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Mini Unmanned Aerial Vehicles (MUAVs) are becoming popular research platform and
drawing considerable attention, particularly during the last decade due to their afford- ability and multi-dimensional applications in almost every walk of life. MUAVs have obvious advantages over manned platforms including their much lower manufacturing and operational costs, risk avoidance for human pilots, flying safely low and slow, and realization of operations that are beyond inherent human limitations. The advancement in Micro Electro-Mechanical System (MEMS) technology, Avionics and miniaturization of sensors also played a significant role in the evolution of MUAVs. These vehicles range from simple toys found at electronic supermarkets for entertainment purpose to highly sophisticated commercial platforms performing novel assignments like offshore wind power station inspection and 3D modelling of buildings etc. MUAVs are also more environment friendly as they cause less air pollution and noise. Unmanned is therefore unmatched. Recent research focuses on use of multiple inexpensive vehicles flying together, while maintaining required relative separations, to carry out the tasks efficiently compared to a single exorbitant vehicle. Redundancy also does away the risk of loss of a single whole-mission dependent vehicle. Some of the valuable applications in the domain of cooperative control include joint load transportation, search and rescue, mobile communication relays, pesticide spraying and weather monitoring etc. Though realization of multi-UAV coupled flight is complex, however obvious advantages justify
the laborious work involved...
While teleoperation of technical highly sophisticated systems has already been a wide field of research, especially for space and robotics applications, the automation industry has not yet benefited from its results. Besides the established fields of application, also production lines with industrial robots and the surrounding plant components are in need of being remotely accessible. This is especially critical for maintenance or if an unexpected problem cannot be solved by the local specialists.
Special machine manufacturers, especially robotics companies, sell their technology worldwide. Some factories, for example in emerging economies, lack qualified personnel for repair and maintenance tasks. When a severe failure occurs, an expert of the manufacturer needs to fly there, which leads to long down times of the machine or even the whole production line. With the development of data networks, a huge part of those travels can be omitted, if appropriate teleoperation equipment is provided.
This thesis describes the development of a telemaintenance system, which was established in an active production line for research purposes. The customer production site of Braun in Marktheidenfeld, a factory which belongs to Procter & Gamble, consists of a six-axis cartesian industrial robot by KUKA Industries, a two-component injection molding system and an assembly unit. The plant produces plastic parts for electric toothbrushes.
In the research projects "MainTelRob" and "Bayern.digital", during which this plant was utilised, the Zentrum für Telematik e.V. (ZfT) and its project partners develop novel technical approaches and procedures for modern telemaintenance. The term "telemaintenance" hereby refers to the integration of computer science and communication technologies into the maintenance strategy. It is particularly interesting for high-grade capital-intensive goods like industrial robots. Typical telemaintenance tasks are for example the analysis of a robot failure or difficult repair operations. The service department of KUKA Industries is responsible for the worldwide distributed customers who own more than one robot. Currently such tasks are offered via phone support and service staff which travels abroad. They want to expand their service activities on telemaintenance and struggle with the high demands of teleoperation especially regarding security infrastructure. In addition, the facility in Marktheidenfeld has to keep up with the high international standards of Procter & Gamble and wants to minimize machine downtimes. Like 71.6 % of all German companies, P&G sees a huge potential for early information on their production system, but complains about the insufficient quality and the lack of currentness of data.
The main research focus of this work lies on the human machine interface for all human tasks in a telemaintenance setup. This thesis provides own work in the use of a mobile device in context of maintenance, describes new tools on asynchronous remote analysis and puts all parts together in an integrated telemaintenance infrastructure. With the help of Augmented Reality, the user performance and satisfaction could be raised. A special regard is put upon the situation awareness of the remote expert realized by different camera viewpoints. In detail the work consists of:
- Support of maintenance tasks with a mobile device
- Development and evaluation of a context-aware inspection tool
- Comparison of a new touch-based mobile robot programming device to the former teach pendant
- Study on Augmented Reality support for repair tasks with a mobile device
- Condition monitoring for a specific plant with industrial robot
- Human computer interaction for remote analysis of a single plant cycle
- A big data analysis tool for a multitude of cycles and similar plants
- 3D process visualization for a specific plant cycle with additional virtual information
- Network architecture in hardware, software and network infrastructure
- Mobile device computer supported collaborative work for telemaintenance
- Motor exchange telemaintenance example in running production environment
- Augmented reality supported remote plant visualization for better situation awareness
In the first part of his work, the causes for the sudden degradation of useable capacity of lithium-ion cells have been studied by means of complementary methods such as computed tomography, Post-Mortem studies and electrochemical analyses. The results obtained point unanimously to heterogeneous aging as a key-factor for the sudden degradation of cell capacity, which in turn is triggered by differences in local compression.
At high states of health, the capacity fade rate is moderate but some areas of the graphite electrode degrade faster than others. Still, the localized changes are hardly noticeable on cell level due to averaging effects. Lithium plating occurs first in unevenly compressed areas, creating patterns visible to the human eye. As lithium plating leads to rapid consumption of active lithium, a sudden drop in capacity is observed on cell level. Lithium plating appears to spread out from the initial areas over the whole graphite electrode, quickly consuming the remaining useful lithium and active graphite. It can be hypothesized that a self-amplifying circle of reciprocal acceleration of local lithium loss and material loss causes rapid local degradation.
Battery cell designers can improve cycle life by homogeneous pressure distribution in the cell and using negative active materials that are resilient to elevated discharge potentials such as improved carbons or lithium titanate. Also, a sufficiently oversized negative electrode and suitable electrolyte additives can help to avoid lithium plating. When packs are designed, care must be taken not to exert local pressure on parts of cells and to avoid both very high and low states of charge.
In the second part of this dissertation the resilience of cylindrical and pouchbag cells to shocks and different vibrations was investigated. Stresses inflicted by vibration and shock tests according to the widely recognized UN38.3 transport test were compared to a long-time test that exposed cells to a 186 days long ordeal of sine sweep vibrations with a profile based on real-world applications. All cells passed visual and electric inspection performed by TU München after the vibration tests. Only cylindrical cells subjected to long-term vibrations in axial direction showed an increase in impedance and a loss of capacity that could be recuperated in part.
The detailed analyses presented in this thesis gave more details on the damages inflicted by vibrations and shocks and revealed drastic damages in some cases. In cylindrical cells, only movement in axial direction caused damage. Long term vibrations were found to be especially detrimental.
No damage whatsoever could be detected for pouch cells, regardless of the test protocol and the direction of movement. The extreme resilience of pouchbag cells shows that the electrode stack of lithium-ion cells is resistant to vibrations, and that damages are caused by design imperfections that can be improved at low cost.
The findings of this work, and the general state of research show that it is most crucial to control the lithiation and thus potential of the graphite electrode.
In the last part of this work, a new, direct method for charge estimation based on changing transmission is presented. A correlation between transmission of short ultrasonic pulses and state of charge is found. This new technology allows direct measurement of the state of charge. The method is demonstrated for batteries with different positive active materials, showing its versatility. As the observed changes can be traced to the lithiation of graphite, it can be determined without a reference electrode. Already at this early stage of development, the found correlations allow estimation of state of charge. The present hysteresis in the signal height of the slow wave, which is unneglectable especially during discharging at higher currents, will be subject to further investigation.
The observed effects can be explained by effects on different length scales. Biot’s theory explains the second wave’s slowness based on the active material particles size in the range of 0.01 mm and electrolyte-filled pores. Lithiation of graphite changes the porosity of the electrode and thereby the velocity and wavelength of the impulse. When the wavelength approaches the length scale of the layers, 0.1 mm, scattering effects dampen the transmitted signal. Finally, the wavelength of the pulse should be shorter than the transducers diameter to obtain a homogeneous wave front.
To conclude, the new method allows the control of each individual cell in a pack independent from the electrical connections of the cells.
As the method shows great promise, further studies regarding factors such as long-term behavior, temperature and current rates should be conducted. In this thesis hysteresis was observed and a deeper understanding of the reasons behind it may allow further improvements of measurement precision.
This dissertation contributes to deepen our understanding of constructs that play a key role in individuals’ vocational career construction. In this regard, many previous studies have focused exclusively on a specific phase of an individual’s career. Yet, modern societies
require continuous investments in one’s career to adapt to changing Environments throughout the life span. Consequently, this dissertation takes a broad approach to capture a wide spectrum of career construction processes.
According to Super’s (1990) developmental stage framework, individuals have to manage vocational developmental tasks corresponding to each of the developmental life stages in order to be career mature across the life span. As the two stages exploration and
maintenance set the stage for individuals’ future career pathways, they are especially important in individuals’ vocational career construction. Therefore, both of them are addressed in this dissertation.
By answering open research questions relevant to career choice in early career stages and to career development in later career stages, this dissertation contributes to the overarching goal of shedding more light on constructs relevant to individuals’ vocational career construction processes across the life span. Beyond the results presented within each study’s horizon, this dissertation aimed at offering practical guidance to career counselors,
trainees, and training and development (T&D) professionals. Career counselors and T&D professionals are involved in guiding vocational career construction processes of individuals across the life span. Thus, on the one hand, this dissertation supports career counselors’ work so that they can help deliberating individuals make optimal and effective career choices. On
the other hand, this dissertation facilitates T&D professionals’ work so that they can effectively design and evaluate e‐learning and classroom trainings in corporate educational settings. Identifying individuals’ vocational interests combined with cognitive abilities through adequate test measures and maximizing success of learning and success of transfer through fostering evidence‐based transfer support actions will help individuals adapt quickly to the changing nature of work environments in the 21st century and to continue to successfully construct careers across the life span.
Soft x-ray spectroscopic study of methanol and glycine peptides in different physical environments
(2017)
Ion-specific effects occur in a huge variety of aqueous solutions of electrolytes and larger molecules like peptides, altering properties such as viscosity, enzyme activity, protein stability, and salting-in and salting-out behavior of proteins. Typically, these type of effects are rationalized in terms of the Hofmeister series, which originally orders cations and anions according to their ability to enhance or suppress the solubility of proteins in water. This empirical order, however, is still not understood yet. Quite some effort was made to gain a molecular level understanding of this phenomenon, yet no consensus has been found about the underlying mechanisms and the determination and localization of the interaction sites.
Resonant inelastic soft x-ray scattering (RIXS) combines x-ray emission (XES) and absorption spectroscopies (XAS), probing the partial local density of states of both occupied and unoccupied electronic states and is thus a promising candidate to shed more light onto the issue. The studies presented in this work are directed towards an improved understanding of the interaction between salts and peptides. In order to address this topic, the impact of different physical environments on the electronic structure of small molecules (i.e., methanol and glycine derived peptides) is investigated systematically using soft x-ray spectroscopic methods, corroborated with density functional theory (DFT) calculations.
In a first step, molecules without any interactions to the surrounding are investigated, using gas-phase methanol as a model system. Thereby, the local and element specific character of RIXS is demonstrated and used to separately probe the local electronic structure of methanol’s hydroxyl and methyl group, respectively. The attribution of the observed emission features to distinct molecular orbitals is confirmed by DFT calculations, which also quantitatively explain the different relative intensities of the emission features. For resonant excitation of the O K pre-edge absorption resonance, strong isotope effects are found that are explained by dynamical processes at the hydroxyl group. This serves as an excellent example for possible consequences of a local change in the geometric structure or symmetry of a molecule on its electronic structure.
In the following, the sample system is expanded to the amino acid glycine and its smallest derived peptides diglycine and triglycine. As a first step, they are studied in their crystalline form in solid state. Again, a comprehensive picture of the electronic structure is developed by measuring RIXS maps at the oxygen and nitrogen K absorption edge, corroborated by DFT calculations. Similar to the case of methanol, dynamic processes at the protonated amino group of the molecules after exciting the nitrogen atom have a strong influence on the emission spectra. Furthermore, it is shown that RIXS can be used to selectively excite the peptide nitrogen to probe the electronic structure around it. A simple building block approach for XES spectra is applied to separate the contribution of the emission attributed to transitions into core holes at the peptide and the amino nitrogen, respectively.
In the aqueous solution, the surrounding water molecules slightly change the electronic structure, probably via interactions with the charged functional groups. The effects on the x-ray emission spectra, however, are rather small. Much bigger changes are observed when manipulating the protonation state of the functional groups by adjusting the pH value of the solution. A protonation of the carboxyl group at low pH values, as well as a deprotonation of the amino group at high pH values lead to striking changes in the shape of the RIXS maps. In a comprehensive study of glycine’s XES spectra at varying pH values, changes in the local electronic structure are not only observed in the immediate surrounding of the manipulated functional groups but also in more distant moieties of the molecule.
Finally, the study is extended to mixed aqueous solutions of diglycine and a variety of different salts as examples for systems where Hofmeister effects are observed. To investigate the influence of different cations and anions on the electronic structure of diglycine, two series of chlorine and potassium salts are used. Ion-specific effects are identified for both cases. Some of the changes in the x-ray emission spectra of diglycine in the mixed solutions qualitatively follow the Hofmeister series as a function of the used salt. The observed trends thereby indicate an increased interaction between the electron density around the peptide oxygen with the cations, whereas anions seem to interact with the amino group of the peptide.
Neoplasms of the skin represent the most frequent tumors worldwide; fortunately, most of them are benign or semi-malignant and well treatable. However, the two most aggressive and deadly forms of malignant skin-neoplasms are melanoma and Merkel cell carcinoma (MCC), being responsible for more than 90% of skin-cancer related deaths. The last decade has yielded enormous progress in melanoma therapy with the advent of targeted therapies, like BRAF or MEK inhibitors, and immune-stimulating therapies, using checkpoint antibodies targeting CTLA- 4, PD-1 or PD-L1. Very recent studies suggest that also MCC patients benefit from a treatment with checkpoint antibodies. Nevertheless, in an advanced metastatic stage, a cure for both of these aggressive malignancies is still hard to achieve: while only a subset of patients experience durable benefit from the immune-based therapies, the widely applicable targeted therapies struggle with development of resistances that inevitably occur in most patients, and finally lead to their death. The four articles included in this thesis addressed current questions concerning therapy and carcinogenesis of melanoma and MCC. Moreover, they are discussed in the light of the up-to-date research regarding targeted and immune-based therapies. In article I we demonstrated that besides apoptosis, MAPK pathway inhibition in BRAF-mutated melanoma cells also induces senescence, a permanent cell cycle arrest. These cells may provide a source for relapse, as even permanently arrested cancer cells can contribute to a pro-tumorigenic milieu. To identify molecular factors determining the differential response, we established M14 melanoma cell line derived single cell clones that either undergo cell death or arrest when treated with BRAF/MEK inhibitors. Using these single cell clones, we demonstrated in article IV that downregulation of the pro-apoptotic BH3-only protein BIK via epigenetic silencing is involved in apoptosis deficiency, which can be overcome by HDAC inhibitors. These observations provide a possible explanation for the lack of a complete and durable response to MAPK inhibitor treatment in melanoma patients, and suggest the application of HDAC inhibitors as a complimentary therapy to MAPK pathway inhibition. Concerning MCC, we scrutinized the interactions between the Merkel cell polyomavirus’ (MCV) T antigens (TA) and the tumor suppressors p53 and Rb in article II and III, respectively. In article III, we demonstrated that the cell cycle master regulator Rb is the crucial target of MCV large T (LT), while it - in contrast to other polyomavirus LTs - exhibits much lower affinity to the related proteins p107 and p130. Knockdown of MCV LT led to proliferation arrest in MCC cells, which can be rescued by knockdown of Rb, but not by knockdown of p107 and p130. Contrary to Rb, restriction of p53 in MCC seems to be independent of the MCV TAs, as we demonstrated in article II. In conclusion, the presented thesis has revealed new molecular details, regarding the response of melanoma cells towards an important treatment modality and the mechanisms of viral carcinogenesis in MCC.
It was the scope of this work to gain a deeper understanding of the correlation between Interface energetics of molecular semiconductors in planar organic solar cells and the corresponding optoelectronic characteristics. For this aim, different approaches were followed. At first, a direct variation of donor/acceptor (D/A) interface energetics of bilayer cells was achieved by utilizing systematically modified donor compounds. This change could be correlated to the macroscopic device performance. At second, the impact of interface energetics was illustrated, employing a more extended device architecture. By introducing a thin interlayer between a planar D/A heterojunction, an energetic staircase was established. Exciton dissociation in such devices could be linked to the cascade energy level alignment of the photo-active materials. Finally, two different fullerene molecules C60 and C70 were employed in co-evaporated acceptor phases. The expected discrepancy in their electronic structure was related to the transport properties of the corresponding organic photovoltaic cells (OPVCs). The fullerenes are created simultaneously in common synthesis procedures. Next to the photo-physical relevance, the study was carried-out to judge on the necessity of separating the components from each other by purification which constitutes the cost-determining step in the total production costs.
Describing the light-to-energy conversion in OSCs requires a multiscale understanding of the involved optoelectronic processes, i.e., an understanding from the molecular, intermolecular, and aggregate perspective. This thesis presents such a multiscale description to provide insight into the processes in the vicinity of the organic::organic interface, which are crucial for the overall performance of OSCs. Light absorption, exciton diffusion, photoinduced charge transfer at the donor-acceptor interface, and charge separation are included. In order to establish structure-property relationships, a variety of different molecular p-type semiconductors are combined at the organic donor-acceptor heterojunction with fullerene C60, one of the most common acceptors in OSCs. Starting with a comprehensive analysis of the accuracy of diverse ab initio, DFT, and semiempiric methods for the properties of the individual molecules, the intermolecular, and aggregate/device stage are subsequently addressed. At all stages, both methodological concepts and physical aspects in OSCs are discussed to extend the microscopic understanding of the charge generation processes.
Nowadays, more than half of the biotherapeutics are produced in mammalian cell lines as a result of correct protein folding and assembly as well as their faculty to bring about a variety of post-translational modifications. The widespread progression of biosimilars has moved the focus in mammalian cell-culture process development. Thereby, the modulation of quality attributes of recombinant therapeutic proteins has increasingly gained importance from early process development stages. Protein quality directly shapes the clinical efficacy and safety in vivo, and therefore, the control of the complex post-translational modifications, such as glycosylation (e.g. high mannose, fucosylation, galactosylation and sialylation), charge variants, aggregates and low-molecular-weight species formation, is pivotal for efficient receptor binding and for triggering the desired immune responses in patients. In the frame of biosimilar development, product quality modulation methods using the potential of the host cell line are particularly sought after to match the quality profile of the targeted reference medicinal product (RMP) as closely as possible. The environment the cell is dwelling in directly influences its metabolism and the resulting quality profile of the expressed protein. Thereby the cell culture medium plays a central role in upstream manufacturing. In this work, concentration adjustment of selected media components and supplementation with a variety of compounds was performed to alter various metabolic pathways, enzyme activities and in some cases the gene expression levels of Chinese Hamster Ovary (CHO) cells in culture. The supplementation of cell culture medium with the trisaccharide raffinose in fed-batch cultures entailed an increase of the abundance of high mannose glycans in two different CHO cell lines. Raffinose especially favored mannose 5 glycans. At the same time, it impaired cell culture performance, induced changes on the intracellular nucleotide levels and even varied the expression levels of glycosylation-related genes. Supplementation with a number of galactosyltransferase inhibiting compounds, in particular fluorinated galactose analogs (alpha- and beta-2F-peracetyl-galactose), consistently decreased the production of galactosylated monoclonal antibodies (mAb). By means of targeted addition during the culture rather than at the beginning, the inhibition was further increased, while limiting detrimental effects on both growth and productivity. High-throughput screening in 96-deepwell plates showed that spermine and L-ornithine also reduced the level of galactosylation. On the other hand, exploratory screening of a variety of potentially disulfide-bridge-reducing agents highlighted that the inherent low-molecular-species level of the proprietary platform cell culture process was likely due to favored reduction. This hypothesis was reinforced by the observation that supplementation of cysteine and N-acetylcysteine promoted fragmentation. Additionally, fragmentation decreased with higher protein expression.
At that point, aiming to improve the efficiency in process development, a rational experimental design method was developed to identify and to define the optimal concentration range of quality modulating compounds by calling on a combination of high throughput fed-batch testing and multivariate data analysis. Seventeen medium supplements were tested in five parallel 96-deepwell plate experiments. The selection process of promising modulators for the follow-up experiment in shake tubes consisted in a three-step procedure, including principal component analysis, quantitative evaluation of their performance with respect to the specifications for biosimilarity and selection following a hierarchical order of decisions using a decision tree. The method resulted in a substantial improvement of the targeted glycosylation profile in only two experimental rounds. Subsequent development stages, namely validation and transfer to industrial-scale facilities require tight control of product quality. Accordingly, further mechanistic understanding of the underlying processes was acquired by non-targeted metabolomic profiling of a CHO cell line expressing a mAb cultured in four distinct process formats. Univariate analysis of intra- and extracellular metabolite and temporal glycosylation profiles provided insights in various pathways. The numerous of parameters were the main driver to carry out principal component analysis, and then, using the methodology of partial-least-square (PLS) projection on latent structures, a multivariate model was built to correlate the extracellular data with the distinct glycosylation profiles. The PLS observation model proved to be reliable and showed its great benefit for glycan pattern control in routine manufacturing, especially at large scale. Rather than relying on post-production interpretation of glycosylation results, glycosylation can be predicted in real-time based on the extracellular metabolite levels in the bioreactor.
Finally, for the bioactivity assessment of the glycan differences between the biosimilar and the reference medicinal product (RMP), the health agencies may ask for in the drug registration process, extended ranges of glycan variants need to be generated so that the in vitro assays pick up the changes. The developed glycosylation modulator library enabled the generation of extreme glycosylation variants, including high mannose, afucosylated, galactosylated as well as sialic acid species of both a mAb and an antibody fusion molecule with three N-glycosylation sites. Moreover, to create increased variety, enzymatic glycoengineering was explored for galactosylation and sialylation. The glyco variants induced significant responses in the respective in vitro biological activity assays. The data of this work highlight the immense potential of cell culture medium optimization to adjust product quality. Medium and feed supplementation of a variety of compounds resulted in reproducible and important changes of the product quality profile of both mAbs and a fusion antibody. In addition to the intermediate modulation ranges that largely met the requirements for new-biological-entity and biosimilar development, medium supplementation even enabled quick and straightforward generation of extreme glycan variants suitable for biological activity testing.
Content Delivery Networks (CDNs) are networks that distribute content in the Internet. CDNs are increasingly responsible for the largest share of traffic in the Internet. CDNs distribute popular content to caches in many geographical areas to save bandwidth by avoiding unnecessary multihop retransmission. By bringing the content geographically closer to the user, CDNs also reduce the latency of the services.
Besides end users and content providers, which require high availability of high quality content, CDN providers and Internet Service Providers (ISPs) are interested in an efficient operation of CDNs. In order to ensure an efficient replication of the content, CDN providers have a network of (globally) distributed interconnected datacenters at different points of presence (PoPs). ISPs aim to provide reliable and high speed Internet access. They try to keep the load on the network low and to reduce cost for connectivity with other ISPs.
The increasing number of mobile devices such as smart phones and tablets, high definition video content and high resolution displays result in a continuous growth in mobile traffic. This growth in mobile traffic is further accelerated by newly emerging services, such as mobile live streaming and broadcasting services. The steep increase in mobile traffic is expected to reach by 2018 roughly 60% of total network traffic, the majority of which will be video. To handle the growth in mobile networks, the next generation of 5G mobile networks is designed to have higher access rates and an increased densification of the network infrastructure. With the explosion of access rates and number of base stations the backhaul of wireless networks will become congested.
To reduce the load on the backhaul, the research community suggests installing local caches in gateway routers between the wireless network and the Internet, in base stations of different sizes, and in end-user devices. The local deployment of caches allows keeping the traffic within the ISPs network. The caches are organized in a hierarchy, where caches in the lowest tier are requested first. The request is forwarded to the next tier, if the requested object is not found. Appropriate evaluation methods are required to optimally dimension the caches dependent on the traffic characteristics and the available resources. Additionally methods are necessary that allow performance evaluation of backhaul bandwidth aggregation systems, which further reduce the load on the backhaul.
This thesis analyses CDNs utilizing locally available resources and develops the following evaluations and optimization approaches: Characterization of CDNs and distribution of resources in the Internet, analysis and optimization of hierarchical caching systems with bandwidth constraints and performance evaluation of bandwidth aggregation systems.
The focus of the work concerned the development of a series of MRI techniques that were specifically designed and optimized to obtain quantitative and spatially resolved information about characteristic parameters of the lung. Three image acquisition techniques were developed. Each of them allows to quantify a different parameter of relevant diagnostic interest for the lung, as further described below:
1) The blood volume fraction, which represents the amount of lung water in the intravascular compartment expressed as a fraction of the total lung water. This parameter is related to lung perfusion.
2) The magnetization relaxation time T\(_2\) und T*\(_2\)
, which represents the component of T\(_2\) associated with the diffusion of water molecules through the internal magnetic field gradients of the lung. Because the amplitude of these internal gradients is related to the alveolar size, T\(_2\) und T*\(_2\) can be used to obtain information about the microstructure of the lung.
3) The broadening of the NMR spectral line of the lung. This parameter depends on lung inflation and on the concentration of oxygen in the alveoli. For this reason, the spectral line broadening can be regarded as a fingerprint for lung inflation; furthermore, in combination with oxygen enhancement, it provides a measure for lung ventilation.
Marine sponge-associated actinomycetes are considered as promising source for the discovery of novel biologically active compounds. Metabolomics coupled multivariate analysis can efficiently reduce the chemical redundancy of re-isolating known compounds at the very early stage of natural product discovery. This Ph.D. project aimed to isolate biologically active secondary metabolites from actinomycetes associated with different Mediterranean sponges with the assistance of metabolomics tools to implement a rapid dereplication and chemically distinct candidate targeting for further up-scaling compounds isolation.
This study first focused on the recovery of actinomycetes from marine sponges by various cultivation efforts. Twelve different media and two separate pre-treatments of each bacterial extract were designed and applied to facilitate actinomycete diversity and richness. A total of 64 actinomycetes were isolated from 12 different marine sponge species. The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full-length 16S rRNA gene sequencing. Four putatively novel species belonging to the genera Geodermatophilus, Microlunatus, Rhodococcus, and Actinomycetospora were identified based on a sequence similarity <98.5% to validly described 16S rRNA gene sequences. 20% of the isolated actinomycetes was shown to exhibit diverse biological properties, including antioxidant, anti-Bacillus sp., anti-Aspergillus sp., and antitrypanosomal activities.
The metabolomics approaches combined with the bioassay results identified two candidate strains Streptomyces sp. SBT348 and Streptomyces sp. SBT345 for further up-scaling cultivation and compounds isolation. Four compounds were isolated from Streptomyces sp. SBT348. Three of these compounds including the new cyclic dipeptide petrocidin A were previously highlighted in the metabolomics analyses, corroborating the feasibility of metabolomics approaches in novel compounds discovery. These four compounds were also tested against two pathogen microorganisms since the same activities were shown in their crude extract in the preliminary bioassay screening, however none of them displayed the expected activities, which may ascribe to the insufficient amount obtained. Streptomyces sp. SBT345 yielded 5 secondary metabolites, three of which were identified as new natural products, namely strepthonium A, ageloline A and strepoxazine A. Strepthonium A inhibited the production of Shiga toxin produced by enterohemorrhagic Escherichia coli at a concentration of 80 μM, without interfering with the bacterial growth. Ageloline A exhibited antioxidant activity and inhibited the inclusion of Chlamydia trachomatis with an IC50 value of 9.54 ± 0.36 μM. Strepoxazine A displayed antiproliferative property towards human promyelocytic HL-60 cells with an IC50 value of 16 μg/ml.
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These results highlighted marine sponges as a rich source for novel actinomycetes and further exhibited the significance of marine sponge-associated actinomycetes as promising producers of novel biologically active compounds. The chemometrics coupled metabolomics approach also demonstrated its feasibility and efficacy in natural product discovery.
Summary
Platelet activation and aggregation at sites of vascular injury is critical to prevent excessive blood loss, but may also lead to life-threatening ischemic disease states, such as myocardial infarction and stroke. Glycoprotein (GP) VI and C type lectin-like receptor 2 (CLEC-2) are essential platelet activating receptors in hemostasis and thrombo-inflammatory disease which signal through a (hem)immunoreceptor tyrosine-based activation motif (ITAM)-dependent pathway. The adapter molecules Src-like adapter protein (SLAP) and SLAP2 are involved in the regulation of immune cell receptor surface expression and signaling, but their function in platelets is unknown. As revealed in this thesis, single deficiency of SLAP or SLAP2 in mice had only moderate effects on platelet function, while SLAP/SLAP2 double deficiency resulted in markedly increased signal transduction, integrin activation, granule release, aggregation, procoagulant activity and thrombin generation following (hem)ITAM-coupled, but not G protein-coupled receptor activation. Slap-/-/Slap2-/- mice displayed accelerated occlusive arterial thrombus formation and a dramatically worsened outcome after focal cerebral ischemia. These results establish SLAP and SLAP2 as critical inhibitors of platelet (hem)ITAM signaling in the setting of arterial thrombosis and ischemic stroke.
GPVI has emerged as a promising novel pharmacological target for treatment of thrombotic and inflammatory disease states, but the exact mechanisms of its immunodepletion in vivo are incompletely understood. It was hypothesized that SLAP and SLAP2 may be involved in the control of GPVI down-regulation because of their role in the internalization of immune cell receptors. As demonstrated in the second part of the thesis, SLAP and SLAP2 were dispensable for antibody-induced GPVI down-regulation, but anti-GPVI treatment resulted in prolonged strong thrombocytopenia in Slap-/-/Slap2-/- mice. The profound thrombocytopenia likely resulted from the powerful platelet activation which the anti-GPVI antibody induced in Slap-/-/Slap2-/- platelets, but importantly, not in wild-type platelets. These data indicate that the expression and activation state of key modulators of the GPVI signaling cascade may have important implications for the safety profile and efficacy of anti-GPVI agents.
Small GTPases of the Rho family, such as RhoA and Cdc42, are critically involved in the regulation of cytoskeletal rearrangements during platelet activation, but little is known about the specific roles and functional redundancy of both proteins in platelet biogenesis. As shown in the final part of the thesis, combined deficiency of RhoA and Cdc42 led to marked alterations in megakaryocyte morphology and the generation of platelets of heterogeneous size and granule content. Despite severe hemostatic defects and profound thrombo¬cytopenia, circulating RhoA-/-/Cdc42-/- platelets were still capable of granule secretion and the formation of occlusive thrombi. These results implicate the existence of both distinct and overlapping roles of RhoA and Cdc42 in platelet production and function.
Work is seen by many thinkers as the fundamental dimension of man`s existence on earth. Through work, he provides his basic necessities on earth and co-operate with God in the work of creation.
He received this mandate to work from the very beginning of creation by God. In carrying out this mandate, man every human being reflects the very action of the creator of the Universe.
God worked and intended that man who is created in His image and likeness continues the work of creation by working.
Even though Man suffers and sweats through work and yet, in spite of all this toil-perhaps in a sense because of it – work is a good thing for man. It is not only good in the sense that it is useful or something to enjoy; it is also good as being something worthy, that is to say something that corresponds to man's dignity that expresses this dignity and increases it.
This project examines man as a creature called to work and born into work. It is true that through work, man provides himself and his family with the basic necessities of life and everyday needs for the reason he charges wages for his sweat. Work goes beyond and should exceed the boundaries of the material benefit that comes out of it to the satisfaction and fulfilment for the very purpose we should work. The modern society has attached so much importance to money and material possession, the question then is how do we go along working in the spirit of improvement and renewal of the earth? The modern man understands work only as a means of making his daily bread. For this reason, he engages himself in an occupation that he has little or no interest in. He ends up quarrelling everyday with the people that he or she is supposed to serve through work. The result is low work output and waste of talents and the society loses an opportunity for improvement as every creature is supposed to contribute uniquely.
A good example is Nigeria, Africa’s most populous nation with a population estimate of about over 170,000,000 people and the sixth Oil producing Nation.
Endogenous clocks help animals to anticipate the daily environmental changes. These
internal clocks rely on environmental cues, called Zeitgeber, for synchronization. The
molecular clock consists of transcription-translation feedback loops and is located in
about 150 neurons (Helfrich-Förster and Homberg, 1993; Helfrich-Förster, 2005). The
core clock has the proteins Clock (CLK) and Cycle (CYC) that together act as a
transcription activator for period (per) and timeless (tim) which then, via PER and TIM
block their own transcription by inhibiting CLK/CYC activity (Darlington et al., 1998;
Hardin, 2005; Dubruille and Emery, 2008). Light signals trigger the degradation of TIM
through a blue-light sensing protein Cryptochrome (CRY) and thus, allows CLK/CYC to
resume per and tim transcription (Emery et al., 1998; Stanewsky et al., 1998).
Therefore, light acts as an important Zeitgeber for the clock entrainment. The
mammalian clock consists of similarly intertwined feedback loops.
Endogenous clocks facilitate appropriate alterations in a variety of behaviors
according to the time of day. Also, these clocks can provide the phase information to the
memory centers of the brain to form the time of day related associations (TOD). TOD
memories promote appropriate usage of resources and concurrently better the survival
success of an animal. For instance, animals can form time-place associations related to
the availability of a biologically significant stimulus like food or mate. Such memories will
help the animal to obtain resources at different locations at the appropriate time of day.
The significance of these memories is supported by the fact that many organisms
including bees, ants, rats and mice demonstrate time-place learning (Biebach et al.
1991; Mistlberger et al. 1997; Van der Zee et al. 2008; Wenger et al. 1991). Previous
studies have shown that TOD related memories rely on an internal clock, but the identity
of the clock and the underlying mechanism remain less well understood. The present
study demonstrates that flies can also form TOD associated odor memories and further
seeks to identify the appropriate mechanism.
Hungry flies were trained in the morning to associate odor A with the sucrose
reward and subsequently were exposed to odor B without reward. The same flies were
exposed in the afternoon to odor B with and odor A without reward. Two cycles of the
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reversal training on two subsequent days resulted in the significant retrieval of specific
odor memories in the morning and afternoon tests. Therefore, flies were able to
modulate their odor preference according to the time of day. In contrast, flies trained in
a non-reversal manner were unable to form TOD related memories. The study also
demonstrates that flies are only able to form time-odor memories when the two
reciprocal training cycles occur at a minimum 6 h interval.
This work also highlights the role of the internal state of flies in establishing timeodor
memories. Prolonged starvation motivates flies to appropriate their search for the
food. It increases the cost associated with a wrong choice in the T-maze test as it
precludes the food discovery. Accordingly, an extended starvation promotes the TOD
related changes in the odor preference in flies already with a single cycle of reversal
training. Intriguingly, prolonged starvation is required for the time-odor memory
acquisition but is dispensable during the memory retrieval.
Endogenous oscillators promote time-odor associations in flies. Flies in constant
darkness have functional rhythms and can form time-odor memories. In contrast, flies
kept in constant light become arrhythmic and demonstrated no change in their odor
preference through the day. Also, clock mutant flies per01 and clkAR, show compromised
performance compared to CS flies when trained in the time-odor conditioning assay.
These results suggest that flies need a per and clk dependent oscillator for establishing
TOD related memories. Also, the clock governed rhythms are necessary for the timeodor
memory acquisition but not for the retrieval.
Pigment-Dispersing Factor (PDF) neuropeptide is a clock output factor (Park and
Hall, 1998; Park et al., 2000; Helfrich-Förster, 2009). pdf01 mutant flies are unable to
form significant time-odor memories. PDF is released by 8 neurons per hemisphere in
the fly brain. This cluster includes the small (s-LNvs) and large (l-LNvs) ventral lateral
neurons. Restoring PDF in these 16 neurons in the pdf01 mutant background rescues
the time-odor learning defect. The PDF neuropeptide activates a seven transmembrane
G-protein coupled receptor (PDFR) which is broadly expressed in the fly brain (Hyun et
al., 2005). The present study shows that the expression of PDFR in about 10 dorsal
neurons (DN1p) is sufficient for robust time-odor associations in flies.
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In conclusion, flies use distinct endogenous oscillators to acquire and retrieve
time-odor memories. The first oscillator is light dependent and likely signals through the
PDF neuropeptide to promote the usage of the time as an associative cue during
appetitive conditioning. In contrast, the second clock is light independent and
specifically signals the time information for the memory retrieval. The identity of this
clock and the underlying mechanism are open to investigation.
Sex determination (SD) is a complex and diverse developmental process that leads to the decision whether the bipotential gonad anlage will become a testis or an ovary. This mechanism is regulated by gene cascades, networks and/or chromosomal systems, and can be influenced by fluctuations of extrinsic factors like temperature, exposure to hormones and pollution. Within vertebrates, the group of fish show the widest variety of sex determination mechanism. This whole diversity of processes and mechanisms converges to the formation of two different gametes, the eggs and the sperm, the first bigger and static, and the second smaller and motile. Meiosis is crucial for the formation of both types of gametes, and the timing of meiosis entry is one of the first recognizable differences between male and female in vertebrates. The germ cells go into meiosis first in female than in male, and in mammals, this event has been shown to be regulated by retinoic acid (RA). This small polar molecule induces in the germ cells the expression of the pre-meiotic marker Stra8 (stimulated by retinoic acid gene 8), which is necessary for meiosis initiation. Interestingly, genome analyzes have shown that the majority of fish (including medaka) lack the stra8 gene, adding a question mark to the role of RA in meiosis induction in this group. Since a role of RA in entry of meiosis and sexual development of fish is still far from being understood, I investigated in medaka (Oryzias latipes) a possible signaling function of RA during the SD period in embryos and in reproductively active gonads of adults. I generated a transgenic medaka line that reports responsiveness to RA in vivo. With this tool, I compared RA responsiveness with the expression of the main gene involved in the synthesis of RA. My results show that there is a de-correlation between the action of RA with its source. In adults, expression of the RA metabolizing enzymes show sexually dimorphic RA levels, with aldh1a2 levels being higher in testis, and cyp26a1 stronger in female gonad. In ovary, the responsiveness is restricted to the early meiotic oocytes. In testis, RA is acting directly in the pre-meiotic cells, but also in Sertoli and Leydig cells. Treatment experiments on testis organ culture showed that RA pathway activation leads to a decrease in meiosis markers expression levels. During the development, RA responsiveness in the germ cells was observed in both sexes much earlier than the first female meiosis entry. Treatments with RA-synthesis inhibitor show a decrease in meiosis markers expression levels only after the sex differentiation period in female. Expression analyzes of embryos treated with exogenous RA showed induction of dmrt1a at the gonad levels and an increase of amh levels. Both genes are not only involved in male formation, but also in the regulation of germ cell proliferation and differentiation. RA is important in meiosis induction and gametogenesis in adult medaka. However, there is no evidence for a similar role of RA in initiating the first meiosis in female germ cells at the SD stage. Moreover, contrary to common expectation, RA seems to induce sex related genes that are involved indirectly in meiosis inhibition. In this thesis, I showed for the first time that RA can be involved in both induction and inhibition of meiosis entry, depending on the sex and the developmental stage in a stra8-independent model organism.
1. Today honey bee colonies face a wide range of challenges in modern agricultural landscapes which entails the need for a comprehensive investigation of honey bees in a landscape context and the assessment of environmental risks. Within this dissertation the pollen foraging of honey bee colonies is studied in different agricultural landscapes to gain insight into the use of pollen resources and the influence of landscape structure across the season. General suggestions for landscape management to support honey bees and other pollinators are derived.
2. Decoding of waggle dances and a subsequent spatial foraging analysis are used as methods in Chapters 4 and 5 to study honey bee colonies in agricultural landscapes. The recently developed metabarcoding of mixed pollen samples was applied for the first time in honey bee foraging ecology and allowed for a detailed analysis of pollen, that was trapped from honey bees in front hive entrances (Chapter 6).
3. Pollen identification through molecular sequencing and DNA barcoding has been proposed as an alternative approach to light microscopy, which still is a tedious and error-prone task. In this study we assessed mixed pollen probes through next-generation sequencing and developed a bioinformatic workflow to analyse these high-throughput data with a newly created reference database. To evaluate the feasibility, we compared results from classical identification based on light microscopy from the same samples with our sequencing results. Abundance estimations from sequencing data were significantly correlated with counted abundances through light microscopy. Next-generation sequencing thus presents a useful and efficient workflow to identify pollen at the genus and species level without requiring specialized palynological expert knowledge.
4. During maize flowering, four observation hives were placed in and rotated between 11 landscapes covering a gradient in maize acreage. A higher foraging frequency on maize fields compared to other landuse types showed that maize is an intensively used pollen resource for honey bee colonies. Mean foraging distances were significantly shorter for maize pollen than for other pollen origins, indicating that effort is put into collecting a diverse pollen diet. The percentage of maize pollen foragers did not increase with maize acreage in the landscape and was not reduced by grassland area as an alternative pollen resource. Our findings allow estimating the distance-related exposure risk of honey bee colonies to pollen from surrounding maize fields treated with systemic insecticides.
5. It is unknown how an increasing area of mass-flowering crops like oilseed rape (OSR) or a decrease of semi-natural habitats (SNH) change the temporal and spatial availability of pollen resources for honey bee colonies, and thus foraging distances and frequency in different habitat types. Sixteen observation hives were placed in and rotated between 16 agricultural landscapes with independent gradients of OSR and SNH area within 2 km to analyze foraging distances and frequencies. SNH and OSR reduced foraging distance at different spatial scales and depending on season, with possible benefits for the performance of honey bee colonies. Frequency of pollen foragers per habitat type was equally high for SNH, grassland and OSR fields, but lower for other crops and forest. In landscapes with a small proportion of SNH a significantly higher density of pollen foragers on SNH was observed, indicating the limitation of pollen resources in simple agricultural landscapes and the importance of SNH.
6. Quantity and diversity of collected pollen can influence the growth and health of honey bee colonies, but little is known about the influence of landscape structure on pollen diet. In a field experiment we rotated 16 honey bee colonies across 16 agricultural landscapes (see also Chapter 5), used traps to get samples of collected pollen and observed the intra-colonial dance communication to gain information about foraging distances. Neither the amount of collected pollen nor pollen diversity were related to landscape diversity. The revealed increase of foraging distances with decreasing landscape diversity suggests that honey bees compensate for a lower landscape diversity by increasing their pollen foraging range in order to maintain pollen amount and diversity.
7. Our results show the importance of diverse pollen resources for honey bee colonies in agricultural landscapes. Beside the risk of exposure to pesticides honey bees face the risk of nutritional deficiency with implications for their health. By modifying landscape composition and therefore availability of resources we are able to contribute to the wellbeing of honey bees. Agri-environmental schemes aiming to support pollinators should focus on possible spatial and temporal gaps in pollen availability and diversity in agricultural landscapes.
Platelets are small anucleate cell fragments derived from bone marrow megakaryocytes (MKs) and are important players in hemostasis and thrombosis. Platelet granules store factors which are released upon activation. There are three major types of platelet granules: alpha-granules, dense granules and lysosomes. While dense granules contain non-proteinacious factors which support platelet aggregation and adhesion, platelet alpha-granules contain more than 300 different proteins involved in various functions such as inflammation, wound healing and the maintenanceof vascular integrity, however, their functional significance in vivo remains unknown. This thesis summarizes analyses using three mouse models generated to investigate the role of platelet granules in thrombosis, hemostasis, stroke and inflammation.
Unc13d-/- mice displayed defective platelet dense granule secretion, which resulted in abrogated thrombosis and hemostasis. Remarkably, Munc13-4-deficient mice were profoundly protected from infarct progression following transient middle cerebral artery occlusion (tMCAO) and this was not associated with increased intracranial bleeding indicating an essential involvementof dense granule secretion in infarct progression but not intracranial hemostasis during acute stroke with obvious therapeutic implications.
In the second part of this thesis, the role of platelet alpha-granules was investigated using the Nbeal2-/- mouse. Mutations in NBEAL2 have been linked to the gray platelet syndrome (GPS), a rare inherited bleeding disorder. Nbeal2-/- mice displayed the characteristics of human GPS, with defective alpha-granule biogenesis in MKs and their absence from platelets. Nbeal2-deficiency did not affect MK differentiation and proplatelet formation in vitro or platelet life span in vivo. Nbeal2-/- platelets displayed impaired adhesion, aggregation, and coagulant activity ex vivo that translated into defective arterial thrombus formation and protection from thrombo-inflammatory brain infarction in vivo. In a model of skin wound repair, Nbeal2-/- mice exhibited impaired development of functional granulation tissue due to severely reduced differentiation of myofibroblasts.
In the third part, the effects of combined deficiency of alpha- and dense granule secretion were analyzed using Unc13d-/-/Nbeal2-/- mice. Platelets of these mice showed impaired aggregation and adhesion to collagen under flow ex vivo, which translated into infinite tail bleeding times and severely defective arterial thrombus formation in vivo. When subjected to in vivo models of skin or lung inflammation, the double mutant mice showed no signs of hemorrhage. In contrast, lack of platelet granule release resulted in impaired vascular integrity in the ischemic brain following tMCAO leading to increased mortality. This indicates that while defective dense granule secretion or the paucity of alpha-granules alone have no effect on vascular integrity after stroke, the combination of both impairs vascular integrity and causes an increase in mortality.
Within this thesis, synthetic strategies for self-assembled organic cage compounds have been developed that allow for both stimuli-responsive control over assembly/disassembly processes and spatial control over functionalization. To purposefully operate the reversible assembly of organic cages, boron-nitrogen dative bonds have been exploited for the formation of a well-defined, discrete bipyramidal organic assembly in solution. Thermodynamic association equilibria for cage formation have been investigated by Isothermal Titration Calorimetry (ITC). Temperature-dependent NMR studies revealed a reversible cage opening upon heating and quantitative reassembly upon cooling. For the spatial functionalization of organic cages, two divergent molecular building units have been designed and synthesized, namely tribenzotriquinacene derivatives possessing a terminal alkyne moiety at the apical position and a meta-diboronic acid having a pyridyl group at the 2-position. Facile access to a variety of apically functionalized tribenzotriquinacenes has been illustrated by post-synthetic modifications at the terminal alkyne group by Sonogashira cross-coupling and azide-alkyne click reactions. Finally, these apically functionalized tribenzotriquinacene building blocks have been implemented into boronate ester-based organic cage compounds showing modular exohedral functionalities.
Posttranslational modifications (PTMs) play a crucial role in many cellular processes. They are reversible, dynamic, and highly regulated events that alter the properties of proteins and increase their functional diversity. The identification and quantification of PTMs are critical for deciphering the molecular mechanisms of PTMs-related biological processes and disease treatment and prevention. Two of the most common and important PTMs that regulate many protein functions are acetylation and phosphorylation.
An important role of acetylation is the regulation of DNA/RNA-protein interactions. A prominent example for this are histones, whose tail regions are lysine-rich and can be highly acetylated at their N-terminal domain. In spite of the utmost importance of this PTM, methods that allow the accurate measuring the site-specific acetylation degree are missing. One of the challenges in quantifying the acetylation degree at an individual lysine residue of the histones N-termini is the occurrence of multiple lysines in close proximity. Herein, we describe the development of the ”Fragment Ion Patchwork Quantification,” a new mass spectrometry-based approach for the highly accurate quantification of sites-pecific acetylation degrees. This method combines 13C1-acetyl derivatization on the protein level, proteolysis by low-specificity proteases and quantification on the fragment ion level. Acetylation degrees are determined from the isotope patterns of acetylated b and y ions. We have shown that this approach allows determining the site-specific acetylation degrees of all lysine residues for all core histones of Trypanosoma brucei. In addition, we demonstrate the use of this approach to identify the substrate sites of histone acetyltransferases and to monitor the changes in acetylation of the histones of canonical nucleosome and transcription start site nucleosomes.
Phosphorylation is one of the most common and most important PTMs. The analysis of the human genome showed that there are about 518 kinases and more than 500,000 phosphorylation sites are believed to exist in the cellular proteome. Protein phosphorylation plays a crucial role in signaling many different cell processes, such as intercellular communication, cell growth, differentiation of proliferation and apoptosis. Whereas MS-based identification and relative quantification of singly phosphorylated peptides have been greatly improved during the last decade, and large-scale analysis of thousands of phosphopeptides can now be performed on a routine-base, the analysis of multi-phosphorylated peptides is still lagging vastly behind. The low pKa value of phosphate group and the associated negative charge are considered the major source of the problems with the analysis of
multi-phosphorylated peptides. These problems include the formation of phosphopeptide-metal complexes during liquid chromatography (e.g. Fe 3+), which leads to a drastic deterioration of the chromatographic properties of these peptides (peak tailing), the decreased ionization efficiencies of phosphorylated peptides compared to their unphosphorylated counterparts, the labile nature of phosphate during CID/HCD fragmentation, and the unsuitability of low-charged phosphopeptides for ETD fragmentation are the most important factors that hinder phosphorylation analysis by LC-MS/MS. Here we aimed to develop a method for improving the identification of multi-phosphorylated peptides as well as the localization of phosphorylation sites by charge-reversal derivatization of the phosphate groups. This method employs a carbodiimide-mediated phosphoramidation to converted the phosphates to stable aromatic phosphoramidates. This chemical modification of phosphosite(s) reversed the negative charge of the phosphate group(s) and increased the number of the positive charges within the phosphopeptide. This modification prevented the formation of phosphopeptide-metal ion complexes that dramatically decreases or completely diminishes the signal intensity of protonated phosphopeptides, specifically multi-phosphorylated peptides. Furthermore, the increased net charge the (phospho-)peptides made them suitable for ETD fragmentation, which generated a high number of fragment ions with high intensities that led to a better phosphopeptide identification and localization of phosphosite(s) with high confidence.
Starting from conception till death, man as a being relates with others. In this relationship he often encounters lots of problems that threaten his existence. One of them is the threat to his dignity. This experience is vivid in many countries particularly in Africa. But my work is limited to an ethnic group in Nigeria, namely Igbo people. The work discloses the extent 'displacement of value' in Igboland has contributed to the devaluation of human dignity and the attempts made to combat it. This displacement resulted in what we can call "value crisis". Some elements, like Igbo culture and cultural communication with foreign cultures that have tentacles in modernized orientation, are discussed as 'transmission carriers'. In order to x-ray properly the heart of this research and communicate the necessary messages, the work is presented in six chapters. However, this summary will not be presented in chapters.
Thus the need for a research on the reason for the failings and crisis of approach regarding this aspect of Igbo life that deals with the value of human dignity. This comes to term with the question which asked has the interest in the enhancement of the dignity of man waned because the effort towards this goal seem futile and unnecessary…Or is human dignity something we care about but take for granted as a cultural inheritance that no longer needs defence?” This question arouses thoughts on the value of HD. The entire work tried to justify the view that the protection of HD is for all times a true assignment of all. This must neither be considered to be relevant only for a time nor only for a portion or a group of individuals. Thus a special attention on this regard is demanded especially in modern day Igbo society.
Optical antennas work similar to antennas for the radio-frequency regime and convert electromagnetic radiation into oscillating electrical currents. Charge density accumulations form at the antenna surface leading to strong and localized near-fields. Since most optical antennas have dimensions of a few hundred nanometers, their near-fields allow the focusing of electromagnetic fields to volumes much smaller than the diffraction limit, with intensities several orders of magnitude larger than achievable with classical diffractive and refractive optical elements. The task to maximize the emission of a quantum emitter, a point-like entity capable of reception and emission of single photons, is identical to the task to maximize the field intensity at the position of the quantum emitter. Therefore it is desirable to optimize the capabilities of focusing optical antennas.
Radio-frequency-antenna designs scaled to optical dimensions of several hundred nanometers show already a decent performance. However, optical frequencies lie near the plasma frequency of the metals used for optical antennas and the mass of electrons cannot be neglected anymore. This leads to new physical phenomena. Light can couple to charge density oscillations, yielding a so-called Plasmon. Effects emerge which have no equivalent in the very advanced field of radio-frequency-technology, e.g.~volume currents and shortened effective wavelengths. Additionally the conductivity is not infinite anymore, leading to thermal losses. Therefore, the question for the optimal geometry of a focusing optical antenna is not easy to answer. However, up to now there was no evidence that there exist better alternatives for optical antennas than down-scaled radio-frequency designs.
In this work the optimization of focusing optical antennas is based on an approach, which often proved successful for radio-frequency-antennas in complex applications (e.g.~broadband and isotropic reception): evolutionary algorithms. The first implementation introduced here allows a large freedom regarding particle shape and count, as it arranges cubic voxels on a planar, square grid. The geometries are encoded in a binary matrix, which works as a genome and enables the methods of mutation and crossing as mechanism of improvement. Antenna geometries optimized in this way surpass a comparable dipolar geometry by a factor of 2. Moreover, a new working principle can be deduced from the optimized antennas: a magnetic split-ring resonance can be coupled conductively to dipolar antennas, to form novel and more effective split-ring-antennas, as their currents add up constructively near the focal point.
In a next step, the evolutionary algorithm is adapted so that the binary matrices describe geometries with realistic fabrication constraints. In addition a 'printer driver' is developed which converts the binary matrices into commands for focused ion-beam milling in mono-crystalline gold flakes. It is shown by means of confocal two-photon photo-luminescence microscopy that antennas with differing efficiency can be fabricated reliably directly from the evolutionary algorithm. Besides, the concept of the split-ring antenna is further improved by adding this time two split-rings to the dipole-like resonance.
The best geometry from the second evolutionary algorithm inspires a fundamentally new formalism to determine the power transfer between an antenna and a point dipole, best termed 'three-dimensional mode-matching'. Therewith, for the first time intuitive design rules for the geometry of an focusing optical antenna can be deduced. The validity of the theory is proven analytically at the case of a point dipole in from of a metallic nano sphere.
The full problem of focusing light by means of an optical antenna can, thus, be reduced to two simultaneous mode-matching conditions -- on the one hand with the fields of a point dipole, on the other hand with a plane wave. Therefore, two types of ideal focusing optical antenna mode patterns are identified, being fundamentally different from the established dipolar antenna mode. This allows not only to explain the functionality of the evolutionary antennas and the split-ring antenna, but also helps to design novel plamonic cavity antennas, which lead to an enhanced focusing of light. This is proven numerically in direct comparison to a classical dipole antenna design.
Multimodal interfaces (MMIs) are a promising human-computer interaction paradigm.
They are feasible for a wide rang of environments, yet they are especially suited if interactions are spatially and temporally grounded with an environment in which the user is (physically) situated.
Real-time interactive systems (RISs) are technical realizations for situated interaction environments, originating from application areas like virtual reality, mixed reality, human-robot interaction, and computer games.
RISs include various dedicated processing-, simulation-, and rendering subsystems which collectively maintain a real-time simulation of a coherent application state.
They thus fulfil the complex functional requirements of their application areas. Two contradicting principles determine the architecture of RISs: coupling and cohesion.
On the one hand, RIS subsystems commonly use specific data structures for multiple purposes to guarantee performance and rely on close semantic and temporal coupling between each other to maintain consistency.
This coupling is exacerbated if the integration of artificial intelligence (AI) methods is necessary, such as for realizing MMIs.
On the other hand, software qualities like reusability and modifiability call for a decoupling of subsystems and architectural elements with single well-defined purposes, i.e., high cohesion.
Systems predominantly favour performance and consistency over reusability and modifiability to handle this contradiction.
They thus accept low maintainability in general and hindered scientific progress in the long-term.
This thesis presents six semantics-based techniques that extend the established entity-component system (ECS) pattern and pose a solution to this contradiction without sacrificing maintainability: semantic grounding, a semantic entity-component state, grounded actions, semantic queries, code from semantics, and decoupling by semantics.
The extension solves the ECS pattern's runtime type deficit, improves component granularity, facilitates access to entity properties outside a subsystem's component association, incorporates a concept to semantically describe behavior as complement to the state representation, and enables compatibility even between RISs.
The presented reference implementation Simulator X validates the feasibility of the six techniques and may be (re)used by other researchers due to its availability under an open-source licence.
It includes a repertoire of common multimodal input processing steps that showcase the particular adequacy of the six techniques for such processing.
The repertoire adds up to the integrated multimodal processing framework miPro, making Simulator X a RIS platform with explicit MMI support.
The six semantics-based techniques as well as the reference implementation are validated by four expert reviews, multiple proof of concept prototypes, and two explorative studies.
Informal insights gathered throughout the design and development supplement this assessment in the form of lessons learned meant to aid future development in the area.
In daily life, olfactory stimuli are potential generators of affective states, but also have a strong influence on social interaction. Pleasant odors have been shown to increase perceived attractiveness and pro-social behavior, whereas unpleasant body odors are often associated with negative personality traits. Since both pleasant odors and positive affective state facilitate pro-social behavior, it is conceivable that the influence of the odors on social interaction is mediated by the induced affective state elicited by the odor itself. The present thesis aims at exploring the impact of hedonic, i.e., pleasant or unpleasant, odors on the processing and evaluation of social stimuli as assessed by verbal, physiological, and behavioral indices. First, I investigate the effects of initially neutral odors which gained threatening value through an aversive conditioning procedure on social stimuli (Study 1). Second, I study the influence of naturally hedonic odors on social interaction. Third, this thesis aims at disentangling differences in the effects of an odor attributed to either a social interaction partner or the environment where the social encounter takes place (Study 2, 3, and 4).
In the first study, a context conditioning procedure was applied, during which one out of two long-lasting neutral odors was paired with an unpredictable aversive unconditioned stimulus (US, i.e., white noise). This odor (CTX+) thereby gained threatening value, while another odor (CTX-) remained unpaired and therefore signaled safety. During a test session, facial stimuli were presented within both conditioned olfactory contexts. Results indicate that autonomic arousal was increased to faces when presented in the threatening odor context. Additionally, participants rated facial stimuli as more aversive when presented in the threatening odor as compared to the safety odor, indicating that faces acquire hedonic value from the odor they were presented in. Strikingly, angry facial expressions received additional processing resources when presented within a threatening olfactory context, as reflected on verbal reports and electrodermal activity (EDA). This latter finding suggests that threat-related stimuli, here angry faces, are preferentially processed within an olfactory context where a threat might happen.
Considering that the hedonic value of an odor may be quite subjective, I conducted a pilot study in order to identify odors with pleasant vs. unpleasant properties for most participants. Seven odors (four pleasant and three unpleasant) were rated with respect to their valence (pleasant vs. unpleasant), arousal (arousing vs. calm), and intensity. Additionally, EDA was measured. Two pleasant (Citral and Eucalyptol) and two unpleasant (“Animalis” and Isobutyraldehyde) odors were chosen from the original seven. The unpleasant odors were rated as more negative, arousing, and intense than the positive ones, but no differences were found regarding EDA.
These four odors were subsequently used in a virtual reality (VR) paradigm with two odor attribution groups. Participants of the social attribution group (n = 59) were always passively guided into the same room (an office) towards one out of two virtual agents who were either paired with the pleasant or the unpleasant odor. Participants of the contextual attribution group (n = 58) were guided into one out of two rooms which were either paired with the pleasant or the unpleasant odor and where they always met the same agent. For both groups, the agents smiled, frowned or remained with a neutral facial expression. This design allowed evaluating the influence of odor valence as a within-subjects factor and the influence of odor attribution as a between-subjects factor. Unpleasant odors facilitated the processing of social cues as reflected by increased verbal and physiological arousal as well as reduced active approach behavior. Specific influence of odor valence on emotional facial expressions was found for ratings, EDA, and facial mimicry, with the unpleasant odor causing a levelling effect on the differences between facial expressions. The social attribution group exhibited larger differences between odors than the contextual group with respect to some variables (i.e., ratings and EDA), but not to others (i.e., electrocortical potentials – ERPs – and approach behavior). In sum, unpleasant in comparison to pleasant odors diminished emotional responses during social interaction, while an additional enhancing effect of the social attribution was observed on some variables. Interestingly, the awareness that an interaction partner would smell (pleasantly or unpleasantly) boosted the emotional reactivity towards them.
In Study 3, I adapted the VR paradigm to a within-subjects design, meaning that the different attribution conditions were now manipulated block-wise. Instead of an approach task, participants had to move away from the virtual agent (withdrawal task). Results on the ratings were replicated from Study 2. Specifically, the difference between pleasant and unpleasant odors on valence, arousal, and sympathy ratings was larger in the social as compared to the contextual attribution condition. No effects of odor or attribution were found on EDA, whereas heart rate (HR) showed a stronger acceleration to pleasant odors while participants were passively guided towards the agent. Instead of an approach task, I focused on withdrawal behavior in this study. Interestingly, independently of the attribution condition, participants spent more time withdrawing from virtual agents, when an unpleasant odor was presented. In sum, I demonstrated that the attribution of the odors to the social agent itself had an enhancing effect on their influence on social interaction.
In the fourth and last study, I applied a similar within-subjects protocol as in Study 3 with an additional Ultimatum Game task as a measure of social interaction. Overall findings replicated the results of Study 3 with respect to HR and EDA. Strikingly, participants offered less money to virtual agents in the bad smelling room than in the good smelling room. In contrast to Study 3, no effects of odor attribution were found in Study 4. In sum, again I demonstrated that unpleasant odor may lessen social interaction not only when the interaction partner smells badly, but also in more complex interaction situations.
In conclusion, I demonstrated that hedonic odors in general influence social interaction. Thus, pleasant odors seem to facilitate, while unpleasant odors seem to reduce interpersonal exchanges. Therefore, the present thesis extends the body of literature on the influence of odors on the processing of social stimuli. Although I found a direct influence of odors on social preferences as well as on the physiological and behavioral responses to social stimuli, I did not disentangle impact of odor per se from the impact of the affective state. Interestingly, odor attribution might play an additional role as mediator of social interactions such as odor effects in social interactions might be boosted when the smell is attributed to an individual. However, the results in this regard were less straightforward, and therefore further investigations are needed. Future research should also take into account gender or other inter-individual differences like social anxiety.
Effects of timing and herbivory on a grass-endophyte association and its trophic interactions
(2017)
I.) Plant associated microorganisms can affect the plant`s interaction with herbivores and higher trophic levels. For instance, endophytic fungi infecting aerial plant parts of grass species produce bioactive alkaloids that can negatively affect species from higher trophic levels, indicating a defensive mutualism between the grass and the endophyte. However, beneficial insects can also be negatively affected by the endophyte, which might question the mutualistic effect of endophytic fungi. On the other hand, grass-endophytes are affected by environmental conditions and species interactions. Grazing can increase endophyte frequencies in natural habitats. Furthermore, endophyte mediated effects on herbivores are most pronounced during warm summers following rainy springs. In this study, we investigated whether endophyte derived alkaloids cascade up a food chain (chapter II) and whether their concentrations depend on plant age and season (chapter III). Further we analysed, whether altered herbivore phenology affects the endophytic fungus (chapter IV) and whether endophyte derived alkaloid production is induced by different herbivore species (chapter V).
II.) In our first experimental study we analysed whether grass-endophyte derived alkaloids decreased the performance of two ladybird species feeding on aphids exclusively reared on endophyte infected grass (6 weeks young grass). Further, we screened species from three trophic levels (grass, herbivores and aphid predators) for their alkaloid content using two year old infected grass as diet for herbivores. We established an UPLC-MS method to detect and quantify the amount of the endophyte derived alkaloids peramine and lolitrem B extracted from the organic plant and insect material. Performance parameters of ladybirds revealed little differences between ladybirds fed on aphids reared on endophyte infected and non-infected grass, which probably resulted from low alkaloid concentrations in the young (6-weeks old) endophyte infected grass used in this part of the study. Alkaloid quantification of the two year old endophyte infected grass, herbivores and aphid predators revealed similar concentrations between grass and aphids, while aphid predators contained approximately half of that amount which still exceeded the bioactive threshold. We conclude that alkaloids produced by grass-endophytes cascade up the food chain and are responsible for fitness disadvantages of higher trophic levels.
III.) In the second study we investigated the impact of plant age and seasonal timing on grass-endophyte growth and alkaloid production. Plants were sown in April of 2013 and sampled monthly over 30 consecutive months. Endophyte growth was quantified with real-time PCR (qPCR) and alkaloid concentrations with UPLC-MS. We showed that alkaloid concentrations and fungal growth followed a seasonal rhythmicity and that alkaloid concentrations increased with plant age. Alkaloid concentrations peak during summer, when also herbivore abundances are high. Consequently, we conclude that plant age and season contribute to the toxicity of endophytes on grass herbivores
IV.) In the third study we simulated earlier spring arrival of aphids by enhancing aphid abundance on endophyte infected and endophyte-free grass in spring and analysed responses across three trophic levels. Enhanced aphid abundance in spring caused higher aphid abundances during the study period. Predators stayed unaffected by increased herbivore abundances; however they did level aphid numbers within two weeks after arrival on the plants, independent of aphid abundance. Grass-endophyte showed a time delayed growth, two weeks after aphid abundance peak and after predators already controlled aphid infestations on the plants. We conclude that phenology shifts of herbivorous insects can affect multi-trophic interactions leading to desynchronizations between phenologies of interacting species and mismatches in food-webs.
V.) In the fourth study we analysed whether herbivores induce endophyte growth and alkaloid production and whether different types of herbivores induce specific alkaloid production. We applied three different herbivore treatments on endophyte infected grass over 18 weeks. Locust herbivory increased the insect deterring alkaloid peramine and clipping of plants (simulation of grazing livestock) increased the vertebrate toxic alkaloid lolitrem B. Aphid herbivory did not affect endophyte derived alkaloid concentrations. Endophyte responses to herbivory were species specific which indicates a primarily plant protecting role of alkaloid synthesis in endophyte infected plants and a close chemical crosstalk between interacting species.
VI.) In summary, we showed that endophyte derived alkaloids affect higher trophic levels and that alkaloid concentrations in the plant depend on prevalent herbivore species, plant age and seasonal timing. Our results indicate a close chemical crosstalk between the host plant and the endophytic fungus which is susceptible to environmental changes altering the endophyte`s alkaloid production in plants. We gained insights into the grass-endophyte symbiosis in ecological contexts and conclude that several factors determine the herbivore toxic potential of endophytic fungi and thereby their plant mutualistic or parasitic character. Future studies should investigate the mechanisms behind the herbivore induced alkaloid concentration increase, shown in this thesis, especially whether plant signals mediate the endophyte response. Furthermore it would be interesting to study the induction of indirect endophyte mediated defence and how it affects multi-trophic level interactions.
An explicit Runge-Kutta discontinuous Galerkin (RKDG) method is used to device numerical schemes for both the compressible Euler equations of gas dynamics and the ideal magneto- hydrodynamical (MHD) model. These systems of conservation laws are known to have discontinuous solutions. Discontinuities are the source of spurious oscillations in the solution profile of the numerical approximation, when a high order accurate numerical method is used. Different techniques are reviewed in order to control spurious oscillations. A shock detection technique is shown to be useful in order to determine the regions where the spurious oscillations appear such that a Limiter can be used to eliminate these numeric artifacts. To guarantee the positivity of specific variables like the density and the pressure, a positivity preserving limiter is used. Furthermore, a numerical flux, proven to preserve the entropy stability of the semi-discrete DG scheme for the MHD system is used. Finally, the numerical schemes are implemented using the deal.II C++ libraries in the dflo code. The solution of common test cases show the capability of the method.
Optogenetics is a method to control the cell activity with light by expression of a natural or engineered photoreceptor via genetic modification technology. Optogenetics early success came with the light-gated cation channel "Channelrhodopsin-2" in neurons and expanded from neuroscience to other research fields such as cardiac research and cell signaling, also due to the enrichment by new photoreceptors. In this study, I focus on searching and characterizing new photoreceptors to expand the optogenetic tool box. In this work I characterize three newly discovered microbial rhodopsins and some engineered mutants of them.
The first rhodopsin is a proton pump from the diatom Fragilariopsis cylindrus, Fragilariopsis Rhodopsin or abbreviated: FR. I cloned the full-length FR and proved it to be a light-activated proton pump with high efficacy in comparison to Bacteriorhodopsin (BR). During this study, I also developed a new method to improve the plasma membrane targeting of several microbial rhodopsins. I also obtained a FR mutant (channel-like FR or chFR) which behaves like a light-gated proton channel. FR can be used for optogenetic hyperpolarization or alkalization of a cell while the chFR could be used for depolarization or lowering of the cellular pH. The induction of FR expression under iron-limited conditions in the diatom indicated an alternative energy generation mechanism of F. cylindrus when iron-containing enzymes are scarce.
I then characterized a new microbial rhodopsin with novel light-regulated Guanylyl Cyclase (GC) activity. This rhodopsin guanylyl cyclase from the fungus Blastocladiella emersonii (B.e. CyclaseOpsin or BeCyclOp) has been proven by me to be an efficient light-gated GC with high specificity and fast kinetics. BeCyclOp also has a novel structure with eight transmembrane helices, containing a long cytosolic N-terminus which participates in the tight regulation of the GC activity. In collaboration with Prof. Alexander Gottschalk (Univ. Frankfurt/M.), BeCyclOp has been tested in muscle cells and sensory neurons of Caenorhabditis elegans and proven to be a powerful optogenetic tool in a living animal. I also generated a BeCyclOp mutant with enhanced light sensitivity.
Already more than ten years ago, guanylyl cyclase rhodopsins were suggested to exist in Chlamydomonas reinhardtii by analyzing genomic sequence data. But until now no functional proof existed. By further cloning and sequencing I discovered such a rhodopsin with light-regulated guanylyl cyclase activity. This functional Cyclaseopsin (COP6c) is quite different to BeCyclOp, as it was proven to be a light-inhibited GC. Cop6c is much larger than BeCyclOp with a His-Kinase and a response regulator domain between the rhodopsin and the cyclase domain.
I also introduced a new strategy for generating optogenetic tools by fusing the photoactivated adenylyl cyclase bPAC to two different CNG channels. These new tools function via light-gated cAMP production and subsequent CNG channel activation. These tools combined the properties of bPAC (highly sensitive to blue light) and CNG channels (high single-channel conductance and high Ca2+ permeability), as demonstrated by expression in Xenopus oocytes. As a further benefit the fusing of bPAC to CNG channels leads to a bPAC with a more than tenfold reduced dark activity which is a valuable improvement for bPAC itself as an optogenetic tool.
Recent advances in the field of cancer immunotherapy have enabled this therapeutic approach to enter the mainstream of modern cancer treatment. In particular, adoptive T cell therapy (ACT) is a potentially powerful immunotherapy approach that relies on the administration of tumor-specific T cells into the patient. There are several strategies to obtain tumor-reactive cytotoxic T lymphocytes (CTLs), which have already been shown to induce remarkable responses in the clinical setting. However, there are concerns and limitations regarding the conventional approaches to obtain tumor-reactive T cells, such as accuracy of the procedure and reproducibility. Therefore, we aimed to develop two approaches to improve the precision and efficacy of tumor-reactive T cells therapy. These two techniques could constitute effective, safe and broadly applicable alternatives to the conventional methods for obtaining tumor-specific CTLs.
The first approach of this study is the so called “Doublet Technology”. Here, we demonstrate that peptide-human leukocyte antigen-T cell receptor (pHLA-TCR) interactions that involve immune reactive peptides are stable and strong. Therefore, the CTLs that are bound by their TCR to tumor cells can be selected and isolated through FACS-based cell sorting taking advantage of this stable interaction between the CTLs and the target cells. The CTLs from acute myeloid leukemia (AML) patients obtained with this technique show cytolytic activity against blast cells suggesting a potential clinical use of these CTLs. “Doublet Technology” offers a personalized therapy in which there is no need for a priori knowledge of the exact tumor antigen.
The second approach of this study is the Chimeric Antigen Receptor (CAR) Technology. We design several CARs targeting the B-Cell Maturation Antigen (BCMA). BCMA CAR T cells show antigen-specific cytolytic activity, production of cytokines including IFN-γ and IL-2, as well as productive proliferation. Although we confirm the presence of soluble BCMA in serum of multiple myeloma (MM) patients, we demonstrate that the presence of soluble protein does not abrogate the efficacy of BCMA CAR T cells suggesting that BCMA CAR T cells can be used in the clinical setting to treat MM patients. The high antigen specificity of CAR T cells allows efficient tumor cell eradication and makes CAR Technology attractive for broadly applicable therapies.
The topic of this thesis is the theoretical and numerical analysis of optimal control problems, whose differential constraints are given by Fokker-Planck models related to jump-diffusion processes. We tackle the issue of controlling a stochastic process by formulating a deterministic optimization problem. The
key idea of our approach is to focus on the probability density function of the process,
whose time evolution is modeled by the Fokker-Planck equation. Our control framework is advantageous since it allows to model the action of the control over the entire range of the process, whose statistics are characterized by the shape of its probability density function.
We first investigate jump-diffusion processes, illustrating their main properties. We define stochastic initial-value problems and present results on the existence and uniqueness of their solutions. We then discuss how numerical solutions of stochastic problems are computed, focusing on the Euler-Maruyama method.
We put our attention to jump-diffusion models with time- and space-dependent coefficients and jumps given by a compound Poisson process. We derive the related Fokker-Planck equations, which take the form of partial integro-differential equations. Their differential term is governed by a parabolic operator, while the nonlocal integral operator is due to the presence of the jumps. The derivation is carried out in two cases. On the one hand, we consider a process with unbounded range. On the other hand, we confine the dynamic of the sample paths to a bounded domain, and thus the behavior of the process in proximity of the boundaries has to be specified. Throughout this thesis, we set the barriers of the domain to be reflecting.
The Fokker-Planck equation, endowed with initial and boundary conditions, gives rise to Fokker-Planck problems. Their solvability is discussed in suitable functional spaces. The properties of their solutions are examined, namely their regularity, positivity and probability mass conservation. Since closed-form solutions to Fokker-Planck problems are usually not available, one has to resort to numerical methods.
The first main achievement of this thesis is the definition and analysis of conservative and positive-preserving numerical methods for Fokker-Planck problems. Our SIMEX1 and SIMEX2 (Splitting-Implicit-Explicit) schemes are defined within the framework given by the method of lines. The differential operator is discretized by a finite volume scheme given by the Chang-Cooper method, while the integral operator is approximated by a mid-point rule. This leads to a large system of ordinary differential equations, that we approximate with the Strang-Marchuk splitting method. This technique decomposes the original problem in a
sequence of different subproblems with simpler structure, which are separately solved and linked to each other through initial conditions and final solutions. After performing the splitting step, we carry out the time integration with first- and second-order time-differencing methods. These steps give rise to the SIMEX1 and SIMEX2 methods, respectively.
A full convergence and stability analysis of our schemes is included. Moreover, we are able to prove that the positivity and the mass conservation of the solution to Fokker-Planck problems are satisfied at the discrete level by the numerical solutions computed with the SIMEX schemes.
The second main achievement of this thesis is the theoretical analysis and the numerical solution of optimal control problems governed by Fokker-Planck models. The field of optimal control deals with finding control functions in such a way that given cost functionals are minimized. Our framework aims at the minimization of the difference between a known sequence of values and the first moment of a jump-diffusion process; therefore, this formulation can also be considered as a parameter estimation problem for stochastic processes. Two cases are discussed, in which the form of the cost functional is continuous-in-time and discrete-in-time, respectively.
The control variable enters the state equation as a coefficient of the Fokker-Planck partial integro-differential operator. We also include in the cost functional a $L^1$-penalization term, which enhances the sparsity of the solution. Therefore, the resulting optimization problem is nonconvex and nonsmooth. We derive the first-order optimality systems satisfied by the optimal solution. The computation of the optimal solution is carried out by means of proximal iterative schemes in an infinite-dimensional framework.
This thesis contributes to several issues in the context of SDN and NFV, with an emphasis on performance and management.
The main contributions are guide lines for operators migrating to software-based networks, as well as an analytical model for the packet processing in a Linux system using the Kernel NAPI.
Latrophilin, alternatively named calcium-independent receptor of α-latrotoxin (CIRL), resembles a prototype of the adhesion class G-protein coupled receptors (GPCRs). Initially identified as a high-affinity receptor for α-latrotoxin, a component of the black widow spider, latrophilins are now associated with various distinct functions, such as synaptic exocytosis, tissue polarity and fertility (Tobaben et al., 2002; Langenhan et al., 2009; Promel et al., 2012). Despite these exploratory efforts the precise subcellular localisation as well as the endogenous ligand of CIRL still remains elusive. In this work genetic experiments, imaging approaches and behavioural studies have been used to unravel the localisation and physiological function of the latrophilin homolog dCirl in Drosophila melanogaster. Containing only one latrophilin homolog together with its genetic accessibility and well-established transgenic approaches, Drosophila seemed an ideally suited model organism. The present study showed that dCirl is widely expressed in the larval central nervous system including moto- and sensory neurons. Further, this work revealed that removal of the latrophilin homolog does not greatly affect synaptic transmission but it seems that aspects of the postsynaptic structural layout are controlled by dCIRL in the fruit fly. Additionally, dCirl expression at the transcriptional level was confirmed in larval and adult chordotonal organs, specialised mechanosensors implicated in proprioception (Eberl, 1999). Expression of dCIRL at the protein level could not yet been confirmed in moto- and sensory neurons likely due to low endogenous expression. However, behavioural studies using dCirl knockout mutant larvae indicated a putative mechanosensory function of dCIRL regarding touch sensitivity and locomotion behaviour.
The second part of this thesis presents a strategy to examine interactions between several presynaptic proteins in living cells. The attempt described in this work is based on the discovery that GFP when split into two non-fluorescent fragments can form a fluorescent complex. The association of the fragments can be facilitated by fusing them to two proteins that interact with each other. Therefore, the split GFP method enables direct visualization of synaptic protein interactions in living cells. In initial experiments I could show that full length reporter protein fusions with n-Synaptobrevin (n-Syb), Synaptotagmin (Syt) and Syntaxin (Syx) allow expression in Drosophila and confirmed that fusion to either end of each synaptic protein did not impair expression or influence the viability of transgenic flies. Further, transgenes containing protein fusions of Syx, Syt, and n-Syb with split GFP fragments were established in previous studies (Gehring, 2010). The present work characterises the interaction of these protein fusions during different stages of synaptic vesicle turnover at active zones such as synaptic vesicle docking at the presynaptic membrane and vesicle fusion. These results suggest that the spGFP assay seems only partly suitable for resolving fast and transient protein-protein interactions at larval Drosophila active zones in vivo.
The prediction and the experimental discovery of topological insulators has set the stage for a novel type of electronic devices. In contrast to conventional metals or semiconductors, this new class of materials exhibits peculiar transport properties at the sample surface, as conduction channels emerge at the topological boundaries of the system.
In specific materials with strong spin-orbit coupling, a particular form of a two-dimensional topological insulator, the quantum spin Hall state, can be observed.
Here, the respective one-dimensional edge channels are helical in nature, meaning that there is a locking of the spin orientation of an electron and its direction of motion.
Due to the symmetry of time-reversal, elastic backscattering off interspersed impurities is suppressed in such a helical system, and transport is approximately ballistic.
This allows in principle for the realization of novel energy-efficient devices, ``spintronic`` applications, or the formation of exotic bound states with non-Abelian statistics, which could be used for quantum computing.
The present work is concerned with the general transport properties of one-dimensional helical states. Beyond the topological protection mentioned above, inelastic backscattering can arise from various microscopic sources, of which the most prominent ones will be discussed in this Thesis. As it is characteristic for one-dimensional systems, the role of electron-electron interactions can be of major importance in this context.
First, we review well-established techniques of many-body physics in one dimension such as perturbative renormalization group analysis, (Abelian) bosonization, and Luttinger liquid theory. The latter allow us to treat electron interactions in an exact way.
Those methods then are employed to derive the corrections to the conductance in a helical transport channel, that arise from various types of perturbations.
Particularly, we focus on the interplay of Rashba spin-orbit coupling and electron interactions as a source of inelastic single-particle and two-particle backscattering. It is demonstrated, that microscopic details of the system, such as the existence of a momentum cutoff, that restricts the energy spectrum, or the presence of non-interacting leads attached to the system, can fundamentally alter the transport signature.
By comparison of the predicted corrections to the conductance to a transport experiment, one can gain insight about the microscopic processes and the structure of a quantum spin Hall sample.
Another important mechanism we analyze is backscattering induced by magnetic moments. Those findings provide an alternative interpretation of recent transport measurements in InAs/GaSb quantum wells.
The Minimal Self
(2017)
The aim of The Minimal Self is to undertake a conceptual analysis of the term ‘self’ and thereby establish the minimal conditions that must be met to ascribe selfhood to an entity. This conceptual analysis focuses on what is termed ‘intrinsic reflexivity’, which is taken as the defining feature of selfhood. Three underlying categories of intrinsic reflexivity are distinguished: self-maintenance, self-reproduction and self-containment. These three fundamental categories provide a framework within which it is possible to distinguish entities that can be designated ‘selves’ from entities that are merely ‘self-like’, thus establishing the logical preconditions for the ‘emergence’ of selfhood. By examining the fuzzy borderlines between selves and the merely self-like as manifest in phenomena such as dissipative systems, genetic material, viruses and bacteria, it becomes possible to ascertain a form of ‘minimal selfhood’, a mode of being shared by all selves qua selves. Free-living single-celled organisms such as protozoa are paradigmatic instances of minimal selfhood to the extent that they can be characterized in terms of the three intrinsically reflexive processes of self-maintenance, self-reproduction and self-containment. Minimal selfhood is also presupposed by more complex multicellular selves such as animals. Such an analysis is found to shed light on the origin of life and on the nature of organisms and biological individuals.
The genetic information encoded with in the genes are transcribed and translated to give rise to
the functional proteins, which are building block of a cell. At first, it was thought that the
regulation of gene expression particularly occurs at the level of transcription by various
transcription factors. Recent discoveries have shown the vital role of gene regulation at the level
of RNA also known as post-transcriptional gene regulation (PTGR). Apart from non-coding RNAs
e.g. micro RNAs, various RNA binding proteins (RBPs) play essential role in PTGR. RBPs have
been implicated in different stages of mRNA life cycle ranging from splicing, processing,
transport, localization and decay. In last 20 years studies have shown the presence of hundreds
of RBPs across eukaryotic systems many of which are widely conserved. Given the rising number
of RBPs and their link to human diseases it is quite evident that RBPs have major role in cellular
processes and their regulation. The current study is aimed to describe the so far unknown
molecular mechanism of CCHC-type Zinc Finger Nucleic Acid Binding Protein (CNBP/ZNF9)
function in vivo.
CNBP is ubiquitously expressed across various human tissues and is a highly conserved RBP in
eukaryotes. It is required for embryonic development in mammals and has been implicated in
transcriptional as well as post-transcriptional gene regulation; however, its molecular function
and direct target genes remain elusive. Here, we use multiple systems-wide approaches to
identify CNBP targets and document the consequences of CNBP binding. We established CNBP as
a cytoplasmic RNA-binding-protein and used Photoactivatable Ribonucleoside Enhanced
Crosslinking and Immunoprecipitation (PAR-CLIP) to identify direct interactions of CNBP with
4178 mRNAs. CNBP preferentially bound a G-rich motif in the target mRNA coding sequences.
Functional analyses, including ribosome profiling, RNA sequencing, and luciferase assays
revealed the CNBP mode of action on target transcripts. CNBP binding was found to increase the
translational efficiency of its target genes. We hypothesize that this is consistent with an RNA
chaperone function of CNBP helping to resolve secondary structures, thus promoting
translation. Altogether this study provides a novel mechanism of CNBP function in vivo and acts
as a step-stone to study the individual CNBP targets that will bring us closer to understand the
disease onset.
Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea, has the potential to spread in the human host and cause a severe complication called disseminated gonococcal infection (DGI). The expression of the major outer membrane porin PorBIA is a characteristic of most gonococci associated with DGI. PorBIA binds to the scavenger receptor expressed on endothelial cells (SREC-I), which mediates the so-called low phosphate-dependent invasion (LPDI). This uptake mechanism enables N. gonorrhoeae to rapidly invade epithelial and endothelial cells in a phosphate-sensitive manner.
We recently demonstrated that the neutral sphingomyelinase, which catalyses the hydrolysis of sphingomyelin to ceramide and phosphorylcholine, is required for the LPDI of gonococci in non-phagocytic cells. Neutral sphingomyelinase 2 (NSM2) plays a key role in the early PorBIA signaling by recruiting the PI3 kinase to caveolin. The following activation of the PI3 kinase-dependent downstream signaling leads to the engulfment of the bacteria. As a part of this work, I could confirm the involvement of the NSM2. The role of the enzyme was further elucidated by the generation of antibodies directed against NSM2 and the construction of an epithelium-based NSM2 knockout cell line using CRISPR/Cas9. The knockout of the NSM2 strongly inhibits the LPDI. The invasion could be, however, restored by the complementation of the knockout using an NSM2-GFP construct. However, the results could not be reproduced.
In this work, I could show the involvement of further members of the sphingolipid pathway in the PorBIA-mediated invasion. Lipidome analysis revealed an increase of the bioactive molecules ceramide and sphingosine due to gonococcal infection. Both molecules do not only affect the host cell, but seem to influence the bacteria as well: while ceramide seems to be incorporated by the gonococci, sphingosine is toxic for the bacteria. Furthermore, the sphingosine kinase 2 (SPHK2) plays an important role in invasion, since the inhibition and knockdown of the enzyme revealed a negative effect on gonococcal invasion. To elucidate the role of the sphingosine kinases in invasion in more detail, an activity assay was established in this study. Additionally, the impact of the sphingosine-1-phosphate lyase (S1PL) on invasion was investigated. Inhibitor studies and infection experiments conducted with a CRISPR/Cas9 HeLa S1PL knockout cell line revealed a role of the enzyme not only in the PorBIA-mediated invasion, but also in the Opa50/HSPG-mediated gonococcal invasion. The signaling experiments allowed the categorization of the SPHK and S1PL activation in the context of infection. Like the NSM2, both enzymes play a role in the early PorBIA signaling events leading to the uptake of the bacteria. All those findings indicate an important role of sphingolipids in the invasion and survival of N. gonorrhoeae.
In the last part of this work, the role of the NSM2 in the inhibition of apoptosis in neutrophils due to gonococcal infection was investigated. It could be demonstrated that the delayed onset of apoptosis is independent of neisserial porin and Opa proteins. Furthermore, the influence of neisserial peptidoglycan on PMN apoptosis was analysed using mutant strains, but no connection could be determined. Since the NSM2 is the most prominent sphingomyelinase in PMNs, fulfils manifold cell physiological functions and has already been connected to apoptosis, the impact of the enzyme on apoptosis inhibition due to gonococcal infection was investigated using inhibitors, with no positive results.
In contrast to normal vessels, tumor vasculature is structurally and functionally abnormal. Tumor vessels are highly disorganized, tortuous and dilated, with uneven diameter and excessive branching. Consequently, tumor blood flow is chaotic, which leads to hypoxic and acidic regions in tumors. These conditions lower the therapeutic effectiveness and select for cancer cells that are more malignant and metastatic. The therapeutic outcome could be improved by increasing the functionality and density of the tumor vasculature. Tumor angiogenesis also shows parallels to epithelial to mesenchymal transition (EMT), a process enabling metastasis. Metastasis is a multi-step process, during which tumor cells have to invade the surrounding host tissue to reach the circulation and to be transported to distant sites.
We hypothesize that the variability in the phenotype of the tumor vasculature is controlled by the differential expression of key transcription factors. Inhibiting these transcription factors might be a promising way for angiogenic intervention and vascular re-engineering. Therefore, we investigated the interdependence of tumor-, stroma- and immune cell-derived angiogenic factors, transcription factors and resulting vessel phenotypes. Additionally, we evaluated whether transcription factors that regulate EMT are promising targets for vascular remodeling.
We used formalin fixed paraffin embedded samples from breast cancer patients, classified according to estrogen-, progesterone- and human epidermal growth factor receptor (HER) 2 status. Establishing various techniques (CD34 staining, laser microdissection, RNA isolation and expression profiling) we systematically analyzed tumor and stroma-derived growths factors. In addition, vascular parameters such as microvessel size, area, circularity and density were assessed. Finally the established expression profiles were correlated with the observed vessel phenotype. As the SNAI1 transcriptional repressor is a key regulator of EMT, we examined the effect of vascular knockdown of Snai1 in murine cancer models (E0771, B16-F10 and lewis lung carcinoma).
Among individual mammary carcinomas, but not among subtypes, strong differences of vascular parameters were observed. Also, little difference between lobular carcinomas and ductal carcinomas was found. Vessel phenotype of Her2 enriched carcinomas was similar to that of lobular carcinomas. Vessel morphology of luminal A and B and basal-like tumors resembled each other. Expression of angiogenic factors was variable across subtypes. We discovered an inverse correlation of PDGF-B and VEGF-A with vessel area in luminal A tumors. In these tumors expression of IL12A, an inhibitor of angiogenesis, was also correlated with vessel size. Treatment of endothelial cells with growth factors revealed an increased expression of transcription factors involved in the regulation of EMT. Knockdown of Snai1 in endothelial cells of mice increased tumor growth and decreased hypoxia in the E0771 and the B16-F10 models. In the lewis lung carcinomas, tumor vascularity and biodistribution of doxorubicin were improved. Here, doxorubicin treatment in combination with the endothelial cell-specific knockdown did slow tumor growth. This shows that SNAI1 is important for a tumor's vascularization, with the significance of its role depending on the tumor model.
The methods established in this work open the way for the analysis of the expression of key transcription factors in vessels of formalin fixed paraffin embedded tumors. This research enables us to find novel targets for vascular intervention and to eventually design novel targeted drugs to inhibit these targets.
Host–microbe interactions are the key to understand why and how microbes inhabit specific environments. With the scientific fields of microbial genomics and metagenomics, evolving on an unprecedented scale, one is able to gain insights in these interactions on a molecular and ecological level. The goal of this PhD thesis was to make (meta–)genomic data accessible, integrate it in a comparative manner and to gain comprehensive taxonomic and functional insights into bacterial strains and communities derived from two different environments: the phyllosphere of Arabidopsis thaliana and the mesohyl interior of marine sponges.
This thesis focused first on the de novo assembly of bacterial genomes. A 5–step protocol was developed, each step including a quality control. The examination of different assembly software in a comparative way identified SPAdes as most suitable. The protocol enables the user to chose the best tailored assembly. Contamination issues were solved by an initial filtering of the data and methods normally used for the binning of metagenomic datasets. This step is missed in many published assembly pipelines. The described protocol offers assemblies of high quality ready for downstream analysis.
Subsequently, assemblies generated with the developed protocol were annotated and explored
in terms of their function. In a first study, the genome of a phyllosphere bacterium, Williamsia sp. ARP1, was analyzed, offering many adaptions to the leaf habitat: it can deal with temperature shifts, react to oxygen species, produces mycosporins as protection against UV–light, and is able to uptake photosynthates. Further, its taxonomic position within the Actinomycetales was infered from 16S rRNA and comparative genomics showing the close relation between the genera Williamsia and Gordonia.
In a second study, six sponge–derived actinomycete genomes were investigated for secondary metabolism. By use of state–of–the–art software, these strains exhibited numerous gene clusters, mostly linked to polykethide synthases, non–ribosomal peptide synthesis, terpenes, fatty acids and saccharides. Subsequent predictions on these clusters offered a great variety of possible produced compounds with antibiotic, antifungal or anti–cancer activity. These analysis highlight the potential for the synthesis of natural products and the use of genomic data as screening toolkit.
In a last study, three sponge–derived and one seawater metagenomes were functionally compared. Different signatures regarding the microbial composition and GC–distribution were observed between the two environments. With a focus on bacerial defense systems, the data indicates a pronounced repertoire of sponge associated bacteria for bacterial defense systems, in particular, Clustered Regularly Interspaced Short Palindromic Repeats, restriction modification system, DNA phosphorothioation and phage growth limitation. In addition, characterizing genes for secondary metabolite cluster differed between sponge and seawater microbiomes. Moreover, a variety of Type I polyketide synthases were only found within the sponge microbiomes. With that, metagenomics are shown to be a useful tool for the screening of secondary metabolite genes. Furthermore, enriched defense systems are highlighted as feature of sponge-associated microbes and marks them as a selective trait.
3D point clouds are a de facto standard for 3D documentation and modelling. The advances in laser scanning technology broadens the usability and access to 3D measurement systems. 3D point clouds are used in many disciplines such as robotics, 3D modelling, archeology and surveying. Scanners are able to acquire up to a million of points per second to represent the environment with a dense point cloud. This represents the captured environment with a very high degree of detail. The combination of laser scanning technology with photography adds color information to the point clouds. Thus the environment is represented more realistically. Full 3D models of environments, without any occlusion, require multiple scans. Merging point clouds is a challenging process. This thesis presents methods for point cloud registration based on the panorama images generated from the scans. Image representation of point clouds introduces 2D image processing methods to 3D point clouds. Several projection methods for the generation of panorama maps of point clouds are presented in this thesis. Additionally, methods for point cloud reduction and compression based on the panorama maps are proposed. Due to the large amounts of data generated from the 3D measurement systems these methods are necessary to improve the point cloud processing, transmission and archiving. This thesis introduces point cloud processing methods as a novel framework for the digitisation of archeological excavations. The framework replaces the conventional documentation methods for excavation sites. It employs point clouds for the generation of the digital documentation of an excavation with the help of an archeologist on-site. The 3D point cloud is used not only for data representation but also for analysis and knowledge generation. Finally, this thesis presents an autonomous indoor mobile mapping system. The mapping system focuses on the sensor placement planning method. Capturing a complete environment requires several scans. The sensor placement planning method solves for the minimum required scans to digitise large environments. Combining this method with a navigation system on a mobile robot platform enables it to acquire data fully autonomously. This thesis introduces a novel hole detection method for point clouds to detect obscured parts of a captured environment. The sensor placement planning method selects the next scan position with the most coverage of the obscured environment. This reduces the required number of scans. The navigation system on the robot platform consist of path planning, path following and obstacle avoidance. This guarantees the safe navigation of the mobile robot platform between the scan positions. The sensor placement planning method is designed as a stand alone process that could be used with a mobile robot platform for autonomous mapping of an environment or as an assistant tool for the surveyor on scanning projects.
This thesis aimed at the coherent investigation of the electrical and thermal transport properties of the low-dimensional organic conductor (DCNQI)2M (DCNQI: dicyanoquinonediimine; M: metallic counterion). These radical anion salts present a promising, new material class for thermoelectric applications and hence, a consistent characterization of the key parameters is required to evaluate and to optimize their performance. For this purpose, a novel experimental measurement setup enabling the determination of the electrical conductivity, the Seebeck coefficient and the thermal conductivity on a single crystalline specimen has been designed and implemented in this work. The novel measurement setup brought to operation within this thesis enabled a thorough investigation of the thermal transport properties in the (DCNQI)2M system. The thermal conductivity of (DCNQI-h8)2Cu at RT was determined to κ=1.73 W m^(-1) K^(-1). By reducing of the copper content in isostructural, crystalline (DMe-DCNQI)2CuxLi1-x alloys, the electrical conductivity has been lowered by one order of magnitude and the correlated changes in the thermal conductivity allowed for a verification of the Wiedemann-Franz (WF) law at RT. A room temperature Lorenz number of L=(2.48±0.45)⋅〖10〗^(-8) WΩK^(-2) was obtained in agreement with the standard Lorenz number L_0=2,44⋅〖10〗^(-8) WΩK^(-2) for 3D bulk metals. This value appears to be significantly reduced upon cooling below RT, even far above the Debye temperature of θ_D≈82 K, below which a breakdown of the WF law is caused by different relaxation times in response to thermal and to electric field perturbations. The experimental data enabled the first consistent evaluation of the thermoelectric performance of (DCNQI)$_2$Cu. The RT power factor of 110 μWm^(-1) K^(-2) is comparable to values obtained on PEDOT-based thermoelectric polymers. The RT figure of merit amounts to zT=0.02 which falls short by a factor of ten compared to the best values of zT=0.42 claimed for conducting polymers. It originates from the larger thermal conductivity in the organic crystals of about 1.73 W m^(-1) K^(-1) in (DCNQI)2Cu. Yet, more elaborate studies on the anisotropy of the thermal conductivity in PEDOT polymers assume their figure of merit to be zT=0.15 at most, recently. Therefore, (DCNQI)2Cu can be regarded as thermoelectric material of similar performance to polymer-based ones. Moreover, it represents one of the best organic n-type thermoelectric materials to date and as such, may also become important in hybrid thermoelectrics in combination with conducting polymers. Upon cooling below room temperature, (DCNQI)2Cu reveals its full potential attaining power factors of 50 mW K^(-2) m^(-1) and exceeding values of zT>0.15 below 40 K. These values represent the best thermoelectric performance in this low-temperature regime for organic as well as inorganic compounds and thus, low-dimensional organic conductors might pave the way toward new applications in cryogenic thermoelectrics. Further improvements may be expected from optimizing the charge carrier concentration by taking control over the CT process via the counterion stack of the crystal lattice. The concept has also been demonstrated in this work. Moreover, the thermoelectric performance in the vicinity of the CDW transition in (MeBr-DCNQI)2Cu was found to be increased by a factor of 5. Accordingly, the diversity of electronic ground states accessible in organic conductors provides scope for further improvements. Finally, the prototype of an all-organic thermoelectric generator has been built in combination with the p-type organic metal TTT2I3. While it only converts about 0.02% of the provided heat into electrical energy, the specific power output per active area attains values of up to 5 mW cm^(-2). This power output, defining the cost-limiting factor in the recovery of waste heat, is three orders of magnitude larger than in conducting polymer devices and as such, unrivaled in organic thermoelectrics. While the thermoelectric key parameters of (DCNQI)2Cu still lack behind conventional thermoelectrics made of e.g. Bi2Te3, the promising performance together with its potential for improvements make this novel material class an interesting candidate for further exploration. Particularly, the low-cost and energy-efficient synthesis routes of organic materials highlight their relevance for technological applications.
The Role of DREAM/MMB-mediated mitotic gene expression downstream of mutated K-Ras in lung cancer
(2017)
The evolutionary conserved Myb-MuvB (MMB) multiprotein complex has an essential role in transcriptional activation of mitotic genes. MMB target genes as well as the MMB associated transcription factor B-Myb and FoxM1 are highly expressed in a range of different cancer types. The elevated expression of these genes correlates with an advanced tumor state and a poor prognosis. This suggests that MMB could contribute to tumorigenesis by mediating overexpression of mitotic genes. Although MMB has been extensively characterized biochemically, the requirement for MMB to tumorigenesis in vivo remains largely unknown and has not been tested directly so far.
In this study, conditional knockout of the MMB core member Lin9 inhibits tumor formation in vivo in a mouse model of lung cancer driven by oncogenic K-Ras and loss of p53. The incomplete recombination observed within tumors points towards an enormous selection pressure against the complete loss of Lin9. RNA interference (RNAi)-mediated depletion of Lin9 or the MMB associated subunit B-Myb provides evidence that MMB is required for the expression of mitotic genes in lung cancer cells. Moreover, it was demonstrated that proliferation of lung cancer cells strongly depends on MMB. Furthermore, in this study, the relationship of MMB to the p53 tumor suppressor was investigated in a primary lung cancer cell line with restorable p53 function. Expression analysis revealed that mitotic genes are downregulated after p53 re-expression. Moreover, activation of p53 induces formation of the repressive DREAM complex and results in enrichment of DREAM at mitotic gene promoters. Conversely, MMB is displaced at these promoters.
Based on these findings the following model is proposed: In p53-negative cells, mitogenic stimuli foster the switch from DREAM to MMB. Thus, mitotic genes are overexpressed and may promote chromosomal instability and tumorigenesis.
This study provides evidence that MMB contributes to the upregulation of G2/M phase-specific genes in p53-negative cells and suggests that inhibition of MMB (or its target genes) might be a strategy for treatment of lung cancer.
The topic of this PhD thesis is the combination of topologically non-trivial phases with correlation effects stemming from Coulomb interaction between the electrons in a condensed matter system. Emphasis is put on both emerging benefits as well as hindrances, e.g. concerning the topological protection in the presence of strong interactions.
The physics related to topological effects is established in Sec. 2. Based on the topological band theory, we introduce topological materials including Chern insulators, topological insulators in two and three dimensions as well as Weyl semimetals. Formalisms for a controlled treatment of Coulomb correlations are presented in Sec. 3, starting with the topological field theory. The Random Phase Approximation is introduced as a perturbative approach, while in the strongly interacting limit the theory of quantum Hall ferromagnetism applies. Interactions in one dimension are special, and are treated through the Luttinger liquid description. The section ends with an overview of the expected benefits offered by the combination of topology and interactions, see Sec. 3.3.
These ideas are then elaborated in the research part. In Chap. II, we consider weakly interacting 2D topological insulators, described by the Bernevig-Hughes-Zhang model. This is applicable, e.g., to quantum well structures made of HgTe/CdTe or InAs/GaSb. The bulk band structure is here a mixture stemming from linear Dirac and quadratic Schrödinger fermions. We study the low-energy excitations in Random Phase Approximation, where a new interband plasmon emerges due to the combined Dirac and Schrödinger physics, which is absent in the separate limits. Already present in the undoped limit, one finds it also at finite doping, where it competes with the usual intraband plasmon. The broken particle-hole symmetry in HgTe quantum wells allows for an effective separation of the two in the excitation spectrum for experimentally accessible parameters, in the right range for Raman or electron loss spectroscopy. The interacting bulk excitation spectrum shows here clear differences between the topologically trivial and topologically non-trivial regime. An even stronger signal in experiments is expected from the optical conductivity of the system. It thus offers a quantitative way to identify the topological phase of 2D topological insulators from a bulk measurement.
In Chap. III, we study a strongly interacting system, forming an ordered, quantum Hall ferromagnetic state. The latter can arise also in weakly interacting materials with an applied strong magnetic field. Here, electrons form flat Landau levels, quenching the kinetic energy such that Coulomb interaction can be dominant. These systems define the class of quantum Hall topological insulators: topologically non-trivial states at finite magnetic field, where the counter-propagating edge states are protected by a symmetry (spatial or spin) other than time-reversal. Possible material realizations are 2D topological insulators like HgTe heterostructures and graphene. In our analysis, we focus on the vicinity of the topological phase transition, where the system is in a strongly interacting quantum Hall ferromagnetic state. The bulk and edge physics can be described by a nonlinear \sigma-model for the collective order parameter of the ordered state. We find that an emerging, continuous U(1) symmetry offers topological protection. If this U(1) symmetry is preserved, the topologically non-trivial phase persists in the presence of interactions, and we find a helical Luttinger liquid at the edge. The latter is highly tunable by the magnetic field, where the effective interaction strength varies from weakly interacting at zero field, K \approx 1, to diverging interaction strength at the phase transition, K -> 0.
In the last Chap. IV, we investigate whether a Weyl semimetal and a 3D topological insulator phase can exist together at the same time, with a combined, hybrid surface state at the joint boundaries. An overlap between the two can be realized by Coulomb interaction or a spatial band overlap of the two systems. A tunnel coupling approach allows us to derive the hybrid surface state Hamiltonian analytically, enabling a detailed study of its dispersion relation. For spin-symmetric coupling, new Dirac nodes emerge out of the combination of a single Dirac node and a Fermi arc. Breaking the spin symmetry through the coupling, the dispersion relation is gapped and the former Dirac node gets spin-polarized. We propose experimental realizations of the hybrid physics, including compressively strained HgTe as well as heterostructures of topological insulator and Weyl semimetal materials, connected to each other, e.g., by Coulomb interaction.
The role of miR-21 in the pathophysiology of neuropathic pain using the model of B7-H1 knockout mice
(2017)
The impact of microRNA (miRNA) as key players in the regulation of immune and neuronal gene expression and their role as master switches in the pathophysiology of neuropathic pain is increasingly recognized. miR-21 is a promising candidate that could be linked to the immune and the nociceptive system. To further investigate the pathophysiological role of miR-21 in neuropathic pain, we assesed mice deficient of B7 homolog 1 (B7-H1 ko), a protein with suppressive effect on inflammatory responses.
B7-H1 ko mice and wildtype littermates (WT) of three different age-groups, young (8 weeks), middle-aged (6 months), and old (12 months) received a spared nerve injury (SNI). Thermal withdrawal latencies and mechanical withdrawal thresholds were determined. Further, we investigated anxiety-, depression-like and cognitive behavior. Quantitative real time PCR was used to determine miR-21 relative expression in peripheral nerves, dorsal root ganglia and white blood cells (WBC) at distinct time points after SNI.
Naïve B7-H1 ko mice showed mechanical hyposensitivity with increasing age. Young and middle-aged B7-H1 ko mice displayed lower mechanical withdrawal thresholds compared to WT mice. From day three after SNI both genotypes developed mechanical and heat hypersensitivity, without intergroup differences. As supported by the results of three behavioral tests, no relevant differences were found for anxiety-like behavior after SNI in B7-H1 ko and WT mice. Also, there was no indication of depression-like behavior after SNI or any effect of SNI on cognition in both genotypes. The injured nerves of B7-H1 ko and WT mice showed higher miR-21 expression and invasion of macrophages and T cells 7 days after SNI without intergroup differences. Perineurial miR-21 inhibitor injection reversed SNI-induced mechanical and heat hypersensitivity in old B7-H1 ko and WT mice.
This study reveals that reduced mechanical thresholds and heat withdrawal latencies are associated with miR-21 induction in the tibial and common peroneal nerve after SNI, which can be reversed by perineurial injection of a miR-21 inhibitor. Contrary to expectations, miR-21 expression levels were not higher in B7-H1 ko compared to WT mice. Thus, the B7-H1 ko mouse may be of minor importance for the study of miR-21 related pain. However, these results spot the contribution of miR-21 in the pathophysiology of neuropathic pain and emphasize the crucial role of miRNA in the regulation of neuronal and immune circuits that contribute to neuropathic pain.
Investigation of Nanostructure-Induced Localized Light Phenomena Using Ultrafast Laser Spectroscopy
(2017)
In recent years, the interaction of light with subwavelength structures, i.e., structures that are smaller than the optical wavelength, became more and more interesting to scientific research, since it provides the opportunity to manipulate light-induced dynamics below the optical diffraction limit. Specifically designed nanomaterials can be utilized to tailor the temporal evolution of electromagnetic fields at the nanoscale. For the investigation of strongly localized processes, it is essential to resolve both their spatial and their temporal behavior. The aim of this thesis was to study and/or control the temporal evolution of three nanostructure-induced localized light phenomena by using ultrafast laser spectroscopy with high spatial resolution.
In Chapter 4, the absorption of near-infrared light in thin-film a-Si:H solar cells was investigated. Using nanotextured instead of smooth interfaces for such devices leads to an increase of absorption from < 20% to more than 50% in the near-infrared regime. Time-resolved experiments with femtosecond laser pulses were performed to clarify the reason for this enhancement. The coherent backscattered radiation from nanotextured solar cell devices was measured as a function of the sample position and evaluated via spectral interferometry. Spatially varying resonance peaks in the recorded spectra indicated the formation of localized photonic modes within the nanotextured absorber layers. In order to identify the modes separately from each other, coherent two-dimensional (2D) nanoscopy was utilized, providing a high spatial resolution < 40 nm. In a nanoscopy measurement on a modified device with an exposed nanotextured a-Si:H absorber layer, hot-spot electron emission was observed and confirmed the presence of localized modes. Fitting the local 2D nanospectra at the hot-spot positions enabled the determination of the resonance frequencies and coherence lifetimes of the modes. The obtained lifetime values varied between 50 fs and 130 fs. Using a thermionic emission model allowed the calculation of the locally absorbed energy density and, with this, an estimation of the localization length of the photonic modes (≈1 μm). The localization could be classified by means of the estimated localization length and additional data evaluation of the backscattered spectra as strong localization ─ the so-called Anderson localization.
Based on the experimental results, it was concluded that the enhanced absorption of near-infrared light in thin-film silicon solar cells with nanotextured interfaces is caused by the formation of strongly localized photonic modes within the disordered absorber layers. The incoming near-infrared light is trapped in these long-living modes until absorption occurs.
In Chapter 5, a novel hybridized plasmonic device was introduced and investigated in both theory and experiment. It consists of two widely separated whispering gallery mode (WGM) nanoantennas located in an elliptical plasmonic cavity. The goal was to realize a periodic long-range energy transfer between the nanoantennas. In finite-difference time-domain (FDTD) simulations, the device was first optimized with respect to strong coupling between the localized antenna modes and the spatially-extended cavity mode. The geometrical parameters of the antennas and the cavity were adjusted separately so that the m="0" antenna mode and the cavity mode were resonant at λ="800 nm" . A high spatial overlap of the modes was achieved by positioning the two antennas in the focal spots of the cavity, leading to a distance between the antenna centers of more than twice the resonant wavelength of the modes. The spectral response of the optimized device revealed an energy splitting of the antenna and the cavity mode into three separated hybridized eigenmodes within an energy range of about 90 meV due to strong coupling. It could be well reproduced by a simple model of three coupled Lorentzian oscillators. In the time domain, an oscillatory energy transfer between both antennas with a period of 86 fs and an energy transfer efficiency of about 7% was observed for single-pulse excitation. For the experiments, devices with cavities and antennas of varying size were fabricated by means of focused-ion-beam (FIB) milling. Time-resolved correlation measurements were performed with high spatial and temporal resolution by using sequences of two femtosecond laser pulses for excitation and photoemission electron microscopy (PEEM) for detection. Local correlation traces at antennas in resonant devices, i.e., devices with enhanced electron emission at both antenna positions, were investigated and reconstructed by means of the coupled-oscillator model. The corresponding spectral response revealed separated peaks, confirming the formation of hybridized eigenmodes due to strong coupling. In a subsequent simulation for single-pulse excitation, one back-and-forth energy transfer between both antennas with an energy transfer efficiency of about 10% was observed.
Based on the theoretical and experimental results, it was demonstrated that in the presented plasmonic device a periodic long-range energy transfer between the two nanoantennas is possible. Furthermore, the coupled-oscillator model enables one to study in depth how specific device properties impact the temporal electric-field dynamics within the device. This can be exploited to further optimize energy transfer efficiency of the device. Future applications are envisioned in ultrafast plasmonic nanocircuitry. Moreover, the presented device can be employed to realize efficient SPP-mediated strong coupling between widely separated quantum emitters.
In Chapter 6, it was investigated in theory how the local optical chirality enhancement in the near field of plasmonic nanostructures can be optimized by tuning the far-field polarization of the incident light. An analytic expression was derived that enables the calculation of the optimal far-field polarizations, i.e., the two far-field polarizations which lead to the highest positive and negative local optical chirality, for any given nanostructure geometry. The two optimal far-field polarizations depend on the local optical response of the respective nanostructure and thus are functions of both the frequency ω and the position r. Their ellipticities differ only in their sign, i.e., in their direction of rotation in the time domain, and the angle between their orientations, i.e., the angle between the principal axes of their ellipses, is ±π/"2" . The handedness of optimal local optical chirality can be switched by switching between the optimal far-field polarizations. In numerical simulations, it was exemplarily shown for two specific nanostructure assemblies that the optimal local optical chirality can significantly exceed the optical chirality values of circularly polarized light in free space ─ the highest possible values in free space. The corresponding optimal far-field polarizations were different from linear and circular and varied with frequency. Using femtosecond polarization pulse shaping provides the opportunity to coherently control local optical chirality over a continuous frequency range. Furthermore, symmetry properties of nanostructures can be exploited to determine which far-field polarization is optimal.
The theoretical findings can have impact on future experimental studies about local optical chirality enhancement. Tuning the far-field polarization of the incident light offers a promising tool to enhance chirally specific interactions of local electromagnetic fields with molecular and other quantum systems in the vicinity of plasmonic nanostructures. The presented approach can be utilized for applications in chiral sensing of adsorbed molecules, time-resolved chirality-sensitive spectroscopy, and chiral quantum control.
In conclusion, each of the localized light phenomena that were investigated in this thesis ─ the enhanced local absorption of near-infrared light due to the formation of localized photonic modes, the periodic long-range energy transfer between two nanoantennas within an elliptical plasmonic cavity, and the optimization of local optical chirality enhancement by tuning the far-field polarization of the incident light ─ can open up new perspectives for a variety of future applications.
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Pancreatic cancer (PC) remains one of the most challenging solid tumors to treat with a high unmet medical need as patients poorly respond to standard-of-care-therapies. Prominent desmoplastic reaction involving cancer-associated fibroblasts (CAFs) and the immune cells in the tumor microenvironment (TME) and their cross-talk play a significant role in tumor immune escape and progression. To identify the key cellular mechanisms induce an immunosuppressive tumor microenvironment, we established 3D co-culture model with pancreatic cancer cells, CAFs, monocyte as well as T cells.
Using this model, we analysed the influence of tumor cells and fibroblasts on monocytes and their immune suppressive phenotype. Phenotypic characterization of the monocytes after 3D co-culture with tumor/fibroblast spheroids was performed by analysing the expression of defined cell surface markers and soluble factors. Functionality of these monocytes and their ability to influence T cell phenotype and proliferation was investigated.
3D co-culture of monocytes with pancreatic cancer cells and fibroblasts induced the production of immunosuppressive cytokines which are known to promote polarization of M2 like macrophages and myeloid derived suppressive cells (MDSCs). These co-culture spheroid polarized monocyte derived macrophages (MDMs) were poorly differentiated and had an M2 phenotype. The immunosuppressive function of these co-culture spheroids polarized MDMs was demonstrated by their ability to inhibit autologous CD4+ and CD8+ T cell activation and proliferation in vitro, which we could partially reverse by 3D co-culture spheroid treatment with therapeutic molecules that are able to re-activate spheroid polarized MDMs or block immune suppressive factors such as Arginase-I.
In conclusion, we generated a physiologically relevant 3D co-culture model, which can be used as a promising tool to study complex cell-cell interactions between different cell types within the tumor microenvironment and to support drug screening and development. In future, research focused on better understanding of resistance mechanisms to existing cancer immunotherapies will help to develop new therapeutic strategies in order to combat cancer.
The Micromegas technology is one of the most successful modern gaseous detector concepts and widely utilized in nuclear and particle physics experiments. Twenty years of R & D rendered the technology sufficiently mature to be selected as precision tracking detector for the New Small Wheel (NSW) upgrade of the ATLAS Muon spectrometer. This will be the first large scale application of Micromegas in one of the major LHC experiments. However, many of the fundamental microscopic processes in these gaseous detectors are still not fully understood and studies on several detector aspects, like the micromesh geometry, have never been addressed systematically.
The studies on signal formation in Micromegas, presented in the first part of this thesis, focuses on the microscopic signal electron loss mechanisms and the amplification processes in electron gas interaction. Based on a detailed model of detector parameter dependencies, these processes are scrutinized in an iterating comparison between exper- imental results, theory prediction of the macroscopic observables and process simulation on the microscopic level. Utilizing the specialized detectors developed in the scope of this thesis as well as refined simulation algorithms, an unprecedented level of accuracy in the description of the microscopic processes is reached, deepening the understanding of the fundamental process in gaseous detectors.
The second part is dedicated to the challenges arising with the large scale Micro- megas production for the ATLAS NSW. A selection of technological choices, partially influenced or determined by the herein presented studies, are discussed alongside a final report on two production related tasks addressing the detectors’ core components: For the industrial production of resistive anode PCBs a detailed quality control (QC) and quality assurance (QA) scheme as well as the therefore required testing tools have been developed. In parallel the study on micromesh parameter optimization and production feasibility resulted in the selection of the proposed mesh by the NSW community and its full scale industrial manufacturing. The successful completion of both tasks were im- portant milestones towards the construction of large size Micromegas detectors clearing the path for NSW series production.
The dissertation aims at investigating how information about jobs arriving to a service facility in the future can be used for capacity planning and control. Nowadays, technical equipment such as aircraft engines are equipped with sensors transferring condition data to central data warehouses in real-time. By jointly analyzing condition data and future usage information with machine learning algorithms, future equipment conditions and maintenance requirements can be forecasted. In the thesis, information regarding the arrival times of aircraft engine at a maintenance facility and the corresponding service requirements are used in order to optimally plan and control the flexible capacity of the facility. Queueing models are developed and analyzed to optimally size and control the facility's capacity and determine the implications on cost and job waiting time. It is demonstrated analytically and numerically that cost and waiting time can be reduced significantly when future information is available.
The thesis deals with the automated generation and efficient evaluation of scattering amplitudes in general relativistic quantum field theories at one-loop order in perturbation theory. At the
present time we lack signals beyond the Standard Model which, in the past, have guided the
high-energy physics community, and ultimately led to the discovery of new physics phenomena.
In the future, precision tests could acquire this guiding role by systematically probing the Standard Model and constraining Beyond the Standard Model theories. As current experimental
constraints strongly favour Standard Model-like theories, only small deviations with respect to the Standard Model are expected which need to be studied in detail. The required precision
demands one-loop corrections in all future analyses, ideally in a fully automated way, allowing
to test a variety of observables in different models and in an effective field theory approach.
In the process of achieving this goal we have developed an enhanced version of the tool
Recola and on this basis the generalization Recola2. These tools represent fully automated
tree- and one-loop-amplitude providers for the Standard Model, or in the case of Recola2
for general models. Concerning the algorithm, we use a purely numerical and fully recursive
approach allowing for extreme calculations of yet unmatched complexity. Recola has led to the first computation involving 9-point functions. Beyond the Standard Model theories and Effective Field theories are integrated into the Recola2 framework as model files. Renormalized model files are produced with the newly developed tool Rept1l, which can perform the renormalization in a fully automated way, starting from nothing but Feynman rules. In view of validation, we have extended Recola2 to new gauges such as the Background-Field Method and the class of Rxi gauges. In particular, the Background-Field Method formulation for new theories serves as an automated validation, and is very useful in practical calculations and the formulation of renormalization conditions. We have applied the system to produce the first results for Higgs-boson production in Higgs strahlung and vector-boson fusion in the Two-Higgs-Doublet Model and the Higgs-Singlet Extension of the Standard Model. All in all, we have laid the foundation for an automated generation and computation of one-loop amplitudes within a large class of phenomenologically interesting theories. Furthermore, we enable the use of our system via a very flexible and dynamic control which does not require any intermediate intervention.
Adult human skeletal stem cells are considered to give rise to the bone marrow stromal
compartment, including bone-forming osteoblasts and marrow adipocytes. Reduced osteogenesis
and enhanced adipogenesis of these skeletal progenitors may contribute to the bone loss and
marrow fat accumulation observed during aging and osteoporosis, the main disorder of bone
remodeling. Concordantly, in vitro evidence indicates that adipogenic and osteogenic
differentiation of human bone marrow stromal cells (hBMSCs) display an inverse relationship
under numerous conditions. Hence, the identification of factors modulating inversely both
differentiation pathways is of great therapeutic interest.
Based on mRNA expression analysis of inversely regulated genes after switching differentiation
conditions, our group had previously proposed that fibroblast growth factor 1 (FGF1) might play
such a modulator role in hBMSC differentiation. The main aim of this work was, therefore, to
investigate the role of FGF1 signaling in the adipogenic and osteogenic differentiation of hBMSCs
using a three-dimensional (3D) culture system based on collagen type I hydrogels in order to
better mimic the natural microenvironment.
Adipogenic and osteogenic differentiation of hBMSCs embedded in collagen gels was successfully
established. Treatment with recombinant human FGF1 (rhFGF1), as well as rhFGF2, throughout
differentiation induction was found to exert a dose-dependent inhibitory effect on adipogenesis
in hBMSCs. This inhibitory effect was found to be reversible and dependent on FGF receptors
(FGFR) signaling, given that simultaneous pharmacological blockage of FGFRs rescued adipogenic
differentiation. Additionally, matrix mineralization under osteogenic induction was also inhibited
by rhFGF1 and rhFGF2 in a dose-dependent manner. A transient treatment with rhFGF1 and
rhFGF2 during an expansion phase, however, enhanced proliferation of hBMSCs without affecting
the differentiation capacity, although matrix mineralization under osteogenic conditions was
hindered.
Additionally, rhFGF1 and rhFGF2 treatments affected the matrix remodeling ability of hBMSCs,
which displayed alterations in the cytoskeletal phenotype and the expression patterns of matrix
metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs).
On the other hand, inhibition of FGFR signaling throughout differentiation induction elicited a
strong enhancement of matrix mineralization under osteogenic conditions but had no significant
effect on adipocyte formation under adipogenic induction.
IX
In conclusion, FGF1 and FGF2 signaling was found to support the expansion of bone marrow
stromal precursors with adipogenic and osteogenic capacities, to hinder adipogenic and
osteogenic differentiation if continuously present during differentiation induction and to alter the
matrix remodeling ability of hBMSCs within a 3D collagenous microenvironment.
Chapter 2 concerns the audit market for German credit institutions (excluding savings banks and cooperative banks), and the presented study allows conclusions to be drawn regarding recent concentration levels of this particular audit market. The last reliable (statistical) studies concerning the audit market for German credit institutions were published several years ago (Grothe 2005; Lenz 1996b; Lenz 1997; Lenz 1998). This is surprising because parts of the new regulations concerning the audit market for public-interest entities—which should also apply to credit institutions (European Commission 2006c)—in Europe would require analyses of the audit market concentration to be performed on a regular basis. Therefore, this study begins to fill this research gap, and it reveals that the audit market for German credit institutions was highly concentrated (market leadership: KPMG AG WPG and PricewaterhouseCoopers AG WPG) in 2006 and 2010. Moreover, the findings also highlight that between these years, neither a notable trend toward higher levels of concentration nor a deconcentration process was evident. Finally, it is illustrated that the regulatory requirements for publishing audit fees and the corresponding right to claim exemption (§§ 285 Sentence 1 No. 17, 314 (1) No. 9 Commercial Code) do not allow the calculation of concentration figures that cover the entire audit market for credit institutions. Thus, it will continue to be necessary to use surrogates for audit fees, and analyses reveal that the arithmetic mean of the total business volume (or total assets) of a credit institution and its square root is a very good surrogate for calculating concentration measures based on audit fees.
Chapter 3 seeks to determine whether public oversight of public-interest entities (PIEs) increases audit fees specifically in the financial industry, which is already a highly regulated industry characterized by intense supervision. To answer this question, a sample of 573 German credit institutions is examined over the 2009–2011 period, as not all credit institutions were considered PIEs in Germany (until very recently). First, the results show that a credit institution’s business risk is related to audit fees. In addition, the findings reveal not only that PIE credit institutions pay statistically significantly higher audit fees but also that this effect is economically substantial (representing an audit fee increase of 31.38%). Finally, there are several indications that the relationship between (other) credit institutions’ business risks and audit fees is greater for PIE credit institutions.
Chapter 4 examines the association between the results of auditor ratification votes and perceived external financial reporting quality. As has been recently remarked by Wei et al. (2015), far too little is known about shareholders’ interests in and perceptions of the election, approval or ratification of auditors. Although auditor ratification by shareholders is normally a routine, non-binding action and the voting ratios are in the range of 95% or higher, the SEC emphasized the importance of this process by amending the disclosure requirements for such voting results in 2010 (SEC 2009; SEC 2010). This study demonstrates that the results of auditor ratification votes are associated with market reactions to earnings surprises (SEC registrants; 2010 to 2013). Moreover, there are moderate indications that this effect may be positively related to higher levels of information asymmetry between managers and shareholders, that such voting results contain incremental informational content beyond that of other publicly available audit-related information, and that the time lag between the ratification of an auditor and the earnings announcement influences the vote’s importance. Finally, the study sheds additional light on an overlooked audit-related topic (e.g., Dao et al. 2012; Hermanson et al. 2009; Krishnan and Ye 2005; Sainty et al. 2002), and illustrates its relation to accounting. More importantly, the provided evidence indicates that disclosure of the results of auditor ratification votes might benefit (prospective) shareholders.
Chapter 5 addresses the question of whether and when shareholders may have a negative perception of an auditor’s economic dependence on the client. The results for a Big 4 client sample in the U.S. (2010 to 2014) show that the economic importance of the client—measured at the audit office-level—is negatively associated with shareholders’ perceptions of external financial reporting quality—measured in terms of the earnings response coefficient and the ex ante cost of equity capital—and, therefore, is perceived as a threat to auditor independence. Moreover, the study reveals that shareholders primarily regard independence due to client dependence as a problem for firms that are more likely to be in financially distressed conditions.
High-throughput sequencing (HTS) has revolutionized bacterial genomics. Its unparalleled sensitivity has opened the door to analyzing bacterial evolution and population genomics, dispersion of mobile genetic elements (MGEs), and within-host adaptation of pathogens, such as Escherichia coli.
One of the defining characteristics of intestinal pathogenic E. coli (IPEC) pathotypes is a specific repertoire of virulence factors (VFs). Many of these IPEC VFs are used as typing markers in public health laboratories to monitor outbreaks and guide treatment options. Instead, extraintestinal pathogenic E. coli (ExPEC) isolates are genotypically diverse and harbor a varied set of VFs -- the majority of which also function as fitness factors (FFs) for gastrointestinal colonization.
The aim of this thesis was the genomic characterization of pathogenic and commensal E. coli with respect to their virulence- and antibiotic resistance-associated gene content as well as phylogenetic background. In order to conduct the comparative analyses, I created a database of E. coli VFs, ecoli_VF_collection, with a focus on ExPEC virulence-associated proteins (Leimbach, 2016b). Furthermore, I wrote a suite of scripts and pipelines, bac-genomics-scripts, that are useful for bacterial genomics (Leimbach, 2016a). This compilation includes tools for assembly and annotation as well as comparative genomics analyses, like multi-locus sequence typing (MLST), assignment of Clusters of Orthologous Groups (COG) categories, searching for protein homologs, detection of genomic regions of difference (RODs), and calculating pan-genome-wide association statistics.
Using these tools we were able to determine the prevalence of 18 autotransporters (ATs) in a large, phylogenetically heterogeneous strain panel and demonstrate that many AT proteins are not associated with E. coli pathotypes. According to multivariate analyses and statistics the distribution of AT variants is instead significantly dependent on phylogenetic lineages. As a consequence, ATs are not suitable to serve as pathotype markers (Zude et al., 2014).
During the German Shiga toxin-producing E. coli (STEC) outbreak in 2011, the largest to date, we were one of the teams capable of analyzing the genomic features of two isolates. Based on MLST and detection of orthologous proteins to known E. coli reference genomes the close phylogenetic relationship and overall genome similarity to enteroaggregative E. coli (EAEC) 55989 was revealed. In particular, we identified VFs of both STEC and EAEC pathotypes, most importantly the prophage-encoded Shiga toxin (Stx) and the pAA-type plasmid harboring aggregative adherence fimbriae. As a result, we could show that the epidemic was caused by an unusual hybrid pathotype of the O104:H4 serotype. Moreover, we detected the basis of the antibiotic multi-resistant phenotype on an extended-spectrum beta-lactamase (ESBL) plasmid through comparisons to reference plasmids. With this information we proposed an evolutionary horizontal gene transfer (HGT) model for the possible emergence of the pathogen (Brzuszkiewicz et al., 2011).
Similarly to ExPEC, E. coli isolates of bovine mastitis are genotypically and phenotypically highly diverse and many studies struggled to determine a positive association of putative VFs. Instead the general E. coli pathogen-associated molecular pattern (PAMP), lipopolysaccharide (LPS), is implicated as a deciding factor for intramammary inflammation. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype was proposed presumably encompassing strains more adapted to elicit bovine mastitis with virulence traits differentiating them from commensals.
We sequenced eight E. coli isolates from udder serous exudate and six fecal commensals (Leimbach et al., 2016). Two mastitis isolate genomes were closed to a finished-grade quality (Leimbach et al., 2015). The genomic sequence of mastitis-associated E. coli (MAEC) strain 1303 was used to elucidate the biosynthesis gene cluster of its O70 LPS O-antigen. We analyzed the phylogenetic genealogy of our strain panel plus eleven bovine-associated E. coli reference strains and found that commensal or MAEC could not be unambiguously allocated to specific phylogroups within a core genome tree of reference E. coli. A thorough gene content analysis could not identify functional convergence of either commensal or MAEC, instead both have only very few gene families enriched in either pathotype. Most importantly, gene content and ecoli_VF_collection analyses showed that no virulence determinants are significantly associated with MAEC in comparison to bovine fecal commensals, disproving the MPEC hypothesis. The genetic repertoire of bovine-associated E. coli, again, is dominated by phylogenetic background. This is also mostly the case for large virulence-associated E. coli gene cluster previously associated with mastitis. Correspondingly, MAEC are facultative and opportunistic pathogens recruited from the bovine commensal gastrointestinal microbiota (Leimbach et al., 2017). Thus, E. coli mastitis should be prevented rather than treated, as antibiotics and vaccines have not proven effective.
Although traditional E. coli pathotypes serve a purpose for diagnostics and treatment, it is clear that the current typing system is an oversimplification of E. coli's genomic plasticity. Whole genome sequencing (WGS) revealed many nuances of pathogenic E. coli, including emerging hybrid or heteropathogenic pathotypes. Diagnostic and public health microbiology need to embrace the future by implementing HTS techniques to target patient care and infection control more efficiently.