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- Elementarteilchenphysik (9)
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- signal transduction (9)
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- evolution (8)
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- climate change (7)
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- melanoma (7)
- memory (7)
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- ATLAS <Teilchendetektor> (6)
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- Epigenetic (4)
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- Hypoxia (4)
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- Impfung (4)
- Implantat (4)
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- Infrarotspektroskopie (4)
- Innate immunity (4)
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- Krebsforschung (4)
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- LEED (4)
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- Perylenbisdicarboximide <Perylen-3,4:9,10-bis(dicarboximide)> (4)
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- Zelle (4)
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- active zone (4)
- antennal lobe (4)
- antibiotics (4)
- attention (4)
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- bees (4)
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- borylation (4)
- cAMP (4)
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Sonstige beteiligte Institutionen
- Fraunhofer-Institut für Silicatforschung ISC (5)
- Helmholtz Institute for RNA-based Infection Research (HIRI) (5)
- Technische Hochschule Nürnberg Georg Simon Ohm (3)
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ResearcherID
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- D-1250-2010 (1)
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EU-Project number / Contract (GA) number
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- 320377 (1)
- EU (FP7/ 2007-2013) (1)
Electrochemical impedance spectroscopy (EIS) is a valuable technique analyzing electrochemical behavior of biological systems such as electrical characterization of cells and biomolecules, drug screening, and biomaterials in biomedical field. In EIS, an alternating current (AC) power signal is applied to the biological system, and the impedance of the system is measured over a range of frequencies.
In vitro culture models of endothelial or epithelial barrier tissue can be achieved by culturing barrier tissue on scaffolds made with synthetic or biological materials that provide separate compartments (apical and basal sides), allowing for further studies on drug transport. EIS is a great candidate for non-invasive and real-time monitoring of the electrical properties that correlate with barrier integrity during the tissue modeling. Although commercially available transendothelial/transepithelial electrical resistance (TEER) measurement devices are widely used, their use is particularly common in static transwell culture. EIS is considered more suitable than TEER measurement devices in bioreactor cultures that involve dynamic fluid flow to obtain accurate and reliable measurements. Furthermore, while TEER measurement devices can only assess resistance at a single frequency, EIS measurements can capture both resistance and capacitance properties of cells, providing additional information about the cellular barrier's characteristics across various frequencies. Incorporating EIS into a bioreactor system requires the careful optimization of electrode integration within the bioreactor setup and measurement parameters to ensure accurate EIS measurements. Since bioreactors vary in size and design depending on the purpose of the study, most studies have reported using an electrode system specifically designed for a particular bioreactor. The aim of this work was to produce multi-applicable electrodes and established methods for automated non-invasive and real-time monitoring using the EIS technique in bioreactor cultures. Key to the electrode material, titanium nitride (TiN) coating was fabricated on different substrates (materials and shape) using physical vapor deposition (PVD) and housed in a polydimethylsiloxane (PDMS) structure to allow the electrodes to function as independent units. Various electrode designs were evaluated for double-layer capacitance and morphology using EIS and scanning electron microscopy (SEM), respectively. The TiN-coated tube electrode was identified as the optimal choice. Furthermore, EIS measurements were performed to examine the impact of influential parameters related to culture conditions on the TiN-coated electrode system. In order to demonstrate the versatility of the electrodes, these electrodes were then integrated into in different types of perfusion bioreactors for monitoring barrier cells. Blood-brain barrier (BBB) cells were cultured in the newly developed dynamic flow bioreactor, while human umblical vascular endothelial cells (HUVECs) and Caco-2 cells were cultured in the miniature hollow fiber bioreactor (HFBR). As a result, the TiN-coated tube electrode system enabled investigation of BBB barrier integrity in long-term bioreactor culture. While EIS measurement could not detect HUVECs electrical properties in miniature HFBR culture, there was the possibility of measuring the barrier integrity of Caco-2 cells, indicating potential usefulness for evaluating their barrier function. Following the bioreactor cultures, the application of the TiN-coated tube electrode was expanded to hemofiltration, based on the hypothesis that the EIS system may be used to monitor clotting or clogging phenomena in hemofiltration. The findings suggest that the EIS monitoring system can track changes in ion concentration of blood before and after hemofiltration in real-time, which may serve as an indicator of clogging of filter membranes. Overall, our research demonstrates the potential of TiN-coated tube electrodes for sensitive and versatile non-invasive monitoring in bioreactor cultures and medical devices.
Barth Syndrome (BTHS) is an inherited X-chromosomal linked disorder, characterized by early development of cardiomyopathy, immune system defects, skeletal muscle myopathy and growth retardation. The disease displays a wide variety of symptoms including heart failure, exercise intolerance and fatigue due to the muscle weakness. The cause of the disease are mutations in the gene encoding for the mitochondrial transacylase Tafazzin (TAZ), which is important for remodeling of the phospholipid cardiolipin (CL). All mutations result in a pronounced decrease of the functional enzyme leading to an increase of monolysocardiolipin (MLCL), the precursor of mature CL, and a decrease in mature CL itself. CL is a hallmark phospholipid of mitochondrial membranes, highly enriched in the inner mitochondrial membrane (IMM). It is not only important for the formation of the cristae structures, but also for the function of different protein complexes associated with the mitochondrial membrane. Reduced levels of mature CL cause remodeling of the respiratory chain supercomplexes, impaired respiration, defects in the Krebs cycle and a loss of mitochondrial calcium uniporter (MCU) protein. The defective Ca2+ handling causes impaired redox homeostasis and energy metabolism resulting in cellular arrhythmias and defective electrical conduction. In an uncompensated situation, blunting mitochondrial Ca2+ uptake provokes increased mitochondrial emission of H2O2 during workload transitions, related to oxidation of NADPH, which is required to regenerate anti-oxidative enzymes. However, in the hearts and cardiac myocytes of mice with a global knock-down of the Taz gene (Taz-KD), no increase in mitochondrial ROS was observed, suggesting that other metabolic pathways may have compensated for reduced Krebs cycle activation.
The healthy heart produces most of its energy by consuming fatty acids. In this study, the fatty acid uptake into mitochondria and their further degradation was investigated, which showed a switch of the metabolism in general in the Taz-KD mouse model. In vivo studies revealed an increase of glucose uptake into the heart and decreased fatty acid uptake and oxidation. Disturbed energy conversion resulted in activation of retrograde signaling pathways, implicating overall changes in the cell metabolism. Upregulated integrated stress response (ISR) was confirmed by increased levels of the downstream target, i.e., the activating transcription factor 4 (ATF4). A Tafazzin knockout mouse embryonal fibroblast cell model (TazKO) was used to inhibit the ISR using siRNA transfection or pharmaceutical inhibition. This verified the central role of
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the ISR in regulating the metabolism in BTHS. Moreover, an increased metabolic flux into glutathione biosynthesis was observed, which supports redox homeostasis. In vivo PET-CT scans depicted elevated activity of the xCT system in the BTHS mouse heart, which transports essential amino acids for the biosynthesis of glutathione precursors. Furthermore, the stress induced signaling pathway also affected the glutamate metabolism, which fuels into the Krebs cycle via -ketoglutarate and therefore supports energy converting pathways. In summary, this thesis provides novel insights into the energy metabolism and redox homeostasis in Barth syndrome cardiomyopathy and its regulation by the integrated stress response, which plays a central role in the metabolic alterations. The aim of the thesis was to improve the understanding of these metabolic changes and to identify novel targets, which can provide new possibilities for therapeutic intervention in Barth syndrome.
Platelets play an important role in haemostasis by mediating blood clotting at sites of blood vessel damage. Platelets, also participate in pathological conditions including thrombosis and inflammation. Upon vessel damage, two glycoprotein receptors, the GPIb-IX-V complex and GPVI, play important roles in platelet capture and activation.
GPIb-IX-V binds to von Willebrand factor and GPVI to collagen. This initiates a signalling cascade resulting in platelet shape change and spreading, which is dependent on the actin cytoskeleton. This thesis aimed to develop and implement different super-resolution microscopy techniques to gain a deeper understanding of the conformation and location of these receptors in the platelet plasma membrane, and to provide insights into their signalling pathways. We suggest direct stochastic optical reconstruction microscopy (dSTORM) and structured illumination microscopy (SIM) as the best candidates for imaging single platelets, whereas expansion microscopy (ExM) is ideal for imaging platelets aggregates.
Furthermore, we highlighted the role of the actin cytoskeleton, through Rac in GPVI signalling pathway. Inhibition of Rac, with EHT1864 in human platelets induced GPVI and GPV, but not GPIbα shedding. Furthermore, EHT1864 treatment did not change GPVI dimerisation or clustering, however, it decreased phospholipase Cγ2 phosphorylation levels, in human, but not murine platelets, highlighting interspecies differences. In summary, this PhD thesis demonstrates that; 1) Rac alters GPVI signalling pathway in human but not mouse platelets; 2) our newly developed ExM protocol can be used to image platelet aggregates labelled with F(ab’) fragments
Early-onset torsion dystonia (DYT-TOR1A, DYT1) is an inherited hyperkinetic movement disorder caused by a mutation of the TOR1A gene encoding the torsinA protein. DYT-TOR1A is characterized as a network disorder of the central nervous system (CNS), including predominantly the cortico-basal ganglia-thalamo-cortical loop resulting in a severe generalized dystonic phenotype. The pathophysiology of DYTTOR1A is not fully understood. Molecular levels up to large-scale network levels of the CNS are suggested to be affected in the pathophysiology of DYT-TOR1A. The reduced penetrance of 30% - 40% indicates a gene-environmental interaction, hypothesized as “second hit”. The lack of appropriate and phenotypic DYT-TOR1A animal models encouraged us to verify the “second hit” hypothesis through a unilateral peripheral nerve trauma of the sciatic nerve in a transgenic asymptomatic DYT-TOR1A rat model (∆ETorA), overexpressing the human mutated torsinA protein. In a multiscale approach, this animal model was characterized phenotypically and pathophysiologically.
Nerve-injured ∆ETorA rats revealed dystonia-like movements (DLM) with a partially generalized phenotype. A physiomarker of human dystonia, describing increased theta oscillation in the globus pallidus internus (GPi), was found in the entopeduncular nucleus (EP), the rodent equivalent to the human GPi, of nerve-injured ∆ETorA rats. Altered oscillation patterns were also observed in the primary motor cortex. Highfrequency stimulation (HFS) of the EP reduced DLM and modulated altered oscillatory activity in the EP and primary motor cortex in nerve-injured ∆ETorA rats. Moreover, the dopaminergic system in ∆ETorA rats demonstrated a significant increased striatal dopamine release and dopamine turnover. Whole transcriptome analysis revealed differentially expressed genes of the circadian clock and the energy metabolism, thereby pointing towards novel, putative pathways in the pathophysiology of DYTTOR1A dystonia.
In summary, peripheral nerve trauma can trigger DLM in genetically predisposed asymptomatic ΔETorA rats leading to neurobiological alteration in the central motor network on multiple levels and thereby supporting the “second hit” hypothesis. This novel symptomatic DYT-TOR1A rat model, based on a DYT-TOR1A genetic background, may prove as a valuable chance for DYT-TOR1A dystonia, to further investigate the pathomechanism in more detail and to establish new treatment strategies.
Chapter I: Introduction
Temperature is a major driver of biodiversity and abundance patterns on our planet, which becomes particularly relevant facing the entanglement of an imminent biodiversity and climate crisis. Climate shapes the composition of species assemblages either directly via abiotic filtering mechanisms or indirectly through alterations in biotic interactions. Insects - integral elements of Earth’s ecosystems - are affected by climatic variation such as warming, yet responses vary among species. While species’ traits, antagonistic biotic interactions, and even species’ microbial mutualists may determine temperature-dependent assembly processes, the lion’s share of these complex relationships remains poorly understood due to methodological constraints. Mountains, recognized as hotspots of diversity and threatened by rapidly changing climatic conditions, can serve as natural experimental settings to study the response of insect assemblages and their trophic interactions to temperature variation, instrumentalizing the high regional heterogeneity of micro- and macroclimate. With this thesis, we aim to enhance our mechanistic understanding of temperature-driven assembly processes within insect communities, exemplified by Orthoptera, that are significant herbivores in temperate mountain grassland ecosystems. Therefore, we combined field surveys of Orthoptera assemblages on grassland sites with molecular tools for foodweb reconstruction, primarily leveraging the elevational gradients offered by the complex topography within the Berchtesgaden Alpine region (Bavaria, Germany) as surrogate for temperature variation (space-for-time substitution approach). In this framework, we studied the effects of temperature variation on (1) species richness, abundance, community composition, and interspecific as well as intraspecific trait patterns, (2) ecological feeding specialisation, and (3) previously neglected links to microbial associates found in the faeces.
Chapter II: Temperature-driven assembly processes
Climate varies at multiple scales. Since microclimate is often overlooked, we assessed effects of local temperature deviations on species and trait compositions of insect communities along macroclimatic temperature gradients in Chapter II. Therefore, we employed joint species distribution modelling to explore how traits drive variation in the climatic niches of Orthoptera species at grassland sites characterized by contrasting micro- and macroclimatic conditions. Our findings revealed two key insights: (1) additive effects of micro- and macroclimate on the diversity, but (2) interactive effects on the abundance of several species, resulting in turnover and indicating that species possess narrower climatic niches than their elevational distributions might imply. This chapter suggests positive effects of warming on Orthoptera, but also highlights that the interplay of macro- and microclimate plays a pivotal role in structuring insect communities. Thus, it underscores the importance of considering both elements when predicting the responses of species to climate change. Additionally, this chapter revealed inter- and intraspecific effects of traits on the niches and distribution of species.
Chapter III: Dietary specialisation along climatic gradients
A crucial trait linked to the position of climatic niches is dietary specialisation. According to the ‘altitudinal niche-breadth hypothesis’, species of high-elevation habitats should be less specialized compared to their low-elevation counterparts. However, empirical evidence on shifts in specialization is scarce for generalist insect herbivores and existing studies often fail to control for the phylogeny and abundance of interaction partners. In Chapter III, we used a combination of field observations and amplicon sequencing to reconstruct dietary relationships between Orthoptera and plants along an extensive temperature gradient. We did not find close but flexible links between individual grasshopper and plant taxa in space. While interaction network specialisation increased with temperature, the corrected dietary specialisation pattern peaked at intermediate elevations on assemblage level. These nuanced findings demonstrate that (1) resource availability, (2) phylogenetic relationships, and (3) climate can affect empirical foodwebs intra- and interspecifically and, hence, the dietary specialisation of herbivorous insects. In this context, we discuss that the underlying mechanisms involved in shaping the specialisation of herbivore assemblages may switch along temperature clines.
Chapter IV: Links between faecal microbe communities, feeding habits, and climate
Since gut microbes affect the fitness and digestion of insects, studying their diversity could provide novel insights into specialisation patterns. However, their association with insect hosts that differ in feeding habits and specialisation has never been investigated along elevational climatic gradients. In Chapter IV, we utilized the dietary information gathered in Chapter III to characterize links between insects with distinct feeding behaviour and the microbial communities present in their faeces, using amplicon sequencing. Both, feeding and climate affected the bacterial communities. However, the large overlap of microbes at site level suggests that common bacteria are acquired from the shared feeding environment, such as the plants consumed by the insects. These findings emphasize the influence of a broader environmental context on the composition of insect gut microbial communities.
Chapter V: Discussion & Conclusions
Cumulatively, the sections of this dissertation provide support for the hypothesis that climatic conditions play a role in shaping plant–herbivore systems. The detected variation of taxonomic and functional compositions contributes to our understanding of assembly processes and resulting diversity patterns within Orthoptera communities, shedding light on the mechanisms that structure their trophic interactions in diverse climates. The combined results presented suggest that a warmer climate could foster an increase of Orthoptera species richness in Central European semi-natural grasslands, also because the weak links observed between insect herbivores and plants are unlikely to limit decoupled range shifts. However, the restructuring of Orthoptera communities in response to warmer temperatures depends on species' traits such as moisture preferences or phenology. Notably, we were able to demonstrate a crucial role of microclimate for many species, partly unravelling narrower climatic niches than their elevational ranges suggest. We found evidence that not only Orthoptera community composition, specialisation, and traits varied along elevational gradients, but even microbial communities in the faeces of Orthoptera changed, which is a novel finding. This complex restructuring and reassembly of communities, coupled with the nonlinear specialisation of trophic interactions and a high diversity of associated bacteria, emphasize our currently incomplete comprehension of how ecosystems will develop under future climatic conditions, demanding caution in making simplified predictions for biodiversity change under climate warming. Since these predictions may benefit from including biotic interactions and both, micro- and macroclimate based on our findings, conservation authorities and practitioners must not neglect improving microclimatic conditions to ensure local survival of a diverse set of threatened and demanding species. In this context, mountains can play a pivotal role for biodiversity conservation since these offer heterogeneous microclimatic conditions in proximity that can be utilized by species with distinct niches.
The detection of smallest mechanical loads plays an increasingly important role in many areas of advancing automation and manufacturing technology, but also in everyday life. In this doctoral thesis, various microparticle systems were developed that are able to indicate mechanical shear stress via simple mechanisms. Using a toolbox approach, these systems can be spray-dried from various nanoscale primary particles (silica and iron oxide) to micrometer-sized units, so-called supraparticles. By varying the different building blocks and in combination with different dyes, a new class of mechanochromic shear stress indicators was developed by constructing hierarchically structured core-shell supraparticles that can indicate mechanical stress via an easily detectable color change. Three different mechanisms can be distinguished. If a signal becomes visible only by a mechanical load, it is a turn-on indicator. In the opposite case, the turn-off indicator, the signal is switched off by a mechanical load. In the third mechanism, the color-change indicator, the color changes as a result of a mechanical load. In principle, these indicators can be used in two different ways. First, they can be incorporated into a coating as an additive. These coatings can be applied to a wide range of products, including food packaging, medical devices, and generally any sensitive surface where mechanical stress, such as scratches, is difficult to detect but can have serious consequences. Second, these shear stress indicators can also be used directly in powder form and for example then applied in 3D-printing or in ball mills. A total of six different shear stress indicators were developed, three of which were used as additives in coatings and three were applied in powder form. Depending on their composition, these indicators were readout by fluorescence, UV-Vis or Magnetic Particle Spectroscopy. The development of these novel shear stress indicator supraparticles were successfully combined molecular chemistry with the world of nano-objects to develop macroscopic systems that can enable smart and communicating materials to indicate mechanical stress in a variety of applications.
Lung cancer is the main cause of cancer-related deaths worldwide. Despite the availability of several targeted therapies and immunotherapies in the clinics, the prognosis for lung cancer remains poor. A major problem for the low benefit of these therapies is intrinsic and acquired resistance, asking for pre-clinical models for closer investigation of predictive biomarkers for refined personalized medicine and testing of possible combination therapies as well as novel therapeutic approaches to break resistances.
One third of all lung adenocarcinoma harbor mutations in the KRAS gene, of which 39 % are transitions from glycine to cysteine in codon 12 (KRASG12C). Being considered “undruggable” in previous decades, KRASG12C-inhibitors now paved the way into the standard-of-care for lung adenocarcinoma treatment in the clinics. Still, the overall response rates as well as overall survival of patients treated with KRASG12C-inhibitors are sobering. Therefore, 3D KRASG12C-biomarker in vitro models were developed based on a decellularized porcine jejunum (SISmuc) using commercial and PDX-derived cell lines and characterized in regards of epithelial-mesenchymal-transition (EMT), stemness, proliferation, invasion and c-MYC expression as well as the sensitivity towards KRASG12C-inhibiton. The phenotype of lung tumors harboring KRAS mutations together with a c-MYC overexpression described in the literature regarding invasion and proliferation for in vivo models was well represented in the SISmuc models. A higher resistance towards targeted therapies was validated in the 3D models compared to 2D cultures, while reduced viability after treatment with combination therapies were exclusively observed in the 3D models. In the test system neither EMT, stemness nor the c-MYC expression were directly predictive for drug sensitivity. Testing of a panel of combination therapies, a sensitizing effect of the aurora kinase A (AURKA) inhibitor alisertib for the KRASG12C-inhibitor ARS-1620 directly correlating with the level of c-MYC expression in the corresponding 3D models was observed. Thereby, the capability of SISmuc tumor models as an in vitro test system for patient stratification was demonstrated, holding the possibility to reduce animal experiments.
Besides targeted therapies the treatment of NSCLC with oncolytic viruses (OVs) is a promising approach. However, a lack of in vitro models to test novel OVs limits the transfer from bench to bedside. In this study, 3D NSCLC models based on the SISmuc were evaluated for their capability to perform efficacy and risk assessment of oncolytic viruses (OVs) in a pre-clinical setting. Hereby, the infection of cocultures of tumor cells and fibroblasts on the SISmuc with provided viruses demonstrated that in contrast to a wildtype herpes simplex virus 1 (HSV-1) based OV, the attenuated version of the OV exhibited specificity for NSCLC cells with a more advanced and highly proliferative phenotype, while fibroblasts were no longer permissive for infection. This approach introduced SISmuc tumor models as novel test system for in vitro validation of OVs.
Finally, a workflow for validating the efficacy of anti-cancer therapies in 3D tumor spheroids was established for the transfer to an automated platform based on a two-arm-robot system. In a proof-of-concept process, H358 spheroids were characterized and treated with the KRASG12C-inhibitor ARS-1620. A time- and dose-dependent reduction of the spheroid area after treatment was defined together with a live/dead-staining as easy-to-perform and cost-effective assays for automated drug testing that can be readily performed in situ in an automated system.
After priming in Peyer's patches (PPs) and mesenteric lymph nodes (mLN) T- cells infiltrate the intestine through lymphatic draining and homing through the bloodstream. However, we found that in mouse models of acute graft-versus-host disease (GvHD), a subset of alloreactive T-cells directly migrates from PPs to the adjacent intestinal lamina propria (LP), bypassing the normal lymphatic drainage and vascular trafficking routes. Notably, this direct migration occurred in irradiated and unirradiated GvHD models, indicating that irradiation is not a prerequisite for this observed behavior.
Next, we established a method termed serial intravascular staining (SIVS) in mouse models to systematically investigate the trafficking and migration of donor T- cells in the early stages of acute GvHD initiation. We found that the direct migration of T-cells from PPs to LP resulted in faster recruitment of cells after allogeneic hematopoietic cell transplantation (allo-HCT). These directly migrating T-cells were found to be in an activated and proliferative state, exhibiting a TH1/TH17-like phenotype and producing cytokines such as IFN-γ and TNF-α. Furthermore, we observed that the directly migrating alloreactive T-cells expressed specific integrins (α4+, αE+) and chemokine receptors (CxCR3+, CCR5+, and CCR9+). Surprisingly, blocking these integrins and chemokine-coupled receptors did not hinder the direct migration of T- cells from PPs to LP, suggesting the involvement of alternative mechanisms. Previous experiments ruled out the involvement of S1PR1 and topographical features of macrophages, leading us to hypothesize that mediators of cytoskeleton reorganization, such as Coro1a, Dock2, or Cdc42, may play a role in this unique migration process.
Additionally, we observed that directly migrating T-cells created a local inflammatory microenvironment, which attracts circulating T-cells. Histological analysis confirmed that alloreactive PPs-derived T-cells and bloodborne T-cells colocalized. We employed two experimental approaches, including either photoconversion of T-cells in PPs or direct transfer of activated T-cells into the vasculature, to demonstrate this colocalization. We hypothesize that cytokines released by migrating T-cells, such as IFN-γ and TNF-α, may play a role in recruiting T-cells from the vasculature, as inhibiting chemokine-coupled receptors did not impair recruitment.
Gastroesophageal junction (GEJ), demarcating the region where the distal esophagus meets with the proximal stomach region, is known for developing pathological conditions, including metaplasia and esophageal adenocarcinoma (EAC). It is essential to understand the mechanisms of developmental stages which lead to EAC since the incidence rate of EAC increased over 7-fold during the past four decades, and the overall five years survival rate is 18.4%. In most cases, patients are diagnosed in the advanced stage without prior symptoms. The main precursor for the development of EAC is a pre-malignant condition called Barrett's esophagus (BE). BE is the metaplastic condition where the multilayered squamous epithelium of the native esophagus is replaced by specialized single-layered columnar epithelium, which shows the molecular characteristics of the gastric as well as intestinal epithelium. The main risk factors for BE development include chronic gastro-esophageal acid reflux disease (GERD), altered microbiota, and altered retinoic acid signaling (RA). The cell of origin of BE is under debate due to a lack of clear evidence demonstrating the process of BE initiation. Here, I investigated how GEJ homeostasis is maintained in healthy tissue by stem cell regulatory morphogens, the role of vitamin A (RA signaling), and how its alteration contributes to BE development.
In the first part of my thesis, I showed the presence of two types of epithelial cells, the squamous type in the esophagus and the columnar type in the stomach region in the GEJ, using single-molecule RNA in situ hybridization (smRNA-ISH) and immunohistochemistry. Employing lineage tracing in the mouse model, I have demonstrated that the esophageal epithelial and stomach epithelial cells derived from two distinct epithelial stem cell lineages in the GEJ. The border between squamous and columnar epithelial cells in the Squamo-columnar junction (SCJ) of GEJ is regulated by opposing Wnt microenvironments. The regeneration of stomach columnar epithelial stem cells is maintained by Wnt activating signal from the stromal compartment while squamous epithelial stem cells of the esophagus are maintained by the Wnt inhibitory signals. I recapitulated the in vivo GEJ epithelial stem cell maintenance by using in vitro epithelial 3D organoid culture model. The growth and propagation of stomach columnar epithelial organoids depend on Wnt growth factors, while squamous epithelial organoids' development needs Wnt-deficient culture conditions.
Further, single-cell RNA sequence (scRNA-seq) analysis of organoid-derived epithelial cells revealed the non-canonical Wnt/ planar cell polarity (PCP) pathway involvement in regulating the squamous epithelial cells. In contrast, columnar stomach epithelial cells are regulated by the canonical Wnt/ beta-catenin and non-canonical Wnt/Ca2+ pathways. My data indicate that the SCJ epithelial cells that merge at the GEJ are regulated by opposing stromal Wnt factors and distinct Wnt pathway signaling in the epithelial cells.
In the second part of the thesis, I investigated the role of Vitamin A-derived bioactive compound RA on esophageal and stomach epithelial stem cells. In vitro treatment of esophageal and stomach, epithelial organoids with RA or its pharmacological inhibitor BMS 493 revealed that each cell type was regulated distinctly. I observed that enhanced RA promoted esophageal stem cell differentiation and loss of stratification, while RA inhibition led to enhanced stemness and regeneration of the esophagus stratified epithelium. As opposed to the esophagus, RA signaling is active in the stomach organoids, and inhibition of RA reduces the growth of stomach organoids. Global transcriptomic data and scRNA-seq data revealed that RA signaling induces dormancy phenotype in the esophageal cells. In contrast, the absence of RA in stomach epithelial cells induces the expression of genes associated with BE. Thus, spatially defined regulation of Wnt and RA signaling at GEJ is critical for healthy homeostasis, and its perturbation leads to disease development.
The unicellular pathogen Trypanosoma brucei is the causative agent of African
trypanosomiasis, an endemic disease prevalent in sub-Saharan Africa. Trypanosoma brucei alternates between a mammalian host and the tsetse fly vector. The extracellular parasite survives in the mammalian bloodstream by periodically exchanging their ˈvariant surface glycoproteinˈ (VSG) coat to evade the host immune response. This antigenic variation is achieved through monoallelic expression of one VSG variant from subtelomeric ˈbloodstream
form expression sitesˈ (BES) at a given timepoint. During the differentiation from the bloodstream form (BSF) to the procyclic form (PCF) in the tsetse fly midgut, the stage specific surface protein is transcriptionally silenced and replaced by procyclins. Due to their subtelomeric localization on the chromosomes, VSG transcription and silencing is partly regulated by homologues of the mammalian telomere complex such as TbTRF, TbTIF2 and TbRAP1 as well as by ˈtelomere-associated proteinsˈ (TelAPs) like TelAP1. To gain more insights into transcription regulation of VSG genes, the identification and characterization of other TelAPs is critical and has not yet been achieved. In a previous study, two biochemical approaches were used to identify other novel TelAPs. By using ˈco-immunoprecipitationˈ (co-IP) to enrich possible interaction partners of TbTRF and by affinity chromatography using telomeric repeat oligonucleotides, a listing of TelAP candidates has been conducted. With this approach TelAP1 was identified as a novel component of the telomere complex, involved in the kinetics of transcriptional BES silencing during BSF to PCF differentiation. To gain further insights into the telomere complex composition, other previously enriched proteins were characterized through a screening process using RNA interference to deplete potential candidates. VSG expression profile changes and overall proteomic changes after depletion were analyzed by mass spectrometry. With this method, one can gain insights into the functions of the proteins and their involvement in VSG expression site regulation. To validate the interaction of proteins enriched by co-IP with TbTRF and TelAP1 and to identify novel interaction proteins, I performed reciprocal affinity purifications of the four most promising candidates (TelAP2, TelAP3, PPL2 and PolIE) and additionally confirmed colocalization of two candidates with TbTRF via immunofluorescence (TelAP2, TelAP3). TelAP3 colocalizes with TbTRF and potentially interacts with TbTRF, TbTIF2, TelAP1 and TelAP2, as well as with two translesion polymerases PPL2 and PolIE in BSF. PPL2 and PolIE seem to be in close contact to each other at the telomeric ends and fulfill different roles as only PolIE is involved in VSG regulation while PPL2 is not. TelAP2 was previously characterized to be associated with telomeres by partially colocalizing with TbTRF and cells show a VSG derepression phenotype when the protein was depleted. Here I show that TelAP2 interacts with the telomere-binding proteins TbTRF and TbTIF2 as well as with the telomere-associated protein TelAP1 in BSF and that TelAP2 depletion results in a loss of TelAP1 colocalization with TbTRF in BSF.
In conclusion, this study demonstrates that characterizing potential TelAPs is effective in gaining insights into the telomeric complex's composition and its role in VSG regulation in Trypanosoma brucei. Understanding these interactions could potentially lead to new therapeutic targets for combatting African trypanosomiasis.
The current study presents a new a group of Demotic ostraca in the belongings of the Cairo Museum. A large part of this group stem from Medinet Habu in the western bank of modern Luxor in Upper Egypt and was discovered in the beginning of the thirties of the last century by the Chicago Oriental Institute (recently renamed as Institute for the Study of Ancient Cultures ‘ISAC’). A small portion of the collection under consideration come from other Upper Egyptian provenances including Gebelein, Edfu, Kom Ombo, and possibly elsewhere in Thebes. The main goal of the present dissertation is to decipher, translate, and provide a philological, paleographical, and cultural analysis of the group of texts in question. The results of this study are spread over two main parts, the first of which is dedicated to the main and largest part of the collection, i.e. ostraca from Medinet Habu, while the second is concerned with ostraca from other places. The first part comprises of five sections beginning with receipts of money and in-kind payments including some receipts for the payments of the different capitation charges in the Ptolemaic and Roman Periods, a few for land-related payments, as well as others related to different Ptolemaic monopolies or trades such as a receipt for the price of oil, one for the linen tax, in addition to a unique receipt for the rarely attested fish tax. The second section includes accounts and lists of different kinds be it monetary, in-kind, agriculture, or any other type of lists or accounts that record different everyday transactions. The following section presents a relatively different type of lists, namely lists of personal names. The fourth section incorporates a variety of texts of different concerns, e.g. texts of religious nature, letters, temples oaths, or other private documents. Unidentified texts occupy the fifth and final section of the first part. The second part of the study, which comprises texts that originate from different Upper Egyptian localities, includes three sections, i.e. receipts, accounts, and lists of names.
The mold Aspergillus fumigatus (A. fumigatus) is known as human pathogen and can cause life-threatening infections in humans with a weakened immune system. This is a known complication in patients receiving glucocorticoids, e.g. after hematopoietic stem cell transplantation or solid organ transplantation. Although research in the field of immune cell/fungus interaction has discovered key strategies how immune cells fight against infectious fungi, our knowledge is still incomplete. In order to develop effective treatment options against fungal infections, a detailed understanding of their interactions is crucial. Thus, visualization of immune cell and fungus is an excellent approach to gain further knowledge. For a detailed view of such interaction processes, a high optical resolution on nanometer scale is required. There is a variety of super resolution microscopy techniques, enabling fluorescence imaging beyond the diffraction limit. This work combines the use of three complementary super resolution microscopy techniques, in order to study immune cell/fungus interaction from different points of view.
Aim of this work is the introduction of the recently invented imaging technique named expansion microscopy (ExM) for the study of immune cell/fungus interactions. The core aspect of this method is the physical magnification of the specimen, which increases the distance between protein structures that are close to each other and which can therefore be imaged separately.
The simultaneous magnification of primary human natural killer (NK) cells and A. fumigatus hyphae was established in this work using ExM. Reorganization of cytoskeletal components of interacting NK cells was demonstrated here, by expansion of the immunological synapse (IS), formed between NK cells and A. fumigatus. In addition, reorganization of the microtubule-organizing center (MTOC) towards fungal hyphae and an accumulation of actin at the IS has been observed. Furthermore, ExM has been used to visualize lytic granules of NK cells after degranulation. After magnification of the specimen, lysosome associated protein 1 (LAMP1) was shown to surround perforin. In absence of the plasma membrane-exposed degranulation marker LAMP1, a “ring-shaped” structure was often observed for fluorescently labeled perforin. Volume calculation of lytic granules demonstrated the benefit of ExM. Compared to pre-expansion images, analyses of post-expansion images showed two volume distributions for degranulated and non-degranulated NK cells. In addition, this work emphasizes the importance of determining the expansion factor for a structure in each species, as variations of expansion factors have been observed. This factor, as well as possible sample distortions should be considered, when ExM is used in order to analyze the interaction between two species.
A second focus of this work is the visualization of a chimeric antigen receptor (CAR), targeting an epitope on the cell wall of A. fumigatus. Structured illumination microscopy (SIM) revealed that the CAR is part of the immunological synapse of primary human CAR T cells and CAR-NK-92 cells. At the interaction site, an accumulation of the CAR was observed, as well as the presence of perforin. CAR accumulation at fungal hyphae was further demonstrated by automated live cell imaging of interacting CAR-NK-92 cells, expressing a fluorescent fusion protein.
Additionally, the use of direct stochastic optical reconstruction microscopy (dSTORM) gave first insights in CAR expression levels on the basal membrane of CAR-NK-92 cells, with single molecule sensitivity. CAR cluster analyses displayed a heterogeneous CAR density on the basal membrane of transfected NK 92 cells.
In summary, this work provides insights into the application of ExM for studying the interaction of primary human NK cells and A. fumigatus for the first time. Furthermore, this thesis presents first insights regarding the characterization of an A. fumigatus-targeting CAR, by applying super-resolution fluorescence microscopy, like SIM and dSTORM.
Theory and simulation of ultrafast autodetachment dynamics and nonradiative relaxation in molecules
(2024)
In this thesis, theoretical approaches for the simulation of electron detachment processes in molecules following vibrational or electronic excitation are developed and applied. These approaches are based on the quantum-classical surface-hopping methodology, in which nuclear motion is treated classically as an ensemble of trajectories in the potential of quantum-mechanically described electronic degrees of freedom.
This compilation focuses on adolescent mental disorders and their prevention. It comprises three distinct studies, each contributing to a deeper understanding of this critical topic. This work addresses a critical gap in the understanding of, and approach to, adolescent mental health, and as a result reveals a critically important and urgently needed policy implication for action. The thematic structure of these studies begins with an examination of the epidemiology of child and adolescent mental disorders. Baseline data were collected from N = 877 adolescents with a mean age of 12.43 years (SD = 0.65). Mental health problems, such as depressive symptoms, non-suicidal self-injury, suicidal ideation, symptoms of eating disorders, and gender differences, are thoroughly examined. Results revealed a significant portion of our sample displaying mental health problems as early as the 6th and 7th grades, with girls generally being more affected than boys. The findings underscore the importance of early adolescence in the emergence of mental health problems and thereby emphasize the need for preventive measures. Moving beyond prevalence estimates, the compilation delves into the etiology of these disorders, exploring their potential correlation with a COVID-19 infection. Understanding the early signs and risk factors is crucial for timely support. While numerous studies have investigated potential risk and protective factors during the pandemic, our focus shifts to adolescents’ coping when an infection with the virus was involved (N = 2,154, M = 12.31, SD = 0.67). We hypothesized that students infected or with close family members infected, would exhibit an increased psychopathology and a decreased functioning of protective factors such as self-efficacy or self-esteem. We found no connection between infection and the mental health status within our sample, but protective factors and mental well-being were positively associated. Thus, universal primary prevention appears to be the preferred approach for promoting mental health. Lastly, the compilation introduces LessStress, a noteworthy contribution to more evidence-based prevention programs. This universal approach is designed to reduce stress in schools, accompanied by a cluster-randomized trial to evaluate its effectiveness (estimated sample size N = 1,894). Existing studies have demonstrated the effectiveness of stress prevention, leading us to introduce a short and easy-to-implement prevention program. There is positive evidence for one-lesson interventions in schools for promoting well-being and health behaviors among adolescents. LessStress is designed based on a life skills approach that not only imparts psychoeducational content but also teaches skills relevant to everyday life and directly applicable. Throughout these studies, a common thread emerges: the pressing need to address mental disorders during childhood and adolescence. These formative years play a pivotal role in the development of mental health problems. These formative years play a crucial role in the development of mental health problems. They highlight the importance of epidemiological data collection and analysis based on the latest models to develop prevention interventions that are not only effective but also reach young people on a global level.
Dipolar merocyanines are very attractive supramolecular building blocks, as they combine interesting functional properties with strong, directional intermolecular interactions. The pyridine dioxocyano-pyridine (PYOP) chromophore (Chapter 2.2), used in this thesis, stands out because of its exceptionally high ground state dipole moment (g ~ 17 D), in combination with the option to retain good solubility also in unpolar solvents, by decoration with solubilizing groups.
The reliable binding motif of anti-parallel -stacking due to dipole-dipole interactions has allowed the design of molecular building blocks that form assemblies of predictable geometry. The intense unstructured charge transfer UV/Vis absorption band (eg ~ 10.7 D) is a result of the dominant contribution of the zwitterionic resonance structure which brings the PYOP chromophore just beyond the cyanine limit in solvents of low polarity (c2 = 0.60, 1,4 dioxane). The high sensitivity of the S0 – S1 UV/Vis absorption band to the environment manifests itself in a pronounced negative solvatochromism and strong H-type exciton coupling within -stacked PYOP assemblies. In accordance with the classical molecular exciton theory, an increasing hypsochromic shift of the dominant absorption band of these H aggregates can be observed as the stack size increases up to about six chromophores, where it levels out at about max ~ 440 nm (CHCl3). This allows a uniquely simple estimation of the number of interacting chromophores within the self-assembled structure from a single UV/Vis absorption spectrum of an aggregate.
The defined and well investigated PYOP dimer formation was employed in this thesis to probe the applicability and limitations of concentration-, temperature-, and solvent-dependent self-assembly studies (Chapter 3). Straightforward theoretical models to evaluate datasets of concentration-, temperature-, and solvent-dependent UV/Vis absorption by nonlinear regression analysis were derived for the case of dimer formation (Chapter 2.1). Although the dimer model is well known and widely applied in literature, this detailed derivation is helpful to understand assumptions and potential problems of the different approaches for the determination of thermodynamic parameters. This helps to decide on the most appropriate method to analyse a system of interest. In this regard it should be noted that covering a large portion of the self-assembly process with the experimental data is a prerequisite for the accuracy of the analysis. Additionally, many of the insights can also be transferred to other self-assembly systems like supramolecular polymerization or host-guest interactions.
The concentration-dependent analysis is the most straightforward method to investigate self-assembly equilibria. No additional assumptions, besides mass balance and mass action law, are required. Since it includes the least number of parameters (only K, if M/D are known), it is the most, or even only, reliable method, to elucidate the self-assembly mechanism of an unknown system by model comparison. To cover a large concentration range, however, the compound must be soluble enough and generally sample amounts at least in the low mg scale must be available.
The temperature-dependent analysis has the advantage that all thermodynamic parameters G0, H0 and S0 can be obtained from a single sample in one automated measurement. However, the accessible temperature-range is experimentally often quite limited and dependent on the solvent. For systems which do not show the transition from monomer to aggregate in a narrow temperature range, as given for, e.g., cooperative aggregation or processes with a high entropy contribution, often not the entire self-assembly process can be monitored. Furthermore, the assumptions of temperature-independent extinction coefficients of the individual species as well as temperature-independent H0 and S0 must be met. Monte Carlo simulations of data sets demonstrated that even minor changes in experimental data can significantly impact the optimized values for H0 and S0. This is due to the redundancy of these two parameters within the model framework and even small thermochromic effects can significantly influence the results. The G0 value, calculated from H0 and S0, is, however, still rather reliable.
Solvent-dependent studies can often cover the entire self-assembly process from monomeric (agg = 0) to the fully aggregated state (agg = 1). However, for dyes with strong solvatochromic effects, such as the dipolar merocyanines investigated in this thesis, the results are affected. Also, the assumption of a linear relation of the binding energy G0 and the fraction of denaturating solvent f, which is based on linear free energy relationships between G0 and the solvent polarity, can lead to errors. Especially when specific solvent effects are involved.
For the evaluation of experimental data by nonlinear regression, general data analysis software can be used, where user-defined fit models and known parameters can be implemented as desired. Alternatively, multiple specialized programs for analysing self-assembly data are available online. While the latter programs are usually more user-friendly, they have the disadvantage of being a “black box” where only pre-implemented models can be used without the option for the user to adapt models or parameters for a specific system.
In Chapter 3 comprehensive UV/Vis absorption datasets are presented for the dimerization of merocyanine derivative 1 in 1,4-dioxane, which allowed for the first time a direct comparison of the results derived from concentration-, temperature-, and solvent-dependent self-assembly studies.
The results for the binding constant K and corresponding G0 from the concentration- and temperature-dependent analysis were in very good agreement, also in comparison to the results from ITC. For the temperature-dependent analysis, though, multiple datasets of samples with different concentration had to be evaluated simultaneously to cover a meaningful part of the self-assembly process. Furthermore, a significant dependence of the optimized parameters H0 and S0 on the wavelength chosen for the analysis was observed. This can be rationalized by the small thermochromic shifts of both the monomer and the dimer UV/Vis absorption band. The results from the solvent-dependent evaluation showed the largest deviation, as expected for the highly solvatochromic merocyanine dye.
However, even here by evaluation at 491 and 549 nm the deviation for G0 was only 2.5 kJ mol1 (9%) with respect to the results from the concentration-dependent analysis (G0 = 29.1 kJ mol1). Thus, despite the strong solvatochromism of the dipolar chromophore, it can still be considered a reliable method for estimating the binding strength. Furthermore, multiple repetitions of the concentration-, temperature-, and solvent-dependent studies provided insight into the reproducibility of the results and possible sources of experimental errors. In all cases, the deviations of the results were small (G0 < 0.4 kJ mol1) and within the same range as the fit error from the nonlinear regression analysis.
The insights from these studies were an important basis for the in-depth investigation of a more complex supramolecular system in Chapter 4, as a single method is often not enough to capture the full picture of a more complicated self-assembly process. To elucidate the anti-cooperative self-assembly of the chiral merocyanine 2, a combination of multiple techniques had to be applied.
Solvent-dependent UV/Vis absorption studies in CH2Cl2/MCH mixtures showed the step-wise assembly of the merocyanine monomer (max(M) = 549 nm, CH2Cl2) to first a dimer (max(D) = 498 nm, CH2Cl2/MCH 15:85) by dipole-dipole interactions, and then a -stacked higher aggregate (max(H) = 477 nm, MCH), with pronounced H-type coupling.
The thermodynamic evaluation of this data, however, suffered from the severe solvatochromism, especially of the monomeric species (max(M, CH2Cl2) = 549 nm, max(M, MCH) = 596 nm). Therefore, concentration-dependent studies were performed at three different temperatures (298, 323, 353 K) to elucidate the self-assembly mechanism and determine reliable thermodynamic parameters. The studies at elevated temperatures were hereby necessary, to obtain experimental data over a larger agg--range. Due to the pronounced difference in the thermodynamic driving force for dimerization and higher aggregate formation (KD/K5 = 6500) a concentration range exists in MCH where almost exclusively the dimer species of 2 is present, before further self-assembly by dispersion interactions occurs. Therefore, the data could be evaluated independently for the two self-assembly steps. The self-assembly of dimers into the higher aggregate could not be described by the isodesmic model but was fitted satisfactorily to a pentamer model. This rather small size of about ten -stacked PYOP chromophores was, furthermore, consistently indicated by AFM, VPO and DOSY NMR measurements. Based on 1D and 2D NMR data as well as the strong bisignate CD signal of the higher aggregate in combination with TD-DFT calculations, a P-helical stack is proposed as its structure. The small size can be rationalized by the anti-cooperative self-assembly mechanism and the sterical demand of the solubilizing trialkoxyphenyl and the chiral tetralin substituents. Additionally, the aliphatic shell formed by the solubilizing chains around the polar chromophore stack, can account for the exceptionally high solubility of 2 in MCH (> 15 mg mL1). These combined studies of the self-assembly process enabled the identification of suitable conditions for the investigation of fluorescence properties of the individual aggregate species. Aggregation-induced emission enhancement was observed for the almost non-emissive monomer (Fl(M) = 0.23%), which can be rationalized by the increasing rigidification within the dimer (Fl(D) = 2.3%) and the higher aggregate (Fl(H) = 4.5%). The helical chirality of the PYOP decamer stack, furthermore, gave rise to a strong CPL signal with a large glum value of 0.011.
The important conclusion of this thesis is that the temperature- and solvent-dependent analyses are valid alternatives to the classical concentration-dependent analysis to determine thermodynamic parameters of self-assembly equilibria. Although, for a specific supramolecular system, one approach might be favourable over the others for a variety of reasons. The experimental limitations often demand a combination of techniques to fully elucidate a self-assembly process and to gain insights in the aggregate structure. The anti-cooperative merocyanine self-assembly, which was described here for the first time for the PYOP merocyanine 2, is no exception. Besides the interest in the merocyanine assemblies from a structural and functional point of view, the insights gained from the presented studies can also be transferred to other self-assembly systems and be a guide to find the most appropriate analysis technique.
This work aims at elucidating chemical processes involving homogeneous catalysis and photo–physical relaxation of excited molecules in the solid state. Furthermore, compounds with supposedly small singlet–triplet gaps and therefore biradicaloid character are investigated with respect to their electro–chemical behavior. The work on hydroboration catalysis via a reduced 9,10–diboraanthracene (DBA) was preformed in collaboration with the Wagner group in Frankfurt, more specifically Dr. Sven Prey, who performed all laboratory experiments. The investigation of delayed luminescence properties in arylboronic esters in their solid state was conducted in collaboration with the Marder group in Würzburg. The author of this work took part in the synthesis of the investigated compounds while being supervised by Dr. Zhu Wu. The final project was a collaboration with the group of Anukul Jana from Hyderabad, India who provided the experimental data.
In this thesis, we apply the information-theoretic approach in the context of quantum dynamics and wave packet motion: Information-theoretic measures are calculated from position and momentum densities, which are obtained from time-dependent quantum wave functions. The aim of this thesis is to benchmark, analyze and interpret these quantities and relate their features to the wave packet dynamics. Firstly, this is done for the harmonic oscillator (HO) with and without static disorder. In the unperturbed HO, the analytical study of coherent and squeezed states reveals time-dependent entropy expressions related to the localization of the wave function. In the disordered HO, entropies from classical and quantum dynamics are compared for short and long times. In the quantum case, imprints of wave packet revivals are found in the entropy. Then, the energy dependence of the entropy for very long times is discussed. Secondly, this is donefor correlated electron-nuclear motion. Here, entropies derived from the total, electronic and nuclear density, respectively, are calculated in position and momentum space for weak and strong adiabatic electronic coupling. The correlation between electron and nucleus is investigated using different correlation measures, where some of these functions are sensitive to the nodal structure of the wave function. An analytic ansatz to interpret the information-theoretical quantities is applied as well.
This doctoral thesis investigates magneto-optical properties of mercury telluride layers grown tensile strained on cadmium telluride substrates. Here, layer thicknesses start above the usual quantum well thickness of about 20 nm and have a upper boundary around 100 nm due to lattice relaxation effects. This kind of layer system has been attributed to the material class of three-dimensional topological insulators in numerous publications. This class stands out due to intrinsic boundary states which cross the energetic band gap of the layer's bulk.
In order to investigate the band structure properties in a narrow region around the Fermi edge, including possible boundary states, the method of highly precise time-domain Terahertz polarimetry is used. In the beginning, the state of the art of Teraherz technology at the start of this project is discussed, moving on to a detailed description and characterization of the self-built measurement setup. Typical standard deviation of a polarization rotation or ellipticity measurement are on the order of 10 to 100 millidegrees, according to the transmission strength through investigated samples. A range of polarization spectra, depending on external magnetic fields up to 10 Tesla, can be extracted from the time-domain signal via Fourier transformation.
The identification of the actual band structure is done by modeling possible band structures by means of the envelope function approximation within the framework of the k·p method. First the bands are calculated based on well-established model parameters and from them the possible optical transitions and expected ellipticity spectra, all depending on external magnetic fields and the layer's charge carrier concentration. By comparing expected with measured spectra, the validity of k·p models with varying depths of detail is analyzed throughout this thesis. The rich information encoded in the ellipitcity spectra delivers key information for the attribution of single optical transitions, which are not part of pure absorption spectroscopy. For example, the sign of the ellipticity signals is linked to the mix of Landau levels which contribute to an optical transition, which shows direct evidence for bulk inversion asymmetry effects in the measured spectra.
Throughout the thesis, the results are compared repeatedly with existing publications on the topic. It is shown that the models used there are often insufficient or, in worst case, plainly incorrect. Wherever meaningful and possible without greater detours, the differences to the conclusions that can be drawn from the k·p model are discussed.
The analysis ends with a detailed look on remaining differences between model and measurement. It contains the quality of model parameters as well as different approaches to integrate electrostatic potentials that exist in the structures into the model.
An outlook on possible future developments of the mercury cadmium telluride layer systems, as well as the application of the methods shown here onto further research questions concludes the thesis.
mRNA is co- or post-transcriptionally processed from a precursor mRNA to a mature mRNA. In addition to 5'capping and splicing, these modifications also include polyadenylation, the addition of a polyA tail to the 3'end of the mRNA. In recent years, alternative polyadenylation in particular has increasingly been taken into account as a mechanism for regulating gene expression. It is assumed that approximately 70-75 % of human protein coding genes contain alternative polyadenylation signals, which are often located within intronic sequences of protein-coding genes. The use of such polyadenylation signals leads to shortened mRNA transcripts and thus to the generation of C-terminal shortened protein isoforms.
Interestingly, the majority of microRNAs, small non-coding RNAs that play an essential role in post-transcriptional gene regulation, are also encoded in intronic sequences of protein-coding genes and are co-transcriptionally expressed with their host genes. The biogenesis of microRNA has been well studied and is well known, but mechanisms that may influence the expression regulation of mature microRNAs are just poorly understood.
In the presented work, I aimed to investigate the influence of alternative intronic polyadenylation on the biogenesis of microRNAs. The human ion channel TRPM1 could already be associated with melanoma pathogenesis and truncated isoforms of this protein have already been described in literature. In addition, TRPM1 harbors a microRNA, miR211, in its sixth intron, which is assumed to act as a tumor suppressor. Since both, TRPM1 and miR211 have already been associated with melanoma pathogenesis, the shift towards truncated transcripts during the development of various cancers is already known and it has been shown that certain microRNAs play a crucial role in the development and progression of melanoma, melanoma cell lines were used as an in vitro model for these investigations.
Integrative, three-dimensional \(in\) \(silico\) modeling of gas exchange in the human alveolus
(2024)
The lung plays a vital role by exchanging respiratory gases. At the core of this gas exchange is a simple yet crucial passive diffusion process occurring within the alveoli. These balloon-like structures, connected to the peripheral airways, are surrounded by a dense network
of small capillaries. Here, inhaled air comes into close proximity with deoxygenated blood coming from the heart, enabling the exchange of oxygen and carbon dioxide across their concentration gradients.
The efficiency of gas exchange can be measured through indicators such as the diffusion capacity of the lung for oxygen and the reaction half-time. A notable discrepancy exists in humans between physiological estimates of diffusion capacity and the theoretical maximum capacity under optimal structural conditions (morphological estimate). This discrepancy is influenced by a range of interrelated factors, including structural elements like the surface area and thickness of the diffusion barrier, as well as physiological factors such as blood flow dynamics. To unravel the different roles of these factors, we investigated how morphological and physiological properties of the human alveolar micro-environment collectively and individually influence the process of gas exchange. To this end, we developed an integrative in silico approach combining 3D morphological modeling and simulation of blood flow and of oxygen transport.
At the core of our approach lies the simulation software Alvin, serving as an interactive platform for the underlying mathematical model of oxygen transport within the alveolus. Developed by integrating and expanding existing mathematical models, our spatio-temporal model produces results in agreement with experimental data. Alvin allows for real-time parameter adjustments and the execution of multiple simultaneous simulation instances and provides detailed quantitative feedback, offering an immersive exploration of the simulated gas exchange process. The morphological and physiological parameters at play were further investigated with a focus on the microvasculature. By compiling a stereological database from the literature and 3D geometric modeling, we created a sheet-flow model as a realistic representation of the morphology of the human alveolar capillary network. Blood flow was simulated using computational fluid dynamics. Our findings were in line with previous estimations and highlighted the crucial role of viscosity models in predicting pressure drop across the microvasculature. Furthermore, we showcased how our approach can be harnessed to explore structural details, such as the connectivity of the alveolar capillary network with the vascular tree, using blood flow indices. It is important to emphasize that
so far we have relied on different data sources and that experimental validation is needed to move forward.
Integration of our findings into Alvin allowed quantification of the simulated gas exchange process through the diffusion capacity for oxygen and reaction half-time. In addition to evaluating the collective influences of the morphological and physiological properties, our interactive software facilitates the assessment of individual parameter value changes. Exploring blood volume and surface area available for gas exchange revealed linear correlations with diffusion capacity. The blood flow velocity had a positive, non-linear effect on diffusion capacity. The reaction half-time confirmed that under normal conditions, the gas exchange process is not diffusion-limited. Collectively, our alveolar model yielded a diffusion capacity value that fell in the middle of previous physiological and morphological estimates, implying that alveolar-level phenomena contribute to 50% of the diffusion capacity limitations that occur in vivo.
In summary, our integrative in silico approach disentangles various structural and functional influences on alveolar gas exchange, complementing traditional investigations in respiratory
research. We further showcase its utility in teaching and the interpretation of published data. To advance our understanding, future work should prioritize obtaining a cohesive experimental data set and identifying an appropriate viscosity model for blood flow simulations.
π-Conjugated organic polymers have attracted tremendous attention in the last decades, and the interest in these materials is mainly driven by their applicability in next-generation electronic and optoelectronic devices (OLEDs, OFETs, photovoltaics). The partial or complete replacement of carbon atoms by main group elements in conjugated polymers can significantly change the characteristics and applications of these macromolecules. In this work, a class of inorganic polymers comprising a backbone of exclusively boron and nitrogen atoms (poly(iminoborane)s, PIBs) and their monodisperse oligomers is described. In addition, novel inorganic–organic hybrid polymers containing BN units in their polymer backbone were synthesized and characterized.
In chapter 2.1, the development of catalytic B–N coupling routes for the controlled synthesis of macromolecular materials is described. While the reaction of an N-silyl-B-chloro-aminoborane with the electrophilic reagent trimethylsilyl triflate led to effective B–N coupling, the reaction with a silver(I) salt resulted in an intramolecular Cl/Me exchange between the boron and silicon centers.
In chapter 2.2-2.4, the study of oligo- and poly(iminoborane)s is discussed. Monodisperse and cyclolinear oligo(iminoborane)s based on diazaborolidines with up to 7 boron and 8 nitrogen atoms were synthesized by successively extending the B-N main chain. However, the use of benzodiazaborolines only led to limited BN catenation. Furthermore, the redistribution processes resulting from the reaction of longer oligomers with non-stoichiometric amounts of (di)halogenated boranes is reported.
In chapter 2.5-2.6, the synthesis of 1,2,5-azadiborolanes as building blocks for the synthesis of poly(iminoborane)s and inorganic-organic hybrid polymers is described. While the attempt to apply an azadiborolane with sterically demanding groups on the boron-bridging ethylene unit for the construction of PIB was unfeasible, it was successfully incorporated in inorganic-organic hybrid polymers. Photophysical studies indicated π-conjugation along the polymer chain. A first attempt to synthesize PIBs based on azadiborolanes with unsubstituted ethylene units showed promising results.
In chapter 2.7-2.8, a comprehensive study of poly(arylene iminoborane)s, which are BN analogs of poly(arylene vinylene)s is described, and the properties of four polymers as well as twelve monodisperse oligomers were investigated. Photophysical investigations of the monomers, dimers and polymers showed a systematic bathochromic shift of the absorption maximum with increasing chain length and thiophene content. Based on TD-DFT calculations of the model oligomers, the lowest-energy absorption band could be assigned to HOMO to LUMO transitions with π-π* character. The oligo- and poly(arylene iminoborane)s showed only very weak to no emission in solution but they were emissive in the solid state. For four oligomers the aggregation induced emission (AIE) in a THF/water mixture was investigated and DLS studies confirmed the formation of nanoaggregates.
In chapter 2.9, oligo- and polymerizations of sulfur-containing building blocks and subsequent pH-triggered degradation of the products is described. While a sulfilimine-containing oligomer could not be isolated, the sulfone-, sulfoximine-, and sulfoxide-containing molecular oligomers and polymers could be successfully synthesized by B=N or B–O bond formation reactions. The sulfur-containing building blocks were successfully released under acidic or basic conditions, which was confirmed by NMR spectroscopy and mass spectrometry.
Introduction.
Mobile health (mHealth) integrates mobile devices into healthcare, enabling remote monitoring, data collection, and personalized interventions. Machine Learning (ML), a subfield of Artificial Intelligence (AI), can use mHealth data to confirm or extend domain knowledge by finding associations within the data, i.e., with the goal of improving healthcare decisions. In this work, two data collection techniques were used for mHealth data fed into ML systems: Mobile Crowdsensing (MCS), which is a collaborative data gathering approach, and Ecological Momentary Assessments (EMA), which capture real-time individual experiences within the individual’s common environments using questionnaires and sensors. We collected EMA and MCS data on tinnitus and COVID-19. About 15 % of the world’s population suffers from tinnitus.
Materials & Methods.
This thesis investigates the challenges of ML systems when using MCS and EMA data. It asks: How can ML confirm or broad domain knowledge? Domain knowledge refers to expertise and understanding in a specific field, gained through experience and education. Are ML systems always superior to simple heuristics and if yes, how can one reach explainable AI (XAI) in the presence of mHealth data? An XAI method enables a human to understand why a model makes certain predictions. Finally, which guidelines can be beneficial for the use of ML within the mHealth domain? In tinnitus research, ML discerns gender, temperature, and season-related variations among patients. In the realm of COVID-19, we collaboratively designed a COVID-19 check app for public education, incorporating EMA data to offer informative feedback on COVID-19-related matters. This thesis uses seven EMA datasets with more than 250,000 assessments. Our analyses revealed a set of challenges: App user over-representation, time gaps, identity ambiguity, and operating system specific rounding errors, among others. Our systematic review of 450 medical studies assessed prior utilization of XAI methods.
Results.
ML models predict gender and tinnitus perception, validating gender-linked tinnitus disparities. Using season and temperature to predict tinnitus shows the association of these variables with tinnitus. Multiple assessments of one app user can constitute a group. Neglecting these groups in data sets leads to model overfitting. In select instances, heuristics outperform ML models, highlighting the need for domain expert consultation to unveil hidden groups or find simple heuristics.
Conclusion.
This thesis suggests guidelines for mHealth related data analyses and improves estimates for ML performance. Close communication with medical domain experts to identify latent user subsets and incremental benefits of ML is essential.
We analyze the mathematical models of two classes of physical phenomena. The first class of phenomena we consider is the interaction between one or more insulating rigid bodies and an electrically conducting fluid, inside of which the bodies are contained, as well as the electromagnetic fields trespassing both of the materials. We take into account both the cases of incompressible and compressible fluids. In both cases our main result yields the existence of weak solutions to the associated system of partial differential equations, respectively. The proofs of these results are built upon hybrid discrete-continuous approximation schemes: Parts of the systems are discretized with respect to time in order to deal with the solution-dependent test functions in the induction equation. The remaining parts are treated as continuous equations on the small intervals between consecutive discrete time points, allowing us to employ techniques which do not transfer to the discretized setting. Moreover, the solution-dependent test functions in the momentum equation are handled via the use of classical penalization methods.
The second class of phenomena we consider is the evolution of a magnetoelastic material. Here too, our main result proves the existence of weak solutions to the corresponding system of partial differential equations. Its proof is based on De Giorgi's minimizing movements method, in which the system is discretized in time and, at each discrete time point, a minimization problem is solved, the associated Euler-Lagrange equations of which constitute a suitable approximation of the original equation of motion and magnetic force balance. The construction of such a minimization problem is made possible by the realization that, already on the continuous level, both of these equations can be written in terms of the same energy and dissipation potentials. The functional for the discrete minimization problem can then be constructed on the basis of these potentials.
Neisseria meningitidis (the meningococcus) is one of the major causes of bacterial meningitis, a life-threatening inflammation of the meninges. Traversal of the meningeal blood-cerebrospinal fluid barrier (mBCSFB), which is composed of highly specialized brain endothelial cells (BECs), and subsequent interaction with leptomeningeal cells (LMCs) are critical for disease progression. Due to the human-exclusive tropism of N. meningitidis, research on this complex host-pathogen interaction is mostly limited to in vitro studies. Previous studies have primarily used peripheral or immortalized BECs alone, which do not retain relevant barrier phenotypes in culture. To study meningococcal interaction with the mBCSFB in a physiologically more accurate context, BEC-LMC co-culture models were developed in this project using BEC-like cells derived from induced pluripotent stem cells (iBECs) or hCMEC/D3 cells in combination with LMCs derived from tumor biopsies.
Distinct BEC and LMC layers as well as characteristic expression of cellular markers were observed using transmission electron microscopy (TEM) and immunofluorescence staining. Clear junctional expression of brain endothelial tight and adherens junction proteins was detected in the iBEC layer. LMC co-culture increased iBEC barrier tightness and stability over a period of seven days, as determined by sodium fluorescein (NaF) permeability and transendothelial electrical resistance (TEER). Infection experiments demonstrated comparable meningococcal adhesion and invasion of the BEC layer in all models tested, consistent with previously published data. While only few bacteria crossed the iBEC-LMC barrier initially, transmigration rates increased substantially over 24 hours, despite constant high TEER. After 24 hours of infection, deterioration of the barrier properties was observed including loss of TEER and altered expression of tight and adherens junction components. Reduced mRNA levels of ZO-1, claudin-5, and VE-cadherin were detected in BECs from all models. qPCR and siRNA knockdown data suggested that transcriptional downregulation of these genes was potentially but not solely mediated by Snail1. Immunofluorescence staining showed reduced junctional coverage of occludin, indicating N. meningitidis-induced post-transcriptional modulation of this protein, as previous studies have suggested. Together, these results suggest a potential combination of transcellular and paracellular meningococcal traversal of the mBCSFB, with the more accessible paracellular route becoming available upon barrier disruption after prolonged N. meningitidis infection. Finally, N. meningitidis induced cellular expression of pro-inflammatory cytokines and chemokines such as IL-8 in all mBCSFB models. Overall, the work described in this thesis highlights the usefulness of advanced in vitro models of the mBCSFB that mimic native physiology and exhibit relevant barrier properties to study infection with meningeal pathogens such as N. meningitidis.
The demand for LIB with enhanced energy densities leads to increased utilization of the space within the confinements of the battery housing or to the use of electrode material with increased intrinsic specific energy densities. Both requirements result in more stress on the battery electrodes and separator during cycling or aging. However, the effect of mechanical strain on the cell’s electrochemistry and thus the performance of batteries is rather unexplored compared to the impact of current or temperature, for example. The objective of this thesis was to give a better understanding of the electrochemical and mechanical interplay in current- and next-generation lithium based battery cells. Therefore, the thesis was structured into the investigations on SoA and next-generation LIBs. For SoA LIBs, the investigations of the interplay started at laboratory scale. Here, the expansion of various electrodes and also the impact of mechanical pressure and its distribution on the performance of the cells were
studied. The investigations at laboratory scale was followed by an examination of the electrochemical and mechanical interactions on large format commercial LIBs which are used in BEVs. Accordingly, the effect of bracing and its effect on the performance was studied in an aging and post-mortem study. To gain a deeper understanding of the mechanical changes in LIBs, an ultrasonic study was performed for pouch cells. Here, the mechanical changes were further investigated in dependence of SoC and SoH. The effects of the mechanical stress on the performance for next-generation batteries were studied at laboratory scale. In the beginning, the expansion of next-generation anode materials such as silicon and lithium was compared with today’s anode materials. Furthermore, the effect of mechanical pressure and electrolyte on the irreversible dilation and performance was investigated for lithium metal cells. Overall, it was shown that pressure has a significant effect on the performance of today’s and also future LIBs. The interplay of the electrochemical and mechanical effects inside a LIB has a considerable impact on the lifetime, capacity fading and impedance increase of the batteries.
Development Of A Human iPSC-Derived Cortical Neuron Model Of Adaptor- Protein-Complex-4-Deficiency
(2024)
Adaptor-protein-4-deficiency (AP-4-deficiency) is an autosomal-recessive childhood- onset form of complicated hereditary spastic paraplegia (HSP) caused by bi-allelic loss- of-function mutations in one of the four subunits of the AP-4-complex. These four conditions are named SPG47 (AP4B1, OMIM #614066), SPG50 (AP4M1, OMIM #612936), SPG51 (AP4E1, OMIM #613744) and SPG52 (AP4S1, OMIM #614067), respectively and all present with global developmental delay, progressive spasticity and seizures. Imaging features include a thinning of the corpus callosum, ventriculomegaly and white matter changes. AP-4 is a highly conserved heterotetrameric complex, which is responsible for polarized sorting of transmembrane cargo including the autophagy- related protein 9 A (ATG9A). Loss of any of the four subunits leads to an instable complex and defective sorting of AP-4-cargo. ATG9A is implicated in autophagosome formation and neurite outgrowth. It is missorted in AP-4-deficient cells and CNS-specific knockout of Atg9a in mice results in a phenotype reminiscent of AP-4-deficiency. However, the AP-4-related cellular phenotypes including ATG9A missorting have not been investigated in human neurons.
Thus, the aim of this study is to provide the first human induced pluripotent stem cell- derived (iPSC) cortical neuron model of AP-4-deficiency to explore AP-4-related phenotypes in preparation for a high-content screening. Under the hypothesis that AP-4- deficiency leads to ATG9A missorting, elevated ATG9A levels, impaired autophagy and neurite outgrowth in human iPSC-derived cortical neurons, in vitro biochemical and imaging assays including automated high-content imaging and analysis were applied. First, these phenotypes were investigated in fibroblasts from three patients with compound heterozygous mutations in the AP4B1 gene and their sex-matched parental controls. The same cell lines were used to generate iPSCs and differentiate them into human excitatory cortical neurons.
This work shows that ATG9A is accumulating in the trans-Golgi-network in AP-4- deficient human fibroblasts and that ATG9A levels are increased compared to parental controls and wild type cells suggesting a compensatory mechanism. Protein levels of the AP4E1-subunit were used as a surrogate marker for the AP-4-complex and were decreased in AP-4-deficient fibroblasts with co-immunoprecipitation confirming the instability of the complex. Lentiviral re-expression of the AP4B1-subunit rescues this corroborating the fact that a stable AP-4-complex is needed for ATG9A trafficking. Surprisingly, autophagic flux was present in AP-4-deficient fibroblasts under nutrient- rich and starvation conditions. These phenotypic markers were evaluated in iPSC-derived cortical neurons and here, a robust accumulation of ATG9A in the juxtanuclear area was seen together with elevated ATG9A protein levels. Strikingly, assessment of autophagy markers under nutrient-rich conditions showed alterations in AP-4-deficient iPSC- derived cortical neurons indicating dysfunctional autophagosome formation. These findings point towards a neuron-specific impairment of autophagy and need further investigation. Adding to the range of AP-4-related phenotypes, neurite outgrowth and branching are impaired in AP-4-deficient iPSC-derived cortical neurons as early as 24h after plating and together with recent studies point towards a distinct role of ATG9A in neurodevelopment independent of autophagy.
Together, this work provides the first patient-derived neuron model of AP-4-deficiency and shows that ATG9A is sorted in an AP-4-dependent manner. It establishes ATG9A- related phenotypes and impaired neurite outgrowth as robust markers for a high-content screening. This disease model holds the promise of providing a platform to further study AP-4-deficiency and to search for novel therapeutic targets.
In the scope of climate warming and the increase in frequency and intensity of severe heat waves in Central Europe, identification of temperate tree species that are suited to cope with these environmental changes is gaining increasing importance. A number of tree physiological characteristics are associated with drought-stress resistance and survival following severe heat, but recent studies have shown the importance of plant hydraulic and anatomical traits for predicting drought-induced tree mortality, such as vessel diameter, and their potential to predict species distribution in a changing climate.
A compilation of large global datasets is required to determine traits related to drought-induced embolism and test whether embolism resistance can be determined solely by anatomical traits. However, most measurements of plant hydraulic traits are labour-intense and prone to measurement artefacts. A fast, accurate and widely applicable technique is necessary for estimating xylem embolism resistance (e.g., water potential at 50% loss of conductivity, P50), in order to improve forecasts of future forest changes. These traits and their combination must have evolved following the selective pressure of the environmental conditions in which each species occurs. Describing these environmental-trait relationships can be useful to assess potential responses to environmental change and mitigation strategies for tree species, as future warmer temperatures may be compounded by drier conditions.
RNA viruses rely entirely on the host machinery for their protein synthesis and harbor non-canonical translation mechanisms, such as alternative initiation and programmed –1 ribosomal frameshifting (–1PRF), to suit their specific needs. On the other hand, host cells have developed a variety of defensive strategies to safeguard their translational apparatus and at times transiently shut down global translation. An infection can lead to substantial translational remodeling in cells and translational control is critical during antiviral response. Due to their sheer diversity, this control is likely unique to each RNA virus and the intricacies of post-transcriptional regulation are unclear in certain viral species.
Here, we explored different aspects of translational regulation in virus-infected cells in detail. Using ribosome profiling, we extensively characterized the translational landscape in HIV-1 infected T cells, uncovering novel features of gene regulation in both host and virus. Additionally, we show that substantial pausing occurs prior to the frameshift site indicating complex regulatory mechanisms involving upstream viral RNA elements that can act as cis- regulators of frameshifting.
We also characterized the mechanistic details of trans- modulation of frameshifting by host- and virus-encoded proteins. Host antiviral protein ZAP-S binds to the SARS-CoV-2 frameshift site and destabilizes the stimulatory structure, leading to frameshift inhibition. On the other hand, EMCV 2A protein stabilizes the viral frameshift site, thereby, activating EMCV frameshifting. While both proteins were shown to be antagonistic in their mechanism, they interact with the host translational machinery. Furthermore, we showed that frameshifting can be regulated not just by proteins, but also by small molecules. High-throughput screening of natural and synthetic compounds identified two potent frameshift inhibitors that also impeded viral replication, namely trichangion and compound 25. Together, this work largely enhances our understanding of gene regulation mechanisms in virus-infected cells and further validates the druggability of viral –1 PRF site.
Poor or variable oral bioavailability is of major concern regarding safety and efficacy for the treatment of patients with poorly water-soluble drugs (PWSDs). The problem statement of this work involves a pharmaceutical development perspective, the physicochemical basis of the absorption process and physiological / biopharmaceutical aspects. A methodology was developed aiming at closing the gap between drug liberation and dissolution on the one hand and the appearance of drug in the blood on the other. Considering what is out of control from a formulation development perspective, a clear differentiation between bioavailability and bioaccessibility was necessary. Focusing on the absorption process, bioaccessibility of a model compound, a poorly soluble but well permeable weak base, was characterized by means of flux across artificial biomimetic membranes. Such setups can be considered to reasonably mimic relevant oral absorption resistances in vitro in terms of diffusion through an unstirred water layer (UWL) and a lipidic barrier. Mechanistic understanding of the driving force for permeation was gained by differentiating drug species and subsequently linking them to the observed transfer rates using a bioaccessibility concept. The three key species that need to be differentiated are molecularly dissolved drug, drug associated in solution with other components (liquid reservoir) and undissolved drug (solid reservoir). An innovative approach to differentiate molecularly dissolved drug from the liquid reservoir using ultracentrifugation in combination with dynamic light scattering as control is presented. A guidance for rational formulation development of PWSDs is elaborated based on the employed model compound. It is structured into five guiding questions to help drug formulation scientists in selecting drug form, excipients and eventually the formulation principle. Overall, the relevance but also limitations of characterizing bioaccessibility were outlined with respect to practical application e.g. in early drug formulation development.
Hereditary spastic paraplegias (HSPs) are genetically-determined, neurodegenerative disorders characterized by progressive weakness and spasticity of the lower limbs. Spastic paraplegia type 11 (SPG11) is a complicated form of HSP, which is caused by mutations in the SPG11 gene encoding spatacsin, a protein possibly involved in lysosomal reformation. Based on our previous studies demonstrating that secondary neuroinflammation can be a robust amplifier of various genetically-mediated diseases of both the central and peripheral nervous system, we here test the possibility that neuroinflammation may modify the disease outcome also in a mouse model for SPG11. Spg11-knockout (Spg11-/-) mice develop early walking pattern and behavioral abnormalities, at least partially reflecting motor, and behavioral changes typical for patients. Furthermore, we detected a progressive increase in axonal damage and axonal spheroid formation in the white and grey matter compartments of the central nervous system of Spg11-/- mice. This was accompanied by a concomitant substantial increase of secondary inflammation by cytotoxic CD8+ and CD4+ T-lymphocytes. We here provide evidence that disease-related changes can be ameliorated/delayed by the genetic deletion of the adaptive immune system. Accordingly, we provide evidence that repurposing clinically approved immunomodulators (fingolimod/FTY720 or teriflunomide), that are in use for treatment of multiple sclerosis (MS), also improve disease symptoms in mice, when administered in an early (before neural damage) or late (after/during neural damage) treatment regime.
This work provides strong evidence that immunomodulation can be a therapeutic option for the still untreatable SPG11, including its typical neuropsychological features. This poses the question if inflammation is not only a disease amplifier in SPG11 but can act as a unifying factor also for other genetically mediated disorders of the CNS. If true, this may pave the way to therapeutic options in a wide range of still untreatable, primarily genetic, neurological disorders by repurposing approved immunomodulators.
Different effects of conditional Knock-Out of Stat3 on the sensory epithelium of the Organ of Corti
(2024)
The mammalian cochlea detects sound in response to vibration at frequency-dependent positions along the cochlea duct. The sensory outer hair cells, which are surrounded by supporting cells, act as a signal amplifier by changing their cell length. This is called electromotility. To ensure correct electrical transmission during mechanical forces, a certain resistance of the sensory epithelium is a prerequisite for correct transduction of auditory information. This resistance is managed by microtubules and its posttranslational modification in the supporting cells of the sensory epithelium of the cochlea. Stat3 is a transcription factor, with its different phosphorylation sites, is involved in many cellular processes like differentiation, inflammation, cell survival and microtubule dynamics, depending on cell type and activated pathway. While Stat3 has a wide range of intracellular roles, the question arose, how and if Stat3 is involved in cells of the organ of Corti to ensure a correct hearing.
To test this, Cre/loxp system were used to perform conditional Knock-Out (cKO) of Stat3 in outer hair cells or supporting cells either before hearing onset or after hearing onset. Hearing performances included DPOAE and ABR measurements, while molecular were performed by sequencing. Additionally, morphological examination was used by immunohistochemistry and electron microscopy.
A cKO of Stat3 before and after hearing onset in outer hair cells leads to hearing impairments, whereas synapses, nerve fibers and mitochondria were not affected. Bulk sequencing analyzation of outer hair cells out of cKO mice before hearing onset resulted in a disturbance of cellular homeostasis and extracellular signals. A cKO of Stat3 in the outer hair cells after hearing onset resulted in inflammatory signaling pathway with increased cytokine production and upregulation of NF-kb pathway. In supporting cells, cKO of Stat3 only after hearing onset resulted in a hearing impairment. However, synapses, nerve soma and fibers were not affected of a cKO of Stat3 in supporting cells. Nevertheless, detyronisated modification of microtubules were altered, which can lead to an instability of supporting cells during hearing.
In conclusion, Stat3 likely interact in a cell-specific and function-specific manner in cells of the organ of Corti. While a cKO in outer hair cells resulted in increased cytokine production, supporting cells altered its stability due to decreased detyronisated modification of microtubules. Together the results indicated that Stat3 is an important protein for hearing performances. However, additional investigations of the molecular mechanism are needed to understand the role of Stat3 in the cells of the organ of Corti.
Even though the international combat against Neglected Tropical Diseases such as schistosomiasis or soil-transmitted helminthiases depends on reliable therapeutics, anthelminthic pharmacovigilance has been neglected on many national African drug markets. Therefore, quality and composition of 88 different batches of Albendazole, Mebendazole and Praziquantel locally collected from randomly selected facilities in Western Burkina Faso, Southeast Côte d’Ivoire, Southwest Ghana and Northwest Tanzania were analysed.
Visual examination of both packaging and samples was performed according to the WHO ‘Be Aware’ tool. Products were then screened with the GPHF Minilab, consisting of tests of mass uniformity, disintegration times and thin-layer chromatography (TLC). Confirmatory tests were performed according to international pharmacopoeiae, applying assays for dissolution profiles and high-performance liquid chromatography (HPLC).
Despite minor irregularities, appearance of the products did not hint at falsified medicines. However, 19.6 % of the brands collected in Ghana and Tanzania were not officially licensed for sale. Mass uniformity was confirmed in 53 out of 58 brands of tablets. 41 out of 56 products passed disintegration times; 10 out of the 15 failing products did not disintegrate at all.
TLC results did not reveal any falsifications or pronounced dosing errors. HPLC findings confirmed the TLC results despite shifted specification limits: ten of the 83 tested batches contained less than 90 %, none more than 110 % label claim. However, no more than 46.3 % (31 / 67) of the tablet batches assayed passed the respective criteria for dissolution.
In the four study countries, no falsified anthelminthic medicine was encountered. The active pharmaceutical ingredient was not found to either exceed or distinctively fall below specification limits. Galenic characteristics as most critical criteria however, especially dissolution profiles, revealed substantial deficits.
According to the WHO, foodborne derived enteric infections are a global disease burden and often manifest in diseases that can potentially reach life threatening levels, especially in developing countries. These diseases are caused by a variety of enteric pathogens and affect the gastrointestinal tract, from the gastric to the intestinal to the rectal tissue. Although the complex mucosal structure of these organs is usually well prepared to defend the body against harmful agents, specialised pathogens such as Salmonella enterica can overcome the intestinal defence mechanism. After ingestion, Salmonella are capable of colonising the gut and establishing their proliferative niche, thereby leading to inflammatory processes and tissue damage of the host epithelium. In order to understand these processes, the scientific community in the last decades mostly used cell line based in vitro approaches or in vivo animal studies. Although these approaches provide fundamental insights into the interactions between bacteria and host cells, they have limited applicability to human pathology. Therefore, tissue engineered primary based approaches are important for modern infection research. They exhibit the human complexity better than traditional cell lines and can mimic human-obligate processes in contrast to animal studies.
Therefore, in this study a tissue engineered human primary model of the small intestinal epithelium was established for the application of enteric infection research with the exemplary pathogen Salmonella Typhimurium.
To this purpose, adult stem cell derived intestinal organoids were used as a primary human cell source to generate monolayers on biological or synthetic scaffolds in a Transwell®-like setting. These tissue models of the intestinal epithelium were examined for their comparability to the native tissue in terms of morphology, morphometry and barrier function. Further, the gene expression profiles of organotypical mucins, tight junction-associated proteins and claudins were investigated. Overall, the biological scaffold-based tissue models showed higher similarity to the native tissue - among others in morphometry and polarisation. Therefore, these models were further characterised on cellular and structural level. Ultrastructural analysis demonstrated the establishment of characteristic microvilli and tight-junction connections between individual epithelial cells. Furthermore, the expression pattern of typical intestinal epithelial protein was addressed and showed in vivo-like localisation. Interested in the cell type composition, single cell transcriptomic profiling revealed distinct cell types including proliferative cells and stem cells, progenitors, cellular entities of the absorptive lineage, Enterocytes and Microfold-like cells. Cells of the secretory lineage were also annotated, but without distinct canonical gene expression patterns. With the organotypical polarisation, protein expression, structural features and the heterogeneous cell composition including the rare Microfold-like cells, the biological scaffold-based tissue model of the intestinal epithelium demonstrates key requisites needed for infection studies with Salmonella.
In a second part of this study, a suitable infection protocol of the epithelial tissue model with Salmonella Typhimurium was established, followed by the examination of key features of the infection process. Salmonella adhered to the epithelial microvilli and induced typical membrane ruffling during invasion; interestingly the individual steps of invasion could be observed. After invasion, time course analysis showed that Salmonella resided and proliferated intracellularly, while simultaneously migrating from the apical to the basolateral side of the infected cell. Furthermore, the bacterial morphology changed to a filamentous phenotype; especially when the models have been analysed at late time points after infection. The epithelial cells on the other side released the cytokines Interleukin 8 and Tumour Necrosis Factor α upon bacterial infection in a time-dependent manner. Taken together, Salmonella infection of the intestinal epithelial tissue model recapitulates important steps of the infection process as described in the literature, and hence demonstrates a valid in vitro platform for the investigation of the Salmonella infection process in the human context.
During the infection process, intracellular Salmonella populations varied in their bacterial number, which could be attributed to increased intracellular proliferation and demonstrated thereby a heterogeneous behaviour of Salmonella in individual cells. Furthermore, by the application of single cell transcriptomic profiling, the upregulation of Olfactomedin-4 (OLFM4) gene expression was detected; OLFM4 is a protein involved in various functions including cell immunity as well as proliferating signalling pathways and is often used as intestinal stem cell marker. This OLFM4 upregulation was time-dependent, restricted to Salmonella infected cells and seemed to increase with bacterial mass. Investigating the OLFM4 regulatory mechanism, nuclear factor κB induced upregulation could be excluded, whereas inhibition of the Notch signalling led to a decrease of OLFM4 gene and protein expression. Furthermore, Notch inhibition resulted in decreased filamentous Salmonella formation. Taken together, by the use of the introduced primary epithelial tissue model, a heterogeneous intracellular bacterial behaviour was observed and a so far overlooked host cell response – the expression of OLFM4 by individual infected cells – could be identified; although Salmonella Typhimurium is one of the best-studied enteric pathogenic bacteria. This proves the applicability of the introduced tissue model in enteric infection research as well as the importance of new approaches in order to decipher host-pathogen interactions with higher relevance to the host.
This thesis provides an edition and commentary of a manuscript discovered by Michael Stolberg in the archives of the central library in Zurich under the title “Mon aprendisage à l'Hôtel Dieu de Paris 1704.” (My apprenticeship at the Hôtel-Dieu de Paris 1704). The manuscript contains records of a midwifery student at the Hôtel-Dieu de Paris, an old hospital famous among others for its education in midwifery in the maternity ward. We read about managing different births, recipes for common remedies, direct questions answered by the maîtresse sage-femme, the leading midwife at the Hôtel-Dieu de Paris and more.
Although other accounts exist of the maternity ward at the Hôtel-Dieu de Paris, \(Mon\) \(Aprendisage\) is the first and only account from a midwife’s perspective that gives more than just instructions on obstetrical techniques. It takes us into the day-to-day experience of a woman as she progressed through her training at the Hôtel-Dieu.
Based on previous results showing that thioether modification of gold nanoparticles (AuNPs), especially coating with a multivalent system, yielded in excellent colloidal stability, the first aim of this thesis was to prove whether functionalization of silver nanoparticles (AgNPs) with thioether also has a comparable or even enhanced stabilization efficacy compared with the gold standard of coating with thiols and, particularly, whether the multivalency of polymers leads to stable AgNPs conjugates. Herein, AgNPs coated with mono- and multivalent thiol- and thioether polymers were prepared to systematically investigate the adsorption kinetics onto the silver surface as well as the colloidal stability after exposure to different conditions relevant for biomedical application. Although the thioether-polymers showed a slower immobilization onto AgNPs, same or mostly even better stabilization was exhibited than for the thiol analogs.
As multivalent thioether-poly(glycidol) (PG) is already proven as a promising candidate for AuNP modification and stabilization, the second aim of this thesis was to examine the stealth behavior of thioether-PG, side-chain functionalized with various hydrophobic (alkyl and cholesteryl) units, to gain a deeper understanding of AuNP surface functionalization in terms of protein adsorption and their subsequent cellular uptake by human monocyte-derived macrophages. For this purpose, citrate-stabilized AuNPs were modified with the amphiphilic polymers by ligand exchange reaction, followed by incubation in human serum. The various surface amphiphilicities affected protein adsorption to a certain extent, with less hydrophobic particle layers leading to a more inhibited protein binding. Especially AuNPs functionalized with PG carrying the longest alkyl chain showed differences in the protein corona composition compared to the other polymer-coated NPs. In addition, PGylation, and especially prior serum incubation, of the NPs exhibited reduced macrophage internalization.
As the use of mammals for in vivo experiments faces various challenges including increasing regulatory hurdles and costs, the third aim of this thesis was to validate larvae of the domestic silkworm Bombyx mori as an alternative invertebrate model for preliminary in vivo research, using AuNPs with various surface chemistry (one PEG-based modification and three PG-coatings with slightly hydrophobic functionalization, as well as positively and negatively charges) for studying their biodistribution and elimination. 6 h and 24 h after intra-hemolymph injection the Au content in different organ compartments was measured with ICP-MS, showing that positively charged particles appeared to be eliminated most rapidly through the midgut, while AuNPs modified with PEG, alkyl-functionalized PG and negatively charged PG exhibited long-term bioavailability in the silkworm body.
After myocardial infarction, an inflammatory response is induced characterized by a sterile inflammation, followed by a reparative phase in order to induce cardiac healing. Neutrophils are the first immune cells that enter the ischemic tissue. Neutrophils have various functions in the ischemic heart, such as phagocytosis, production of reactive oxygen species or release of granule components. These functions can not only directly damage cardiac tissue, but are also necessary for initiating reparative effects in post-ischemic healing, indicating a dual role of neutrophils in cardiac healing after infarction.
In recent years, evidence has been growing that neutrophils show phenotypic and functional differences in distinct homeostatic and pathogenic settings.
Preliminary data of my working group using single-cell RNA-sequencing revealed the time- dependent heterogeneity of neutrophils, with different populations showing distinct gene expression profiles in ischemic hearts of mice, including the time-dependent appearance of a SiglecFhigh neutrophil population. To better understand the dynamics of neutrophil heterogeneity in the ischemic heart, my work aimed to validate previous findings at the protein level, as well as to investigate whether the distinct neutrophil populations show functional differences. Furthermore, in vivo depletion experiments were performed in order to modulate circulating neutrophil levels.
Hearts, blood, bone marrow and spleens were processed and analyzed from mice after 1 day and 3 days after the onset of cardiac ischemia and analyzed using flow cytometry.
Results showed that the majority of cardiac neutrophils isolated at day 3 after myocardial infarction were SiglecFhigh, whereas nearly no SiglecFhigh neutrophils could be isolated from ischemic hearts at day 1 after myocardial infarction.
No SiglecFhigh neutrophils could be found in the blood, spleen and bone marrow either after 1 day or 3 days after myocardial infarction, indicating that the SiglecFhigh state of neutrophils is unique to the ischemic cardiac tissue.
When I compared SiglecFhigh and SiglecFlow neutrophils regarding their phagocytosis activity and ROS production, SiglecFhigh neutrophils showed a higher phagocytosis ability than their SiglecFlow counterparts, as well as higher ROS production capacity.
In vivo depletion experiments could not achieve successful and efficient depletion of cardiac neutrophils either 1 day or 3 days after myocardial infarction, but led to a shift of a higher percentage of SiglecFhigh expressing neutrophils in the depletion group. Bone marrow neutrophil levels only showed partial depletion at day 3 after MI. Regarding blood neutrophils, depletion efficiently reduced circulating neutrophils at both time points, 1 and 3 days after MI. To summarize, this work showed the time-dependent presence of different neutrophil states in the ischemic heart. The main population of neutrophils isolated 3 days after MI showed a high expression of SiglecF, a unique state that could not be detected at different time points or other organs. These SiglecFhigh neutrophils showed functional differences regarding their phagocytosis ability and ROS production. Further investigation is needed to reveal what role these SiglecFhigh neutrophils could play within the ischemic heart.
To better target neutrophil depletion in vivo, more efficient or different anti-neutrophil strategies are needed.
The ongoing and evolving usage of networks presents two critical challenges for current and future networks that require attention: (1) the task of effectively managing the vast and continually increasing data traffic and (2) the need to address the substantial number of end devices resulting from the rapid adoption of the Internet of Things. Besides these challenges, there is a mandatory need for energy consumption reduction, a more efficient resource usage, and streamlined processes without losing service quality. We comprehensively address these efforts, tackling the monitoring and quality assessment of streaming applications, a leading contributor to the total Internet traffic, as well as conducting an exhaustive analysis of the network performance within a Long Range Wide Area Network (LoRaWAN), one of the rapidly emerging LPWAN solutions.
Deep Learning (DL) models are trained on a downstream task by feeding (potentially preprocessed) input data through a trainable Neural Network (NN) and updating its parameters to minimize the loss function between the predicted and the desired output. While this general framework has mainly remained unchanged over the years, the architectures of the trainable models have greatly evolved. Even though it is undoubtedly important to choose the right architecture, we argue that it is also beneficial to develop methods that address other components of the training process. We hypothesize that utilizing domain knowledge can be helpful to improve DL models in terms of performance and/or efficiency. Such model-agnostic methods can be applied to any existing or future architecture. Furthermore, the black box nature of DL models motivates the development of techniques to understand their inner workings. Considering the rapid advancement of DL architectures, it is again crucial to develop model-agnostic methods.
In this thesis, we explore six principles that incorporate domain knowledge to understand or improve models. They are applied either on the input or output side of the trainable model. Each principle is applied to at least two DL tasks, leading to task-specific implementations. To understand DL models, we propose to use Generated Input Data coming from a controllable generation process requiring knowledge about the data properties. This way, we can understand the model’s behavior by analyzing how it changes when one specific high-level input feature changes in the generated data. On the output side, Gradient-Based Attribution methods create a gradient at the end of the NN and then propagate it back to the input, indicating which low-level input features have a large influence on the model’s prediction. The resulting input features can be interpreted by humans using domain knowledge.
To improve the trainable model in terms of downstream performance, data and compute efficiency, or robustness to unwanted features, we explore principles that each address one of the training components besides the trainable model. Input Masking and Augmentation directly modifies the training input data, integrating knowledge about the data and its impact on the model’s output. We also explore the use of Feature Extraction using Pretrained Multimodal Models which can be seen as a beneficial preprocessing step to extract useful features. When no training data is available for the downstream task, using such features and domain knowledge expressed in other modalities can result in a Zero-Shot Learning (ZSL) setting, completely eliminating the trainable model. The Weak Label Generation principle produces new desired outputs using knowledge about the labels, giving either a good pretraining or even exclusive training dataset to solve the downstream task. Finally, improving and choosing the right Loss Function is another principle we explore in this thesis. Here, we enrich existing loss functions with knowledge about label interactions or utilize and combine multiple task-specific loss functions in a multitask setting.
We apply the principles to classification, regression, and representation tasks as well as to image and text modalities. We propose, apply, and evaluate existing and novel methods to understand and improve the model. Overall, this thesis introduces and evaluates methods that complement the development and choice of DL model architectures.
The variant surface glycoprotein (VSG) of African trypanosomes plays an essential role in protecting the parasites from host immune factors. These trypanosomes undergo antigenic variation resulting in the expression of a single VSG isoform out of a repertoire of around 2000 genes. The molecular mechanism central to the expression and regulation of the VSG is however not fully understood.
Gene expression in trypanosomes is unusual due to the absence of typical RNA polymerase II promoters and the polycistronic transcription of genes. The regulation of gene expression is therefore mainly post-transcriptional. Regulatory sequences, mostly present in the 3´ UTRs, often serve as key elements in the modulation of the levels of individual mRNAs. In T. brucei VSG genes, a 100 % conserved 16mer motif within the 3´ UTR has been shown to modulate the stability of VSG transcripts and hence their expression. As a stability-associated sequence element, the absence of nucleotide substitutions in the motif is however unusual. It was therefore hypothesised that the motif is involved in other essential roles/processes besides stability of the VSG transcripts.
In this study, it was demonstrated that the 100 % conservation of the 16mer motif is not essential for cell viability or for the maintenance of functional VSG protein levels. It was further shown that the intact motif in the active VSG 3´ UTR is neither required to promote VSG silencing during switching nor is it needed during differentiation from bloodstream forms to procyclic forms. Crosstalk between the VSG and procyclin genes during differentiation to the insect vector stage is also unaffected in cells with a mutated 16mer motif. Ectopic overexpression of a second VSG however requires the intact motif to trigger silencing and exchange of the active VSG, suggesting a role for the motif in transcriptional VSG switching. The 16mer motif therefore plays a dual role in VSG in situ switching and stability of VSG transcripts. The additional role of the 16mer in the essential process of antigenic variation appears to be the driving force for the 100 % conservation of this RNA motif.
A screen aimed at identifying candidate RNA-binding proteins interacting with the 16mer motif, led to the identification of a DExD/H box protein, Hel66. Although the protein did not appear to have a direct link to the 16mer regulation of VSG expression, the DExD/H family of proteins are important players in the process of ribosome biogenesis. This process is relatively understudied in trypanosomes and so this candidate was singled out for detailed characterisation, given that the 16mer story had reached a natural end point. Ribosome biogenesis is a major cellular process in eukaryotes involving ribosomal RNA, ribosomal proteins and several non-ribosomal trans-acting protein factors. The DExD/H box proteins are the most important trans-acting protein factors involved in the biosynthesis of ribosomes. Several DExD/H box proteins have been directly implicated in this process in yeast. In trypanosomes, very few of this family of proteins have been characterised and therefore little is known about the specific roles they play in RNA metabolism. Here, it was shown that Hel66 is involved in rRNA processing during ribosome biogenesis. Hel66 localises to the nucleolus and depleting the protein led to a severe growth defect. Loss of the protein also resulted in a reduced rate of global translation and accumulation of rRNA processing intermediates of both the small and large ribosomal subunits. Hel66 is therefore an essential nucleolar DExD/H protein involved in rRNA processing during ribosome biogenesis. As very few protein factors involved in the processing of rRNAs have been described in trypanosomes, this finding represents an important platform for future investigation of this topic.
Cardiovascular disease is one of the leading causes of death worldwide and, so far, echocardiography, nuclear cardiology, and catheterization are the gold standard techniques used for its detection. Cardiac magnetic resonance (CMR) can replace the invasive imaging modalities and provide a "one-stop shop" characterization of the cardiovascular system by measuring myocardial tissue structure, function and perfusion of the heart, as well as anatomy of and flow in the coronary arteries. In contrast to standard clinical magnetic resonance imaging (MRI) scanners, which are often operated at a field strength of 1.5 or 3 Tesla (T), a higher resolution and subsequent cardiac parameter quantification could potentially be achieved at ultra-high field, i.e., 7 T and above.
Unique insights into the pathophysiology of the heart are expected from ultra-high field MRI, which offers enhanced image quality in combination with novel contrast mechanisms, but suffers from spatio-temporal B0 magnetic field variations. Due to the resulting spatial misregistration and intra-voxel dephasing, these B0-field inhomogeneities generate a variety of undesired image artifacts, e.g., artificial image deformation. The resulting macroscopic field gradients lead to signal loss, because the effective transverse relaxation time T2* is shortened. This affects the accuracy of T2* measurements, which are essential for myocardial tissue characterization. When steady state free precession-based pulse sequences are employed for image acquisition, certain off-resonance frequencies cause signal voids. These banding artifacts complicate the proper marking of the myocardium and, subsequently, systematic errors in cardiac function measurements are inevitable. Clinical MR scanners are equipped with basic shim systems to correct for occurring B0-field inhomogeneities and resulting image artifacts, however, these are not sufficient for the advanced measurement techniques employed for ultra-high field MRI of the heart.
Therefore, this work focused on the development of advanced B0 shimming strategies for CMR imaging applications to correct the spatio-temporal B0 field variations present in the human heart at 7 T. A novel cardiac phase-specific shimming (CPSS) technique was set up, which featured a triggered B0 map acquisition, anatomy-matched selection of the shim-region-of-interest (SROI), and calibration-based B0 field modeling. The influence of technical limitations on the overall spherical harmonics (SH) shim was analyzed. Moreover, benefits as well as pitfalls of dynamic shimming were debated in this study. An advanced B0 shimming strategy was set up and applied in vivo, which was the first implementation of a heart-specific shimming approach in human UHF MRI at the time.
The spatial B0-field patterns which were measured in the heart throughout this study contained localized spots of strong inhomogeneities. They fluctuated over the cardiac cycle in both size and strength, and were ideally addressed using anatomy-matched SROIs. Creating a correcting magnetic field with one shim coil, however, generated eddy currents in the surrounding conducting structures and a resulting additional, unintended magnetic field. Taking these shim-to-shim interactions into account via calibration, it was demonstrated for the first time that the non-standard 3rd-order SH terms enhanced B0-field homogeneity in the human heart. However, they were attended by challenges for the shim system hardware employed in the presented work, which was indicated by the currents required to generate the optimal 3rd-order SH terms exceeding the dynamic range of the corresponding shim coils. To facilitate dynamic shimming updated over the cardiac cycle for cine imaging, the benefit of adjusting the oscillating CPSS currents was found to be vital. The first in vivo application of the novel advanced B0 shimming strategy mostly matched the simulations.
The presented technical developments are a basic requirement to quantitative and functional CMR imaging of the human heart at 7 T. They pave the way for numerous clinical studies about cardiac diseases, and continuative research on dedicated cardiac B0 shimming, e.g., adapted passive shimming and multi-coil technologies.
Human-environment interaction has significantly altered the pedosphere since the Neolithic, if not since the early Holocene. In the course of clearance, agriculture, and (wood) pasture soils have been deeply modified or eroded. These types of land use practices but above all forms of sedentariness spread alongside floodplains and trajectories were oriented towards loess covered areas where fertile soils could develop. Besides this, also peripheral / marginal regions were settled due to population pressure or other factors. Evidence for landscape history and development can be found within archeological sites but also overbank deposits and anthropogenic slope deposits document vast transformation processes.
The presented investigations took place within the natural region of the Windsheimer Bucht which is locat-ed in the district of Middle Franconia in northern Bavaria, Germany. In this area, Holocene soils predomi-nantly developed within mudstones of the Middle to Upper Triassic. The soil texture is extremely clay-rich which renders the soils problematic with regard to cultivation management. As a peculiarity, the gypsum underlying the mudstones is prone to karstification processes and resulting proceeding geomorphological processes shape the surface of the landscape. In the course of gypsum mining the karst forms are being exposed and archeological findings are being documented. The latter mainly date back to a span from the Neolithic to the Iron Age, but partly are of Younger Paleolithic origin. Especially subsidence sinkholes are capable of storing pedosediments of several meters in thickness. Despite the high clay content and connect-ed pedoturbation processes, the excavated sequences are stratigraphically and pedologically well-differentiated. The archives occur in the context of settlement structures such as pits and postholes; there-fore, they developed at the interface of natural developments and human impact on their surroundings.
The main original research questions that were formulated within the general frame of a project funded by the Deutsche Forschungsgemeinschaft (DFG-projects Te295/15-1 and -2 and Fa390/9-1 and -2) focused on the attractors of the peripheral region for early settlers, the pedological conditions before land use, but also the impact of humans on soils and karst dynamics through time. In the course of the in hand study, the pedosedimentary archives have been approached with a multimethodological toolset which consisted of field analyses, soil morphological analyses from micro- to macro-scale, spectrophotometric (color), (laser) granulometric, and (iron-) pedochemical analyses. The numerical chronological frame was spanned by radiocarbon dating of different organic remains and bulk material if soil organic carbon was supposed-ly high. The result is a multi-dimensional data set that consists of analyses on different spatial scales but also on different levels of measurement. Thus, qualitative, semi-quantitative, and quantitative data consti-tute the basis for discussion. While the grain-size analyses underline the general sedimentological differen-tiation of the records and further affirm the high clay content within the pedosedimentary layers, iron-pedochemical analyses indicate an interplay between oxidation of iron and its chemical reduction. This is also manifested within the spectrophotometric record. Especially the versatile pedogenic characteristics that have been identified by field analyses are confirmed within the thin sections and, by considering all different analyses, the polygenic character of the pedosediments is emphasized.
After stressing the general pedological specificities among the different investigated sites within the re-search area, for the collected data, the research further branches into the subjects of general notions on pedogenesis in clayey material and the classification of the respective pedosediments according to paleo-pedological concepts but also recent schemes. Concerning the latter, it becomes evident that established principles cannot be applied to the studied pedosediments without major adaptions. This underlines the specific characteristics of the material.
The basis for further interpretations is the evaluation of the multi-level data set for the single records with regard to profile development and pedogenic processes. Hereby, the main drivers of pedogenesis could be identified, which are karst dynamics, land use, and subtle changes in parent material due to the admixture of slope deposits that contain allochthonous eolian material. The latter underlines the importance of Pleis-tocene preconditioning for understanding Holocene landscape dynamics. At the same time, a differentia-tion between the mentioned factors and Holocene climate development is difficult. The following compila-tion of record and localities within the given time frame unveils synchronous as well as asynchronous de-velopments; however, a clear connection between phases of Holocene climate and pedogenesis within the pedosediments cannot be established. Instead, it becomes evident that site specific factors or those that act on the scale of the micro-catchment of the investigated records are decisive.
The aforementioned main topics of the project are also considered in the in hand study from a soil-geographic perspective: it is possible that before land use, there was an insular or thin cover by loess sedi-ments or at least upper layers (according to the concept of periglacial cover beds) which constituted the parent material for Holocene soil formation. The according soils, which were superior for agricultural purposes compared to those developed on the autochthonous mudstones, were eroded which exposed the clayey Upper to Middle Triassic beds. Erosion was aggravated due to the impermeable mudstones which enhanced overland flow and interflow within the overlying silty (loessic) material. This is further support-ed by the notions on erodibility of the clayey material that are derived from the comparison of conven-tional and laser granulometric analyses: probably, the clayey pedosediments are capable of forming micro-aggregates that can easily be eroded during heavy rainfall events despite the general consent that material with heavy texture should be rather resistant.
The study presents a comprehensive view on clay-rich pedosediments and the complex effects of human-environment interaction on pedogenic as well as sedimentary processes through time that have not been investigated in such detail before. In this context, the multi-level soil morphological analyses and their necessity for a genetic interpretation with regard to the influence of natural versus anthropogenic factors need to be emphasized. Based on quantitative laboratory analytical data only, a respective differentiation would not be possible. This underlines the importance of the chosen soil-geographic multi-methodological approach for answering questions with regard to human-environment interaction but also geoarcheology in general.
Gold nanoparticles of diameter ca. 60 nm have been synthesized based on Turkevich and Frens protocols. We have demonstrated that the carboxyl-modified gold nanoparticles can be coupled covalently with antibodies (Ab) of interest using the EDC/NHS coupling procedure. Binding studies with Ab-grafted AuNPs and GpL fusion proteins proved that conjugation of AuNPs with antibodies enables immobilization of antibodies with preservation of a significant antigen binding capacity. More importantly, our findings showed that the conjugation of types of anti-TNF receptors antibodies such as anti-Fn14 antibodies (PDL192 and 5B6) (Aido et al., 2021), anti-CD40, anti-4-1BB and anti-TNFR2 with gold nanoparticles confers them with potent agonism. Thus, our results suggest that AuNPs can be utilized as a platform to immobilize anti-TNFR antibodies which, on the one hand, helps to enhance their agonistic activity in comparison to “free” inactive antibodies by mimicking the effect of cell-anchored antibodies or membrane-bound TNF ligands and, on the other hand, allows to develop new generations of drug delivery systems. These constructs are characterized with their biocompatibility and their tunable synthesis process.
In a further work part, we combined the benefits of the established system of Ab-AuNPs with materials used widely in the modern biofabrication approaches such as the photo-crosslinked hydrogels, methacrylate-modified gelatin (GelMA), combined with embedded variants of human cell lines. The acquired results demonstrated clearly that the attaching of proteins like antibodies to gold nanoparticles might reduce their release rate from the crosslinked hydrogels upon the very low diffusion of gold nanoparticles from the solid constructs to the surrounding medium yielding long-term local functioning proteins-attached particles. Moreover, our finding suggests that hydrogel-embedded AuNP-immobilized antibodies, e.g. anti-TNFα-AuNPs or anti-IL1-AuNPs enable local inhibitory functions,
To sum up, our results demonstrate that AuNPs can act as a platform to attach anti-TNFR antibodies to enhance their agonistic activity by resembling the output of cell-anchoring or membrane bounding. Gold nanoparticles are considered, thus, as promising tool to develop the next generation of drug delivery systems, which may contribute to cancer therapy. On top of that, the embedding of anti-inflammatory-AuNPs in the biofabricated hydrogel presents new innovative strategy of the treatment of autoinflammatory diseases.
Most medicines are taken orally. To enter the systemic circulation, they dissolve in the intestinal fluid, cross the epithelial barrier, and pass through the liver. Intestinal absorption is driven by the unique features of the gastrointestinal tract, including the bile colloids formed in the lumen and the mucus layer covering the intestinal epithelium. Neglecting this multifaceted environment can lead to poor drug development decisions, especially for poorly water-soluble drugs that interact with bile and mucus. However, there is a lack of a rationale nexus of molecular interactions between oral medicines and gastrointestinal components with drug bioavailability. Against this background, this thesis aims to develop biopharmaceutical strategies to optimize the presentation of oral therapeutics to the intestinal epithelial barrier.
In Chapter 1, the dynamics of bile colloids upon solubilization of the poorly-water soluble drug Perphenazine was studied. Perphenazine impacted molecular arrangement, structure, binding thermodynamics, and induced a morphological transition from vesicles to worm-like micelles. Despite these dynamics, the bile colloids ensured stable relative amounts of free drug substance. The chapter was published in Langmuir.
Chapter 2 examined the impact of pharmaceutical polymeric excipients on bile-mediated drug solubilization. Perphenazine and Imatinib were introduced as model compounds interacting with bile, whereas Metoprolol did not. Some polymers altered the arrangement and geometry of bile colloids, thereby affecting the molecularly soluble amount of those drugs interacting with bile. These insights into the bile-drug-excipient interplay provide a blueprint to optimizing formulations leveraging bile solubilization. The chapter was published in Journal of Controlled Release.
Chapter 3 deals with the impact of bile on porcine intestinal mucus. Mucus exposed to bile solution changed transiently, it stiffened, and the overall diffusion rate increased. The bile-induced changes eased the transport of the bile-interacting drug substance Fluphenazine, whereas Metoprolol was unaffected. This dichotomous pattern was linked to bioavailability in rats and generalized based on two previously published data sets. The outcomes point to a bile-mucus interaction relevant to drug delivery. The chapter is submitted.
The Appendix provides a guide for biopharmaceutical characterization of drug substances by nuclear magnetic resonance spectroscopy aiming at establishing a predictive algorithm.
In summary, this thesis deciphers bile-driven mechanisms shaping intestinal drug absorption. Based on these molecular insights, pharmaceuticals can be developed along a biopharmaceutical optimization, ultimately leading to better oral drugs of tomorrow.
The reprogramming of metabolic pathways is a hallmark of cancer: Tumour cells are dependent on the supply with metabolites and building blocks to fulfil their increased need as highly proliferating cells. Especially de novo synthesis pathways are upregulated when the cells of the growing tumours are not able to satisfy the required metabolic levels by uptake from the environment.
De novo synthesis pathways are often under the control of master transcription factors which regulate the gene expression of enzymes involved in the synthesis process. The master regulators for de novo fatty acid synthesis and cholesterogenesis are sterol regulatory element-binding proteins (SREBPs). While SREBP1 preferably controls the expression of enzymes involved in fatty acid synthesis, SREBP2 regulates the transcription of the enzymes of the mevalonate pathway and downstream processes namely cholesterol, isoprenoids and building blocks for ubiquinone synthesis.
SREBP activity is tightly regulated at different levels: The post-translational modification by ubiquitination decreases the stability of active SREBPs. The attachment of K48-linked ubiquitin chains marks the transcription factors for the proteasomal degradation. In tumour cells, high levels of active SREBPs are essential for the upregulation of the respective metabolic pathways. The increased stability and activity of SREBPs were investigated in this thesis.
SREBPs are ubiquitinated by the E3 ligase Fbw7 which leads to the subsequential proteolysis of the transcription factors. The work conducted in this thesis identified the counteracting deubiquitination enzyme USP28 which removes the ubiquitin chains from SREBPs and prevents their proteasomal degradation.
It further revealed that the stabilization of SREBP2 by USP28 plays an important role in the context of squamous cancers. Increased USP28 levels are associated with a poor survival in patients with squamous tumour subtypes. It was shown that reduced USP28 levels in cell lines and in vivo result in a decrease of SREBP2 activity and downregulation of the mevalonate pathway. This manipulation led to reduced proliferation and tumour growth.
A direct comparison of adenocarcinomas and squamous cell carcinomas in lung cancer patients revealed an upregulation of USP28 as well as SREBP2 and its target genes. Targeting the USP28-SREBP2 regulatory axis in squamous cell lines by inhibitors also reduced cell viability and proliferation.
In conclusion, this study reports evidence for the importance of the mevalonate pathway regulated by the USP28-SREBP2 axis in tumour initiation and progression of squamous cancer. The combinatorial inhibitor treatment of USP28 and HMGCR, the rate limiting enzyme of the mevalonate pathway, by statins opens the possibility for a targeted therapeutic treatment of squamous cancer patients.
Ecophysiological adaptations of the cuticular water permeability within the Solanaceae family
(2024)
The cuticle, a complex lipidic layer synthesized by epidermal cells, covers and protects primary organs of all land plants. Its main function is to avoid plant desiccation by limiting non-stomatal water loss. The cuticular properties vary widely among plant species. So far, most of the cuticle-related studies have focused on a limited number of species, and studies addressing phylogenetically related plant species are rare. Moreover, comparative studies among organs from the same plant species are still scarce.
Thus, this study focus on organ-specificities of the cuticle within and between plant species of the Solanaceae family. Twenty-seven plant species of ten genera, including cultivated and non- cultivated species, were investigated to identify potential cuticular similarities. Structural, chemical and functional traits of fully expanded leaves, inflated fruiting calyces, and ripe fruits were analyzed.
The surface morphology was investigated by scanning electron microscopy. Leaves were mainly amphistomatic and covered by an epicuticular wax film. The diversity and distribution of trichomes varied among species. Only the leaves of S. grandiflora were glabrous. Plant species of the Leptostemonum subgenus had numerous prickles and non-glandular stellate trichomes. Fruits were stomata-free, except for S. muricatum, and a wax film covered their surface. Last, lenticel- like structures and remaining scars of broken trichomes were found on the surface of some Solanum fruits.
Cuticular water permeability was used as indicators of the cuticular transpiration barrier efficiency. The water permeability differed among plant species, organs and fruit types with values ranging up to one hundred-fold. The minimum leaf conductance ranged from 0.35 × 10-5 m s-1 in S. grandiflora to 31.54 × 10-5 m s-1 in S. muricatum. Cuticular permeability of fruits ranged from 0.64 × 10-5 m s-1 in S. dulcamara (fleshy berry) to 34.98 × 10-5 m s-1 in N. tabacum (capsule). Generally, the cuticular water loss of dry fruits was about to 5-fold higher than that of fleshy fruits.
Interestingly, comparisons between cultivated and non-cultivated species showed that wild species have the most efficient cuticular transpiration barrier in leaves and fruits. The average permeability of leaves and fruits of wild plant species was up to three-fold lower in comparison to the cultivated ones. Moreover, ripe fruits of P. ixocarpa and P. peruviana showed two-times lower cuticular transpiration when enclosed by the inflated fruiting calyx.
The cuticular chemical composition was examined using gas chromatography. Very-long-chain aliphatic compounds primarily composed the cuticular waxes, being mostly dominated by n- alkanes (up to 80% of the total wax load). Primary alkanols, alkanoic acids, alkyl esters and branched iso- and anteiso-alkanes were also frequently found. Although in minor amounts, sterols, pentacyclic triterpenoids, phenylmethyl esters, coumaric acid esters, and tocopherols were identified in the cuticular waxes. Cuticular wax coverages highly varied in solanaceous (62- fold variation). The cuticular wax load of fruits ranged from 0.55 μg cm−2 (Nicandra physalodes) to 33.99 μg cm−2 (S. pennellii), whereas the wax amount of leaves varied from 0.90 μg cm−2 (N. physalodes) to 28.42 μg cm−2 (S. burchellii). Finally, the wax load of inflated fruiting calyces ranged from 0.56 μg cm−2 in P. peruviana to 2.00 μg cm−2 in N. physalodes.
For the first time, a comparative study on the efficiency of the cuticular transpiration barrier in different plant organs of closely related plant species was conducted. Altogether, the cuticular chemical variability found in solanaceous species highlight species-, and organ-specific wax biosynthesis. These chemical variabilities might relate to the waterproofing properties of the plant cuticle, thereby influencing leaf and fruit performances. Additionally, the high cuticular water permeabilities of cultivated plant species suggest a potential existence of a trade-off between fruit organoleptic properties and the efficiency of the cuticular transpiration barrier. Last, the high cuticular water loss of the solanaceous dry fruits might be a physiological adaptation favouring seed dispersion.
Background: That a differentiated treatment of subjects with low and high levels of disabling pain might be necessarily has only been suspected but not sufficiently confirmed so far. Furthermore, the effectiveness of extraoral therapy methods for TMD is still controversial in the literature. The present work could make an important contribution to this.
Objectives: Five systematic reviews with meta-analysis were conducted to investigate the efficacy of extraoral therapies (acupuncture, laser, medication, psychosocial interventions, and physiotherapy) in the treatment of TMD in relation to the degree of chronicity of pain.
Literature sources: With this objective, the databases Pubmed/MEDLINE, EMBASE, Cochrane Library, Livivo, OpenGrey, drks.de, Clinicaltrials.gov. were searched.
Criteria for the selection of suitable studies: Adults suffering from painful TMD and treated with either acupuncture, laser, medication, psychosocial interventions, or physiotherapy. The studies were then examined for evidence in the subjects' characteristics suggesting that they were suffering from chronic TMD in terms of pain dysfunction. These included a high score on the GCPS, resistance to undergone treatments, multilocular pain, depression, and regular use of pain medication. The effectiveness of the five interventions was then differentiated according to the suspected degree of chronicity. Effectiveness was assessed by the following outcomes: patient- related current pain intensity, MMO, pain on palpation, temporomandibular joint sounds, depression, and somatization.
Study evaluation: After the assessment of the studies, the quality assessment (Risk of Bias Tool of the Cochrane Institute) and the extraction of the data were conducted. After that five meta-analyses were carried out for each of the five interventions using the Review Manager of the Cochrane Institute (RevMan 5.3)
Results: Acupuncture and dry needling were statistically significantly more effective in providing short-term pain relief compared to the control group in patients with low disability pain (p=0.04) and (p=0.02), respectively. Acupuncture or dry needling did not show a significant result in the improvement of MMO in the short-term period. Laser therapy is more effective in relieving pain (p<0.0001) and functional outcomes (p=0.03) in the short term compared to placebo for low disability pain. Botulinum toxin (p=0.003) and NSAIDs (p=0.03) showed significantly better short-term improvement in pain intensity for high disability pain. Low disability pain is significantly better treated by psychosocial interventions than by other treatments in terms of long-term pain relief (more than 12 months) (p=0.02). Patients with high disability pain had significantly lower depression scores after psychosocial interventions than after other treatments (p=0.008). Physiotherapy showed a statistically significant short-term analgesic effect in patients with high disability pain compared to placebo (p=0.04). Manual Therapy (MT) showed a statistically significant short-term analgesic effect in high disability pain compared to the control group (p=0.01). Patients with low disability pain showed a statistically significant short-term pain-relieving effect with the single intervention of MT in combination with exercise compared to the control groups (p=0.003). A statistically significant result in the improvement of MMO was found in the short-term period in low disability pain for the single interventions of physiotherapy (p=0.008) and physiotherapy in combination with another treatment compared to other treatments (p=0.03), MT compared to the control group (p=0.03) and physiotherapy compared to splint therapy (p=0.03). Clinical conclusion: Individual interventions of the five extraoral therapies confirm the hypothesis that painful TMDs respond differently to established therapies depending on the degree of chronic pain-related disability and that the prognosis of therapy is significantly influenced by the degree of chronic pain- related disability of the condition, according to the GCPS.
Registration number of the review at PROSPERO: CRD42020202558
Keywords: meta-analysis, systematic review, temporomandibular disorders, extra oral therapy, acupuncture, laser, medication, psychosocial interventions, physiotherapy, low disability, high disability, pain, chronification
Maintaining the balance between CO2 uptake and transpiration is important for plants and depends on tightly controlled turgor changes caused by the activity of various anion and cation channels. These channels are part of signaling cascades triggered, for example, by phytohormones such as ABA (abscisic acid) and JA (jasmonate), both of which act during drought stress in guard cells. In addition, JA is known to be involved in the plant's response to pathogen attack or wounding.
GORK (guard cell outward rectifying K+ channel) is the only known outward rectifying K+ channel in guard cells and therefore responsible for K+ efflux during stomatal closure.
In the course of this work it could be demonstrated by stomatal aperture assays, that GORK is an essential part of JA-induced stomatal closure. This is true for both triggers, leaf wounding as well as direct MeJA (methyl jasmonate) application. Patch clamp experiments on guard cell protoplasts backed this finding by revealing GORK K+ outward currents as a target of JA signaling in guard cells. As cytosolic Ca2+ signals are known to be involved in both ABA as well as JA signaling, the interaction of GORK with Ca2+-dependent kinases was examined consequently. An antagonistic regulation of GORK by
CIPK5-CBL1/9 complexes and ABI2 was identified by DEVC (double electrode voltage clamp) and protein-protein interaction experiments and backed up by in vitro kinase assays. Patch-clamp recordings on guard cell protoplasts of cipk5-2 kinase loss-of-function mutant revealed the importance of CIPK5 for JA-triggered stomatal closure via activation of GORK. The interaction of different CDPKs (Ca2+-dependent protein kinases) with GORK was also investigated.
Besides Ca2+ signaling also ROS (reactive oxygen species) production is essential in ABA and MeJA signaling. In DEVC experiments a reversible effect of ROS on GORK channel activity could be demonstrated, which could be one piece in the explanation of those ROS effects in ABA and MeJA signaling.
Ownership and usage of personal voice assistant devices like Amazon Echo or Google Home have increased drastically over the last decade since their market launch. This thesis builds upon existing computers are social actors (CASA) and media equation research that is concerned with humans displaying social reactions usually exclusive to human-human interaction when interacting with media and technological devices. CASA research has been conducted with a variety of technological devices such as desktop computers, smartphones, embodied virtual agents, and robots. However, despite their increasing popularity, little empirical work has been done to examine social reactions towards these personal stand-alone voice assistant devices, also referred to as smart speakers. Thus, this dissertation aims to adopt the CASA approach to empirically evaluate social responses to smart speakers. With this goal in mind, four laboratory experiments with a total of 407 participants have been conducted for this thesis. Results show that participants display a wide range of social reactions when interacting with voice assistants. This includes the utilization of politeness strategies such as the interviewer-bias, which led to participants giving better evaluations directly to a smart speaker device compared to a separate computer. Participants also displayed prosocial behavior toward a smart speaker after interdependence and thus a team affiliation had been induced. In a third study, participants applied gender stereotypes to a smart speaker not only in self-reports but also exhibited conformal behavior patterns based on the voice the device used. In a fourth and final study, participants followed the rule of reciprocity and provided help to a smart speaker device that helped them in a prior interaction. This effect was also moderated by subjects’ personalities, indicating that individual differences are relevant for CASA research. Consequently, this thesis provides strong empirical support for a voice assistants are social actors paradigm. This doctoral dissertation demonstrates the power and utility of this research paradigm for media psychological research and shows how considering voice assistant devices as social actors lead to a more profound understanding of voice-based technology. The findings discussed in this thesis also have implications for these devices that need to be carefully considered both in future research as well as in practical design.
In this thesis, a new approach of a qNMR method has been investigated to demonstrate the reliability and importance of this method as an alternative solution for analyzing oil quality parameters, especially in RFO, which has particular characteristics (red color). This study also includes the chemometric evaluation of spectral data for authentication, visual grouping, and prediction of RFO quality based on the degree of unsaturation, FFA value, and unsaturated fatty acid content.
The analytical measurement procedure of NMR spectroscopy begins with optimization of the analytical acquisition parameters, including effect of solvent, effect of sample concentration, selection of appropriate internal standards, determination of T1, and method validation. Furthermore, the results of the method development were interpreted to RFO samples evaluation, which began with determining the assignment of signal spectra for the determination of AV, SV, EV, and IV simultaneously with: the hydrolysis approach and standard addition of palmitic acid.
Adoptive immunotherapy using chimeric antigen receptor (CAR)-modified T cells is an effective treatment for hematological malignancies that are refractory to conventional chemotherapy. To address a wider variety of cancer entities, there is a need to identify and characterize additional target antigens for CAR-T cell therapy. The two members of the receptor tyrosine kinase-like orphan receptor family, ROR1 and ROR2, have been found to be overexpressed on cancer cells and to correlate with aggressive cancer phenotypes. Recently, ROR1-specific CAR-T cells have entered testing in phase I clinical trials, encouraging us to assess the suitability of ROR2 as a novel target for CAR-T cell therapy. To study the therapeutic potential of targeting ROR2 in solid and hematological malignancies, we selected two representative cancer entities with high unmet medical need: renal cell carcinoma and multiple myeloma.
Our data show that ROR2 is commonly expressed on primary samples and cell lines of clear cell renal cell carcinoma and multiple myeloma. To study the efficacy of ROR2-specific CAR T cell therapy, we designed two CAR constructs with 10-fold binding affinity differences for the same epitope of ROR2. We found both cell products to exhibit antigen-specific anti-tumor reactivity in vitro, including tumor cell lysis, secretion of the effector cytokines interleukin-2 (IL-2) and interferon-gamma (IFNγ), and T cell proliferation. In vivo studies revealed ROR2 specific CAR-T cells to confer durable responses, significant survival benefits and long-term persistence of CAR-expressing T cells. Overall, there was a trend towards more potent anti-tumor efficacy upon treatment with T cells that expressed the CAR with higher affinity for ROR2, both in vitro and in vivo.
We performed a preclinical safety and toxicology assessment comprising analyses of ROR2 expression in healthy human and murine tissues, cross-reactivity, and adoptive T cell transfer in immunodeficient mice. We found ROR2 expression to be conserved in mice, and low-level expression was detectable in the male and female reproductive system as well as parts of the gastrointestinal tract. CAR-T cells targeting human ROR2 were found to elicit similarly potent reactivity upon recognition of murine ROR2. In vivo analyses showed transient tissue-specific enrichment and activation of ROR2-specific CAR-T cells in organs with high blood circulation, such as lung, liver, or spleen, without evidence for clinical toxicity or tissue damage as determined by histological analyses.
Furthermore, we humanized the CAR binding domain of ROR2-specific CAR-T cells to mitigate the risk of adverse immune reactions and concomitant CAR-T cell rejection. Functional analyses confirmed that humanized CARs retained their specificity and functionality against ROR2-positive tumor cells in vitro.
In summary, we show that ROR2 is a prevalent target in RCC and MM, which can be addressed effectively with ROR2-specific CAR-T cells in preclinical models. Our preliminary toxicity studies suggest a favorable safety profile for ROR2-specific CAR-T cells. These findings support the potential to develop ROR2-specific CAR-T cells clinically to obtain cell products with broad utility.
Virtual humans (VHs) hold immense potential for collaboration in social virtual reality (VR). As VR technology advances, it's vital to assess the psychological effects on VH trust and user privacy to build meaningful social interactions in VR. In social VR, users must be able to trust the VHs they interact with as they navigate through socio-cultural activities. The evaluation of trustworthiness in VHs profoundly impacts interaction quality and user willingness to engage. Conversely, untrustworthy VHs can harm user experiences, privacy, and VR engagement. To address this, we conducted immersive VR studies, exploring how psychological factors influence user's VH trust evaluation under various psychological conditions. This research is pivotal for developing strategies to enhance user privacy, establish secure VR environments, and create a foundation of trust that supports immersive socio-cultural experiences in VR.
To date, there are no established interpersonal trust measurement tools specifically for VHs in VR. In study 1 (the familiarity study) of the current thesis the VR-adjusted version of the social conditioned place preference paradigm (SCPP) by Kiser et al., (2022) was identified as a potential trust measurement tool. We tested whether the familiarity of a VH influenced trust as measured with the SCPP paradigm and other self-defined outcome measures, in a Computer Augmented Virtual Environment (CAVE). The CAVE is a VR system that combines immersive VR with real-world elements. It consists of a room-sized space where the walls are used as projection screens to display virtual scenes and objects. In this within - subject design (n = 20), half of the participants were familiarized with one VH and tasked to explore and interact in a realistic looking virtual art museum environment. The participant’s evaluation of the VH’s trustworthiness was measured as well as their subsequent trust behaviours. Results revealed no significant differences in the evaluation of the VH’s trustworthiness nor any behavioural differences between conditions. The findings of the impact of a VH’s familiarity on trust is inconclusive due to the major limitations of the paradigm. We concluded that the SCPP paradigm needs further validation and the proposed proxies of trust need to be re-evaluated. The findings were considered in the following study.
The virtual maze paradigm design of Hale, (2018) was identified as a potential trust measurement tool, however several limitations are associated with its use to measure trust in VR. In study 2 (a validation study), improvements were made to the virtual maze paradigm of Hale, (2018) and a variant of this paradigm was implemented. We conducted a validation study with 70 participants in a between-subject design with VH trustworthiness as the between-subject factor. Participants wore a head-mounted display (HMD), to deliver an immersive VR experience. In our version of the virtual maze, it was the task of the users (the trustors) to navigate through a maze in VR, where they could interact with a VH (the trustee). They could choose to ask for advice and follow the advice from the VH if they wanted to. The number of times participants asked and followed advice and the time it took to respond to the given advice served as behavioural proxies/measures of trust. The two conditions (trustworthy vs. untrustworthy) did not differ in the content of the advice but in the appearance, tone of voice and engagement of the trustees (allegedly an avatar controlled by other participants). Results indicated that the experimental manipulation was successful, as participants rated the VH as more trustworthy in the trustworthy condition compared with the VH in the untrustworthy condition. Importantly, this manipulation affected the trust behaviour of participants, who, in the trustworthy condition, asked for advice and followed advice more often, indicating that the paradigm is sensitive to differences in VH’s trustworthiness. Thus, our paradigm can be used to measure differences in interpersonal trust towards VHs and may serve as a valuable research tool for researchers who study trust in VR. Therefore, study 2 fills the gap in the literature, for an interpersonal trust measurement tool specifically for VHs in VR.
Two experimental studies, with a sample size of 50 participants each, utilized the virtual maze paradigm where participants entered 12 rooms under different conditions. We examined the influence of cognitive load (CL) on trust towards VH in VR in study 3 (Cognitive load study), and the influence of emotional affect (Emotional affect study) on trust towards VH in VR in study 4 (EA study). In both studies, we assessed participant’s evaluation of a VH’s trustworthiness, along with three behavioural indicators of trust in the maze task: 1) frequency of advice asked, 2) frequency of advice followed, and 3) the time taken by participants to execute the received advice. In study 3, the CL was manipulated with the auditory 1-back task in the high cognitive load condition (HCL). In study 4, the Autobiographical Emotional Memory Task (AEMT) was used to manipulate the EA of participants in the negative emotional affect (NEA) condition. As an additional manipulation, while participants were immersed in VR, they were exposed to 12 negative pictures and sounds that was presented simultaneously to strengthen the initial manipulation. The manipulation of the within-subject factors (CL and EA) was successful in both studies, as significant differences between conditions were observed in both studies (higher CL in the HCL condition and a more negative EA in the NEA condition). However, only CL influenced participant’s evaluation of the VH’s trustworthiness. The VH were evaluated as significantly more trustworthy after the HCL condition. Despite the difference in trust evaluation, there was no difference in advice asking or following. Participants in study 4 asked and followed advice due to their trust in the VH and asked and followed advice equally often in both conditions. Importantly, significant differences were observed in the participants response times in both studies. In study 3 during the HCL condition participants followed advice quicker. The order in which the conditions were presented influenced the experience of CL. Participants experienced higher levels of CL and responded to advice significantly faster when low cognitive load (LCL) was presented as the first condition compared with LCL as the second condition. In study 4 participants in the NEA condition followed advice slower similar to the findings of study 3. The order in which the conditions were presented had a significant effect on the EA. Participants asked and followed advice less when the NEA condition was presented first compared with when it is presented second. Possible explanations for the findings are discussed in the thesis.
Overall, this thesis offers a novel tool for trust measurement (the virtual maze paradigm) and contributes to understanding the role of psychological factors in trust towards virtual humans in virtual reality.
Biofabrication technologies must address numerous parameters and conditions to reconstruct tissue complexity in vitro. A critical challenge is vascularization, especially for large constructs exceeding diffusion limits. This requires the creation of artificial vascular structures, a task demanding the convergence and integration of multiple engineering approaches. This doctoral dissertation aims to achieve two primary objectives: firstly, to implement and refine engineering methods for creating artificial microvascular structures using Melt Electrowriting (MEW)-assisted sacrificial templating, and secondly, to deepen the understanding of the critical factors influencing the printability of bioink formulations in 3D extrusion bioprinting.
In the first part of this dissertation, two innovative sacrificial templating techniques using MEW are explored. Utilizing a carbohydrate glass as a fugitive material, a pioneering advancement in the processing of sugars with MEW with a resolution under 100 microns was made. Furthermore, by introducing the “print-and-fuse” strategy as a groundbreaking method, biomimetic branching microchannels embedded in hydrogel matrices were fabricated, which can then be endothelialized to mirror in vivo vascular conditions.
The second part of the dissertation explores extrusion bioprinting. By introducing a simple binary bioink formulation, the correlation between physical properties and printability was showcased. In the next step, employing state-of-the-art machine-learning approaches revealed a deeper understanding of the correlations between bioink properties and printability in an extended library of hydrogel formulations.
This dissertation offers in-depth insights into two key biofabrication technologies. Future work could merge these into hybrid methods for the fabrication of vascularized constructs, combining MEW's precision with fine-tuned bioink properties in automated extrusion bioprinting.
Biological systems are in dynamic interaction. Many responses reside in the core concepts of biological systems interplay (competition and cooperation). In infection situation, the competition between a bacterial system and a host is shaped by many stressors at spatial and temporal determinants. Reactive chemical species are universal stressors against all biological systems since they potentially damage the basic requirements of these systems (nucleic acids, proteins, carbohydrates, and lipids). Either produced endogenously or exogenously, reactive chemical species affect the survival of pathogens including the gram-positive
Staphylococcus aureus (S. aureus). Therefore, bacteria developed strategies to overcome the toxicity of reactive species.
S. aureus is a widely found opportunistic pathogen. In its niche, S. aureus is in permanent contact with surrounding microbes and host factors. Deciphering the deterministic factors
in these interactions could facilitate pinpointing novel bacterial targets. Identifying
the aforementioned targets is crucial to develop new strategies not only to kill the pathogenic organisms but also to enhance the normal flora to minimize the pathogenicity and virulence of potential pathogens. Moreover, targeting S. aureus stress response can be used
to overcome bacterial resistance against host-derived factors. In this study, I identify a novel
S. aureus stress response factor against reactive electrophilic, oxygen, and hypochlorite species to better understand its resilience as a pathogen.
Although bacterial stress response is an active research field, gene function is a current bottleneck in characterizing the understudied bacterial strategies to mediate stress conditions. I aimed at understanding the function of a novel protein family integrated
in many defense systems of several biological systems.
In bacteria, fungi, and plants, old yellow enzymes (OYEs) are widely found. Since the first isolation of the yellow flavoprotein, OYEs are used as biocatalysts for decades to reduce activated C=C bonds in α,β-unsaturated carbonyl compounds. The promiscuity
of the enzymatic catalysis is advantageous for industrial applications.
However, the physiological function of OYEs, especially in bacteria, is still puzzling.
Moreover, the relevance of the OYEs in infection conditions remained enigmatic.
Here, I show that there are two groups of OYEs (OYE flavin oxidoreductase, OfrA and OfrB) that are encoded in staphylococci and some firmicutes. OfrA (SAUSA300_0859) is more conserved than OfrB (SAUSA300_0322) in staphylococci and is a part of the staphylococcal core genome.
A reporter system was established to report for ofrA in S. aureus background.
The results showed that ofrA is induced under electrophilic, oxidative, and hypochlorite stress. OfrA protects S. aureus against quinone, methylglyoxal, hydrogen peroxide,
and hypochlorite stress. Additionally, the results provide evidence that OfrA supports
thiol-dependent redox homeostasis. At the host-pathogen interface, OfrA promotes S. aureus fitness in murine macrophage cell line. In whole human blood, OfrA is involved in S. aureus survival indicating a potential clinical relevance to bacteraemia.
In addition, ofrA mutation affects the production of the virulence factor staphyloxanthin via the upper mevalonate pathway. In summary, decoding OfrA function and its proposed mechanism of action in S. aureus shed the light on a conserved stress response within multiple organisms.
Plasmonic nanostructures are considered promising candidates for essential components of integrated quantum technologies because of their ability to efficiently localize broad-band electromagnetic fields on the nanoscale. The resulting local near field can be understood as a spatial superposition of spectrally different plasmon-polariton modes due to the spectrally broad optical excitation, and thus can be described as a classical wave packet. Since plasmon polaritons, in turn, can transmit and receive non-classical light states, the exciting question arises to what extent they have to be described as quantum mechanical wave packets, i.e. as a superposition of different quantum states.
But how to probe, characterize and eventually manipulate the quantum state of such plasmon polaritons? Up to now, probing at room temperatures relied completely on analyzing quantum optical properties of the corresponding in-going and out-going far-field photon modes. However, these methods so far only allow a rather indirect investigation of the plasmon-polariton quantum state by means of transfer into photons. Moreover, these indirect methods lack spatial resolution and therefore do not provide on-site access to the plasmon-polariton quantum state. However, since the spectroscopic method of coherent two-dimensional (2D) nanoscopy offers the capability to follow the plasmon-
polariton quantum state both in Hilbert space and in space and time domain a complete characterization of the plasmon polariton is possible.
In this thesis a versatile coherent 2D nanoscopy setup is presented combining spectral tunability and femtosecond time resolution with spatial resolution on the nanometer scale due to the detection of optically excited nonlinear emitted electrons via photoemission electron microscopy (PEEM). Optical excitation by amplitude- and phase-shaped, systematically-modified and interferometric-stable multipulse sequences is realized, and characterized via Fourier-transform spectral interferometry (FTSI). This linear technique enables efficient data acquisition in parallel to a simultaneously performed experiment. The full electric-field reconstruction of every generated multipulse sequence is used to analyze the effect of non-ideal pulse sequences on the two-dimensional spectral data of population-based multidimensional spectroscopy methods like, e.g., the coherent 2D nanoscopy applied in this thesis. Investigation of the spatially-resolved nonlinear electron emission yield from plasmonic gold nanoresonators by coherent 2D nanoscopy requires a quasi-particle treatment of the addressed plasmon-polariton mode and development of a quantum model to adequately describe the plasmon-assisted multi-quantum electron emission from nanostructures. Good agreement between simulated and experimental data enables to connect certain spectral features to superpositions of non-adjacent plasmon-polariton quantum states, i.e, non-adjacent occupation-number states of the underlying quantized, harmonic oscillator, thus direct probing of the plasmon-polariton quantum wave packet at the location of the nanostructure.
This is a necessary step to locally control and manipulate the plasmon-polariton quantum state and thus of general interest for the realization of nanoscale quantum optical devices.
In aqueous environment, hydrophobic interactions play an important role for DNA. The introduction of modifications based on hydrophobic aromatic moieties offers additional ways for controlling recognition and reactivity of functional groups in DNA. Modifications are introduced through an artificial backbone or in the form of an extension of the nucleobases, resulting in additional properties of the DNA.
This dissertation focuses on the use of hydrophobic units for the functionalization of DNA.
In the first part of the work, the tolane (i. e. diphenylacetylene) motif was used in combination with the acyclic backbone of GNA and BuNA to generate recognition units in the DNA context. Fluorination of the aromatic rings in the tolane moiety provided the basis for a supramolecular language based on arene-fluoroarene interactions. The specific recognition was investigated by thermodynamic, kinetic and NMR spectroscopic methods.
In the second part of the work, deoxyuridine derivatives with a hydrophobic aromatic modification were prepared and incorporated into DNA duplexes. The irradiation with UV light led to a [2+2] cycloaddition reaction between two modified nucleosides in the DNA. This reaction product was structurally characterized and the reaction was used in various biochemical and nanotechnological DNA applications.
The slowly activating vacuolar SV/TPC1 channel is ubiquitously expressed in plants and provides a large cation conductance in the vacuolar membrane. Thereby, monovalent (K+, Na+) and in principle also divalent cations, such as Ca2+, can pass through the channel. The SV/TPC1 channel is activated upon membrane depolarization and cytosolic Ca2+ but inhibited by luminal calcium. With respect to the latter, two luminal Ca2+ binding sites (site 1 Asp240/Asp454/Glu528, site 2 Glu239/Asp240/Glu457) were identified to coordinate luminal Ca2+. In this work, the characteristics of the SV/TPC1 channels in terms of regulation and function were further elucidated, focusing on the TPC1s of Arabidopsis thaliana and Vicia faba. For electrophysiological analysis of the role of distinct pore residues for channel gating and luminal Ca2+ sensing, TPC1 channel variants were generated by site-directed mutagenesis and transiently expressed as eGFP/eYFP-fusion constructs in Arabidopsis thaliana mesophyll protoplasts of the TPC1 loss-of-function mutant attpc1-2.
1. As visualized by confocal fluorescence laser-scanning microscopy, all AtTPC1 (WT, E605A/Q, D606N, D607N, E605A/D606N, E605Q/D606N/D607N, E457N/E605A/D606N) and VfTPC1 channel variants (WT, N458E/A607E/ N608D) were correctly targeted to the vacuole membrane.
2. Patch-clamp studies revealed that removal of one of the negative charges at position Glu605 or Asp606 was already sufficient to promote voltage-dependent channel activation with higher voltage sensitivity. The combined neutralization of these residues (E605A/D606N), however, was required to additionally reduce the luminal Ca2+ sensitivity of the AtTPC1 channel, leading to hyperactive AtTPC1 channels. Thus, the residues Glu605/Asp606 are functionally coupled with the voltage sensor of AtTPC1 channel, thereby modulating channel gating, and form a novel luminal Ca2+ sensing site 3 in AtTPC1 at the luminal entrance of the ion transport pathway.
3. Interestingly, this novel luminal Ca2+ sensing site 3 (Glu605/Asp606) and Glu457 from the luminal Ca2+ sensing site 2 of the luminal Ca2+-sensitive AtTPC1 channel were neutralized by either asparagine or alanine in the TPC1 channel from Vicia faba and many other Fabaceae. Moreover, the VfTPC1 was validated to be a hyperactive TPC1 channel with higher tolerance to luminal Ca2+ loads which was in contrast to the AtTPC1 channel features. As a result, VfTPC1 but not AtTPC1 conferred the hyperexcitability of vacuoles. When AtTPC1 was mutated for the three VfTPC1-homologous polymorphic site residues, the AtTPC1 triple mutant (E457N/E605A/D606N) gained VfTPC1-like characteristics. However, when VfTPC1 was mutated for the three AtTPC1-homologous polymorphic site residues, the VfTPC1 triple mutant (N458E/A607E/N608D) still sustained VfTPC1-WT-like features. These findings indicate that the hyperactivity of VfTPC1 is achieved in part by the loss of negatively charged amino acids at positions that - as part of the luminal Ca2+ sensing sites 2 and 3 – are homologous to AtTPC1-Glu457/Glu605/Asp606 and are likely stabilized by other unknown residues or domains.
4.The luminal polymorphic pore residues (Glu605/Asp606 in AtTPC1) apparently do not contribute to the unitary conductance of TPC1. Under symmetrical K+ conditions, a single channel conductance of about 80 pS was determined for AtTPC1 wild type and the AtTPC1 double mutant E605A/D606A. This is in line with the three-fold higher unitary conductance of VfTPC1 (232 pS), which harbors neutral luminal pore residues at the homologous sites to AtTPC1.
In conclusion, by studying TPC1 channel from Arabidopsis thaliana and Vicia faba, the present thesis provides evidence that the natural TPC1 channel variants exhibit differences in voltage gating, luminal Ca2+ sensitivity and luminal Ca2+ binding sites.
The RNAs of many viruses contain a frameshift stimulatory element (FSE) that grants access to an alternate reading frame via −1 programmed ribosomal frameshifting (PRF). This −1PRF is essential for effective viral replication. The −1PRF efficiency relies on the presence of conserved RNA elements within the FSE, such as a slippery sequence, spacer, and a downstream secondary structure – often a hairpin or a pseudoknot. The PRF efficiency is also affected by trans-acting factors such as proteins, miRNAs and metabolites. The interactions of these factors with the RNA and the translation machinery have not yet been completely understood. Traditional ensemble methods used previously to study these events focus on the whole population of molecular species. This results in innate averaging of the molecular behavior and a loss of heterogeneity information.
Here, we first established the experimental workflow to study the RNA structures and the effect of potential trans-acting factors using single-molecule force spectroscopy technique, optical tweezers. Additionally, to streamline the data analysis, we developed an algorithm for automatized data processing.
Next, we harnessed this knowledge to study viral RNA elements responsible for stimulation of PRF and how the presence of trans-acting factors affects the RNA behavior. We further complemented these single-molecule structural data with ensemble functional assays to gain a complex view on the dynamics behind the programmed ribosomal frameshifting.
Specifically, two different viral RNA elements have been studied in the presented work. First, the dynamics of SARS-CoV-2 FSE and the role of extended sequences have been explored. Then, the mode of action of the host-encoded trans-acting factor ZAP-S inhibition of SARS-CoV-2 PRF has been examined. Finally, the mechanism of the trans-acting viral factor induced PRF in Encephalomyocarditis virus (EMCV) has been uncovered.
Western societies are steadily becoming older undergoing a clear trend of delayed parenthood. Children of older fathers have an undeniably higher risk for certain neurodevelopmental disorders and other medical conditions. Changes in the epigenetic landscape and especially in DNA methylation patterns are likely to account for a portion of this inherited disease susceptibility. DNA methylation changes during the ageing process are a well-known epigenetic feature. These so-called age-DMRs exist in developmentally important genes in the methylome of several mammalian species. However, there is only a minor overlap between the age-DMR datasets of different studies. We therefore replicated age-DMRs (which were obtained from a genome wide technique) by applying a different technical approach in a larger sample number. Here, this study confirmed 10 age-DMRs in the human and 4 in the bovine sperm epigenome from a preliminary candidate list based on RRBS. For this purpose, we used bisulphite Pyrosequencing in 94 human and 36 bovine sperm samples. These Pyrosequencing results confirm RRBS as an effective and reliable method to screen for age-DMRs in the vertebrate genome. To decipher whether paternal age effects are an evolutionary conserved feature of mammalian development, we compared methylation patterns between human and bovine sperm in orthologous regulatory regions. We discovered that the level of methylation and the age effect are both species-specific and speculate that these methylation marks reflect the lineage-specific development of each species to hit evolutionary requirements and adaptation processes. Different methylation levels between species in developmentally important genes also imply a differing mutational burden, representing a potential driver for point mutations and consequently deviations in the underlying DNA sequence of different species. Using the example of different haplotypes, this study showed the great effect of single base variations on the methylation of adjacent CpGs. Nonetheless, this study could not provide further evidence or a mechanism for the transfer of epigenetic marks to future generations. Therefore, further research in tissues from the progeny of old and young fathers is required to determine if the observed methylation changes are transmitted to the next generation and if they are associated with altered transcriptional activity of the respective genes. This could provide a direct link between the methylome of sperm from elderly fathers and the development potential of the next generation.
Ischemia-reperfusion injury (I/R injury) is a common complication in ischemic stroke (IS) treatment, which is characterized by a paradoxical perpetuation of tissue damage despite the successful re-establishment of vascular perfusion. This phenomenon is known to be facilitated by the detrimental interplay of platelets and inflammatory cells at the vascular interface. However, the spatio-temporal and molecular mechanisms underlying these cellular interactions and their contribution to infarct progression are still incompletely understood. Therefore, this study intended to clarify the temporal mechanisms of infarct growth after cerebral vessel recanalization. The data presented here could show that infarct progression is driven by early blood-brain-barrier perturbation and is independent of secondary thrombus formation. Since previous studies unravelled the secretion of platelet granules as a molecular mechanism of how platelets contribute to I/R injury, special emphasis was placed on the role of platelet granule secretion in the process of barrier dysfunction. By combining an in vitro approach with a murine IS model, it could be shown that platelet α-granules exerted endothelial-damaging properties, whereas their absence (NBEAL2-deficiency) translated into improved microvascular integrity. Hence, targeting platelet α-granules might serve as a novel treatment option to reduce vascular integrity loss and diminish infarct growth despite recanalization.
Recent evidence revealed that pathomechanisms underlying I/R injury are already instrumental during large vessel occlusion. This indicates that penumbral tissue loss under occlusion and I/R injury during reperfusion share an intertwined relationship. In accordance with this notion, human observational data disclosed the presence of a neutrophil dominated immune response and local platelet activation and secretion, by the detection of the main components of platelet α-granules, within the secluded vasculature of IS patients. These initial observations of immune cells and platelets could be further expanded within this thesis by flow cytometric analysis of local ischemic blood samples. Phenotyping of immune cells disclosed a yet unknown shift in the lymphocyte population towards CD4+ T cells and additionally corroborated the concept of an immediate intravascular immune response that is dominated by granulocytes. Furthermore, this thesis provides first-time evidence for the increased appearance of platelet-leukocyte-aggregates within the secluded human vasculature. Thus, interfering with immune cells and/or platelets already under occlusion might serve as a potential strategy to diminish infarct expansion and ameliorate clinical outcome after IS.
Within this thesis, three main approaches for the assessment and investigation of altered hemodynamics like wall shear stress, oscillatory shear index and the arterial pulse wave velocity in atherosclerosis development and progression were conducted:
1. The establishment of a fast method for the simultaneous assessment of 3D WSS and PWV in the complete murine aortic arch via high-resolution 4D-flow MRI
2. The utilization of serial in vivo measurements in atherosclerotic mouse models using high-resolution 4D-flow MRI, which were divided into studies describing altered hemodynamics in late and early atherosclerosis
3. The development of tissue-engineered artery models for the controllable application and variation of hemodynamic and biologic parameters, divided in native artery models and biofabricated artery models, aiming for the investigation of the relationship between atherogenesis and hemodynamics
Chapter 2 describes the establishment of a method for the simultaneous measurement of 3D WSS and PWV in the murine aortic arch at, using ultra high-field MRI at 17.6T [16], based on the previously published method for fast, self-navigated wall shear stress measurements in the murine aortic arch using radial 4D-phase contrast MRI at 17.6 T [4]. This work is based on the collective work of Dr. Patrick Winter, who developed the method and the author of this thesis, Kristina Andelovic, who performed the experiments and statistical analyses. As the method described in this chapter is basis for the following in vivo studies and undividable into the sub-parts of the contributors without losing important information, this chapter was not split into the single parts to provide fundamental information about the measurement and analysis methods and therefore better understandability for the following studies. The main challenge in this chapter was to overcome the issue of the need for a high spatial resolution to determine the velocity gradients at the vascular wall for the WSS quantification and a high temporal resolution for the assessment of the PWV without prolonging the acquisition time due to the need for two separate measurements. Moreover, for a full coverage of the hemodynamics in the murine aortic arch, a 3D measurement is needed, which was achieved by utilization of retrospective navigation and radial trajectories, enabling a highly flexible reconstruction framework to either reconstruct images at lower spatial resolution and higher frame rates for the acquisition of the PWV or higher spatial resolution and lower frame rates for the acquisition of the 3D WSS in a reasonable measurement time of only 35 minutes. This enabled the in vivo assessment of all relevant hemodynamic parameters related to atherosclerosis development and progression in one experimental session. This method was validated in healthy wild type and atherosclerotic Apoe-/- mice, indicating no differences in robustness between pathological and healthy mice.
The heterogeneous distribution of plaque development and arterial stiffening in atherosclerosis [10, 12], however, points out the importance of local PWV measurements. Therefore, future studies should focus on the 3D acquisition of the local PWV in the murine aortic arch based on the presented method, in order to enable spatially resolved correlations of local arterial stiffness with other hemodynamic parameters and plaque composition.
In Chapter 3, the previously established methods were used for the investigation of changing aortic hemodynamics during ageing and atherosclerosis in healthy wild type and atherosclerotic Apoe-/- mice using the previously established methods [4, 16] based on high-resolution 4D-flow MRI. In this work, serial measurements of healthy and atherosclerotic mice were conducted to track all changes in hemodynamics in the complete aortic arch over time. Moreover, spatially resolved 2D projection maps of WSS and OSI of the complete aortic arch were generated. This important feature allowed for the pixel-wise statistical analysis of inter- and intragroup hemodynamic changes over time and most importantly – at a glance. The study revealed converse differences of local hemodynamic profiles in healthy WT and atherosclerotic Apoe−/− mice, with decreasing longWSS and increasing OSI, while showing constant PWV in healthy mice and increasing longWSS and decreasing OSI, while showing increased PWV in diseased mice. Moreover, spatially resolved correlations between WSS, PWV, plaque and vessel wall characteristics were enabled, giving detailed insights into coherences between hemodynamics and plaque composition. Here, the circWSS was identified as a potential marker of plaque size and composition in advanced atherosclerosis. Moreover, correlations with PWV values identified the maximum radStrain could serve as a potential marker for vascular elasticity. This study demonstrated the feasibility and utility of high-resolution 4D flow MRI to spatially resolve, visualize and analyze statistical differences in all relevant hemodynamic parameters over time and between healthy and diseased mice, which could significantly improve our understanding of plaque progression towards vulnerability. In future studies the relation of vascular elasticity and radial strain should be further investigated and validated with local PWV measurements and CFD.
Moreover, the 2D histological datasets were not reflecting the 3D properties and regional characteristics of the atherosclerotic plaques. Therefore, future studies will include 3D plaque volume and composition analysis like morphological measurements with MRI or light-sheet microscopy to further improve the analysis of the relationship between hemodynamics and atherosclerosis.
Chapter 4 aimed at the description and investigation of hemodynamics in early stages of atherosclerosis. Moreover, this study included measurements of hemodynamics at baseline levels in healthy WT and atherosclerotic mouse models. Due to the lack of hemodynamic-related studies in Ldlr-/- mice, which are the most used mouse models in atherosclerosis research together with the Apoe-/- mouse model, this model was included in this study to describe changing hemodynamics in the aortic arch at baseline levels and during early atherosclerosis development and progression for the first time. In this study, distinct differences in aortic geometries of these mouse models at baseline levels were described for the first time, which result in significantly different flow- and WSS profiles in the Ldlr-/- mouse model. Further basal characterization of different parameters revealed only characteristic differences in lipid profiles, proving that the geometry is highly influencing the local WSS in these models. Most interestingly, calculation of the atherogenic index of plasma revealed a significantly higher risk in Ldlr-/- mice with ongoing atherosclerosis development, but significantly greater plaque areas in the aortic arch of Apoe-/- mice. Due to the given basal WSS and OSI profile in these two mouse models – two parameters highly influencing plaque development and progression – there is evidence that the regional plaque development differs between these mouse models during very early atherogenesis.
Therefore, future studies should focus on the spatiotemporal evaluation of plaque development and composition in the three defined aortic regions using morphological measurements with MRI or 3D histological analyses like LSFM. Moreover, this study offers an excellent basis for future studies incorporating CFD simulations, analyzing the different measured parameter combinations (e.g., aortic geometry of the Ldlr-/- mouse with the lipid profile of the Apoe-/- mouse), simulating the resulting plaque development and composition. This could help to understand the complex interplay between altered hemodynamics, serum lipids and atherosclerosis and significantly improve our basic understanding of key factors initiating atherosclerosis development.
Chapter 5 describes the establishment of a tissue-engineered artery model, which is based on native, decellularized porcine carotid artery scaffolds, cultured in a MRI-suitable bioreactor-system [23] for the investigation of hemodynamic-related atherosclerosis development in a controllable manner, using the previously established methods for WSS and PWV assessment [4, 16]. This in vitro artery model aimed for the reduction of animal experiments, while simultaneously offering a simplified, but completely controllable physical and biological environment. For this, a very fast and gentle decellularization protocol was established in a first step, which resulted in porcine carotid artery scaffolds showing complete acellularity while maintaining the extracellular matrix composition, overall ultrastructure and mechanical strength of native arteries. Moreover, a good cellular adhesion and proliferation was achieved, which was evaluated with isolated human blood outgrowth endothelial cells. Most importantly, an MRI-suitable artery chamber was designed for the simultaneous cultivation and assessment of high-resolution 4D hemodynamics in the described artery models. Using high-resolution 4D-flow MRI, the bioreactor system was proven to be suitable to quantify the volume flow, the two components of the WSS and the radStrain as well as the PWV in artery models, with obtained values being comparable to values found in literature for in vivo measurements. Moreover, the identification of first atherosclerotic processes like intimal thickening is achievable by three-dimensional assessment of the vessel wall morphology in the in vitro models. However, one limitation is the lack of a medial smooth muscle cell layer due to the dense ECM. Here, the utilization of the laser-cutting technology for the generation of holes and / or pits on a microscale, eventually enabling seeding of the media with SMCs showed promising results in a first try and should be further investigated in future studies. Therefore, the proposed artery model possesses all relevant components for the extension to an atherosclerosis model which may pave the way towards a significant improvement of our understanding of the key mechanisms in atherogenesis.
Chapter 6 describes the development of an easy-to-prepare, low cost and fully customizable artery model based on biomaterials. Here, thermoresponsive sacrificial scaffolds, processed with the technique of MEW were used for the creation of variable, biomimetic shapes to mimic the geometric properties of the aortic arch, consisting of both, bifurcations and curvatures. After embedding the sacrificial scaffold into a gelatin-hydrogel containing SMCs, it was crosslinked with bacterial transglutaminase before dissolution and flushing of the sacrificial scaffold. The hereby generated channel was subsequently seeded with ECs, resulting in an easy-to-prepare, fast and low-cost artery model. In contrast to the native artery model, this model is therefore more variable in size and shape and offers the possibility to include smooth muscle cells from the beginning. Moreover, a custom-built and highly adaptable perfusion chamber was designed specifically for the scaffold structure, which enabled a one-step creation and simultaneously offering the possibility for dynamic cultivation of the artery models, making it an excellent basis for the development of in vitro disease test systems for e.g., flow-related atherosclerosis research. Due to time constraints, the extension to an atherosclerosis model could not be achieved within the scope of this thesis. Therefore, future studies will focus on the development and validation of an in vitro atherosclerosis model based on the proposed bi- and three-layered artery models.
In conclusion, this thesis paved the way for a fast acquisition and detailed analyses of changing hemodynamics during atherosclerosis development and progression, including spatially resolved analyses of all relevant hemodynamic parameters over time and in between different groups. Moreover, to reduce animal experiments, while gaining control over various parameters influencing atherosclerosis development, promising artery models were established, which have the potential to serve as a new platform for basic atherosclerosis research.
Drug Discovery based on Oxidative Stress and HDAC6 for Treatment of Neurodegenerative Diseases
(2024)
Most antioxidants reported so far only achieved limited success in AD clinical trials. Growing evidences suggest that merely targeting oxidative stress will not be sufficient to fight AD. While multi-target directed ligands could synergistically modulate different steps in the neurodegenerative process, offering a promising potential for treatment of this complex disease.
Fifteen target compounds have been designed by merging melatonin and ferulic acid into the cap group of a tertiary amide HDAC6 inhibitor. Compound 10b was screened as the best hybrid molecule exhibit potent HDAC6 inhibition and potent antioxidant capacity. Compound 10b also alleviated LPS-induced microglia inflammation and led to a switch from neurotoxic M1 to the neuroprotective M2 microglial phenotype. Moreover, compound 10b show pronounced attenuation of spatial working memory and long-term memory damage in an in vivo AD mouse model. Compound 10b can be a potentially effective drug candidate for treatment of AD and its druggability worth to be further studied.
We have designed ten novel neuroprotectants by hybridizing with several common antioxidants, including ferulic acid, melatonin, lipoic acid, and trolox. The trolox hybrid compound exhibited the most potent neuroprotective effects in multiple neuroprotection assays. Besides, we identified the synergistic effects between trolox and vitamin K derivative, and our trolox hybrid compound showed comparable neuroprotection with the mixture of trolox and vitamin K derivative.
We have designed and synthesized 24 quinone derivatives based on five kinds of different quinones including ubiquinone, 2,3,5-trimethyl-1,4-benzoquinone, memoquin, thymoquinone, and anthraquinone. Trimethylbenzoquinone and thymoquinone derivatives showed more potent neuroprotection than other quinones in oxytosis assay. Therefore, trimethylbenzoquinone and thymoquinone derivatives can be used as lead compounds for further mechanism study and drug discovery for treatment of neurodegenerative disease.
We designed a series of photoswitchable HDAC inhibitors, which could be effective molecular tools due to the high spatial and temporal resolution. In total 23 target compounds were synthesized and photophysicochemically characterized. Azoquinoline-based compounds possess more thermally stable cis-isomers in buffer solution, which were further tested in enzyme-based HDAC inhibition assay. However, none of those tested compounds show significant differences in activities between trans-isomers and corresponding cis-isomers.
The ongoing and evolving usage of networks presents two critical challenges for current and future networks that require attention: (1) the task of effectively managing the vast and continually increasing data traffic and (2) the need to address the substantial number of end devices resulting from the rapid adoption of the Internet of Things. Besides these challenges, there is a mandatory need for energy consumption reduction, a more efficient resource usage, and streamlined processes without losing service quality. We comprehensively address these efforts, tackling the monitoring and quality assessment of streaming applications, a leading contributor to the total Internet traffic, as well as conducting an exhaustive analysis of the network performance within a Long Range Wide Area Network (LoRaWAN), one of the rapidly emerging LPWAN solutions.
Motor neuron diseases (MNDs) encompass a variety of clinically and genetically heterogeneous disorders, which lead to the degeneration of motor neurons (MNs) and impaired motor functions. MNs coordinate and control movement by transmitting their signal to a target muscle cell. The synaptic endings of the MN axon and the contact site of the muscle cell thereby form the presynaptic and postsynaptic structures of the neuromuscular junction (NMJ). In MNDs, synaptic dysfunction and synapse elimination precede MN loss suggesting that the NMJ is an early target in the pathophysiological cascade leading to MN death. In this study, we established new experimental strategies to analyze human MNDs by patient derived induced pluripotent stem cells (iPSCs) and investigated pathophysiological mechanisms in two different MNDs.
To study human MNDs, specialized cell culture systems that enable the connection of MNs to their target muscle cells are required to allow the formation of NMJs. In the first part of this study, we established and validated a human neuromuscular co-culture system consisting of iPSC derived MNs and 3D skeletal muscle tissue derived from myoblasts. We generated 3D muscle tissue by culturing primary myoblasts in a defined extracellular matrix in self-microfabricated silicone dishes that support the 3D tissue formation. Subsequently, iPSCs from healthy donors and iPSCs from patients with the progressive MND Amyotrophic Lateral Sclerosis (ALS) were differentiated into MNs and used for 3D neuromuscular co-cultures. Using a combination of immunohistochemistry, calcium imaging, and pharmacological stimulations, we characterized and confirmed the functionality of the 3D muscle tissue and the 3D neuromuscular co-cultures. Finally, we applied this system as an in vitro model to study the pathophysiology of ALS and found a decrease in neuromuscular coupling, muscle contraction, and axonal outgrowth in co-cultures with MNs harboring ALS-linked superoxide dismutase 1 (SOD1) mutation. In summary, this co-culture system presents a human model for MNDs that can recapitulate aspects of ALS pathophysiology.
In the second part of this study, we identified an impaired unconventional protein secretion (UPS) of Sod1 as pathological mechanisms in Pleckstrin homology domain-containing family G member 5 (Plekhg5)-associated MND. Sod1 is a leaderless cytosolic protein which is secreted in an autophagy-dependent manner. We found that Plekhg5 depletion in primary MNs and NSC34 cells leads to an impaired secretion of wildtype Sod1, indicating that Plekhg5 drives the UPS of Sod1 in vitro. By interfering with different steps during the biogenesis of autophagosomes, we could show that Plekhg5-regulated Sod1 secretion is determined by autophagy. To analyze our findings in a clinically more relevant model we utilized human iPSC MNs from healthy donors and ALS patients with SOD1 mutations. We observed reduced SOD1 secretion in ALS MNs which coincides with reduced protein expression of PLEKHG5 compared to healthy and isogenic control MNs. To confirm this correlation, we depleted PLEKHG5 in control MNs and found reduced extracellular SOD1 levels, implying that SOD1 secretion depends on PLEKHG5. In summary, we found that Plekh5 regulates the UPS of Sod1 in mouse and human MNs and that Sod1 secretion occurs in an autophagy dependent manner. Our data shows an unreported mechanistic link between two MND-associated proteins.
This Ph.D. thesis has addressed several main issues in current ASSB research within four studies. Ceramic ASSBs are meant to enable the implementation of Li-metal anodes and high voltage cathode materials, which would increase energy density, power density, life time as well as safety aspects in comparison with commercially available liquid electrolyte LiBs. In this thesis, several scientific questions arising on the cathode side of ASSBs have been focused on. With respect to the target system of a ternary composite bulk cathode consisting of ceramic active material, ceramic SSE and an electrically conductive component, studies about the thermal stabilities of these components and their impact on the electrochemical performance have been conducted. Particulate bulk cathode composites have to fulfil electrochemical, chemical, mechanical and structural requirements in order to compete with commercial LiBs. Particularly, the production process requires high-temperature sintering to obtain firmly bonded contacts in order to maximize the electrochemically active area, charge transfer and ionic conduction. However, interdiffusion, intermixing and decomposition of the initial components during sintering result in low-performing ASSBs so far.
These side reactions during high-temperature treatment have been investigated in order to gain a better understanding of these mechanisms and to enable a better controlling of the manufacturing process as well as to simplify the choice of material combinations. The first two parts of this thesis deal with the thermal stability of the ceramic SSE LATP in combination with various active materials and with the validation of a probable improvement of the sintering process due to liquid phase sintering of LATP by adding Li3PO4. In the third and fourth parts, the impact of interdiffusion, intermixing and decomposition on the electrochemical performance of TF-SSBs based on the active material LMO and the ceramic SSE Ga-LLZO has been investigated.
In the face of threat, animals react with a defensive reaction to avoid or reduce harm. This defensive reaction encompasses apart from behavioral changes also physiological, analgetic, and endocrine adaptations. Nonetheless, most animal studies on fear and anxiety are based on behavioral observations only, disregarding other aspects of the defensive reaction, or integrating their inter-related dynamics only insufficiently. The first part of this thesis aimed in characterizing patterned associations of behavioral and physiological responses, termed integrated defensive states. Analyzing cardiac and behavioral responses in mice undergoing multiple fear and anxiety paradigms revealed a complex and dynamic interaction of those readouts on both, short and long timescales. Microstates, stereotypical combinations of i.e. freezing and decelerating heart rates, are short-lasting and were, in turn, shown to be influenced by slow acting macrostate changes. One of those higher order macrostates, called `rigidity`, was defined as a latent process that constrains the range of momentary displayed heart rate values. Furthermore, integrated defensive states were found to be highly dependent on the cue and the context the animals are confronted with. Importantly, same behavioral observations, i.e. freezing, were associated with distinct cardiac responses, highlighting the importance of multivariate analysis of integrated defensive states. Defensive states are orchestrated by the brain, which has evolved evolutionary conserved survival circuits. A central brain area of these circuits is the periaqueductal gray (PAG) in the midbrain. It plays a pivotal role in mediating defensive states, as it receives signals about external and internal information from multiple brain regions and sends information to both, higher order brain areas as well as to the brainstem ultimately causing the execution of threat responses. In the second part of this thesis, different neuronal circuit elements in the PAG were optically manipulated in order to gain mechanistic insight into the defense network in the brain underlying the previously delineated cardio-behavioral defensive states. Optical activation of glutamatergic PAG neurons evoked heterogeneous, light-intensity dependent responses. However, a further molecular restriction of the glutamatergic neuronal population targeting only Chx10+ neurons, led to a cardio-behavioral state that resembled spontaneous freezing-bradycardia bouts.
In summary, this thesis presents a multivariate description of defensive states, which includes the complex interaction of cardiac and behavioral responses on different timescales and, furthermore, functionally dissects different excitatory and inhibitory PAG circuit elements mediating these defensive states.
Acceleration is a central aim of clinical and technical research in magnetic resonance imaging (MRI) today, with the potential to increase robustness, accessibility and patient comfort, reduce cost, and enable entirely new kinds of examinations. A key component in this endeavor is image reconstruction, as most modern approaches build on advanced signal and image processing. Here, deep learning (DL)-based methods have recently shown considerable potential, with numerous publications demonstrating benefits for MRI reconstruction. However, these methods often come at the cost of an increased risk for subtle yet critical errors. Therefore, the aim of this thesis is to advance DL-based MRI reconstruction, while ensuring high quality and fidelity with measured data. A network architecture specifically suited for this purpose is the variational network (VN). To investigate the benefits these can bring to non-Cartesian cardiac imaging, the first part presents an application of VNs, which were specifically adapted to the reconstruction of accelerated spiral acquisitions. The proposed method is compared to a segmented exam, a U-Net and a compressed sensing (CS) model using qualitative and quantitative measures. While the U-Net performed poorly, the VN as well as the CS reconstruction showed good output quality. In functional cardiac imaging, the proposed real-time method with VN reconstruction substantially accelerates examinations over the gold-standard, from over 10 to just 1 minute. Clinical parameters agreed on average.
Generally in MRI reconstruction, the assessment of image quality is complex, in particular for modern non-linear methods. Therefore, advanced techniques for precise evaluation of quality were subsequently demonstrated.
With two distinct methods, resolution and amplification or suppression of noise are quantified locally in each pixel of a reconstruction. Using these, local maps of resolution and noise in parallel imaging (GRAPPA), CS, U-Net and VN reconstructions were determined for MR images of the brain. In the tested images, GRAPPA delivers uniform and ideal resolution, but amplifies noise noticeably. The other methods adapt their behavior to image structure, where different levels of local blurring were observed at edges compared to homogeneous areas, and noise was suppressed except at edges. Overall, VNs were found to combine a number of advantageous properties, including a good trade-off between resolution and noise, fast reconstruction times, and high overall image quality and fidelity of the produced output. Therefore, this network architecture seems highly promising for MRI reconstruction.
Articular cartilage defects represent one of the most challenging clinical problem for orthopedic surgeons and cartilage damage after trauma can result in debilitating joint pain, functional impairment and in the long-term development of osteoarthritis. The lateral cartilage-cartilage integration is crucial for the long-term success and to prevent further tissue degeneration. Tissue adhesives and sealants are becoming increasingly more popular and can be a beneficial approach in fostering tissue integration, particularly in tissues like cartilage where alternative techniques, such as suturing, would instead introduce further damage. However, adhesive materials still require optimization regarding the maximization of adhesion strength on the one hand and long-term tissue integration on the other hand. In vitro models can be a valuable support in the investigation of potential candidates and their functional mechanisms. For the conducted experiments within this work, an in vitro disc/ring model obtained from porcine articular cartilage tissue was established. In addition to qualitative evaluation of regeneration, this model facilitates the implementation of biomechanical tests to quantify cartilage integration strength. Construct harvesting for histology and other evaluation methods could be standardized and is ethically less questionable compared to in vivo testing. The opportunity of cell culture technique application for the in vitro model allowed a better understanding of cartilage integration processes.
Tissue bonding requires chemical or physical interaction of the adhesive material and the substrate. Adhesive hydrogels can bind to the defect interface and simultaneously fill the gap of irregularly shaped defect voids. Fibrin gels are derived from the physiological blood-clot formation and are clinically applied for wound closure. Within this work, comparisons of different fibrin glue formulations with the commercial BioGlue® were assessed, which highlighted the need for good biocompatibility when applied on cartilage tissue in order to achieve satisfying long-term integration. Fibrin gel formulations can be adapted with regard to their long-term stability and when applied on cartilage disc/ring constructs improved integrative repair is observable. The kinetic of repairing processes was investigated in fibrin-treated cartilage composites as part of this work. After three days in vitro cultivation, deposited extracellular matrix (ECM) was obvious at the glued interface that increased further over time. Interfacial cell invasion from the surrounding native cartilage was detected from day ten of tissue culture. The ECM formation relies on molecular factors, e.g., as was shown representatively for ascorbic acid, and contributes to increasing integration strengths over time. The experiments performed with fibrin revealed that the treatment with a biocompatible adhesive that allows cartilage neosynthesis favors lateral cartilage integration in the long term. However, fibrin has limited immediate bonding strength, which is disadvantageous for use on articular cartilage that is subject to high mechanical stress. The continuing aim of this thesis was to further develop adhesive mechanisms and new adhesive hydrogels that retain the positive properties of fibrin but have an increased immediate bonding strength.
Two different photochemical approaches with the advantage of on-demand bonding were tested. Such treatment potentially eases the application for the professional user. First, an UV light induced crosslinking mechanism was transferred to fibrin glue to provide additional bonding strength. For this, the cartilage surface was functionalized with highly reactive light-sensitive diazirine groups, which allowed additional covalent bonds to the fibrin matrix and thus increased the adhesive strength. However, the disadvantages of this approach were the multi-step bonding reactions, the need for enzymatic pretreatment of the cartilage, expensive reagents, potential UV-light damage, and potential toxicity hazards. Due to the mentioned disadvantages, no further experiments, including long-term culture, were carried out. A second photosensitive approach focused on blue light induced crosslinking of fibrinogen (RuFib) via a photoinitiator molecule instead of using thrombin as a crosslinking mediator like in normal fibrin glue. The used ruthenium complex allowed inter- and intramolecular dityrosine binding of fibrinogen molecules. The advantage of this method is a one-step curing of fibrinogen via visible light that further achieved higher adhesive strengths than fibrin. In contrast to diazirine functionalization of cartilage, the ruthenium complex is of less toxicological concern. However, after in vitro cultivation of the disc/ring constructs, there was a decrease in integration strength. Compared to fibrin, a reduced cartilage synthesis was observed at the defect. It is also disadvantageous that a direct adjustment of the adhesive can only be made via protein concentration, since fibrinogen is a natural protein that has a fixed number of tyrosine binding sites without chemical modification.
An additional cartilage adhesive was developed that is based on a mussel-inspired adhesive mechanism in which reactivity to a variety of substrates is enabled via free DOPA amino acids. DOPA-based adhesion is known to function in moist environments, a major advantage for application on water-rich cartilage tissue surrounded by synovial liquid. Reactive DOPA groups were synthetically attached to a polymer, here POx, to allow easy chemical modifiability, e.g. insertion of hydrolyzable ester motifs for tunable degradation. The possibility of preparing an adhesive hybrid hydrogel of POx in combination with fibrinogen led to good cell compatibility as was similarly observed with fibrin, but with increased immediate adhesive strength. Degradation could be adjusted by the amount of ester linkages on the POx and a direct influence of degradation rates on the development of integration in the in vitro model could be shown.
Hydrogels are well suited to fill defect gaps and immediate integration can be achieved via adhesive properties. The results obtained show that for the success of long-term integration, a good ability of the adhesive to take up synthesized ECM components and cells to enable regeneration is required. The degradation kinetics of the adhesive must match the remodeling process to avoid intermediate loss of integration power and to allow long-term firm adhesion to the native tissue.
Hydrogels are not only important as adhesives for smaller lesions, but also for filling large defect volumes and populating them with cells to produce tissue engineered cartilage. Many different hydrogel types suitable for cartilage synthesis are reported in the literature. A long-term stable fibrin formulation was tested in this work not only as an adhesive but also as a bulk hydrogel construct. Agarose is also a material widely used in cartilage tissue engineering that has shown good cartilage neosynthesis and was included in integration assessment. In addition, a synthetic hyaluronic acid-based hydrogel (HA SH/P(AGE/G)) was used. The disc/ring construct was adapted for such experiments and the inner lumen of the cartilage ring was filled with the respective hydrogel. In contrast to agarose, fibrin and HA-SH/P(AGE/G) gels have a crosslink mechanism that led to immediate bonding upon contact with cartilage during curing. The enhanced cartilage neosynthesis in agarose compared to the other hydrogel types resulted in improved integration during in vitro culture. This shows that for the long-term success of a treatment, remodeling of the hydrogel into functional cartilage tissue is a very high priority. In order to successfully treat larger cartilage defects with hydrogels, new materials with these properties in combination with chemical modifiability and a direct adhesion mechanism are one of the most promising approaches.
The emergence of human induced pluripotent stem cells (iPSCs) and the rise of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) gene editing technology innovated the research platform for scientists based on living human pluripotent cells. The revolutionary combination of both Nobel Prize-honored techniques enables direct disease modeling especially for research focused on genetic diseases. To allow the study on mutation-associated pathomechanisms, we established robust human in vitro systems of three inherited cardiomyopathies: arrhythmogenic cardiomyopathy (ACM), dilated cardiomyopathy with juvenile cataract (DCMJC) and dilated cardiomyopathy with ataxia (DCMA).
Sendai virus vectors encoding OCT3/4, SOX2, KLF4, and c-MYC were used to reprogram human healthy control or mutation-bearing dermal fibroblasts from patients to an embryonic state thereby allowing the robust and efficient generation of in total five transgene-free iPSC lines. The nucleofection-mediated CRISPR/Cas9 plasmid delivery in healthy control iPSCs enabled precise and efficient genome editing by mutating the respective disease genes to create isogenic mutant control iPSCs. Here, a PKP2 knock-out and a DSG2 knock-out iPSC line were established to serve as a model of ACM. Moreover, a DNAJC19 C-terminal truncated variant (DNAJC19tv) was established to mimic a splice acceptor site mutation in DNAJC19 of two patients with the potential of recapitulating DCMA-associated phenotypes. In total eight self-generated iPSC lines were assessed matching internationally defined quality control criteria. The cells retained their ability to differentiate into cells of all three germ layers in vitro and maintained a stable karyotype. All iPSC lines exhibited a typical stem cell-like morphology as well as expression of characteristic pluripotency markers with high population purities, thus validating the further usage of all iPSC lines in in vitro systems of ACM, DCMA and DCMJC.
Furthermore, cardiac-specific disease mechanisms underlying DCMA were investigated using in vitro generated iPSC-derived cardiomyocytes (iPSC-CMs). DCMA is an autosomal recessive disorder characterized by life threatening early onset cardiomyopathy associated with a metabolic syndrome. Causal mutations were identified in the DNAJC19 gene encoding an inner mitochondrial membrane (IMM) protein with a presumed function in mitochondrial biogenesis and cardiolipin (CL) remodeling. In total, two DCMA patient-derived iPSC lines (DCMAP1, DCMAP2) of siblings with discordant cardiac phenotypes, a third isogenic mutant control iPSC line (DNAJC19tv) as well as two control lines (NC6M and NC47F) were directed towards the cardiovascular lineage upon response to extracellular specification cues. The monolayer cardiac differentiation approach was successfully adapted for all five iPSC lines and optimized towards ventricular subtype identity, higher population purities and enhanced maturity states to fulfill all DCMA-specific requirements prior to phenotypic investigations. To provide a solid basis for the study of DCMA, the combination of lactate-based metabolic enrichment, magnetic-activated cell sorting, mattress-based cultivation and prolonged cultivation time was performed in an approach-dependent manner. The application of the designated strategies was sufficient to ensure adult-like characteristics, which included at least 60-day-old iPSC-CMs. Therefore, the novel human DCMA platform was established to enable the study of the pathogenesis underlying DCMA with respect to structural, morphological and functional changes.
The disease-associated protein, DNAJC19, is constituent of the TIM23 import machinery and can directly interact with PHB2, a component of the membrane bound hetero-oligomeric prohibitin ring complexes that are crucial for phospholipid and protein clustering in the IMM. DNAJC19 mutations were predicted to cause a loss of the DnaJ interaction domain, which was confirmed by loss of full-length DNAJC19 protein in all mutant cell lines. The subcellular investigation of DNAJC19 demonstrated a nuclear restriction in mutant iPSC-CMs. The loss of DNAJC19 co-localization with mitochondrial structures was accompanied by enhanced fragmentation, an overall reduction of mitochondrial mass and smaller cardiomyocytes. Ultrastructural analysis yielded decreased mitochondria sizes and abnormal cristae providing a link to defects in mitochondrial biogenesis and CL remodeling. Preliminary data on CL profiles revealed longer acyl chains and a more unsaturated acyl chain composition highlighting abnormities in the phospholipid maturation in DCMA.
However, the assessment of mitochondrial function in iPSCs and dermal fibroblasts revealed an overall higher oxygen consumption that was even more enhanced in iPSC-CMs when comparing all three mutants to healthy controls. Excess oxygen consumption rates indicated a higher electron transport chain (ETC) activity to meet cellular ATP demands that probably result from proton leakage or the decoupling of the ETC complexes provoked by abnormal CL embedding in the IMM.
Moreover, in particular iPSC-CMs presented increased extracellular acidification rates that indicated a shift towards the utilization of other substrates than fatty acids, such as glucose, pyruvate or glutamine. The examination of metabolic features via double radioactive tracer uptakes (18F-FDG, 125I-BMIPP) displayed significantly decreased fatty acid uptake in all mutants that was accompanied by increased glucose uptake in one patient cell line only, underlining a highly dynamic preference of substrates between mutant iPSC-CMs.
To connect molecular changes directly to physiological processes, insights on calcium kinetics, contractility and arrhythmic potential were assessed and unraveled significantly increased beating frequencies, elevated diastolic calcium concentrations and a shared trend towards reduced cell shortenings in all mutant cell lines basally and upon isoproterenol stimulation. Extended speed of recovery was seen in all mutant iPSC-CMs but most striking in one patient-derived iPSC-CM model, that additionally showed significantly prolonged relaxation times. The investigations of calcium transient shapes pointed towards enhanced arrhythmic features in mutant cells comprised by both the occurrence of DADs/EADs and fibrillation-like events with discordant preferences.
Taken together, new insights into a novel in vitro model system of DCMA were gained to study a genetically determined cardiomyopathy in a patient-specific manner upon incorporation of an isogenic mutant control. Based on our results, we suggest that loss of full-length DNAJC19 impedes PHB2-complex stabilization within the IMM, thus hindering PHB-rings from building IMM-specific phospholipid clusters. These clusters are essential to enable normal CL remodeling during cristae morphogenesis. Disturbed cristae and mitochondrial fragmentation were observed and refer to an essential role of DNAJC19 in mitochondrial morphogenesis and biogenesis. Alterations in mitochondrial morphology are generally linked to reduced ATP yields and aberrant reactive oxygen species production thereby having fundamental downstream effects on the cardiomyocytes` functionality. DCMA-associated cellular dysfunctions were in particular manifested in excess oxygen consumption, altered substrate utilization and abnormal calcium kinetics. The summarized data highlight the usage of human iPSC-derived CMs as a powerful tool to recapitulate DCMA-associated phenotypes that offers an unique potential to identify therapeutic strategies in order to reverse the pathological process and to pave the way towards clinical applications for a personalized therapy of DCMA in the future.
In the initiation phase of acute graft-versus-host disease (aGvHD), CD4+ T cells are activated by hematopoietic antigen presenting cells in secondary lymphoid organs whereas in effector phase by non-hematopoietic cells in the small intestine. We hypothesized that alloreactive CD4+ T cells primarily home to the secondary lymphoid organs subsequent to allogeneic hematopoietic cell transplantation in the initiation phase of aGvHD and are activated by the non-hematopoietic lymph node stromal cells via MHC class II. To test this hypothesis, we employed CD4+ T cell-dependent major mismatch aGvHD mouse model to study this correlation.
Upon analyzing the early events following allo-HCT with bioluminescence imaging, flow cytometry and whole-mount light sheet fluorescence microscopy, we found that allogeneic T cells exclusively home to the spleen, lymph nodes and the Peyer’s patches and not to the intestinal lamina propria in the initiation phase of aGvHD. Utilizing mice devoid of partial or complete hematopoietic antigen presentation we could show allogeneic CD4+ T cells activation in the lymphoid organs of MHCIIΔCD11c and MHCIIΔ BM chimeric mice early after allo-HCT. MHCIIΔ BM chimeras failure of thymic negative selection and developing tissue wasting disease upon syn-HCT deemed them unsuitable to study non-hematopoietic antigen presentation in aGvHD. To overcome this challenge, we generated MHCIIΔVav1 mice that lack MHC class II expression on all hematopoietic cells. MHCIIΔVav1 mice were susceptible to aGvHD and LNSCs from these animals activated allogeneic CD4+ T cells in mixed lymphocyte reaction. Likewise, mesenteric lymph nodes from CD11c.DTR mice surgically transplanted into a MHCIIΔ mouse could activate CD4+ T cells in vivo, clearly demonstrating LNSCs as non-hematopoietic APCs of the lymphoid organs.
We specifically target lymph node stromal cell subsets via the Cre/loxP system, we employed single cell RNA sequencing and selected Ccl19 and VE-Cadherin to specifically target the fibroblastic reticular cells and endothelial cells of the lymph nodes respectively. In MHCIIΔCcl19 mice, alloreactive CD4+ T cells activation was discreetly reduced in the initiation phase of aGvHD whereas absence of MHCII on fibroblastic reticular cells resulted in hyper-activation of allogeneic CD4+ T cells leading to poor survival. This phenotype was modulated by the regulatory T cells that were able to rescue H2-Ab1fl mice but not the MHCIIΔCcl19 subsequent to GvHD.
Knock-out of MHCII on endothelial cells MHCIIΔVE Cadherin, resulted only in modest reduction of CD4+ T cells activation in the initiation phase of GvHD, conversely MHCIIΔVE Cadherin mice showed a protective phenotype compared against littermates H2-Ab1fl mice in long-term survival. Furthermore, to pin-point endothelial cells MHCII antigen presentation we generated MHCIIΔVE Cadherin ΔVav1 animals devoid of antigen presentation in both endothelial and hematopoietic compartments. LNSCs from MHCIIΔVE Cadherin ΔVav1 were unable to activate alloreactive CD4+ T cells in mixed lymphocyte reaction.
Altogether, we demonstrate for the first time that MHC class II on the lymph node stromal cells plays a crucial role in the modulation of allogeneic CD4+ T cells in the initiation and later in the effector phase of graft-versus-host-disease.
This thesis aimed at searching for new effective agents against Multidrug-Resistant Enterobacteriaceae. This is necessitated by the urgent need for new and innovative antibacterial agents addressing the critical priority pathogens prescribed by the World Health Organization (WHO). Among the available means for antibiotics discovery and development, nature has long remained a proven, innovative, and highly reliable gateway to successful antibacterial agents. Nevertheless, numerous challenges surrounding this valuable source of antibiotics among other drugs are limiting the complete realization of its potential. These include the availability of good quality data on the highly potential natural sources, limitations in methods to prepare and screen crude extracts, bottlenecks in reproducing biological potentials observed in natural sources, as well as hurdles in isolation, purification, and characterization of natural compounds with diverse structural complexities.
Through an extensive review of the literature, it was possible to prepare libraries of plant species and phytochemicals with reported high potentials against Escherichia coli and Klebsiella pneumnoniae. The libraries were profiled to highlight the existing patterns and relationships between the reported antibacterial activities and studied plants’ families and parts, the type of the extracting solvent, as well as phytochemicals’ classes, drug-likeness and selected parameters for enhanced accumulation within the Gram-negative bacteria. In addition, motivations, objectives, the role of traditional practices and other crucial experimental aspects in the screening of plant extracts for antibacterial activities were identified and discussed.
Based on the implemented strict inclusion criteria, the created libraries grant speedy access to well-evaluated plant species and phytochemicals with potential antibacterial activities. This way, further studies in yet unexplored directions can be pursued from the indicated or related species and compounds. Moreover, the availability of compound libraries focusing on related bacterial species serves a great role in the ongoing efforts to develop the rules of antibiotics penetrability and accumulation, particularly among Gram-negative bacteria. Here, in addition to hunting for potential scaffolds from such libraries, detailed evaluations of large pool compounds with related antibacterial potential can grant a better understanding of structural features crucial for their penetration and accumulation. Based on the scarcity of compounds with broad structural diversity and activity against Gram-negative bacteria, the creation and updating of such libraries remain a laborious but important undertaking.
A Pressurized Microwave Assisted Extraction (PMAE) method over a short duration and low-temperature conditions was developed and compared to the conventional cold maceration over a prolonged duration. This method aimed at addressing the key challenges associated with conventional extraction methods which require long extraction durations, and use more energy and solvents, in addition to larger quantities of plant materials. Furthermore, the method was intended to replace the common use of high temperatures in most of the current MAE applications. Interestingly, the yields of 16 of 18 plant samples under PMAE over 30 minutes were found to be within 91–139% of those obtained from the 24h extraction by maceration. Additionally, different levels of selectivity were observed upon an analytical comparison of the extracts obtained from the two methods. Although each method indicated selective extraction of higher quantities or additional types of certain phytochemicals, a slightly larger number of additional compounds were observed under maceration. The use of this method allows efficient extraction of a large number of samples while sparing heat-sensitive compounds and minimizing chances for cross-reactions between phytochemicals.
Moreover, findings from another investigation highlighted the low likelihood of reproducing antibacterial activities previously reported among various plant species, identified the key drivers of poor reproducibility, and proposed possible measures to mitigate the challenge. The majority of extracts showed no activities up to the highest tested concentration of 1024 µg/mL. In the case of identical plant species, some activities were observed only in 15% of the extracts, in which the Minimum Inhibitory Concentrations (MICs) were 4 – 16-fold higher than those in previous reports. Evaluation of related plant species indicated better outcomes, whereby about 18% of the extracts showed activities in a range of 128–512 μg/mL, some of the activities being superior to those previously reported in related species.
Furthermore, solubilizing plant crude extracts during the preparation of test solutions for Antibacterial Susceptibility Testing (AST) assays was outlined as a key challenge. In trying to address this challenge, some studies have used bacteria-toxic solvents or generally unacceptable concentrations of common solubilizing agents. Both approaches are liable to give false positive results. In line with this challenge, this study has underscored the suitability of acetone in the solubilization of crude plant extracts. Using acetone, better solubility profiles of crude plant extracts were observed compared to dimethyl sulfoxide (DMSO) at up to 10 %v/v. Based on lacking toxicity against many bacteria species at up to 25 %v/v, its use in the solubilization of poorly water-soluble extracts, particularly those from less polar solvents is advocated.
In a subsequent study, four galloylglucoses were isolated from the leaves of Paeonia officinalis L., whereby the isolation of three of them from this source was reported for the first time. The isolation and characterization of these compounds were driven by the crucial need to continually fill the pre-clinical antibiotics pipeline using all available means. Application of the bioautography-guided isolation and a matrix of extractive, chromatographic, spectroscopic, and spectrometric techniques enabled the isolation of the compounds at high purity levels and the ascertainment of their chemical structures.
Further, the compounds exhibited the Minimum Inhibitory Concentrations (MIC) in a range of 2–256 µg/mL against Multidrug-Resistant (MDR) strains of E. coli and K. pneumonia exhibiting diverse MDR phenotypes. In that, the antibacterial activities of three of the isolated compounds were reported for the first time. The observed in vitro activities of the compounds resonated with their in vivo potentials as determined using the Galleria mellonella larvae model. Additionally, the susceptibility of the MDR bacteria to the galloylglucoses was noted to vary depending on the nature of the resistance enzymes expressed by the MDR bacteria. In that, the bacteria expressing enzymes with higher content of aromatic amino acids and zero or positive net charges were generally more susceptible. Following these findings, a plausible hypothesis for the observed patterns was put forward.
The generally challenging pharmacokinetic properties of galloylglucoses limit their further development into therapeutic agents. However, the compounds can replace or reduce the use of antibiotics in livestock keeping as well as in the treatment of septic wounds and topical or oral cavity infections, among other potential uses.
Using nature-inspired approaches, a series of glucovanillin derivatives were prepared following feasible synthetic pathways which in most cases ensured good yields and high purity levels. Some of the prepared compounds showed MIC values in a range of 128 – 512 μg/mL against susceptible and MDR strains of Klebsiella pneumoniae, Methicillin-Resistant Staphylococcus aureus (MRSA) and Vancomycin-Resistant Enterococcus faecium (VRE). These findings emphasize the previously reported essence of small molecular size, the presence of protonatable amino groups and halogen atoms, as well as an amphiphilic character, as crucial features for potential antibacterial agents.
Due to the experienced limited success in the search for new antibacterial agents using purely synthetic means, pursuing semi-synthetic approaches as employed in this study are highly encouraged. This way, it is possible to explore broader chemical spaces around natural scaffolds while addressing their inherent limitations such as solubility, toxicity, and poor pharmacokinetic profiles.
The recent pandemic has reminded the public that basic research in virology is pivotal for human health. Understanding the mechanisms of successful viral replication and the role of host factors can help to combat viral infections and prevent future pandemics.
Our lab has published the first SARS-CoV-2 RNA-protein interaction atlas, laying the foundation to investigate the interplay between viral RNA and host RNA binding proteins (RBP). Based on this, my project created the largest collection of binding profiles of host and viral RBPs on SARS-CoV-2 RNA to date. This revealed the host protein SND1 as the first human RBP that specifically binds negative sense viral RNA at the 5´ end, a region associated with viral transcription initiation. The binding profile shares similarities with the viral RBP nsp9, which binds the 5´ ends of positive and negative sense SARS-CoV-2 RNA. Depletion of SND1 shows reduced levels of viral RNA revealing it as a proviral host factor. To decode the underlying molecular mechanism, I characterized the protein-protein interactions of SND1 in SARS-CoV-2 infected and uninfected cells. Infection remodels the protein interactors of SND1 from general RNA biology to membrane association and viral RNA synthesis. Upon infection, SND1 specifically interacts with nsp9, the RBP that shares the same binding region on the negative strand of SARS-CoV-2 RNA. Recent work demonstrates that nsp9 is NMPylated in vitro suggesting a functional role of nsp9 in priming of viral RNA synthesis. I was able to show that nsp9 is covalently linked to the 5´ ends of SARS-CoV-2 RNA during infection of human cells. Analysing the covalent bond of nsp9 with the viral RNA on nucleotide level shows close proximity to the initiation sites of viral RNA synthesis, suggesting that nsp9 acts as a protein-primer of SARS-CoV-2 RNA synthesis. SND1 modulates the distribution of nsp9 on the viral RNA, since depletion of SND1 results in imbalanced occupancy of nsp9 at the 5´ends of viral RNA.
This study is the first to provide evidence for the priming mechanism of SARS-CoV-2 in authentic viral replication and further reveals how this mechanism is modulated by the host RBP SND1. Detailed knowledge about priming of viral RNA synthesis can help to find targeted antivirals that could be used to fight coronaviral infections.
In this thesis, the usage of onion-like carbon (OLC) for energy storage applications was researched regarding sustainability, performance and processability. This work targets to increase the scientific understanding regarding the role of OLC in electrodes and to facilitate a large-scale production, which is the foundation for commercial application. Research was devoted to increase the knowledge in the particular field, to yield synergistic approaches and a shared value regarding sustainability and performance.
Effect of Tjap1 knock-down on blood-brain barrier properties under normal and hypoxic conditions
(2023)
Stroke is one of the leading causes of mortality and disability worldwide. The blood-brain barrier (BBB) plays an important role in maintaining brain homeostasis by tightly regulating the exchange of substances between circulating blood and brain parenchyma. BBB disruption is a common pathologic feature of stroke and traumatic brain injury. Understanding the cellular and molecular events that affect the BBB after ischaemic brain injury is important to improve patient prognosis.
We have previously shown that microRNA-212/132 is elevated in hypoxic brain microvascular endothelial cells and acts through suppressing the expression of direct microRNA-212/132 target genes with function at the BBB: claudin-1, junctional adhesion molecule 3 (Jam3) and tight-junction associated protein 1 (Tjap1). While the role of claudin-1 and Jam3 at the BBB is well known, the role of Tjap1 is still unclear. The aim of this work was therefore to characterize the role of Tjap1 in brain endothelial cells using a knock-down (KD) approach in established murine in vitro BBB models cEND and cerebEND. Tjap1 KD was established by stable transfection of a plasmid expressing shRNA against Tjap1. The successful downregulation of Tjap1 mRNA and protein was demonstrated by qPCR and Western blot. Tjap1 KD resulted in impaired barrier properties of endothelial cells as shown by lower TEER values and higher paracellular permeability. Interestingly, the Tjap1 KD cells showed lower cell viability and proliferation but migrated faster in a wound healing assay. In the tube formation assay, Tjap1 KD cell lines showed a lower angiogenic potential due to a significantly lower tube length and number as well as a lower amount of branching points in formed capillaries. Tjap1 KD cells showed changes in gene and protein expression. The TJ proteins claudin-5, Jam3 and ZO-1 were significantly increased in Tjap1 KD cell lines, while occludin was strongly decreased. In addition, efflux pump P-glycoprotein was downregulated in Tjap1 KD cells. Oxygen-glucose deprivation (OGD) is a method to mimic stroke in vitro. Brain endothelial cell lines treated with OGD showed lower barrier properties compared to cells cultured under normal condition. These effects were more severe in Tjap1 KD cells, indicating active Tjap1 involvement in the OGD response in brain microvascular endothelial cells.
We thus have shown that Tjap1 contributes to a tight barrier of the BBB, regulates cell viability and proliferation of endothelial cells, suppresses their migration and promotes new vessel formation. This means that Tjap1 function is important for mature BBB structure in health and disease.
This thesis consists of three studies investigating the influence media literacy has on political variables, cognitive variables, and learning. Adolescents from 13 years of age and young adults are included in the studies. This thesis is divided into three chapters. Study I and II are one comprehensive study, but will be presented separately for better readability. Chapter I provides the reader with background knowledge for the original studies presented in chapter II includes information about media use, different conceptualizations of media literacy and its development over the lifetime, as well as media literacy’s impact on cognitive and political variables. Additionally, current literature on the comparison of the learning outcomes of different kinds of texts (written, auditory, and audiovisual) is presented, with a differentiation between text-based information and inferences. In chapter II, the original studies are placed in the current state of research and presented in detail. In chapter III, a critical discussion of the studies is conducted, and a general model of the influence media literacy has on the investigated cognitive and political factors is presented, followed by a conclusion of the research.
The theoretical foundation of this thesis is three models of media literacy proposed by Groeben (2002, 2004), Hobbs (1997), and Potter (1998, 2016). These three models are similar in that they define media literacy as a multifactorial construct with skills that develop further in the course of life. Their ideas are integrated and developed further, leading to our own model of media literacy. It encompasses five scales: media sign literacy, distinction between reality and fiction, knowledge of media law, knowledge of media effects, and production skills. Thereupon, the assessment tool Würzburg Media Literacy Test (WMK; Würzburger Medienkompetenztest) is designed.
There is evidence that media use and media literacy influence socio-political factors. Young adults name the internet as the main source of information on political topics (see Pasek et al., 2006), and knowledge demonstrably fosters political participation (Delli Carpini & Keeter, 1996). However, the kind of participation activity regarded is important (Quintelier & Vissers, 2008), as sometimes real-life participation is supplemented by online activities (Quan-Haase & Wellman, 2002). Media literacy is the key to evaluating the quality of information from media. Whether or not a direct link between media literacy and political interest exists has, as far as I know, not yet been investigated. Several studies have shown that precursors and subcomponents of media literacy have the capacity to influence cognitive variables. For instance, children with higher media sign literacy possess better reading proficiency (Nieding et al., 2017) and are better at collecting information and drawing inferences from hypermedia and films (Diergarten et al., 2017) as compared to children with low literacy. These precursors and subcomponents are more efficient in processing medial sign systems, reducing cognitive load, and consequently, liberating cognitive capacity for other mental tasks (Sweller, 1988). Paino and Renzulli (2012) showed that highly computer-proficient adolescents exhibit better mathematics and reading abilities. Different types of media influence the learning process differently, and the learning process can be enhanced by combining these different types of media, if the material is prepared according to the research findings and Mayer’s (2002) cognitive theory of multimedia learning. Similarly, a reduction in cognitive load takes place and more resources can be invested in the learning process itself (Mayer & Moreno, 2003; Sweller, 1988). It is not easy to answer the question of whether one medium is superior for learning to another. Generally, adults learn best from written texts (e.g., Byrne & Curtis, 2000), and audiovisual and auditory texts are comparable (e.g., Hayes et al., 1986); however, there is little research regarding the comparison of the latter two.
Study I examined whether media literacy has a positive impact on interest in politics and the political self-concept. A sample of 101 13-to 20-year-olds was drawn. The control variables were intelligence, socio-economic status (SES), openness to experiences, perspective-taking, age, and sex. Additionally, an evaluation of the WMK was conducted, which indicated good construct validity and excellent overall reliability. Media literacy was positively associated with interest in politics, political self-concept, and perspective-taking but not with openness. In hierarchical regressions and path analysis, a direct influence of media literacy and openness on interest in politics could be found. Political self-concept was solely influenced by interest in politics. Although media literacy had no direct influence on political self-concept, it influenced its precursor interest in politics and was thus expected to have distal influence. The results of the first study confirm previous findings (e.g., Vecchione & Caprara, 2009), where political self-concept is regarded as a precursor of political participation. In conclusion, the findings of study I suggested that by stimulating political interest, media literacy could, mediated through political self-concept, foster political participation.
Study II (which was conducted on the same sample as study I) was concerned with the question of whether highly media-literate adolescent and young adult participants exhibit better academic skills (mathematics; reading) and academic achievement (grades) compared to less media-literate participants. Additionally, to obtain information about potential development during adolescence, a group of 50 13-year-olds was compared with a group of 51 19-year-olds in terms of their media literacy. The control variables were intelligence, SES, sex, and age. The results showed that a significant development of media literacy took place during adolescence (∆M = .17), agreeing with Potter’s (1998, 2013) development theory of media literacy. Media literacy was significantly correlated with reading skills and school grades. Regarding adults, media literacy was also significantly correlated with mathematical skills; the association was greater than that with reading skills. However, no connection with mathematical skills was found for adolescents. To control for the influence of age and intelligence, which were both associated with media literacy, hierarchical regressions and path analyses were conducted. The results revealed that media literacy had a greater impact on grades and academic abilities than intelligence. These results are in line with those obtained by Paino and Renzulli (2012).
Study III investigated whether media literacy helps young adults to better learn from three kinds of media, a written, an auditory, and an audio-visual text, and which medium achieves the best learning results. Three groups of 91 young adults were compared (written, auditory, and audio-visual text) in terms of their learning outcomes. These outcomes were conceptualized as directly stated information in the text (assessed by text-based questions) and inferential learning (inference questions). A computer-based short version of the WMK was applied to assess media literacy, which should be optimized in the future. The control variables were intelligence, verbal ability, media usage, prior knowledge, and SES. In hierarchical regression, media literacy turned out to be a significant predictor of text inferences, even when other relevant variables, such as intelligence, were controlled for. Inferences foster the building of the situation model, which is believed by many authors to be true comprehension of a text (Zwaan & Radvansky, 1998). The outcomes of study III support Ohler’s (1994) assumption that media literacy fosters the creation of a more elaborated situational model. Text-based questions were only influenced by prior knowledge. As assumed by Potter (1998, 2016), the media literacy of young adults in the Western world suffices to extract relevant facts from educational learning material. Both subjects were best in the written text condition for text-based and inference question results. Audiovisual and auditory texts showed no significant differences. The written text condition did not excel in the auditory text condition for inferences. The results accord with those obtained by, for instance, Byrne and Curtis (2000).
Taken together, these studies show that media literacy can influence several cognitive and political variables. It stimulates political interest, reading comprehension, school grades, and mathematical abilities in young adults, as well as drawing inferences from different kinds of texts. Additionally, media literacy develops further during adolescence.
Permafrost degradation is observed all over the world as a consequence of climate change and the associated Arctic amplification, which has severe implications for the environment. Landslides, increased rates of surface deformation, rising likelihood of infrastructure damage, amplified coastal erosion rates, and the potential turnover of permafrost from a carbon sink to a carbon source are thereby exemplary implications linked to the thawing of frozen ground material. In this context, satellite earth observation is a potent tool for the identification and continuous monitoring of relevant processes and features on a cheap, long-term, spatially explicit, and operational basis as well as up to a circumpolar scale.
A total of 325 articles published in 30 different international journals during the past two decades were investigated on the basis of studied environmental foci, remote sensing platforms, sensor combinations, applied spatio-temporal resolutions, and study locations in an extensive review on past achievements, current trends, as well as future potentials and challenges of satellite earth observation for permafrost related analyses. The development of analysed environmental subjects, utilized sensors and platforms, and the number of annually published articles over time are addressed in detail. Studies linked to atmospheric features and processes, such as the release of greenhouse gas emissions, appear to be strongly under-represented. Investigations on the spatial distribution of study locations revealed distinct study clusters across the Arctic. At the same time, large sections of the continuous permafrost domain are only poorly covered and remain to be investigated in detail. A general trend towards increasing attention in satellite earth observation of permafrost and related processes and features was observed. The overall amount of published articles hereby more than doubled since the year 2015. New sources of satellite data, such as the Sentinel satellites and the Methane Remote Sensing LiDAR Mission (Merlin), as well as novel methodological approaches, such as data fusion and deep learning, will thereby likely improve our understanding of the thermal state and distribution of permafrost, and the effects of its degradation. Furthermore, cloud-based big data processing platforms (e.g. Google Earth Engine (GEE)) will further enable sophisticated and long-term analyses on increasingly larger scales and at high spatial resolutions.
In this thesis, a specific focus was put on Arctic permafrost coasts, which feature increasing vulnerability to environmental parameters, such as the thawing of frozen ground, and are therefore associated with amplified erosion rates. In particular, a novel monitoring framework for quantifying Arctic coastal erosion rates within the permafrost domain at high spatial resolution and on a circum-Arctic scale is presented within this thesis. Challenging illumination conditions and frequent cloud cover restrict the applicability of optical satellite imagery in Arctic regions. In order to overcome these limitations, Synthetic Aperture RADAR (SAR) data derived from Sentinel-1 (S1), which is largely independent from sun illumination and weather conditions, was utilized. Annual SAR composites covering the months June–September were combined with a Deep Learning (DL) framework and a Change Vector Analysis (CVA) approach to generate both a high-quality and circum-Arctic coastline product as well as a coastal change product that highlights areas of erosion and build-up. Annual composites in the form of standard deviation (sd) and median backscatter were computed and used as inputs for both the DL framework and the CVA coastal change quantification. The final DL-based coastline product covered a total of 161,600 km of Arctic coastline and featured a median accuracy of ±6.3 m to the manually digitized reference data. Annual coastal change quantification between 2017–2021 indicated erosion rates of up to 67 m per year for some areas based on 400 m coastal segments. In total, 12.24% of the investigated coastline featured an average erosion rate of 3.8 m per year, which corresponds to 17.83 km2 of annually eroded land area. Multiple quality layers associated to both products, the generated DL-coastline and the coastal change rates, are provided on a pixel basis to further assess the accuracy and applicability of the proposed data, methods, and products.
Lastly, the extracted circum-Arctic erosion rates were utilized as a basis in an experimental framework for estimating the amount of permafrost and carbon loss as a result of eroding permafrost coastlines. Information on permafrost fraction, Active Layer Thickness (ALT), soil carbon content, and surface elevation were thereby combined with the aforementioned erosion rates. While the proposed experimental framework provides a valuable outline for quantifying the volume loss of frozen ground and carbon release, extensive validation of the utilized environmental products and resulting volume loss numbers based on 200 m segments are necessary. Furthermore, data of higher spatial resolution and information of carbon content for deeper soil depths are required for more accurate estimates.
From simply ringing a bell to preparing a five-course menu, human behavior commonly causes changes in the environment. Such episodes where an agent acts, thereby causing changes in their environment constitute the sense of agency. In this thesis four series of experi-ments elucidate how the sense of agency is represented in complex action-event sequences, thereby bridging a gap between basic cognitive research and real-life practice. It builds upon extensive research on the sense of agency in unequivocal sequences consisting of single ac-tions and distinct, predominantly auditory, outcomes. Employing implicit as well as explicit measures, the scope is opened up to multi-step sequences.
The experiments show that it is worthwhile devoting more research to complex action-event sequences. With a newly introduced auditory measure (Chapter II), common phenomena such as temporal binding and a decrease in agency ratings following distorted feedback were replicated in multi-step sequences. However, diverging results between traditional implicit and explicit measures call for further inspection. Multisensory integration appears to gain more weight when multiple actions have to be performed to attain a goal leading to more accurate representations of the own actions (Chapter III). Additionally, freedom of choice (Chapter III) as well as early spatial ambiguity altered the perceived timing of outcomes, while late spatial ambi-guity (Chapter IV) and the outcome’s self-relevance did not (Chapter V). The data suggests that the cognitive system is capable of representing multi-step action-event sequences implicitly and explicitly. Actions and sensory events show a temporal attraction stemming from a bias in the perception of outcomes. Explicit knowledge about causing an event-sequence facilitates neither feelings of control nor taking authorship. The results corroborate current theorizing on the un-derpinnings of temporal binding and the divergence between traditional implicit and explicit measures of the sense of agency. Promising avenues for further research include structured analyses of how much inferred causality contributes to implicit and explicit measures of agency as well as finding alternative measures to capture conceptual as well as non-conceptual facets of the agency experience with one method.
Single-molecule dynamics at a bottleneck: a systematic study of the narrow escape problem in a disc
(2023)
Diffusion facilitates numerous reactions within the biological context of a cell. It is remarkable how the cost-efficient random process of Brownian motion promotes fast reactions. From the narrow escape theory, it is possible to determine the mean first passage time of such processes based on their reaction space and diffusion coefficient. The narrow escape theory of Brownian particles is characterized by a confining domain with reflective boundaries and a small reaction site. In this thesis, the mean first passage time was systematically tested in a disc as a function of the escape opening size in vitro and in silico. For the in vitro experiments, a model system of patterned supported-lipid bilayers (SLB) was established. Such a model is prepared by a combined colloid metalization approach, where a gold scaffold on glass facilitates assembly of SLB patches of distinct sizes through vesicle fusion. The model setup was evaluated and found to match all necessary requirements to test the nar- row escape problem in vitro. In particular, the reflectivity of the boundaries, the unhindered, free diffusion of the tracer lipids, and the distinct area were assessed. Observed results of the mean first passage time agreed with the theory of the narrow escape problem. There was excellent agreement in both absolute values and across a range of small escape opening sizes. Additionally, I developed a straightforward method, a correction factor, to calculate the mean first passage time from incomplete experimental traces. By re-scaling the mean first passage time to the fraction of particles that escaped, I was able to overcome the lifetime limitations of fluorescent probes. Previously inaccessible measurements of the mean first passage time relying on fluorescent probes will be made possible through this approach. The in vitro experiments were complemented with various in silico experiments. The latter were based on random walk simulations in discs, mimicking the in vitro situation with its uncertainties. The lifetime of single particles was either set sufficiently long to allow all particles to escape, or was adjusted to meet the lifetime limitations observed in the in vitro experiments. A comparison of the mean first passage time from lifetime-unlimited particles to the corrected, lifetime-limited particles did support the use of the correction factor. In agreement with the narrow escape theory, it was experimentally found that the mean first passage time is independent of the start point of the particle within the domain. This is when the particle adheres to a minimum distance to the escape site. In general, the presented random walk simulations do accurately represent the in vitro experiments in this study. The required hardware for the establishment of an astigmatism-based 3D system was installed in the existing microscope. The first attempts to analyze the obtained 3D imaging data gave insight into the potential of the method to investigate molecule dynamics in living trypanosome cells. The full functionality will be realized with the ongoing improvement of image analysis outside of this thesis.
Allogenic hematopoietic stem cell transplantation (allo-HCT) is a curative therapy for the treatment of malignant and non-malignant bone marrow diseases. The major complication of this treatment is a highly inflammatory reaction known as Graft-versus-Host Disease (GvHD). Cyclosporin A (CsA) and tacrolimus are used to treat GvHD which limits inflammation but also interferes with the anticipated Graft-versus-Leukemia (GvL) effect. These drugs repress conventional T cells (Tcon) along with regulatory T cells (Treg), which are important for both limiting GvHD and supporting GvL. Both of these drugs inhibit calcineurin (CN), which dephosphorylates and activates the nuclear factor of activated T-cells (NFAT) family of transcription factors. Here, we make use of our Cd4cre.Cas9+ mice and developed a highly efficient non-viral CRISPR/Cas9 gene editing method by gRNA-only nucleofection. Utilizing this technique, we demonstrated that unstimulated mouse T cells upon NFATc1 or NFATc2 ablation ameliorated GvHD in a major mismatch mouse model. However, in vitro pre-stimulated mouse T cells could not achieve long-term protection from GvHD upon NFAT single-deficiency. This highlights the necessity of gene editing and transferring unstimulated human T cells during allo-HCT. Indeed, we established a highly efficient ribonucleoprotein (RNP)-mediated CRISPR/Cas9 gene editing for NFATC1 and/or NFATC2 in pre-stimulated as well as unstimulated primary human T cells. In contrast to mouse T cells, not NFATC1 but NFATC2 deficiency in human T cells predominantly affected proinflammatory cytokine production. However, either NFAT single-knockout kept cytotoxicity of human CD3+ T cells untouched against tumor cells in vitro. Furthermore, mouse and human Treg were unaffected upon the loss of a single NFAT member. Lastly, NFATC1 or NFATC2-deficient anti-CD19 CAR T cells, generated with our non-viral ‘one-step nucleofection’ method validated our observations in mouse and human T cells. Proinflammatory cytokine production was majorly dependent on NFATC2 expression, whereas, in vitro cytotoxicity against CD19+ tumor cells was undisturbed in the absence of either of the NFAT members. Our findings emphasize that NFAT single-deficiency in donor T cells is superior to CN-inhibitors as therapy during allo-HCT to prevent GvHD while preserving GvL in patients.
The main objective of this study was to test whether subjects with different degrees of bruxism differ regarding EMG parameters and whether CES intervention affects those parameters. The hypothesis was that CES influences EMG parameters and after its’ cessation, all EMG parameters return to baseline (exposure–response relationship).
For this purpose, forty subjects were examined, 16 men and 24 women, matched for age and gender and assigned randomly in the intervention (N=20) and control group (N=20). The procedure was as follows: 1-week inactive GC (N=40), 2 weeks inactive/active GC (N=20/N=20), 2 weeks inactive GC (N=40). Each interval was followed by a surface EMG recording from eight muscle parts (right and left anterior -, medial -, and posterior masseter and right and left anterior temporalis) under force-controlled feedback (BiteFork®) with three submaximal bite forces. The resulting EMG activity is expressed as RMS % MVC and RMS at MVC. The statistics is performed with t-test, one-way rmANOVA, and Friedman rmANOVA on ranks, according to the distribution of the data. The significance level was set at p≤0.05.
The results generated from the within-groups and between-groups comparison were mostly not statistically significant and could therefore not offer clinically relevant conclu-sions.
However, it cannot be excluded that a higher submaximal bite force and an extended intervention interval would have rendered different outcomes. The insufficient study sample resulted in a low observed power which makes the findings prone to Type II er-ror. It can be concluded that this study did not find any substantiating differences be-tween the EMG values of participants with various bruxism activity and that CES could not influence the studied EMG parameters in the two weeks intervention time.
Our hypothesis which supposes that subjects with high and low bruxism activity differ in RMS % MVC could not be verified. However, with the gained knowledge, it is recom-mended to further elaborate a definite bruxism diagnosis by using portable EMG devices.
Serum half-life elongation as well as the immobilization of small proteins like cytokines is still one of the key challenges for biologics. This accounts also for cytokines, which often have a molecular weight between 5 and 40 kDa and are therefore prone to elimination by renal filtration and sinusoidal lining cells. To solve this problem biologics are often conjugated to poly(ethylene glycol) (PEG), which is the gold standard for the so called PEGylation. PEG is a synthetic, non-biodegradable polymer for increasing the hydrodynamic radius of the conjugated protein to modulate their pharmacokinetic performance and prolong their therapeutic outcome. Though the benefits of PEGylation are significant, they also come with a prize, which is a loss in bioactivity due to steric hindrance and most often the usage of heterogeneous bioconjugation chemistries. While PEG is a safe excipient in most cases, an increasing number of PEG related side-effects, such as immunological responses like hypersensitivity and accelerated blood clearance upon repetitive exposure occur, which highlights the need for PEG alternative polymers, that can replace PEG in such cases.
Another promising method to significantly prolong the residence time of biologics is to immobilize them at a desired location. To achieve this, the transglutaminase (TG) Factor XIIIa (FXIIIa), which is an important human enzyme during blood coagulation can be used. FXIIIa can recognize specific peptide sequences that contain a lysine as substrates and link them covalently to another peptide sequence, that contains a glutamine, forming an isopeptide bond. This mechanism can be used to link modified proteins, which have a N- or C-terminal incorporated signal peptide by mutation, to the extracellular matrix (ECM) of tissues.
Additionally, both above-described methods can be combined. By artificially introducing a TG recognition sequence, it is possible to attach an azide group containing peptide site-specifically to the TG, recognition sequence. This allows the creation of a site-selective reactive site at the proteins N- or C-terminus, which can then be targeted by cyclooctyne functionalized polymers, just like amber codon functionalized proteins.
This thesis has focused on the two cytokines human Interferon-α2a (IFN-α2a) and human, as well as murine Interleukin-4 (IL-4) as model proteins to investigate the above-described challenges. IFN-α2a has been chosen as a model protein because it is an approved drug since 1986 in systemic applications against some viral infections, as well as several types of cancer. Furthermore, IFN-α2 is also approved in three PEGylated forms, which have different molecular weights and use different conjugation techniques for polymer attachment. This turns it into an ideal candidate to compare new polymers against the gold standard PEG. Interleukin-4 (IL-4) has been chosen as the second model protein due to its similar size and biopotency. This allows to compare found trends from IFN-α2a with another bioconjugate platform and distinguish between IFN-α2a specific, or general trends. Furthermore, IL-4 is a promising candidate for clinical applications as it is a potent anti-inflammatory protein, which polarizes macrophages from the pro-inflammatory M1 state into the anti-inflammatory M2 state.
The chirality of the interlocked bay-arylated perylene motif is investigated upon its material prospect and the enhancement of its chiroptical response to the NIR spectral region. A considerable molecular library of inherently chiral perylene bisimides (PBIs) was utilized as acceptors in organic solar cells to provide decent device performances and insights into the structure-property relationship of PBI materials within a polymer blend. For the first time in the family of core-twisted PBIs, the effects of enantiopurity on the device performance was thoroughly investigated. The extraordinary structural sensitivity of CD spectroscopy served as crucial analytical tool to bridge the highly challenging gap between molecular properties and device analytics by proving the excitonic chirality of a helical PBI dimer. The chirality of this perylene motif could be further enhanced on a molecular level by both the expansion and the enhanced twisting of the π-scaffold to achieve a desirable strong chiroptical NIR response introducing a new family of twisted QBI-based nanoribbons. These achievements could be substantially further developed by expanding this molecular concept to a supramolecular level. The geometrically demanding supramolecular arrangement necessary for the efficient excitonic coupling was carefully encoded into the molecular design. Accordingly, the QBIs could form the first J-type aggregate constituting a fourfold-stranded superhelix of a rylene bisimide with strong excitonic chirality. Therefore, this thesis has highlighted the mutual corroboration of experimental and theoretical data from the molecular to the supramolecular level. It has demonstrated that for rylene bisimide dyes, the excitonic contribution to the overall chiroptical response can be designed and rationalized. This can help to pave the way for new organic functional materials to be used for
chiral sensing or chiral organic light-emitting devices.
In this work, dRNA-seq (differential RNA sequencing) and RNAtag-seq were applied to first define the global transcriptome architecture of C. difficile, followed by Hfq RIP-seq (RNA immunoprecipitation followed by RNA-seq) and RIL-seq (RNA interaction by ligation and sequencing) to characterize the Hfq-mediated sRNA interactome on a transcriptome-wide scale. These approaches resulted in the annotation of > 60 novel sRNAs. Notably, it not only revealed 50 Hfq-bound sRNAs, but also > 1000 mRNA-sRNA interactions, confirming Hfq as a global RNA matchmaker in C. difficile. Similar to its function in Gram-negative species, deletion of Hfq resulted in decreased sRNA half-lives, providing evidence that Hfq affects sRNA stability in C. difficile. Finally, several sRNAs and their function in various infection relevant conditions were characterized. The sRNA nc085 directly interacts with the two-component response regulator eutV, resulting in regulation of ethanolamine utilization, an abundant intestinal carbon and nitrogen source known to impact C. difficile pathogenicity. Meanwhile, SpoY and SpoX regulate translation of the master regulator of sporulation spo0A in vivo, thereby affecting sporulation initiation. Furthermore, SpoY and SpoX deletion significantly impacts C. difficile gut colonization and spore burden in a mouse model of C. difficile infection.
Forkhead box O transcription factors are a family of proteins involved in cellular processes downstream of the Insulin-PI3K-PKB pathway. In response to extra- or intracellular stresses, for example starvation or oxidative stress, FoxOs are required to direct cell cycle progression and apoptosis. In endothelial cells, they induce apoptosis, and their deregulation is linked to diseases involving the insulin pathway, such as diabetes. FoxOs also exhibit a complex role in tumour transformation: here their main function is to suppress tumorigenesis. In both physiological and cancer contexts, FoxO activation leads to the transcription of some general targets, such as p27kip1 or IGFBP1. The FoxOs can also induce tissue-specific genes, as ANGPT2 and BIM in the endothelium.
In endothelial cells, another pathway with a pivotal function is the MEK5/ERK5 MAPK signalling way. Its activation promotes cell survival and proliferation in stressful conditions, e.g., when blood vessels are exposed to the shear forces exerted by the blood stream. Furthermore, recent data described ERK5 as a kinase directing tumour resistance upon therapy-induced stress.
Comparing their reported roles in various tumours and in the endothelium, FoxO proteins and the MEK5/ERK5 MAPK cascade appear to exert opposite functions. First non-published data confirmed the hypothesis that FoxO factors are subject to a negative modulation by the MEK5/ERK5 pathway. Hence, one goal of this PhD project was to further characterise this crosstalk at molecular level. The major mechanism of FoxO regulation is the balance among several post translational modifications, such as phosphorylation, acetylation, and ubiquitination. Most importantly, the PKB dependent phosphorylation of FoxOs negatively controls their activity, and it is critical for their subcellular localization. Therefore, the regulation of FoxO localization as mechanism of ERK5 dependent suppression was studied, but the results presented in this thesis argue against this hypothesis. However, additional experiments are required to explore the impact of ERK5 activity on FoxO post-translational modifications.
FoxO activity can also be modulated by the interaction with other proteins, which in turn could explain general- and tissue-specific gene expression. Thus, another objective of this work was to investigate FoxO3-interactome in endothelial cells and the impact of MEK5/ERK5 activation on it. As published in (Fusi et al. 2022) and presented here, this analysis unveiled TRRAP as new FoxO bound protein in several cell types. Moreover, the interaction did not rely on the capacity of the FoxOs to bind their consensus DNA sequences at the promoter of target genes. Functional data demonstrated that TRRAP is required for FoxO-dependent gene transcription in endothelial and osteosarcoma cells. In addition, TRRAP expression in the endothelium is important for FoxO induced apoptosis. In summary, the interaction between FoxO factors and TRRAP revealed a new regulatory mechanism of FoxO-dependent gene transcription. It remains to be analysed whether the MEK5/ERK5 cascade may exert its suppressive effect on FoxO activity by interfering with their binding to TRRAP and whether such a mechanism may be relevant for tumorigenesis.
Regulatory T cells (Tregs) are the masters of immune regulation controlling inflammation and tolerance, tissue repair and homeostasis. Multiple immunological diseases result from altered Treg frequencies and Treg dysfunction. We hypothesized that augmenting Treg function and numbers would prevent inflammatory disease whereas inhibiting or depleting Tregs would improve cancer immunotherapy.
In the first part of this thesis, we explored whether in vivo activation and expansion of Tregs would impair acute graft-versus-host disease (aGvHD). In this inflammatory disease, Tregs are highly pathophysiological relevant and their adoptive transfer proved beneficial on disease outcome in preclinical models and clinical studies. IL-2 has been recognized as a key cytokine for Treg function. Yet, attempts in translating Treg expansion via IL-2 have remained challenging, due to IL-2s extremely broad action on other cell types including effector T cells, NK cells, eosinophils and vascular leakage syndrome, and importantly, due to poor pharmacokinetics in vivo. We addressed the latter issue using an IL-2-IgG-fusion protein (irrIgG-IL-2) with improved serum retention and demonstrated profound Treg expansion in vivo in FoxP3-luciferase reporter mice. Further, we augmented Treg numbers and function via the selective-TNF based agonists of TNFR2 (STAR2). Subsequently, we tested a next-generation TNFR2 agonist, termed NewSTAR, which proved even more effective. TNFR2 stimulation augmented Treg numbers and function and was as good as or even superior to the IL-2 strategy. Finally, in a mouse model of aGvHD we proved the clinical relevance of Treg expansion and activation with irrIgG-IL-2, STAR2 and NewSTAR. Notably, the TNFR2 stimulating constructs were outstanding as we observed not the IL-2 prototypic effects on other cell populations and no severe side effects.
In the second part of this thesis, we explored Tregs in pancreatic ductal adenocarcinoma (PDAC) and developed targeting strategies. Among several tumor entities in which Tregs impact survival, preclinical and clinical data demonstrated their negative role on PDAC. In our studies we employed the orthotopic syngeneic Panc02 model in immunocompetent mice. Based on flow cytometric analysis of the tumor microenvironment we propose TIGIT and TNFRSF members as novel therapeutic targets. Surprisingly, we found that blocking TNFR2 did not interfere with intratumoral Treg accumulation. However, we decreased the highly abundant intratumoral Tregs when we disrupted the tumor extracellular matrix. In PDAC, Treg manipulation alone did not lead to tumor regression and we propose that an additional immune boost may be necessary for efficient tumor immune surveillance and cancer clearance. This contrasts with aGvHD, in which Treg manipulation alone was sufficient to improve disease outcome.
Conclusively, we demonstrated the enormous medical benefit of Treg manipulation. Our promising data obtained with our newly developed powerful tools highlight the potential to translate our findings into clinical practice to therapeutically target human Tregs in patients. With novel TNFR2 agonists (STAR2, NewSTAR) we augmented Treg numbers and function as (or even more) effectively than with IL-2, without causing adverse side effects. Importantly, exogenous in vivo Treg expansion protected mice from aGvHD. For the therapy of PDAC, we identified novel targets on Tregs, notably TIGIT and members of the TNFRSF. We demonstrated that altering the extracellular tumor matrix can efficiently disrupt the Treg abundance in tumors. These novel targeting strategies appear as attractive new treatment options and they may benefit patients suffering from inflammatory disease and cancer in the future.
Many arthropods such as mosquitoes, ticks, bugs, and flies are vectors for the transmission of pathogenic parasites, bacteria, and viruses. Among these, the unicellular parasite Trypanosoma brucei (T. brucei) causes human and animal African trypanosomiases and is transmitted to the vertebrate host by the tsetse fly. In the fly, the parasite goes through a complex developmental cycle in the alimentary tract and salivary glands ending with the cellular differentiation into the metacyclic life cycle stage. An infection in the mammalian host begins when the fly takes a bloodmeal, thereby depositing the metacyclic form into the dermal skin layer. Within the dermis, the cell cycle-arrested metacyclic forms are activated, re-enter the cell cycle, and differentiate into proliferative trypanosomes, prior to dissemination throughout the host.
Although T. brucei has been studied for decades, very little is known about the early events in the skin prior to systemic dissemination. The precise timing and the mechanisms controlling differentiation of the parasite in the skin continue to be elusive, as does the characterization of the proliferative skin-residing trypanosomes. Understanding the first steps of an infection is crucial for developing novel strategies to prevent disease establishment and its progression.
A major shortcoming in the study of human African trypanosomiasis is the lack of suitable infection models that authentically mimic disease progression. In addition, the production of infectious metacyclic parasites requires tsetse flies, which are challenging to keep. Thus, although animal models - typically murine - have produced many insights into the pathogenicity of trypanosomes in the mammalian host, they were usually infected by needle injection into the peritoneal cavity or tail vein, bypassing the skin as the first entry point. Furthermore, animal models are not always predictive for the infection outcome in human patients. In addition, the relatively small number of metacyclic parasites deposited by the tsetse flies makes them difficult to trace, isolate, and study in animal hosts.
The focus of this thesis was to develop and validate a reconstructed human skin equivalent as an infection model to study the development of naturally-transmitted metacyclic parasites of T. brucei in mammalian skin. The first part of this work describes the development and characterization of a primary human skin equivalent with improved mechanical properties. To achieve this, a computer-assisted compression system was designed and established. This system allowed the improvement of the mechanical stability of twelve collagen-based dermal equivalents in parallel through plastic compression, as evaluated by rheology. The improved dermal equivalents provided the basis for the generation of the skin equivalents and reduced their contraction and weight loss during tissue formation, achieving a high degree of standardization and reproducibility. The skin equivalents were characterized using immunohistochemical and histological techniques and recapitulated key anatomical, cellular, and functional aspects of native human skin. Furthermore, their cellular heterogeneity was examined using single-cell RNA sequencing - an approach which led to the identification of a remarkable repertoire of extracellular matrix-associated genes expressed by different cell subpopulations in the artificial skin. In addition, experimental conditions were established to allow tsetse flies to naturally infect the skin equivalents with trypanosomes.
In the second part of the project, the development of the trypanosomes in the artificial skin was investigated in detail. This included the establishment of methods to successfully isolate skin-dwelling trypanosomes to determine their protein synthesis rate, cell cycle and metabolic status, morphology, and transcriptome. Microscopy techniques to study trypanosome motility and migration in the skin were also optimized. Upon deposition in the artificial skin by feeding tsetse, the metacyclic parasites were rapidly activated and established a proliferative population within one day. This process was accompanied by: (I) reactivation of protein synthesis; (II) re-entry into the cell cycle; (III) change in morphology; (IV) increased motility. Furthermore, these observations were linked to potentially underlying developmental mechanisms by applying single-cell parasite RNA sequencing at five different timepoints post-infection.
After the initial proliferative phase, the tsetse-transmitted trypanosomes appeared to enter a reversible quiescence program in the skin. These quiescent skin-residing trypanosomes were characterized by very slow replication, a strongly reduced metabolism, and a transcriptome markedly different from that of the deposited metacyclic forms and the early proliferative trypanosomes. By mimicking the migration from the skin to the bloodstream, the quiescent phenotype could be reversed and the parasites returned to an active proliferating state. Given that previous work has identified the skin as an anatomical reservoir for T. brucei during disease, it is reasonable to assume that the quiescence program is an authentic facet of the parasite's behavior in an infected host.
In summary, this work demonstrates that primary human skin equivalents offer a new and promising way to study vector-borne parasites under close-to-natural conditions as an alternative to animal experimentation. By choosing the natural transmission route - the bite of an infected tsetse fly - the early events of trypanosome infection have been detailed with unprecedented resolution. In addition, the evidence here for a quiescent, skin-residing trypanosome population may explain the persistence of T. brucei in the skin of aparasitemic and asymptomatic individuals. This could play an important role in maintaining an infection over long time periods.
The cancer stem cell hypothesis is a cancer development model which elicited great interest in the last decades stating that cancer heterogeneity arises from a stem cell through asymmetrical division. The Cancer Stem Cell subset is described as the only population to be tumorigenic and having the potential to renew. Conventional therapy often fails to eradicate CSC resulting in tumor relapse. Consequently, it is of great inter-est to eliminate this subset of cells to provide the best patient outcome. In the last years several approaches to target CSC were developed, one of them being immunotherapeu-tic targeting with antibodies. Since markers associated with CSC are also expressed on normal stem cells or healthy adjacent tissue in colorectal cancer, dual targeting strate-gies are preferred over targeting only a single antigen. Subsequently, the idea of dual targeting two CSC markers in parallel by a newly developed split T cell-engaging anti-body format termed as Hemibodies emerged. In a preliminary single cell RNA sequenc-ing analysis of colorectal cancer cells CD133, CD24, CD166 and CEA were identified as suitable targets for the combinatorial targeting strategy. Therefore, this study focused on trispecific and trivalent Hemibodies comprising a split binding moiety against CD3 and a binding moiety against either CD133, CD24, CD166 or CEA to overcome the occurrence of resistance and to efficiently eradicate all tumor cells including the CSC compartment. The study showed that the Hemibody combinations CD133xCD24, CD133xCD166 and CD133xCEA are able to eliminate double positive CHO cells with high efficacy while having a high specificity indicated by no killing of single antigen positive cells. A thera-peutic window ranging between one to two log levels could be achieved for all combina-tions mentioned above. The combinations CD133xCD24 and CD133xCD166 further-more proved its efficacy and specificity on established colorectal cancer cell lines. Be-sides the evaluation of specificity and efficacy the already introduced 1st generation of Hemibodies could be improved into a 2nd generation Hemibody format with increased half-life, stability and production yield. In future experiments the applicability of above-mentioned Hemibodies will be proven on patient-derived micro tumors to also include variables like tumor microenvironment and infiltration.
The bile system in vertebrates is an evolutionary conserved endogenous solubilization system for hydrophobic fats and poorly water-soluble vitamins. Bile pours out from the gallbladder through the common bile duct into the duodenum triggered by cholecystokinin. Cholecystokinin is released from enteroendocrine cells after food intake. The small intestine is also the absorption site of many orally administered drugs. Most emerging drug candidates belong to the class of poorly water-soluble drugs (PWSDs). Like hydrophobic vitamins, these PWSDs might as well be solubilized by bile. Therefore, this natural system is of high interest for drug formulation strategies. Simulated intestinal fluids containing bile salts (e.g., taurocholate TC) and phospholipids (e.g., lecithin L) have been widely applied over the last decade to approximate the behavior of PWSDs in the intestine. Solubilization by bile can enhance the oral absorption of PWSDs being at least in part responsible for the positive “food effect”. The dissolution rate of PWSDs can be also enhanced by the presence of bile. Furthermore, some PWSDs profit from supersaturation stabilization by bile salts. Some excipients solubilizing PWSDs seemed to be promising candidates for drug formulation when investigated in vitro without bile. When tested in vivo, these excipients reduced the bioavailability of drugs. However, these observations have been hardly examined on a molecular level and general links between bile interaction in vitro and bioavailability are still missing.
This thesis investigated the interplay of bile, PWSDs, and excipients on a molecular level, providing formulation scientists a blueprint for rational formulation design taking bile/PWSD/excipient/ interaction into account. The first chapter focus on an in silico 1H nuclear magnetic resonance (NMR) spectroscopy-based algorithm for bile/drug interaction prediction. Chapter II to IV report the impact of excipients on bioavailability of PWSDs interacting with bile. At last, we summarized helpful in vitro methods for drug formulation excipient choice harnessing biopharmaceutic solubilization in chapter V.
Chapter I applies 1H NMR studies with bile and drugs on a large scale for quantitative structure-property relationship analysis. 141 drugs were tested in simulated intestinal media by 1H NMR. Drug aryl-proton signal shifts were correlated to in silico calculated molecular 2D descriptors. The probability of a drug interacting with bile was dependent on its polarizability and lipophilicity, whereas interaction with lipids in simulated intestinal media components was dependent on molecular symmetry, lipophilicity, hydrogen bond acceptor capability, and aromaticity. The probability of a drug to interact with bile was predictive for a positive food effect. This algorithm might help in the future to identify a bile and lipid interacting drug a priori.
Chapter II investigates the impact of excipients on bile and free drug fraction. Three different interaction patterns for excipients were observed. The first pattern defined excipients that interacted with bile and irreversibly bound bile. Therefore, the free drug fraction of bile interacting drugs increased. The second pattern categorized excipients that formed new colloidal entities with bile which had a high affinity to bile interacting drugs. These colloids trapped the drug and decreased the free drug fraction. The last excipient pattern described excipients that formed supramolecular structures in coexistence with bile and had no impact on the free drug fraction. These effects were only observed for drugs interacting with bile (Perphenazine and Imatinib). Metoprolol’s free drug fraction, a compound not interacting with bile, was unaffected by bile or bile/excipient interaction. We hypothesized that bile/excipient interactions may reduce the bioavailability of bile interacting drugs.
Chapter III addresses the hypothesis from chapter II. A pharmacokinetic study in rats revealed that the absorption of Perphenazine was reduced by bile interacting excipients due to bile/excipient interaction. The simultaneous administration of excipient patterns I and II did not further reduce or enhance Perphenazine absorption. Conversely, the absorption of Metoprolol was not impacted by excipients. This reinforced the hypothesis, that drugs interacting with bile should not be formulated with excipients also interacting with bile.
Chapter IV further elaborates which in vitro methods using simulated intestinal fluids are predictive for a drug’s pharmacokinetic profile. The PWSD Naporafenib was analyzed in vitro with simulated intestinal fluids and in presence of excipients regarding solubility, supersaturation, and free drug fraction. Naporafenib showed a strong interaction with TC/L from simulated bile. Assays with TC/L, but not without identified one excipient as possibly bioavailability reducing, one as supersaturation destabilizing, and the last as bile not interacting and supersaturation stabilizing excipient. A pharmacokinetic study in beagle dogs outlined and confirmed the in vitro predictions.
The Appendix summarizes in vivo predictive methods as presented in chapter I to IV and rationalizes experimental design paving the way towards a biopharmaceutic excipient screening. The first presented preliminary decision tree is transformed into a step-by-step instruction. The presented decision matrix might serve as a blueprint for processes in early phase drug formulation development.
In summary, this thesis describes how a drug can be defined as bile interacting or non-interacting and gives a guide as well how to rate the impact of excipients on bile. We showed in two in vivo studies that bile/excipient interaction reduced the bioavailability of bile interacting drugs, while bile non-interacting drugs were not affected. We pointed out that the bile solubilization system must be incorporated during drug formulation design. Simulated gastrointestinal fluids offer a well-established platform studying the fate of drugs and excipients in vivo. Therefore, rational implementation of biopharmaceutic drug and excipient screening steers towards efficacy of oral PWSD formulation design.
Adrenocortical carcinoma (ACC) is a rare, but highly aggressive endocrine malignancy. Tumor-related hypercortisolism is present in 60 % of patients and associated with worse outcome. While cancer immunotherapies have revolutionized the treatment of many cancer entities, the results of initial studies of different immune checkpoint inhibitors in ACC were heterogeneous. Up to now, five small clinical trials with a total of 121 patients have been published and demonstrated an objective response in only 17 patients. However, one of the studies, by Raj et al., reported a clinically meaningful disease control rate of 52 % and a median overall survival of almost 25 months suggesting that a subgroup of ACC patients may benefit from immunotherapeutic approaches. Following the hypothesis that some ACCs are characterized by a glucocorticoid-induced T lymphocytes depletion, several studies were performed as part of the presented thesis. First, the immune cell infiltration in a large cohort of 146 ACC specimens was investigated. It was demonstrated for the first time, and against the common assumption, that ACCs were infiltrated not only by FoxP3+ regulatory T cells (49.3 %), but also that a vast majority of tumor samples was infiltrated by CD4+ TH cells (74 %) and CD8+ cytotoxic T cells (84.3 %), albeit the immune cell number varied heterogeneously and was rather low (median: 7.7 CD3+ T cells / high power field, range: 0.1-376). Moreover, the presence of CD3+-, CD4+- and CD8+ ACC-infiltrating lymphocytes was associated with an improved recurrence-free (HR: 0.31 95 % CI 0.11-0.82) and overall survival (HR: 0.47 96 % CI 0.25-0.87). Particularly, patients with tumor-infiltrating CD4+ TH cells without glucocorticoid excess had a significantly longer overall survival compared to patients with T cell-depleted ACC and hypercortisolism (121 vs. 27 months, p = 0.004). Hence, the impact of glucocorticoids might to some extent be responsible for the modest immunogenicity in ACC as hypercortisolism was reversely correlated with the number of CD4+ TH cells. Accordingly, CD3+ T cells co-cultured with steroidogenic NCI-H295R ACC cells demonstrated in vitro an enhanced anti-tumoral cytotoxicity by secreting 747.96 ±225.53 pg/ml IFN-γ in a therapeutically hormone-depleted microenvironment (by incubation with metyrapone), versus only 276.02 ±117.46 pg/ml IFN-γ in a standard environment with glucocorticoid excess.
Other potential biomarkers to predict response to immunotherapies are the immunomodulatory checkpoint molecules, programmed cell death 1 (PD-1) and its ligand PD-L1, since both are targets of antibodies used therapeutically in different cancer entities. In a subcohort of 129 ACCs, expressions of both molecules were heterogeneous (PD-1 17.4 %, range 1-15; PD-L1 24.4 %, range 1 - 90) and rather low. Interestingly, PD-1 expression significantly influenced ACC patients´ overall (HR: 0.21 95 % CI 0.53-0.84) and progression- free survival (HR: 0.30 95 % CI 0.13-0.72) independently of established factors, like ENSAT tumor stage, resection status, Ki67 proliferation index and glucocorticoid excess, while PD-L1 had no impact.
In conclusion, this study provides several potential explanations for the heterogeneous results of the immune checkpoint therapy in advanced ACC. In addition, the establishment of PD-1 as prognostic marker can be easily applied in routine clinical care, because it is nowadays anyway part of a detailed histo-pathological work-up. Furthermore, these results provide the rationale and will pave the way towards a combination therapy using immune checkpoint inhibitors as well as glucocorticoid blockers. This will increase the likelihood of re-activating the immunological anti-tumor potential in ACC. However, this will have to be demonstrated by additional preclinical in vivo experiments and finally in clinical trials with patients.
The human African trypanosomiasis is a neglected tropical disease, which is caused by the protozoan Trypanosoma brucei and transmitted by the bite of the tsetse fly. An untreated infection leads to death. However, only a few drugs with significant drawbacks are currently available for treatment. In this thesis, quinolone amides with an antitrypanosomal activity were synthesized and their biological and physicochemical properties were measured. New structure-activity relationships and a promising lead structure were discovered.
Bone morphogenetic proteins (BMPs) are involved in various aspects of cell-cell communication in complex life forms. They act as morphogens, help differentiate different cell types from different progenitor cells in development, and are involved in many instances of intercellular communication, from forming a body axis to healing bone fractures, from sugar metabolism to angiogenesis. If the same protein or protein family carries out many functions, there is a demand to regulate and fine-tune their biological activities, and BMPs are highly regulated to generate cell- and context-dependent outcomes.
Not all such instances can be explained yet. Growth/differentiation factor (GDF)5 (or BMP14) synergizes with BMP2 on chondrogenic ATDC5 cells, but antagonizes BMP2 on myoblastic C2C12 cells. Known regulators of BMP2/GDF5 signal transduction failed to explain this context-dependent difference, so a microarray was performed to identify new, cell-specific regulatory components. One identified candidate, the fibroblast growth factor receptor (FGFR)2, was analyzed as a potential new co-receptor to BMP ligands such as GDF5: It was shown that FGFR2 directly binds BMP2, GDF5, and other BMP ligands in vitro, and FGFR2 was able to positively influence BMP2/GDF5-mediated signaling outcome in cell-based assays. This effect was independent of FGFR2s kinase activity, and independent of the downstream mediators SMAD1/5/8, p42/p44, Akt, and p38. The elevated colocalization of BMP receptor type IA and FGFR2 in the presence of BMP2 or GDF5 suggests a signaling complex containing both receptors, akin to other known co-receptors of BMP ligands such as repulsive guidance molecules.
This unexpected direct interaction between FGF receptor and BMP ligands potentially opens a new category of BMP signal transduction regulation, as FGFR2 is the second receptor tyrosine kinase to be identified as BMP co-receptor, and more may follow. The integration of cell surface interactions between members of the FGF and BMP family especially may widen the knowledge of such cellular communication mechanisms which involve both growth factor families, including morphogen gradients and osteogenesis, and may in consequence help to improve treatment options in osteochodnral diseases.
Infectious diseases caused by pathogenic microorganisms are one of the largest socioeconomic burdens today. Although infectious diseases have been studied for decades, in numerous cases, the precise mechanisms involved in the multifaceted interaction between pathogen and host continue to be elusive. Thus, it still remains a challenge for researchers worldwide to develop novel strategies to investigate the molecular context of infectious diseases in order to devise preventive or at least anti-infective measures. One of the major drawbacks in trying to obtain in-depth knowledge of how bacterial pathogens elicit disease is the lack of suitable infection models to authentically mimic the disease progression in humans. Numerous studies rely on animal models to emulate the complex temporal interactions between host and pathogen occurring in humans. While they have greatly contributed to shed light on these interactions, they require high maintenance costs, are afflicted with ethical drawbacks, and are not always predictive for the infection outcome in human patients. Alternatively, in-vitro two-dimensional (2D) cell culture systems have served for decades as representatives of human host environments to study infectious diseases. These cell line-based models have been essential in uncovering virulence-determining factors of diverse pathogens as well as host defense mechanisms upon infection. However, they lack the morphological and cellular complexity of intact human tissues, limiting the insights than can be gained from studying host-pathogen interactions in these systems.
The focus of this thesis was to establish and innovate intestinal human cell culture models to obtain in-vitro reconstructed three-dimensional (3D) tissue that can faithfully mimic pathogenesis-determining processes of the zoonotic bacterium Campylobacter jejuni (C. jejuni). Generally employed for reconstructive medicine, the field of tissue engineering provides excellent tools to generate organ-specific cell culture models in vitro, realistically recapitulating the distinctive architecture of human tissues. The models employed in this thesis are based on decellularized extracellular matrix (ECM) scaffolds of porcine intestinal origin. Reseeded with intestinal human cells, application of dynamic culture conditions promoted the formation of a highly polarized mucosal epithelium maintained by functional tight and adherens junctions. While most other in-vitro infection systems are limited to a flat monolayer, the tissue models developed in this thesis can display the characteristic 3D villi and crypt structure of human small intestine.
First, experimental conditions were established for infection of a previously developed, statically cultivated intestinal tissue model with C. jejuni. This included successful isolation of bacterial colony forming units (CFUs), measurement of epithelial barrier function, as well as immunohistochemical and histological staining techniques. In this way, it became possible to follow the number of viable bacteria during the infection process as well as their translocation over the polarized epithelium of the tissue model. Upon infection with C. jejuni, disruption of tight and adherens junctions could be observed via confocal microscopy and permeability measurements of the epithelial barrier. Moreover, C. jejuni wildtype-specific colonization and barrier disruption became apparent in addition to niche-dependent bacterial localization within the 3D microarchitecture of the tissue model. Pathogenesis-related phenotypes of C. jejuni mutant strains in the 3D host environment deviated from those obtained with conventional in-vitro 2D monolayers but mimicked observations made in vivo. Furthermore, a genome-wide screen of a C. jejuni mutant library revealed significant differences for bacterial factors required or dispensable for interactions with unpolarized host cells or the highly prismatic epithelium provided by the intestinal tissue model. Elucidating the role of several previously uncharacterized factors specifically important for efficient colonization of a 3D human environment, promises to be an intriguing task for future research.
At the frontline of the defense against invading pathogens is the protective, viscoelastic mucus layer overlying mucosal surfaces along the human gastrointestinal tract (GIT). The development of a mucus-producing 3D tissue model in this thesis was a vital step towards gaining a deeper understanding of the interdependency between bacterial pathogens and host-site specific mucins. The presence of a mucus layer conferred C. jejuni wildtype-specific protection against epithelial barrier disruption by the pathogen and prevented a high bacterial burden during the course of infection. Moreover, results obtained in this thesis provide evidence in vitro that the characteristic corkscrew morphology of C. jejuni indeed grants a distinct advantage in colonizing mucous surfaces.
Overall, the results obtained within this thesis highlight the strength of the tissue models to combine crucial features of native human intestine into accessible in-vitro infection models. Translation of these systems into infection research demonstrated their ability to expose in-vivo like infection outcomes. While displaying complex organotypic architecture and highly prismatic cellular morphology, these tissue models still represent an imperfect reflection of human tissue. Future advancements towards inclusion of human primary and immune cells will strive for even more comprehensive model systems exhibiting intricate multicellular networks of in-vivo tissue. Nevertheless, the work presented in this thesis emphasizes the necessity to investigate host-pathogen interactions in infection models authentically mimicking the natural host environment, as they remain among the most vital parts in understanding and counteracting infectious diseases.
A closer look at long-established drugs: enantioselective protein binding and stability studies
(2023)
The aim of this work was to investigate older, established drugs. The extent of the protein binding of chiral ephedra alkaloids to AGP and of ketamine to albumin was determined. Since enantiomers of these drugs are individual available, the focus was on possible enantioselective binding and structural moieties involved in the binding.
Previously published work suggested that ephedrine and pseudoephedrine can bind stereoselectively to proteins other than albumin in serum. For the determination of the extent of protein binding, the established ultrafiltration with subsequent chiral CE analysis was used. To determine the influence of basicity on binding, the drugs methylephedrine and norephedrine were also analyzed. Drug binding to AGP increased with increasing basicity as follows: norephedrine < methylephedrine < ephedrine < pseudoephedrine. pKaff was determined both graphically using the Klotz plot and mathematical indicating a low affinity of the ephedra alkaloids to AGP. Using STD-NMR spectroscopy experiments the aromatic protons and the C-CH3 side chain were shown to be most strongly involved in binding, which could be confirmed by molecular docking experiments in more detail. For all drugs, van der Waals-, π π , cationic interactions, hydrogen bonds, and a formation of a salt bridge were observed. The individual enantiomers showed no significant differences and thus the binding of ephedra alkaloids to AGP is not significant.
In contrast to the ephedra alkaloids, the possible enantioselective binding to albumin was investigated for R and S ketamine. Again, ultrafiltration followed by CE analysis was performed. The binding of ketamine to one main binding site could be identified. A non-linear fit was used for the determination of pKaff. Using the NMR methods STD-NMR, waterLOGSY-NMR, and CPMG-NMRspectroscopy: the aromatic protons as well as the protons of the NCH3 methyl group showed the largest signal intensity changes, while the cyclohexanone protons showed the smallest changes. pKaff was also determined by the change in the chemical shift at different drug-protein ratios. These obtained values confirm the values obtained from ultrafiltration. Based on this, ketamine is classified as a low-affinity ligand to albumin. There were no significant differences between the individual enantiomers and thus the binding of ketamine to albumin is not a stereoselective process.
Using statistical design of experiments an efficient chiral CE method for determining the extent of protein binding of R and S ketamine to albumin was developed and validated according to ICH Q2 (R1) guideline.
The stability of ketamine was also investigated because a yellowish discoloration of an aqueous solution of ketamine developed under heat. XRPD investigations showed the same crystal structure for all batches examined. An untargeted screening using LC HRMS as well as LC UV measurements showed no degradation of ketamine or the presence of impurities in stress and non-stressed ketamine solutions, confirming the stability of ketamine under the stress conditions investigated. The lower the quality of the water used in the stress tests, the more intense the yellow discoloration occurred. The impurity or the mechanism that causes the yellow discoloration could not be identified.
Fabry disease (FD), an X-linked lysosomal storage disorder, is caused by variants in the gene α-galactosidase A (GLA). As a consequence, the encoded homonymous enzyme GLA is not produced in sufficient amount or does not function properly. Subsequently, globotriaosylceradmide (Gb3), the target substrate of GLA, starts accumulating in several cell types, especially neurons and endothelial cells. FD patients suffer from multiorgan symptoms including cardiomyopathy, nephropathy, stroke, and acral burning pain. It is suggested that the impact of pathological Gb3 accumulation, inflammatory and hypoxic processes, and vasculopathy are contributing to the specific FD pain phenotype. Thus, we investigated the role of inflammation, hypoxia, and vasculopathy on molecular level in dorsal root ganglia (DRG) of the GLA knockout (KO) mouse model. Further, we investigated pain-like characteristics of GLA KO mice at baseline (BS), after capsaicin administration, and after repeated enzyme replacement therapy (ERT) administration for a period of 1.5 years. Acquired data showed disturbances in immune response markers represented by downregulated inflammation-associated genes and lower numbers of CD206+ macrophages in DRG of GLA KO mice. Hypoxic mechanisms were active in DRG of GLA KO mice reflected by increased gene expression of hypoxia- and DNA damage-associated targets, higher numbers of hypoxia-inducible factor 1α-positive (HIF1α+) and carbonic anhydrase 9-positive (CA9+) neurons in DRG of GLA KO mice, and DRG neuronal HIF1α cytosolic-nuclear translocation in GLA KO mice. Vascularization in DRG of GLA KO mice was reduced including lower numbers of blood vessel branches and reduced total blood vessel length. Pain-like behavior of the GLA KO mouse model revealed no mechanical hypersensitivity at BS but age-dependent heat hyposensitivity, which developed also age-matched wild type (WT) mice. Capsaicin administration under isoflurane anesthesia did not elicit the development of nocifensive behavior in GLA KO mice after mechanical or heat stimulation. Repeated ERT administration did not show a clear effect in GLA KO mice in terms of restored heat hyposensitivity to BS paw withdrawal latencies. In summary, we demonstrated the impact of disturbed immune response markers, active hypoxic mechanisms, and reduced vascularization on molecular FD pathophysiology.
Regulatory T cells (Treg) are critical immune cells to ensure immune homeostasis. Treg do so by establishing tolerance to self-antigens as well as food-derived antigens. Additionally, they fine-tune immune responses to limit the damage caused by inevitable inflammation during the resolution of an ongoing infection or anti-tumor response. Despite countless efforts to gain a detailed understanding of the mechanisms Treg utilize to regulate adaptive immune responses, in vivo evidence is rather limited. We were interested in the cell-cell interactions of Treg and their spatio-temporal dynamics during a viral infection. We sought to address Interleukin-2 (IL-2) competition as a viable mechanism to control anti-viral CD8 T cell responses. We used intra-vital 2-photon imaging to analyze the interactions between Treg and activated T cells during viral infection. Additionally, we performed multiple loss- and gain-of-function experiments, addressing the IL-2 active signaling of CD8, CD4, and regulatory T cells to understand the competitive sensing of IL-2. Finally, we performed single-cell RNA sequencing to understand the cell-intrinsic differences in Treg caused by infection. We found that IL-2 competition by Treg limits the CD8 T cell response and can alter the differentiation of CD8 T cells. Furthermore, we show that Treg do not arrest in proximity to CD8 T cells for prolonged periods and therefore are unlikely to regulate CD8 T cells via contact-dependent mechanisms previously proposed. Our data support an area control model in which Treg scavenge IL-2 while actively migrating through the LN, constantly limiting access to IL-2. Establishing CD4 T cells as the major source of IL-2 during the later phases of infection, we provide direct evidence that Treg compete with CD8 T cells for CD4-derived IL-2. Finally, we show that IL-2 limitation is in correlation with CD25 expression levels and has an impact on the differentiation of CD8 T cells. Altering the differentiation of CD8 T cells to increase effector or memory functions has huge implications in clinical treatments, e.g ’checkpoint immunotherapy’. Especially in scenarios like checkpoint immunotherapy, where an efficient expansion of CD8 T cells is vital to the success of the treatment, it is invaluable to understand the spatio-temporal dynamics of Treg. Not only can the expansion phase be optimized, but also side effects can be better controlled by ensuring the adequate timing of treatments and boosting the anti-inflammatory response after the initial establishment of CD8 T cells. On top of this, the gained understanding of the regulatory mechanism of Treg can help to enhance the efficacy of autoimmune disorder treatments. Overall, this study addressed highly relevant questions in the Treg field and answered aspects of Treg regulation, refining their mode of action and the spatio-temporal dynamics during viral infection, providing evidence for IL-2 competition as a major regulatory mechanism controlling antiviral CD8 T cell responses.
Strong correlations caused by interaction in systems of electrons can bring about unusual physical phenomena due to many-body quantum effects that cannot properly be captured by standard electronic structure methods like density functional theory. In this thesis, we apply the state-of-the-art continuous-time quantum Monte Carlo algorithm in hybridization expansion (CT-HYB) for the strongly correlated multi-orbital Anderson impurity model (AIM) to the solution of models of magnetic impurities on metallic surfaces and, via dynamical mean-field theory (DMFT), to the solution of a lattice model, the multi-orbital Hubbard model with Hund's coupling.
A concise introduction to the theoretical background focuses on information directly relevant to the understanding of applied models, methods, and the interpretation of results. It starts with a discussion of the AIM with its parameters and its solution in the path integral formalism, the basis of the CT-HYB algorithm. We consider its derivation and implementation in some detail before reviewing the DMFT approach to correlated lattice models and the interpretation of the single-particle Green's function.
We review two algorithmic developments for the CT-HYB algorithm that help to increase the performance of calculations especially in case of a complex structure of the interaction matrix and allow the precise calculation of self-energies and vertex functions also at intermediate and higher frequencies.
Our comparative analysis of Kondo screening in the cobalt on copper impurity system points out the importance of an accurate interaction matrix for qualitatively correct Kondo temperatures and the relevance of all d-orbitals in that case. Theoretical modeling of cobalt impurities in copper "atomic wires" fails to reproduce variations and partial absence of Kondo resonances depending on the wire size. We analyze the dependence of results on parameters and consider possible reasons for the discrepancy. Different Kondo temperatures of iron adatoms adsorbed on clean or oxygen-reconstructed niobium in the normal state are qualitatively reproduced, with the adsorption distance identified as major factor and implications for the superconducting state pointed out.
Moving on to lattice problems, we demonstrate the connection between Hund's coupling, shown to cause first-order character of the interaction-driven Mott transition at half-filling in the two-orbital Hubbard model, and a phase separation zone ending in a quantum critical point at finite doping. We touch on similarities in realistic models of iron-pnictide superconductors. We analyze the manifestation of the compressibility divergence at the finite-temperature critical points away from half-filling in the eigenbasis of the two-particle generalized susceptibility. A threshold for impurity susceptibility eigenvalues that indicates divergence of the DMFT lattice compressibility and distinguishes thermodynamic stability and instability of DMFT solutions is determined.
Platelets have a key physiological role in haemostasis however, inappropriate thrombus formation can lead to cardiovascular diseases such as myocardial infarction or stroke. Although, such diseases are common worldwide there are comparatively few anti-platelet drugs, and these are associated with an increased risk of bleeding. Platelets also have roles in thrombo-inflammation, immuno-thrombosis and cancer, in part via C-type lectin-like receptor 2 (CLEC-2) and its ligand podoplanin. Although CLEC-2 contributes to these diseases in mice, as well as to thrombus stability, it is unclear whether CLEC-2 has similar roles in humans, particularly as human CLEC-2 (hCLEC-2) cannot be investigated experimentally in vivo.
To investigate hCLEC-2 in vivo, we generated a humanised CLEC-2 mouse (hCLEC-2KI) model, as well as a novel monoclonal antibody, HEL1, that binds to a different site than an existing antibody, AYP1. Using these antibodies, we have provided proof of principle for the use of hCLEC-2KI mice to test potential therapeutics targeting hCLEC-2, and shown for the first time that hCLEC-2 can be immunodepleted, with little effect on haemostasis. However, our results have also suggested that there are species differences in the role of CLEC-2 in arterial thrombosis. We further confirmed this using human blood where blocking CLEC-2 ligand binding had no effect on thrombosis, whereas we confirmed a minor role for mouse CLEC-2 in thrombus stability. We also investigated the effect of blocking CLEC-2 signalling using the Bruton’s tyrosine kinase inhibitor PRN473 on CLEC-2 mediated immuno-thrombosis in a Salmonella typhimurium infection model. However, no effect on thrombosis was observed suggesting that CLEC-2 signalling is not involved.
Overall, our results suggest that there may be differences in the role of human and mouse CLEC-2, at least in arterial thrombosis, which could limit the potential of CLEC-2 as an anti-thrombotic target. However, it appears that the interaction between CLEC-2 and podoplanin is conserved and therefore CLEC-2 could still be a therapeutic target in immuno-thrombosis, thrombo-inflammation and cancer. Furthermore, any potential human specific therapeutics could be investigated in vivo using hCLEC-2KI mice.
Conspiracy theories and fake news are receiving wide media coverage and their proliferation has motivated academic research on the driving factors irrational cognition and behavior. This dissertation focuses on individuals' beliefs about knowledge and knowing, which are commonly referred to as epistemic beliefs. The term post-truth epistemic beliefs is proposed and defined as a strong trust in one’s intuition, a low need to align opinions with evidence, and the strong conviction that truth is a matter of power. Across six online studies, a mediation model is proposed and tested. It includes the core of all dark traits, the Dark Factor of Personality (D), as an antecedent of post-truth epistemic beliefs, and irrational cognition and behavior as consequences. Manuscript #1 comprises four studies showing that post-truth epistemic beliefs are rooted in D and predict increased endorsement of COVID-19 conspiracy theories as well as less engagement in health-protective behavior against COVID-19. Manuscript #2 includes a US nationally representative study suggesting that post-truth epistemic beliefs and D predict a lower probability of having been vaccinated against COVID-19. Manuscript #3 presents a repeated measures experiment indicating that the nexus of D and post-truth epistemic beliefs also predicts less discernment between fake and accurate news. These findings highlight a major insight and a serious challenge for rational communication: Some individuals deliberately disregard (scientific) evidence and rational decision-making. Against this background, the need to foster the epistemological development of students and educators is emphasized.
Calcium ion (Ca2+) and protons (H+) are both regarded as second messengers, participating in plant growth and stress mechanisms. However, H+ signals in plant physiology are less well investigated compared to Ca2+ signals. If interconnections between these two second messengers exist remains to be uncovered because appropriate imaging tools to monitor Ca2+ and H+ simultaneously in the same cell as well as accurate bioinformatics analysis remain to be developed. To overcome this problem and unravel the role and possible interconnection of Ca2+ and H+ in plants, a new biosensor named CapHensor was developed and optimized to visualize intracellular Ca2+ and H+ changes simultaneously and ratiometrically in the same cell. The CapHensor consisted of an optimized green fluorescent pH sensor (PRpHluorin) and an established red fluorescent Ca2+ sensor (R-GECO1) that were combined in one construct via a P2A sequence. A P2A self-cleavage site between the two sensors allowed to express equal amounts but spatially separated sensors, which enabled artifact-free and ratiometric imaging of cellular Ca2+ and pH side-by-side. The function of the CapHensor was verified in pollen tubes, since they possess standing Ca2+ and pH gradients. We found better imaging quality and the signal-to-noise ratio to be enhanced in live-cell imaging when two R-GECO1 proteins were fused in tandem within the CapHensor construct. To guarantee exclusive subcellular localization and avoid mixed signals from different compartments, Nuclear Export Sequence (NES) and Nuclear Localization Sequence (NLS) were used to target PRpHluorin and R-GECO1 to distinct compartments. After optimization and verification its function, CapHensor was successfully expressed in different cell types to investigate the role of Ca2+ and H+ signals to control polar growth of pollen tube, stomatal movement or leaf defense signaling. Results obtained in the past indicated both Ca2+ gradients and pH gradients in pollen tubes play roles in polar growth. However, the role and temporal relationship between the growth process and changes in Ca2+ and pH have not been conclusively resolved. Using CapHensor, I found cytosolic acidification at the tip could promote and alkalization to suppress growth velocity in N. tabacum pollen tubes, indicating that cytosolic H+ concentrations ([H+]cyt) play an important role in regulation pollen tubes growth despite the accompanied changes in cytosolic Ca2+ concentrations ([Ca2+]cyt). Moreover, growth correlated much better with the tip [H+]cyt regime than with the course of the tip [Ca2+]cyt regime. However, surprisingly, tip-focused [Ca2+]cyt andII [H+]cyt oscillations both lagged behind growth oscillations approximately 33 s and 18 s, respectively, asking for a re-evaluation of the role that tip [Ca2+]cyt may play in pollen tube growth. Live-cell CapHensor imaging combined with electrophysiology uncovered that oscillatory membrane depolarization correlated better with tip [H+]cyt oscillations than with tip [Ca2+]cyt oscillations, indicative for a prominent role of [H+]cyt to also control electrogenic membrane transport. Using CapHensor, reading out cellular movement at the same time enabled to provide a precise temporal and spatial resolution of ion signaling events, pointing out a prominent role of [H+]cyt in pollen tube tip growth. For leaf cells, a special CapHensor construct design had to be developed, containing additional NES localization sequences to avoid overlapping of fluorescense signals from the nucleus and the cytosol. Once this was achieved, the role of Ca2+ and pH changes in guard cells, another typical single-cell system was investigated. Cytosolic pH changes have been described in stomatal movement, but the physiological role of pH and the interaction with changing Ca2+ signals were still unexplored. Combining CapHensor with the here developed technique to monitor stomatal movement in parallel, the role of Ca2+ and H+ in stomatal movement was studied in detail and novel aspects were identified. The phytohormone ABA and the bacterial elicitor flagellin (flg22) are typical abiotic and biotic stresses, respectively, to trigger stomatal closure. What kind of Ca2+ and H+ signals by ABA and flg22 are set-off in guard cells and what their temporal relationship and role for stomatal movement is were unknown. Similar [Ca2+]cyt increases were observed upon ABA and flg22 triggered stomatal closure, but [H+]cyt dynamics differed fundamentally. ABA triggered pronounced cytosolic alkalization preceded the [Ca2+]cyt responses significantly by 57 s while stomata started to close ca. 205 s after phytohormone application. With flg22, stomatal closure was accompanied only with a mild cytosolic alkalization but the [Ca2+]cyt response was much more pronounced compared to the ABA effects. Where the cytosolic alkalization originates from was unclear but the vacuole was speculated to contribute in the past. In this thesis, vacuolar pH changes were visualized by the dye BCECF over time, basically displaying exactly the opposite course of the concentration shift in the vacuole than observed in the cytosol. This is indicative for the vacuolar pH dynamics to be coupled strongly to the cytosolic pH changes. In stomatal closure signalling, reactive oxygen species (ROS) were proposed to play a major role, however, only very high concentration of H2O2 (> 200 µM), which resulted in the loss of membrane integrity, induced stomatal closure. Unexpectedly, physiological concentrations of ROS led to cytosolic acidificationIII which was associated with stomatal opening, but not stomatal closure. To study the role of [H+]cyt to steer stomatal movement in detail, extracellular and intracellular pH variations were evoked in N. tabacum guard cells and their behaviour was followed. The results demonstrated cytosolic acidification stimulated stomatal opening while cytosolic alkalization triggered stomatal closure accompanied by [Ca2+]cyt elevations. This demonstrated pH regulation to be an important aspect in stomatal movement and to feed-back on the Ca2+-dynamics. It was remarkable that cytosolic alkalization but not [Ca2+]cyt increase seemed to play a crucial role in stomatal closure, because more pronounced cytosolic alkalization, evoked stronger stomatal closure despite similar [Ca2+]cyt increases. Increases in [Ca2+]cyt, which are discussed as an early stomatal closure signal in the past, could not trigger stomatal closure alone in my experiments, even when extremely strong [Ca2+]cyt signals were triggered. Regarding the interaction between the two second messengers, [Ca2+]cyt and [H+]cyt were negatively correlated most of the times, which was different from pollen tubes showing positive correlation of [Ca2+]cyt and [H+]cyt regimes. [Ca2+]cyt elevations were always associated with a cytosolic alkalization and this relationship could be blocked by the presence of vanadate, a plasma membrane H+-pump blocker, indicating plasma membrane H+-ATPases to contribute to the negative correlation of [Ca2+]cyt and [H+]cyt. To compare with guard cells, cytosolic and nuclear versions of CapHensor were expressed in N. benthamiana mesophyll cells, a multicellular system I investigated. Mesophyll cell responses to the same stimuli as tested in guard cells demonstrated that ABA and H2O2 did not induce any [Ca2+]cyt and [H+]cyt changes while flg22 induced an increase in [Ca2+]cyt and [H+]cyt, which is different from the response in guard cells. I could thus unequivocally demonstrate that guard cells and mesophyll cells do respond differently with [Ca2+]cyt and [H+]cyt changes to the same stimuli, a concept that has been proposed before, but never demonstrated in such detail for plants. Spontaneous Ca2+ oscillations have been observed for a long time in guard cells, but the function or cause is still poorly understood. Two populations of oscillatory guard cells were identified according to their [Ca2+]cyt and [H+]cyt phase relationship in my study. In approximately half of the oscillatory cells, [H+]cyt oscillations preceded [Ca2+]cyt oscillations whereas [Ca2+]cyt was the leading signal in the other half of the guard cells population. Strikingly, natural [H+]cyt oscillations were dampened by ABA but not by flg22. This effect could be well explained by dampening of vacuolar H+ oscillations in the presence of ABA, but not through flg22. Vacuolar pH contributes to spontaneous [H+]cyt oscillations and ABA but not flg22 can block the interdependence of naturalIV [Ca2+]cyt and [H+]cyt signals. To study the role of [Ca2+]cyt oscillations in stomatal movement, solutions containing high and low KCl concentrations were applied aiming to trigger [Ca2+]cyt oscillations. The triggering of [Ca2+]cyt oscillations by this method was established two decades ago leading to the dogma that [Ca2+]cyt increases are the crucial signal for stomatal closure. However, I found stomatal movement by this method was mainly due to osmotic effects rather than [Ca2+]cyt increases. Fortunately, through this methodology, I found a strong correlation between cytosolic pH and the transport of potassium across the plasma membrane and vacuole existed. The plasma membrane H+-ATPases and H+-coupled K+ transporters were identified as the cause of [H+]cyt changes, both very important aspects in stomata physiology that were not visualized experimentally before. Na+ transport is also important for stomatal regulation and leaves generally since salt can be transported from the root to the shoot. Unlike well-described Ca2+- dependent mechanisms in roots, how leaves process salt stress is not at all understood. I applied salt on protoplasts from leaves, mesophyll cells and guard cells and combined live-cell imaging with Vm recordings to understand the transport and signaling for leaf cells to cope with salt stress. In both, mesophyll and guard cells, NaCl did not trigger Ca2+-signals as described for roots but rather triggered Ca2+ peaks when washing salt out. However, membrane depolarization and pronounced alkalinization were very reliably triggered by NaCl, which could presumably act as a signal for detoxification of high salt concentrations. In line with this, I found the vacuolar cation/H+ antiporter NHX1 to play a role in sodium transport, [H+]cyt homeostasis and the control of membrane potential. Overexpression of AtNHX1 enabled to diminish [H+]cyt changes and resulted in a smaller depolarization responses druing NaCl stress. My results thus demonstrated in contrast to roots, leaf cells do not use Ca2+-dependent signalling cascades to deal with salt stress. I could show Na+ and K+ induced [H+]cyt and Vm responses and Cl- transport to only have a minor impact. Summing all my results up briefly, I uncovered pH signals to play important roles to control pollen tube growth, stomatal movement and leaf detoxification upon salt. My results strongly suggested pH changes might be a more important signal than previously thought to steer diverse processes in plants. Using CapHensor in combination with electrophysiology and bioinformatics tools, I discovered distinct interconnections between [Ca2+]cyt and [H+]cyt in different cell types and distinct [Ca2+]cyt and [H+]cyt signals are initiated through diverse stimuli and environmental cues. The CapHensor will be very useful in the future to further investigate the coordinated role of Ca2+ and pH changes in controlling plant physiology.
This thesis is aimed at establishing modalities of time-resolved photoelectron spectroscopy (tr-PES) conducted at a free-electron laser (FEL) source and at a high harmonic generation (HHG) source for imaging the motion of atoms, charge and energy at photoexcited hybrid organic/inorganic interfaces. Transfer of charge and energy across interfaces lies at the heart of surface science and device physics and involves a complex interplay between the motion of electrons and atoms. At hybrid organic/inorganic interfaces involving planar molecules, such as pentacene and copper(II)-phthalocyanine (CuPc), atomic motions in out-of-plane direction are particularly apparent. Such hybrid interfaces are of importance to, e.g., next-generation functional devices, smart catalytic surfaces and molecular machines. In this work, two hybrid interfaces – pentacene atop Ag(110) and copper(II)-phthalocyanine (CuPc) atop titanium disulfide (1T-TiSe2) – are characterized by means of modalities of tr-PES. The experiments were conducted at a HHG source and at the FEL source FLASH at Deutsches Elektronen-Synchrotron DESY (Hamburg, Germany). Both sources provide photon pulses with temporal widths of ∼ 100 fs and thus allow for resolving the non-equilibrium dynamics at hybrid interfaces involving both electronic and atomic motion on their intrinsic time scales. While the photon energy at this HHG source is limited to the UV-range, photon energies can be tuned from the UV-range to the soft x-ray-range at FLASH. With this increased energy range, not only macroscopic electronic information can be accessed from the sample’s valence and conduction states, but also site-specific structural and chemical information encoded in the core-level signatures becomes accessible. Here, the combined information from the valence band and core-level dynamics is obtained by performing time- and angle-resolved photoelectron spectroscopy (tr-ARPES) in the UV-range and subsequently performing time-resolved x-ray photoelectron spectroscopy (tr-XPS) and time-resolved photoelectron diffraction (tr-XPD) in the soft x-ray regime in the same experimental setup. The sample’s bandstructure in energy-momentum space and time is captured by a time-of-flight momentum microscope with femtosecond temporal and sub-Ångström spatial resolutions. In the investigated systems, out-of-equilibrium dynamics are traced that are connected to the transfer of charge and energy across the hybrid interfaces. While energetic shifts and complementary population dynamics are observed for molecular and substrate states, the shapes of involved molecular orbitals change in energy-momentum space on a subpicosecond time scale. In combination with theory support, these changes are attributed to iiiatomic reorganizations at the interface and transient molecular structures are reconstructed with sub-Ångström precision. Unique to the material combination of CuPc/TiSe2, a structural rearrangement on the macroscopic scale is traced simultaneously: ∼ 60 % of the molecules undergo a concerted, unidirectional in-plane rotation. This surprising observation and its origin are detailed in this thesis and connected to a particularly efficient charge transfer across the CuPc/TiSe2 interface, resulting in a charging of ∼ 45 % of CuPc molecules.
The goal of this thesis was the development and application of higher-order spectroscopic techniques. In contrast to ordinary pump–probe (PP) and two-dimensional (2D) spectroscopy, higher-order coherently detected spectroscopic methods measure a polarization that has an order of nonlinearity higher than three. The key idea of the techniques in this thesis is to isolate the higher-order signals from the lower-order signals either by their excitation frequency or by their excitation intensity dependence. Due to the increased number of interactions in higher-order spectroscopy, highly excited states can be probed. For excitonic systems such as aggregates and polymers, the fifth-order signal allows one to directly measure exciton–exciton annihilation (EEA). In polymers and aggregates, the exciton transport is not connected to a change of the absorption and can therefore not be investigated with conventional third-order techniques. In contrast, EEA can be used as a probe to study exciton diffusion in these isonergetic systems. As a part of this thesis, anisotropy in fifth-order 2D spectroscopy was investigated and was used to study geometric properties in polymers.
In 2D spectroscopy, the multi-quantum signals are separated from each other by their spectral position along the excitation axis. This concept can be extended systematically to higher signals. Another approach to isolate multi-quantum signals in PP spectroscopy utilizes the excitation intensity. The PP signal is measured at specific excitation intensities and linear combinations of these measurements result in different signal contributions. However, these signals do not correspond to clean nonlinear signals because the higher-order signals contaminate the lower-order multi-quantum signals. In this thesis, a correction protocol was derived that uses the isolated multiquantum signals, both from 2D spectroscopy and from PP spectroscopy, to remove the contamination of higher-order signals resulting in clean nonlinear signals. Using the correction on the third-order signal allows one to obtain annihilation-free signals at high excitation intensities, i.e., with high signal-to-noise ratio. Isolation and correction in PP and 2D spectroscopy were directly compared by measuring the clean third-order signals of squaraine oligomers at high excitation intensities. Furthermore, higher-order PP spectroscopy was used to isolate up to the 13th nonlinear order of squaraine polymers.
The demonstrated spectroscopic techniques represent general procedures to isolate clean signals in terms of perturbation theory. The technique of higher-order PP spectroscopy needs only small modifications of ordinary PP setups which opens the field of higher-order spectroscopy to the broad scientific community. The technique to obtain clean nonlinear signals allows one to systematically increase the number of interacting (quasi)particles in a system and to characterize their interaction energies and dynamics.