), healthy subjects were asked to adopt a bipedal stance under single- and dual-task conditions. Three trials were conduced each with a different sampling duration: 30, 60, and 300 seconds [s]. 2) 26 young (28.15 ± 5.86 years) and 13 elderly (72 ± 7 years) subjects stood quietly for 60 s on five different surfaces which imposed different biomechanical constraints: level ground (LG), one foot on a step (ST), uphill (UH), downhill (DH), and slope (SL). Additional to COP recordings, limb load symmetry was assessed via foot pressure insoles.
Results: We found a higher sensitivity of structural COP parameters to modulations of postural control and partly an improved evaluation of sway dynamics in longer COP recordings. WT revealed a reweighing of frequency bands in response to altered standing conditions. Scaling exponents and entropy values of COP signals were task-dependent. Higher entropy values were found under the dual-task and condition ST. The time scales affected under the altered standing positions differed between groups and sway directions. Mainly larger posturograms were found in the elderly. Age effects were especially revealed in position ST and concerning medial-lateral COP signals. Load asymmetry was stronger in elderly subjects for LG, UH, and DH positions.
Discussion: Modifications of multiple time scales corresponds to an interplay of control subsystems to cope with the altered task demands. The affected time scales are age-dependent suggesting a change of control processes. Higher irregularity under the dual-task indicates a more complex motor output which is interpreted as less attentional investment into postural control. Larger complexity is evident for ST in contrast to LG position. ST obviously challenges lateral sway which is counteracted differently between groups. Load asymmetry suggests that especially elderly subjects adopt a step-initiation strategy.
Conclusion: A continued application of nonlinear methods is necessary to broaden the understanding of postural control mechanisms and to identify classifiers for balance dysfunctions. Structural COP parameters provide a more comprehensive indication of postural control system properties between groups and task demands. COP recordings of at least 60 s are recommended to adequately quantify COP signal structure. The analysis of postural strategies in everyday activities increases the ecological validity of postural control studies and can provide valuable information regarding the development of effective rehabilitation programs.
This work presents a biochemical, functional and structural characterization of Aquifex aeolicus F1FO ATP synthase obtained using both a native form (AAF1FO) and a heterologous form (EAF1FO) of this enzyme.
F1FO ATP synthases catalyze the synthesis of ATP from ADP and inorganic phosphate driven by ion motive forces across the membrane and therefore play a key cellular function. Because of their central role in supporting life, F1FO ATP synthases are ubiquitous and have been remarkably conserved throughout evolution. For their biological importance, F1FO ATP synthases have been extensively studied for many decades and many of them were characterized from both a functional and a structural standpoint. However, important properties of ATP synthases – specifically properties pertaining to their membrane embedded subunits – have yet to be determined and no structures are available to date for the intact enzyme complex. Therefore, F1FO ATP synthases are still a major focus of research worldwide. Our research group had previously reported an initial characterization of AAF1FO and had indicated that this enzyme presents unique features, i.e. a bent central stalk and a putatively heterodimeric peripheral stalk. Based on such a characterization, this enzyme revealed promising for structural and functional studies on ATP synthases and became the focus of this doctoral thesis. Two different lines of research were followed in this work.
First, the characterization of AAF1FO was extended by bioinformatic, biochemical and enzymatic analyses. The work on AAF1FO led to the identification of a new detergent that maintains a higher homogeneity and integrity of the complex, namely the detergent trans-4-(trans-4’-propylcyclohexyl)cyclohexyl-α-D-maltoside (α-PCC). The characterization of AAF1FO in this new detergent showed that AAF1FO is a proton-dependent, not a sodium ion-dependent ATP synthase and that its ATP hydrolysis mechanism needs to be triggered and activated by high temperatures, possibly inducing a conformational switch in subunit γ. Moreover, this approach suggested that AAF1FO may present unusual features in its membrane subunits, i.e. short N-terminal segments in subunits a and c with implications for the membrane insertion mechanism of these subunits.
Investigating on these unique features of A. aeolicus F1FO ATP synthase could not be done using A. aeolicus cells, because these require a harsh and dangerous environment for growth and they are inaccessible to genetic manipulations. Therefore, a second approach was pursued, in which an expression system was created to produce the enzyme in the heterologous host E. coli. This second approach was experimentally challenging, because A. aeolicus F1FO ATP synthase is a 500-kDa multimeric membrane enzyme with a complicated and still not entirely determined stoichiometry and because its encoding genes are scattered throughout A. aeolicus genome, rather than being organized in one single operon. However, an artificial operon suitable for expression was created in this work and led to the successful production of an active and fully assembled form of Aquifex aeolicus F1FO ATP synthase. Such artificial operon was created using a stepwise approach, in which we expressed and studied first individual subunits, then subcomplexes, and finally the entire F1FO ATP synthase complex. We confirmed experimentally that subunits b1 and b2 form a heterodimeric subcomplex in the E. coli membranes, which is a unique case among ATP synthases of non-photosynthetic organisms. Moreover, we determined that the b1b2 subcomplex is sufficient to recruit the soluble F1 subcomplex to the membranes, without requiring the presence of the other membrane subunits a and c. The latter subunits can be produced in our expression system only when the whole ATP synthase is expressed, but not in isolation nor in the context of smaller FO subcomplexes. These observations led us to propose a novel mechanism for the assembly of ATP synthases, in which first the F1 subcomplex attaches to the membrane via subunit b1b2, and then cring and subunits a assemble to complete the FO subcomplex. Furthermore, we could purify the heterologous ATP synthase (EAF1FO) to homogeneity by chromatography and electro-elution. Enzymatic assays showed that the purified form of EAF1FO is as active as AAF1FO. Peptide mass fingerprinting showed that EAF1FO is composed of the same subunits as AAF1FO and all soluble and membrane subunits could be identified. Finally, single-particle electron microscopy analysis revealed that the structure of EAF1FO is identical to that of AAF1FO. Therefore, the EAF1FO expression system serves as a reliable platform for investigating on properties of AAF1FO.
Specifically, in this work, EAF1FO was used to study the membrane insertion mechanism of rotary subunit c. Subunits c possess different lengths and levels of hydrophobicity across species and by analyzing their N-terminal variability, four phylogenetic groups of subunits c were distinguished (groups 1 to 4). As a member of group 2, the subunit c from A. aeolicus F1FO ATP synthase is characterized by an N-terminal segment that functions as a signal peptide with SRP recognition features, a unique case for bacterial F1FO ATP synthases. By accurately designing mutants of EAF1FO, we determined that such a signal peptide is strictly necessary for membrane insertion of subunit c and we concluded that A. aeolicus subunit c inserts into E. coli membranes using a different pathway than E. coli subunit c. Such a property may be common to other ATP synthases from extremophilic organisms, which all cluster in the same phylogenetic group.
In conclusion, the successful production of the fully assembled and active F1FO ATP synthase from A. aeolicus in E. coli reported in this work provides a novel genetic system to study A. aeolicus F1FO ATP synthase. To a broader extent, it will also serve in the future as a solid reference for designing strategies aimed at producing large multi-subunit complexes with complicated stoichiometry.
Characterization of mouse NOA1 : subcellular localizaion, G-Quadruplex binding and proteolysis
(2013)
Mitochondria contain their own protein synthesis machinery with mitoribosomes that are similar to prokaryotic ribosomes. The thirteen proteins encoded in the mitochondrial genome are members of the respiratory chain complexes that generate a proton gradient, which is the electromotoric force for ATP synthesis.
NOA1 (Nitric Oxide Associated Protein-1) is a nuclear encoded GTPase that positively influences mitochondrial respiration and ATP production. Although a role in mitoribosome assembly was assigned to NOA1 the underlying molecular mechanism is poorly understood. This work shows that the multi-domain protein NOA1 serves multiple purposes for the function of mitochondria. NOA1 is a dual localized protein that makes a detour through the nucleus before mitochondrial import. The nuclear shuttling is mediated by a nuclear localization signal and the now identified nuclear export signal. SELEX (Systemic Evolution of Ligands by Exponential Enrichment) analysis revealed a G-quadruplex binding motif that characterizes NOA1 as ribonucleoprotein (RNP). G-quadruplex binding was coupled to the GTPase activity and increased the GTP hydrolysis rate. The sequence of localization events and the identification of NOA1 being a RNP lead to the discussion of an alternative import pathway for RNPs into mitochondria. The short-lived NOA1 contains ClpX recognition motifs and is specifically degraded by the mitochondrial matrix protease ClpXP. NOA1 is the first reported substrate of ClpXP in higher eukaryotes and augments the contribution of the ClpXP protease for mitochondrial metabolism. To assess the direct action of NOA1 on the mitoribosome co-sedimentation assays were performed. They showed that the interaction of NOA1 and the mitoribosome is dependent on the GTPase function and the nascent peptide chain. In vitro, NOA1 facilitated the membrane insertion of newly translated and isotope labeled mitochondrial translation products into inverted mitochondrial inner membrane vesicles. In conclusion, NOA1 is a G-quadruplex-RNP that acts as mitochondrial membrane insertion factor for mtDNA-encoded proteins.
This thesis provides a comprehensive model of the molecular function of NOA1 and is the basis for future research. The identification of NOA1 as ClpXP substrate is a major contribution to the field of mitochondrial research.
Cheating and Cheaters in Pfaffe Amis and Reinhart Fuchs An Alsatian poet named Heinrich, writing around 1180, composed a beast epic, based on French sources, about a trickster fox named Reinhart. Some sixty years later, a poet known to us only as Der Stricker composed a work of similar length and structure, about a trickster priest named Amis, and his diligent efforts to cheat various anonymous individuals out of their money. Other works by this poet bear out the Stricker's consistent emphasis on strategy over brute force, prudence and intelligence over unconsidered actions. These stories both illustrate that power, when not directed by intelligence, is useless or dangerous, even to the one who wields it. Tricksters and cheating also appear in a surprising range of works contemporary to the Stricker's Pfaffe Amis and Heinrich's Reinhart Fuchs. Romances have their own trickster characters, conducting their cheats using methods and structures that recall those of these two Schwank-type epics. Cheaters like Amis, and Tristan's Isolde generate twin situations. One of them is true/hidden, and can influence the characters, and one is false/apparent, to which the victim characters are forced to respond. This artificial, apparent reality persists even after the cheater has left the scene, occasionally taking on a truth of its own. Both Reinhart and Amis, whatever their motivations, work evil everywhere they go; and yet the audience is expected to treat them as sympathetic characters. Because the trickster universe functions to turn systems upside-down, it also rejects the concepts of good and evil, forming a universe in which all that matters is who wins and who loses. The place of the villain belongs now to the fool; any character who becomes deceived deserves to be, and is treated with indignation by the narrator, just as the traditional villain might be.
The biogenesis and function of photosynthetically active chloroplasts relies on the import of thousands of nuclear encoded proteins via the coordinated actions of two multiprotein translocon machineries in the outer and inner envelope membrane. Trafficking of preproteins across the soluble compartment of InterMembrane Space (IMS) is currently envisioned to be facilitated by an IMS complex composed of outer envelope proteins Toc64 and Toc12, a soluble IMS component, Tic22 and an IMS-localized Hsp70. Among them, currently Tic22 is the only component that stands undisputed in terms of its existence. Having two closely related homologs in A. thaliana, their biochemical and functional characterization was still lacking. A critical analysis of Tic22 knockout mutants displayed growth phenotype reminiscent of ppi1, the mutant of Toc33. However, both the genes have similar expression patterns with no clear preference for photosynthetic or nonphotosynthetic tissues, which explained the absence of a detectable phenotype in single mutants. In addition, transgenic complementation study with either of the homolog affirmed the identical localization of both proteins in the IMS which characterizes the two homologs as functionally redundant. Based on the pale-yellow phenotype exhibited by the double mutant plants, an attempt to analyze the import capacity of a stromal substrate in the double mutant revealed threefold reduction when compared to wild-type acknowledging the essential role of Tic22 in the import mechanism. Initially, Tic22 was identified together with another protein, Tic20, which has been heavily discussed as a protein conducting channel in the inner membrane. Despite being characterized, in A. thaliana, two out of four homologs of Tic20 are differentially localized with one being additionally localized in mitochondria and the other, exclusively residing in the thylakoids.
According to in silico analysis, for all the Tic20 proteins, a four-helix transmembrane topology was predicted. Accordingly, its topology was mapped by employing the recently established selfassembling GFP-based in vivo experiments. Astonishingly, the expression of one of the inner envelope localized Tic20 homolog enforces inner membrane proliferation affecting the shape and organization of the membrane. Therefore this study focuses on analyzing the effects of high envelope protein concentrations on membrane structures, which together with the existing results, an imbalance in the lipid to protein ratio and a possible role of signaling pathway regulating membrane biogenesis is discussed.
Paging is one of the most prominent problems in the field of online algorithms. We have to serve a sequence of page requests using a cache that can hold up to k pages. If the currently requested page is in cache we have a cache hit, otherwise we say that a cache miss occurs, and the requested page needs to be loaded into the cache. The goal is to minimize the number of cache misses by providing a good page-replacement strategy. This problem is part of memory-management when data is stored in a two-level memory hierarchy, more precisely a small and fast memory (cache) and a slow but large memory (disk). The most important application area is the virtual memory management of operating systems. Accessed pages are either already in the RAM or need to be loaded from the hard disk into the RAM using expensive I/O. The time needed to access the RAM is insignificant compared to an I/O operation which takes several milliseconds.
The traditional evaluation framework for online algorithms is competitive analysis where the online algorithm is compared to the optimal offline solution. A shortcoming of competitive analysis consists of its too pessimistic worst-case guarantees. For example LRU has a theoretical competitive ratio of k but in practice this ratio rarely exceeds the value 4.
Reducing the gap between theory and practice has been a hot research issue during the last years. More recent evaluation models have been used to prove that LRU is an optimal online algorithm or part of a class of optimal algorithms respectively, which was motivated by the assumption that LRU is one of the best algorithms in practice. Most of the newer models make LRU-friendly assumptions regarding the input, thus not leaving much room for new algorithms.
Only few works in the field of online paging have introduced new algorithms which can compete with LRU as regards the small number of cache misses.
In the first part of this thesis we study strongly competitive randomized paging algorithms, i.e. algorithms with optimal competitive guarantees. Although the tight bound for the competitive ratio has been known for decades, current algorithms matching this bound are complex and have high running times and memory requirements. We propose the algorithm OnlineMin which processes a page request in O(log k/log log k) time in the worst case. The best previously known solution requires O(k^2) time.
Usually the memory requirement of a paging algorithm is measured by the maximum number of pages that the algorithm keeps track of. Any algorithm stores information about the k pages in the cache. In addition it can also store information about pages not in cache, denoted bookmarks. We answer the open question of Bein et al. '07 whether strongly competitive randomized paging algorithms using only o(k) bookmarks exist or not. To do so we modify the Partition algorithm of McGeoch and Sleator '85 which has an unbounded bookmark complexity, and obtain Partition2 which uses O(k/log k) bookmarks.
In the second part we extract ideas from theoretical analysis of randomized paging algorithms in order to design deterministic algorithms that perform well in practice. We refine competitive analysis by introducing the attack rate
parameter r, which ranges between 1 and k. We show that r is a tight bound on the competitive ratio of deterministic algorithms.
We give empirical evidence that r is usually much smaller than k and thus r-competitive algorithms have a reasonable performance on real-world traces. By introducing the r-competitive priority-based algorithm class OnOPT we obtain a collection of promising algorithms to beat the LRU-standard. We single out the new algorithm RDM and show that it outperforms LRU and some of its variants on a wide range of real-world traces.
Since RDM is more complex than LRU one may think at first sight that the gain in terms of lowering the number of cache misses is ruined by high runtime for processing pages. We engineer a fast implementation of RDM, and compare it
to LRU and the very fast FIFO algorithm in an overall evaluation scheme, where we measure the runtime of the algorithms and add penalties for each cache miss.
Experimental results show that for realistic penalties RDM still outperforms these two algorithms even if we grant the competitors an idealistic runtime of 0.
Silicon wafers such as Silicon on Insulator (SOI) and strained silicon on Insulator (sSOI) are the essential and basic materials of advanced microelectronic devices. However, they often show various kinds of crystal defects which impair the function of these devices. The most efficient method to date, for detecting such defects and for determining their density, is to delineate them by etching the wafers with a suitable etching solution and characterise them via light optical microscopy. Etch pits are formed at defect sites which are etched at a faster rate than at the perfect lattice. The standard etching solution used for SOI and sSOI is a dilute version of Secco. As Secco contains carcinogenic and environmentally hazardous chromium (VI), the use of which is or will be restricted by law in many countries, suitable chromium (VI)-free etching solutions like Organic Peracid Etches (OPE), modified Chemical Polishing Etches (CP) like CP4 mod and mixtures with organic oxidizing agents like chloranil (CA) have been developed for the successful delineation of various types of crystal defects.
However there are still nanometer-sized defects which are hard to detect or escape detection by this method. Copper decoration is a well known method to magnify these defects. It consists in applying a copper nitrate solution to the back of the SOI or sSOI wafer. On annealing, copper diffuses through the substrate and the BOX (buried oxide) to the SOI/sSOI film and on quenching to room temperature, copper precipitates as copper silicide, SiCu3, foremost at crystal defects where the lattice strain is greater than at perfect lattice sites. These silicides increase the volume in these parts of the crystal lattice and defect magnification occurs. A considerable disadvantage of this method is its tendency for artefact formation, when the copper concentration used is too high, with the copper precipitating at the film surface. The consequence is a higher density of etch pits whereby true defect etch pits cannot be differentiated from those caused by artefacts.
The aim of this thesis is to show that the processes of decorating and etching can be combined successfully to delineate all crystal defects in SOI and sSOI. An ideal result would have been to find a copper decoration procedure that decorates all existing crystal defects at a copper concentration that avoids artefact formation.
Development of prototype components for the Silicon Tracking System of the CBM experiment at FAIR
(2013)
The CBM experiment at future accelerator facility FAIR will investigate the properties of nuclear matter under extreme conditions. The experimental programm is different from the heavy-ion experiments at RHIC (BNL) and LHC (CERN) that create nuclear matter at high temperatures. In contrast, the study of the QCD phase diagram in the region of the highest net baryon densities and moderate temperatures that is weakly explored will be performed with high precision. For this, collisions of different heavy-ion beams at the energies of 10–45GeV/nucleon with nuclear target will be measured.
The physics programme of the CBM experiment includes measurement of both rare probes and bulk observables that originate from various phases of a nucleus-nucleus collision. In particular, decay of particles with charm quarks can be registered by reconstructing the decay vertex detached from the primary interaction point by several hundreds of micrometers (e.g., decay length c Tau = 123 µm for D0 meson). For this, precise tracking and full event reconstruction with up to 600 charged particle tracks per event within acceptance are required. Other rare probes require operation at interaction rate of up to 10MHz. The detector system that performs tracking has to provide high position resolution on the order of 10 µm, operate at high rates and have radiation tolerant design with low material budget.
The Silicon Tracking System (STS) is being designed for charged-particle tracking in a magnetic field. The system consists of eight tracking station located in the aperture of a dipole magnet with 1T field. For tracks with momentum above 1GeV, momentum resolution of such a system is expected to be about 1%. In order to fulfill this task, thorough optimization of the detector design is required. In particular, minimal material budget has to be achieved.
Production of a detector module requires research and development activities with respect to the module components and their integration. A detector module is a basic functional unit that includes a sensor, an analogue microcable and frontend electronics mounted on a support structure. The objective of the thesis is to perform quality assurance tests of the prototype module components in order to validate the concept of the detector module and to demonstrate its operation using radioactive sources and particle beams.
Double-sided silicon microstrip detectors have been chosen as sensor technology for the STS because of the combination of a good spatial resolution, two-dimensional coordinate measurement achieved within low material budget (0.3%X0), high readout speed and sufficient radiation tolerance. Several generations of double-sided silicon microstrip sensors have been manufactured in order to explore the radiation hard design features and the concept of a large-area sensor compatible with ladder-type structure of the detector module. In particular, sensors with double metal layer on both sides and active area of 62×62mm2 have been produced. Electrical characterization of the sensors has been performed in order to establish the overall operability as well as to extract the device parameters. Current-voltage, capacitance-voltage characteristics and interstrip parameters have been measured.
Readout of the sensors has been done using self-triggering front-end electronics. A front-end board has been developed based on the n-XYTER readout chip with data driven architecture and capable of operating at 32MHz readout rate. The front-end board included an external analog-to-digital converter (ADC). Calibration of the ADC has been performed using both 241Am X-ray source and external pulse generator. Threshold calibration and investigation of temperature dependence of chip parameters has been carried out.
Low-mass support structures have been developed using carbon fibre that has the rigidity to hold the detector modules and introduce minimal Coulomb scattering of the particle tracks. Analogue microcables have been produced with aluminium traces on a polyimide substrate, thus combining good electrical connection with low material budget. Microcable structure includes several layers optimized for low trace capacitance and thus low-noise performance.
A demonstrator tracking telescope has been constructed and operated in several beam tests including 2.5GeV proton beam at COSY synchrotron (Jülich). Three tracking stations have been complemented with several beam hodoscopes. Analysis of the beam data has yielded information on analogue and timing response, beam profile. Tracking and alignment information has been obtained. Beam stability has been evaluated using specially developed monitoring tools.
As a result of conducted studies, performance of the module components have been evaluated and requirements to the detector module have been formulated. Practical suggestions have been made with respect to the structure of the detector module, whereas precise definition of the final detector module design was outside of the scope of this thesis.
Heterodyne array receivers are employed in radio astronomy to reduce the observing time needed for mapping extended sources. One of the main factors limiting the amount of pixels in terahertz receivers is the difficulty of generating a sufficient amount of local oscillator power. Another challenge is efficient diplexing and coupling of local oscillator and signal power to the detectors. These problems are attacked in this dissertation by proposing the application of two vacuum electronic terahertz amplifier types for the amplification of the LO-signal and by introducing a new method for finding the defects in a quasioptical diplexer.
A traveling wave tube (TWT) design based on a square helix slow wave structure (SWS) at 825 GHz is introduced. It exhibits a simulated small-signal gain of 18.3 dB and a 3-dB bandwidth of 69 GHz. In order to generate LO-power at even higher frequencies, the operation of an 850-GHz square helix TWT as a frequency doubler has been studied. A simulated conversion efficiency of 7% to 1700 GHz, comparable with the state-of-art solid-state doublers, has been achieved for an input power of 25 mW.
The other amplifier type discussed in this work is a 1-THz cascade backward wave amplifier based on a double corrugated waveguide SWS. Specifically, three input/output coupler types between a rectangular waveguide and the SWS are presented. The structures have been realized with microfabrication, and the results of loss measurements at 1 THz will be shown.
Diplexing of the LO- and signal beams is often performed with a Martin-Puplett interferometer. Misalignment and deformation of the quasioptical components causes the polarization state of the output signal to be incorrect, which leads to coupling losses. A ray-tracing program has been developed for studying the influence of such defects. The measurement results of the diplexer of a multi-pixel terahertz receiver operated at the APEX telescope have been analyzed with the program, and the results are presented. The program allows the quasioptical configuration of the diplexer to be corrected in order to obtain higher receiver sensitivity.
In der vorliegenden Arbeit wird untersucht, wie das Gehirn Bewusstsein erzeugt. Diese Frage wird als eines der größten Rätsel der heutigen Wissenschaft angesehen: Wie kann es sein, dass aus der Aktivität der Nervenzellen unsere subjektive Welt entsteht? Es ist offensichtlich nicht einfach, diese Frage wissenschaftlich zu untersuchen. Eine der vorgeschlagenen Strategien für die Untersuchung von Bewusstsein behauptet, dass man zunächst die neuronalen Korrelate des Bewusstseins finden sollte (Koch, 2004). Einer Definition zufolge sind die neuronalen Korrelate des Bewusstseins die kleinste Menge neuronaler Prozesse, die hinreichend für eine bestimmte bewusste Erfahrung sind (zum Beispiel für die bewusste Erfahrung des Blaubeergeschmacks). Manche behaupteten, die Entdeckung der neuronalen Korrelate des Bewusstseins würde es erlauben, dem Rätsel des Bewusstseins näher zu kommen (Crick & Koch, 1990). Nur wie soll man die neuronalen Korrelate des Bewusstseins finden? Eine relativ einfache Strategie dafür wurde schon vor mehr als 20 Jahren beschrieben. Es sollten einfach experimentelle Bedingungen erschaffen werden, in welchen ein Reiz manchmal bewusst wahrgenommen wird und manchmal nicht (Baars, 1989). Solche Analysen, die Bedingungen mit und ohne bewusste Wahrnehmung vergleichen, werden als „Kontrastierungsanalyse“ bezeichnet (da zwei Bedingungen miteinander kontrastiert werden). Es existieren viele verschiedene experimentelle Paradigmen, bei welchen man den Reiz unter denselben Bedingungen präsentieren kann, so dass er bei manchen Versuchsdurchgängen bewusst wahrgenommen wird, bei anderen nicht (Kim & Blake, 2005). Mit solchen experimentellen Paradigmen kann man angeblich die neuronalen Korrelate des Bewusstseins finden, wenn man a) bei jedem Durchgang die Versuchsperson fragt, ob oder was die Versuchsperson bei dem Durchgang wahrgenommen hat und b) gleichzeitig die neuronalen Prozesse misst (zum Beispiel mit EEG, MEG oder fMRT). Anschließend kann man die erhobenen neuronalen Daten unter den Bedingungen mit und ohne bewusste Wahrnehmung vergleichen.
Mittlerweile gibt es viele Studien, in denen solche experimentelle Paradigmen – und damit die Kontrastierungsanalyse – angewendet wurden. Insofern könnte man glauben, die neuronalen Korrelate des Bewusstseins seien schon gefunden worden. Allerdings ist dies nicht der Fall. Es existiert in der Literatur weiterhin Uneinigkeit darüber, ob die Korrelate des Bewusstseins früh oder spät in der Zeit liegen, und ob die Korrelate in sensorischen Arealen oder eher im hierarchisch höheren fronto-parietalen Kortex zu finden sind.
Nach unserer Meinung sind die experimentellen Paradigmen, die üblicherweise zum Auffinden der neuronalen Korrelate des Bewusstseins verwendet werden, nicht spezifisch genug, um diese eindeutig zu lokalisieren. Eher glauben wir, dass die klassische Kontrastierungsanalyse auch andere Prozesse als Ergebnisse hervorbringt und uns deshalb prinzipiell nicht zu den neuronalen Korrelaten des Bewusstseins führen kann.
Im Kapitel 2 wird erklärt, wieso die typischen experimentellen Paradigmen nicht die neuronalen Korrelate des Bewusstseins ausfindig machen können. Wir behaupten, dass der Vergleich neuronaler Daten aus experimentellen Bedingungen mit und ohne bewusste Wahrnehmung auch die neuronalen Prozesse widerspiegeln könnte, die bewussten Wahrnehmungen entweder vorausgehen oder folgen. Es ist beispielsweise bekannt, dass neuronale Prozesse vor Auftreten des Reizes darüber bestimmen können, ob der Reiz bewusst wahrgenommen wird oder nicht (Busch, Dubois, & VanRullen, 2009; Mathewson, Gratton, Fabiani, Beck, & Ro, 2009). Wenn man experimentelle Bedingungen mit und ohne bewusster Wahrnehmung miteinander vergleicht, werden auch solche Prozesse als Ergebnis auftauchen, obwohl diese zeitlich klar vor dem Reiz stattfinden und deshalb keine neuronalen Korrelate des Bewusstseins sein können. Es ist natürlich einfach zu entscheiden, dass diese Prozesse, die schon vor dem Reiz stattfinden, der bewussten Wahrnehmung vorausgehen müssen, aber es ist unmöglich zu sagen, ob ein neuronaler Prozess 100 oder 200 Millisekunden nach der Präsentation des Reizes immer noch ein Vorläuferprozess ist schon ein neuronales Korrelat des Bewusstseins darstellt. Deshalb ist die typische Kontrastierungsanalyse nicht spezifisch genug und wir wissen nicht, ob neuronale Prozesse, die durch die Kontrastierungsanalyse aufgedeckt werden, direkt die neuronalen Korrelate des Bewusstseins oder eher Prozesse vor der bewussten Wahrnehmung widerspiegeln.
Nicht nur die Vorläuferprozesse der bewussten Warnehmung stellen ein Problem dar. Auch Konsequenzen der bewussten Verarbeitung werden durch die Kontrastierungsanalyse gefunden. Beispielsweise wurden im medialen Temporallappen Neurone gefunden, die nur dann feuern, wenn ein Patient eine Person auf einem Bild bewusst erkennt, aber nicht feuern, wenn der Patient die Person auf dem Bild nicht bewusst wahrnimmt (Quiroga, Mukamel, Isham, Malach, & Fried, 2008). So könnte man vorerst meinen, dass das Feuern dieser Neurone das neuronale Korrelat des Bewusstseins sein könnte. Nach einer Läsion, sprich neuronalen Schädigung des medialen Temporallappens kann man die Welt jedoch weiterhin bewusst wahrnehmen (man hat jedoch Probleme mit dem Gedächtnis und Wiedererkennen). Insofern kann das Feuern dieser Neurone nicht das neuronale Korrelat des Bewusstseins sein und ist eher ein Beispiel für die Konsequenz der bewussten Verarbeitung. Wir behaupten, dass es noch viele andere solcher Vorläuferprozesse und Konsequenzen gibt, die notwendigerweise als Ergebnis bei der Kontrastierungsanalyse auftauchen, und also ist die typische Kontrastierungsanalyse extrem unspezifisch bezüglich der neuronalen Korrelate des Bewusstseins. In anderen Worten: Die typische Kontrastierungsanalyse, bei welcher man experimentelle Bedingungen mit und ohne bewusste Wahrnehmung miteinander vergleicht, wird uns nicht helfen die neuronalen Korrelate des Bewusstseins zu finden.
Wir glauben, dass neue experimentelle Paradigmen entwickelt werden sollten, um die neuronalen Korrelate des Bewusstseins ausfindig zu machen. Wahrscheinlich gibt es kein einfaches Experiment, mit dem man die Vorläuferprozesse und Konsequenzen vollständig vermeiden kann, um damit direkt die neuronalen Korrelate des Bewusstseins zu bestimmen. Eher braucht man viele verschiedene Experimente, die Schritt für Schritt unser Wissen über die neuronalen Korrelate des Bewusstseins erweitern.
In der vorliegenden Arbeit (in Kapiteln 3, 4 und 5) wird ein neues experimentelles Paradigma angewandt. Dieses Paradigma wird nicht alle oben erwähnten Probleme lösen, wird aber hoffentlich erlauben, einige Vorläuferprozesse der bewussten Wahrnehmung von den neuronalen Korrelaten des Bewusstseins auseinanderzuhalten. Der Vorteil unseres experimentellen Paradigmas besteht darin, dass die bewusste Wahrnehmung durch zwei verschiedene Vorläuferprozesse beeinflusst wird. Die Versuchspersonen müssen auf schnell präsentierten und mittels Rauschens undeutlich gemachten Bildern eine Person detektieren. Die experimentellen Bedingungen sind derart gestaltet, dass die Versuchspersonen nicht bei jedem Durchgang die Person auf dem Bild wahrnehmen können. Damit können wir den Wahrnehmungsprozess manipulieren. Bei einer Manipulation variieren wir den Anteil des Rauschens auf dem Bild und damit die sensorische Evidenz. Je weniger Rauschen, desto besser können die Versuchspersonen die Bilder wahrnehmen und desto öfter sehen sie auch bewusst die Person auf dem Bild. Bei der anderen experimentellen Manipulation der Wahrnehmung werden einige Bilder den Versuchspersonen vorher klar und ohne Rauschen gezeigt. Damit erschafft man Wissen über bestimmte Bilder, die später mit Rauschen präsentiert werden. Man kann zeigen, dass solch bestehendes Wissen tatsächlich die Wahrnehmung beeinflusst. Wenn die Versuchspersonen bestehendes Wissen über ein Bild haben, ist es wahrscheinlicher, dass sie die Person auf dem Bild bewusst wahrnehmen. Damit haben wir zwei verschiedene Vorläuferprozesse – sensorische Evidenz und bestehendes Wissen, die beide die bewusste Wahrnehmung beeinflussen. Beide Vorläuferprozesse erhöhen den Anteil der Durchgänge, in welchen die Versuchspersonen die Person auf dem Bild bewusst wahrnehmen.
Mit diesem experimentellen Paradigma möchten wir einige Aussagen über die neuronalen Korrelate des Bewusstseins testen. Wenn über einen neuronalen Prozess behauptet wird, dass er einem neuronalen Korrelat des Bewusstseins entspricht, müsste dieser Prozess von den beiden manipulierten Vorläuferprozessen in ähnlicher Weise beeinflusst werden, da bewusste Wahrnehmung durch beide manipulierten Vorläuferprozessen in ähnlicher Weise erleichtert wird. Wenn aber der Prozess, über den behauptet wird, er sei ein neuronales Korrelat des Bewusstseins, nicht durch beide Manipulationen geändert wird, kann dieser Prozess kein neuronales Korrelat des Bewusstseins sein, da er nicht beeinflusst wird, obwohl die bewusste Wahrnehmung geändert wurde.
Mit diesem experimentellen Paradigma und dieser Logik haben wir zwei unterschiedliche neuronale Prozesse getestet, von denen behauptet wird, dass sie den neuronalen Korrelaten des Bewusstseins entsprechen könnten. In Kapitel 3 wurde untersucht, ob lokale kategorienspezifische Gammabandaktivität die neuronalen Korrelate des Bewusstseins reflektieren könnte. In Kapitel 4 wurde mit diesem experimentellen Paradigma untersucht, ob die neuronale Synchronisierung dem neuronalen Korrelat des Bewusstseins entsprechen könnte.
Unsere Arbeit im Kapitel 3 baut auf der von Fisch und Kollegen (2009) auf. Fisch und Kollegen (2009) zogen aus ihrer experimentellen Arbeit den Schluss, dass lokale kategorienspezifische Gammabandaktivität die neuronalen Korrelate des Bewusstseins reflektieren könnte. Sie hatten Elektroden auf dem visuellen Kortex von Epilepsiepatienten implantiert und von diesen Elektroden die Gammabandaktivität abgeleitet. Im ersten Schritt suchten sie nach Elektroden, die kategorienspezifische Antworten zeigen. Bei den kategorienspezifischen Elektroden ist die Gammabandaktivität abhängig vom präsentierten Stimulusmaterial. Zum Beispiel kann man bei einer Elektrode auf dem Fusiform Face Area starke Gammabandaktivität nur dann messen, wenn ein Gesicht auf dem Bild zu sehen ist. Die Autoren benutzten solche kategorienspezifischen Elektroden, um nach den neuronalen Korrelaten des Bewusstseins zu suchen. Sie zeigten den Patienten Bilder von Gesichtern, Häusern und Objekten, die direkt nach der kurzen Präsentation maskiert wurden, so dass die Patienten nur bei manchen Durchgängen erkannten, was auf dem Bild war, bei anderen Durchgängen nicht. Dies entspricht der typischen Kontrastierungsanalyse. Die Ergebnisse haben klar gezeigt, dass bei diesen kategorienspezifischen Elektroden die Gammabandaktivität erhöht wurde, als die Patienten bewusst wahrnahmen, was auf dem Bild zu sehen war. Aus diesen Ergebnissen zogen die Autoren den Schluss, dass lokale kategorienspezifische Gammabandaktivität dem neuronalen Korrelat des Bewusstseins entspricht. Diese Aussage wollten wir mit unserem experimentellen Paradigma testen.
Um diese Behauptung zu untersuchen, erhoben wir sehr ähnliche Daten wie Fisch et al. (2009) und analysierten die Daten auf ähnliche Weise. Unsere experimentelle Frage war, ob die lokale kategorienspezifische Gammabandaktivität durch unsere beiden Manipulationen – sensorische Evidenz und bestehendes Wissen – in ähnlicher Weise erhöht wird. Dies sollte der Fall sein, wenn die lokale kategorienspezifische Gammabandaktivität dem neuronalen Korrelat des Bewusstseins entspricht, da sensorische Evidenz und bestehendes Wissen beide den Anteil der Durchgänge, in welchen die Versuchsperson die Person auf dem Bild bewusst wahrnimmt, erhöhen. Dieses Ergebnis wurde nicht gefunden. Stattdessen fanden wir, dass die lokale kategorien-spezifische Gammabandaktivität nur durch sensorische Evidenz erhöht wurde, bestehendes Wissen aber keinen Effekt auf diese Aktivierung hatte. Da bestehendes Wissen auch den Anteil der Durchgänge mit bewusster Wahrnehmung erhöht, die kategorienspezifische Gammabandaktivität aber nicht durch bestehendes Wissen erhöht wurde, kann man schlussfolgern, dass die kategorienspezifische Gammabandaktivität nicht die neuronalen Korrelate des Bewusstseins reflektieren kann.
Als nächstes (Kapitel 4) haben wir die Hypothese getestet, dass Synchronizität dem neuronalen Korrelat des Bewusstseins entspricht. Um diese Idee zu testen, maßen wir mittels Magnetoenzephalographie die magnetischen Felder des Gehirns, schätzten aus diesen Daten mittels Beamforming die neuronalen Aktivitätsquellen und quantifizierten die Synchronizität zwischen diesen Quellen. Wenn die interareale Synchronizität dem neuronalen Korrelat des Bewusstseins entspräche, sollte die Synchronizität für Bedingungen mit mehr sensorischer Evidenz und mit bestehendem Wissen erhöht sein. Dies wurde nicht beobachtet. Wir fanden, dass Synchronizität (gemittelt über die Quellen) nur bei den Bildern erhöht war, für die bestehendes Wissen vorlag. Ein ähnlicher Effekt für sensorische Evidenz wurde nicht gefunden. Insofern können wir sagen, dass unsere Befunde dagegen sprechen, dass neuronale Synchronizität den Mechanismus für Bewusstsein darstellt. Allerdings können wir das in diesem Fall auch nicht völlig ausschließen, denn Synchronizität könnte die Informationsverarbeitung auf einem kleineren Maßstab koordinieren als wir es mit dem MEG messen können (Singer, in press).
Im Kapitel 5 untersuchten wir, wie schnell bestehendes Wissen bewusste Verarbeitung beeinflussen kann. Um dies herauszufinden machten wir uns die intraindividuellen Unterschiede der perzeptuellen Leistung zu Nutze. Wir fanden, dass bestehendes Wissen bewusste Verarbeitung schon innerhalb der ersten 100 Millisekunden nach der Präsentation des Reizes beeinflusst. Wir beobachteten auch, dass ein größerer perzeptueller Effekt des bestehenden Wissens in geringerer neuronaler Aktivität in Durchgängen mit bestehendem Wissen hervorruft. Diese Ergebnisse sind im Einklang mit Theorien, die besagen, dass unsere Wahrnehmung bestehendes Wissen nutzt, um vorherzusagen, wie die visuelle Welt sich ändert und um die neuronalen Antworten zu verringern (Friston, 2010).
In der vorliegenden Arbeit wurde diskutiert, warum die typische Kontrastierungsanalyse uns nicht zu den neuronalen Korrelaten des Bewusstseins führen kann. Wir schlugen vor, dass neue experimentelle Paradigmen nötig sind, um näher an die neuronalen Korrelate des Bewusstseins heranzukommen. Es wurde ein neues Paradigma benutzt, um zwischen Vorläuferprozessen und neuronalen Korrelate des Bewusstseins zu unterscheiden. Mit diesem Paradigma wurden zwei sehr unterschiedliche Hypothesen getestet und gefunden, dass die kategorienspezifische Gammabandaktivität nicht die neuronalen Korrelate des Bewusstseins widerspiegeln kann. Wir hoffen, dass unsere Experimente eine Entwicklung von vielen weiteren und besseren experimentellen Paradigmen stimuliert, die zwischen den Vorläuferprozessen, den Konsequenzen und den eigentlichen Korrelaten des Bewusstseins unterscheiden können. Wenn man über die Kontrastierungsanalyse hinausgeht, kann man die gegenwärtigen Theorien des Bewusstseins testen und damit Schritt für Schritt näher an die neuronalen Grundlagen des Bewusstseins kommen.
In der vorliegenden Arbeit wurden mikroskopische Studien zur Äquilibrierung von partonischer und hadronischer Materie im Rahmen einer Nichtgleichgewichts-Transporttheorie durchgeführt, die sowohl hadronische als partonische Freiheitsgrade enthält und den Übergang zwischen beiden Phasen dynamisch beschreibt. Des Weiteren wurden die thermischen Eigenschaften des Gleichgewichtszustandes der stark wechselwirkenden Materie untersucht, insbesondere Fluktuationen in der Teilchenzahl wie auch höhere Momente von Observablen und deren Verhältnisse. Besonderes Interesse galt dabei den Transportkoeffizienten wie Scher- und Volumenviskosität sowie der elektrischen Leitfähigkeit.
Die Methode der Nichtgleichgewichts-Green'schen Funktionen - initiiert von Schwinger sowie Kadanoff und Baym - wurde vorgestellt um hochenergetische Kern-Kern Kollisionen zu beschreiben. Weiterhin wurde der Schwinger-Keldysh Formalismus benutzt um im Sinne einer Zweiteilchen-irrediziblen Näherung (2PI) die Dynamik von 'resummierten' Propagatoren und Kopplungen in konsistenter Weise zu beschreiben. Des Weiterhin wurden generalisierte Transportgleichungen auf der Basis der Kadanoff-Baym Gleichungen (in Phasenraumdarstellung) abgeleitet und ein Testteilchenverfahren zur Lösung dieser Gleichungen vorgestellt. Damit wurde der formale Rahmen der Parton-Hadron-String Dynamik (PHSD) abgesteckt.
Das PHSD Transportmodell wurde sodann für die Lösung der expliziten Fragestellungen in dieser Arbeit verwendet. Die 'Eingangsgrößen' des Modells wurden in Kapitel 3 aufgeführt. Weiterhin wurde aufgezeigt, dass das Transportmodell alle Phasen einer relativistischen Schwerionenkollision konsistent beschreibt, d.h. angefangen von den primären harten Stoßprozessen und der Bildung von 'Strings' zur Formierung einer partonischen Phase, den Wechselwirkungen in dieser Phase sowie die
dynamische Beschreibung der Hadronisierung. Weiterhin enthält das Modell zudem die hadronischen Endzustandswechselwirkungen bis zum Ausfrieren der hadronischen Freiheitsgrade bei geringer Dichte. ...
Mantle convection is the process by which heat from the Earth’s core is transferred upwards to the surface and it is accepted to explain the dynamics of the Earth’s interior. On geological time-scales, mantle material flows like a viscous fluid as a consequence of the buoyancy forces arising from thermal expansion. Indeed, mantel convection provides a framework which links together the major disciplines, such as seismology, mineral physics, geochemistry tectonic and geology. The numerical model has been applied to understand the dynamic, structure and evaluation of the Earth, and other terrestrial planets and the investigations continue to explore, different aspects of the mantle convection.
In fact, to model this phenomenon, two complementary approaches are possible. On the one hand, one can solve self-consistently the equations of thermal convection, including parameters and employing physical relationships derived from mineral physics. Our understanding of mantle convection depends ultimately upon the success of such fully self-consistent dynamic models in explaining observable features of the flow. Although, these models presently unable to predict the actual convection pattern of the Earth, they are extremely useful to investigate general characteristics of given physical systems. On the other hand, to permit comparison with specific observables associated with the flow, one can consider a more restricted problem. Instead of focusing on the time evolution of mantle flow, if we know a priori the temperature - and hence presumably the density - anomalies that drive the convection, we can try to build a snapshot of the present-day flow pattern, consistent with those anomalies, that can successfully predict the observables. As matter of fact, the aim of this study is to investigate both approaches in comparison with the main geophysical constraints on mantle structure. These constraints include the geoid anomalies, the dynamic surface and core-mantle boundary topography and tectonic plate motions.
The most appropriate mathematical basis functions for describing a bounded and continuous function on a spherical surface are spherical harmonics. We may therefore expand the geodynamic observables in terms of spherical harmonics. We have investigated two methods of the global spherical harmonic analysis by specific attention to the dynamic geoid computation of the geodynamic models. The first method is the quadrature method in which the loss of the orthogonality of the Legendre functions in transition from continues to discrete case is the major drawback to the method. Particularly, we showed that in the absence of the tesseral harmonics, quadrature formulation leads to obtain inaccurate results. The second method is the least-squares which can be considered as the best linear unbiased estimator that provides the exact results. We showed that even with a low resolution grid data it is possible to reconstruct the data and achieve an accurate result by using this method, which is extremely remarkable in three-dimensional global convection studies. However, special care has to be taken since there is some source of errors that might influence the efficiency of this method.
In general, to better understanding of the properties of the mantle, it is useful to assess observable characteristics of plumes in the mantle, including geoid, topography and heat flow anomalies. However, only few studies exist on geoid and topography for axi-symmetric convection and their models were restricted to isoviscous (or stratified) mantle and low Rayleigh numbers. We studied fully coupled depth and temperature dependent Arrhenius type of viscosity in axi-symmetric spherical shell geometry in order to investigate the shape of geoid anomalies and dynamic topography above a plume. Indeed, the topography and geoid anomalies produced from plumes are sensitive to rheology of the mantle and rheology of the plume; both have effects on shape and amplitude of the geoid anomalies. As results we are able to define different classes of plumes by their geoid signals.
Mainly depth-dependent viscosity models show a geoid with negative sign above the plume which can turn to the positive sign by decrease the viscosity contrast. This can be considered as a transition between the strongly depth dependent and the constant viscosity case. Our results basically support the idea by Morgan [1965] and McKenzie [1977]. They have shown the magnitude and even the sign of the total gravity anomaly depend on the spatial variation in effective viscosity. In addition, Hager [1984] has concluded that the total gravity field is depend on the radial distribution of effective viscosity, and a small change in viscosity contrast leads to varying sign of the response function.
In the case of temperature-dependent viscosity, the formation of an immobile lithosphere is a natural result, and the flow as well as the total geoid becomes strongly time dependent. When we increase the activation energy, all geoids associated with the first arriving plumes look like bell shaped whereas for typical plumes, after reaching a statistical steady state, bell-shaped geoids with decreasing amplitude as well as linear flank shaped geoids are observed. It is surprising that in spite of large differences in lateral and depth varying viscosities, the shapes of the geoid anomalies remained rather similar. We also identified different behaviors in the combined model with temperature-and pressure-dependent viscosity. In fact, in spite of the strongly different rheology, the geoid anomalies in all cases were surprisingly similar. Furthermore, we proposed a scaling law for the geoid which makes our results directly applicable to other planets. Moreover, we can apply the results of our calculation to find relations between different rheology and sub-lid temperature, since we know that the mantle temperature can change significantly with variation in pressure-temperature dependent viscosity. It is also possible to define a range of stagnant lid thickness related to the amplitude of the geoid which can be reasonable for study of the lid thickness in Venus or Mars.
Nevertheless, in these series of models, we simplified a number of complexities within the Earth. One of the most important of such simplification is the Boussinesq approximation. This approximation is valid if the temperature scale height (i.e. the depth over which temperature increases by a factor of “ ” due to adiabatic compression) is much greater than the convection depth. However, a temperature scale height in the Earth’s mantle is at best only slightly greater than the mantle depth. Hence, the Boussinesq approximation could mask some very important stratification and compressibility effects that influence both the spatial and temporal structure of the convection. Therefore, in more advance models we considered compressibility in our mantle convection models, assuming that density vary both radially and laterally, being determined as a function of pressure and temperature through an appropriate equation of the state. Moreover, thermodynamic properties assumed to be a function of depth.
We examined the details of the structure of the spherical axi-symmetric Anelastic Liquid Approximation model (ALA) with special attention to the Arrhenius rheology, and compare it to the cases of compressible convection without depth dependent thermodynamical properties, and to cases of the extended Boussinesq approximation. At the same time, the effects of the interaction between temperature and pressure-dependent viscosity and thermodynamic parameters in the compressible mantle convection on the geoid and topography have been studied. We showed that assuming compressible convection with depth-dependent thermodynamic properties strongly influence the geoid undulations. Using compressible convection with constant thermodynamic properties is physically inconsistent and may lead to spurious results for the geoid and convection pattern. Indeed, by a systematic study of different approaches of compressibility in the spherical shell convection for different Arrhenius viscosity laws we proved that only in the unrealistic case of zero activation energy the different compressibility modes result in comparable convection and geoid patterns. In all other rheological cases, large differences have been obtained, that stressing the important role of consistent compressible thermodynamic properties for mantle convection.
In addition, we examine the impact of compressibility as well as different rheologies on the power law relation that connects the Nusselt number to the Rayleigh number. We have discovered that the power law index of the relationship is controlled by the rheology, independent of which approximation is used. Instead, the bound of this relation is controlled by a combination of different approximation and rheology.
Next, instead of focusing on the time evolution of mantle flow, we have carried out three-dimensional spherical shell models of mantle circulation to investigate the effects of joint radial and lateral viscosity variations on the Earth’s non-hydrostatic geoid, surface and core-mantle boundary topographies. These models include realistic lateral viscosity variations (LVV) in the lithosphere, upper mantle and lower mantle in combination with different stratified viscosity structures. We have demonstrated that the contradictory results concerning the effects of LVV can be clarified by the most straight-forward problem in geoid modeling; namely, rather poorly known stratified viscosity structure. We explored three classes of dynamic geoid models due to lateral viscosity variations. In the first class, the LVV strongly improved the fit to the observed geoid. Indeed, when the viscosity contrast between lower and upper mantles is not large enough to produce a good fit to geoid the LVVs are able to perform this action by adjusting amplitudes, so that it becomes comparable with observation. In the second class, inducing the LVV moderately improved the fit. Actually, when the geoid induced by a stratified viscosity structure already has a good correlation with observation, then the LVV causes its amplitude to further improve. In the last class, if the viscosity contrast between upper and lower mantle would be high enough, inducing LVV deteriorate the fit to the observed geoid.. Indeed, depending on the stratified viscosity, inducing the LVV may take place in one of these categories.
We also quantified the effects of LVV in the mantle and lithosphere individually. We found that the presence of LVV in the mantle (upper and lower) improves the fit to the observed geoid regardless of stratified viscosity. While LVV in the lithosphere is a crucial parameter, and dependent of the stratified viscosity, may increase or decrease the geoid fit. In fact, when the lower mantle considers being viscous enough, it would support the negative buoyancy of subducting slabs. Thus, it transmits some of the stress back to the top boundary and causes a weak coupling between slab and surface. Therefore, by including the low viscous plate boundaries in this model, the slabs and overriding plates decouples and the fit to the observed geoid degrades. In contrast, when the lower mantle viscosity is not sufficiently stiff, the presence of the low viscous plate boundaries assists to weaken the strong mechanical coupling between slab and surface. Hence, a better fit achieved.
Ziel dieser Arbeit war, die Reaktion von biologischen Gewebeproben auf dünn- und dicht-ionisierende Strahlung zu evaluieren. Dafür wurden die Gewebeproben konventioneller Röntgenstrahlung sowie einem ausgedehnten 12C-Ionen Bragg-Peak ausgesetzt. Zur Bestrahlung der biologischen Proben mit 12C wurde mit dem GSI-eigenen Simulationsprogramm TRiP98 ein Tiefendosisprofil eines ausgedehnten Bragg-peaks erstellt. Ein weiteres Ziel dieser Arbeit war, dieses Tiefendosisprofil mit drei anderen Simulationsprogrammen (ATIMA, MCHIT, TRIM) zu reproduzieren und zu vergleichen.
ATIMA und TRIM sind allgemeine Programme für den Energieverlust von Ionen in Materie. Sie können das von TRiP98 berechnetet Tiefendosisprofil nur ungenügend reproduzieren, da sie aufgrund fehlender Fragmentierung ein linear ansteigendes Tiefendosisprofil berechnen. Das Monte Carlo-Programm MCHIT, welches speziell für die Wechselwirkung von Ionen mit Materie in medizinischer Anwendung entwickelt wurde, zeigt die beste Übereinstimmung mit der TRiP98-Referenzkurve. Bis auf eine leicht höhere Durchschnittsdosis um 0.1 Gy konnte das Tiefendosisprofil nahezu exakt reproduziert werden.
Die biologischen Proben bestanden aus Schnittkulturen gesunder Maus-Lebern und Explantatkulturen gesunder Maus-Pankreata, um Nebenwirkungen ionisierender Strahlen abzuschätzen. Zusätzlich wurde die Reaktion auf 12C-Bestrahlung in neoplastischem Lebergewebe transgener c-myc/TGF-α Mäuse mit induzierbarem Lebertumor bestimmt. Um eine mögliche Tageszeitabhängigkeit der Gewebereaktion auf die Bestrahlung zu untersuchen, wurden die Schnitt- und Explantatkulturen zu zwei unterschiedlichen Tageszeiten präpariert: zur Mitte des subjektiven Tages und zur Mitte der subjektiven Nacht.
Die Präparate wurden für mehrere Tage auf einer Membran an einer Grenzschicht von Flüssigkeit und Luft kultiviert. Leber- und Pankreaskulturen gesunder C3H wildtyp Mäuse wurden mit einer Dosis von 2 Gy, 5 Gy oder 10 Gy Röntgenstrahlen bestrahlt. Leber- und Pankreaskulturen transgener Mäuse wurden mit ausgedehnten C-Ionen Bragg Peaks gleicher Dosen bestrahlt. Als Kontrolle dienten unbestrahlte Proben. Alle Proben wurden 1 h bzw. 24 h nach der Bestrahlung fixiert und immunhistochemisch auf Marker für Proliferation (Ki67), Apoptose (Caspase3) und DNA- Doppelstrangbrüche (γH2AX) untersucht.
Während die Pankreas-Präparate im Hinblick auf die untersuchten Parameter leider keine auswertbaren Ergebnisse ergaben, zeigten die untersuchten Parameter im gesunden Lebergewebe deutliche Tag-Nacht Unterschiede: die Proliferationsrate war zur Mitte des subjektiven Tages signifikant höher als zur Mitte der subjektiven Nacht. Umgekehrt waren die Raten für DNA-Doppelstrangbrüche zur Mitte der subjektiven Nacht signifikant erhöht. Diese Tag-Nacht Unterschiede ließen sich in neoplastischem Lebergewebe nicht nachweisen. Unabhängig von der Art und Dosis, hatte die Bestrahlung im gesunden Lebergewebe keinen Einfluss auf die untersuchten Parameter. In neoplastischem Lebergewebe hingegen wird die Rate an DNA-Doppelstrangbrüchen durch eine Bestrahlung dosisabhängig erhöht.
Die Auswirkungen ionisierender Strahlen auf das circadiane Uhrwerk wurden in Gewebeproben transgener Per2luc-Mäuse überprüft. Per2luc-Mäuse exprimieren das Enzym Luziferase unter der Kontrolle des Promoters von Per2, einem wichtigen Bestandteil des circadianen Uhrwerks. Daher erlaubt die Analyse dieser Tiere, den circadianen Rhythmus des molekularen Uhrwerks in Leber und anderen Geweben durch Messung der Luziferase-Aktivität in Echtzeit aufzuzeichnen. Wie in Leber- und Nebennierenkulturen dieser Tiere gezeigt werden konnte, führten ioniserende Strahlen dosisabhängig zu einem Phasenvorsprung des circadianen Uhrwerks.
Die Ergebnisse erlauben die Schlussfolgerung, dass ionisierende Strahlen das circadiane Uhrwerk verstellen, Proliferation und Apoptose in gesundem Lebergewebe jedoch kaum beeinflussen.
The prevalence of food allergies has increased in the westernized countries during the past decades. Clinical manifestations of food allergies involve the skin (e.g. atopic dermatitis), the respiratory tract (e.g. rhinitis, and asthma), the ocular area (e.g. conjunctivitis), the gastrointestinal tract (e.g. food-protein-induced enterocolitis syndrome, food-induced proctocolitis, and eosinophilic gastroenteropathies), and the cardiovascular system (e.g. anaphylaxis). A curative treatment of these diseases has not been established yet. Oral immunotherapy (OIT) has gained attention as a potential therapy for food allergies. Continuous feeding of allergenic diet applied in the model described here mirrors to a certain extent an OIT treatment. It might be therefore useful to investigate efficacy and safety of OIT pre-clinically.
Mouse models have been widely used to analyse novel treatment approaches. Unfortunately, most of them have focussed on IgE-mediated hyperreactivity. Only a limited number of mouse models presenting mixed IgE- and non-IgE-mediated gastrointestinal symptoms and inflammation upon allergen-challenge are available. To study the mechanisms underlying the induction of food-induced gastrointestinal inflammation and subsequent oral tolerance induction, a mouse model of food-induced gastrointestinal allergy was established. BALB/c mice were sensitised with Ovalbumin (OVA) plus ALUM and subsequently challenged by feeding a diet containing egg white (EW diet). During the first seven days on EW diet, OVA-sensitised mice (OVA/ALUM EW mice) developed gastrointestinal symptoms (e.g. weight loss, ruffed fur, soft stool and less mobility) and inflammation in the small intestines accompanied by a strong induction of OVA-specific IgE antibodies and mouse mast cell protease-1 (mMCP-1). Proliferation of CD4+ T cells from spleen of OVA/ALUM EW mice was reduced compared controls. The result indicated that feeding EW diet induced T cell tolerance systemically. In contrast, CD4+ T cells isolated from MLN of OVA/ALUM EW mice showed stronger proliferation upon OVA stimulation in vitro than mice OVA-sensitised but fed a conventional diet, indicating that tolerance was not induced by short-term EW diet. Histological analysis of the small intestinal tissue of OVA/ALUM EW mice revealed strong inflammation present in the duodenum, jejunum and ileum at this time point.
Interestingly, the observed symptoms in OVA/ALUM EW mice resolved spontaneously after 7 days on EW diet, if the feeding was continued. In the next steps the CD4+ T cell-mediated immune response after 28 days continuous EW diet was assessed and revealed that tolerance was induced systemically as well as locally. This was shown by reduced proliferation and cytokine secretion of CD4+ T cells from MLN of OVA/ALUM EW mice after long-term EW diet. However, the inflammation in the jejunum was aggravated instead of resolved at this time point of allergenic diet. Our results suggest that application of OIT in food-allergic patients with gastrointestinal inflammation may need to be reconsidered, since continuous administration of allergenic food may aggravate inflammation in the local tissue. Interestingly, only the jejunum was affected by a worsened condition, whereas duodenum and ileum resolved inflammation. In accordance to the observed jejunal inflammation mMCP-1 levels in the sera were not changed. Allergen-specific IgE levels did not reach baseline level after long-term EW diet, although they were reduced compared to levels in mice after 7 days on EW diet. This result suggests that residual OVA-specific IgE antibodies would promote the jejunal inflammation by sustained activation of mast cells. Furthermore, our results suggest that IL-4 produced by activated Th2 cells could be an effector molecule to induce intestinal inflammation.
The second part of this thesis was aimed at verifying the hypothesis that IgE-mediated mast cell activation is a major effector mechanism in induction of chronic inflammation induced by long-term EW diet. For that mice deficient for FcεRI, a high affinity IgE receptor, were used. These mice were sensitised with OVA and fed EW diet as described for WT mice. Although FcεRI-deficient mice showed an intact Th2 immunity with IgE production, weight loss in the receptor-deficient mice was moderately induced by EW diet compared to WT mice, suggesting that this clinical symptom during the acute phase of allergic response is associated with IgE-mediated mechanisms. Surprisingly, the deficient mice presented comparable intestinal inflammation on day seven of EW diet as WT mice did. However, if EW diet was continued, recovery of intestinal inflammation was observed in FcεRI-deficient mice in contrast to WT mice. These results suggest that the induction of intestinal inflammation is not IgE-dependent. Nevertheless, this does not rule out a potential role of mast cells in the inflammation, because of their IgE-independent activation pathways. It also suggests the involvement of T cell-mediated mechanisms during induction of jejunal inflammation. Interestingly, the aggravated inflammation seen after long-term EW diet in WT mice seems to be IgE-dependent, considering that it was not observed in FcεRI-deficient mice. The elevated number of mast cells in the intestine of WT mice further led to a hypothesis that their continuous activation might be responsible for the chronification of allergic inflammation observed after long-term EW diet. In the context of OIT it further implies that IgE might be a poor prognostic factor for recovery of intestinal inflammation during and after an OIT treatment. In the third part of this thesis regulatory mechanisms employed by the immune system were analysed. Initial results from CD4+ T cells isolated from MLN from OVA/ALUM EW mice showed elevated IL-10 levels in their supernatants after short-term EW diet. IL-10-deficient mice were used to analyse the effect of this immunosuppressive cytokine in the mouse model presented here. However, IL-10-deficient mice tend to develop a strong Th1-dominated immune response. Nevertheless, an accelerated weight loss and slight inflammation of the jejunum was observed after short-term EW diet. Analysis of OVA-specific proliferation and cytokine production CD4+ T cells from Spleen and MLN of IL-10-deficient mice on EW diet suggested that systemic as well as local tolerance was induced after short-term and long-term EW diet feeding, respectively. The result suggests that IL-10 is dispensable for induction of T cell tolerance in our mouse model.
However, the presence of functionally active Tregs was observed during this study in WT mice fed short-term EW diet, suggesting that Tregs might have an important role in regulating the systemic or local immune response. T cell deletion as an alternative immune regulatory mechanism was also observed. Additionally, the efficacy of continuous EW diet (mirroring to a certain extent an OIT treatment) in induction of permanent tolerance was assessed. In OVA-sensitised WT mice continuous allergenic diet was stopped after resolution of clinical symptoms and reintroduced after a defined period on conventional diet. Evaluating the weight development showed that reintroduction of EW diet induced weight loss again, but not as pronounced as seen after short-term EW diet. Also the CD4+ T cell-mediated response was elevated again upon allergen stimulation in vitro. The results suggested that permanent tolerance was not induced in the chosen feeding regime.
The mouse model established and analysed here was used to investigate inflammatory and regulatory mechanisms underlying food-induced gastrointestinal allergy. It presents clinical symptoms and intestinal inflammation (Burggraf et al., 2011). This model is easy to be reproduced in different laboratories, and is useful for testing novel therapy approaches (Schülke et al., 2011; Bohnen et al., 2013). It further provides an opportunity to investigate basic mechanisms underlying OIT. This therapy approach is currently extensively investigated and our mouse model would help to understand the therapeutic mechanism of OIT.
Essays in behavioral economics - evidence on self-selection into jobs, social networks and leniency
(2013)
Die Dissertation mit dem Titel „Essays in Behavioral Economics – Evidence on Self-Selection into Jobs, Social Networks and Leniency“ besteht aus einer Sammlung von vier wissenschaftlichen Abhandlungen. Alle Arbeiten verbindet die Analyse von theoretischen Konzepten und Erkenntnissen der Verhaltensökonomie unter Verwendung der experimentellen Methode. Die erste wissenschaftliche Abhandlung trägt den Titel „Sorting of Motivated Agents - Empirical Evidence on Self-Selection into the German Police“ und untersucht Selbstselektion bestimmter Individuen in den Polizeiberuf. Die experimentelle Studie untersucht die Frage, ob Polizeibewerber sich hinsichtlich ihrer Präferenzen in Bezug auf ihr Normdurchsetzungsverhalten in den Polizeiberuf selektieren. Die zweite Abhandlung greift diese Erkenntnisse auf und untersucht Polizeianwärter in ihrer Berufsausbildung ebenfalls hinsichtlich ihrer Normdurchsetzungsbereitschaft. Die Arbeit trägt den Titel „Selection and formation of motivated agents -- empirical evidence from the German Police”. In der dritten wissenschaftlichen Abhandlung werden geschlechterspezifische Unterschiede bei der Wahl von Partnern und dem Aufbau des sozialen Netzwerkes untersucht. Diese trägt den Titel „Selectivity and opportunism: two dimensions of gender differences in trust games and network formation“ und wurde zusammen mit Guido Friebel, Marie Lalanne, Paul Seabright und Peter Schwardmann verfasst. Die vierte Abhandlung geht einer aktuellen Fragestellung der Industrieökonomie nach und trägt den Titel „Antitrust, auditing and leniency programs: evidence from the laboratory“, verfasst mit Mehdi Feizi and Ali Mazyaki. In ihrer Gesamtheit liefert meine Dissertation Antworten auf personalpolitische, soziale und industrieökonomische Fragestellungen.
So far clinical human immunodeficiency virus (HIV) therapy is limited to non-curative treatments. However, as recently shown, alternative approaches such as HIV gene therapy have the potential to functionally cure the disease (e.g. the hematopoietic stem cell (HSC)-transplantation with a CCR5Δ32 homozygous transplant) (1). In contrast to the highly personalized medical treatment applied in the ‘Berlin case’, more broadly applicable approaches are currently under intensive investigation.
One example is the adeno-associated-virus (AAV)-mediated delivery of in vivo secreted antiviral entry inhibitors (iSAVE), the concept of which is based on the direct in vivo administration of a broadly applicable highly potent antiviral gene (here: a C46-derived entry inhibitory peptide interfering with HIV-1 membrane fusion). The AAV-based gene delivery is believed to overcome several limitations of gene therapeutic treatments based on ex vivo lentiviral trials in the past. It is (i) targeting differentiated HIV target cells (i.e. liver and differentiated lymphatic cells) reducing the risk of genotoxicity compared to stem cell-based trials, (ii) overcoming the limitation of a low number of genetically modifiable cells as in lentivirally based ex vivo transduction strategies (i.e. limited modifiable cell number due to culture conditions and lower vector titers) and (iii) using the safe AAV vector system, which has not been associated with major genotoxicity in men. (iv) Most importantly, the concept of secretable entry inhibitors does not require transduction of large amounts of cells due to the protective bystander effect. Thus, iSAVE might be a treatment principle for HIV infection that might be able to cure patients irrespective of their viral isolates or adherence.
Accordingly, the iSAVE concept could aim at two different sites in the patient for the production of antiviral transgenes, either the systemic production via suitable producer cells (e.g. hepatocytes) or the local production in the lymphatic system.
In a first approach, we are able to efficiently target hepatocytes using the natural AAV serotype 8 to express high plasma levels of secretable antiviral entry inhibitors in order to systemically suppress viral replication. In this setting we could show that iSAVE peptides are highly expressed in hepatocytes. However, plasma levels of iSAVE were insufficient when using a secretable peptide as sole antiviral transgene.
As a second treatment strategy, the iSAVE project aimed to deliver antiviral genes directly to the site of viral replication, the lymphatic system. Here, (i) a panel of naturally occurring AAV serotypes as well as (ii) AAV retargeting approaches were employed to design a highly efficient and selective AAV vector variant for gene delivery into the lymphatic system after intravenous vector administration.
In detail, (i) screening of the natural occurring serotypes revealed that the AAV serotype 1 (AAV-1) was best in targeting splenic tissue in two humanized mouse models, however at a very low level. After systemic AAV-1 vector administration neither transduction of human lymphocytes did occur nor was iSAVE expressed in the lymphatic system in a humanized mouse model.
(ii) In a second approach, we modified the well-characterized AAV-2 serotype in a tropism-defining region of its capsid gene by insertion of human peripheral blood lymphocytes (hPBL)-tropic peptide ligands. These in turn were selected by M13 in vivo phage display and by in vivo AAV peptide display. Selected variants were cloned and tested for hPBL transduction in vitro. Although the selected variants did not show increased expression efficacies compared to AAV-2 WT, it still might be possible that the selected variant are more specific for hPBLs as these conditions have not been tested.
As these selection processes required a humanized mouse model that comprises a functional lymphatic system, we established the previously described Trimera mouse model in our lab (2). We found that this mouse model could be further improved to allow engraftment of a lower number of gene-modified (gm) human T cells as in the classical Trimera model. These modified Trimera mice (mT3 mice) were conditioned by inclusion of cyclophosphamide (CTX) to the irradiation-conditioning scheme of the classical Trimera model.
Comparison of mT3 mice with established NSG and DKO mice in an adoptive gm T cell transplantation setting revealed that NSG mice were the most robust model providing high reproducibility in human T cell engraftment. MT3 mice allowed a substantial, yet more variable engraftment of gm T cells. Besides comparing engraftment kinetics, the graft quality (i.e. clonality and cytokine milieu) was analyzed. Again, NSG mice showed the most balanced homeostatic repopulation three weeks after transplantation, while mT3 mice were prone to Th1-type, oligloclonal repopulation, indicating an early onset of xenograft-versus-host disease. Finally, the lymphatic infiltration was analyzed. As expected, mT3 mice provided the most intact lymphatic structures, although the normal lymphatic morphology was not restored.
In conclusion, it was demonstrated in this work that AAV-mediated iSAVE gene therapy faces specific limitations depending on the respective targeting approach
In the systemic approach, iSAVE peptides have to be further optimized in terms of transgene design itself, as high-level accumulation in murine plasma was not feasible for the short iSAVE precursor. In the local, lymphatic targeting approach, AAV-mediated expression faces its limits in targeting specificity but foremost expression efficacy. Thus, the AAV vector itself needs further optimization for sufficient local iSAVE expression levels. Independently from the AAV-related approaches, a novel humanized mouse model was established in this work. Despite drawbacks regarding repopulation variability and set-up complexity, the novel mT3 mouse model comprised improved secondary lymphatic structures for adoptive T cell transfer, which might be an interesting platform for studies in lymphoma or leukemia therapy.
The 35 neutron deficient nuclides known as the p nuclei are sysnthesized mainly in the so-called γ process. Taking place in explosive supernova events, the existing seed distribution from prior nucleosynthesis is altered by photodisintegration reactions of the types (γ,n), (γ,p) and (γ,α).
The bulk of reaction rates needed in network calculations of the γ process are predicted by the Hauser-Feshbach Model. When using this theory, the largest uncertainties stem from the interaction between charged particles and nuclei described by optical model potentials.
An improvement of these potentials can be achieved by comparison to measured cross section data. However, because of the low energies of interest for nuclear astrophysics and the resulting low cross sections, suitable data are scarce.
This thesis extends the corresponding database by measurement of the reactions 165Ho(α, n), 166Er(α, n), 169Tm(p,n) and 175Lu(p,n) using the activation technique. While not particularly important for the γ process, the selected (α,n) and (p,n) reactions exhibit nearly exclusive sensitivity to the α- or proton-nucleus potential, respectively. Therefore, the results presented here are well suited to test and improve the predictive power of currently available parameterizations of these potentials
Modern computational molecular quantum chemical studies, such as the present one, typically employ a wide range of theoretical techniques. The latter are often rather complicated and one should not generally expect that an experimental scientist in the area of physical chemistry, a potential reader of this work, should be familiar with all these techniques. To simplify the reading of the Thesis and to make it self-sufficient, it is supplied with an overview of the employed theoretical methodologies (Chapter 1). The overview explains basic quantum-chemical terminology referred to throughout the Thesis, introduces theoretical foundations of the methods and outlines their properties and limitations. In Part 1.1 of Chapter 1, methods for the solution of the molecular Schrödinger equation are introduced, while in the subsequent Parts 1.2 and 1.3 methods for the solution of the electronic Schrödinger equation are presented to find the ground and excited states, respectively. Part 1.4 is dedicated to basis-set effects which are omnipresent in electronic-structure calculations. It contains a number of unusual insights and concepts proposed by the author and, thus, may be insightful also to experts in quantum chemistry.
In Chapter 2, the phenomenon of acetone-water proton exchange catalyzed by tubular as well as amorphous aggregates of calix[4]hydroquinone (CHQ) macromolecules, which has been observed previously in NMR experiments (Ref. D1D), is investigated by means of correlated quantum-chemical methods. The first part of the study (Section 2.3-2.7) considers concerted proton transfer, assisted by several initially neutral OH-groups in the hydrogen-bonded networks of CHQ aggregates. The second part of the study (Section 2.8-2.13) is dedicated to a second mechanism of proton exchange: step-wise proton transfer via formation of ionic intermediates resulting from CHQ pre-dissociation. CHQ application-specific as well as general conclusions, relevant to the main topic of the Thesis (i.e. influence of specific microsolvation on the considered proton transfer processes), are presented in Section 2.14.
The phenomenon of dual fluorescence observed in clusters of methyl 4-N,N-dimethylaminobenzoate ester (DMABME) and two water molecules in the gas phase, is studied in Chapter 3. Experimentally, the dual fluorescence was detected in experiments combining optical and ground-state ion-depletion infrared spectroscopies in ultracold molecular beams (Ref. D2D). In Section 3.3, calculated ground-state infrared spectra are presented that allow to identify the structures of those isomers, which are present in the gas-phase, as well as the structure of the isomer responsible for dual fluorescence. To further understand the reaction mechanism of dual fluorescence, excited-state potential energy surfaces of the identified isomers were computed along the relevant twisted intermolecular charge-transfer formation coordinate and the mechanism of energy dissipation in these complexes was investigated (Section 3.4-3.5) (Ref. D3D). A brief summary of the main results of this chapter and conclusions are given in Section 3.6. Finally, in Section 3.7 a complementary benchmark study of the quality of ground-state potential energy surfaces of prototypical hydrogen-bonded systems (ammonia-water and formic acid-water dimers) obtained at the level of BSSE-corrected MP2 combined with moderate basis sets, has been conducted. The quality of potential energy surfaces was tested with respect to basis-set size, level of electron correlation and anharmonicity effects and the applied methodology to identify the IR spectrum of hydrated DMABME complexes (Section 3.3) has been found to be sufficient to uniquely assign the IR spectra.
This dissertation provides an analysis of Finnish prosody, with a focus on the sentence or phrase level. The thesis analyses Finnish as a phrase language. Thus, it accounts for prosodic variation through prosodic phrasing and explains intonational differences in terms of phrase tones.
Finnish intonation has traditionally been described in terms of accents associated with stressed syllables, i.e. similarly as prototypical intonation languages like English or German. However, accents are usually described as uniform instead of forming an inventory of contrasting accent types. The present thesis confirms the uniformity of Finnish tonal contours and explains it as based on realisations of tones associated with prosodic phrases instead of accents. Two levels of phrasing are discussed: Prosodic phrases (p-phrases) and intonational phrases (i-phrases). Most prominently, the p-phrase is marked by a high tone associated with its beginning and a low tone associated with its end; realisations of these tones form the rise-fall contours traditionally analysed as accents. The i-phrase is associated with a final tone that is either low or high and additionally marked by voice quality and final lengthening. While the tonal specifications of these phrases are thus predominantly invariant, variation arises from different distributions of phrases.
This analysis is based on three studies, two production experiments and one perception study. The first production study investigated systematic variation in information structure, first syllable vowel quantity and the target word's position in the sentence, while the second production experiment induced variation in information structure, first and second syllable type and number of syllables. In addition to fundamental frequency, the materials were analysed regarding duration, the occurrence of pauses and voice quality. The perception study investigated the interpretation of compound/noun phrase minimal pairs with manipulated fundamental frequency contours using a two-alternative forced-choice picture selection task. Additionally, a pilot perception study on variation in peak height and timing supported the assumption of uniform tonal contours.
To reconstruct ocean circulation changes during specific periods of Earth history, benthic and planktic foraminifera were used as proxies in the different parts of this thesis. Both studied time periods, the Late Cretaceous and the early Pleistocene, are characterized by long-term climate cooling and major changes in ocean circulation. The first part of this thesis concentrated in the Late Cretaceous. During the Late Cretaceous long-term cooling phase, benthic foraminiferal δ18O values show a positive shift lasting about 1.5 Myr (71.5–70 Ma). This shift can be observed on a global scale and has become known as the Campanian-Maastrichtian Boundary Event (CMBE). It is proposed that this δ18O excursion is influenced either by changing intermediate- to deep-water circulation or by temporal build-up of Antarctic ice sheets. Benthic foraminiferal assemblage counts from a southern high-latitudinal site near Antarctica (ODP Site 690) are analyzed to test if the influence of the CMBE on the benthic species composition. One of the two discussed hypotheses for the causation of the δ18O transition is a change in intermediate- to deep-water circulation from low-latitude to high-latitude water masses. This change would result in cooler temperatures, higher oxygen concentration, and possibly lower organic-matter flux at the seafloor, causing a major benthic foraminiferal assemblage change. Another possible explanation of the δ18O transition of the CMBE is significant ice formation on Antarctica. However no major benthic foraminiferal assemblage change would be expected in this case. The benthic foraminiferal assemblage of Site 690 shows a separation of the studied succession into two parts with significantly different species composition. The older part (73.0–70.5 Ma) is dominated by species, which are typical for lower bottom water oxygen concentration and more common in low-latitude assemblages. Species dominating the younger part (70.0–68.0 Ma) are indicators for well-oxygenated bottom waters and more common in high-latitude assemblages. This change in the benthic foraminiferal assemblages is interpreted to represent a shift of low-latitude toward high-latitude dominated intermediateto deep-water sources. A change in oceanic circulation was therefore at least a major component of the CMBE. The Pacific Ocean contributed significantly to the climatic development during the Late Cretaceous cooling period. The contribution of ocean circulation changes in the Pacific Ocean to the Late Cretaceous climatic development in general and the CMBE and Mid-Maastrichtian Event (MME) in particular, however, is poorly understood. Previously measured high resolution planktic and benthic stable isotope data and a neodymium (Nd) isotope record from the Pacific ODP Site 1210 (Shatsky Rise, tropical Pacific Ocean) for the Campanian to Maastrichtian (69.5 to 72.5 Ma) are used to reconstruct changes in surface- and bottom water temperatures as well as changes in the source region of deep- to intermediate waters [see Appendix 4; Jung et al. 2013]. The results of the benthic foraminiferal δ18O and Nd isotope records in combination with Nd isotope records from other studies indicate changes in the intensity of intermediate- to deep ocean circulation in the tropical Pacific across the Campanian-Maastrichtian interval [see Appendix 4; Jung et al. 2013]. During the early Maastrichtian (72.5 to 69.5 Ma), a three-million-year-long period of cooler conditions and a simultaneous change towards less radiogenic Nd isotope signatures is interpreted to represent a period of increased admixture and northward flow of deep waters from the Southern Ocean (Southern Component Water, SCW). This change was probably caused by an intensified formation of deep waters in the Southern Ocean. This was reduced again during the MME (69.5 to 68.5 Ma). This early Maastrichtian cold interval is similar to the CMBEδ13C fall and succeeding δ13C rise towards the MME and is therefore also interpreted to represent tectonically forced, long-term changes in the global carbon cycle and thus a tectonic forcing of the early Maastrichtian climate cooling. Overall, the Campanian-Maastrichtian Nd and stable isotope records of Shatsky Rise indicate changes in ocean circulation that are paralleled by global warming and cooling periods. The fluctuating strength of SCW contribution in the tropical Pacific points towards an increased respectively weakened ocean circulation, which is probably related to the strength of deep-water formation in the Southern Ocean [see Appendix 4; Jung et al. 2013]. For this study, the analysis of benthic foraminiferal assemblages of Site 1210 is carried out for the same time interval (69.5 to 72.5 Ma) as Nd and stable isotopes to evaluate the influence of intermediate- to deep ocean circulation changes on the benthic foraminiferal community. The possible reaction of benthic foraminiferal assemblages is compared to the results of stable isotope and neodymium isotopes. The observed changes in species abundances only partly reflect the circulation changes reconstructed with Nd and stable oxygen istopes. For example, Stensioina spp., Aragonia spp. and Lenticulina spp., cold-water preferring species, start to be increasingly abundant at the beginning of enhanced influence of SCW. However, their abundance pattern does not follow the varying strength of the cold SCW influence at Shatsky Rise. Other species prefer lesser oxygen concentrations and warmer bottom water, e.g. Paralabamina spp. and Globorotalites spp. Paralabamina spp. has its highest relativ abundance at the beginning of the studied succession, where the influence of SCW is small. However, this taxa occurs throughout the record, even though the influence of SCW increases. Globorotalites spp. is even most abundance after the CMBE, where bottom waters are till cold and influenced by SCW. This leads to the conclusion that the varying strength of SCW in the tropical Pacific at Shatsky Rise through the studied interval is not facilitating a significant faunal turnover as has been observed at the South Atlantic Site 690 (Chapter 3). These results of the benthic foraminiferal assemblage analysis suggest a rather minor influence of the SCW on the major environmental factors that are generally influencing benthic foraminiferal communities (e.g., oxygen concentration, organic matter flux to the sea floor, bottom-water temperature). The second major part of this thesis focused on the late Pliocene-earliest Pleistocene. The late Pliocene is characterized by a long-term global cooling trend resulting in a major increase of Arctic ice sheets from around 3 Ma onwards, culminating in the Plio-Pleistocene intensification of the Northern Hemisphere glaciation. At around 2.7 Ma, large amplitude glacial-interglacial excursions (~1‰ δ18O in benthic foraminiferal calcite) in benthic oxygen isotopes can be observed. Marine isotope stage (MIS) 100 at around 2.55 Ma is the first glacial, when widespread ice rafted debris has been found in sediments in the North Atlantic Ocean. To gain a deeper understanding of the climatic evolution of the latest Pliocene-early Pleistocene, it is necessary to improve the reconstructions of North Atlantic paleohydrography, as the North Atlantic provides a key region for global climate. The consequences of the intensification of Northern Hemisphere on the early Pleistocene North Atlantic thermocline stratification and intermediate waters are still poorly understood. However, surface hydrography, the history of the thermocline and development of North Atlantic intermediate waters are well-studied for the Last Glacial Maximum (LGM). These well-known mechanisms responsible for the LGM in comparison with the present-day interglacial North Atlantic are used as an analogue for te early Pleistocene glacialinterglacials cycles. In this study, suborbitally resolved stable oxygen and carbon isotope and Mg/Ca records are measured from a deep-dwelling planktic foraminifera (Globorotaliacrassaformis) from Integrated Ocean Drilling Program Site U1313 (North Atlantic, 41°N) covering marine oxygen isotope stages MIS 103 to 95 (early Pleistocene, 2.6 to 2.4 Ma). The results are interpreted to represent a change in intermediate-water masses on glacialinterglacial timescales. During glacials geochemical records in G. crassaformis (~500–1000 m) bear the imprint of Glacial North Atlantic Intermediate Water (GNAIW), while during interglacials this species reflects the signature of the influence of Mediterranean Outflow Water (MOW) in combination with the subtropical gyre. The comparison of this data with the published records from G. ruber from the same samples facilitates the reconstruction of glacial-interglacial stratification changes of the upper water column at Site U1313. The results show that larger gradients of temperature, salinity and δ13C prevailed during glacials, suggesting a stronger stratification of the upper water column. This can be seen to indicate glacial-interglacial changes in ntermediate water masses in the North Atlantic similar to those reconstructed for the latest Pleistocene. As an additional proxy, the clumped isotope paleothermometer is applied for the Late Cretaceous study as well as for the early Pleistocene. This proxy is commonly assumed to be independent of other factors than temperature. Clumped isotopes are measured for the Late Cretaceous Site 690 on the planktic foraminiferal species Archaeoglobigerina australis and compared to already existing stable oxygen isotopes of this species. This is assumed to enable the reconstruction of paleotemperature independent of ice volume and therefore contribute to the long-lasting discussion whether there was a temporal ice build-up on Antarctic during the Campanian-Maastrichtian cooling period. For the early Pleistocene, the planktic foraminiferal species G. crassaformis is used from Site U1313 from MIS 99 (interglacial) and MIS 98 (glacial). This provides the opportunity to separate ice volume, salinity and temperature effects on the measured δ18O record of G. crassaformis. The results of the clumped isotope measurements reveal comparatively large standard errors. For the Late Cretaceous the standard error of the clumped isotope measurements proved too large to allow any conclusions on the temperature component on the δ18O record of A. australis. For the early Pleistocene, the temperature difference is also too small to be reconstructed with the standard error of the clumped isotope measurements in this study. Measuring many replicates of one sample would minimize the standard error considerably. However, the amount necessary to measure replicates cannot be gained for either time period, as almost all foraminifera were picked from the respective samples. It is concluded that the respective questions may be solved with a different method of clumped isotope analysis requiring less sample material. This method is, for example, available at the ETH Zurich.
Nervous system development requires a sequence of processes such as neuronal migration, the development of dendrites and dendritic spines and the formation of synapses. The extracellular matrix protein Reelin plays an important role in these processes, Reelin regulates for example the migration of neurons from proliferative zones to their target positions in the brain. As a consequence, layered structures are formed in the neocortex, the hippocampus and cerebellum (Lambert de Rouvroit et al., 1999). Reelin exerts its functions by binding to two transmembrane receptors, apolipoprotein E receptor 2 (ApoER2) and very-low-density lipoprotein receptor (VLDLR). This binding causes phosphorylation of the intracellular adapter protein Disabled-1 (Dab1) (D’Arcangelo et al., 1999) via activation of Src-family kinases (SFKs) (Bock and Herz, 2003), leading to cytoskeletal reorganization which enables cell migration and morphological changes (Lambert de Rouvroit and Goffinet, 2001). Since ApoER2 and VLDLR do not possess intrinsic kinase activity to activate SFKs, the existence of a co-receptor was suggested. EphrinBs are transmembrane ligands for Eph receptors and have signaling capabilities required for axon guidance (Cowan et al., 2004), dendritic spine maturation (Segura et al., 2007) and synaptic plasticity (Essmann et al., 2008; Grunwald et al., 2004). As stimulation of cultured cortical neurons with soluble EphB receptors causes recruitment of SFKs to ephrinB-containing membrane patches and SFK activation (Palmer et al., 2002), we investigated whether ephrinB ligands would be the missing co-receptors in the Reelin signaling pathway functioning during neuronal migration, dendritic spine maturation and synaptic plasticity. We found that the extracellular part of ephrinBs directly binds to Reelin and that ephrinBs interact with Dab1, phospho-Dab1, ApoER2 and VLDLR. EphrinB3 is localized in the same neurons as ApoER2 and Dab1 in the cortex and hippocampus, and in the cerebellum ephrinB2 is detected in neurons that express Dab1. To investigate the requirement of ephrinBs for neuronal migration, triple knockout mice lacking all ephrinB ligands were analyzed. The cortical layering of ephrinB1, B2, B3 knockout brains is inverted, showing the outside-in pattern typical for the reeler cortex. The hippocampus and cerebellum of triple knockout mice also exhibit reeler-like malformations, although less penetrant than the cortical defects. Dab1 phosphorylation is impaired in mice lacking ephrinB3 and this effect is strongly enhanced in neurons lacking all ephrin ligands. Moreover, activation of ephrinB3 reverse signaling induces Dab1phosphorylation in reeler primary neurons. In agreement with an important regulatory function of ephrinBs in Reelin signaling, activation of ephrinB3 reverse signaling is even able to rescue reeler defects in cortical layering in organotypic slice cultures. In summary, all these results identify ephrinBs as co-receptors for Reelin signaling, playing essential roles in neuronal migration during the development of cortex, hippocampus and cerebellum (Sentürk et al., 2011).
Plants absorb sunlight via photosynthetic pigments and convert light energy intochemical energy in the process of photosynthesis. These pigments are mainly bound to antenna protein complexes that funnel the excitation energy to the photosynthetic reaction centres. The peripheral antenna of plant photosystem II (PSII) consists of the major light-harvesting complex of PSII (LHC-II) and the minor LHCs CP29, CP26 and CP24. Light intensity can change frequently and plants need to adapt to high-light conditions in order to avoid photodamage. When more photons are absorbed than can be utilised by the photosynthetic machinery, excessive excitation energy is dissipated as heat by short-term adaptation processes collectively known as non-photochemical quenching (NPQ). A decrease in PSII antenna chlorophyll (Chl) fluorescence yield and a reduction in the average Chl fluorescence lifetime are associated with NPQ. The main component of NPQ is the so-called energy-dependent quenching (qE), and it is triggered by the rapid drop in thylakoid lumenal pH resulting from the plant’s photosynthetic activity. This process is thought to take place at the PSII antenna complexes, which therefore not only capture and transfer light energy but are also involved in balancing the energy flow. The decrease in lumenal pH acivates the enzyme violaxanthin de-epoxidase (VDE), which converts the xanthophyll violaxanthin (Vio) into zeaxanthin (Zea) in the xanthophyll cycle. In addition, the PSII subunit PsbS was discovered to be essential for qE by screening qE-deficient Arabidopsis thaliana mutants. This membrane protein is considered a member of the LHC superfamily, which also includes LHC-II and the minor LHCs. Previous studies on PsbS isolated either from native source or refolded in vitro have produced inconsistent results on its pigment binding capacity. Interestingly, a pH-dependent change in the quaternary structure of PsbS under high light conditions has been reported. This observed dimer-tomonomer transition very likely follows the protonation of lumenal glutamates upon the drop in pH and is accompanied by a change in PSII supercomplex localisation. PsbS dimers are preferentially found in association with the PSII core, whereas PsbS monomers co-localise with LHC-II.Despite the identification of !pH, Zea and PsbS as key players in qE, both the nature of the quencher(s) as well as the underlying molecular mechanism leading to excess energy dissipation still remain unknown. Several models have been put forward to explain the reversible switch in the antenna from an energy-transmitting to a quenched state. Proposals include a simple pigment exchange of Vio for Zea, and aggregation or an internal conformational change of LHC-II. Charge transfer (CT)quenching in the minor LHCs or quenching by carotenoid dark state (Car S1)-Chl interactions have also been suggested. However, none of these qE models has so far been capable of accommodating all the physiological observations and available experimental data. Most importantly, the function of PsbS remains an enigma. A recent qE model suggested that monomerisation of PsbS enables the protein to transiently bind a carotenoid and form a quenching unit with a Chl of a PSII LHC. In view of the various proposed qE mechanisms, this thesis aimed at understanding the interplay of the different qE components and the contribution of the PSII subunits LHC-II, the minor LHCs and PsbS to qE. The initial approach was to investigate the properties of the PSII subunits in the most simple in vitro model system, namely in detergent solution. For this purpose, LHC-II was isolated either from native source or refolded from recombinantly produced protein. Investigation of the minor LHCs and PsbS required heterologous expression and refolding. In addition, experiments were performed on aggregated LHC-II. Aggregates of LHC-II have been used as a popular model system for qE because they exhibit highly quenched Chl fluorescence. At the final stage of this doctoral work, a more sophisticated model system to approximate the thylakoid membrane was developed by reconstitution of the PSII subunits LHC-II and PsbS into liposomes. This system not only allowed for investigation of these membrane proteins in their native environment, but also for mimicking the xanthophyll cycle by distribution of Zea within the membrane as well as !pH by outside buffer exchange. The role of Zea in qE was first investigated with detergent solubilised antenna proteins. The requirement of this xanthophyll for qE is well-known, but the specific contribution to the molecular quenching mechansim is unclear. Previous work had shown that replacement of Vio for Zea in LHC-II was not sufficient to induce Chl fluorescence quenching in Zea-LHC-II, as suggested by the so-called molecular gearshift mechanism. However, by means of selective two-photon excitation spectroscopy, an increase in electronic interactions between Car S1 and Chls was observed for LHC-II upon lowering the pH of the detergent buffer. Electronic Car S1-Chl coupling became even stronger when Zea-LHC-II was probed. The extent of Car S1-Chl coupling correlated directly with the extent of Chl fluorescence quenching, in a similar way as observed previously in live plants under high-light conditions. However, very similar results were obtained with LHC-II aggregates. This implied that the increase in electronic interactions and fluorescence quenching was independent of Zea and low pH. Further experiments on aggregates of LHC-II Chl mutants indicated that the targeted pigments were also not essential for the observed effects. It is proposed that the same molecular mechanism causes an increase in electronic Car S1-Chl interactions and Chl fluorescence quenching in Zea-LHC-II at low pH as well as in aggregated LHC-II. Most likely, surface exposed pigments form random quenching centres in both cases. On the other hand, it was possible that Zea could act as a direct quencher of excess excitation energy in the minor LHCs. However, enrichment of refolded CP29, CP26 and CP24 with Zea did not lead to a change in the Chl excited state lifetime. Formation of a carotenoid radical cation, previously implied in CT quenching, was also not observed, although artificial generation of such a radical cation was principally possible as shown for CP29. During the course of this work, a study reporting the formation of Zea radical cations in minor LHCs was published. Therefore, Zea-enriched minor LHCs were again investigated on the experimental apparatus used in the reported study. Indeed, the presence of at least one carotenoid radical cation for each minor complex was detected. It is suggested that either the preparation method of incubating the refolded minor LHCs with Zea in contrast to refolding the complexes with only Zea and lutein causes the observed differences or that the observed spectral radical cation signatures are due to experimental artifacts. While the experiments with LHC-II and the minor LHCs gave useful insights into the putative qE mechanism, the quencher site and the mode of action of Zea could still not be unambiguously identified. Most importantly, these studies could not explain the function of the qE keyplayer PsbS. Therefore, the focus of the work was shifted to PsbS protein production, purification and characterisation. In view of inconsistent reports on the pigment binding capacity of this PSII subunit, refolding trials with and without photosynthetic pigments were conducted. The formation of a specific pigmentprotein complex typical for other LHCs was not observed and neither was the earlier reported “activation” of Zea for qE by binding to this protein. Nevertheless, PsbS refolded without pigments displayed secondary structure content in agreement with previous studies, indicating pigment-independent folding. Reconstitution of pigmentfree, refolded PsbS into liposomes confirmed that the protein is stable in the absence of pigments. Zea distributed in PsbS-containing liposomes also showed no spectral alteration that would indicate its “activation”. With the ability to reconstitute PsbS, it was then possible to proceed to modelling qE in a proteoliposome system. For this purpose, PsbS was co-reconstituted with LHC-II, which has been reported to interact with PsbS. One-photon excitation (OPE) and two-photon excitation (TPE) spectroscopy measurements were performed on LHC-II- and LHC-II/PsbS-containing liposomes. This enabled both quantification of Chl fluorescence quenching as well as determination of the extent of electronic Car S1-Chl interactions. The effect of Zea was investigated by incorporating it in the proteoliposome membrane. It was shown that Zea alone was not able to induce significant Chl fluorescence quenching when only LHC-II was present. However, when LHC-II and PsbS were co-reconstituted, pronounced Chl fluorescence quenching and an increase in electronic Car S1-Chl interactions were observed and both effects were enhanced when Zea was present. Western blot analysis indicated the presence of a LHC-II/PsbS-heterodimer in these proteoliposomes. In addition to the OPE and TPE measurements, the average Chl fluorescence lifetime was determined in detergent-free buffer at neutral pH and directly after buffer exchange to low pH. No significant changes in the average lifetime were observed for LHC-II proteoliposomes when either Zea was present or after exchange for low pH buffer. This indicated that Zea alone cannot act as a direct quencher, which concurs with the OPE measurements. Moreover, the complex was also properly reconstituted as no aggregation or significant Chl fluorescence quenching were observed. The average lifetime was not significantly affected in LHC-II/PsbS-proteoliposomes, independent of Zea or pH. However, a shortlived component in the presence of a long-lived component was not resolvable with the time resolution of the fluorescence lifetime apparatus.
Implications for qE model systems and the in vivo quenching mechanism are discussed based on the experiments in detergent solution, on LHC-II aggregates and with the proteoliposome model system.
Fungal organisms, including the most common human pathogens Candida spp., are commensal organisms that are widely present as part of the human flora. Fungal infections are, most frequently, local infections that do not compromise the life of patients. However, mycotic diseases can be life-threatening if they become systemic infections. Systemic fungal infections have risen over the last three decades in parallel to the increased immune-compromised population as a consequence of diseases (e.g. HIV/AIDS) or therapeutic interventions that affect the immune system (e.g. chemotherapy for cancer treatment and immunosuppressors used for patients with organ transplants). This has resulted in the demand of new antifungal drugs that can eradicate the new infections caused by these opportunistic fungal pathogens. However, most of the current compounds have poor pharmaceutical properties such as narrow spectrum of activity, susceptibility to be extruded by efflux pumps or lack of specificity, which make them not suitable for human clinical applications. The treatment of fungal and parasitic infections has been traditionally difficult because the infective organisms are eukaryotic cells that share most of the pathways and enzymes with human cells. To avoid side effects and to develop a targeted therapy, the research has traditionally been centered on the very few enzymes and pathways existing in the infectious organism but absent in humans. Until now, antifungal therapeutic options are limited and are almost dominated by azole class of sterol biosynthesis inhibitors affecting the synthesis of ergosterol, a major constituent of the fungal cell membrane. Because human cells do not have a cell wall, the development of effective and safe antifungal agents has also been directed to enzymes required for the synthesis of the cell wall. Alternatively, it is theoretically possible to target enzymes that are present in fungal organisms and in humans, when: 1) sufficient selectivity can be achieved, and 2) inhibition of the fungal enzyme is lethal to the fungus but does not produce major side effects to humans. In this line, it would be ideal to evaluate the development of selective inhibitors of enzymes which are already known to be drug targets, like protein kinases.
Goethe and the Sublime
(2013)
The dissertation situates the Goethean sublime in an obscured countermovement of resistance to the aestheticization the concept underwent in the 18th century. Before the encounter with the English aesthetic concept of the sublime, the German notion of das Erhabene (the sublime) named not a category of aesthetic experience, but a social affect. In contrast to the Sublime of Edmund Burke's theory, which explicitly excludes melancholy from the sources of the Sublime, das Erhabene is an affect related to the self-overcoming of melancholic subjectivity. As the aestheticized notion of the sublime displaced das Erhabene, Goethe became one of the most radical innovators of the aesthetics of the sublime. But as is demonstrated in chapters on The Sorrows of Young Werther, Elective Affinities, Faust and Wilhelm Meister, he did so with the aim of recovering the displaced meaning of das Erhabene as social affect. Goethe's sublime aims to show at every turn that the so-called "aesthetic experience" of the sublime is really displaced social affect. His treatment of the sublime therefore constitutes a radical critique of the establishment of aesthetics as an independent sphere of inquiry. There is for Goethe no way to understand aesthetic experience independently of its social context. By reconnecting the sublime it to the original social meaning of das Erhabene, Goethe recovers the aesthetics of the sublime as a means of mediating and facilitating the movement of subjectivity from frustrated stasis to divine creativity; i.e., from exclusion to participation in the material creation of reality.
Gridded maps of meteorological variables are needed for the evaluation of weather and climate models and for climate change monitoring. In order to produce them, values at locations where no observing stations are available need to be estimated from point-wise observations. For the interpolation of meteorological observations deterministic and stochastic methods are often combined. Deterministic methods can account for ancillary information such as elevation, continentality or satellite observations. Stochastic methods such as kriging reproduce observed values at the station locations and also account for spatial variability. In the first two studies of this thesis, a flexible interpolation method for the gridding of locally observed daily extreme temperatures is developed that also provides an optimal estimate of the interpolation ncertainty. In the third study, an observational dataset is created using this interpolation method and then applied to evaluate a climate simulation for Africa.
In the first study, the Regression-Kriging-Kriging (RKK) method is tested for the interpolation of daily minimum and maximum temperatures (Tmin and Tmax) in different regions in Europe. RKK accounts for elevation, continentality index and zonal mean temperature and is applicable in regions of differing station density and climate. The accuracy of RKK is compared to Inverse Distance Weighting, a common deterministic interpolation method, and to Ordinary Kriging, a common stochastic interpolation method. The first step in RKK is to use regression kriging, in which multiple linear regression accounts for topographical effects on the temperature field and kriging minimizes the regression error, to interpolate climatological means. In the second step daily deviations from the monthly climatology are interpolated using simple kriging. Owing to the large climatological differences across the investigation area the interpolation is performed in homogeneous subregions defined according to the Köppen-Geiger climate classification. Cross validation demonstrates the superiority of RKK over the simpler algorithms in terms of accuracy and preservation of spatial variability. The interpolation performance however strongly varies across Europe, being considerably higher over Central Europe (highest station density) than over Greenland (few stations along the coast line). This illustrates the strong impact of the station density on the accuracy of the interpolation result. Satellites provide comprehensive observations of climate variables such as land surface temperature (LST) and cloud cover (CC). However, LST is associated with high uncertainty (standard error ~ 1-2°C), preventing its direct application in meteorology and climatology. The second study investigates the usefulness of LST and CC as predictors for the gridding of daily Tmin and Tmax. The RKK algorithm is compared with similar interpolation methods that apply LST and CC in addition to the predictors used with the RKK algorithm. The investigation is conducted in two regions, Central Europe and the Iberian Peninsula, which differ strongly in average cloud cover (Central Europe is approximately 30% cloud free and the Iberian Peninsula approximately 60 % cloud free). RKKLST (in which monthly mean LST is used as an additional predictor) yields for Central Europe no clear improvement over RKK, yet it reduces the interpolation error over the Iberian Peninsula. This finding can be explained by the higher percentage of cloud free pixels over that region in summer which enables a more robust determination of monthly mean LST. Adding a regression step for daily anomalies (using the predictor CC) yields the RKRK method and improves the preservation of spatial variability over the Iberian Peninsula. Moreover, a successive reduction of the station number (from 140 to 10 stations) reveals an increasing superiority of RKKLST and RKRK over RKK in both regions.
The application of a gridded observational dataset for climate monitoring or climate model validation requires knowledge of the uncertainties associated with the dataset. The estimation of the interpolation uncertainty, here the inter quartile range is the used uncertainty measure, is therefore an important issue within the frame of this thesis. By means of cross validation it is shown that the largest uncertainties occur in regions of low station density (e.g. Greenland), in mountainous regions and along coastlines (in these regions model evaluation results should be interpreted carefully). The magnitude of the interpolation error mainly depends on the station density, while the complexity of terrain has substantially less influence. On average over all regions and investigation days the target precision of the uncertainty estimate is reached. However, on local scales and for single days it can be clearly over- or underestimated. The application of satellite-derived predictors (LST and CC) yields no noteworthy improvement of the uncertainty estimate.
In the last study two regional climate simulations for Africa using the ERA-Interim driven COSMO-CLM (CCLM) model at two different horizontal resolutions (0.22° and 0.44°) are validated. It is assessed whether observed patterns and statistical properties of daily Tmin and Tmax are correctly represented in the model. The ERA-Interim reanalysis and a specially created observational dataset are used as reference. The observational dataset is generated by applying the RKRK algorithm (developed within the second study). The investigations show an occasionally large bias in Tmin and Tmax. The hemispheric summers are generally too warm and the temporal variability in temperature is too high, particularly over extra tropical Africa. The diurnal temperature range is overestimated by about 2°C in the northern subtropics but underestimated by about 2°C over large parts of the African tropics. CCLM reproduces the observed frequency distribution of daily Tmin and Tmax in all African climate regions, and the extreme values in the lower percentiles (5, 10, 20%) for Tmin are well simulated. The higher percentiles (80, 90, 95%) for Tmax are however overestimated by 2-5°C. For both Tmin and Tmax the 0.22° simulation is on average 0.5°C warmer than the 0.44° simulation. Additionally, the higher percentiles are about 1°C warmer for both Tmin and Tmax in the higher resolution run, while the lower percentiles in both runs match very well. Although the temperature pattern is represented in more detail along the coastlines and in topographically complex regions, the higher resolution simulation yields no qualitative improvement.
To summarize, the choice of the appropriate algorithm mainly depends on the interpolation conditions. In cases where the station density is high across the target region and the predictor space is adequately covered by observing stations, the computationally less demanding RK algorithm should be preferred. In regions where the station density is low the more robust RKRK algorithm should be the first choice. Due to the strong physical relation of both CC and LST to Tmin and Tmax the missing information is at least partially compensated for. The estimation of the interpolation uncertainty could be improved by applying a normal score transformation to the data prior to a kriging step. This is because the kriging assumption that the increments of the variable of interest are second order stationary can be approximately met by a normal score transformation.
In this thesis, Hanbury-Brown-Twiss (HBT) interferometry is used together with the Ultrarelativistic Quantum Molecular Dynamics (UrQMD) to analyse the time and space structure of heavy-ion collisions.
The first chapter after the introduction gives an overview of the different types of models used in the field of heavy-ion collisions and a introduction of the UrQMD model in more detail. The next chapter explains the basics of Hanbury-Brown-Twiss correlations, including azimuthally sensitive HBT (asHBT).
Results section:
4. Charged Multiplicities from UrQMD
5. Formation time via HBT from pp collisions at LHC
6. HBT analysis of Pb+Pb collisions at LHC energies
7. HBT scaling with particle multiplicity
8. Compressibility from event-by-event HBT
9. Tilt in non-central collisions
10. Shape analysis of strongly-interacting systems
11. Measuring a twisted emission geometry
This thesis covers the standard integrated HBT analyses, extracting the Pratt-Bertsch radii, at LHC energies. The analyses at these energies showed a too soft expansion in UrQMD probably related to the absence of a partonic phase in UrQMD. The most promising results in this thesis at these energies are the restriction of the formation time to a value smaller than 0.8 fm/c and furthermore, the results from the asHBT analyses. In simulations of non-central heavy-ion collisions at energies of Elab= 6, 8 and 30 AGeV the validity of the formulae to calculate the tilt angle via asHBT has been checked numerically, even for the case of non-Gaussian, flowing sources. On this basis has been developed and test in the course of this thesis that allows to measure a scale dependent tilt angle experimentally. The signal should be strongest at FAIR energies.
In the absence of apparent mutations, alteration of gene expression patterns represents the key mechanism by which normal cells evolve to cancer cells.
Gene expression is tightly regulated by posttranscriptional processes. Within this context, RNA-binding proteins (RBPs) represent fundamental factors, since they control mechanisms, such as mRNA-stabilization, -translation and -degradation. Human antigen R (HuR) was among the first RBPs that have been directly associated to carcinogenesis. HuR modulates the stability and translation of mRNAs which encode proteins facilitating various ‘hallmarks of cancer’, namely proliferation, evasion of growth suppression, angiogenesis, cell death resistance, invasion and metastasis. Furthermore, it is well established that tumor-promoting inflammation contributes to tumorigenesis. In this process, monocytes are attracted to the site of the tumor and educated towards a tumor-promoting macrophage phenotype. While HuR has been extensively studied in various tumor cell types, little is known about HuR in hepatocellular carcinoma (HCC). Thus, the aim of my work was to characterize the contribution of HuR to the development of cancer characteristics in HCC. I was particularly interested to investigate if HuR facilitates tumor-promoting inflammation, since a role for HuR has not been described in this context. To this end, I depleted HuR in HepG2 cells (HuR k/d) and used a co-culture model of HepG2 tumor spheroids and infiltrating monocytes to study the impact of HuR on the tumor microenvironment. I could show that depletion of HuR resulted in the reduction of cell numbers. Additionally, the expression of proliferation marker KI-67 and proto-oncogene c-Myc was reduced, supporting a proliferative role of HuR. Furthermore, exposure to cytotoxic staurosporine elevated apoptosis in HuR k/d cells compared to control cells. Concomitantly, the expression of the anti-apoptotic mediator B-cell lymphoma protein-2 (Bcl-2) was markedly reduced in the HuR k/d cells, pointing to an involvement of HuR in cell survival processes.
Accordingly, a pro-survival function of HuR was also observed in tumor spheroids, since HuR k/d spheroids exhibited a larger necrotic core region at earlier time points and showed elevated numbers of dead cells compared to control (Ctr.) spheroids. Interestingly, HuR k/d spheroids isplayed reduced numbers of infiltrated macrophages, suggesting that HuR contributes to a tumor-promoting, inflammatory microenvironment by recruiting monocytes/macrophages to the tumor site. Aiming at identifying HuR-regulated factors responsible for the recruitment of monocytes, I found reduced levels of the chemokine interleukin 8 (IL-8) in supernatants of HuR k/d spheroids, supporting a critical involvement of HuR in the chemoattraction of monocytes. Analyzing supernatants of co-cultures of macrophages and HuR k/d or Ctr. spheroids revealed additional differences in chemokine secretion patterns. Interestingly, protein levels of many chemokines were elevated in co-cultures of HuR k/d spheroids compared to control co-cultures. Albeit enhanced chemokine secretion was observed, less monocytes are recruited into HuR k/d spheroids, further underlining the necessity of HuR in cancer related monocyte/macrophage attraction and infiltration. Differences between chemokine profiles of mono- and co-cultured spheroids could be attributable to changes in spheroid-derived chemokines as a result of the crosstalk with the immune cells. Provided the chemokines originate from monocytes/macrophages, the different secretion patterns suggest that HuR contributes to the modulation of the functional phenotype of infiltrated macrophages, since the tumorenvironment is critically involved in the shaping of macrophage phenotypes. Regions of low-oxygen (hypoxia) represent another critical feature of tumors. Therefore, I next analyzed the impact of HuR on the hypoxic response. Loss of HuR attenuated hypoxia-inducible factor (HIF) 2α expression after exposure to hypoxia, while HIF-1α protein levels remained unaltered. Considering previous results of our group, showing that HIF-2α depletion (HIF-2α k/d) resulted in the enhanced expression of HIF-1α protein, I aimed to determine the involvement of HuR in the compensatory upregulation of HIF-1α protein in HIF-2α k/d cells. I could demonstrate that not only total HuR protein levels, but specifically cytoplasmic HuR was elevated in HIF-2α depleted cells pointing to enhanced HuR activity. Silencing HuR in HIF-2α deficient cells attenuated enhanced HIF-1α protein expression, thus confirming a direct role of HuR in the compensatory upregulation of HIF-1α. This as also reflected on HIF-1α target gene expression. I further investigated the mechanism underlying the compensatory HIF-1α expression in HIF-2α deficient cells. Analyzing HIF-1α mRNA expression, I excluded enhanced HIF1-α transcription and stability to account for elevated HIF-1α expression in HIF-2α k/d cells. HIF-1α promoter activity assays confirmed the mRNA data. Furthermore, HIF-1α protein half-life was not elevated in HIF-2α k/d cells compared to control cells, indicating that HIF-1α protein stability is not altered in HIF-2α k/d cells. Analysis of the association of HIF-1α with the translational machinery using polysomal fractionation finally revealed an increased istribution of HIF-1α mRNA in the heavier polysomal fractions in HIF-2α k/d cells compared to control cells. Since augmented ribosome occupancy is an indicator for more efficient translation, I propose enhanced HIF-1α translation as underlying principle of the compensatory increase in HIF-1α protein levels in HIF-2α k/d cells. In summary, my results demonstrate that HuR is critical for the development of cancer characteristics in HCC. Future work analyzing the impact of HuR on tumor-promoting inflammation, specifically macrophage attraction and activation could provide new trategies to inhibit macrophage-driven tumor progression. Furthermore, I provide evidence that HuR contributes to the hypoxic response by regulating the expression of HIF-1α and HIF-2α. Targeting single HIF-isoforms for tumor therapy should be carefully considered, because of their compensatory regulation when one α-subunit is depleted. Thus, therapeutic strategies targeting factors such as HuR that control both α-subunits and at the same time prevent compensation might be more promising.
Der programmierte Zelltod (Apoptose) ist ein wichtiger Mechanismus zur Eliminierung von beschädigtem Gewebe und entarteten Zellen. Die Deregulierung der Apoptose führt zu zahlreichen Erkrankungen wie neuro-degenerativen Störungen und Krebs. Insbesondere in Tumoren wird der programmierte Zelltod mit Hilfe von hochregulierten, anti-apoptotischen Proteinen umgangen und es entstehen Resistenzen gegen Chemotherapien. Um innovative therapeutische Ansätze zu finden, wurden in diesem Projekt mit Hilfe eines Hefe-Survival-Screens neue, potentiell anti-apoptotische Proteine im Pankreaskarzinom identifiziert. Von den insgesamt 38 identifizierten Genprodukten wurden zwei für eine weiterführende Analyse ausgewählt.
Eins der näher untersuchten Proteine ist die Pyruvoyl-tetrahydrobiopterin-Synthase (PTS), ein wichtiges Enzym für die Biosynthese von Tetrahydrobiopterin (BH4). BH4 ist ein Kofaktor, der von mehreren Enzymen der Zelle für ihre Funktionen benötigt wird. In Zellkultur-Experimenten konnte gezeigt werden, dass eine Überexpression von PTS die Zellen vor Apoptose schützen kann, während eine Herunterregulation durch genetischen knockdown die Zellen gegenüber Apoptose-Stimuli sensibilisiert und ihr Wachstum beeinträchtigt. In Xenograft-Experimenten mit NOD/SCID-Mäusen konnte zudem gezeigt werden, dass Tumore mit einem PTS-Knockdown signifikant langsamer wachsen als die der Kontrollgruppe. Zusammengenommen deuten diese Ergebnisse auf eine Rolle von PTS bei der Apoptose-Regulation und beim Tumorwachstum hin, was das Protein zu einem attraktiven Target für die Krebstherapie macht.
Als zweites wurde ein Protein analysiert, das eine Untereinheit des respiratorischen Komplex I bildet: NDUFB5 (NADH-Dehydrogenase 1 beta Subcomplex, 5). Das besondere an diesem Protein sind die verschiedenen Isoformen, die durch alternatives Splicing zustandekommen. Eine Isoform, der die Exone 2 und 3 fehlen, wurde im Hefe-Survival-Screen identifiziert. Bei Überexpression in Zelllinien konnte sie im Gegensatz zum Volllänge-Protein die Apoptoserate reduzieren. Und auch Ergebnisse aus Versuchen mit Isoformen-spezifischem knockdown deuten an, dass hauptsächlich die verkürzte Isoform sNDUFB5 für die Regulation von Apoptose und Proliferation verantwortlich ist. Diese Beobachtungen konnten mit denselben Zellen im Xenograft-Tiermodell jedoch nicht bestätigt werden. Die Ursachen dafür blieben unklar. Zusätzlich wurden immunhistochemische Analysen von Pankreaskarzinomen und normalem Pankreasgewebe durchgeführt. Sie ergaben, dass die kurze Isoform sNDUFB5 im Tumor stark überexpremiert ist, während die Expression des Volllänge-Proteins in normalem und Tumorgewebe ähnlich hoch ausfällt. Dieser Befund macht NDUFB5 zu einem interessanten therapeutischen Target.
Die näher untersuchten Kandidaten-Gene zeigen beide Potential als neue Angriffspunkte für eine molekulare Krebstherapie. Andere in dem Hefe-Survival-Screen identifizierte Proteine wurden bereits als anti-apoptotisch und/oder in Krebszellen überexprimiert beschrieben. Diese Ergebnisse demonstrieren, dass ein funktionelles, Hefe-basiertes Screeningsystem geeignet ist, neue bisher unbekannte Proteine mit anti-apoptotischer Funktion zu identifizieren. Auch zeigen die Befunde, dass bereits bekannte Proteine weitere bisher unbekannte Funktionen wie z.B. die Inhibition von Apoptose aufweisen können. Basierend auf solchen mehrfachen Proteinfunktionen lassen sich weitere therapeutische Möglichkeiten ableiten.
Diese Dissertation stellt die systematische Einbeziehung von Eichkorrekturen in die Theorie der thermischen Leptogenese vor, welche eine Erklärung für die Frage nach dem Ursprung der Materie in unserem Universum bereitstellt.
Geht man vom weithin anerkannten Urknallmodell aus, so müsste hierbei zu gleichen Teilen Materie sowie Antimaterie entstanden sein. Aufgrund von Annihilationsprozessen sollte demnach die gesamte Materie zerstrahlt sein und ein leeres Universum zurückbleiben. Da dies aber nicht der Fall ist, stellt sich die Frage, wie das Ungleichgewicht zwischen Materie und Antimaterie entstehen konnte. Der Wert der Asymmetrie lässt sich mit Hilfe von Experimenten sehr genau bestimmen. Für eine systematische theoretische Beschreibung dieser Problematik stellte A. Sacharow drei Bedingungen auf: 1. die Verletzung der Baryonenzahl, 2. die Verletzung der Invarianz von Ladungskonjugation C sowie der Zusammensetzung von Ladungskonjugation und Parität CP sowie 3. eine Abweichung vom thermischen Gleichgewicht.
Da das Urknallmodell und das Standardmodell der Teilchenphysik nicht in der Lage sind, diese Asymmetrie zu beschreiben, beschäftigt sich die vorliegende Dissertation mit der Theorie der thermischen Leptogenese, welche statt von einer ursprünglichen Baryonenasymmetrie von einer Leptonenasymmetrie ausgeht. Zu einem späteren Zeitpunkt wird diese dann mittels Sphaleron-Prozesse, welche die Baryonenzahl verletzen, in eine Baryonenasymmetrie übertragen. Hierzu werden neue Teilchen zum Standardmodell hinzugefügt: schwere Majorana-Neutrinos. Diese zerfallen im thermischen Nichtgleichgewicht CP-verletzend in die bekannten Standardmodell-Leptonen und Higgs-Teilchen.
In dieser Arbeit wird eine hierarchische Anordnung der drei schweren Neutrinomassen betrachtet. Dies hat zur Folge, dass zwei der drei Majorana-Neutrinos ausintegriert werden können und eine effektive Theorie aufgestellt werden kann. Dieses Modell wird auch vanilla leptogenesis genannt und im Folgenden verwendet.
Die Dissertation ist wie folgt gegliedert. Die einleitenden Betrachtungen sind Gegenstand der Kapitel 1 und 2. Dort werden weiterhin andere Modelle zur Lösung des Problems der Baryonenasymmetrie kurz vorgestellt. Die thermische Leptogenese wird eingeführt und der See-saw-Mechanismus sowie die CP-Asymmetrie genauer beschrieben. Am Ende des Kapitels wird der klassische Ansatz für Leptogenese über Boltzmann Gleichungen präsentiert.
In Kapitel 3 werden die Grundlagen für Quantenfeldtheorien im Nichtgleichgewicht eingeführt. Die wichtigsten Definitionen im Falle des thermischen Gleichgewichts werden gegeben, anschließend findet sich die Verallgemeinerung auf Nichtgleichgewichtszustände. Die Bewegungsgleichungen, die sogenannten Kadanoff-Baym-Gleichungen, werden im Folgenden sowohl für skalare Teilchen als auch für Fermionen gelöst.
Kapitel 4 stellt die Notwendigkeit der Einbeziehung von Eichkorrekturen im Kontext der thermischen Leptogenese vor. Durch die Definition einer Leptonenzahlmatrix lässt sich die Asymmetrie durch die Kadanoff-Baym Gleichung für Leptonen umschreiben. Da der Vergleich von Boltzmann und Kadanoff-Baym Gleichungen im letzten Teil dieses Kapitels Unterschiede im Zeitverhalten zeigt, werden im Kadanoff-Baym Ansatz thermische Standardmodell-Breiten des Higgsfeldes und der Leptonen per Hand eingeführt. Mit dieser naiven Erweiterung erhält man ein gleiches Verhalten für die Leptonenzahlmatrix, lokal in der Zeit wie die Lösung der Boltzmann Gleichung. Eine systematische Einführung von Standardmodellkorrekturen für thermische Leptogenese ist daher unumgänglich, weshalb im Rahmen der vorliegenden Dissertation von Grund auf Eichkorrekturen der Diagramme, die zur Asymmetrie führen, berücksichtigt werden.
Die vier für diese Arbeit wichtigen Skalenbereich bedingen zwei Resummationsschemata, Hard Thermal Loop (HTL) und Collinear Thermal Loop (CTL), welche in Kapitel 5 vorgestellt werden. Dies führt schließlich auf zwei Differenzialgleichungen für die Berechnung der thermischen Produktionsrate des Majorana-Neutrinos, welche in Kapitel 6 numerisch weiter ausgewertet werden.
In Kapitel 7 erfolgt zunächst eine naive Berechnung aller eichkorrigierter 3-Schleifen-Diagramme, die zu den beiden die Asymmetrie verursachenden Diagrammen gehören. Da eine einfache Berechnung der 3-Schleifen-Diagramme nicht ausreicht, wird an dieser Stelle ein neues, zylindrisches Diagramm eingeführt, welches alle wichtigen Beiträge, insbesondere die HTL- und CTL-resummierten, enthält. Am Ende des Kapitels findet sich der erste geschlossene Ausdruck für die eichkorrigierte Leptonenzahlmatrix in führender Ordnung in allen Kopplungen.
Abschließend gibt es eine kurze Zusammenfassung und einen Ausblick in Kapitel 8. In dieser Dissertation findet sich zum ersten Mal ein systematischer Zugang zur Berücksichtigung aller Eichwechselwirkungen in der Theorie der thermischen Leptogenese. Ein geschlossener Ausdruck für die eichkorrigierte Leptonenasymmetrie konnte vorgestellt werden.
Retroviral vectors are powerful tools in clinical gene therapy as they integrate permanently into the target cell genome and thus guarantee long-term expression of transgenes. Therefore, they belong to the most frequently used application platforms in clinical gene therapy involving a broad range of different target cells and tissues. However, stable genomic integration of retroviral vectors can be oncogenic, as reported in several animal models and in clinical trials. In particular, γ-retroviral vectors, which derive from naturally mutagenic γ-retroviruses, integrate semirandomly into the host genome with regard to the target sequence, but have a preference for regions of active transcription and regulatory elements of transcriptionally active genes. The integration can result in overexpression of adjacent genes or disruption of ‘target’ gene expression. Moreover, γ-retroviral integration can cause modified transcripts and proteins through alternative or aberrant splicing or through premature termination of transcription.
Initially, the event of insertional mutagenesis and subsequent induction of leukemia by the genotoxicity of a γ-retroviral vector was described in a mouse model after genetic modification of hematopoietic stem cells (HSCs). Vector-related activation and overexpression of the oncogene ecotropic viral integration site-1 (Evi1) fostered clonal outgrowth and leukemogenesis. Additional genotoxic events of γ-retroviral vectors were observed in clinical HSC gene therapy trials for X-linked severe combined immune deficiency (SCID-X1), chronic granulomatous disease (X-CGD), and Wiskott-Aldrich Syndrome (WAS). But, genotoxicity induced by γ-retroviral vectors has never been described in clinical gene therapy trials involving adoptive transfer of genetically modified mature T lymphocytes. This fact is surprising, since T cells are long-lived and have a high capacity of self-renewal.
In a previous study, the susceptibility towards oncogenic transformation of mature T cells and HSCs after genetic modification was compared. It could be demonstrated that T-cell receptor (TCR)-polyclonal mature T cells are far less prone to transformation after γ-retroviral transfer of (proto-)oncogenes in vivo than HSCs. Additional experiments revealed that TCR-oligoclonal (OT-I and P14) mature T cells are transformable in the same setting and give rise to mature T-cell lymphomas (MTCLs).
In the present thesis, the susceptibility of mature T cells towards insertional mutagenesis was investigated. Within the first part of the thesis, retroviral integration sites (RISs) from 33 murine MTCLs were retrieved and subsequently analyzed in terms of integration pattern, detection of common integration sites (CIS) and gene ontology (GO). As these bioinformatic results demonstrated that insertional mutagenesis most likely contributed to mature T-cell lymphomagenesis, the susceptibility of mature T cells was directly assessed in a mouse model. Therefore, murine TCR-oligoclonal OT-I T cells were transduced with an enhanced green fluorescent protein (EGFP) encoding γ-retroviral vector and gene-modified T cells were transplanted into RAG1-/- mice. After 16 months, including one round of serial transplantation, a case of MTCL emerged. Tumor cells were characterized by CD3, CD8, TCR and ICOS expression. Integration site analysis via ligation-mediated polymerase chain reaction (LM-PCR) revealed a proviral insertion in the Janus kinase 1 (Jak1) gene. Subsequent overexpression of Jak1 could be demonstrated on transcriptional and protein level. Furthermore, T-cell lymphoma cells were characterized by an activated Jak/STAT-pathway as signal transducer and activator of transcription 3 (STAT3) was highly phosphorylated. The overexpression of Jak1 was causally implicated in tumor growth promotion as specific pharmacological inhibition of Jak1 using Ruxolitinib significantly prolonged survival of mice transplanted with these Jak1-activated tumor cells. A concluding systematic metaanalysis of available gene expression data on human mature T-cell lymphomas/leukemias confirmed the relevance of Jak/STAT overexpression in sporadic human T-cell tumorigenesis.
This was the first reported case of an insertional mutagenesis event in mature T cells in vivo. Thus, the results obtained in this thesis underline the importance of long-term monitoring of genetically modified T cells in vivo and the evaluation of vector toxicology and safety in T-cell based gene therapies. In particular, the transduction of T cells with a recombinant TCR or CAR (chimeric antigen receptor) bears a risk enhancement, as normal T-cell homeostasis is perturbed besides the general risk of insertional mutagenesis.
In this thesis the integral membrane protein diacylglycerol kinase (DAGK) from E.coli is investigated with solid-state NMR. The aim is to gain an insight into the enzyme’s mechanism through integration of kinetic, structural and dynamic data. The biological function of DAGK is the transfer of the γ-phosphate group from Mg*ATP to diacylglycerol (DAG) building phosphatidic acid (PA)[6] as port of the membrane-derived oligosaccharide cycle[31,34]. Surprisingly, DAGK does not share structural or sequential similarities with other kinases[12]. Typical sequence motives found in other kinases, which catalyze phosphoryl transfer reactions, are not found[13]. In its physiological form DAGK is a homo-trimer with nine transmembrane helices, three catalytic centers and a size of 39.6 kDa.
First, the set-up of a real-time 31P MAS NMR experiment is shown. This experiment allows measuring in real-time the simultaneous ATP hydrolysis in the aqueous phase and lipid substrate phos-phorylation in the membrane phase with atomic resolution under magic angle spinning[56]. After fast transfer of the sample into the NMR spectrometer the enzymatic reaction is started with a temperature jump. This approach of real-time MAS NMR in a dual-phase system was demonstrated for the lipid substrate analogs dioleoyl- (DOG) and dibutyrylglycerol (DBG), with a C8 and C4 aliphatic chain, respectively. The combination of 31P direct and cross polarization functions as a dynamic filter. In the 31P direct polarized experiment nuclei in both phases are detected, while in the 31P cross polar-ized experiment, only nuclei in the membrane phase are detected. Rates for substrate turnover, i.e. degradation of γP-, βP, αP-ATP and build-up of βP-, αP-ADP, free phosphate as side reaction, and PA are obtained, which reveal a Michaelis-Menten behavior with regard to Mg*ATP and DBG. Here Mg*ATP and DBG follow a random-equilibrium model, where every substrate can bind indepen-dently from the other substrate. Analyses of the peak integrals from educts and products of the enzymatic reaction, revealed the stoichiometry of the reaction: 1.5 ATP molecules are used to phos-phorylate one DBG molecule. The excess of ATP is attributed to the basal ATPase activity. Further-more, experiments with ATPγS, usually regarded as a non-hydrolysable ATP-analog, where carried out. Surprisingly, DAGK hydrolyzes ATPγS and also transfers the thio-phosphate group to the lipid acceptor DBG, which points to a certain degree of plasticity in the active center. A phosphorylated enzyme intermediate was not detected. These results suggest the building of a ternary complex of Mg*ATP, DBG and DAGK performing a direct-phosphoryl transfer reaction, without passing through a phosphorylated enzyme intermediate. Experiments with the transition state analog ortho-vanadate (Vi) showed a decoupling of the ATP hydrolysis activity from lipid substrate phosphorylation. This indicates a specific transfer site for the γ-phosphate group from ATP to DAG, which can be blocked by Vi.
A general disadvantage of NMR spectroscopy compared to other spectroscopic methods is its inherent low sensitivity. One possible starting point for the improvement of signal-to-noise per unit time is the reduction of the spin-lattice relaxation time of protons[209]. Usually 95 % of the experi-mental time is required for the relaxation of the 1H to equilibrium. The addition of paramagnetic species can be used to reduce the 1H T1[233]. In a comprehensive study four different paramagnetic agents were tested: Cu2+-EDTA, Cu2+-EDTA-tag, Gd3+-TTAHA and Gd3+-DOTA. The titration of these paramagnetic complexes showed the principle feasibility of this approach, but differences between the tested species exist. The most promising complex is Gd3+-DOTA which, at a concentration of 2 mM, causes a 10-time improvement of signal-to-noise ratio per unit time. This allowed measuring 2D 13C-13C correlation spectra of proteoliposomes in one tenth of the usual required experimental time (i.e. 10 hours vs. 4 days) with good signal-to-noise.
For the investigation of structural or dynamic changes in the protein upon substrate interaction with MAS NMR, the spectral properties CP efficiency and resolution of the DAGK in liposomes needed to be improved. The most critical step during sample preparation is the reconstitution of the membrane protein from detergent micelles into a membrane of synthetic lipids under detergent removal. For this procedure the important criteria are enzymatic activity, measured in a coupled ATPase assay[55], and homogeneity of the proteoliposomes, which was tested e.g. on a discontinuous sucrose step gradient. Therefore an extensive study was carried out, in which different detergents, lipids and lipid mixtures, techniques for detergent removal and different protein-to-lipid ratios were tested. A direct correlation between high ATPase activity and good resolution was not found. Moreover, active DAGK in a mixture of DMPC and cholesterol, which emulates the membrane features of a membrane containing DAG, showed the best CP efficiency and resolution.
The assignment of the protein backbone and amino acid side chains the first mandatory step towards the investigation of structural and dynamical features influencing and defining the enzymatic mechanism by MAS NMR. As the assignment procedure is very time consuming for a total protein, a special labeling scheme for DAGK was developed, which allows assigning most of the protein areas presumably involved in enzyme catalysis. The assignment of DAGK with solution NMR[132] was not transferable to the MAS NMR spectra. Most important for the assignment process were the unique pairs[335], two consecutive amino acids which only appear once in the amino acid sequence. These unique pairs served as anchor points. Five different multinuclear MAS NMR experiments (DARR, NCO, NCA, NCACX, NCOCX) were required for the sequential assignment. It was possible to assign 35 % of the total amino acid sequence with one sample and 8 experiments acquired at 850 MHz. The secondary structure analysis showed subtle differences to the DAGK assignment with solution NMR[132], which can be attributed to the different environment in lipid bilayers and detergent micelles.
Data about structural and dynamical changes under substrate interaction can reveal details about the enzymatic mechanism. Therefore changes in chemical shift in 2D heteronuclear correlation experiments in the apo-state and under substrate saturated conditions with the substrates Mg*AMP-PNP, a non-hydrolysable ATP-analog, DOG, a mixture of Mg*AMP-PNP and DOG as well as inhibited by Vi were recorded. The most significant peak changes were observed at the interface membrane-cytoplasm as well as the the N-terminal amphipathic helix. The residues revealing chemical shift perturbations correlate with conserved residues or such residues, for which importance for catalysis and/or folding could be shown in mutation studies[8]. Especially noticeable were the changes at the amino acids Asn 72, Lys 64, His 87, Tyr 86 and Asp 95.
Beside changes of the chemical shift, changes of line width or signal doubling were observable. These changes can point to a correlation with dynamic reorientations in the μs-ms time regime, which are most relevant for enzymatic processes. The protein backbone dynamics in the apo-state as well as saturated with the substrates or inhibited with Vi were investigated with a 15N-CODEX experiment, which is based on the reorientation of the CSA tensor upon dynamical changes[350]. Specific effects of the different substrates or analogs on the protein backbone dynamic were revealed complementing the structural data and the chemical shift perturbation experiments.
This research was conducted in the Rwenzori Region of the Western Branch, East African Rift System (EARS). The EARS is a tectonic structure extending over a length of more than 3000 km from the Afar Triple Junction, in Ethiopia, to Lake Malawi in the south. The Western Rift System is a roughly NE to ENE trending sector of the EARS, which runs along the western boundary of Uganda and the neighboring Democratic Republic of Congo (D.R.C). It stretches 2100 km from Nimule, NW on Uganda-Sudan border, extending to Lake Malawi in the SE of Africa. The unusual uplift of the Rwenzori Mountains within an extensional regime and the mechanisms associated with the high frequency of seismic activity in the region was hardly understood and therefore, had remained a subject of contention that needed to be critically addressed in detail. To my knowledge, this was probably the first study to be performed and documented in great depth within the domains of seismic noise variation, seismic anisotropy and b value analyses beneath the Rwenzori Region. After about six years of operation (2006-2012), the seismology group of the RIFTLINK Research Project (www.riftlink.org) acquired a vast amount of high-quality, digital data that were collected using a seismic network of well calibrated seismic equipment. The project was divided into two phases. Phase I, that operated between February 2006 - September 2007, consisted of thirty-two temporary seismic stations, which were selectively spread out in the Rwenzori Region on the Ugandan side, to detect and record extremely weak as well as strong naturally occurring earthquakes. The seismic equipment used included EDL and REFTEK digitizers, which were coupled with Güralp and MARK sensors respectively (REFTEKS: only short-period MARK sensors, EDLs: short-period MARK plus few broadband Güralp Sensors). Exactly 22375 earthquakes were recorded. The data were processed using the SEISAN software package. About 14413 earthquakes were carefully localized using the velocity model of Bram (1975) that implements a Vp=Vs ratio fixed at 1.74. Phase II, that extended between 2009-2012 consisted of thirty-two seismic stations, which were spread out around the Rwenzori Mountains, both on the Ugandan side and the neighboring D.R.C. Only Taurus digitizers that were coupled with Trillium sensors were used in the D.R.C. On the Ugandan side however, both EDL and Taurus digitizers, which were coupled with Trillium and Güralp sensors were used. ...
In this work the main emphasis is put on the investigation of relativistic shock waves and Mach cones in hot and dense matter using the microscopic transport model BAMPS, based on the relativistic Boltzmann equation. Using this kinetic approach we study the complete transition from ideal-fluid behavior to free streaming. This includes shock-wave formation in a simplified (1+1)-dimensional setup as well as the investigation of Mach-cone formation induced by supersonic projectiles and/or jets in (2+1)- and (3+1)-dimensional static and expanding systems. We further address the question whether jet-medium interactions inducing Mach cones can contribute to a double-peak structure observed in two-particle correlations in heavy-ion collision experiments. Furthermore, BAMPS is used as a benchmark to compare kinetic theory to several relativistic hydrodynamic theories in order to verify their accuracy and to find their limitations.
In this study, the structural and functional properties of the Na+/Betaine symporter BetP were investigated upon K+-induced activation. BetP regulates transport activity dependent on the amount of associated anionic lipids and the cytoplasmic K+-concentration. For this purpose, FTIR spectroscopy was implemented as a non-perturbing biophysical method which shed light on how the membrane lipids contribute to the molecular mechanisms of activation and regulatory response of BetP.