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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.
Plants are exposed to high temperature, especially during hot summer days. Temperatures are typically lowest in the morning and reach a maximum in the afternoon. Plants can tolerate and survive short-term heat stress even on hot summer days. A. thaliana seedlings have been reported to tolerate higher temperatures for different time periods, a phenomenon that has been termed basal thermotolerance. In addition, plants have the inherent capacity to acclimate to otherwise lethal temperatures. Arabidopsis thaliana seedlings acclimate at moderately elevated temperatures between 32–38° C. During heat acclimation, a genetically programmed heat shock response (HSR) is triggered that is characterized by a rapid activation of heat shock transcription factors (HSFs), which trigger a massive accumulation of heat shock proteins that are chiefly involved in protein folding and protection.
Although the HSF-triggered heat-shock response is well characterized, little is known about the metabolic adjustments during heat stress. The aim of this work was to get more insight into heat-responsive metabolism and its importance for thermotolerance.
In order to identify the response of metabolites to elevated temperatures, global metabolite profiles of heat-acclimated and control seedlings were compared. Untargeted metabolite analyses revealed that levels of polyunsaturated triacylglycerols (TG) rapidly increase during heat acclimation. TG accumulation was found to be temperature-dependent in a temperature range from 32–50° C (optimum at 42° C). Heat-induced TG accumulation was localized in extra-chloroplastic compartments by chloroplast isolation as well as by fluorescence microscopy of A. thaliana cell cultures.
Analysis of mutants deficient in all four HSFA1 master regulator genes or the HSFA2 gene revealed that TG accumulation occurred independently to HSF. Moreover, the TG response was not limited to heat stress since drought and salt stress (but not short-term osmotic, cold and high light stress) also triggered an accumulation of TGs.
In order to reveal the origin of TG synthesis, lipid analysis was carried out. Heat-induced accumulation of TGs does not derive from massive de novo fatty acid (FA) synthesis. On the other hand, lipidomic analyses of A. thaliana seedlings indicated that polyunsaturated FA from thylakoid galactolipids are incorporated into cytosolic TGs during heat stress. This was verified by lipidomic analyses of A. thaliana fad7/8 transgenic seedlings, which displayed altered FA compositions of plastidic lipids. In addition, wild type A. thaliana seedlings displayed a rapid conversion of plastidic monogalactosyldiacylglycerols (MGDGs) into oligogalactolipids, acylated MGDGs and diacylglycerols (DGs). For TG synthesis, DG requires a FA from the acyl CoA pool or phosphatidylcholine (PC). Seedlings deficient in phospholipid:diacylglycerol acyltransferase1 (PDAT1) were unable to accumulate TGs following heat stress; thus PC appears to be the major FA donor for TGs during heat treatment. These results suggest that TG and oligogalactolipid accumulation during heat stress is driven by post-translationally regulated plastid lipid metabolism.
TG accumulation following heat stress was found to increase basal thermotolerance. Pdat1 mutant seedlings were more sensitive to severe heat stress without prior acclimatization, as revealed by a more dramatic decline of the maximum efficiency of PSII and lower survival rate compared to wild type seedlings. In contrast, tgd1 mutants over-accumulating TGs and oligogalactolipids displayed a higher basal thermotolerance compared to wild type seedlings. These results therefore suggest that accumulation of TGs increases thermotolerance in addition to the genetically encoded heat shock response.
The limited intrinsic self-healing capability of articular cartilage requires treatment of
cartilage defects. Material assisted and cell based therapies are in clinical practice but
tend to result in formation of mechanical inferior fibro-cartilage in long term follow up. If
a lesion has not been properly restored degenerative diseases are diagnosed as late sequela
causing pain and loss in morbidity. Complex three dimensional tissue models mimicking
physiological situation allow investigation of cartilage metabolism and mechanisms involved
in repair. A standardized and reproducible model cultured under controllable conditions
ex vivo to maintain tissue properties is of relevance for comparable studies.
Topic of this thesis was the establishment of an cartilage defect model that allows for
testing novel biomaterials and investigate the effect of defined defect depths on formation
of repair tissue.
In part I an ex vivo osteochondral defect model was established based on isolation of
porcine osteochondral explants (OCE) from medial condyles, 8 mm in diameter and 5 mm
in height. Full thickness cartilage defects with 1 mm to 4 mm in diameter were created
to define ex vivo cartilage critical size after 28 days culture with custom developed static
culture device. In part II of this thesis hydrogel materials, namely collagen I isolated from
rat tail, commercially available fibrin glue, matrix-metalloproteinase clevable poly(ethylene
glycol) polymerized with heparin (starPEGh), methacrylated poly(N-(2-hydroxypropyl)
methacrylamide mono-dilactate-poly(ethylene glycol) triblock copolymer/methacrylated
hyaluronic acid (MP/HA), thiol functionalized HA/allyl functionalized poly(glycidol)
(P(AGE/G)-HA-SH), were tested cell free and chondrocyte loaded (20 mio/ml) as implant
in 4 mm cartilage defects to investigate cartilage regeneration. Reproducible chondral
defects, 8 mm in diameter and 1 mm in height, were generated with an artificial tissue
cutter (ARTcut®) to investigate effect of defect depth on defect regeneration in part III.
In all approaches OCE were analyzed by Safranin-O staining to visualize proteoglycans
in cartilage and/or hydrogels. Immuno-histological and -fluorescent stainings (aggrecan,
collagen II, VI and X, proCollagen I, SOX9, RUNX2), gene expression analysis (aggrecan,
collagen II and X, SOX9, RUNX2) of chondrocyte loaded hydrogels (part II) and proteoglycan
and DNA content (Part I & II) were performed for detailed analysis of cartilage
regeneration.
Part I: The development of custom made static culture device, consisting of inserts in which OCE is fixed and deep well plate, allowed tissue specific media supply without
supplementation of TGF . Critical size diameter was defined to be 4 mm.
Part II: Biomaterials revealed differences in cartilage regeneration. Collagen I and fibrin
glue showed presence of cells migrated from OCE into cell free hydrogels with indication
of fibrous tissue formation by presence of proCollagen I. In chondrocyte loaded study
cartilage matrix proteins aggrecan, collagen II and VI and transcription factor SOX9 were
detected after ex vivo culture throughout the two natural hydrogels collagen I and fibrin
glue whereas markers were localized in pericellular matrix in starPEGh. Weak stainings resulted
for MP/HA and P(AGE/G)-HA-SH in some cell clusters. Gene expression data and
proteoglycan quantification supported histological findings with tendency of hypertrophy
indicated by upregulation of collagen X and RunX2 in MP/HA and P(AGE/G)-HA-SH.
Part III: In life-dead stainings recruitment of cells from OCE into empty or cell free
collagen I treated chondral defects was seen.
Separated and tissue specific media supply is critical to maintain ECM composition in
cartilage. Presence of OCE stimulates cartilage matrix synthesis in chondrocyte loaded
collagen I hydrogel and reduces hypertrophy compared to free swelling conditions and
pellet cultures. Differences in cartilage repair tissue formation resulted in preference of
natural derived polymers compared to synthetic based materials. The ex vivo cartilage
defect model represents a platform for testing novel hydrogels as cartilage materials, but
also to investigate the effect of cell seeding densities, cell gradients, cell co-cultures on
defect regeneration dependent on defect depth. The separated media compartments allow
for systematic analysis of pharmaceutics, media components or inflammatory cytokines on
bone and cartilage metabolism and matrix stability.
In this thesis, metacognition research is connected with fluency research. Thereby, the focus lies on how disfluency can be used to improve metacognitive monitoring (i.e., students` judgments during the learning process). Improving metacognitive monitoring is important in educational contexts in order to foster performance. Theories about metacognition and self-regulated learning suppose that monitoring affects control and performance. Accurate monitoring is necessary to initiate adequate control and better performance. However, previous research shows that students are often not able to accurately monitor their learning with meaningful text material. Inaccurate monitoring can result in inadequate control and low performance.
One reason for inaccurate monitoring is that students use cues for their judgments that are not valid predictors of their performance. Because fluency might be such a cue, the first aim of this thesis is to investigate under which conditions fluency is used as a cue for judgments during the learning process. A fluent text is easy to process and, hence, it should be judged as easy to learn and as easy to remember. Inversely, a disfluent text is difficult to process, for example because of a disfluent font type (e.g., Mistral) or because of deleted letters (e.g., l_tt_rs). Hence, a disfluent text should be judged as difficult to learn and as difficult to remember. This assumption is confirmed when students learn with both fluent and disfluent material. When fluency is manipulated between persons, fluency seems to be less obvious as a cue for judgments. However, there are only a few studies that investigated the effects of fluency on judgments when fluency is manipulated between persons. Results from Experiment 1 (using deleted letters for disfluent text) and from Experiment 4 (using Mistral for disfluent text) in this thesis support the assumption that fluency is used as a cue for judgments in between-person designs. Thereby, however, the interplay with the type of judgment and the learning stage seems to matter.
Another condition when fluency affects judgments was investigated in Experiment 2 and 3. The aim of these experiments was to investigate if disfluency leads to analytic monitoring and if analytic monitoring sustains for succeeding fluent material. If disfluency activates analytic monitoring that remains for succeeding fluent material, fluency should no longer be used as a cue for judgments. Results widely support this assumption for deleted letters (Experiment 2) as well as for the font type Mistral (Experiment 3). Thereby, again the interplay between the type of judgment and the learning stage matters.
Besides the investigation of conditions when fluency is used as a cue for different types of judgments during the learning process, another aim of this thesis is to investigate if disfluency leads to accurate monitoring. Results from Experiment 3 and 4 support the assumption that Mistral can reduce overconfidence. This is the case when fluency is manipulated between persons or when students first learn with a fluent and then with a disfluent text. Dependent from the type of judgment and the learning stage, disfluency can lead even to underconfidence or to improved relative monitoring accuracy (Experiment 4).
Improving monitoring accuracy is only useful when monitoring is implemented into better control and better performance. The effect of monitoring accuracy on control and performance was in the focus of Experiment 4. Results show that accurate monitoring does not result in improved control and performance. Thus, further research is required to develop interventions that do not only improve monitoring accuracy but that also help students to implement accurate monitoring into better control and performance.
Summing up, the aim of this thesis is to investigate under which conditions fluency is used as a cue for judgments during the learning process, how disfluency can be used to improve monitoring accuracy, and if improved monitoring accuracy leads to improved performance. By connecting metacognition research and fluency research, further theories about metacognition and theories about fluency are specified. Results show that not only the type of fluency and the design, but also the type of judgment, the type of monitoring accuracy, and the learning stage should be taken into account. Understanding conditions that affect the interplay between metacognitive processes and performance as well as understanding the underlying mechanisms is necessary to enable systematic research and to apply findings into educational settings.
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.
Banks perform important functions for the economy. Besides financial intermediation, banks provide information, liquidity, maturity- and risk-transformation (Fama, 1985). Banks ensure the transfer of liquidity from depositors to the most profitable investment projects. In addition, they perform important screening and monitoring services over investments hence contributing steadily to the efficient allocation of resources across the economy (Pathan and Faff, 2013). Since banks provide financial services all across the economy, this exposes banks (as opposed to non-banks) to systemic risk: the recent financial crisis revealed that banks can push economies into severe recessions. However, the crisis also revealed that certain bank types appear far more stable than others. For instance, cooperative banks performed better during the crisis than commercial banks. Different business models may reason these performance-differences: cooperative banks focus on relationship lending across their region, hence these banks suffered less from the collapse of the US housing market.
Since cooperative banks performed better during the crisis than commercial banks, it is quite surprising that research concerning cooperative banks is highly underrepresented in the literature. For this reason, the following three studies aim to contribute to current literature by examining three independent contemporaneous research questions in the context of cooperative banks.
Chapter 2 examines whether cooperative banks benefit from revenue diversification: Current banking literature reveals the recent trend in the overall banking industry that banks may opt for diversification by shifting their revenues to non-interest income. However, existing literature also shows that not every bank benefits from revenue diversification (Mercieca et al., 2007; Stiroh and Rumble, 2006; Goddard et al., 2008). Stiroh and Rumble (2006) find that large commercial banks (US Financial Holding Companies) perceive decreasing performance by shifting revenues towards non-interest income. Revenues from cooperative banks differ from those of commercial banks: commercial banks trade securities and derivatives, sell investment certificates and other trading assets. Concerning the lending business, commercial banks focus on providing loans for medium-sized and large companies rather than for small (private) customers. Cooperative banks rely on commission income (fees) from monetary transactions and selling insurances as a source of non-interest income. They generate most of their interest income by providing loans to small and medium-sized companies as well as to private customers in the region. These differences in revenues raise the question whether findings from Stiroh and Rumble (2006) apply to cooperative banks. For this reason, Chapter 2 evaluates a sample of German cooperative banks over the period 2005 to 2010 and aims to investigate the following research question: which cooperative banks benefit from revenue diversification?
Results show that findings from Stiroh and Rumble (2006) do not apply to cooperative banks. Revenue concentration is positive related to risk-adjusted returns (indirect effect) for cooperative banks. At the same time, non-interest income is more profitable than interest income (direct effect). The evaluation of the underlying non-interest income share shows that banks who heavily focus on non-interest income benefit by shifting towards non-interest income. This finding arises due to the fact, that the positive direct effect dominates the negative indirect effect, leading in a positive (and significant) net effect. Furthermore, results reveal a negative net effect for banks who are heavily exposed to interest generating activities. This indicates that shifting to non-interest income decreases risk-adjusted returns for these banks. Consequently, these banks do better by focusing on the interest business. Overall, results show evidence that banks need time to build capabilities, expertise and experience before trading off return and risk efficiently with regard on revenue diversification.
Chapter 3 deals with the relation between credit risk, liquidity risk, capital risk and bank efficiency: There has been rising competition in the European banking market due to technological development, deregulation and the introduction of the Euro as a common currency in recent decades. In order to remain competitive banks were forced to improve efficiency. That is, banks try to operate closer to a “best practice” production function in the sense that banks improve the input – output relation. The key question in this context is if banks improve efficiency at a cost of higher risk to compensate decreasing earnings. When it comes to bank risk, a large strand of literature discusses the issue of problem loans. Several studies identify that banks hold large shares of non-performing loans in their portfolio before becoming bankrupt (Barr and Siems, 1994; Demirgüc-Kunt, 1989). According to efficiency, studies show that the average bank generates low profits and incorporates high costs compared to the “best practice” production frontier (Fiordelisi et al., 2011; Williams, 2004). At first glance, these two issues do not seem related. However, Berger and DeYoung (1997) show that banks with poor management are less able to handle their costs (low cost-efficiency) as well as to monitor their debtors in an appropriate manner to ensure loan quality. The negative relationship between cost efficiency and non-performing loans leads to declining capital. Existing studies (e.g. Williams, 2004; Berger and DeYoung, 1997) show that banks with a low level of capital tend to engage in moral hazard behavior, which in turn can push these banks into bankruptcy.
However, the business model of cooperative banks is based on the interests of its commonly local customers (the cooperative act: § 1 GenG). This may imply that the common perception of banks engaging in moral hazard behavior may not apply to cooperative banks. Since short-term shareholder interests (as a potential factor for moral hazard behavior) play no role for cooperative banks this may support this notion. Furthermore, liquidity has been widely neglected in the existing literature, since the common perception has been that access to additional liquid funds is not an issue. However, the recent financial crisis revealed that liquidity dried up for many banks due to increased mistrust in the banking sector. Besides investigating moral hazard behavior, using data from 2005 to 2010 this study moves beyond current literature by employing a measure for liquidity risk in order to evaluate how liquidity risk relates to efficiency and capital.
Results mostly apply to current literature in this field since the empirical evaluation reveals that lower cost and profit-efficiency Granger-cause increases in credit risk. At the same time, results indicate that credit risk negatively Granger-causes cost and profit-efficiency, hence revealing a bi-directional relationship between these measures. However, most importantly, results also show a positive relationship between capital and credit risk, thus displaying that moral hazard behavior does not apply to cooperative banks. Especially the business model of cooperative banks, which is based on the interests of its commonly local customers (the cooperative act: § 1 GenG) may reason this finding. Contrary to Fiordelisi et al. (2011), results also show a negative relationship between capital and cost-efficiency, indicating that struggling cooperative banks focus on managing their cost-exposure in following periods. Concerning the employed liquidity risk measure, the authors find that banks who hold a high level of liquidity are less active in market related investments and hold high shares of equity capital. This outcome clearly reflects risk-preferences from the management of a bank.
Chapter 4 examines governance structures of cooperative banks: The financial crisis of 2007/08 led to huge distortions in the banking market. The failure of Lehman Brothers was the beginning of government interventions in various countries all over the world in order to prevent domestic economies from even further disruptions. In the aftermath of the crisis, politicians and regulators identified governance deficiencies as one major factor that contributed to the crisis. Besides existing studies in the banking literature (e.g. Beltratti and Stulz, 2012; Diamond and Rajan, 2009; Erkens et al., 2012) an OECD study from 2009 supports this notion (Kirkpatrick, 2009). Public debates increased awareness for the need of appropriate governance mechanisms at that time. Consequently, politicians and regulators called for more financial expertise on bank boards. Accordingly, the Basel Committee on Banking Supervision states in principle 2 that “board members should remain qualified, individually and collectively, for their positions. They should understand their oversight and corporate governance role and be able to exercise sound, objective judgement about the affairs of the bank.” (BCBS, 2015). Taking these perceptions into consideration the prevailing question is whether financial experts on bank boards do really foster bank stability?
This chapter aims to investigate this question by referring to the study from Minton et al. (2014). In their study, the authors investigate US commercial bank holding companies between the period 2003 and 2008. The authors find that financial experts on the board of US commercial bank holding companies promote pro-cyclical bank performance. Accordingly, the authors question regulators view of more financial experts on the board leading to more banking stability.
However, Minton et al. (2014) do not examine whether their findings accrue due to financial experts who act in the interests of shareholders or due to the issue that financial experts may have a more risk-taking attitude (due to a better understanding of financial instruments) than other board members.
Supposed that their findings accrue due to financial experts who act in the interests of shareholders. Then financial experts on the board of banks where short-term shareholder interests play no role (cooperative banks) may prove beneficial with regard on bank performance during the crisis as well as in normal times. This would mean that they use their skills and expertise to contribute sustainable growth to the bank. Contrary, if this study reveals pro-cyclical bank performance related to financial experts on the board of cooperative banks, this finding may be addressed solely to the risk-taking attitude of financial experts (since short-term shareholder interests play no role). For this reason, this chapter aims to identify the channel for the relation of financial experts and bank performance by examining the following research question: Do financial experts on the board promote pro-cyclical bank performance in a setting where short-term shareholder interests play no role?
Results show that financial experts on the board of cooperative banks (data from 2006 to 2011) do not promote pro-cyclical bank performance. Contrary, results show evidence that financial experts on the board of cooperative banks appear to foster long-term bank stability. This suggests that regulators should consider ownership structure (and hence business model of banks) when imposing new regulatory constraints for financial experts on the bank board.
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.
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.
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.
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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Modern software is often realized as a modular combination of subsystems for, e. g.,
knowledge management, visualization, verification, or the interaction with users. As
a result, software libraries from possibly different programming languages have to
work together. Even more complex the case is if different programming paradigms
have to be combined. This type of diversification of programming languages and
paradigms in just one software application can only be mastered by mechanisms
for a seamless integration of the involved programming languages. However, the
integration of the common logic programming language Prolog and the popular
object-oriented programming language Java is complicated by various interoperability
problems which stem on the one hand from the paradigmatic gap between the
programming languages, and on the other hand, from the diversity of the available
Prolog systems.
The subject of the thesis is the investigation of novel mechanisms for the integration
of logic programming in Prolog and object–oriented programming in Java. We are
particularly interested in an object–oriented, uniform approach which is not specific
to just one Prolog system. Therefore, we have first identified several important
criteria for the seamless integration of Prolog and Java from the object–oriented
perspective. The main contribution of the thesis is a novel integration framework
called the Connector Architecture for Prolog and Java (CAPJa). The framework is
completely implemented in Java and imposes no modifications to the Java Virtual
Machine or Prolog. CAPJa provides a semi–automated mechanism for the integration
of Prolog predicates into Java. For compact, readable, and object–oriented
queries to Prolog, CAPJa exploits lambda expressions with conditional and relational
operators in Java. The communication between Java and Prolog is based
on a fully automated mapping of Java objects to Prolog terms, and vice versa. In
Java, an extensible system of gateways provides connectivity with various Prolog
system and, moreover, makes any connected Prolog system easily interchangeable,
without major adaption in Java.
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.
This dissertation investigates selected causes and effects of worker mobility between firms in three empirical studies for Germany. Chapter 2 investigates the productivity effects of worker inflows to manufacturing establishments, distinguishing inflows by their previous employers’ wage level, as a proxy for productivity. The chapter is motivated by several empirical studies which find that worker inflows from more productive or higher-paying firms increase hiring firms’ productivity. The analyses in chapter 2 are based on a unique linked employer-employee data set. The findings indicate that inflows from higher-paying establishments do not increase hiring establishments’ productivity, but inflows from lower-paying establishments do. Further analyses suggest that this effect is due to a positive selectivity of such inflows from their sending establishments. These findings can be interpreted as evidence of a reallocation process by which the best employees of lower-paying establishments become hired by higher-paying establishments. This process reflects the assortative pattern of worker mobility in Germany documented by Card et al. (2013) for the past decades. The chapter thus contributes to the literature by linking establishment-level productivity analysis to the assortative pattern of inter-firm worker mobility, thereby providing a micro-foundation for the latter.
Chapter 3 focuses on a positive selection of workers moving between firms from another, more specific perspective. The analysis focuses on the importance of regional labor market competition for establishments’ apprentice training and poaching of apprenticeship completers. Previous studies have found that firms provide less training if they are located in regions with strong labor market competition. This finding is usually interpreted as evidence of a higher risk of poaching in these regions. Yet, there is no direct evidence that regional competition is positively correlated with poaching. Building on a recently established approach to ex-post identify poaching of apprenticeship completers, this chapter is the first to directly investigate the correlation between regional labor market competition and poaching. Using German administrative data, it is found that competition indeed increases training establishments’ probability of becoming poaching victims. However, poaching victims do not change their apprenticeship training activity in reaction to poaching. Instead, the findings indicate that the lower training activity in competitive regions can be attributed to lower retention rates, as well as a less adverse selection and lower labor and hiring costs of apprenticeship completers hired from rivals.
Chapter 4 investigates the effects of local broadband internet availability on establishment-level employment growth. The analysis uses data for Germany in the years 2005-2009, when broadband was introduced in rural regions of Western Germany and in large parts of Eastern Germany. Technical frictions in broadband rollout are exploited to obtain exogenous variation in local broadband availability. The results suggest that broadband expansion had a positive effect on employment growth in the Western German service sector and a negative effect in Western German manufacturing, suggesting that broadband expansion has accelerated the reallocation of workers from manufacturing to services. Furthermore, this pattern of results is driven by pronounced positive effects in knowledge- and computer-intensive industries, suggesting that it is the actual use of broadband in the production process that leads to complementary hiring, respectively a slowdown of employment growth, in the respective sectors. For Eastern Germany, no significant employment growth effects are found.
This dissertation is dealing with three mathematical areas, namely polynomial matrices over finite fields, linear systems and coding theory.
Coprimeness properties of polynomial matrices provide criteria for the reachability and observability of interconnected linear systems. Since time-discrete linear systems over finite fields and convolutional codes are basically the same objects, these results could be transfered to criteria for non-catastrophicity of convolutional codes.
We calculate the probability that specially structured polynomial matrices are right prime. In particular, formulas for the number of pairwise coprime polynomials and for the number of mutually left coprime polynomial matrices are calculated. This leads to the probability that a parallel connected linear system is reachable and that a parallel connected convolutional codes is non-catastrophic.
Moreover, the corresponding probabilities are calculated for other networks of linear systems and convolutional codes, such as series connection.
Furthermore, the probabilities that a convolutional codes is MDP and that a clock code is MDS are approximated.
Finally, we consider the probability of finding a solution for a linear network coding problem.
African trypanosomiasis is a disease endemic to sub-Saharan Africa. It affects humans as well as wild and domestic animals. The human form of the disease is known as sleeping sickness and the animal form as nagana, which are usually fatal if left untreated. The cause of African trypanosomiasis is the unicellular parasite Trypanosoma brucei. During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host the parasite multiplies as bloodstream form (BSF) extracellularly in the bloodstream or the lymphatic system. Survival of BSF parasites relies on immune evasion by antigenic variation of surface proteins because its extracellular lifestyle leads to direct exposure to immune responses. At any given time each BSF cell expresses a single type of variant surface glycoprotein (VSG) on its surface from a large repertoire. The active VSG is transcribed from one of 15 specialized subtelomeric domains, termed bloodstream expression sites (BESs). The remaining 14 BESs are silenced. This monoallelic expression and periodic switching of the expressed VSG enables to escape the immune response and to establish a persistent infection in the mammalian host. During developmental differentiation from BSF to the insect vector-resident procyclic form (PCF), the active BES is transcriptionally silenced to stop VSG transcription. Thus, all 15 BESs are inactive in the PCF cells as surface protein expression is developmentally regulated.
Previous reports have shown that the telomere complex components TbTRF, TbRAP1 and TbTIF2 are involved in VSG transcriptional regulation. However, the precise nature of their contribution remains unclear. In addition, no information is available about the role of telomeres in the initiation and regulation of developmental BES silencing. To gain insights into the regulatory mechanisms of telomeres on VSG transcription and developmental repression it is therefore essential to identify the complete composition of the trypanosome telomere complex.
To this end, we used two complementary biochemical approaches and quantitative label-free interactomics to determine the composition of telomere protein complexes in T. brucei. Firstly, using a telomeric pull-down assay we found 17 potential telomere-binding proteins including the known telomere-binding proteins TbTRF and TbTIF2. Secondly, by performing a co-immunoprecipitation experiment to elucidate TbTRF interactions we co-purified five proteins. All of these five proteins were also enriched with telomeric DNA in the pull-down assay.
To validate these data, I characterized one of the proteins found in both experiments (TelBP1). In BSF cells, TelBP1 co-localizes with TbTRF and interacts with already described telomere-binding proteins such as TbTRF, TbTIF2 and TbRAP1 indicating that TelBP1 is a novel component of the telomere complex in trypanosomes. Interestingly, protein interaction studies in PCF cells suggested a different telomere complex composition compared to BSF cells. In contrast to known members of the telomere complex, TelBP1 is dispensable for cell viability indicating that its function might be uncoupled from the known telomere-binding proteins. Overexpression of TelBP1 had also no effect on cell viability, but led to the discovery of two additional shorter isoforms of TelBP1. However, their source and function remained elusive.
Although TelBP1 is not essential for cell viability, western blot analysis revealed a 4-fold upregulation of TelBP1 in the BSF stage compared to the PCF stage supporting the concept of a dynamic telomere complex composition. We observed that TelBP1 influences the kinetics of transcriptional BES silencing during developmental transition from BSF to PCF. Deletion of TelBP1 caused faster BES silencing compared to wild-type parasites.
Taken together, TelBP1 function illustrates that developmental BES silencing is a fine-tuned process, which involves stage-specific changes in telomere complex formation.
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.
In this thesis the excited-state dynamics of radicals and biradicals were characterized with femtosecond pump-probe spectroscopy.
These open-shell molecules play important roles as combustion intermediates, in the formation of soot and polycyclic aromatic hydrocarbons, in atmospheric chemistry and in the formation of complex molecules in the interstellar medium and galactic clouds. In these processes molecules frequently occur in some excited state, excited either by thermal energy or radiation. Knowledge of the reactivity and dynamics of these excited states completes our understanding of these complex processes.
These highly reactive molecules were produced via pyrolysis from suitable precursors and examined in a molecular beam under collision-free conditions. A first laser now excites the molecule, and a second laser ionizes it. Time-of-flight mass spectrometry allowed a first identification of the molecule, photoelectron spectroscopy a complete characterization of the molecule - under the condition that the mass spectrum was dominated by only one mass. The photoelectron spectrum was obtained via velocity-map imaging, providing an insight in the electronic states involved. Ion velocity map imaging allowed separation of signal from direct ionization of the radical in the molecular beam and dissociative photoionization of the precursor. During this thesis a modified pBasex algorithm was developed and implemented in python, providing an image inversion tool without interpolation of data points. Especially for noisy photoelectron images this new algorithm delivers better results.
Some highlighted results:
• The 2-methylallyl radical was excited in the ππ*-state with different internal energies using three different pump wavelengths (240.6 , 238.0 and 236.0 nm). Ionized with 800 nm multi-photon probe, the photoelectron spectra shows a s-Rydberg fingerprint spectrum, a highly positive photoelectron anisotropy of 1.5 and a bi-exponential decay ( τ1= 141\pm43 fs, τ2= 4.0\pm0.2 ps for 240.6 nm pump), where the second time-constant shortens for lower wavelengths. Field-induced surface hopping dynamics calculations confirm that the initially excited ππ*-state relaxes very fast to an s-Rydberg state (first experimentally observed time-constant), and then more slowly to the first excited state/ground state (second time-constant). With higher excitation energies the conical intersection between the s-Rydberg-state and the first excited state is reached faster, resulting in shorter life-times.
• The benzyl radical was excited yith 265 nm and probed with two wavelengths, 798 nm and 398 nm. Probed with 798 nm it shows a bi-exponential decay (\tau_{1}=84\pm5 fs, \tau_{2}=1.55\pm0.12 ps), whereas with 398 nm probe only the first time-constant is observed (\tau_{1}=89\pm5 fs). The photoelectron spectra with 798 nm probe is comparable to the spectrum with 398 nm probe during the first 60 fs, at longer times an additional band appears. This band is due to a [1+3']-process, whereas with 398 nm only signal from a [1+1']-process can be observed. Non-adiabatic dynamic on the fly calculations show that the initially excited, nearly degenerate ππ/p-Rydberg-states relax very fast (first time-constant) to an s-Rydberg state. This s-Rydberg state can no longer be ionized with 398 nm, but with 798 nm ionization via intermediate resonances is still possible. The s-Rydberg state then decays to the first excited state (second time-constant), which is long-lived.
• Para-xylylene, excited with 266 nm into the S2-state and probed with 800 nm, shows a bi-exponential decay (\tau_{1}=38\pm7 fs, \tau_{2}=407\pm9 fs). The initially excited S2-state decays quickly to S1-state, which shows dissociative photoionization. The population of the S1-state is directly visible in the masses of the dissociative photoionization products, benzene and the para-xylylene -H.
• Ortho-benzyne, produced via pyrolysis from benzocyclobutendione, was excited with 266 nm in the S2 state and probed with 800 nm. In its time-resolved mass spectra the dynamic of the ortho-benzyne signal was superposed with the dynamics from dissociative photoionization of the precursor and of the ortho-benzyne-dimer. With time-resolved ion imaging gated on the ortho-benzyne these processes could be seperated, showing that the S2-state of ortho-benzyne relaxes within 50 fs to the S1-state.
The synapse-associated protein of 47 kDa (Sap47) in Drosophila melanogaster is the founding member of a phylogenetically conserved protein family of hitherto unknown molecular function. Sap47 is localized throughout the entire neuropil of adult and larval brains and closely associated with glutamatergic presynaptic vesicles of larval motoneurons. Flies lacking the protein are viable and fertile and do not exhibit gross structural or marked behavioral deficiencies indicating that Sap47 is dispensable for basic synaptic function, or that its function is compensated by other related proteins.
Syap1 - the mammalian homologue of Sap47 - was reported to play an essential role in Akt1 phosphorylation in various non-neuronal cells by promoting the association of mTORC2 with Akt1 which is critical for the downstream signaling cascade for adipogenesis. The function of Syap1 in the vertebrate nervous system, however, is unknown so far.
The present study provides a first description of the subcellular localization of mouse Syap1 in cultured motoneurons as well as in selected structures of the adult mouse nervous system and reports initial functional experiments. Preceding all descriptive experiments, commercially available Syap1 antibodies were tested for their specificity and suitability for this study. One antibody raised against the human protein was found to recognize specifically both the human and murine Syap1 protein, providing an indispensable tool for biochemical, immunocytochemical and immunohistochemical studies.
In the course of this work, a Syap1 knockout mouse was established and investigated. These mice are viable and fertile and do not show obvious changes in morphology or phenotype. As observed for Sap47 in flies, Syap1 is widely distributed in the synaptic neuropil, particularly in regions rich in glutamatergic synapses but it was also detected at perinuclear Golgi-associated sites in certain groups of neuronal somata. In motoneurons the protein is especially observed in similar perinuclear structures, partially overlapping with Golgi markers and in axons, dendrites and axonal growth cones. Biochemical and immunohistochemical analyses showed widespread Syap1 expression in the central nervous system with regionally distinct distribution patterns in cerebellum, hippocampus or olfactory bulb. Besides its expression in neurons, Syap1 is also detected in non-neuronal tissue e.g. liver, kidney and muscle tissue. In contrast, non-neuronal cells in the brain lack the typical perinuclear accumulation.
First functional studies with cultured primary motoneurons on developmental, structural and functional aspects reveal no influence of Syap1 depletion on survival and morphological features such as axon length or dendritic length. Contrary to expectations, in neuronal tissues or cultured motoneurons a reduction of Akt phosphorylation at Ser473 or Thr308 was not detected after Syap1 knockdown or knockout.
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.
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.
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.
In highly polarized cells like neurons, cytoskeleton dynamics play a crucial role in establishing neuronal connections during development and are required for adult plasticity. Actin turnover is particularly important for neurite growth, axon path finding, branching and synaptogenesis. Motoneurons establish several thousand branches that innervate neuromuscular synapses (NMJs). Axonal branching and terminal arborization are fundamental events during the establishment of synapses in motor endplates. Branching process is triggered by the assembly of actin filaments along the axon shaft giving rise to filopodia formation. The unique contribution of the three actin isoforms, α-, β- and γ-actin, in filopodia stability and dynamics during this process is not well characterized. Here, we performed high resolution in situ hybridization and qRT-PCR and showed that in primary mouse motoneurons α-, β- and γ-actin isoforms are expressed and their transcripts are translocated into axons. Using FRAP experiments, we showed that transcripts for α-, β- and γ-actin become locally translated in axonal growth cones and translation hot spots of the axonal branch points. Using live cell imaging, we showed that shRNA depletion of α-actin reduces dynamics of axonal filopodia which correlates with reduced number of collateral branches and impairs axon elongation. Depletion of β-actin correlates with reduced dynamics of growth cone filopoida, disturbs axon elongation and impairs presynaptic differentiation. Also, depletion of γ-actin impairs axonal growth and decreases axonal filopodia dynamics. These findings implicate that actin isoforms accomplish unique functions during development of motor axons. Depletions of β- and γ-actin lead to compensatory upregulation of other two isoforms. Consistent with this, total actin levels remain unaltered and F-actin polymerization capacity is preserved. After the knockdown of either α- or γ-actin, the levels of β-actin increase in the G-actin pool indicating that polymerization and stability of β-actin filaments depend on α- or γ-actin. This study provides evidence both for unique and overlapping function of actin isoforms in motoneuron growth and differentiation. In the soma of developing motoneurons, actin isoforms act redundantly and thus could compensate for each other’s loss. In the axon, α-, β- and γ-actin accomplish specific functions, i.e. β-actin regulates axon elongation and plasticity and α- and γ-actin regulate axonal branching.
Furthermore, we show that both axonal transport and local translation of α-, β- and γ-actin isoforms are impaired in Smn knockout motoneurons, indicating a role for Smn protein in RNA granule assembly and local translation of these actin isoforms in primary mouse motoneurons.
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.
The dissertation deals with the market and welfare effects of different business practices and the firm's incentives to use them: resale price maintenance, revenue sharing of a platform operator, membership fees to buyers using a platform and patent licensing.
In the second chapter we investigate the incentives of two manufacturers with common retailers to use resale price maintenance (RPM). Retailers provide product specific services that increase demand and manufacturers use minimum RPM to compete for favorable services for their products. Minimum RPM increases consumer pricesby voiding retailer price competition and can create a prisoner’s dilemma for manufacturers without increasing, and possibly even decreasing the overall service level. If manufacturer market power is asymmetric, minimum RPM tends to distort the allocation of sales services towards the high-priced products of the manufacturer with more market power. These results challenge the service argument as an efficiency defense for minimum RPM.
The third chapter deals with trade platforms whose operators not only allow third party sellers to offer their products to consumers, but also offer products themselves. In this context, the platform operator faces a hold-up problem if he uses classical two-part tariffs only (which previous literature on two-sided markets has focused on) as potential competition between the platform operator and sellers reduces platform attractiveness. Since some sellers refuse to join the platform, some products that are not known to the platform operator will not be offered at all. We discuss the effects of different platform tariffs on this hold-up problem. We find that revenue-based fees lower the platform operator's incentives to compete with sellers, increasing platform attractiveness. Therefore, charging such proportional fees can be profitable, what may explain why several trade platforms indeed charge proportional fees.
The fourth chapter investigates the optimal tariff system in a model in which buyers are heterogeneous. A platform model is presented in which transactions are modeled explicitly and buyers can differ in their expected valuations when they decide to join the platform. The main effect that the model identifies is that the participation decision sorts buyers according to their expected valuations. This affects the pricing of sellers. Furthermore diffing form the usual approach, in which buyers are ex-ante homogeneous, the platform does not internalize the full transaction surplus. Hence it does not implement the socially efficient price on the platform, also it has control of the price with the transaction fee.
The fifth chapter investigates the effects of licensing on the market outcome after the patent has expired. In a setting with endogenous entry, a licensee has a head start over the competition which translated into a first mover advantage if strategies are strategic substitutes. As competitive strategies quantities and informative advertising are considered explicitly. We find that although licensing increases the joint profit of the patentee and licensee, this does not necessarily come from a reduction in consumer surplus or other firms profits. For the case of quantity competition we show that licensing is welfare improving. For the case of informative advertising, however, we show that licensing increases prices and is thus detrimental to consumer surplus.
The contact of hot melt with liquid water - called Molten Fuel Coolant Interaction (MFCI) - can result in vivid explosions. Such explosions can occur in different scenarios: in steel or powerplants but also in volcanoes. Because of the possible dramatic consequences of such explosions an investigation of the explosion process is necessary.
Fundamental basics of this process are already discovered and explained, such as the frame conditions for these explosions. It has been shown that energy transfer during an MFCI-process can be very high because of the transfer of thermal energy caused by positive feedback mechanisms.
Up to now the influence of several varying parameters on the energy transfer and the explosions is not yet investigated sufficiently. An important parameter is the melt temperature, because the amount of possibly transferable energy depends on it. The investigation of this influence is the main aim of this work. Therefor metallic tin melt was used, because of its nearly constant thermal material properties in a wide temperature range. With tin melt research in the temperature range from 400 °C up to 1000 °C are
possible.
One important result is the lower temperature limit for vapor film stability in the experiments. For low melt temperatures up to about 600 °C the vapor film is so unstable that it already can collapse before the mechanical trigger. As expected the transferred thermal energy all in all increases with higher temperatures. Although this effect sometimes is superposed by other influences such as the premix of melt and water, the result is confirmed after a consequent filtering of the remaining influences. This trend is not only recognizable in the amount of transferred energy, but also in the fragmentation of melt or the vaporizing water. But also the other influences on MFCI-explosions showed interesting results in the frame of this work. To perform the experiments the installation and preparation of the experimental Setup in the laboratory were necessary.
In order to compare the results to volcanism and to get a better investigation of the brittle fragmentation
of melt additional runs with magmatic melt were made. In the results the thermal power during energy transfer could be estimated. Furthermore the model of “cooling fragments “ could be usefully applied.
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.
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.
The obligate human pathogen Neisseria gonorrhoeae is responsible for the widespread sexually transmitted disease gonorrhoea, which in rare cases also leads to the development of disseminated gonococcal infection (DGI). DGI is mediated by PorBIA-expressing bacteria that invade host cells under low phosphate condition by interaction with the scavenger receptor-1 (SREC-I) expressed on the surface of endothelial cells. The interaction of PorBIA and SREC-I was analysed using different in vitro approaches, including surface plasmon resonance experiments that revealed a direct phosphate-independent high affinity interaction of SREC-I to PorBIA. However, the same binding affinity was also found for the other allele PorBIB, which indicates unspecific binding and suggests that the applied methods were unsuitable for this interaction analysis.
Since N. gonorrhoeae was recently classified as a “super-bug” due to a rising number of antibiotic-resistant strains, this study aimed to discover inhibitors against the PorBIA-mediated invasion of N. gonorrhoeae. Additionally, inhibitors were searched against the human pathogen Chlamydia trachomatis, which causes sexually transmitted infections as well as infections of the upper inner eyelid. 68 compounds, including plant-derived small molecules, extracts or pure compounds of marine sponges or sponge-associated bacteria and pipecolic acid derivatives, were screened using an automated microscopy based approach. No active substances against N. gonorrhoeae could be identified, while seven highly antichlamydial compounds were detected.
The pipecolic acid derivatives were synthesized as potential inhibitors of the virulence-associated “macrophage infectivity potentiator” (MIP), which exhibits a peptidyl prolyl cis-trans isomerase (PPIase) enzyme activity. This study investigated the role of C. trachomatis and N. gonorrhoeae MIP during infection. The two inhibitors PipN3 and PipN4 decreased the PPIase activity of recombinant chlamydial and neisserial MIP in a dose-dependent manner. Both compounds affected the chlamydial growth and development in epithelial cells. Furthermore, this work demonstrated the contribution of MIP to a prolonged survival of N. gonorrhoeae in the presence of neutrophils, which was significantly reduced in the presence of PipN3 and PipN4.
SF2446A2 was one of the compounds that had a severe effect on the growth and development of C. trachomatis. The analysis of the mode of action of SF2446A2 revealed an inhibitory effect of the compound on the mitochondrial respiration and mitochondrial ATP
production of the host cell. However, the chlamydial development was independent of proper functional mitochondria, which excluded the connection of the antichlamydial properties of SF2446A2 with its inhibition of the respiratory chain. Only the depletion of cellular ATP by blocking glycolysis and mitochondrial respiratory chain inhibited the chlamydial growth. A direct effect of SF2446A2 on C. trachomatis was assumed, since the growth of the bacteria N. gonorrhoeae and Staphylococcus aureus was also affected by the compound.
In summary, this study identified the severe antichlamydial activity of plant-derived naphthoquinones and the compounds derived from marine sponges or sponge-associated bacteria SF2446A2, ageloline A and gelliusterol E. Furthermore, the work points out the importance of the MIP proteins during infection and presents pipecolic acid derivatives as novel antimicrobials against N. gonorrhoeae and C. trachomatis.
Spliceosomal U-rich small ribonucleoprotein particles (U snRNPs) are the major building
blocks of the nuclear pre-mRNA splicing machinery. The core composition of U snRNPs
includes the name giving U snRNA and a set of seven common (Sm) proteins termed Sm
B/B’, D1, D2, D3, E, F and G. These Sm proteins are arranged in the form of a toroidal ring on
the single stranded conserved sequence element in the snRNA to form the Sm core domain.
Even though U snRNPs assemble spontaneously in vitro, their assembly in vivo requires an
amazingly large number of trans-acting assembly factors united in the Protein Arginine
Methyltransferase 5 (PRMT5) and the Survival Motor Neuron (SMN) complexes. The
cytoplasmic assembly pathway of U snRNPs can be divided into the early and the late phase.
The early phase is dominated by the assembly chaperone, pICln, a subunit of the PRMT5
complex. This factor binds to Sm proteins and delivers them in a pICln-bound form to the
PRMT5 complex. The early assembly phase then segregates into two lines. In one assembly
line, a stable hexameric ring intermediate (6S complex) composed of pICln and the five Sm
proteins D1, D2, F, E and G, is formed. This intermediate forms at the PRMT5 complex but
dissociates from the latter upon completion of its assembly. Within the 6S complex, these Sm
proteins are pre-organized into respective spatial positions adopted in the assembled U
snRNP. The other assembly line forms a protein trimer composed of pICln, Sm B/B’ and D3,
which unlike the 6S complex is not released from the PRMT5 complex. As a consequence of
their association with pICln, Sm proteins are kinetically trapped and fail to proceed in the
assembly pathway. The late phase of the U snRNP formation is dominated by the SMN
complex, which resolves this kinetic trap by dissociating pICln from the pre-organized Sm
proteins and, subsequently catalyzes the loading of the Sm proteins on the U snRNA.
Even though basic principles of U snRNP assembly have been understood in some detail, the
question arises as to why cells employ sophisticated assembly machinery for the assembly
despite the reaction occurring spontaneously in vitro. A few studies have shown that the
system works towards rendering specificity to the assembly reaction. However, Sm proteins
in their free form expose hydrophobic surfaces to the cytosolic solvent. Hence, I reasoned that
the assembly machinery of snRNPs might also prevent Sm protein aggregation.
In this thesis, I describe the work that leads to the discovery of a multi-layered regulatory
network for Sm proteins involving post-transcriptional and post-translational surveillance
mechanisms. Here, I show that the reduced level of SMN (a key assembly factor of the late
phase) leads to the initial tailback of Sm proteins over pICln followed by the transcriptional
down regulation of Sm protein encoding mRNAs. In contrast, depletion of pICln, a key factor
of the early phase, results in the retention of Sm proteins on the ribosomes followed by their
degradation via autophagy. Furthermore, I show that exceeding levels of Sm proteins over
pICln caused by overexpression results in aggregation and mis-localization of Sm proteins.
Thus, my findings uncover a complex regulatory network that helps to maintain the cellular
U snRNP homeostasis by either preventing or clearing the unassembled Sm protein
aggregates when they are not faithfully incorporated into the U snRNPs.
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.
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.
The progress which has been made in semiconductor chip production in recent years enables a multitude of cores on a single die. However, due to further decreasing structure sizes, fault tolerance and energy consumption will represent key challenges. Furthermore, an efficient communication infrastructure is indispensable due to the high parallelism at those systems. The predominant communication system at such highly parallel systems is a Network on Chip (NoC). The focus of this thesis is on NoCs which are based on deflection routing. In this context, contributions are made to two domains, fault tolerance and dimensioning of the optimal link width. Both aspects are essential for the application of reliable, energy efficient, and deflection routing based NoCs.
It is expected that future semiconductor systems have to cope with high fault probabilities. The inherently given high connectivity of most NoC topologies can be exploited to tolerate the breakdown of links and other components. In this thesis, a fault-tolerant router architecture has been developed, which stands out for the deployed interconnection architecture and the method to overcome complex fault situations. The presented simulation results show, all data packets arrive at their destination, even at high fault probabilities. In contrast to routing table based architectures, the hardware costs of the herein presented architecture are lower and, in particular, independent of the number of components in the network.
Besides fault tolerance, hardware costs and energy efficiency are of great importance. The utilized link width has a decisive influence on these aspects. In particular, at deflection routing based NoCs, over- and under-sizing of the link width leads to unnecessary high hardware costs and bad performance, respectively. In the second part of this thesis, the optimal link width at deflection routing based NoCs is investigated. Additionally, a method to reduce the link width is introduced. Simulation and synthesis results show, the herein presented method allows a significant reduction of hardware costs at comparable performance.
Driving simulators are powerful research tools. Countless simulator studies have contributed to traffic safety over the last decades. Constant improvements in simulator technology call for a measureable scale to assess driving simulators with regard to their utility in human factors research. A promising psychological construct to do so is presence. It is commonly defined as the feeling of being located in a remote or virtual environment that seems to be real. Another aspect of presence describes the ability to act there successfully.
The main aim of this thesis is to develop a presence model dedicated to the application in driving simulators. Established models have been combined and extended in order to gain a comprehensive model of presence that allows understanding its emergence and deriving recommendations on how to design or improve driving simulators. The five studies presented in this thesis investigate specific postulated model components and their interactions. All studies deal with motorcycling or a motorcycle riding simulator as exemplary field of application.
The first study used a speed estimation task to investigate the contribution of different sensory cues to presence. While visualization plays a particularly important role, further improvements could be achieved by adding more consistent sensory stimuli to the virtual environment. Auditory, proprioceptive and vestibular cues have been subject to investigation. In the second study, the speed production method was applied. It confirmed the positive contribution of action to presence as predicted by psychocybernetic models. The third study dealt with the effect of training on presence. Hence, no positive effect was observed. The fourth study aimed at replicating previous findings on sensory fidelity and diversity in a more complex riding situation than only longitudinal vehicle control. The riders had to cross an unexpectedly appearing deep pit with the virtual motorcycle. The contribution of more consistent sensory stimulation on presence was successfully shown in this scenario, too. The final study was a real riding experiment that delivered reference values for the speed estimation capabilities of motorcycle riders. Besides higher variations in the simulator data, the general speed estimation performance was on a comparable level. Different measures, such as subjective ratings, behavioral responses, performance, and physiological reactions, have been applied as presence indicators.
These studies’ findings deliver evidence for the meaningful application of the proposed presence model in driving simulator settings. The results suggest that presence can be interpreted as a quality measure for perception in virtual environments. In line with psychocybernetic models, taking action, which is seen as controlling perception, enhances this quality even further. Describing the psychological construct of presence in a theoretical framework that takes the diversity of perception and action in driving simulator settings into account closes a gap in traffic psychological research.
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.
Drug delivery of therapeutic gases – strategies for controlled and local delivery of carbon monoxide
(2017)
The isoenzyme heme oxygenase 1 (HO-1) is a key element for maintaining cellular homeostasis. Upregulated in response to cellular stress, the HO-1 degrades heme into carbon monoxide (CO), biliverdin, and Fe2+. By means of a local cell-protective feedback loop the enzyme triggers numerous effects including anti-oxidative, anti-apoptotic, and anti-inflammatory events associated with complex signalling patterns which are largely orchestrated by CO. Various approaches to mimic this physiological HO-1 / CO system aiming for a treatment of medical conditions have been described [1]. These preclinical studies commonly applied CO systemically via (i) inhalation or (ii) using CO-Releasing Molecules (CORMs) [2]. The clinical use of these approaches, however, is challenged by a lack of practicability and substantial safety issues associated with the toxicity of high systemic doses of CO that are required for triggering therapeutic effects. Therefore, one rational of this thesis is to describe and evaluate strategies for the local delivery of CO aiming for safe and effective CO therapeutics of tomorrow.
Desert ants of the genus Cataglyphis (Formicinae) are widely distributed in arid
areas of the palearctic ecozone. Their habitats range from relatively cluttered environments in the Mediterranean area to almost landmark free deserts. Due to their
sophisticated navigational toolkit, mainly based on the sky-compass, they were
studied extensively for the last 4 decades and are an exceptional model organism
for navigation. Cataglyphis ants exhibit a temporal polyethism: interior workers
stay inside the dark nest and serve as repletes for the first ∼2 weeks of their adult
life (interior I). They then switch to nursing and nest maintenance (interior II)
until they transition to become day-active outdoor foragers after ∼4 weeks. The
latter switch in tasks involves a transition phase of ∼2-3 days during which the
ants perform learning and orientation walks. Only after this last phase do the ants
start to scavenge for food as foragers.
In this present thesis I address two main questions using Cataglyphis desert ants
as a model organism:
1. What are the underlying mechanisms of temporal polyethism?
2. What is the neuronal basis of sky-compass based navigation in Cataglyphis
ants?
Neuropeptides are important regulators of insect physiology and behavior and as
such are promising candidates regarding the regulation of temporal polyethism in
Cataglyphis ants. Neuropeptides are processed from large precursor proteins and undergo substantial post-translational modifications. Therefore, it is crucial to biochemically identify annotated peptides. As hardly any peptide data are available
for ants and no relevant genomic data has been recorded for Cataglyphis, I started
out to identify the neuropeptidome of adult Camponotus floridanus (Formicinae)
workers (manuscript 1). This resulted in the first neuropeptidome described in an
ant species – 39 neuropeptides out of 18 peptide families. Employing a targeted
approach, I identified allatostatin A (AstA), allatotropin (AT), short neuropeptide
F (sNPF) and tachykinin (TK) using mass spectrometry and immunohistology to
investigate the distribution of AstA, AT and TK in the brain (manuscript 2). All
three peptides are localized in the central complex, a brain center for sensory integration and high-order control of locomotion behavior. In addition, AstA and
TK were also found in visual and olfactory input regions and in the mushroom
bodies, the centers for learning and memory formation. Comparing the TK immunostaining in the brain of 1, 7 and 14 days old dark kept animals revealed that
the distribution in the central complex changes, most prominently in the 14 day
old group. In the Drosophila central complex TK modulates locomotor activity
levels. I therefore hypothesize that TK is involved in the internal regulation of the
interior I–interior II transition which occurs after ∼2 weeks of age.
I designed a behavioral setup to test the effect of neuropeptides on the two traits:
’locomotor activity level’ and ’phototaxis’ (manuscript 3). The test showed that
interior I ants are less active than interior II ants, which again are less active
than foragers. Furthermore, interior ants are negatively phototactic compared to
a higher frequency of positive phototaxis in foragers. Testing the influence of AstA
and AT on the ants’ behavior revealed a stage-specific effect: while interior I behavior is not obviously influenced, foragers become positively phototactic and more
active after AT injection and less active after AstA injection. I further tested the
effect of light exposure on the two behavioral traits of interior workers and show that it rises locomotor activity and results in decreased negative phototaxis in
interior ants. However, both interior stages are still more negatively phototactic
than foragers and only the activity level of interior II ants is raised to the forager
level. These results support the hypothesis that neuropeptides and light influence
behavior in a stage-specific manner.
The second objective of this thesis was to investigate the neuronal basis of skycompass navigation in Cataglyphis (manuscript 4). Anatomical localization of the
sky-compass pathway revealed that its general organization is highly similar to
other insect species. I further focused on giant synapses in the lateral complex,
the last relay station before sky-compass information enters the central complex.
A comparison of their numbers between newly eclosed ants and foragers discloses
a rise in synapse numbers from indoor worker to forager, suggesting task-related
synaptic plasticity in the sky-compass pathway. Subsequently I compared synapse
numbers in light preexposed ants and in dark-kept, aged ants. This experiment
showed that light as opposed to age is necessary and sufficient to trigger this rise
in synapse number. The number of newly formed synapses further depends on the
spectral properties of the light to which the ants were exposed to.
Taken together, I described neuropeptides in C. floridanus and C. fortis, and provided first evidence that they influence temporal polyethism in Cataglyphis ants.
I further showed that the extent to which neuropeptides and light can influence
behavior depends on the animals’ state, suggesting that the system is only responsive under certain circumstances. These results provided first insight into the
neuronal regulation of temporal polyethism in Cataglyphis. Furthermore, I characterized the neuronal substrate for sky-compass navigation for the first time in
Cataglyphis. The high level of structural synaptic plasticity in this pathway linked
to the interior–forager transition might be particularly relevant for the initial calibration of the ants’ compass system.
The inhibitory glycine receptors are one of the major mediators of rapid synaptic inhibition in the mammalian brainstem, spinal cord and higher brain centres. They are ligand-gated ion channels that are mainly involved in the regulation of motor functions. Dysfunction of the receptor is associated with motor disorders such as hypereklepxia or some forms of spasticity. GlyR is composed of two glycosylated integral membrane proteins α and β and a peripheral membrane protein of gephyrin. Moreover, there are four known isoforms of the α-subunit (α1-4) of GlyR while there is a single β-subunit. Glycine receptors can be homomeric including α subunits only or heteromeric containing both α and β subunits. To date, strychnine is the ligand that has the highest affinity as glycine receptor ligand. It acts as a competitive antagonist of glycine that results in the inhibition of Cl- ions permeation and consequently reducing GlyR-mediated inhibition.
For a long time, the details of the molecular mechanism of GlyRs inactivation by strychnine were insufficient due to the lack of high-resolution structures of the receptor. Only homology models based on structures of other cys-loop receptors have been available. Recently, 3.0 Å X-ray structure of the human glycine receptor- α3 homopentamer in complex with strychnine, as well as electro cryo-microscopy structures of the zebra fish α1 GlyR in complex with strychnine and glycine were published. Such information provided detailed insight into the molecular recognition of agonists and antagonists and mechanisms of GlyR activation and inactivation.
Very recently, a series of dimeric strychnine analogs obtained by diamide formation of two molecules of 2-aminostrychnine with diacids of different chain length was pharmacologically evaluated at human α1 and α1β glycine receptors. None of the dimeric analogs was superior to strychnine.
The present work focused on the extension of the structure-activity relationships of strychnine derivatives at glycine receptors
All the synthesized compounds were pharmacologically evaluated at human α1 and α1β glycine receptors in a functional FLIPRTM assay and the most potent analogs were pharmacologically evaluated in a whole cell patch-clamp assay and in [3H]strychnine binding studies.
It was reported that 11-(E)-isonitrosostrychnine displayed a 2-times increased binding to both α1 and α1β glycine receptors which prompted us to choose the hydroxyl group as a suitable attachment point to connect two 11-(E)-isonitrosostrychnine molecules using a spacer. In order to explore the GlyR pocket tolerance for oxime extension, a series of oxime ethers with different spacer lengths and sterical/lipophilic properties were synthesized biologically evaluated. Among all the oxime ethers, methyl, allyl and propagyl oxime ethers were the most potent antagonists displaying IC50 values similar to that of strychnine. These findings indicated that strychnine binding site at GlyRs comprises an additional small lipophilic pocket located in close proximity to C11 of strychnine and the groups best accommodated in this pocket are (E)-allyl and (E)-propagyl oxime ethers.
Moreover, 11-aminostrychnine, and the corresponding propionamide were prepared and pharmacologically evaluated to examine the amide function at C11 as potential linker.
A series of dimeric strychnine analogs designed by linking two strychnine molecules through amino groups in position 11 with diacids were synthesized and tested in binding studies and functional assays at human α1 and α1β glycine receptors. The synthesized bivalent ligands were designed to bind simultaneously to two α-subunits of the pentameric glycine receptors causing a possibly stronger inhibition than the monomeric strychnine. However, all the bivalent derivatives showed no significant difference in potency compared to strychnine. When comparing the reference monomeric propionamide containing ethylene spacer to the dimeric ligand containing butylene spacer, a 3-fold increase in potency was observed. Since the dimer containing (CH2)10 spacer length was found to be equipotent to strychnine, it is assumed that one molecule of strychnine binds to the receptor and the ‘additional’ strychnine molecule in the dimer probably protrudes from the orthosteric binding sites of the receptor.
Multiple sclerosis (MS) is the most prevalent neurological disease of the central nervous system (CNS) in young adults and is characterized by inflammation, demyelination and axonal pathology that result in multiple neurological and cognitive deficits. The focus of MS research remains on modulating the immune response, but common therapeutic strategies are only effective in slowing down disease progression and attenuating the symptoms; they cannot cure the disease. Developing an option to prevent neurodegeneration early on would be a valuable addition to the current standard of care for MS. Based on our results we suggest that application of nimodipine could be an effective way to target both neuroinflammation and neurodegeneration. We performed detailed analyses of neurodegeneration in experimental autoimmune encephalomyelitis (EAE), an animal model of MS, and in in vitro experiments regarding the effect of the clinically well-established L-type calcium channel antagonist nimodipine. Nimodipine treatment attenuated the course of EAE and spinal cord histopathology. Furthermore, it promoted remyelination. The latter could be due to the protective effect on oligodendrocytes and oligodendrocyte precursor cells (OPCs) we observed in response to nimodipine treatment. To our surprise, we detected calcium channel-independent effects on microglia, resulting in apoptosis. These effects were cell type-specific and independent of microglia polarization. Apoptosis was accompanied by decreased levels of nitric oxide (NO) and inducible NO synthase (iNOS) in cell culture as well as decreased iNOS expression and reactive oxygen species (ROS) activity in EAE. Overall, application of nimodipine seems to generate a favorable environment for regenerative processes and could therefore be a novel treatment option for MS, combining immunomodulatory effects while promoting neuroregeneration.
Synthesis of Dualsteric Ligands for Muscarinic Acetylcholine Receptors and Cholinesterase Inhibitors
(2017)
The study is dealing with the synthesis and pharmacological investigation of newly designed dualsteric ligands of muscarinic acetylcholine receptors belonging to the superfamily of G protein-coupled receptors. Such bipharmacophoric ligands combine the advantages of the orthosteric binding site (high-affinity) and of the topographically distinct allosteric binding site (subtype-selectivity) resulting in compounds with reduced side effects. This opens the way to a new therapeutic approach in the treatment of e.g. chronic pain, drug withdrawal, Parkinson`s and Alzheimer`s disease. Furthermore, the newly synthesized dualsteric compounds were pharmacologically investigated in order to get a better understanding of the activation and signaling processes in muscarinic acetylcholine receptors, especially with regard to partial agonism.
The development of the “dynamic ligand binding” concept offers new perspectives for ligand binding and signaling at G protein-coupled receptors. GPCRs are no longer considered as simple on/off switches. Dualsteric ligands can bind in a dualsteric pose, reflecting an active receptor state as well as in a purely allosteric binding pose, characterized by an inactive receptor state resulting in partial agonism. The degree of partial agonism depends on the ratio of active versus inactive receptor populations. On this basis, orthosteric/orthosteric hybrid ligands consisting of the antagonist atropine and scopolamine, respectively, as well as of the agonist iperoxo and isoxazole, respectively, linked via different alkyl chain length were synthesized in order to investigate partial agonism (Figure 1).
Figure 1: Structures of the synthesized iperoxo/isoxazole-atropine/scopolamine-hybrids.
Furthermore, different sets of quaternary and tertiary homodimers consisting either of two iperoxo or two acetylcholine units were synthesized in order to study their extent on partial agonism (Figure 2). The two agonists were connected by varying alkyl chain length. Binding studies on CHO-hM2 cells of the quaternary compounds revealed that dimerization of the agonist results in a loss of potency. The iperoxo-dimers reached higher maximum effects on the Gi- as well as on the Gs pathway in comparison to the acetylcholine-dimers. Besides the choice of the orthosteric building block (potency of the agonist), the alkyl chain length is also crucial for the degree of partial agonism.
Figure 2: Structures of the synthesized quat./tert. iperoxo/acetylcholine-homodimers.
Quinolone-based hybrids connected to the superagonist iperoxo and to the endogenous ligand acetylcholine, respectively, linked through an alkyl chain of different length were synthesized in order to develop further partial agonists (Figure 3). FRET studies confirmed M1 subtype-selectivity as well as linker dependent receptor response. The greatest positive FRET signal was observed with quinolone-C6-iper resulting from a positive cooperativity between the two separated moieties, alloster and orthoster. However, the corresponding hybrids with a longer linker led to an inverse FRET signal indicating a different binding mode, e.g. purely allosteric, in contrast to the shorter linked hybrids. Furthermore, the flexible alkyl spacer was replaced by a rigidified linker resulting in the hybrid quinolone-rigid-iperoxo (Figure 3). FRET studies on the M1 receptor showed reduced FRET kinetics, resulting from interactions between the bulky linker and the aromatic lid, located between the orthosteric and allosteric binding site. A bitopic binding mode of the rigidified hybrid is presumed. For further clarity, mutational studies are necessary.
Figure 3: M1-selective hybrid compounds.
Another aim of this work was the design and synthesis of new hybrid compounds, acting as agonists at the M1 and M2 receptor and as inhibitors for AChE and BChE in the context of M. Alzheimer. Several sets of hybrid compounds consisting of different pharmacophoric units (catalytic active site: phthalimide, naphthalimide, tacrine; peripheric anionic site: iperoxo, isoxazole) linked through a polymethylene chain of varying length were synthesized. Tac-C10-iper (Figure 4), consisting of tacrine and the superagonist iperoxo linked by a C10 polymethylene spacer, was found to have excellent anticholinesterase activity for both AChE (pIC50 = 9.81) and BChE (pIC50 = 8.75). Docking experiments provided a structural model to rationalize the inhibitory power towards AChE. Additionally, the tacrine related hybrids showed affinity to the M1 and M2 receptor. Such compounds, addressing more than one molecular target are favorable for multifactorial diseases such as Alzheimer.
Figure 4: Structure of the most active compound regarding anticholinesterase activity.
In summary, the choice of the pharmacophoric units, their connecting point as well as the nature, length, and flexibility of the linker play an important role for the activity of designed bivalent ligands. A shorter linker length cannot bridge both binding sites simultaneously in contrast to longer linker chains. On the other hand, too long linker chains can result in unwanted steric interactions. Further investigations with respect to structural variations of hybrid compounds, with or without quaternary ammonium groups, are necessary in the light of drug development.
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.
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.
In this work fluorescence-based single molecule detection at low concetration is investigated, with an emphasis on the usage of active transport and waveguides.
Active transport allows to overcome the limits of diffusion-based systems in terms of the lowest detectable threshold of concentration.
The effect of flow in single molecule experiments is investigated and a theoretical model is derived for laminar flow.
Waveguides on the other hand promise compact detection schemes and show great potential for their possible integration into lab-on-a-chip applications. Their properties in single molecule experiments are analyzed with help of a method based on the reciprocity theorem of electromagnetic theory.
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.
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.
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
65
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.
66
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.
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.
Nowadays, data centers are becoming increasingly dynamic due to the common adoption of virtualization technologies. Systems can scale their capacity on demand by growing and shrinking their resources dynamically based on the current load. However, the complexity and performance of modern data centers is influenced not only by the software architecture, middleware, and computing resources, but also by network virtualization, network protocols, network services, and configuration. The field of network virtualization is not as mature as server virtualization and there are multiple competing approaches and technologies. Performance modeling and prediction techniques provide a powerful tool to analyze the performance of modern data centers. However, given the wide variety of network virtualization approaches, no common approach exists for modeling and evaluating the performance of virtualized networks.
The performance community has proposed multiple formalisms and models for evaluating the performance of infrastructures based on different network virtualization technologies. The existing performance models can be divided into two main categories: coarse-grained analytical models and highly-detailed simulation models. Analytical performance models are normally defined at a high level of abstraction and thus they abstract many details of the real network and therefore have limited predictive power. On the other hand, simulation models are normally focused on a selected networking technology and take into account many specific performance influencing factors, resulting in detailed models that are tightly bound to a given technology, infrastructure setup, or to a given protocol stack.
Existing models are inflexible, that means, they provide a single solution method without providing means for the user to influence the solution accuracy and solution overhead. To allow for flexibility in the performance prediction, the user is required to build multiple different performance models obtaining multiple performance predictions. Each performance prediction may then have different focus, different performance metrics, prediction accuracy, and solving time.
The goal of this thesis is to develop a modeling approach that does not require the user to have experience in any of the applied performance modeling formalisms. The approach offers the flexibility in the modeling and analysis by balancing between: (a) generic character and low overhead of coarse-grained analytical models, and (b) the more detailed simulation models with higher prediction accuracy.
The contributions of this thesis intersect with technologies and research areas, such as: software engineering, model-driven software development, domain-specific modeling, performance modeling and prediction, networking and data center networks, network virtualization, Software-Defined Networking (SDN), Network Function Virtualization (NFV). The main contributions of this thesis compose the Descartes Network Infrastructure (DNI) approach and include:
• Novel modeling abstractions for virtualized network infrastructures. This includes two meta-models that define modeling languages for modeling data center network performance. The DNI and miniDNI meta-models provide means for representing network infrastructures at two different abstraction levels. Regardless of which variant of the DNI meta-model is used, the modeling language provides generic modeling elements allowing to describe the majority of existing and future network technologies, while at the same time abstracting factors that have low influence on the overall performance. I focus on SDN and NFV as examples of modern virtualization technologies.
• Network deployment meta-model—an interface between DNI and other meta- models that allows to define mapping between DNI and other descriptive models. The integration with other domain-specific models allows capturing behaviors that are not reflected in the DNI model, for example, software bottlenecks, server virtualization, and middleware overheads.
• Flexible model solving with model transformations. The transformations enable solving a DNI model by transforming it into a predictive model. The model transformations vary in size and complexity depending on the amount of data abstracted in the transformation process and provided to the solver. In this thesis, I contribute six transformations that transform DNI models into various predictive models based on the following modeling formalisms: (a) OMNeT++ simulation, (b) Queueing Petri Nets (QPNs), (c) Layered Queueing Networks (LQNs). For each of these formalisms, multiple predictive models are generated (e.g., models with different level of detail): (a) two for OMNeT++, (b) two for QPNs, (c) two for LQNs. Some predictive models can be solved using multiple alternative solvers resulting in up to ten different automated solving methods for a single DNI model.
• A model extraction method that supports the modeler in the modeling process by automatically prefilling the DNI model with the network traffic data. The contributed traffic profile abstraction and optimization method provides a trade-off by balancing between the size and the level of detail of the extracted profiles.
• A method for selecting feasible solving methods for a DNI model. The method proposes a set of solvers based on trade-off analysis characterizing each transformation with respect to various parameters such as its specific limitations, expected prediction accuracy, expected run-time, required resources in terms of CPU and memory consumption, and scalability.
• An evaluation of the approach in the context of two realistic systems. I evaluate the approach with focus on such factors like: prediction of network capacity and interface throughput, applicability, flexibility in trading-off between prediction accuracy and solving time. Despite not focusing on the maximization of the prediction accuracy, I demonstrate that in the majority of cases, the prediction error is low—up to 20% for uncalibrated models and up to 10% for calibrated models depending on the solving technique.
In summary, this thesis presents the first approach to flexible run-time performance prediction in data center networks, including network based on SDN. It provides ability to flexibly balance between performance prediction accuracy and solving overhead. The approach provides the following key benefits:
• It is possible to predict the impact of changes in the data center network on the performance. The changes include: changes in network topology, hardware configuration, traffic load, and applications deployment.
• DNI can successfully model and predict the performance of multiple different of network infrastructures including proactive SDN scenarios.
• The prediction process is flexible, that is, it provides balance between the granularity of the predictive models and the solving time. The decreased prediction accuracy is usually rewarded with savings of the solving time and consumption of resources required for solving.
• The users are enabled to conduct performance analysis using multiple different prediction methods without requiring the expertise and experience in each of the modeling formalisms.
The components of the DNI approach can be also applied to scenarios that are not considered in this thesis. The approach is generalizable and applicable for the following examples: (a) networks outside of data centers may be analyzed with DNI as long as the background traffic profile is known; (b) uncalibrated DNI models may serve as a basis for design-time performance analysis; (c) the method for extracting and compacting of traffic profiles may be used for other, non-network workloads as well.
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...
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.
The present thesis demonstrates the importance of the solid state packing of dipolar merocyanine dyes with regard to charge transport and exciton coupling.
Due to the charge transport theory for disordered materials, it is expected that high ground state dipole moments in amorphous thin films lead to low mobility values due to a broadening of the density of states. However, due to their inherent dipolarity, merocyanine dyes usually align in antiparallel dimers in an ordered fashion. The examination of twenty different molecules with ground state dipole moments up to 15.0 D shows that by a high dipolarity and well-defined sterics, the molecules pack in a highly regular two-dimensional brickwork-type structure, which is beneficial for hole transport. Utilization of these molecules for organic thin-film transistors (OTFTs) leads to hole mobility values up to 0.21 cm²/Vs. By fabrication of single crystal field-effect transistors (SCFETs) for the derivative showing the highest mobility values in OTFTs, even hole mobilities up to 2.34 cm²/Vs are achieved. Hence, merocyanine based transistors show hole mobility values comparable to those of conventional p-type organic semiconductors and therefore high ground state dipole moments are not necessarily disadvantageous regarding high mobility applications.
By examination of a different series of ten merocyanine dyes with the same chromophore backbone but different donor substituents, it is demonstrated that the size of the donor has a significant influence on the optical properties of thin films. For small and rigid donor substituents, a hypsochromic shift of the absorption compared to the monomer absorption in solution is observed due to the card stack like packing of the molecules in the solid state. By utilization of sterical demanding or flexible donor substituents, a zig-zag type packing is observed, leading to a bathochromical shift of the absorption. These packing motifs and spectral shifts with an offset of 0.93 eV of the H- and J-bands comply with the archetype examples of H- and J-aggregates from Kasha’s exciton theory.
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.
Spin- and angle-resolved photoelectron spectroscopy is the prime method to investigate
spin polarized electronic states at solid state surfaces. In how far the spin polarization
of an emitted photoelectron reflects the intrinsic spin character of an electronic state is
the main question in the work at hand. It turns out that the measured spin polarization
is strongly influenced by experimental conditions, namely by the polarization of the
incoming radiation and the excitation energy. The photoemission process thus plays a
non-negligible role in a spin-sensitive measurement. This work is dedicated to unravel
the relation between the result of a spin-resolved measurement and the spin character
in the ground state and, therefore, to gain a deep understanding of the spin-dependent
photoemission process.
Materials that exhibit significant spin-splittings in their electronic structure,
owing to a strong spin-orbit coupling, serve as model systems for the investigations in
this work. Therefore, systems with large Rashba-type spin-splittings as BiTeI(0001)
and the surface alloys BiAg2/Ag(111) and PbAg2/Ag(111) are investigated. Likewise,
the surface electronic structure of the topological insulators Bi2Te2Se(0001) and
Bi2Te3(0001) are analyzed.
Light polarization dependent photoemission experiments serve as a probe of the
orbital composition of electronic states. The knowledge of the orbital structure helps
to disentangle the spin-orbital texture inherent to the different surface states, when
in addition the spin-polarization is probed. It turns out that the topological surface
state of Bi2Te2Se(0001) as well as the Rashba-type surface state of BiTeI(0001) exhibit
chiral spin-textures associated with the p-like in-plane orbitals. In particular, opposite
chiralities are coupled to either tangentially or radially aligned p-like orbitals,
respectively. The results presented here are thus evidence that a coupling between
spin- and orbital part of the wave function occurs under the influence of spin-orbit
coupling, independent of the materials topology.
Systematic photon energy dependent measurements of the out-of-plane spin polarization
of the topological surface state of Bi2Te3(0001) reveal a strong dependence and
even a reversal of the sign of the photoelectron spin polarization with photon energy.
Similarly, the measured spin component perpendicular to the wave vector of the surface
state of BiAg2/Ag(111) shows strong modulations and sign reversals when the photon energy is changed. In BiAg2/Ag(111) the variations in the photoelectron spin
polarization are accompanied by significant changes and even a complete suppression
of the photoemission intensity from the surface state, indicating that the variations of
the spin polarization are strongly related to the photoemission cross section.
This relation is finally analyzed in detail by employing a simple model, which is
based on an evaluation of the transition matrix elements that describe the presented
experiments. The model shows that the underlying cause for the observed photoelectron
spin reversals can be found in the coupling of the spin structure to the spatial part
of the initial state wave function, revealing the crucial role of spin-orbit interaction
in the initial state wave function. The model is supported by ab initio photoemission
calculations, which show strong agreement with the experimental results.
Since the late 20th century, spintroncis has become a very active field of research [ŽFS04]. The prospect of spin based information technology, featuring strongly decreased energy consumption and possibly quantum-computation capabilities, has fueled this interest. Standard materials, like bulk gallium arsenide (GaAs), have experienced new attention in this context by exhibiting extraordinarily long lifetimes for nonequilibrium spin information, which is an important requirement for efficient spin based information storage and transfer. Another important factor is the lengthscale over which spin information can be transported in a given material and the role of external influences. Both aspects have been studied experimentally with innovative optical methods since the late 1990s by the groups of D. D. AWSHALOM and S. A. CROOKER et al. [KA99, CS05, CFL+05]. Although the pioneering experimental approaches presented by these authors led to a variety of insights into spin propagation, some questions were raised as well. Most prominently, the classical Einstein relation, which connects the mobility and diffusivity of a given particle species, seemed to be violated for electron spins in a bulk semiconductor. In essence, nonequilibrium spins appeared to move (diffuse) faster than the electrons that actually carry the spin. However, this contradiction was masked by the fact, that the material of interest was n-type GaAs with a doping concentration directly at the transition between metallic and insulating behavior (MIT). In this regime, the electron mobility is difficult to determine experimentally. Consequently, it was not a priori obvious that the spin diffusion rates determined by the newly introduced optical methods were in contradiction with established electrical transport data.
However, in an attempt to extend the available data of optical spin microscopy, another issue surfaced, concerning the mathematical drift-diffusion model that has been commonly used to evaluate lateral spin density measurements. Upon close investigation, this model appears to have a limited range of applicability, due to systematic discrepancies with the experimental data (chapter 4). These deviations are noticeable in original publications as well, and it is shown in the present work that they originate from the local heating of electrons in the process of optical spin pumping. Based on insights gained during the second half of the 20th century, it is recapitulated why conduction electrons are easily overheated at cryogenic temperatures. The main reason is the poor thermal coupling between electrons and the crystal lattice (chapter 3). Experiments in the present work showed that a significant thermal gradient exists in the conduction band under local optical excitation of electron–hole pairs. This information was used to develop a better mathematical model of spin diffusion, which allowed to derive the diffusivity of the undisturbed system, due to an effective consideration of electron overheating. In this way, spin diffusivities of n-GaAs were obtained as a function of temperature and doping density in the most interesting regime of the metal–insulator-transition.
The experiments presented in this work were performed on a series of n-type bulk GaAs samples, which comprised the transition between metallic conductivity and electrical insulation at low temperatures. Local electron temperature gradients were measured by a hyperspectral photoluminescence imaging technique with subsequent evaluation of the electron–acceptor (e,A$^0$) line shape. The local density of nonequilibrium conduction electron spins was deduced from scanning magneto-optic Kerr effect microscopy. Numerical evaluations were performed using the finite elements method in combination with a least-squares fitting procedure.
Chapter 1 provides an introduction to historical and recent research in the field of spintronics, as far as it is relevant for the understanding of the present work. Chapter 2 summarizes related physical concepts and experimental methods. Here, the main topics are semiconductor optics, relaxation of hot conduction electrons, and the dynamics of nonequilibrium electron spins in semiconductors.
Chapter 3 discusses optical heating effects due to local laser excitation of electron–hole pairs. Experimental evaluations of the acceptor-bound-exciton triplet lines led to the conclusion that the crystal lattice is usually not overheated even at high excitation densities. Here, the heat is efficiently dissipated to the bath, due to the good thermal conductivity of the lattice. Furthermore, the heating of the lattice is inherently limited by the weak heat transfer from the electron system, which on the other hand is also the reason why conduction electrons are easily overheated at temperatures below ≈ 30 K. Spatio-spectral imaging of the electron–acceptor-luminescence line shape allowed to trace the thermal gradient within the conduction band under focused laser excitation. A heat-diffusion model was formulated, which reproduces the experimental electron-temperature trend nicely for low-doped GaAs samples of n- and p-type. For high-doped n-type GaAs samples, it could be shown that the lateral electron-temperature profile is well approximated by a Gaussian. This facilitated easy integration of hot electron influence into the mathematical model of spin diffusion.
Chapter 4 deals with magneto-optical imaging of optically induced nonequilibrium conduction-electron spins in n-GaAs close to the MIT. First, the spectral dependence of the magneto-optic Kerr effect was examined in the vicinity of the fundamental band gap. Despite the marked differences among the investigated samples, the spectral shape of the Kerr rotation could be described in terms of a simple Lorentz-oscillator model in all cases. Based on this model, the linearity of the Kerr effect with respect to a nonequilibrium spin polarization is demonstrated, which is decisively important for further quantitative evaluations.
Furthermore, chapter 4 presents an experimental survey of spin relaxation in n-GaAs at the MIT. Here, the dependence of the spin relaxation time on bath temperature and doping density was deduced from Hanle-MOKE measurements. While all observed trends agree with established literature, the presented results extend the current portfolio by adding a coherent set of data.
Finally, diffusion of optically generated nonequilibrium conduction-electron spins was investigated by scanning MOKE microscopy. First, it is demonstrated that the standard diffusion model is inapplicable for data evaluation in certain situations. A systematic survey of the residual deviations between this model and the experimental data revealed that this situation unfortunately persisted in published works. Moreover, the temperature trend of the residual deviations suggests a close connection to the local overheating of conduction electrons. Consequently, a modified diffusion model was developed and evaluated, in order to compensate for the optical heating effect. From this model, much more reliable results were obtained, as compared to the standard diffusion model. Therefore, it was shown conclusively that the commonly reported anomalously large spin diffusivities were at least in parts caused by overheated conduction electrons.
In addition to these new insights some experimental and technological enhancements were realized in the course of this work. First, the optical resolution of scanning MOKE microscopy was improved by implementing a novel scanning mechanism, which allows the application of a larger aperture objective than in the usual scheme. Secondly, imaging photoluminescence spectroscopy was employed for spatially resolved electron-temperature measurements. Here, two different implementations were developed: One for lattice-temperature measurements by acceptor–bound exciton luminescence and a second for conduction-electron temperature measurements via the analysis of the electron–acceptor luminescence line shape.
It is shown in the present work that the originally stated anomalously high spin diffusivities were caused to a large extent by unwanted optical heating of the electron system. Although an efficient method was found to compensate for the influence of electron heating, it became also evident that the classical Einstein relation was nonetheless violated under the given experimental conditions. In this case however, it could be shown that this discrepancy did not originate from an experimental artifact, but was instead a manifestation of the fermionic nature of conduction electrons.
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.
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
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.
Platelets are continuously produced from megakaryocytes (MK) in the bone marrow by a cytoskeleton-driven process of which the molecular regulation is not fully understood.
As revealed in this thesis, MK/ platelet-specific Profilin1 (Pfn1) deficiency results in micro- thrombocytopenia, a hallmark of the Wiskott-Aldrich syndrome (WAS) in humans, due to accelerated platelet turnover and premature platelet release into the bone marrow. Both Pfn1-deficient mouse platelets and platelets isolated from WAS patients contained abnormally organized and hyper-stable microtubules. These results reveal an unexpected function of Pfn1 as a regulator of microtubule organization and point to a previously unrecognized mechanism underlying the platelet formation defect in WAS patients.
In contrast, Twinfilin2a (Twf2a) was established as a central regulator of platelet reactivity and turnover. Twf2a-deficient mice revealed an age-dependent macrothrombocytopenia that could be explained by a markedly decreased platelet half-life, likely due to the pronounced hyper-reactivity of \(Twf2a^{-/-}\) platelets. The latter was characterized by sustained integrin acti- vation and thrombin generation in vitro that translated into accelerated thrombus formation in vivo. To further elucidate mechanisms of integrin activation, Rap1-GTP-interacting adaptor molecule (RIAM)-null mice were generated. Despite the proposed critical role of RIAM for platelet integrin activation, no alterations in this process could be found and it was concluded that RIAM is dispensable for the activation of β1 and β3 integrins, at least in platelets. These findings change the current mechanistic understanding of platelet integrin activation.
Outside-in signaling by integrins and other surface receptors was supposed to regulate MK migration, but also the temporal and spatial formation of proplatelet protrusions. In this the- sis, phospholipase D (PLD) was revealed as critical regulator of actin dynamics and podo- some formation in MKs. Hence, the unaltered platelet counts and production in \(Pld1/2^{-/-}\) mice and the absence of a premature platelet release in the bone marrow of \(Itga2^{-/-}\) mice question the role of podosomes in platelet production and raise the need to reconsider the proposed inhibitory signaling by α2β1 integrins on proplatelet formation.
Non-muscle myosin IIA (NMMIIA) has been implicated as a downstream effector of the in- hibitory signals transmitted via α2β1 integrins. Besides Rho-GTPase signaling, also \(Mg^{2+}\) and transient receptor potential melastatin-like 7 (TRPM7) channel α-kinase are known regulators of NMMIIA activity. In this thesis, TRPM7 was identified as major regulator of \(Mg^{2+}\) homeostasis in MKs and platelets. Furthermore, decreased \([Mg^{2+}]_i\) led to deregulated NMMIIA activity and altered cytoskeletal dynamics that impaired thrombopoiesis and resulted in macrothrombocytopenia in humans and mice.
Preclinical development of an immunotherapy against antibiotic-resistant Staphylococcus aureus
(2017)
The Gram-positive bacterium Staphylococcus aureus is the leading cause of nosocomial infections. In particular, diseases caused by methicillin-resistant S. aureus (MRSA) are associated with higher morbidity, mortality and medical costs due to showing resistance to several classes of established antibiotics and their ability to develop resistance mechanisms against new antibiotics rapidly. Therefore, strategies based on immunotherapy approaches have the potential to close the gap for an efficient treatment of MRSA.
In this thesis, a humanized antibody specific for the immunodominant staphylococcal antigen A (IsaA) was generated and thoroughly characterized as potential candidate for an antibody based therapy. A murine monoclonal antibody was selected for humanization based on its binding characteristics and the ability of efficient staphylococcal killing in mouse infection models. The murine antibody was humanized by CDR grafting and mouse and humanized scFv as well as scFv-Fc fragments were constructed for comparative binding studies to analyse the successful humanization. After these studies, the full antibody with the complete Fc region was constructed as isotype IgG1, IgG2 and IgG4, respectively to assess effector functions, including antibody-dependent killing of S. aureus. The biological activity of the humanized antibody designated hUK-66 was analysed in vitro with purified human PMNs and whole blood samples taken from healthy donors and patients at high risk of S. aureus infections, such as those with diabetes, end-stage renal disease, or artery occlusive disease (AOD).
Results of the in vitro studies show, that hUK-66 was effective in antibody-dependent killing of S. aureus in blood from both healthy controls and patients vulnerable to S. aureus infections. Moreover, the biological activity of hUK-66 and hUK-66 combined with a humanized anti-alpha-toxin antibody (hUK-tox) was investigated in vivo using a mouse pneumonia model. The in vivo results revealed the therapeutic efficacy of hUK-66 and the antibody combination of hUK-66 and hUK-tox to prevent staphylococcal induced pneumonia in a prophylactic set up.
Based on the experimental data, hUK-66 represents a promising candidate for an antibody-based therapy against antibiotic resistant MRSA.
During my PhD I studied two principal biological aspects employing Drosophila melanogaster. Therefore, this study is divided into Part I and II.
Part I: Bruchpilot and Complexin interact to regulate synaptic vesicle tethering to the
active zone cytomatrix
At the presynaptic active zone (AZ) synaptic vesicles (SVs) are often physically linked to an electron-dense cytomatrix – a process referred to as “SV tethering”. This process serves to concentrate SVs in close proximity to their release sites before contacting the SNARE complex for subsequent fusion (Hallermann and Silver, 2013). In Drosophila, the AZ protein Bruchpilot (BRP) is part of the proteinous cytomatrix at which SVs accumulate (Kittel et al., 2006b; Wagh et al., 2006; Fouquet et al., 2009). Intriguingly, truncation of only 1% of the C-terminal region of BRP results in a severe defect in SV tethering to this AZ scaffold (hence named brpnude; Hallermann et al., 2010b).
Consistent with these findings, cell-specific overexpression of a C-terminal BRP fragment, named mBRPC-tip (corresponds to 1% absent in brpnude; m = mobile) phenocopied the brpnude mutant in behavioral and functional experiments. These data indicate that mBRPC-tip suffices to saturate putative SV binding sites, which induced a functional tethering deficit at motoneuronal AZs. However, the molecular identity of the BRP complement to tether SVs to the presynaptic AZ scaffold remains unknown. Moreover, within larval motoneurons membrane-attached C-terminal portions of BRP were sufficient to tether SVs to sites outside of the AZ. Based on this finding a genetic screen was designed to identify BRP interactors in vivo. This screen identified Complexin (CPX), which is known to inhibit spontaneous SV fusion and to enhance stimulus evoked SV release (Huntwork and Littleton, 2007; Cho et al., 2010; Martin et al., 2011). However, so far CPX has not been associated with a function upstream of priming/docking and release of SVs. This work provides morphological and functional evidence, which suggests that CPX promotes recruitment of SVs to the AZ and thereby curtails synaptic short-term depression. Together, the presented findings indicate a functional interaction between BRP and CPX at Drosophila AZs.
Part II: The Adhesion-GPCR Latrophilin/CIRL shapes mechanosensation
The calcium independent receptor of α-latrotoxin (CIRL), also named Latrophilin, represents a prototypic Adhesion class G-protein coupled-receptor (aGPCR). Initially, Latrophilin was identified based on its capacity to bind the α-component of latrotoxin (α-LTX; Davletov et al., 1996; Krasnoperov et al., 1996), which triggers massive exocytotic activity from neurons of the peripheral nervous system (Scheer et al., 1984; Umbach et al., 1998; Orlova et al., 2000). As a result Latrophilin is considered to play a role in synaptic transmission. Later on, Latrophilins have been associated with other biological processes including tissue polarity (Langenhan et al., 2009), fertility (Prömel et al., 2012) and synaptogenesis (Silva et al., 2011). However, thus far its subcellular localization and the identity of endogenous ligands, two aspects crucial for the comprehension of Latrophilin’s in vivo function, remain enigmatic.
Drosophila contains only one latrophilin homolog, named dCirl, whose function has not been investigated thus far.
This study demonstrates abundant dCirl expression throughout the nervous system of Drosophila larvae. dCirlKO animals are viable and display no defects in development and neuronal differentiation. However, dCirl appears to influence the dimension of the postsynaptic sub-synaptic reticulum (SSR), which was accompanied by an increase in the postsynaptic Discs-large abundance (DLG). In contrast, morphological and functional properties of presynaptic motoneurons were not compromised by the removal of dCirl. Instead, dCirl is required for the perception of mechanical challenges (acoustic-, tactile- and proprioceptive stimuli) through specialized mechanosensory devices, chordotonal organs (Eberl, 1999). The data indicate that dCirl modulates the sensitivity of chordotonal neurons towards mechanical stimulation and thereby adjusts their input-output relation. Genetic interaction analyses suggest that adaption of the molecular mechanotransduction machinery by dCirl may underlie this process. Together, these results uncover an unexpected function of Latrophilin/dCIRL in mechanosensation and imply general modulatory roles of aGPCR in mechanoception.
A promising new approach for the treatment of human cancer is the use of oncolytic viruses, which exhibit tumor tropism. One of the top candidates in this area is the oncolytic vaccinia virus (VACV), which has already shown promising results in animal studies and in clinical trials. However, due to discrepancies in both innate and adaptive immunity between mice and men the evaluation of the vaccinia virus’ interactions with the host immune system in mice are not fully conclusive of what is actually happening in human cancer patients after systemic administration of vaccinia virus. Also, ethical and legal concerns as well as risk of potential toxicity limit research involving human patients. Therefore, a good in vivo model for testing interactions between vaccinia virus and human immune cells, avoiding the numerous limitations and risks associated with human studies, could be a humanized mouse model.
LIVP-1.1.1, GLV-2b372, GLV-1h68, GLV-1h375, GLV-1h376 and GLV-1h377 VACVs were provided by Genelux Corporation. GLV-2b372 was constructed by inserting TurboFP635 expression cassette into the J2R locus of the parental LIVP-1.1.1. GLV-1h375, -1h376 and -1h377 VACVs encode the human CTLA4-blocking single-chain antibody (CTLA4 scAb). Performed replication and cytotoxicity assays demonstrated that all six viruses were able to infect, replicate in and kill human tumor cells in virus-dose- and time-dependent fashion. CTLA4 scAb and β-glucuronidase (GusA) expression as well as viral titers in GLV-1h376-infected cells were analyzed by ELISA, β-glucuronidase assay and standard plaque assay, respectively, and compared. An excellent correlation with correlation coefficients R2>0.9806 were observed. GLV-1h376-encoded CTLA4 scAb was successfully purified from supernatants of infected CV-1 cells and demonstrated in vitro affinity to its human CTLA4 target and lack of cross-reactivity to mouse CTLA4. CTLA4 scAb functionality was confirmed in Jurkat cells. LIVP-1.1.1, GLV-2b372, GLV-1h68 and GLV-1h376 were next studied in non-tumorous and/or tumor-bearing humanized mice.
It was demonstrated that injection of human CD34+ stem cells into the liver of preconditioned newborn NSG mice let to a successful systemic reconstitution with human immune cells. CD19+ B cells, CD4 and CD8 single positive CD3+ T cell, NKp46+CD56- and NKp46+CD56+ NK cells as well as CD33+ myeloid cells developed. At early time points after engraftment, majority of the human hematopoietic cells detected in the mouse blood were CD19+ B cells and only a small portion were CD3+ T cells. With time a significant change in CD19+/CD3+ ratio was reported with a decrease of B cells and an increase of T cells. Implantation of A549 cells under the skin of those humanized NSG mice resulted in a progressive tumor growth, described for the first time in this thesis. Successful colonization of subcutaneous A549 tumors with VACVs was visualized and demonstrated by detection of virus-mediated TurboFP635 and GFP expression as well as by standard plaque assay and immunohistochemistry. The human CD45+ cell population in tumors was represented mainly by NKp46+CD56bright NK cells and a large portion of activated CD4+ and cytotoxic CD8+ T cells. However, no significant differences were observed between control and LIVP-1.1.1-infected tumors, suggesting that the recruitment of NK and activated T cells were more tumor tissue specific than virus-dependent. Unfortunately, virus-mediated CTLA4 scAb expression in the GLV-1h376-infected tumors was also not able to significantly increase activation of T cells compared to control and GLV-1h68-treated mice. Importantly, ELISA, β-glucuronidase and standard plaque assays showed an excellent correlation with correlation coefficients R2>0.9454 between CTLA4 scAb, GusA concentrations and viral titers in tumor samples from those GLV-1h376 treated mice.
T cells isolated from the spleens of such control or GLV-1h68- or -1h376-treated A549 tumor-bearing mice were functional and could successfully be activated with human T cells activation beads. However, although no significant difference was observed between the three mouse groups, a slightly higher percentage of the GLV-1h376-treated mice-derived T cells were expressing CD25 and producing IFN-ɣ after ex vivo activation, probably due to the CTLA4 blockade by the virus-encoded CTLA4 scAb in the GLV-1h376-treated mice. Also, slightly higher levels of IL-2 were detected in the culture supernatant of those splenocytes compared to control samples. In contrast, T cells from all three mouse groups were not able be activated by A549 tumor cells ex vivo.
Our model has the specific advantage that tumors develop under the skin of the humanized mice, which allows accurate monitoring of the tumor growth and evaluation of the oncolytic virotherapy. Therefore it is important to choose the right approaches for its further improvement.
Several important cellular processes, including transcription, nucleotide excision repair and cell cycle control are mediated by the multifaceted interplay of subunits within the general transcription factor II H (TFIIH).
A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these pathways. This becomes especially important in the context of severe diseases like xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy, that arise from single point mutations in some of the TFIIH subunits.
In an attempt to structurally characterize the TFIIH complex, we harnessed the qualities of the eukaryotic thermophile Chaetomium thermophilum, a remarkable fungus, which has only recently been recognized as a novel model organism. Homologues of TFIIH from C. thermophilum were expressed in E. coli, purified to homogeneity and subsequently utilized for crystallization trials and biochemical studies.
The results of the present work include the first crystal structure of the p34 subunit of TFIIH, comprising the N-terminal domain of the protein. The structure revealed a von Willebrand Factor A (vWA) like fold, which is generally known to be involved in a multitude of protein-protein interactions. Structural comparison allowed to delineate similarities as well as differences to already known vWA domains, providing insight into the role of p34 within TFIIH. These results indicate that p34 assumes the role of a structural scaffold for other TFIIH subunits via its vWA domain, while likely serving additional functions, which are mediated through its
C-terminal zinc binding domain and are so far unknown.
Within TFIIH p34 interacts strongly with the p44 subunit, a positive regulator of the XPD helicase, which is required for regulation of RNA Polymerase II mediated transcription and essential for eukaryotic nucleotide excision repair. Based on the p34 vWA structure putative protein-protein interfaces were analyzed and binding sites for the p34 p44 interaction suggested. Continuous crystallization efforts then led to the first structure of a p34 p44 minimal complex, comprising the N-terminal vWA domain of p34 and the C-terminal C4C4 RING domain of p44. The structure of the p34 p44 minimal complex verified the previous hypothesis regarding the involved binding sites. In addition, careful analysis of the complex interface allowed to identify critical residues, which were subsequently mutated and analyzed with respect to their significance in mediating the p34 p44 interaction, by analytical size exclusion chromatography, electrophoretic mobility shift assays and isothermal titration calorimetry. The structure of the p34 p44 complex also revealed a binding mode of the p44 C4C4 RING domain, which differed from that of other known RING domains in several aspects, supporting the hypothesis that p44 contains a novel variation of this domain.
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.
Merkel cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer that has been associated with the Merkel cell polyomavirus (MCPyV). Indeed, MCC is one of the cancers with the best-established viral carcinogenesis. Despite persistence of the virus in MCC cells and the subsequent expression of viral antigens, the majority of MCC tumors are able to escape the surveillance of the immune system. Therefore the aim of the here presented thesis was to scrutinize immune escape mechanisms operative in MCC. A better understanding of their underlying molecular processes should allow to improve immunotherapeutic treatment strategies for MCC patients. The manuscripts included in this thesis characterize three novel immune evasion strategies of MCC.
I) the epigenetic silencing of the NKG2D ligands MICA and MICB via histone H3 hypoacetylation
II) reduced HLA class I surface expression via epigenetic silencing of the antigen processing machinery (APM)
III) the activation of the PI3K-AKT pathway in a mutation independent manner as potential immune escape strategy
MCC tumors and MCC cell lines were analyzed for their expression of MICA/B, HLA and components of the antigen processing machinery as well as for the activation of the PI3K-AKT pathway in situ and in vitro. These analysis reviled MICA and MICB, as well as HLA class I were not expressed or at least markedly reduced in ~80% of MCCs in situ. The PI3K-AKT pathway, that had only recently been demonstrated to play a significant role in tumor immune escape, was activated in almost 90% of MCCs in situ. To determine the underlying molecular mechanisms of these aberrations well characterized MCC cell lines were further analyzed in vitro. The fact that the PI3K-AKT pathway activation was due to oncogenic mutations in the PIK3CA or AKT1 gene in only 10% of MCCs, suggested an epigenetic regulation of this pathway in MCC. In line with this MICA/B as well as components of the APM were indeed silenced epigenetically via histone hypoacetylation in their respective promoter region. Notably MICA/B and HLA class I expression on the cell surface of MCC cells could be restored after treatment with HDAC inhibitors in combination with the Sp1 inhibitor Mithramycin A in all analyzed MCC cell lines in vitro and in a xenotransplantation mouse model in vivo. Moreover inhibition of HDACs increased immune recognition of MCC cell lines in a MICA/B and HLA class I dependent manner.
Several studies have accumulated evidence that immunotherapy is a promising treatment option for MCC patients due to the exquisite immunogenicity of this malignancy. However, current immunotherapeutic interventions towards solid tumors like MCC have to account for the plentitude of tumor immune escape strategies, in order to increase response rates. The immune escape mechanisms of MCC described in this thesis can be reverted by HDAC inhibition, thus providing the rationale to combine ‘epigenetic priming’ with currently tested immunotherapeutic regimens.
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.
Anionic Adducts
Sp2-sp3 tetraalkoxy diboron compounds have gained attention due to the development of new, synthetically useful catalytic reactions either with or without transition-metals. Lewis-base adducts of the diboron(4) compounds were suggested as possible intermediates in Cu catalyzed borylation reactions some time ago. However, intermolecular adducts of tetraalkoxy diboron compounds have not been studied yet in great detail. In preliminary studies, we have synthesized a series of anionic sp2-sp3 adducts of B2pin2 with alkoxy-groups (L = [OMe]–, [OtBu]–), a phenoxy-group (L = [4-tBuC6H4O]–) and fluoride (L = [F]–, with [nBu4N]+ as the counter ion) as Lewis-bases.
Neutral Adducts
Since their isolation and characterization, applications of N-heterocyclic carbenes (NHCs) and related molecules, e.g., cyclic alkylaminocarbenes (CAACs) and acyclic diaminocarbenes (aDCs), have grown rapidly. Their use as ligands in homogeneous catalysis and directly in organocatalysis, including recently developed borylation reactions, is now well established. Recently, several examples of ring expansion reactions (RER) involving NHCs were reported to take place at elevated temperatures, involving Be, B, and Si.
Furthermore, preliminary studies in the group of Marder et al. showed the presence of neutral sp2-sp3 diboron compounds with B2pin2 and the NHC Cy2Im. In this work, we focused on the synthesis and characterization of further neutral sp2-sp3 as well as sp3-sp3 diboron adducts with B2cat2 and B2neop2 and different NHCs. Whereas the mono-NHC adduct is stable for several hours at temperatures up to 60 °C, the bis-NHC adducts undergo thermally induced rearrangement to form the ring expanded products compound 26 and 27. B2neop2 is much more reactive than B2cat2 giving ring expanded product 29 at room temperature in quantitative yields, demonstrating that NHC ring expansion and B–B bond cleavage can be very facile processes.
Whereas the mono-NHC adduct is stable for several hours at temperatures up to 60 °C, the bis-NHC adducts undergo thermally induced rearrangement to form the ring expanded products compound 26 and 27. B2neop2 is much more reactive than B2cat2 giving ring expanded product 29 at room temperature in quantitative yields, demonstrating that NHC ring expansion and B–B bond cleavage can be very facile processes.
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.
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.
Mechanisms of visual memory formation in bees: About immediate early genes and synaptic plasticity
(2017)
Animals form perceptual associations through processes of learning, and retain that information through mechanisms of memory. Honeybees and bumblebees are classic models for insect perception and learning, and despite their small brains with about one million neurons, they are organized in highly social colonies and possess an astonishing rich behavioral repertoire including navigation, communication and cognition. Honeybees are able to harvest hundreds of morphologically divergent flower types in a quick and efficient manner to gain nutrition and, back in the hive, communicate discovered food sources to nest mates. To accomplish such complex tasks, bees must be equipped with diverse sensory organs receptive to stimuli of different modalities and must be able to associatively learn and memorize the acquired information. Particularly color vision plays a prominent role, e.g. in navigation along landmarks and when bees identify inflorescences by their color signals. Once acquired, bees are known to retain visual information for days or even months. Numerous studies on visual perception and color vision have been conducted in the past decades and largely revealed the information processing pathways in the brain. In contrast, there are no data available on how the brain may change in the course of color learning experience and whether pathways differ for coarse and fine color learning. Although long-term memory (LTM) storage is assumed to generally include reorganization of the neuronal network, to date it is unclear where in the bee brain such changes occur in the course of color learning and whether visual memories are stored in one particular site or decentrally distributed over different brain domains. The present dissertation research aimed to dissect the visual memory trace in bees that is beyond mere stimulus processing and therefore two different approaches were elaborated: first, the application of immediate early genes (IEG) as genetic markers for neuronal activation to localize early processes underlying the formation of a stable LTM. Second, the analysis of late consequences of memory formation, including synaptic reorganization in central brain areas and dependencies of color discrimination complexity.
Immediate early genes (IEG) are a group of rapidly and transiently expressed genes that are induced by various types of cellular stimulation. A great number of different IEGs are routinely used as markers for the localization of neuronal activation in vertebrate brains. The present dissertation research was dedicated to establish this approach for application in bees, with focus on the candidate genes Amjra and Amegr, which are orthologous to the two common vertebrate IEGs c-jun and egr-1. First the general requirement of gene transcription for visual LTM formation was proved. Bumblebees were trained in associative proboscis extension response (PER) conditioning to monochromatic light and subsequently injected with an inhibitor of gene transcription. Memory retention tests at different intervals revealed that gene transcription is not required for the formation of a mid-term memory, but for stable LTM. Next, the appliance of the candidate genes was validated. Honeybees were exposed to stimulation with either alarm pheromone or a light pulse, followed by qPCR analysis of gene expression. Both genes differed in their expression response to sensory exposure: Amjra was upregulated in all analyzed brain parts (antennal lobes, optic lobes and mushroom bodies, MB), independent from stimulus modality, suggesting the gene as a genetic marker for unspecific general arousal. In contrast, Amegr was not significantly affected by mere sensory exposure. Therefore, the relevance of associative learning on Amegr expression was assessed. Honeybees were trained in visual PER conditioning followed by a qPCR-based analysis of the expression of all three Amegr isoforms at different intervals after conditioning. No learning-dependent alteration of gene expression was observed. However, the presence of AmEgr protein in virtually all cerebral cell nuclei was validated by immunofluorescence staining. The most prominent immune-reactivity was detected in MB calyx neurons.
Analysis of task-dependent neuronal correlates underlying visual long-term memory was conducted in free-flying honeybees confronted with either absolute conditioning to one of two perceptually similar colors or differential conditioning with both colors. Subsequent presentation of the two colors in non-rewarded discrimination tests revealed that only bees trained with differential conditioning preferred the previously learned color. In contrast, bees of the absolute conditioning group chose randomly among color stimuli. To investigate whether the observed difference in memory acquisition is also reflected at the level of synaptic microcircuits, so called microglomeruli (MG), within the visual domains of the MB calyces, MG distribution was quantified by whole-mount immunostaining three days following conditioning. Although learning-dependent differences in neuroarchitecture were absent, a significant correlation between learning performance and MG density was observed.
Taken together, this dissertation research provides fundamental work on the potential use of IEGs as markers for neuronal activation and promotes future research approaches combining behaviorally relevant color learning tests in bees with examination of the neuroarchitecture to pave the way for unraveling the visual memory trace.
This work is concerned with the syntheses and photophysical properties of para-xylylene bridged macrocycles nPBI with ring sizes from two to nine PBI units, as well as the complexation of polycyclic aromatic guest compounds.
With a reduced but substantial fluorescence quantum yield of 21% (in CHCl3) the free host 2PBI(4-tBu)4 can be used as a dual fluorescence probe. Upon encapsulation of rather electron-poor guests the fluorescence quenching interactions between the chromophores are prevented, leading to a significant fluorescence enhancement to > 90% (“turn-on”). On the other hand, the addition of electron-rich guest molecules induces an electron transfer from the guest to the electron-poor PBI chromophores and thus quenches the fluorescence entirely (“turn-off”). The photophysical properties of the host-guest complexes were studied by transient absorption spectroscopy. These measurements revealed that the charge transfer between guest and 2PBI(4-tBu)4 occurs in the “normal region” of the Marcus-parabola with the fastest charge separation rate for perylene. In contrast, the charge recombination back to the PBI ground state lies far in the “inverted region” of the Marcus-parabola.
Beside complexation of planar aromatic hydrocarbons into the cavity of the cyclophanes an encapsulation of fullerene into the cyclic trimer 3PBI(4-tBu)4 was observed. 3PBI(4-tBu)4 provides a tube-like structure in which the PBI subunits represent the walls of those tubes. The cavity has the optimal size for hosting fullerenes, with C70 fitting better than C60 and a binding constant that is higher by a factor of 10. TA spectroscopy in toluene that was performed on the C60@3PBI(4-tBu)4 complex revealed two energy transfer processes. The first one comes from the excited PBI to the fullerene, which subsequently populates the triplet state. From the fullerene triplet state a second energy transfer occurs back to the PBI to generate the PBI triplet state.
In all cycles that were studied by TA spectroscopy, symmetry-breaking charge separation (SB-CS) was observed in dichloromethane. This process is fastest within the PBI cyclophane 2PBI(4-tBu)4 and slows down for larger cycles, suggesting that the charge separation takes place through space and not through bonds. The charges then recombine to the PBI triplet state via a radical pair intersystem crossing (RP-ISC) mechanism, which could be used to generate singlet oxygen in yields of ~20%.
By changing the solvent to toluene an intramolecular folding of the even-numbered larger cycles was observed that quenches the fluorescence and increases the 0-1 transition band in the absorption spectra. Force field calculations of 4PBI(4-tBu)4 suggested a folding into pairs of dimers, which explains the remarkable odd-even effect with respect to the number of connected PBI chromophores and the resulting alternation in the absorption and fluorescence properties. Thus, the even-numbered macrocycles can fold in a way that all chromophores are in a paired arrangement, while the odd-numbered cycles have open conformations (3PBI(4-tBu)4, 5PBI(4-tBu)4, 7PBI(4-tBu)4) or at least additional unpaired PBI unit (9PBI(4-tBu)4).
With these experiments we could for the first time give insights in the interactions between cyclic PBI hosts and aromatic guest molecules. Associated with the encapsulation of guest molecules a variety of possible applications can be envisioned, like fluorescence sensing, chiral recognition and photodynamic therapy by singlet oxygen generation. Particularly, these macrocycles provide photophysical relaxation pathways of PBIs, like charge separation and recombination and triplet state formation that are hardly feasible in monomeric PBI dyes. Furthermore, diverse compound specific features were found, like the odd-even effect in the folding process or the transition of superficial nanostructures of the tetrameric cycle influenced by the AFM tip. The comprehensive properties of these macrocycles provide the basis for further oncoming studies and can serve as an inspiration for the synthesis of new macrocyclic compounds.
A successful therapy for colorectal cancer (CRC), one of the most common malignancies worldwide, requires the greatest possible research effort. Of critical importance is an understanding of the relevant intracellular networks of signaling cascades, their activation, and the resulting cellular changes that are a prerequisite for a more successful CRC therapy. Vascular endothelial growth factor (VEGF) and the appropriate VEGF receptors represent molecular targets that have already been successfully implemented in the clinic (i.e. using monoclonal antibodies, tyrosine kinase inhibitors). However, for platelet derived growth factor (PDGF) and the relevant PDGF receptors, there are currently no clinically approved molecular therapeutics available. However, there are preliminary data to show that PDGF and its associated signaling pathways play an important role in CRC progression. In particular, the PI3K/Akt/mTOR pathway is emerging as an important intracellular partner of PDGF with which to control proliferation, migration, and angiogenesis in tumor cells.
Therefore it was the objective of this work to investigate the multifactorial influence of PDGF on proliferation and metabolism, depending on CRC mutation status. The intention was to identify new therapeutic targets for future cancer therapy through analyses of PDGF-induced intracellular changes.
For this purpose two human colorectal cancer cell lines were analyzed at gene and/or protein level for components of the PI3K/Akt/mTOR and MAPK signaling pathway, c-Myc, p53, and HIF1α (hypoxia-inducible-factor 1α). Changes in proliferation and metabolism, either during stimulation with PDGF and/or PI3K/Akt/mTOR inhibition, were also investigated. Experiments conducted at protein level during PDGF stimulation and/or PI3K/Akt/mTOR inhibition revealed changes in signaling pathways and crosstalk. The influence of the tumor suppressors (retinoblastoma, Rb), oncogenes (c-Myc, p53mut), and HIF1α during stimulation with PDGF, and their interactions in the tumor cell with respect to proliferation and glycolysis warrant further examination in terms of clinical treatment options. Investigations at the gene level of ex vivo samples (UICC I-IV) complete the study with regards to the clinical relevance of PDGF.
PDGF stimulation increases tumor cell proliferation in HT29 cells via the PI3K/Akt/mTOR pathway rather than the MAPK pathway. However, if the PI3K/Akt/mTOR pathway is pharmacologically blocked, PDGF stimulation is mediated by inhibitory crosstalk through the MAPK pathway. Further analyses revealed that specific Akt inhibition impedes tumor cell growth, while PI3K inhibition had little effect on proliferation. Inhibitory crosstalk was found to be responsible for these different effects. Careful intervention strategies are therefore required if future therapies intend to make use of these specific signaling pathways. One aim of future research should be to gain a better understanding of the crosstalk between these signaling pathways. In this fashion, “over-inhibition” of the signal pathways, which would result in additional clinical side effects for patients, could be prevented.
In late stage UICC, more mutation events occur, with tumorigenicity promoted by an increased mutation rate. Given that PDGF is increasingly expressed in the late UICC stages, our data would indicate that PDGF's effects are amplified with increasing malignancy. The activating effect of PDGF on the PI3K/Akt/mTOR pathway and subsequent changes in the activity of p53mut, Rb, c-Myc, and HIF1α, lead to an unfavorable prognosis for colon cancer patients. PDGF acts on colon cancer cells in an Akt-activating, glycolysis-dependent manner. PDGF increases glycolysis and the ability of CRC cells to adjust their energy metabolism. These activities should be taken as possible starting points with which to design therapeutic interventions for CRC therapy.
PDGF, as another representative of the growth factor family, seems to play a similar role to VEGF in CRC. The data from this study underline the importance of the PDGF - PI3K/Akt/mTOR pathway-axis and its potential as a possible target in colorectal cancer. Thus PDGF represents an attractive therapeutic target, besides the VEGF/EGFR-based therapies already used in CRC.
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.
G protein-coupled receptors (GPCRs) are the major group of cell-surface receptors that transmit extracellular signals via classical, G protein-dependent pathways into the cell. Although GPCRs were long assumed to signal exclusively from the cell-surface, recent investigations have demonstrated a possibly completely new paradigm. In this new view, GPCR continues signaling via 3´,5´-cyclic adenosine monophosphate (cAMP) after their agonist-induced internalization of ligand/receptor complexes into an intracellular compartment, causing persistent cAMP elevation and apparently specific signaling outcomes. The thyroid stimulating hormone (TSH) receptor is one of the first GPCRs, which has been reported to show persistent signaling after ligand removal (Calebiro et al., 2009). In the meantime, signaling by internalized GPCR become a highly investigated topic and has been shown for several GPCRs, including the parathyroid hormone receptor (Ferrandon et al., 2009), D1 dopamine receptor (Kotowski et al., 2011) and beta2-adrenergic receptor (Irannejad et al., 2013). A recent study on the beta2-adrenergic receptor revealed that internalized receptor not only participates in cAMP signaling, but is also involved in gene transcription (Tsvetanova and von Zastrow, 2014). However, a biological effect of GPCR signaling at intracellular sites, which would demonstrate its physiological relevance, still remained to be shown.
To investigate GPCR signaling from intracellular compartment under physiological condition, two different cellular models were utilized in the present study: intact ovarian follicles expressing luteinizing hormone (LH) receptors and primary thyroid cells expressing TSH receptors.
Intact ovarian follicles were obtained from a transgenic mouse expressing, a Förster/Fluorescence Resonance Energy Transfer (FRET) sensor for cAMP to monitor cAMP/LH receptor signaling. This study provides the first accurate spatiotemporal characterization of cAMP signaling, which is derived from different cell layers of an intact ovarian follicle. Additionally, it could be shown that cAMP diffusion via gap junctions is implicated in spreading the LH-induced cAMP signals from one the outermost (mural granulosa) to the innermost (cumulus oophorus) cell layer of an ovarian follicle. Interestingly, LH receptor stimulation was associated with persistent cAMP signaling after LH removal and negligible desensitization of the cAMP signal. Interfering with receptor internalization with a dynamin inhibitor dynasore did not only prevent persistent LH-induced cAMP signaling, but also impaired the resumption of meiosis in follicle-enclosed oocytes, a key biological effect of LH.
In order to investigate the downstream activation of protein kinase A (PKA) in primary thyroid cells, FRET sensors with different subcellular localization (plasma membrane, cytosol and nucleus) were transiently transfected into primary thyroid cells of wild-type mice via electroporation. Interestingly, TSH stimulation causes at least two distinct phases of PKA activation in the global primary thyroid cell, which are temporally separated by approximately 2 min. In addition, PKA activation in different subcellular compartments are characterized by dissimilar kinetics and amplitudes. Pharmacological inhibition of TSH receptor internalization largely prevented the second (i.e. late) phase of PKA activation as well as the subsequent TSH-dependent phosphorylation of CREB and TSH-dependent induction of early genes. These results suggest that PKA activation and nuclear signaling require internalization of the TSH receptor.
Taken together, the data of the present study provide strong evidence that GPCR signaling at intracellular sites is distinct from the one occurring at the cell-surface and is highly physiologically relevant.
Spinal muscular atrophy and amyotrophic lateral sclerosis are the two most common devastating motoneuron diseases. The mechanisms leading to motoneuron degeneration are not resolved so far, although different hypotheses have been built on existing data. One possible mechanism is disturbed axonal transport of RNAs in the affected motoneurons. The underlying question of this study was therefore to characterize changes in transcript levels of distinct RNAs in cell culture models of spinal muscular atrophy and amyotrophic lateral sclerosis, especially in the axonal compartment of primary motoneurons.
To investigate this in detail we first established compartmentalized cultures of Primary mouse motoneurons. Subsequently, total RNA of both compartments was extracted
separately and either linearly amplified and subjected to microarray profiling or whole transcriptome amplification followed by RNA-Sequencing was performed. To make
the whole transcriptome amplification method suitable for compartmentalized cultures, we adapted a double-random priming strategy. First, we applied this method
for initial optimization onto serial dilutions of spinal cord RNA and later on to the compartmentalized motoneurons.
Analysis of the data obtained from wildtype cultures already revealed interesting results. First, the RNA composition of axons turned out to be highly similar to the somatodendritic compartment. Second, axons seem to be particularly enriched for transcripts related to protein synthesis and energy production. In a next step we
repeated the experiments by using knockdown cultures. The proteins depleted hereby are Smn, Tdp-43 and hnRNP R. Another experiment was performed by knocking down the non-coding RNA 7SK, the main interacting RNA of hnRNP R.
Depletion of Smn led to a vast number of deregulated transcripts in the axonal and somatodendritic compartment. Transcripts downregulated in the axons upon Smn depletion were especially enriched for GOterms related to RNA processing and encode proteins located in neuron projections including axons and growth cones.
Strinkingly, among the upregulated transcripts in the somatodendritic compartment we mainly found MHC class I transcripts suggesting a potential neuroprotective role.
In contrast, although knockdown of Tdp-43 also revealed a large number of downregulated transcripts in the axonal compartment, these transcripts were mainly
associated with functions in transcriptional regulation and RNA splicing. For the hnRNP R knockdown our results were again different. Here, we observed
downregulated transcripts in the axonal compartment mainly associated with regulation of synaptic transmission and nerve impulses. Interestingly, a comparison between deregulated transcripts in the axonal compartment of both hnRNP R and 7SK knockdown presented a significant overlap of several transcripts suggesting
some common mechanism for both knockdowns.
Thus, our data indicate that a loss of disease-associated proteins involved in axonal RNA transport causes distinct transcriptome alterations in motor axons.
This dissertation studies the interrelations between housing markets and monetary policy from three different perspectives. First, it identifies housing finance specific shocks and analyzes their impact on the broader economy and, most importantly, the systematic monetary policy reaction to such mortgage sector disturbances. Second, it investigates the implications of the institutional arrangement of a currency union for the potential buildup of a housing bubble in a member country of the monetary union by, inter alia, fostering border-crossing capital flows and ultimately residential investment activity. This dissertation, third, quantifies the effects of autonomous monetary policy shifts on the macroeconomy and, in particular, on housing markets by conditioning on financial sector conditions. From a methodological perspective, the dissertation draws on time-series econometrics like vector autoregressions (VARs) or local projections models.
The basement membrane separates the epithelium from the stroma of any given barrier tissue and is essential in regulating cellular behavior, as mechanical barrier and as structural support. It further plays an important role for new tissue formation, homeostasis, and pathological processes, such as diabetes or cancer. Breakdown of the basement membrane is believed to be essential for tumor invasion and metastasization. Since the basement membrane is crucial for many body functions, the development of artificial basement membranes is indispensable for the ultimate formation of engineered functional tissue, however, challenging due to their complex structure.
Electrospinning enables the production of fibers in the nano- or microscale range with morphological similarities to the randomly orientated collagen and elastic fibers in the basement membrane. However, electrospun fibers often lack the functional similarity to guide cells and maintain tissue-specific functions. Hence, their possible applications as matrix structure for tissue engineering are limited.
Herein, the potential of polyester meshes, modified with six armed star-shaped pre-polymers and cell-adhesion-mediating peptides, was evaluated to act as functional isotropic and bipolar artificial basement membranes. Thereby, the meshes were shown to be biocompatible and stable including under dynamic conditions, and the degradation profile to correlate with the rate of new tissue formation. The different peptide sequences did not influence the morphology and integrity of the fibers. The modified membranes exhibited protein-repellent properties over 12 months, indicating the long-term stability of the cross-linked star-polymer surfaces.
Cell culture experiments with primary fibroblasts and a human keratinocyte cell line (HaCaT) revealed that cell adhesion and growth strongly depends on the peptide sequences and their combinations employed. HaCaT cells grew to confluence on membranes modified with a combination of laminin/collagen type IV derived binding sequences and with a combination of fibronectin/laminin/collagen type IV derived peptide sequences. Fibroblasts strongly adhered to the fibronectin derived binding sequence and to membranes containing a combination of fibronectin/laminin/collagen type IV derived peptide sequences. The adhesion and growth of fibroblasts and HaCaT cells were significantly reduced on membranes modified with laminin, as well as collagen IV derived peptide sequences. HaCaT cells and fibroblasts barely adhered onto meshes without peptide sequences.
Co-culture experiments at the air-liquid interface with fibroblasts and HaCaT cells confirmed the possibility of creating biocompatible, biofunctional and biomimetic isotropic and bipolar basement membranes, based on the functionalized fibers. HaCaT cells grew in several layers, differentiating towards the surface and expressing cytokeratin 10 in the suprabasal and cytokeratin 14 in the basal layers. Migration of fibroblasts into the electrospun membrane was shown by vimentin staining. Moreover, specific staining against laminin type V, collagen type I, III, IV and fibronectin illustrated that cells started to remodel the electrospun membrane and produced new extracellular matrix proteins following the adhesion to the synthetic surface structures.
The culturing of primary human skin keratinocytes proved to be difficult on electrospun fibers. Cells attached to the membrane, but failed to form a multilayered, well-stratified, and keratinized epidermal layer. Changing the fiber composition and fixation methods did not promote tissue development. Further investigations of the membrane demonstrated the tremendous influence of the pore size of the membrane on epithelial formation. Furthermore, primary keratinocytes reacted more sensitive to pH changes in the medium than HaCaT cells did.
Since primary keratinocytes did not adequately develop on the functionalized meshes, polycarbonate membranes were used instead of electrospun meshes to establish oral mucosa models. The tissue-engineered models represented important features of native human oral mucosa. They consisted of a multilayered epithelium with stratum basale, stratum spinosum, stratum granulosum, and stratum corneum. The models formed a physical barrier and the expression of characteristic cell markers was comparable with that in native human oral mucosa. The results from the ET-50 assay and the irritation study reflected the reproducibility of the tissue equivalents.
Altogether, electrospinning enables the production of fibers with structural similarity to the basement membrane. Incorporating extracellular matrix components to mimic the functional composition offers a safe and promising way to modify the fibers so that they can be used for different tissue engineering applications. The resultant biomimetic membranes that can be functionalized with binding sequences derived from widely varying proteins can be used as a toolbox to study the influence of isotropic and bipolar basement membranes on tissue formation and matrix remodeling systematically, with regards to the biochemical composition and the influence and importance of mono- and co-culture. The oral mucosa models may be useful for toxicity and permeation studies, to monitor the irritation potential of oral health care products and biomaterials or as a disease model.
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.
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.
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.
Dementia is a complex neurodegenerative syndrome that by 2050 could affect about 135 Million people worldwide. People with dementia experience a progressive decline in their cognitive abilities and have serious problems coping with activities of daily living, including
orientation and wayfinding tasks. They even experience difficulties in finding their way in a familiar environment. Being lost or fear of getting lost may consequently develop into other psychological deficits such as anxiety, suspicions, illusions, and aggression. Frequent results are social isolation and a reduced quality of life. Moreover, the lives of relatives and
caregivers of people with dementia are also negatively affected.
Regarding navigation and orientation, most existing approaches focus on outdoor environment and people with mild dementia, who have the capability to use mobile devices. However, Rasquin (2007) observe that even a device with three buttons may be too complicated for
people with moderate to severe dementia. In addition, people who are living in care homes mainly perform indoor activities. Given this background, we decided to focus on designing a system for indoor environments for people with moderate to severe dementia, who are unable
or reluctant to use smartphone technology.
Adopting user-centered design approach, context and requirements of people with dementia were gathered as a first step to understand needs and difficulties (especially in spatial disorientation and wayfinding problems) experienced in dementia care facilities. Then, an "Implicit Interactive Intelligent (III) Environment" for people with dementia was proposed emphasizing implicit interaction and natural interface. The backbone of this III Environment is based on supporting orientation and navigation tasks with three systems: a Monitoring system, an intelligent system, and a guiding system. The monitoring system and intelligent system automatically detect and interpret the locations and activities performed by the users i.e. people with dementia. This approach (implicit input) reduces cognitive workload as well as physical workload on the user to provide input. The intelligent system is also aware of context, predicts next situations (location, activity), and decides when to provide an appropriate service to the users. The guiding system with intuitive and dynamic environmental cues (lighting with color) has the responsibility for guiding the users to the places they need to be.
Overall, three types of a monitoring system with Ultra-Wideband and iBeacon technologies, different techniques and algorithms were implemented for different contexts of use.
They showed a high user acceptance with a reasonable price as well as decent accuracy and precision. In the intelligent system, models were built to recognize the users’ current activity, detect the erroneous activity, predict the next location and activity, and analyze the
history data, detect issues, notify them and suggest solutions to caregivers via visualized web interfaces. About the guiding systems, five studies were conducted to test and evaluate the effect of lighting with color on people with dementia. The results were promising. Although
several components of III Environment in general and three systems, in particular, are in place (implemented and tested separately), integrating them all together and employing this in the dementia context as a fully properly evaluation with formal stakeholders (people with
dementia and caregivers) are needed for the future step.
Social life is organized around rules and norms. The present experiments investigate the cognitive architecture of rule violations. To do so, a setting with arbitrary rules that had to be followed or broken was developed, and breaking these rules did not have any negative consequences. Removed from any social influences that might further encourage or hinder the rule breaker, results suggest that simply labeling a behavior as a rule violation comes with specific costs: They are more difficult to plan and come with specific behavioral markers during execution. In essence, rule violations resemble rule negations, but they also trigger additional processes.
The question of what makes rule violations more difficult than rule inversions is the major focus of the remaining experiments. These experiments revealed negative affective consequences of rule violation and rule inversions alike, while rule violations additionally prime authority-related concepts, thus sensitizing towards authority related stimuli.
Next, the question how these burdens of non-conformity can be mitigated was investigated, and the influence of having executed the behavior in question frequently and recently was tested in both negations and rule violations. The burdens of non-conformity can best be reduced by a combination of having violated/negated a rule very frequently and very recently. Transfer from another task, however, could not be identified.
To conclude, a model that accounts for the data that is currently presented is proposed. As a variant of a task switching model, it describes the cognitive processes that were investigated and highlights unique processing steps that rule violations seem to require.
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.
The subject of this thesis is the control of strain in HgTe thin-film crystals. Such systems are members of the new class of topological insulator materials and therefore of special research interest. A major task was the experimental control of the strain in the HgTe films. This was achieved by a new epitaxial approach and confirmed by cristallographic analysis and magneto-transport measurements.
In this work, strain was induced in thin films by means of coherent epitaxy on substrate crystals. This means that the film adopts the lattice constant of the substrate in the plane of the substrate-epilayer interface. The level of strain is determined by the difference between the strain-free lattice constants of the substrate and epilayer material (the so-called lattice mismatch). The film responds to an in-plane strain with a change of its lattice constant perpendicular to the interface. This relationship is crucial for both the correct interpretation of high resolution X-ray diffraction (HRXRD) measurements, and the precise determination of the band dispersion. The lattice constant of HgTe is smaller than the lattice constant of CdTe. Therefore, strain in HgTe is tensile if it is grown on a CdTe substrate. In principle, compressive strain can be achieved by using an appropriate \(\text{Cd}_{1-x}\text{Zn}_{x}\text{Te}\) substrate. This concept was modified and applied in this work.
Epilayers have been fabricated by molecular-beam epitaxy (MBE). The growth of thick buffer layers of CdTe on GaAs:Si was established as an alternative to commercial CdTe and \(text{Cd}_{0.96}\text{Zn}_{0.04}\text{Te}\) substrates. The growth conditions have been optimized by an analysis of atomic force microscopy and HRXRD studies. HRXRD measurements reveal a power-law increase of the crystal quality with increasing thickness. Residual strain was found in the buffer layers, and was attributed to a combination of finite layer thickness and mismatch of the thermal expansion coefficients of CdTe and GaAs. In order to control the strain in HgTe epilayers, we have developed a new type of substrate with freely adjustable lattice constant.
CdTe-\(\text{Cd}_{0.5}\text{Zn}_{0.5}\text{Te}\) strained-layer-superlattices have been grown by a combination of MBE and atomic-layer epitaxy (ALE), and have been analyzed by HRXRD. ALE of the \(\text{Cd}_{0.5}\text{Zn}_{0.5}\text{Te}\) layer is self-limiting to one monolayer, and the effective lattice constant can be controlled reproducibly and straightforward by adjusting the CdTe layer thickness. The crystal quality has been found to degrade with increasing Zn-fraction. However, the effect is less drastic compared to single layer \(\text{Cd}_{1-x}\text{Zn}_{x}\text{Te}\) solid solutions. HgTe quantum wells (QWs) sandwiched in between CdHgTe barriers have been fabricated in a similar fashion on superlattices and conventional CdTe and \(\text{Cd}_{0.96}\text{Zn}_{0.04}\text{Te}\) substrates. The lower critical thickness of the CdHgTe barrier material grown on superlattice substrates had to be considered regarding the sample design. The electronic properties of the QWs depend on the strain and thickness of the QW. We have determined the QW thickness with an accuracy of \(\pm\)0.5 nm by an analysis of the beating patterns in the thickness fringes of HRXRD measurements and X-ray reflectometry measurements. We have, for the first time, induced compressive strain in HgTe QWs by an epitaxial technique (i.e. the effective lattice constant of the superlattice is lower compared to the lattice constant of HgTe). The problem of the lattice mismatch between superlattice and barriers has been circumvented by using CdHgTe-ZnHgTe superlattices instead of CdHgTe as a barrier material. Furthermore, the growth of compressively strained HgTe bulk layers (with a thickness of at least 50 nm) was demonstrated as well.
The control of the state of strain adds a new degree of freedom to the design of HgTe epilayers, which has a major influence on the band structure of QWs and bulk layers. Strain in bulk layers lifts the degeneracy of the \(\Gamma_8\) bands at \(\mathbf{k}=0\). Tensile strain opens an energy gap, compressive strain shifts the touching points of the valence- and conduction band to positions in the Brillouin zone with finite \(\mathbf{k}\). Such a situation has been realized for the first time in the course of this work. For QWs in the inverted regime, it is demonstrated that compressive strain can be used to significantly enhance the thermal energy gap of the two-dimensional electron gas (2DEG). In addition, semi-metallic and semiconducting behavior is expected in wide QWs, depending on the state of strain. An examination of the temperature dependence of the subband ordering in QWs revealed that the band gap is only temperature-stable for appropriate sample parameters and temperature regimes. The band inversion is always lifted for sufficiently high temperatures.
A large number of models investigate the influence of the band gap on the stability of the quantum-spin-Hall (QSH) effect. An enhancement of the stability of QSH edge state conductance is expected for enlarged band gaps. Furthermore, experimental studies on the temperature dependence of the QSH conductance are in contradiction to theoretical predictions. Systematic studies of these aspects have become feasible based on the new flexibility of the sample design.
Detailed low-temperature magnetotransport studies have been carried out on QWs and bulk layers. For this purpose, devices have been fabricated lithographically, which consist of two Hall-bar geometries with different dimensions. This allows to discriminate between conductance at the plane of the 2DEG and the edge of the sample. The Fermi energy in the 2DEG has been adjusted by means of a top gate electrode. The strain-induced transition from semi-metallic to semiconducting characteristics in wide QWs was shown. The magnitude of the semi-metallic overlap of valence- and conduction band was determined by an analysis of the two-carrier conductance and is in agreement with band structure calculations. The band gap of the semiconducting sample was determined by measurements of the temperature dependence of the conductance at the charge-neutrality point. Agreement with the value expected from theory has been achieved for the first time in this work. The influence of the band gap on the stability of QSH edge state conductance has been investigated on a set of six samples. The band gap of the set spans a range of 10 to 55 meV. The latter value has been achieved in a highly compressively strained QW, has been confirmed by temperature-dependent conductance measurements, and is the highest ever reported in the inverted regime. Studies of the carrier mobility reveal a degradation of the sample quality with increasing Zn-fraction in the superlattice, in agreement with HRXRD observations. The enhanced band gap does not suppress scattering mechanisms in QSH edge channels, but lowers the conductance in the plane of the 2DEG. Hence, edge state conductance is the dominant conducting process even at elevated temperatures. An increase in conductance with increasing temperature has been found, in agreement with reports from other groups. The increase follows a power-law dependency, the underlying physical mechanism remains open. A cause for the lack of an increase of the QSH edge state conductance with increasing energy gap has been discussed. Possibly, the sample remains insulating even at finite carrier densities, due to localization effects. The measurement does not probe the QSH edge state conductance at the situation where the Fermi energy is located in the center of the energy gap, but in the regime of maximized puddle-driven scattering. In a first set of measurements, it has been shown that the QSH edge state conductance can be influenced by hysteretic charging effects of trapped states in the insulating dielectric. A maximized conductance of \(1.6\ \text{e}^2/\text{h}\) was obtained in a \(58\ \mu\text{m}\) edge channel. Finally, measurements on three dimensional samples have been discussed. Recent theoretical works assign compressively strained HgTe bulk layers to the Weyl semi-metal class of materials. Such layers have been synthesized and studied in magnetotransport experiments for the first time. Pronounced quantum-Hall- and Shubnikov-de-Haas features in the Hall- and longitudinal resistance indicate two-dimensional conductance on the sample surface. However, this conductance cannot be assigned definitely to Weyl surface states, due to the inversion of \(\Gamma_6\) and \(\Gamma_8\) bands. If a magnetic field is aligned parallel to the current in the device, a decrease in the longitudinal resistance is observed with increasing magnetic field. This is a signature of the chiral anomaly, which is expected in Weyl semi-metals.
In the 1960s, when most African nations gained their independence after the age of colonialism, several theories and strategies emerged with the goal of "developing" these apparently "underdeveloped" territories. One of the most influential approaches for this task was represented in Julius K. Nyerere´s idea of Ujamaa, the Tanzanian version of African socialism.
Even before the Arusha Declaration established Ujamaa as a national development strategy in 1967, several groups of politicized young farmers took to the empty countryside of Tanzania to implement their own version of cooperative development. From one of these attempts emerged the Ruvuma Development Association (RDA), which organized up to 18 villages in southwestern Tanzania. The RDA became the inspiration for Nyerere´s concretization of Ujamaa and its implementation on national level. Yet, the central state could not replicate the success of the peasants, which was based on voluntariness and intrinsic motivation.
In 2015, this exploratory study has revisited the Region of Ruvuma. Through a case study approach, relying mostly on qualitative methods, new insights into the local history of Ujamaa and its perception have been gathered. In particular, narrative interviews with contemporary witnesses and group interviews with the present-day farmers’ groups have been conducted. Furthermore, NGOs active within the region, as well as regional and local government institutions were among the key stakeholders identified to concretize the local narrative of Ujamaa development. All interviews were analyzed according to the principles of qualitative content analysis. Additionally, individual villager questionnaires were used to achieve a more holistic picture of the local perception of development, challenges and the Ujamaa era.
None of the original Ujamaa groups of the times of the RDA was still operational at the time of research and no case of village-wide organization of collective agriculture could be observed. Nevertheless, in all of the three case study villages, several farmers’ groups (vikundi) were active in organizing development activities for their members. Furthermore, the perception of the Ujamaa era was generally positive throughout all of the case study sites. Yet, there have been significant differences in this perception, based on the village, age, gender and field size of the recipients. Overall, the period of Ujamaa was seen as an inspiration for present-day group activities, and the idea of such activities as a remedy for the developmental challenges of these villages was common among all stakeholders.
This thesis concludes that the positive perception of group activities as a vehicle for village development and the perception of Ujamaa history as a positive asset for the inception and organization of farmers’ groups would be highly beneficial to further attempts to support such development activities. However, the limitations in market access and capital availability for these highly-motivated group members have to be addressed by public and private development institutions. Otherwise, "the smell of Ujamaa" will be of little use for the progress of these villages.
This thesis reports a successful fabrication and characterisation of ferromagnetic/superconductor junction (F/S) on graphene. The thesis preposes a fabrication method to produce F/S junctions on graphene which make use of ALD grown Al2O3 as the tunnel barrier for the ferromagnetic contacts. Measurements done on F/G/S/G/F suggests that by injecting spin polarised current into the superconductor, a spin imbalance is created in the quasiparticle density of states of the superconductor which then diffuses through the graphene channel. The observed characteristic curves are similar to the ones which are already reported on metallic ferromagnet/superconductor junctions where the spin imbalance is created using Zeeman splitting. Further measurements also show that the curves loose their characteristic shapes when the temperature is increased above the critical temperature (Tc) or when the external magnetic field is higher then the critical field (Hc) of the superconducting contact. But to prove conclusively and doubtlessly the existence of spin imbalance in ferromagnet/superconductor junctions on graphene, more devices have to be made and characterised preferably in a dilution refrigerator.
The thesis focuses on Quality of Experience (QoE) of HTTP adaptive video streaming (HAS) and traffic management in access networks to improve the QoE of HAS. First, the QoE impact of adaptation parameters and time on layer was investigated with subjective crowdsourcing studies. The results were used to compute a QoE-optimal adaptation strategy for given video and network conditions. This allows video service providers to develop and benchmark improved adaptation logics for HAS. Furthermore, the thesis investigated concepts to monitor video QoE on application and network layer, which can be used by network providers in the QoE-aware traffic management cycle. Moreover, an analytic and simulative performance evaluation of QoE-aware traffic management on a bottleneck link was conducted. Finally, the thesis investigated socially-aware traffic management for HAS via Wi-Fi offloading of mobile HAS flows. A model for the distribution of public Wi-Fi hotspots and a platform for socially-aware traffic management on private home routers was presented. A simulative performance evaluation investigated the impact of Wi-Fi offloading on the QoE and energy consumption of mobile HAS.
RNA-binding proteins (RBPs) have been extensively studied in eukaryotes, where they post-transcriptionally regulate many cellular events including RNA transport, translation, and stability. Experimental techniques, such as cross-linking and co-purification followed by either mass spectrometry or RNA sequencing has enabled the identification and characterization of RBPs, their conserved RNA-binding domains (RBDs), and the regulatory roles of these proteins on a genome-wide scale. These developments in quantitative, high-resolution, and high-throughput screening techniques have greatly expanded our understanding of RBPs in human and yeast cells. In contrast, our knowledge of number and potential diversity of RBPs in bacteria is comparatively poor, in part due to the technical challenges associated with existing global screening approaches developed in eukaryotes.
Genome- and proteome-wide screening approaches performed in silico may circumvent these technical issues to obtain a broad picture of the RNA interactome of bacteria and identify strong RBP candidates for more detailed experimental study. Here, I report APRICOT (“Analyzing Protein RNA Interaction by Combined Output Technique”), a computational pipeline for the sequence-based identification and characterization of candidate RNA-binding proteins encoded in the genomes of all domains of life using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences of an input proteome using position-specific scoring matrices and hidden Markov models of all conserved domains available in the databases and then statistically score them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them according to functionally relevant structural properties. APRICOT performed better than other existing tools for the sequence-based prediction on the known RBP data sets. The applications and adaptability of the software was demonstrated on several large bacterial RBP data sets including the complete proteome of Salmonella Typhimurium strain SL1344. APRICOT reported 1068 Salmonella proteins as RBP candidates, which were subsequently categorized using the RBDs that have been reported in both eukaryotic and bacterial proteins. A set of 131 strong RBP candidates was selected for experimental confirmation and characterization of RNA-binding activity using RNA co-immunoprecipitation followed by high-throughput sequencing (RIP-Seq) experiments. Based on the relative abundance of transcripts across the RIP-Seq libraries, a catalogue of enriched genes was established for each candidate, which shows the RNA-binding potential of 90% of these proteins. Furthermore, the direct targets of few of these putative RBPs were validated by means of cross-linking and co-immunoprecipitation (CLIP) experiments.
This thesis presents the computational pipeline APRICOT for the global screening of protein primary sequences for potential RBPs in bacteria using RBD information from all kingdoms of life. Furthermore, it provides the first bio-computational resource of putative RBPs in Salmonella, which could now be further studied for their biological and regulatory roles. The command line tool and its documentation are available at https://malvikasharan.github.io/APRICOT/.
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 field of genetics faces a lot of challenges and opportunities in both research and diagnostics due to the rise of next generation sequencing (NGS), a technology that allows to sequence DNA increasingly fast and cheap.
NGS is not only used to analyze DNA, but also RNA, which is a very similar molecule also present in the cell, in both cases producing large amounts of data.
The big amount of data raises both infrastructure and usability problems, as powerful computing infrastructures are required and there are many manual steps in the data analysis which are complicated to execute.
Both of those problems limit the use of NGS in the clinic and research, by producing a bottleneck both computationally and in terms of manpower, as for many analyses geneticists lack the required computing skills.
Over the course of this thesis we investigated how computer science can help to improve this situation to reduce the complexity of this type of analysis.
We looked at how to make the analysis more accessible to increase the number of people that can perform OMICS data analysis (OMICS groups various genomics data-sources).
To approach this problem, we developed a graphical NGS data analysis pipeline aimed at a diagnostics environment while still being useful in research in close collaboration with the Human Genetics Department at the University of Würzburg.
The pipeline has been used in various research papers on covering subjects, including works with direct author participation in genomics, transcriptomics as well as epigenomics.
To further validate the graphical pipeline, a user survey was carried out which confirmed that it lowers the complexity of OMICS data analysis.
We also studied how the data analysis can be improved in terms of computing infrastructure by improving the performance of certain analysis steps.
We did this both in terms of speed improvements on a single computer (with notably variant calling being faster by up to 18 times), as well as with distributed computing to better use an existing infrastructure.
The improvements were integrated into the previously described graphical pipeline, which itself also was focused on low resource usage.
As a major contribution and to help with future development of parallel and distributed applications, for the usage in genetics or otherwise, we also looked at how to make it easier to develop such applications.
Based on the parallel object programming model (POP), we created a Java language extension called POP-Java, which allows for easy and transparent distribution of objects.
Through this development, we brought the POP model to the cloud, Hadoop clusters and present a new collaborative distributed computing model called FriendComputing.
The advances made in the different domains of this thesis have been published in various works specified in this document.
The importance of enterprise systems is increasingly growing and they are in the center of attention and consideration by organizations in various types of business and industries from extra-large public or private organizations to small and medium-sized service sector business. These systems are continuously advancing functionally and technologically and are inevitable and ineluctable for the enterprises to maximize their productivity and integration in current competitive national and global business environments.
Also, since local software solutions could not meet the requirements of especially large enterprises functionally and technically, and as giant global enterprise software producers like SAP, Oracle and Microsoft are improving their solutions rapidly and since they are expanding their market to more corners of the globe, demand for these globally branded low-defect software solutions is daily ascending. The agreements for international ERP implementation project consultancy are, therefore, exponentially increasing, while the research on the influencing factors and know-hows is scattered and rare, and thus, a timely urgency for this field of research is being felt.
The final developed five-in-five framework of this study, for the first time, collects all mentioned-in-the-history critical success factors and project activities, while sequencing them in five phases and categorizing them in five focus areas for international ERP implementation projects. This framework provides a bird’s-eye view and draws a comprehensive roadmap or instruction for such projects.
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.
Using color in user interface design is both art and science. Often, designers focus on aesthetic properties of color, but neglect that it also carries meaning and entails profound psychological consequences. Color psychology, filling this gap, is in its infancy, and lacks a theoretical approach that predicts and explains color-meaning associations shared by a large group of people in a large variety of contexts.
To amend this situation, this work develops Conceptual Metaphor Theory of Color (CMToC), which predicts and explains cross-cultural and experience-based semantic color associations. The theory is based on the idea from cognitive linguistics that the study of metaphorical language provides valuable insights into our mental models involving color. A discussion of three types of metaphors that cover associations with physical and abstract concepts in light of existing empirical evidence provides the basis for deriving empirical research questions.
The first research question addresses the use of color for conveying physical information like weight in user interfaces. The results of four online surveys involving a total of 295 German and Japanese participants show the relative impact of hue, saturation and brightness for associations with 16 physical properties. Two thirds of these color associations were correctly predicted by CMToC. Participants frequently matched physical properties to colors based on sensorimotor correspondences and participants of both cultures did not considerably vary in their performance.
The second research question addresses the use of color for conveying abstract information like importance in user interfaces. In one experimental study, a total of 75 German and Japanese participants validated color-to-abstract mappings in form of color population stereotypes like important is dark. The majority of these color associations (86%) were correctly predicted by CMToC. Again, participants of both cultures did not considerably vary in their performance.
The third research question addresses whether predicted color associations with physical and abstract information are processed automatically as a precondition for intuitive use. The results of three studies involving a total of 85 German and Japanese participants show on the example of temperature that color automatically influences the identification speed of related physical properties, but not vice versa. Color and abstract information were not automatically associated.
As a result of these studies it can be concluded that predictions of CMToC are cross-culturally valid for user interface design. Derived implicit associations with physical properties and explicit associations with abstract concepts can inform design decisions in both hard- and software user interface design.
Site Directed Immobilization of BMP-2: Two Approaches for the Production of Osteoinductive Scaffolds
(2017)
Bone fractures typically heal without surgical intervention. However, pathological situations exist which impede the healing process resulting in so-called non-union fractures. Such fractures are nowadays treated with scaffold material being introduced into the defect area. These scaffolds can be doped with osteogenic factors, such as bone morphogenetic protein (BMP)2. BMP2 belongs to the most osteogenic growth factors known to date. Its medical use, efficiency and safety have been approved by FDA for certain applications. Currently, BMP2 is distributed with a stabilizing scaffold, which is simply soaked with the growth factor. Due to fast release kinetics supraphysiological high doses of BMP2 are required which are causally associated with severe side effects observed in certain applications being most harmful in the area of the cervical spine. These side-effects include inflammation, swelling and breathing problems, leading to disastrous consequences or secondary surgical interventions. Since it could be shown that a retardation of BMP2 release from the scaffold resulted in superior bone forming properties in vivo, it seems obvious to further reduce this release to a minimum. This can be achieved by covalent coupling which in the past was already elaborated using mainly classical EDC/NHS chemistry. Using this technique coupling of the protein occurs non-site-directedly leading mainly to an unpredictable product outcome with variable osteogenic activities. In order to improve the reproducibility of scaffold functionalization by BMP2 we created variants one of which contains a unique unnatural amino acid substitution within the mature polypeptide sequence (BMP2-K3Plk) and another, BMP2-A2C, in which an N-terminal alanine has been substituted by cysteine. These modifications enable site-specific and covalent immobilization of BMP2 e.g. onto polymeric beads. Both proteins were expressed in E. coli, renatured and purified by cation-exchange chromatography. Both variants were extensively analyzed in terms of purity and biological activity which was tested by in vitro interaction analyses as well as in cell based assays. Both proteins could be successfully coupled to polymeric beads. The different BMP2 functionalized beads were shown to interact with the ectodomain of the type I receptor BMPR-IA in vitro indicating that the biological activity of both BMP2 variants retained upon coupling. Both functionalized beads induced osteogenic differentiation C2C12 cells but only of those cells which have been in close contact to the particular beads. This strongly indicates that the BMP2 variant are indeed covalently coupled and not just adsorbed.
We claim that we have developed a system for a site-specific and covalent immobilization of BMP-2 onto solid scaffolds, potentially eliminating the necessity of high-dose scaffold loading. Since immobilized proteins are protected from removal by extracellular fluids, their activities now rely mainly on the half-life of the used scaffold and the rate of proteolytic degradation. Assuming that due to prolonged times much lower loading capacities might be required we propose that the immobilization strategy employed in this work may be further refined and optimized to replace the currently used BMP2-containing medical products.
This doctoral thesis provides a classification of equivariant star products (star products together with quantum momentum maps) in terms of equivariant de Rham cohomology. This classification result is then used to construct an analogon of the Kirwan map from which one can directly obtain the characteristic class of certain reduced star products on Marsden-Weinstein reduced symplectic manifolds from the equivariant characteristic class of their corresponding unreduced equivariant star product. From the surjectivity of this map one can conclude that every star product on Marsden-Weinstein reduced symplectic manifolds can (up to equivalence) be obtained as a reduced equivariant star product.
In this work, multi-particle quantum optimal control problems are studied in the framework of time-dependent density functional theory (TDDFT).
Quantum control problems are of great importance in both fundamental research and application of atomic and molecular systems. Typical applications are laser induced chemical reactions, nuclear magnetic resonance experiments, and quantum computing.
Theoretically, the problem of how to describe a non-relativistic system of multiple particles is solved by the Schrödinger equation (SE). However, due to the exponential increase in numerical complexity with the number of particles, it is impossible to directly solve the Schrödinger equation for large systems of interest. An efficient and successful approach to overcome this difficulty is the framework of TDDFT and the use of the time-dependent Kohn-Sham (TDKS) equations therein.
This is done by replacing the multi-particle SE with a set of nonlinear single-particle Schrödinger equations that are coupled through an additional potential.
Despite the fact that TDDFT is widely used for physical and quantum chemical calculation and software packages for its use are readily available, its mathematical foundation is still under active development and even fundamental issues remain unproven today.
The main purpose of this thesis is to provide a consistent and rigorous setting for the TDKS equations and of the related optimal control problems.
In the first part of the thesis, the framework of density functional theory (DFT) and TDDFT are introduced. This includes a detailed presentation of the different functional sets forming DFT. Furthermore, the known equivalence of the TDKS system to the original SE problem is further discussed.
To implement the TDDFT framework for multi-particle computations, the TDKS equations provide one of the most successful approaches nowadays. However, only few mathematical results concerning these equations are available and these results do not cover all issues that arise in the formulation of optimal control problems governed by the TDKS model.
It is the purpose of the second part of this thesis to address these issues such as higher regularity of TDKS solutions and the case of weaker requirements on external (control) potentials that are instrumental for the formulation of well-posed TDKS control problems. For this purpose, in this work, existence and uniqueness of TDKS solutions are investigated in the Galerkin framework and using energy estimates for the nonlinear TDKS equations.
In the third part of this thesis, optimal control problems governed by the TDKS model are formulated and investigated. For this purpose, relevant cost functionals that model the purpose of the control are discussed.
Henceforth, TDKS control problems result from the requirement of optimising the given cost functionals subject to the differential constraint given by the TDKS equations. The analysis of these problems is novel and represents one of the main contributions of the present thesis.
In particular, existence of minimizers is proved and their characterization by TDKS optimality systems is discussed in detail.
To this end, Fréchet differentiability of the TDKS model and of the cost functionals is addressed considering \(H^1\) cost of the control.
This part is concluded by deriving the reduced gradient in the \(L^2\) and \(H^1\) inner product.
While the \(L^2\) optimization is widespread in the literature, the choice of the \(H^1\) gradient is motivated in this work by theoretical consideration and by resulting numerical advantages.
The last part of the thesis is devoted to the numerical approximation of the TDKS optimality systems and to their solution by gradient-based optimization techniques.
For the former purpose, Strang time-splitting pseudo-spectral schemes are discussed including a review of some recent theoretical estimates for these schemes and a numerical validation of these estimates.
For the latter purpose, nonlinear (projected) conjugate gradient methods are implemented and are used to validate the theoretical analysis of this thesis with results of numerical experiments with different cost functional settings.
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 current dissertation addresses the analysis of technology-enhanced learning processes by using Process Mining techniques. For this purpose, students’ coded think-aloud data served as the measurement of the learning process, in order to assess the potential of this analysis method for evaluating the impact of instructional support.
The increasing use of digital media in higher education and further educational sectors enables new potentials. However, it also poses new challenges to students, especially regarding the self-regulation of their learning process. To help students with optimally making progress towards their learning goals, instructional support is provided during learning. Besides the use of questionnaires and tests for the assessment of learning, researchers make use increasingly of process data to evaluate the effects of provided support. The analysis of observed behavioral traces while learning (e.g., log files, eye movements, verbal reports) allows detailed insights into the student’s activities as well as the impact of interventions on the learning process. However, new analytical challenges emerge, especially when going beyond the analysis of pure frequencies of observed events. For example, the question how to deal with temporal dynamics and sequences of learning activities arises. Against this background, the current dissertation concentrates on the application of Process Mining techniques for the detailed analysis of learning processes. In particular, the focus is on the additional value of this approach in comparison to a frequency-based analysis, and therefore on the potential of Process Mining for the evaluation of instructional support.
An extensive laboratory study with 70 university students, which was conducted to investigate the impact of a support measure, served as the basis for pursuing the research agenda of this dissertation. Metacognitive prompts supported students in the experimental group (n = 35) during a 40-minute hypermedia learning session; whereas the control group (n = 35) received no support. Approximately three weeks later, all students participated in another learning session; however, this time all students learned without any help. The participants were instructed to verbalize their learning activities concurrently while learning. In the three analyses of this dissertation, the coded think aloud data were examined in detail by using frequency-based methods as well as Process Mining techniques.
The first analysis addressed the comparison of the learning activities between the experimental and control groups during the first learning session. This study concentrated on the research questions whether metacognitive prompting increases the number of metacognitive learning activities, whether a higher number of these learning activities corresponds with learning outcome (mediation), and which differences regarding the sequential structure of learning activities can be revealed. The second analysis investigated the impact of the individual prompts as well as the conditions of their effectiveness on the micro level. In addition to Process Mining, we used a data mining approach to compare the findings of both analysis methods. More specifically, we classified the prompts by their effectiveness, and we examined the learning activities preceding and following the presentation of instructional support. Finally, the third analysis considered the long-term effects of metacognitive prompting on the learning process during another learning session without support. It was the key objective of this study to examine which fostered learning activities and process patterns remained stable during the second learning session.
Overall, all three analyses indicated the additional value of Process Mining in comparison to a frequency-based analysis. Especially when conceptualizing the learning process as a dynamic sequence of multiple activities, Process Mining allows identifying regulatory loops and crucial routing points of the process. These findings might contribute to optimizing intervention strategies. However, before drawing conclusions for the design of instructional support based on the revealed process patterns, additional analyses need to investigate the generalizability of results. Moreover, the application of Process Mining remains challenging because guidelines for analytical decisions and parameter settings in technology-enhanced learning context are currently missing. Therefore, future studies need to examine further the potential of Process Mining as well as related analysis methods to provide researchers with concrete recommendations for use. Nevertheless, the application of Process Mining techniques can already contribute to advance the understanding of the impact of instructional support through the use of fine-grained process data.
Sponges (phylum Porifera) are evolutionary ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. Throughout this thesis project, I aimed at exploring the adaptations of these symbionts to life within their sponge host by sequencing and analyzing the genomes of a variety of bacteria from the microbiome of the Mediterranean sponge Aplysina aerophoba. Employed methods were fluorescence-activated cell sorting with subsequent multiple displacement amplification and single-cell / ‘mini-metagenome’ sequencing, and metagenomic sequencing followed by differential coverage binning. These two main approaches both aimed at obtaining genome sequences of bacterial symbionts of A. aerophoba, that were then compared to each other and to references from other environments, to gain information on adaptations to the host sponge environment and on possible interactions with the host and within the microbial community.
Cyanobacteria are frequent members of the sponge microbial community. My ‘mini-metagenome’ sequencing project delivered three draft genomes of “Candidatus Synechococcus spongiarum,” the cyanobacterial symbiont of A. aerophoba and many more sponges inhabiting the photic zone. The most complete of these genomes was compared to other clades of this symbiont and to closely related free-living cyanobacterial references in a collaborative project published in Burgsdorf I*, Slaby BM* et al. (2015; *shared first authorship). Although the four clades of “Ca. Synechococcus spongiarum” from the four sponge species A. aerophoba, Ircinia variabilis, Theonella swinhoei, and Carteriospongia foliascens were approximately 99% identical on the level of 16S rRNA gene sequences, they greatly differed on the genomic level. Not only the genome sizes were different from clade to clade, but also the gene content and a number of features including proteins containing the eukaryotic-type domains leucine-rich repeats or tetratricopeptide repeats. On the other hand, the four clades shared a number of features such as ankyrin repeat domain-containing proteins that seemed to be conserved also among other microbial phyla in different sponge hosts and from different geographic locations. A possible novel mechanism for host phagocytosis evasion and phage resistance by means of an altered O antigen of the lipopolysaccharide was identified.
To test previous hypotheses on adaptations of sponge-associated bacteria on a broader spectrum of the microbiome of A. aerophoba while also taking a step forward in methodology, I developed a bioinformatic pipeline to combine metagenomic Illumina short-read sequencing data with PacBio long-read data. At the beginning of this project, no pipelines to combine short-read and long-read data for metagenomics were published, and at time of writing, there are still no projects published with a comparable aim of un-targeted assembly, binning and analysis of a metagenome. I tried a variety of assembly programs and settings on a simulated test dataset reflecting the properties of the real metagenomic data. The developed assembly pipeline improved not only the overall assembly statistics, but also the quality of the binned genomes, which was evaluated by comparison to the originally published genome assemblies.
The microbiome of A. aerophoba was studied from various angles in the recent years, but only genomes of the candidate phylum Poribacteria and the cyanobacterial sequences from my above-described project have been published to date. By applying my newly developed assembly pipeline to a metagenomic dataset of A. aerophoba consisting of a PacBio long-read dataset and six Illumina short-read datasets optimized for subsequent differential coverage binning, I aimed at sequencing a larger number and greater diversity of symbionts. The results of this project are currently in review by The ISME Journal. The complementation of Illumina short-read with PacBio long-read sequencing data for binning of this highly complex metagenome greatly improved the overall assembly statistics and improved the quality of the binned genomes. Thirty-seven genomes from 13 bacterial phyla and candidate phyla were binned representing the most prominent members of the microbiome of A. aerophoba. A statistical comparison revealed an enrichment of genes involved in restriction modification and toxin-antitoxin systems in most symbiont genomes over selected reference genomes. Both are defense features against incoming foreign DNA, which may be important for sponge symbionts due to the sponge’s filtration and phagocytosis activity that exposes the symbionts to high levels of free DNA. Also host colonization and matrix utilization features were significantly enriched. Due to the diversity of the binned symbiont genomes, a within-symbionts genome comparison was possible, that revealed three guilds of symbionts characterized by i) nutritional specialization on the metabolization of carnitine, ii) specialization on sulfated polysaccharides, and iii) apparent nutritional generalism. Both carnitine and sulfated polysaccharides are abundant in the sponge extracellular matrix and therefore available to the sponge symbionts as substrates. In summary, the genomes of the diverse community of symbionts in A. aerophoba were united in their defense features, but specialized regarding their nutritional preferences.
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.
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.