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Institute
- Theodor-Boveri-Institut für Biowissenschaften (97)
- Graduate School of Life Sciences (51)
- Physikalisches Institut (44)
- Medizinische Klinik und Poliklinik II (33)
- Institut für Psychologie (32)
- Institut für Anorganische Chemie (27)
- Institut für Organische Chemie (27)
- Neurologische Klinik und Poliklinik (27)
- Institut für deutsche Philologie (24)
- Neuphilologisches Institut - Moderne Fremdsprachen (24)
Schriftenreihe
Sonstige beteiligte Institutionen
- VolkswagenStiftung (24)
- Johns Hopkins School of Medicine (2)
- Bio-Imaging Center Würzburg (1)
- CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - the development agency of the Brazilian Federal Government (1)
- Center for Nanosystems Chemistry (CNC), Universität Würzburg (1)
- DAAD - Deutscher Akademischer Austauschdienst (1)
- Department of Hematology and Oncology, Sana Hospital Hof, Hof, Germany (1)
- Department of Laboratory Medicine and Medicine Huddinge, Karolinska Institutet and University Hospital, Stockholm, Sweden (1)
- Department of Medicine A, University Hospital of Münster, Münster, Germany (1)
- Ernst Strüngmann Institute for Neuroscience in Cooperation with Max Planck Society (ESI) (1)
ResearcherID
- B-4606-2017 (1)
Metal nanostructures have been known for a long time to exhibit optical resonances via localized surface plasmons. The high electric fields in close proximity to the metal surface have prospects to dramatically change the dynamics of electronic transitions, such as an enhanced spontaneous decay rate of a single emitter. However, there have been two major issues which impede advances in the experimental realization of enhanced light-matter interaction. (i) The fabrication of high-quality resonant structures requires state-of-the-art patterning techniques in combination with superior materials. (ii) The tiny extension of the optical near-field requires precise control of the single emitter with respect to the nanostructure. This work demonstrates a solution to these problems by combining scanning probe and optical confocal microscopy. Here, a novel type of scanning probe is introduced which features a tip composed of the edge of a single crystalline gold sheet. The patterning via focused ion beam milling makes it possible to introduce a plasmonic nanoresonator directly at the apex of the tip. Numerical simulations demonstrate that the optical properties of this kind of scanning probe are ideal to analyze light-matter interaction. Detailed experimental studies investigate the coupling mechanism between a localized plasmon and single colloidal quantum dots by dynamically changing coupling strength via their spatial separation. The results have shown that weak interaction affects the shape of the fluorescence spectrum as well as the polarization. For the best probes it has been found that it is possible to reach the strong coupling regime at the single emitter level at room temperature. The resulting analysis of the experimental data and the proposed theoretical models has revealed the differences between the established far-field coupling and near-field coupling. It has been found that the broad bandwidth of plasmonic resonances are able to establish coherent coupling to multiple transitions simultaneously giving rise to an enhanced effective coupling strength. It has also been found that the current model to numerically calculate the effective mode volume is inaccurate in case of mesoscopic emitters and strong coupling. Finally, light-matter interaction is investigated by the means of a quantum-dot-decorated microtubule which is traversing a localized nearfield by gliding on kinesin proteins. This biological transport mechanism allows the parallel probing of a meta-surface with nm-precision. The results that have been put forward throughout this work have shed new light on the understanding of plasmonic light-matter interaction and might trigger ideas on how to more efficiently combine the power of localized electric fields and novel excitonic materials.
Metabolic adaptation to the host cell is important for obligate intracellular pathogens such as Chlamydia trachomatis (Ct). Here we infer the flux differences for Ct from proteome and qRT-PCR data by comprehensive pathway modeling. We compare the comparatively inert infectious elementary body (EB) and the active replicative reticulate body (RB) systematically using a genome-scale metabolic model with 321 metabolites and 277 reactions. This did yield 84 extreme pathways based on a published proteomics dataset at three different time points of infection. Validation of predictions was done by quantitative RT-PCR of enzyme mRNA expression at three time points. Ct’s major active pathways are glycolysis, gluconeogenesis, glycerol-phospholipid (GPL) biosynthesis (support from host acetyl-CoA) and pentose phosphate pathway (PPP), while its incomplete TCA and fatty acid biosynthesis are less active. The modeled metabolic pathways are much more active in RB than in EB. Our in silico model suggests that EB and RB utilize folate to generate NAD(P)H using independent pathways. The only low metabolic flux inferred for EB involves mainly carbohydrate metabolism. RB utilizes energy -rich compounds to generate ATP in nucleic acid metabolism. Validation data for the modeling include proteomics experiments (model basis) as well as qRT-PCR confirmation of selected metabolic enzyme mRNA expression differences. The metabolic modeling is made fully available here. Its detailed insights and models on Ct metabolic adaptations during infection are a useful modeling basis for future studies.
Plant–pathogen interactions have been widely studied, but mostly from the site of the plant secondary defense. Less is known about the effects of pathogen infection on plant primary metabolism. The possibility to transform a fluorescing protein into prokaryotes is a promising phenotyping tool to follow a bacterial infection in plants in a noninvasive manner. In the present study, virulent and avirulent Pseudomonas syringae strains were transformed with green fluorescent protein (GFP) to follow the spread of bacteria in vivo by imaging Pulse-Amplitude-Modulation (PAM) fluorescence and conventional binocular microscopy. The combination of various wavelengths and filters allowed simultaneous detection of GFP-transformed bacteria, PAM chlorophyll fluorescence, and phenolic fluorescence from pathogen-infected plant leaves. The results show that fluorescence imaging allows spatiotemporal monitoring of pathogen spread as well as phenolic and chlorophyll fluorescence in situ, thus providing a novel means to study complex plant–pathogen interactions and relate the responses of primary and secondary metabolism to pathogen spread and multiplication. The study establishes a deeper understanding of imaging data and their implementation into disease screening.
Supramolecular self-assembly of perylene bisimide (PBI) dyes via non-covalent forces gives rise to a high number of different PBI architectures with unique optical and functional properties. As these properties can be drastically influenced by only slightly structural changes of the formed supramolecular ensembles (Chapter 2.1) the controlled self-assembly of PBI dyes became a central point of current research to design innovative materials with a high potential for different applications as for example in the fields of organic electronics or photovoltaics.
As PBI dyes show a strong tendency to form infinite aggregated structures (Chapter 2.2) the aim of this thesis was to precisely control their self-assembly to create small, structurally well-defined PBI assemblies in solution. Chapter 2.3 provides an overview on literature known strategies that were established to realize this aim. It could be demonstrated that especially backbone-directed intra- and intermolecular self-assembly of covalently linked Bis-PBI dyes evolved as one of the most used strategies to define the number of stacked PBI chromophores by using careful designed spacer units with regard to their length and flexibility.
By using conventional spectroscopic methods like UV/Vis and fluorescence experiments in combination with NMR measurements an in-depth comparison of the molecular and optical properties in solution both in the non-stacked and aggregated state of the target compounds could be elucidated to reveal structure-property relationships of different PBI architectures. Thus, it could be demonstrated, that spacer units that pre-organize two PBI chromophores with an inter-planar distance of r < 7 Å lead to an intramolecular folding, whereas linker moieties with a length between 7 to 11 Å result in an intermolecular self-assembly of the respective Bis-PBIs dyes via dimerization to form well-defined quadruple PBI pi-stacks. Hence, if the used spacer units ensure an inter-planar distance r > 14 Å larger oligomeric PBI pi-stacks are generated.
In Chapter 4 a detailed analysis of the exciton coupling in a highly defined H-aggregate quadruple PBI pi-stack is presented. Therefore, bay-tethered PBI dye Bis-PBI 1 was investigated by concentration-dependent UV/Vis spectroscopy in THF and toluene as well as by 2D-DOSY-NMR spectroscopy, ESI mass spectrometry and AFM measurements confirming that Bis-PBI 1 self-assembles exclusively into dimers with four closely pi-stacked PBI chromophores. Furthermore, with the aid of broadband fluorescence upconversion spectroscopy (FLUPS) ensuring broadband detection range and ultrafast time resolution at once, ultrafast Frenkel exciton relaxation and excimer formation dynamics in the PBI quadruple pi-stack within 1 ps was successfully investigated in cooperation with the group of Dongho Kim. Thus, it was possible to gain for the first time insights into the exciton dynamics within a highly defined synthetic dye aggregate beyond dimers. By analysing the vibronic line shape in the early-time transient fluorescence spectra in detail, it could be demonstrated that the Frenkel exciton is entirely delocalized along the quadruple stack after photoexcitation and immediately loses its coherence followed by the formation of the excimer state.
In Chapter 5 four well-defined Bis-PBI folda-dimers Bis-PBIs 2-4 were introduced, where linker units of different length (r < 7 Å) and steric demand were used to gain distinct PBI dye assemblies in the folded state. Structural elucidation based on in-depth UV/Vis, CD and fluorescence experiments in combination with 1D and 2D NMR studies reveals a stacking of the two PBI chromophores upon folding, where geometry-optimized structures obtained from DFT calculations suggest only slightly different arrangements of the PBI units enforced by the distinct spacer moieties. With the resulting optical signatures of Bis-PBIs 2-4 ranging from conventional Hj-type to monomer like absorption features, the first experimental proof of a PBI-based “null-aggregate” could be presented, in which long- and short-range exciton coupling fully compensate each other. Hence, the insights of this chapter pinpoint the importance of charge-transfer mediated short-range exciton coupling that can significantly influence the properties of pi-stacked PBI chromophores
In the last part of this thesis (Chapter 6), spacer-controlled self-assembly of four bay-linked Bis-PBI dyes Bis-PBIs 5-8 into well-defined supramolecular architectures was investigated, where the final aggregate structures are substantially defined by the nature of the used spacer units. By systematically extending the backbone length from 7 to 15 Å defining the inter-planar distance between the tethered chromophores, different assemblies from defined quadruple PBI pi-stacks to larger oligomeric pi-stacks could be gained upon aggregation.
In conclusion, the synthesis of nine covalently linked PBI dyes in combination with a detailed investigation of their spacer-mediated self-assembly behaviour in solution concerning structure-properties-relationships was presented within this thesis. The results confirm a strong exciton coupling in different types of Bis-PBI architectures e.g. folda-dimers or highly defined quadruple pi-stacks, which significantly influences their optical properties upon self-assembly.
Space- and time-resolved UV-to-NIR surface spectroscopy and 2D nanoscopy at 1 MHz repetition rate
(2019)
We describe a setup for time-resolved photoemission electron microscopy (TRPEEM) with aberration correction enabling 3 nm spatial resolution and sub-20 fs temporal resolution. The latter is realized by our development of a widely tunable (215–970 nm) noncollinear optical parametric amplifier (NOPA) at 1 MHz repetition rate. We discuss several exemplary applications. Efficient photoemission from plasmonic Au nanoresonators is investigated with phase-coherent pulse pairs from an actively stabilized interferometer. More complex excitation fields are created with a liquid-crystal-based pulse shaper enabling amplitude and phase shaping of NOPA pulses with spectral components from 600 to 800 nm. With this system we demonstrate spectroscopy within a single plasmonic nanoslit resonator by spectral amplitude shaping and investigate the local field dynamics with coherent two-dimensional (2D) spectroscopy at the nanometer length scale (“2D nanoscopy”). We show that the local response varies across a distance as small as 33 nm in our sample. Further, we report two-color pump–probe experiments using two independent NOPA beamlines. We extract local variations of the excited-state dynamics of a monolayered 2D material (WSe2) that we correlate with low-energy electron microscopy (LEEM) and reflectivity (LEER) measurements. Finally, we demonstrate the in-situ sample preparation capabilities for organic thin films and their characterization via spatially resolved electron diffraction and dark-field LEEM.
This thesis elucidates patterns and drivers of invertebrate herbivory, herbivore diversity, and community-level biomass along elevational and land use gradients at Mt. Kilimanjaro, Tanzania.
Chapter I provides background information on the response and predictor variables, study system, and the study design. First, I give an overview of the elevational patterns of species diversity/richness and herbivory published in the literature. The overview illuminates existing debates on elevational patterns of species diversity/richness and herbivory. In connection to these patterns, I also introduce several hypotheses and mechanisms put forward to explain macroecological patterns of species richness. Furthermore, I explain the main variables used to test hypotheses. Finally, I describe the study system and the study design used.
Chapter II explores the patterns of invertebrate herbivory and their underlying drivers along extensive elevational and land use gradients on the southern slopes of Mt. Kilimanjaro. I recorded standing leaf herbivory from leaf chewers, leaf miners and gall-inducing insects on 55 study sites located in natural and anthropogenic habitats distributed from 866 to 3060 meters above sea level (m asl) on Mt. Kilimanjaro. Standing leaf herbivory was related to climatic variables [mean annual temperature - (MAT) and mean annual precipitation - (MAP)], net primary productivity (NPP) and plant functional traits (leaf traits) [specific leaf area (SLA), carbon to nitrogen ratio (CN), and nitrogen to phosphorous ratio (NP)]. Results revealed an unimodal pattern of total leaf herbivory along the elevation gradient in natural habitats. Findings also revealed differences in the levels and patterns of herbivory among feeding guilds and between anthropogenic and natural habitats. Changes in NP and CN ratios which were closely linked to NPP were the strongest predictors of leaf herbivory. Our study uncovers the role of leaf nutrient stoichiometry and its linkages to climate in explaining the variation in leaf herbivory along climatic gradients.
Chapter III presents patterns and unravels direct and indirect effects of resource (food) abundance (NPP), resource (food) diversity [Functional Dispersion (FDis)], resource quality (SLA, NP, and CN rations), and climate variables (MAT and MAP) on species diversity of phytophagous beetles. Data were collected from 65 study sites located in natural and anthropogenic habitats distributed from 866 to 4550 m asl on the southern slopes of Mt. Kilimanjaro. Sweep net and beating methods were used to collect a total of 3,186 phytophagous beetles representing 21 families and 304 morphospecies. Two groups, weevils (Curculionidae) and leaf beetles (Chrysomelidae) were the largest and most diverse families represented with 898 and 1566 individuals, respectively. Results revealed complex (bimodal) and dissimilar patterns of Chao1-estimated species richness (hereafter referred to as species diversity) along elevation and land use gradients. Results from path analysis showed that temperature and climate-mediated changes in NPP had a significant positive direct and indirect effect on species diversity of phytophagous beetles, respectively. The results also revealed that the effect of NPP (via beetles abundance and diversity of food resources) on species diversity is stronger than that of temperature. Since we found that factors affecting species diversity were intimately linked to climate, I concluded that predicted climatic changes over the coming decades will likely alter the species diversity patterns which we observe today.
Chapter IV presents patterns and unravels the direct and indirect effects of climate, NPP and anthropogenic disturbances on species richness and community-level biomass of wild large mammals which represent endothermic organisms and the most important group of vertebrate herbivores. Data were collected from 66 study sites located in natural and anthropogenic habitats distributed from 870 to 4550 m asl on the southern slopes of Mt. Kilimanjaro. Mammals were collected using camera traps and used path analysis to disentangle the direct and indirect effects of climatic variables, NPP, land use, land area, levels of habitat protection and occurrence of domesticated mammals on the patterns of richness and community-level biomass of wild mammals, respectively. Results showed unimodal patterns for species richness and community-level biomass of wild mammals along elevation gradients and that the patterns differed depending on the type of feeding guild. Findings from path analysis showed that net primary productivity and levels of habitat protection had a strong direct effect on species richness and community-level biomass of wild mammals whereas temperature had an insignificant direct effect. Findings show the importance of climate-mediated food resources in determining patterns of species richness of large mammals. While temperature is among key predictors of species richness in several ectotherms, its direct influence in determining species richness of wild mammals was insignificant. Findings show the sensitivity of wild mammals to anthropogenic influences and underscore the importance of protected areas in conserving biodiversity.
In conclusion, despite a multitude of data sets on species diversity and ecosystem functions along broad climatic gradients, there is little mechanistic understanding of the underlying causes. Findings obtained in the three studies illustrate their contribution to the scientific debates on the mechanisms underlying patterns of herbivory and diversity along elevation gradients. Results present strong evidence that plant functional traits play a key role in determining invertebrate herbivory and species diversity along elevation gradients and that, their strong interdependence with climate and anthropogenic activities will shape these patterns in future. Additionally, findings from path analysis demonstrated that herbivore diversity, community-level biomass, and herbivory are strongly influenced by climate (either directly or indirectly). Therefore, the predicted climatic changes are expected to dictate ecological patterns, biotic interactions, and energy and nutrient fluxes in terrestrial ecosystems in the coming decades with stronger impacts probably occurring in natural ecosystems. Furthermore, findings demonstrated the significance of land use effects in shaping ecological patterns. As anthropogenic pressure is advancing towards more pristine higher elevations, I advocate conservation measures which are responsive to and incorporate human dimensions to curb the situation. Although our findings emanate from observational studies which have to take several confounding factors into account, we have managed to demonstrate global change responses in real ecosystems and fully established organisms with a wide range of interactions which are unlikely to be captured in artificial experiments. Nonetheless, I recommend additional experimental studies addressing the effect of top-down control by natural enemies on herbivore diversity and invertebrate herbivory in order to deepen our understanding of the mechanisms driving macroecological patterns along elevation gradients.
Breast cancer is the most common cancer among women worldwide and the second most common cause of cancer death in the developed countries. As the current state of the art in first-line drug screenings is highly ineffective, there is an urgent need for novel test systems that allow for reliable predictions of drug sensitivity.
In this study, a tissue engineering approach was used to successfully establish and standardize a 3-dimensional (3D) mamma carcinoma test system that was optimized for the testing of anti-tumour therapies as well as for the investigation of tumour biological issues. This 3D test system is based on the decellularised scaffold of a porcine small intestinal segment and represents the three molecular subsets of oestrogen receptor-positive, HER2/Neu-overexpressing and triple negative breast cancer (TNBC). The characterization of the test system with respect to morphology as well as the expression of markers for epithelial-mesenchymal transition (EMT) and differentiation indicate that the 3D tumour models cultured under static and dynamic conditions reflect tumour relevant features and have a good correlation with in vivo tumour tissue from the corresponding xenograft models. In this respect, the dynamic culture in a flow bioreactor resulted in the generation of tumour models that exhibited best reflection of the morphology of the xenograft material. Furthermore, the proliferation indices of 3D models were significantly reduced compared to 2-dimensional (2D) cell culture and therefore better reflect the in vivo situation. As this more physiological proliferation index prevents an overestimation of the therapeutic effect of cytostatic compounds, this is a crucial advantage of the test system compared to 2D culture. Moreover, it could be shown that the 3D models can recapitulate different tumour stages with respect to tumour cell invasion. The scaffold SISmuc with the preserved basement membrane structure allowed the investigation of invasion over this barrier which tumour cells of epithelial origin have to cross in in vivo conditions during the process of metastasis formation. Additionally, the data obtained from ultrastructural analysis and in situ zymography indicate that the invasion observed is connected to a tumour cell-associated change in the basement membrane in which matrix metalloproteinases (MMPs) are also involved. This features of the model in combination with the mentioned methods of analysis could be used in the future to mechanistically investigate invasive processes and to test anti-metastatic therapy strategies.
The validation of the 3D models as a test system with respect to the predictability of therapeutic effects was achieved by the clinically relevant targeted therapy with the monoclonal antibody trastuzumab which induces therapeutic response only in patients with HER2/Neu-overexpressing mamma carcinomas due to its specificity for HER2. While neither in 2D nor in 3D models of all molecular subsets a clear reduction of cell viability or an increase in apoptosis could be observed, a distinct increase in antibody-dependent cell-mediated cytotoxicity (ADCC) was detected only in the HER2/NEU-overexpressing 3D model with the help of an ADCC reporter gene assay that had been adapted for the application in the 3D model in the here presented work. This correlates with the clinical observations and underlines the relevance of ADCC as a mechanism of action (MOA) of trastuzumab. In order to measure the effects of ADCC on the tumour cells in a direct way without the indirect measurement via a reporter gene, the introduction of an immunological component into the models was required. This was achieved by the integration of peripheral blood mononuclear cells (PBMCs), thereby allowing the measurement of the induction of tumour cell apoptosis in the HER2/Neu-overexpressing model. Hence, in this study an immunocompetent model could be established that holds the potential for further testing of therapies from the emergent field of cancer immunotherapies.
Subsequently, the established test system was used for the investigation of scientific issues from different areas of application. By the comparison of the sensitivity of the 2D and 3D model of TNBC towards the water-insoluble compound curcumin that was applied in a novel nanoformulation or in a DMSO-based formulation, the 3D test system was successfully applied for the evaluation of an innovative formulation strategy for poorly soluble drugs in order to achieve cancer therapy-relevant concentrations. Moreover, due to the lack of targeted therapies for TNBC, the TNBC model was applied for testing novel treatment strategies. On the one hand, therapy with the WEE1 kinase inhibitor MK 1775 was evaluated as a single agent as well as in combination with the chemotherapeutic agent doxorubicin. This therapy approach did not reveal any distinct benefits in the 3D test system in contrast to testing in 2D culture. On the other hand, a novel therapy approach from the field of cellular immunotherapies was successfully applied in the TNBC 3D model. The treatment with T cells that express a chimeric antigen receptor (CAR) against ROR1 revealed in the static as well as in the dynamic model a migration of T cells into the tumour tissue, an enhanced proliferation of T cells as well as an efficient lysis of the tumour cells via apoptosis and therefore a specific anti-cancer effect of CAR-transduced T cells compared to control T cells. These results illustrate that the therapeutic application of CAR T cells is a promising strategy for the treatment of solid tumours like TNBC and that the here presented 3D models are suitable for the evaluation and optimization of cellular immunotherapies.
In the last part of this work, the 3D models were expanded by components of the tumour stroma for future applications. By coculture with fibroblasts, the natural structures of the intestinal scaffold comprising crypts and villi were remodelled and the tumour cells formed tumour-like structures together with the fibroblasts. This tissue model displayed a strong correlation with xenograft models with respect to morphology, marker expression as well as the activation of dermal fibroblasts towards a cancer-associated fibroblast (CAF) phenotype. For the integration of adipocytes which are an essential component of the breast stroma, a coculture with human adipose-derived stromal/stem cells (hASCs) which could be successfully differentiated along the adipose lineage in 3D static as well as dynamic models was established. These models are suitable especially for the mechanistic analysis of the reciprocal interaction between tumour cells and adipocytes due to the complex differentiation process.
Taken together, in this study a human 3D mamma carcinoma test system for application in the preclinical development and testing of anti-tumour therapies as well as in basic research in the field of tumour biology was successfully established. With the help of this modular test system, relevant data can be obtained concerning the efficacy of therapies in tumours of different molecular subsets and different tumour stages as well as for the optimization of novel therapy strategies like immunotherapies. In the future this can contribute to improve the preclinical screening and thereby to reduce the high attrition rates in pharmaceutical industry as well as the amount of animal experiments.
Tumor necrosis factor (TNF)-like weak inducer of apoptosis (TWEAK) is a member of the TNF superfamily (TNFSF) and is as such initially expressed as type II class transmembrane glycoprotein from which a soluble ligand form can be released by proteolytic processing. While the expression of TWEAK has been detected at the mRNA level in various cell lines and cell types, its cell surface expression has so far only been documented for dendritic cells, monocytes and interferon-γ stimulated NK cells. The fibroblast growth factor-inducible-14 (Fn14) is a TRAF2-interacting receptor of the TNF receptor superfamily (TNFRSF) and is the only receptor for TWEAK. The expression of Fn14 is strongly induced in a variety of non-hematopoietic cell types after tissue injury. The TWEAK/Fn14 system induces pleiotropic cellular activities such as induction of proinflammatory genes, stimulation of cellular angiogenesis, proliferation, differentiation, migration and in rare cases induction of apoptosis. On the other side, Toll-like receptor3 (TLR3) is one of DNA- and RNA-sensing pattern recognition receptors (PRRs), plays a crucial role in the first line of defense against virus and invading foreign pathogens and cancer cells. Polyinosinic-polycytidylic acid poly(I:C) is a synthetic analog of dsRNA, binds to TLR3 which acts through the adapter TRIF/TICAM1, leading to cytokine secretion, NF-B activation, IRF3 nuclear translocation, inflammatory response and may also elicit the cell death. TWEAK sensitizes cells for TNFR1-induced apoptosis and necroptosis by limiting the availability of protective TRAF2-cIAP1 and TRAF2-cIAP2 complexes, which interact with the TNFR1-binding proteins TRADD and RIPK1. In accordance with the fact that poly(I:C)-induced signaling also involves these proteins, we found enhanced necroptosis-induction in HaCaT and HeLa-RIPK3 by poly(I:C) in the presence of TWEAK (Figure 24). Analysis of a panel of TRADD, FADD, RIPK1 and caspase-8 knockout cells revealed furthermore similarities and differences in the way how these molecules act in cell death signaling by poly(I:C)/TWEAK and TNF and TRAIL. RIPK1 turned out to be essential for poly(I:C)/TWEAK-induced caspase-8-mediated apoptosis but was dispensable for these responses in TNF and TRAIL signaling. Lack of FADD protein abrogated TRAIL- but not TNF- and poly(I:C)-induced necroptosis. Moreover, we observed that both long and short FLIP rescued HaCaT and HeLa-RIPK3 cells from poly(I:C)-induced apoptosis or necroptosis.
To sum up, our results demonstrate that TWEAK, which is produced by interferon stimulated myeloid cells, controls the induction of apoptosis and necroptosis by the TLR3 ligand poly(I:C) and may thus contribute to cancer or anti-viral immunity treatment.
The etiology of anxiety disorders is multifactorial with contributions from both
genetic and environmental factors. Several susceptibility genes of anxiety disorders or
anxiety-related intermediate phenotypes have been identified, including the
serotonin transporter gene (5-HTT) and the neuropeptide S receptor gene (NPSR1),
which have been shown to modulate responses to distal and acute stress experiences.
For instance, gene-environment interaction (GxE) studies have provided evidence
that both 5-HTT and NPSR1 interact with environmental stress, particularly
traumatic experiences during childhood, in the moderation of anxiety traits, and
both 5-HTT and NPSR1 have been implicated in hypothalamic-pituitary-adrenal
(HPA) axis reactivity – an intermediate phenotype of mental disorders – in response
to acute stress exposure. The first part of this thesis aimed to address the interplay of
variations in both 5-HTT and NPSR1 genes and distal stress experiences, i.e.
childhood trauma, in the moderation of anxiety-related traits, extended by
investigation of the potentially protective effect of positive influences, i.e. elements of
successful coping such as general self-efficacy (GSE), on a GxE risk constellation by
introducing GSE as an indicator of coping ability (“C”) as an additional dimension in
a GxExC approach conferring – or buffering – vulnerability to anxiety. Increased
anxiety was observed in 5-HTTLPR/rs25531 LALA genotype and NSPR1 rs324981 AA
genotype carriers, respectively, with a history of childhood maltreatment but only in
the absence of a person’s ability to cope with adversity, whereas a dose-dependent
effect on anxiety traits as a function of maltreatment experiences irrespective of
coping characteristics was observed in the presence of at least one 5-HTT S/LG or
NSPR1 T allele, respectively. The second part of this thesis addressed the respective
impact of 5-HTT and NPSR1 variants on the neuroendocrine, i.e. salivary cortisol
response to acute psychosocial stress by applying the Maastricht Acute Stress Test
(MAST). A direct effect of NPSR1 – but not 5-HTT – on the modulation of acute
stress reactivity could be discerned, with carriers of the more active NPSR1 T allele
Summary
III
displaying significantly higher overall salivary cortisol levels in response to the MAST
compared to AA genotype carriers.
In summary, study 1 observed a moderating effect of GSE in interaction with
childhood maltreatment and 5-HTT and NPSR1, respectively, in an extended GxExC
model of anxiety risk, which may serve to inform targeted preventive interventions
mitigating GxE risk constellations and to improve therapeutic interventions by
strengthening coping ability as a protective mechanism to promote resilient
functioning. In study 2, a modulation of HPA axis function, considered to be an
endophenotype of stress-related mental disorders, by NPSR1 gene variation could be
discerned, suggesting neuroendocrine stress reactivity as an important potential
intermediate phenotype of anxiety given findings linking NPSR1 to dimensional and
categorical anxiety. Results from both studies may converge within the framework of
a multi-level model of anxiety risk, integrating neurobiological, neuroendocrine,
environmental, and psychological factors that act together in a highly complex
manner towards increasing or decreasing anxiety risk.
The aim of this thesis was to develop new automatic enhanced sampling methods by extending the idea of Parrinello’s metadynamics to multistate problems and by introducing new quantum-mechanical electronic collective variables. These methods open up a rich perspective for applications to the photophysical processes in complex molecular systems, which play a major role in many natural processes such as vision and photosynthesis, but also in the development of new materials for organic electronics, whose function depends on specific electronic properties such as biradicalicity.
This dissertation employs gauge/gravity duality to investigate features
of ( 2 + 1 ) -dimensional quantum gravity in Anti-de Sitter space (AdS)
and its relation to conformal field theory (CFT) in 1 + 1 dimensions.
Concretely, we contribute to research on the frontier of gauge/gravity
with condensed matter as well as the frontier with quantum informa-
tion.
The first research topic of this thesis is motivated by the Kondo
model, which describes the screening of magnetic impurities in metals
by conduction electrons at low temperatures. This process has a de-
scription in the language of string theory via fluctuating surfaces in
spacetime, called branes. At high temperatures the unscreened Kondo
impurity is modelled by a stack of pointlike branes. At low tempera-
tures this stack condenses into a single spherical, two-dimensional brane
which embodies the screened impurity.
This thesis demonstrates how this condensation process is naturally
reinvoked in the holographic D1/D5 system. We find brane configu-
rations mimicking the Kondo impurities at high and low energies and
establish the corresponding brane condensation, where the brane grows
two additional dimensions. We construct supergravity solutions, which
fully take into account the effect of the brane on its surrounding space-
time before and after the condensation takes place. This enables us
to compute the full impurity entropies through which we confirm the
validity of the g-theorem.
The second research topic is rooted in the connection of geometry
with quantum information. The motivation stems from the “complexity
equals volume” proposal, which relates the volume of wormholes to
the cicruit complexity of a thermal quantum state. We approach this
proposal from a pragmatic point of view by studying the properties of
certain volumes in gravity and their description in the CFT.
We study subregion complexities, which are the volumes of the re-
gions subtended by Ryu-Takayanagi (RT) geodesics. On the gravity
side we reveal their topological properties in the vacuum and in ther-
mal states, where they turn out to be temperature independent. On the
field theory side we develop and proof a formula using kinematic space
which computes subregion complexities without referencing the bulk.
We apply our formula to global AdS 3 , the conical defect and a black
hole. While entanglement, i.e. minimal boundary anchored geodesics,
suffices to produce vacuum geometries, for the conical defect we also
need geodesics windings non-trivially around the singularity. The black
hole geometry requires additional thermal contributions.
The indepth metabolic profiling of the crude extracts of two African Ancistrocladus species viz. A. likoko from Central Africa and A. abbreviatus from West Africa, resulted in a total of 87 alkaloids among them 54 new ones. All of the compounds were intensely elucidated by 1D and 2D NMR, HRESIMS, as well as chemical and chiroptical techniques.
Among the newly discovered compounds are quinoid naphthylisoquinolines with an ortho-diketone in the naphthalene portion, nor-naphthylisoquinoline alkaloid lacking the always present methyl group at C-1, seco-(ring cleaved) naphthylisoquinolines, and a newly discovered class of natural products called the naphthylisoindolinones.
Some of the compounds displayed strong antitumoral activities against human pancreatic cancer cells and leukemia cells in-vitro.
This work deals with a class of nonlinear dynamical systems exhibiting both continuous and discrete dynamics, which is called as hybrid dynamical system.
We provide a broader framework of generalized hybrid dynamical systems allowing us to handle issues on modeling, stability and interconnections.
Various sufficient stability conditions are proposed by extensions of direct Lyapunov method.
We also explicitly show Lyapunov formulations of the nonlinear small-gain theorems for interconnected input-to-state stable hybrid dynamical systems.
Applications on modeling and stability of hybrid dynamical systems are given by effective strategies of vaccination programs to control a spread of disease in epidemic systems.
In Tissue Engineering, scaffolds composed of natural polymers often show a distinct lack in stability. The natural polymer gelatin is highly fragile under physiological conditions, nevertheless displaying a broad variety of favorable properties. The aim of this study was to fabricate electrospun gelatin nanofibers, in situ functionalized and stabilized during the spinning process with highly reactive star polymer NCO-sP(EO-stat-PO) (“sPEG”). A spinning protocol for homogenous, non-beaded, 500 to 1000 nm thick nanofibers from different ratios of gelatin and sPEG was successfully established. Fibers were subsequently characterized and tested with SEM imaging, tensile tests, water incubation, FTIR, EDX, and cell culture. It was shown that adding sPEG during the spinning process leads to an increase in visible fiber crosslinking, mechanical stability, and stability in water. The nanofibers were further shown to be biocompatible in cell culture with RAW 264.7 macrophages.
Besides external characteristics and reading a piece of DNA (barcode), the DNA weight per nucleus (genome size) via flow cytometry is a key value to detect species and hybrids and determine ploidy. In addition, the DNA weight appears to be related to various properties, such as the size of the cell and the nucleus, the duration of mitosis and meiosis and the generation time. Sometimes it is even possible to distinguish between groups or sections, which can lead to new classification of the genera. The variation in DNA weight is also useful to analyze biodiversity, genome evolution and relationships between related taxa. Moreover, it is important to know how large a genome is before one determines the base sequence of the DNA of a plant. Flow cytometry is also important for understanding fundamental processes in plants such as growth and development and recognizing chimeras. In the literature, DNA weight measurements are usually limited to one genus and often only locally (Siljak et al. 2010; Bai et al. 2012). In this study, however, it was decided to investigate all vascular plants from one country. This can also contribute to the protection of rare plants. This study is the first flora in the world whose weight of DNA per nucleus and peak patterns has been determined. More than 6400 plants, representing more than 2350 (sub)species (more than 90%) have been collected, thanks to the help of almost 100 volunteers of Floristisch Onderzoek Nederland (Floron). Multiple specimens of many species have therefore been measured, preferably from different populations, in some cases more than fifty. For 1370 species, these values were not previously published. Moreover, a good number of the remaining 45% are new for The Netherlands. In principle, each species has a fixed weight of DNA per nucleus. It has also been found that, especially between the genera, there are strong differences in the number of peaks that determine the DNA weight, from one to five peaks. This indicates that in a plant or organ there are sometimes nuclei with multiples of its standard DNA weight (multiple ploidy levels). It is impossible to show graphs of more than 2350 species. Therefore, we have chosen to show the peak pattern in a new way in a short formula. Within most genera there are clear differences in the DNA weights per nucleus between the species, in some other genera the DNA weight is hardly variable. Based on about twenty genera that were previously measured completely in most cases (‘t Hart et al. 2003: Veldkamp and Zonneveld 2011; Soes et al. 2012; Dirkse et al. 2014, 2015; Verloove et al. 2017; Zonneveld [et al.] 2000−2018), it can be noted that even if all species of a genus have the same number of chromosomes, there can still be a difference of up to three times in the weight of the DNA. Therefore, a twice larger DNA weight does not have to indicate four sets of chromosomes. Finally, this research has also found clues to examine further the current taxonomy of a number of species or genera.
G protein-coupled receptor research looks out for new technologies to elucidate the complex
processes of receptor activation, function and downstream signaling with spatiotemporal
resolution, preferably in living cells and organisms. A thriving approach consists in making use
of the unsurpassed properties of light, including its high precision in space and time, noninvasiveness
and high degree of orthogonality regarding biological processes. This is realized
by the incorporation of molecular photoswitches, which are able to effectively respond to light,
such as azobenzene, into the structure of a ligand of a given receptor. The muscarinic
acetylcholine receptors belong to class A GPCRs and have received special attention in this
regard due to their role as a prototypic pharmacological system and their therapeutic potential.
They mediate the excitatory and inhibitory effects of the neurotransmitter acetylcholine and
thus regulate diverse important biological processes, especially many neurological functions in
our brain.
In this work, the application of photopharmacological tool compounds to muscarinic receptors
is presented, consisting of pharmacophores extended with azobenzene as light-responsive
motif. Making use of the dualsteric concept, such photochromic ligands can be designed to bind
concomitantly to the orthosteric and allosteric binding site of the receptor, which is
demonstrated for BQCAAI (M1) and PAI (M2) and may lead to subtype- and functionalselective
photoswitchable ligands, suitable for further ex vivo and in vivo studies.
Moreover, photoswitchable ligands based on the synthetic agonist iperoxo were investigated
extensively with regard to their photochemical behavior and pharmacological profile, outlining
the advantages and challenges of using red-shifted molecular photoswitches, such as tetraortho-
fluoro azobenzene. For the first time on a GPCR it was examined, which impact the
different substitution pattern has on both the binding and the activity on the M1 receptor. Results
show that substituted azobenzenes in photopharmacological compounds (F4-photoiperoxo and
F4-iper-azo-iper) not just represent analogs with other photophysical properties but can exhibit
a considerably different biological profile that has to be investigated carefully.
The achievements gained in this study can give important new insights into the binding mode
and time course of activation processes, enabling precise spatial and temporal resolution of the
complex signaling pathway of muscarinic receptors. Due to their role as exemplary model
system, these findings may be useful for the investigation into other therapeutically relevant
GPCRs.
Since its first experimental implementation in 2005, single-molecule localization microscopy (SMLM) emerged as a versatile and powerful imaging tool for biological structures with nanometer resolution. By now, SMLM has compiled an extensive track-record of novel insights in sub- and inter- cellular organization.\\
Moreover, since all SMLM techniques rely on the analysis of emission patterns from isolated fluorophores, they inherently allocate molecular information $per$ $definitionem$.\\
Consequently, SMLM transitioned from its origin as pure high-resolution imaging instrument towards quantitative microscopy, where the key information medium is no longer the highly resolved image itself, but the raw localization data set.\\
The work presented in this thesis is part of the ongoing effort to translate those $per$ $se$ molecular information gained by SMLM imaging to insights into the structural organization of the targeted protein or even beyond. Although largely consistent in their objectives, the general distinction between global or segmentation clustering approaches on one side and particle averaging or meta-analyses techniques on the other is usually made.\\
During the course of my thesis, I designed, implemented and employed numerous quantitative approaches with varying degrees of complexity and fields of application.\\ \\
In my first major project, I analyzed the localization distribution of the integral protein gp210 of the nuclear pore complex (NPC) with an iterative \textit{k}-means algorithm. Relating the distinct localization statistics of separated gp210 domains to isolated fluorescent signals led, among others, to the conclusion that the anchoring ring of the NPC consists of 8 homo-dimers of gp210.\\
This is of particular significance, both because it answered a decades long standing question about the nature of the gp210 ring and it showcased the possibility to gain structural information well beyond the resolution capabilities of SMLM by crafty quantification approaches.\\ \\
The second major project reported comprises an extensive study of the synaptonemal complex (SNC) and linked cohesin complexes. Here, I employed a multi-level meta-analysis of the localization sets of various SNC proteins to facilitate the compilation of a novel model of the molecular organization of the major SNC components with so far unmatched extend and detail with isotropic three-dimensional resolution.\\
In a second venture, the two murine cohesin components SMC3 and STAG3 connected to the SNC were analyzed. Applying an adapted algorithm, considering the disperse nature of cohesins, led to the realization that there is an apparent polarization of those cohesin complexes in the SNC, as well as a possible sub-structure of STAG3 beyond the resolution capabilities of SMLM.\\ \\
Other minor projects connected to localization quantification included the study of plasma membrane glycans regarding their overall localization distribution and particular homogeneity as well as the investigation of two flotillin proteins in the membrane of bacteria, forming clusters of distinct shapes and sizes.\\ \\
Finally, a novel approach to three-dimensional SMLM is presented, employing the precise quantification of single molecule emitter intensities. This method, named TRABI, relies on the principles of aperture photometry which were improved for SMLM.\\
With TRABI it was shown, that widely used Gaussian fitting based localization software underestimates photon counts significantly. This mismatch was utilized as a $z$-dependent parameter, enabling the conversion of 2D SMLM data to a virtual 3D space. Furthermore it was demonstrated, that TRABI can be combined beneficially with a multi-plane detection scheme, resulting in superior performance regarding axial localization precision and resolution.\\
Additionally, TRABI has been subsequently employed to photometrically characterize a novel dye for SMLM, revealing superior photo-physical properties at the single-molecule level.\\
Following the conclusion of this thesis, the TRABI method and its applications remains subject of diverse ongoing research.
γ-Aminobutyric acid type A receptors (GABAARs) mediate the majority of fast synaptic inhibition in the central nervous system (CNS). GABAARs belong to the Cys-loop superfamily of pentameric ligand-gated ion channels (pLGIC) and are assembled from 19 different subunits. As dysfunctional GABAergic neurotransmission manifests itself in neurodevelopmental disorders including epilepsy and anxiety, GABAARs are key drug targets. The majority of synaptic GABAARs are anchored at the inhibitory postsynaptic membrane by the principal scaffolding protein gephyrin, which acts as the central organizer in maintaining the architecture of the inhibitory postsynaptic density (iPSD). This interaction is mediated by the long intracellular loop located in between transmembrane helices 3 and 4 (M3–M4 loop) of the receptors and a universal receptor-binding pocket residing in the C-terminal domain of gephyrin. In 2014, the crystal structure of the β3-homopentameric GABAAR provided crucial information regarding the architecture of the receptor; however, an understanding of the structure and assembly of heteropentameric receptors at the atomic level was lacking. This review article will highlight recent advances in understanding the structure of heteropentameric synaptic GABAARs and how these structures have provided fundamental insights into the assembly of these multi-subunit receptors as well as their modulation by diverse ligands including the physiological agonist GABA. We will further discuss the role of gephyrin in the anchoring of synaptic GABAARs and glycine receptors (GlyRs), which are crucial for maintaining the architecture of the iPSD. Finally, we will also summarize how anti-malarial artemisinin drugs modulate gephyrin-mediated inhibitory neurotransmission.
This dissertation deals with composite-based methods for structural equation models with latent variables and their enhancement. It comprises five chapters. Besides a brief introduction in the first chapter, the remaining chapters consisting of four essays cover the results of my PhD studies.Two of the essays have already been published in an international journal.
The first essay considers an alternative way of construct modeling in structural equation modeling.While in social and behavioral sciences theoretical constructs are typically modeled as common factors, in other sciences the common factor model is an inadequate way construct modeling due to its assumptions. This essay introduces the confirmatory composite analysis (CCA) analogous to confirmatory factor analysis (CFA). In contrast to CFA, CCA models theoretical constructs as composites instead of common factors. Besides the theoretical presentation of CCA and its assumptions, a Monte Carlo simulation is conducted which demonstrates that misspecifications of the composite model can be detected by the introduced test for overall model fit.
The second essay rises the question of how parameter differences can be assessed in the framework of partial least squares path modeling. Since the standard errors of the estimated parameters have no analytical closed-form, the t- and F-test known from regression analysis cannot be directly used to test for parameter differences. However, bootstrapping provides a solution to this problem. It can be employed to construct confidence intervals for the estimated parameter differences, which can be used for making inferences about the parameter difference in the population. To guide practitioners, guidelines were developed and demonstrated by means of empirical examples.
The third essay answers the question of how ordinal categorical indicators can be dealt with in partial least squares path modeling. A new consistent estimator is developed which combines the polychoric correlation and partial least squares path modeling to appropriately deal with the qualitative character of ordinal categorical indicators. The new estimator named ordinal consistent partial least squares combines consistent partial least squares with ordinal partial least squares. Besides its derivation, a Monte Carlo simulation is conducted which shows that the new estimator performs well in finite samples. Moreover, for illustration, an empirical example is estimated by ordinal consistent partial least squares.
The last essay introduces a new consistent estimator for polynomial factor models.
Similarly to consistent partial least squares, weights are determined to build stand-ins for the latent variables, however a non-iterative approach is used.
A Monte Carlo simulation shows that the new estimator behaves well in finite samples.
Polygonum cuspidatum (Japanese knotweed, also known as Huzhang in Chinese), a plant that produces bioactive components such as stilbenes and quinones, has long been recognized as important in traditional Chinese herbal medicine. To better understand the biological features of this plant and to gain genetic insight into the biosynthesis of its natural products, we assembled a draft genome of P. cuspidatum using Illumina sequencing technology. The draft genome is ca. 2.56 Gb long, with 71.54% of the genome annotated as transposable elements. Integrated gene prediction suggested that the P. cuspidatum genome encodes 55,075 functional genes, including 6,776 gene families that are conserved in the five eudicot species examined and 2,386 that are unique to P. cuspidatum. Among the functional genes identified, 4,753 are predicted to encode transcription factors. We traced the gene duplication history of P. cuspidatum and determined that it has undergone two whole-genome duplication events about 65 and 6.6 million years ago. Roots are considered the primary medicinal tissue, and transcriptome analysis identified 2,173 genes that were expressed at higher levels in roots compared to aboveground tissues. Detailed phylogenetic analysis demonstrated expansion of the gene family encoding stilbene synthase and chalcone synthase enzymes in the phenylpropanoid metabolic pathway, which is associated with the biosynthesis of resveratrol, a pharmacologically important stilbene. Analysis of the draft genome identified 7 abscisic acid and water deficit stress-induced protein-coding genes and 14 cysteine-rich transmembrane module genes predicted to be involved in stress responses. The draft de novo genome assembly produced in this study represents a valuable resource for the molecular characterization of medicinal compounds in P. cuspidatum, the improvement of this important medicinal plant, and the exploration of its abiotic stress resistance.