Naturwissenschaftliche Fakultät

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  • Doctoral thesis
    Open Access
    Dissection of astrocyte-mediated cerebral homeostasis in synucleinopathies
    (2024) Schneider, Yanni; Winkler, Jürgen
    Multiple system atrophy (MSA) represents a rare atypical parkinsonian disorder characterized by a rapid and fatal course currently lacking causal therapies. Clinical features of MSA com- prise classical parkinsonism, cerebellar ataxia and pronounced autonomic failure occurring in the mean of the 6th decade of life. So far, the disease is classified as a sporadic disease with rare cases of familial MSA. Data concerning environmental factors causing the disease is still controversial. Dependent on the clinical manifestation, MSA is subdivided into a parkinsonian or a cerebellar type. Due to the low frequency of the disease and the fact that a definitive diagnosis is based on post mortem, animal models have been developed to mirror the molec- ular and motor phenotype of the disease. The MBP29-haSyn mouse model expresses human α-synuclein (aSyn) under the myelin basic protein (MBP) promotor specifically in oligodendro- cytes thus resembling MSA-related molecular pathology, such as glial cytoplasmic aSyn inclu- sions, severe demyelination, and microgliosis. Moreover, MBP29-haSyn mice display motor impairments, gait instability and a reduced lifespan. So far, comprehensive molecular profiling of astrocytes in MSA is lacking. Astrocytic expres- sion of glial fibrillary acidic protein (GFAP) was assessed as an indicator for astrocytic re- sponse to alterations in the microenvironment of MBP29-haSyn mice. Reactive astrogliosis was observed in the cortex and striatum on protein and RNA level analyzing expression levels of GFAP and vimentin. Moreover, focusing on cortex and striatum, an impaired capacity of upregulation of homeostasis-associated aquaporin-4, growth-associated protein 43, and glu- tamine synthetase was observed in the striatum of MBP29-haSyn-Syn mice compared to cor- tex. Additionally, expression of glutamate reuptake transporters was downregulated in the stri- atum of MBP29-haSyn mice, but not altered in the cortex. Based on these differences, a magnetic-activated cell sorting protocol for astrocyte isolation was adapted to ensure a high yield of pure astrocytes and bulk RNA sequencing was per- formed subsequently. Using these datasets, a transcriptomic landscape was generated high- lighting altered gene expression in astrocytes in the cortex and the striatum of MBP29-haSyn mice. Comprehensive analysis of both astrocyte populations revealed a dichotomous profile of astrocytes in the regions analyzed. Striatal astrocytes exhibit a pronounced immuno-active profile with upregulated pro-inflammatory transcripts involved in cytokine-cytokine interaction, toll-like receptor signaling, and phagocytosis. Conversely, analysis of the cortical astrocyte population demonstrated a decreased expression of transcripts associated with the inflamma- tory response, such as cytokine-cytokine interaction, and chemokine signaling. Since an increased presence of oligodendrocyte-associated transcripts was found upregulat-ed, the cellular components were further analyzed using gene set enrichment. Notably, the results indicated an enrichment of upregulated transcripts predominantly in the myelin sheath and the maintenance of axon implying a supportive role of astrocytes in the cortex of MBP29-haSyn mice. To examine the presence of oligodendroglial transcripts in astrocytes, in situ RNA hybridization was performed targeting Sry-related HMG-box 10 (SOX10) and myelin regulatory factor (MYRF) as prototypical oligodendroglial transcription factor. SOX10 and MYRF were identified in the proximity of astrocytic processes suggesting a potential oligoden-droglia-astroglia interaction in the cortex of MBP29-haSyn mice. Finally, reactive astrogliosis was investigated in human MSA-P patients post mortem. MSA-P patients display a strong reactive astrogliosis in the cortex, the striatum, and the substantia nigra. Moreover, expression of excitatory amino acid transporter 2 (EAAT2) was investigated expand the analysis of astrocytic characteristics. While no general decrease in expression of EAAT2 was detected, astrocytes in MSA-P patients show a re-distribution of EAAT2 from the branches towards the soma. The re-distribution of EAAT2 implies altered astrocyte functions in MSA-P patients, with EAAT2 as a potential target for a more detailed investigation of the glutamate metabolism in MSA. In conclusion, the findings of this thesis strongly demonstrate the heterogeneity of astrocytes within the CNS dependent on the region and the predominant pathology. The MBP29-haSyn mouse model provided a powerful tool to generate a transcriptomic landscape, thus highlight-ing the dynamic characteristic of astrocytes, displaying distinguished molecular profiles de-spite showing a similar upregulation pattern of GFAP. This work highlights the necessity of a comprehensive profiling of astrocytes to unravel the molecular complexity of this cell type to identify dysregulated pathways. Identification of potential interventional targets may be a promising approach to modulate the astrocytic phenotype in MSA-related pathology and thus slowing disease progression.
  • Doctoral thesis
    Open Access
    Perylene Bisimide Cyclophanes and Fullerene Derivatives as Supramolecular Architectures
    (2024) Solymosi, Iris; Hirsch, Andreas; Perez-Ojeda Rodríguez, M. Eugenia

    The present work deals with perylene bisimide (PBI) based cyclophanes and fullerene derivatives as supramolecular systems. The majority of the molecules were synthesized and characterised, but most importantly the intra- and intermolecular interactions in the different assemblies were investigated, either between macrocyclic PBI building blocks or in complexes consisting of various host and guest molecules. For this purpose, PBI cyclophanes of different sizes were synthesised in a condensation reaction with malonyl dichloride and subsequently isolated (publication 1). The flexible malonate linkers caused the two-membered ring to exhibit different properties compared to the larger macrocycles containing three or four PBI units. The π-π stacking of the two-membered ring was intensively investigated by low-temperature NMR spectroscopy and it was found that the homochiral arrangement of the PBI units is preferred at low temperatures due to a solvent-dependent diastereoselectivity. Furthermore, the two-membered ring was functionalised with fullerene pentakisadducts, thereby modifying the macrocycle's external environment and further enhancing the π-π stacking within the cyclophane. Additionally, the photophysical properties of the cyclophanes and hybrid molecules were measured and compared with one another. After the extensive characterisation in solution, the π-stacking behaviour of the PBI units in the solid state was investigated (publication 2). A slip-stack arrangement of the PBI units could be observed. As a special feature, there are both intramolecular and intermolecular π-π interactions, which lead to the formation of a one-dimensional π-stacking, polymer-like structure. This particular solid state structure could not have been deduced from the properties in solution and from theoretical calculations.

    Moreover, the two-membered ring and a structurally similar open molecule structure with only one PBI unit were functionalised with pristine fullerene C60 and the respective target compounds subsequently characterised (publication 3). For the dumbbell-like molecule with two PBI units, the low-temperature NMR measurements revealed that there is a lower diastereoselectivity in favour of the homochiral arrangement of the PBI units than for the unsubstituted two-membered ring or the hybrid molecule with fullerene pentakisadducts as substituents, which were presented in publication 1. In addition, the influence of the bridging unit on the complexation of the fullerene substituents with [10]cycloparaphenylene ([10]CPP) was investigated in o-DCB. With the help of fluorescence as well as NMR spectroscopies and, especially, ITC titrations it could be shown that the single or double PBI bridge has no significant influence on the enthalpically driven bis-pseudorotaxane formation. However, in other derivatives the bridging unit demonstrated to play a crucial role on the supramolecular interaction. Thus, the complexation behaviour of four other dumbbell molecules with carbohydrate based (isosorbide or isomannide) bridging units and [10]CPP was also investigated (publication 4). Although the four dumbbell molecules have the same molecular weight and very similar electrochemical properties, the isosorbide derivatives are thermally more stable. In the ITC titrations with [10]CPP, characteristic 1:1 ([10]CPPdumbbell molecule) and 2:1 complexes (([10]CPP)2dumbbell molecule) could be detected for the furan-fused dumbbell molecules. In contrast, the fullerene derivatives with cyclopropane rings on the fullerene substituents also formed oligomer-like structures in addition to the complexes mentioned, which was assumed by NMR measurements.

    Besides the dumbbell molecules, the binding affinities and thermodynamic parameters of pristine C60 and C70 with [10]CPP were determined using ITC (publication 5). It was found for the first time that when the fullerenes were saturated with [10]CPP in o-DCB, not only the 1:1 complex ([10]CPPC60/70) but also the 2:1 complex (([10]CPP)2C60/70) was formed. The binding constants for the complexation of C60 and [10]CPP are between Ka = (2.5-3.8) · 105 M-1 and about an order of magnitude lower for C70 and [10]CPP. In addition to the 1:1 complexes, the 2:1 complexes could also be observed in the gas phase, which was further supported by theoretical calculations. Finally, the interaction of the endohedral fullerene [Li+@C60](PF6)- with [10]CPP was investigated by ITC titrations (publication 6). Unlike C60 and C70, the 2:1 complex could only be observed in the gas phase, but not in solution. However, the binding affinity in o-DCB is two orders of magnitude higher than for C60, most likely due to the charge distribution throughout the entire complex and additional charge-transfer interactions.

    These investigations help to gain a deeper understanding of the supramolecular interactions between perylene bisimide units in a predefined arrangement and the host-guest systems based on fullerene derivatives and [10]CPP.

  • Doctoral thesis
    Open Access
    Energy Storage in Derivatized Norbornadiene/Quadricyclane as Molecular Solar Thermal System Investigated by XPS
    (2024) Hemauer, Felix; Papp, Christian
    The indispensable transition to renewable energy sources goes hand in hand with appropriate energy storage solutions. Molecular solar thermal (MOST) systems combine the utilization of solar power with the direct storage of the gained energy in a chemical manner. Upon irradiation, an energy-lean compound is converted into its energy-rich photoisomer, whereby the release of the stored energy can be catalytically triggered on demand. The molecule pair norbornadiene (NBD) and quadricyclane (QC) appears promising for MOST-based applications. By suitable derivatization of its molecular framework, the conversion and storage properties are optimized. In particular, the overlap of the absorption profile of NBD with the solar spectrum defines the overall efficiency and requires novel molecular design. Not only the photoconversion yield from NBD to QC is essential for the general applicability, but also the back reaction from QC to NBD must occur in a controlled and efficient way. In this thesis, several 2,3-disubstituted NBD derivatives and their corresponding QC isomers were surveyed on model catalyst surfaces (Pt, Ni, Au) by synchrotron radiation-based X-ray photoelectron spectroscopy (XPS). Specifically, the derivatization included cyano moieties, phenyl-ester substitution, and ester-substituted oxa-NBD/QC of various size. Investigations on the adsorption at low temperatures and subsequent temperature-programmed experiments allowed for information on the respective systems on the molecular level, which enabled the deduction of thermally induced surface reactions. The focus was set on the conditions and the extent of the energy-releasing cycloreversion reactions of the QC derivatives, by which the feasibility of the different molecule and catalyst combinations was assessed.
  • Doctoral thesis
    Open Access
    Myeloid ZEB1 in the gastrointestinal tumor and metastatic microenvironment
    (2024) Fuchs, Kathrin; Brabletz, Thomas
    Cancer is one of the leading causes of morbidity worldwide. Colorectal (CRC) and pancreatic (PDAC) cancer will account for almost 20% of all expected cancer deaths in 2023. While cancer research mainly focused on the malignant tumor cells for many years, the critical impact of the tumor microenvironment (TME) on tumor progression has recently come into focus. In particular, tumor associated macrophages (TAMs) in the TME play a dual role in influencing clinical outcome of cancer patients, depending on their polarization towards tumor suppressive or supportive subtypes. The transcription factor ZEB1 conveys plasticity to numerous cell types, for example the epithelial-to-mesenchymal transition in tumor cells, which fosters malignant progression. Interestingly, ZEB1 is also present in stromal cells of TME. In this study, we therefore sought to investigate how plasticity factor ZEB1 can alter TAM polarization and functions and thereby affect gastrointestinal tumor development and metastatic colonization. Based on clinical data, we demonstrate the expression of ZEB1 in TAMs in primary tumors and metastases. Employment of a mouse model with conditional homozygous knockout of myeloid Zeb1 (ZEB1LysMDel) revealed no evident impact of myeloid ZEB1 on organ development, tissue and immune homeostasis in mice. In contrast, myeloid ZEB1 depletion resulted in increased tumor growth and tumorgenicity of subcutaneous syngeneic allografts of CRC cell line CMT 93. These results were partially reproduced in CRC cell line MC 38 and PDAC cell line KPCz661. Moreover, metastatic lung colonization of KPCz661 was also considerably enhanced in ZEB1LysMDel compared to control mice. Surprisingly, in vitro characterization of macrophages derived from ZEB1LysMDel mice did not reveal ZEB1 as a master regulator of macrophage polarization transcription, but rather as fine tuner of specific macrophage effectors. Remarkably, we provide evidence that the secretion of cytokines CCL2 and CCL22 by ZEB1 proficient macrophages may be responsible for macrophage-mediated chemotaxis of cytotoxic T cells into the TME. ZEB1 deficient macrophages were incapable of recruiting sufficient cytotoxic T cells into the TME, resulting in diminished tumor cell apoptosis and subsequently increased tumor or metastatic colony burden. Collectively, our data provide evidence for a novel and unanticipated tumor suppressive function of ZEB1 in TAMs by chemokine mediated cytotoxic T cell recruitment. This study reinforces the importance of the complex interactions in the TME and their influence on cancer biology.
  • Doctoral thesis
    Open Access
    Interplay between membrane fluctuations and the kinetics of a membrane-anchored receptor
    (2024) Janeš, Josip Augustin; Smith, Ana-Sunčana
    The main topic of this dissertation is the interplay between a bendable thin sheet (membrane) and its highly localized pinning. The most general formulation of the problem allows for the reversible breaking and formation of the membrane pinning, with the kinetic rates depending on the dynamics of the membrane. In order to break the problem into more manageable parts, we first investigate the effect of a permanent pinning on the static and dynamic properties of the pinned membrane, such as its shape and fluctuations. After that we explore how are the kinetic rates for the pinning breaking and formation affected by membrane fluctuations. A paradigmatic example that motivates investigation of such problems is a biological membrane anchoring receptors which interact with environmental ligands. The receptor-ligand ”lock-key” interactions are effective only when receptors and their corresponding ligands are in close proximity for a certain amount of time, which in turn depends on the fluctuations of the receptor-anchoring membrane. On the other hand, the formed ligand-receptor bond pins the membrane locally, affecting membrane dynamics and consequently the rate for bond rupture. Of course, the described problem of a bendable sheet locally pinned by a stochastic pinning is more general than the biological case and can be applied to many different systems. However, we will frame our investigations mostly through the biological perspective. Along the way we will build on the corresponding literature which already offers many useful attempts at a general descriptive model. In the General Introduction, we discuss the theoretical frameworks that define the problems we aim to solve. We first review the continuum Canham-Helfrich model of the membrane energetics [1, 2], which describes the membrane by only two coarsegrained parameters; bending rigidity and tension. We then describe the extensions of the model that account for the non-specific interactions of the membrane with the environment, and introduce the Hamiltonian that accounts for the local, specific interactions. After that, we present the Langevin formalism used for modeling membrane dynamics in a hydrodynamic surrounding [3], together with the obtainable analytic solutions for the case of non-specific interactions. Finally, we consider the available models for the receptor-ligand interactions in situations in which at least one of the interacting molecules is anchored to a fluctuating membrane. We start with the frequently used phenomenological models [4, 5] and end with the coarse-grained kinetic rates that account for the effect of membrane fluctuations [6]. Publication P1 treats the classical Canham-Helfrich model of the membrane extended by two additional terms; one representing the non-specific interactions with the environment, and the other representing a localized pinning of the membrane modeling specific receptor-ligand interaction. We assume that the pinning is permanent and immobile and explore its consequences on the thermal equilibrium properties of the membrane, such as its mean shape, spatial two-point correlation function and shape fluctuations. Interestingly, we find that the correlation function of a pinned membrane is proportional to the free-membrane correlation, and consequently that the correlation length of a pinned membrane does not depend on the pinning properties. However, we find a non-monotonous dependence of the correlation length on the membrane tension, indicating that the effect of the pinning cannot be accounted for by a constant effective tension. We explore the corresponding tension regimes of the correlation length and show its universally exponential decay. We use these results to gain insight into the membrane-mediated interactions between two pinnings and find that interactions are present even in the absence of the mean shape deformation, solely due to the effect of thermal fluctuations of the membrane. Publication P2 extends the treatment of the pinned membrane by exploring the membrane dynamics in the context of the Langevin formalism accounting for the hydrodynamic effects of the surrounding solution. We resolve the membrane dynamics by analytically calculating the Green’s function of the differential equation defining the problem. We use this result to focus on the case of thermal forces and calculate the power spectral density (PSD) of a thermally agitated pinned membrane in a hydrodynamic surrounding. We validate the correctness of the analytical result with explicit numerical simulations of the membrane dynamics. We then propose several experimental protocols that can use the derived theoretical results for the extraction of system parameters from the measurements of membrane spatio-temporal dynamics. In publication P3 we tackle the problem of the reversible ligand-receptor (LR) interactions, with the aim to account for the effect of membrane fluctuations on these interactions by developing effective LR reaction rates. First, we give a firstprinciple derivation of the otherwise phenomenologically introduced rates with familiar Bell-Dembo properties [4, 5]. We then assume that the receptor is anchored on a fluctuating membrane and account for the effect of membrane fluctuations by calculating the expected (un)binding rates with respect to the time-independent probability distribution of membrane fluctuations. Based on the fluctuation measurements in non-activated and activated human macrophages and red blood cells, we construct a general model that captures both Gaussian and non-Gaussian fluctuations exhibited by both cell types. Thus, the introduced fluctuation model, which is a convolution of Gaussian and exponential distributions, enables us to model the effect of active fluctuations in a cell-type-independent way. Finally, we show that even the calculated non-Gaussian LR rates have a Bell-Dembo structure in the biologically relevant regime in which the receptor is much stiffer than the membrane. This result emphasizes the robustness of the Bell-Dembo assumptions and gives a framework that unifies the treatment of the effective LR rates under passive and active membrane fluctuations. Work in this dissertation builds a theoretical framework for the investigation of the interplay between membrane fluctuations and the kinetics and affinity of the membrane-anchored receptors. The framework is based on a few simple principles and as such offers well-defined metrics for testing the validity of the corresponding models. Furthermore, it offers a way to bridge the gap between the models of passive and active fluctuations, as well as between different fluctuation sources in the active case, thus tying separate models into a single, coherent picture. All of this should facilitate analytical modeling of complex systems that were out of reach until now, as well as increase the spatio-temporal scales on which the systems can be effectively simulated
  • Doctoral thesis
    Open Access
    Transport phenomena on the nanoscale: from isotropic systems to extreme confinement
    (2024-04-29) Baer, Andreas; Smith, Ana-Suncana
    Nanoscale systems, including particles or macromolecules as well as fluids confined to nanochannels and liquid films, are fascinating as they feature a transition between macroscopic continuum hydrodynamics and the intrinsically discrete molecular scale. A wealth of new phenomena arises due to this cross over as the separation of time or length scales between the different components (liquid – confinement – particle) is often not satisfied. The present thesis tackles this transition region focusing on diffusive transport in a series of six peer-reviewed articles [P1] to [P6]. Molecular dynamics (MD) simulations are applied as primary method, that is a unique tool allowing to resolve molecular details and sampling statistical averages on the mesoscopic scale. The thesis starts with addressing the validity of the Stokes-Einstein-Sutherland (SES) equation [P1]. It captures a fundamental relation between the diffusion coefficient of a particle or molecule, its hydrodynamic radius and the surrounding fluid viscosity. The derivation of the SES equation at equilibrium assumes a continuous description of the fluid and a separation of time and length scales: the particle is required to be large and heavy compared to solvent molecules such that the momentum of the particle changes slowly compared to molecular time scales of the fluid. With these conditions violated for a nanoparticle, a breakdown at the nanoscale was often proposed and the latter even confirmed by several MD studies. Contrastingly, most experiments including those of our collaborators confirmed its validity for particles down to 1 nm in diameter. This discrepancy is tackled in the thesis by extensive MD simulations of the C60 buckminsterfullerene diffusing in toluene. This system clearly violates crucial conditions underlying the SES equation, yet the law is restored in simulations in the framework of the linear response to a constant drag force. This explains the success of the experiments that typically rely on the analysis of particle sedimentation when applying the SES equation. Notably, consistent with the Knudsen number, small deviations from perfect stick boundary conditions at the particle interface are required to obtain uniform results in experiments and simulations. The study of bulk systems is extended to understand diffusion in confined liquids. Here the ordering of the solvent at the interface with the solid or the vapour phase may occur on similar length scales as the characteristic length scale of the confinement and the size of the diffusing object. Similarly, the characteristic time scales of diffusion life times of structural fluctuations become comparable to those of interactions of molecules with interfaces and other molecules. The anisotropy due to confinement also requires separate handling of the directions parallel and orthogonal to the confining walls when analysing transport properties. These issues are first tackled in MD simulations of the solvent phase within solid pores or thin films in [P2] to [P4]. Using the analysis tools developed in the PULS group it is possible to show that significant anisotropic oscillations of transport coefficients may take place due to effective interactions with the interfaces. Understanding the behaviour of confined solvents is a prerequisite for the investigation of diffusive transport of nanoparticles as solutes in such confined systems [P5]. Using the fullerenes C60 and C70 in toluene filled alumina pores as model systems, it is shown that an effective diffusion coefficient can be well estimated by measuring the diffusivity in the centre of a pore and at the interface, as well as the transition rates between these two regions. These rates are estimated from the potential of mean force (PMF) of the particle with the solid. This approach is of particular relevance for understanding separation techniques including chromatography, as the direct relation between the effective transport coefficients in the pore and the particle retention time is established. With equilibrium transport properties at the nanoscale extensively analysed, the attention finally shifts towards non-equilibrium systems, specifically addressing the viscosity of water in electric fields [P6]. Due to their dipole moment, water molecules couple to such fields, altering its intrinsic structure as well as relaxation processes in an anisotropic manner. In the extensive analysis of relaxations of thermal excitations and changes in the first and second hydration shell it is possible to study the competition between order imposed by the intrinsic tetrahedral structure and order imposed by the field. It is furthermore possible to assign different modes to time dependent viscosity, each relating to different molecular relaxation processes, and ultimately explain the anisotropic response of the system. The transport phenomena of nanoscale systems tackled in the present thesis demand further research to be conducted in this area. The theoretical foundations of the SES equation are recapped and brought into the context of experiments and simulations, providing a solid framework for studying the diffusion of small dispersed nanoparticles. Relaxing the stick boundary condition demands an in-depth analysis covering various systems and particle sizes to allow for an a priori estimate of the boundary condition, e.g. from the Knudsen number. Furthermore, the study on the transport of dispersions through narrow pores paves the way for establishing a unified view of the relationship between interactions and transport properties of such systems in general. For systems with polar components, the investigations of water in an electric field furthermore provide valuable insights, into how the transport phenomena are altered in the presence of these fields, most relevant for water-filled nanopores. Therefore, the tools and concepts developed in this work shall find applications well beyond the systems studied herein.
  • Doctoral thesis
    Open Access
    Impacts of supraglacial lakes and snowmelt on glacier velocity on the example of the Baltoro Glacier in Pakistan
    (2024) Wendleder, Anna; Braun, Matthias
    Millions of people live along the Indus River in Pakistan and are dependent on the meltwater from the glaciers in the Karakoram. Glacial meltwater also mainly controls the glacier dynamics which is a key information on glacier evolution in a changing climate. Timing and amount of meltwater influences the easonal evolution and the variation of glacier dynamic. Though, the glaciers in the Karakoram are not yet been sufficiently researched to better understand their glacier dynamics and their drivers. In addition, most of the glaciers are covered with an extensive debris cover and thus react more complex to climate changes than glaciers without debris. The focus of this work is to better understand the dynamics of Baltoro Glacier in Pakistan and hydrological drainage within the glacier. The long-term time series of glacier velocity fields derived from multi-mission Synthetic Aperutre Radar (SAR) data with high temporal and spatial resolution enable the monitoring of (intra-)seasonal and annual glacier dynamics. In combination with time series of supraglacial lakes derived from Earth observation data and precipitation and temperature from reanalysis and satellite-based data complex relationships were found between winter precipitation, summer melt, supraglacial lakes, crevasses and glacier acceleration. The high winter precipitation is associated with an acceleration of the glaciers in spring, while the heavy precipitation in spring leads to an increase in supraglacial lakes. The higher temperatures during the early melting season also influenced the formation of lakes and thus the increase in meltwater in the glacier. The mapping of supraglacial lakes is based on an annual resolution and little is known about their seasonal behaviour. The multi-temporal and multi-sensor summer time series made it possible to determine the characteristic filling and discharge periods, the lake area change over the years, and how the seasonal development varies over the years. The supraglacial lakes filled between mid-April to mid-June and drained between mid-June to mid-September and expanded faster than they contracted. A tendency towards the formation of larger lakes (>0.04 km2 ) over time is visible. The combination of the dense and high-temporal time series of supraglacial lakes with the glacier surface velocity, snowmelt, runoff, precipitation, and temperature derived of earth observation and reanalysis data enables to analyze influence of supraglacial lakes and snowmelt and the drivers of glacier velocity. The prolonged period of positive air temperatures in spring affected both snowmelt and supraglacial lake formation. Snow and ice melt had the greatest influence on the spring acceleration and the high glacier velocities in summer. The drainage of the supraglacial lakes caused the glacier acceleration in fall. The influence of melting and drainage of supraglacial lakes on glacier dynamics is therefore surprisingly large, with the former also leading to efficient drainage. Despite the insulation provided by the debris cover on the main branch, the Baltoro glacier is sensitive to temperature rise, leading to additional ice loss.
  • Doctoral thesis
    Open Access
    Grundlegende Untersuchungen zur Entwicklung Bioorthogonaler Reaktionssysteme auf Basis von Olefinmetathesereaktionen
    (2024) Benkert, Tobias; Schatz, Jürgen
    Carrying out artificial chemical reactions in living cells is one of the greatest challenges in modern chemistry. To date, there are only a few reactions that are able to fulfil the strict constraints of a bioorthogonal reaction. In this work, fundamental studies on a bioorthogonal reaction system based on olefin metathesis have been investigated. Several synthetic routes to different systems were investigated and carried out. Particular attention was paid to the preparation of piperidine-labelled systems for future targeted use in cell lysosomes. Three different approaches were studied in detail and led to the conclusion that the detailed investigation of suitable fluorescent dyes prior to their direct synthesis is a more promising strategy, as no surprising discrepancies arise between the existing and the required properties of the systems for use in cells.
  • Doctoral thesis
    Open Access
    Signaling circuits involved in the selection of high-affinity antigen-specific B cells in the germinal center
    (2024) Kuria, Timothy Chege; Winkler, Thomas
    The germinal center (GC) serves as the site for somatic hypermutation, affinity maturation, and the selection of high-affinity B cells. Two selection models have been proposed to take place in the GC: a death-limited model and a birth-limited model. In the simplified death-limited model, low-affinity GC B cells undergo apoptosis, while high-affinity B cells do not. In the more pragmatic birth-limited model, selection signals are mediated through increased upregulation of metabolic factors in high-affinity cells, promoting faster proliferation compared to low-affinity GC B cells. Regardless of the selection model, high-affinity B cells consistently outcompete low-affinity B cells in the GC. However, the signaling circuits that mediate this selection are not yet fully understood. An adoptive experimental approach utilizing a 4-hydroxy-3-nitrophenyl (NP) antibody mouse model (B1-8 mouse model) coupled to a non-responsive NP recipient mouse model was employed. Donor high and low-affinity B cells were competitively transferred into the recipient mice. On days 6 and 9 of the GC response, recipient mice were sacrificed, and the GC response was analyzed. RNA was also extracted from the donor B cells, followed by bulk RNA sequencing and differential gene expression analysis to identify potential genes mediating selection in the GC. High-affinity B cells consistently outcompeted low-affinity B cells, even with a starting ratio of high-affinity to low-affinity B cells of 1:138. Differential expression analysis of low-affinity and high-affinity GC B cells revealed a panel of genes, including the B cell co-receptor, CD72. In multiple follow-up experiments, high-affinity B cells downregulated the expression of CD72 not only at the transcriptome level but also at the protein level. CD72 is expressed on all B cells except in antibody-secreting cells, and the downregulation of CD72 likely serves to prepare high-affinity GC B cells for differentiation into antibody-secreting cells. Additionally, CD72 knock-out B cells were outcompeted by wild-type B cells owing to the lack of CD72-CD100 mediated activation and proliferation. In this thesis, novel genes were identified, including the B cell co-receptor CD72, which may play a role in mediating the GC selection process and differentiation into antibody-secreting cells. We have gained meaningful insights through the possible identification of a new GC selection signaling pathway that CD72 mediates.
  • Doctoral thesis
    Open Access
    Methods to monitor and improve cell viability and behaviour during and after bioprinting
    (2024) Fischer, Lena; Thievessen, Ingo
    The ultimate goal of biofabrication is to create biologically functional constructs that mimic human tissues and organs in structure and complexity. To achieve this, living cells immersed in biomaterials are printed into three-dimensional (3-D) tissue-constructs using methods such as laser-assisted, inkjet or extrusion-based bioprinting. Due to many advantages, extrusion-based bioprinting is the most commonly used method. However, it inevitably subjects cells to shear stress due to the application of hydrostatic pressure to pass cells through a thin printing needle. This shear stress can cause damage to the cellular plasma membrane and possibly intracellular organelles, which can impair cell survival or functional performance. Despite this inherent problem of extrusion bioprinting, methods to monitor shear stress-induced plasma membrane damages, and to decrease the vulnerability of cells to shear stress are not well established. In this work, a fluorescence-based assay using the styryl dye FM 1-43 was developed to visualize and quantify bioprinting-induced plasma membrane damages. FM 1-43 is incorporated into the outer lipid layer of the plasma membrane without crossing it and becomes fluorescent upon insertion. Following plasma membrane damage, e.g. through shear stress, the dye enters the cell and additionally stains intracellular membrane systems (e.g. mitochondria), resulting in an increased fluorescence intensity. Using FM 1-43 in confocal microscopy and microfluidic setups, it could be confirmed that the fluorescence intensity increases with applied shear stress and resulting cell deformation. Moreover, it could be shown in this work that bioprinting at high pneumatic pressure (6 bar) leads to cellular plasma membrane damages and impaired cell survival. Calcium ions play a fundamental and well-described role in the immediate repair of plasma membrane lesions. Based on this, it was shown in this work that supplementing the bioink with 1.9 mM CaCl2 improved cell survival during bioprinting in all tested bioinks (alginate, GelMA) and cell types (NIH/3T3, A125, MDA-MB-231, hiPSC, HUVEC/Tert2). Importantly, stiffer cells (hiPSC, HUVEC/Tert2) underwent less cell deformation than softer cells (NIH/3T3, A125, MDA-MB-231) at similar shear stress, resulting in less plasma membrane damage and cell death. This result strongly suggests that it is the shear stress-induced cell deformation, rather than the shear stress itself, that results in cell damage and death. In addition to providing tools for visualizing and improving the immediate effects of bioprinting on cell survival, methods for long-term monitoring of cell behavior were developed in this work. Lentiviral genetic reporter constructs for different cellular processes (proliferation, morphology and apoptosis) were generated and stably integrated into different cell types. Notably, bioprinting experiments using NIH/3T3-FUCCI proliferation reporter cells revealed that the application of high shear stress (6 bar) did not impair the proliferation of surviving cells. Moreover, NIH/3T3-tdTomato-Farnesyl morphology reporter cells exhibited increased spreading and elongation in biomaterials containing adhesion motifs (collagen) compared to non-adhesive bioinks (alginate), emphasizing the relevance of efÏcient adhesive functionalization of bioinks. As demonstrated by those experiments, genetically encoded reporter for cell behaviour can be used for the optimization of printing processes as well as the characterization of bioinks, and for live monitoring of the same cells over a longer period of time.
  • Doctoral thesis
    Open Access
    Die Rolle der miR-101-3p als Tumorsuppressor in Bezug auf die genomische Integrität des malignen Melanoms
    (2024) Lämmerhirt, Lisa; Boßerhoff, Anja Katrin
    Das maligne Melanom ist nach wie vor die tödlichste Form von Hautkrebs mit einer sehr schlechten Prognose nach Bildung von Fernmetastasen. MicroRNAs (miRNAs) spielen eine entscheidende Rolle bei der Entwicklung und Progression des Melanoms durch die Regulierung von Onkogenen und Tumorsuppressorgenen. Wir definierten den Verlust der miR-101-3p-Expression in Melanomzellen im Vergleich zu normalen humanen epidermalen Melanozyten (NHEM) und Melanoblasten-verwandten Zellen (MBrC, engl.: melanoblast related cells) als ein frühes Ereignis in der Tumorentwicklung. Unsere Forschung zielt darauf ab, die tumorsuppressive Rolle der miR-101-3p und ihre Funktion in der Regulierung wichtiger zellulärer Prozesse zu verstehen. Die Re-Expression der miR-101-3p führte zu einer Hemmung der Proliferation, Beeinflussung des Zellzyklus, einer Zunahme der DNA-Schäden und einer Induktion der Apoptose. Wir identifizierten Lamin B1 (LMNB1) und dessen Rezeptor (LBR) als wichtige direkte bzw. indirekte Zielgene von miR-101-3p, die Kernprozesse wie die transkriptionelle Repression von Genen und die Heterochromatinstruktur beeinflussen. Veränderungen in den Kernstrukturen von Zellen werden bei verschiedenen Krankheiten, einschließlich Krebs, beobachtet. Sie führen zu Veränderungen der Kernaktivität, der strukturellen Dynamik und der zellulären Signaltransduktion. Ihre molekulare Charakterisierung könnte somit zu einem tieferen Verständnis und zur Entwicklung neuer Therapieansätze führen. Im Rahmen dieser Doktorarbeit analysierten wir die funktionellen Auswirkungen der Fehlregulation von LMNB1 und LBR. RNA-Sequenzierung und Genexpressionsanalysen nach Knockdown (KD) von LMNB1 bzw. LBR zeigten, dass sie an wichtigen zellulären Prozessen beteiligt sind, die zu Seneszenz und Chromatinveränderungen führen. Wir stellten fest, dass Melanomzellen beide Moleküle unabhängig voneinander benötigen, um Seneszenz zu verhindern. Die verminderte Expression von LMNB1 bzw. LBR in einem BRAFV600E-Melanozyten-Seneszenzmodell sowie in Etoposid-behandelten Melanomzellen deutete auf ihre Rolle als potenzielle Seneszenzmarker im Melanom hin. Unsere Ergebnisse legten nahe, dass LMNB1 und LBR einen Einfluss auf die Seneszenz haben und sich auf nukleare Vorgänge wie die Kondensation von Chromatin auswirken könnten, was für die Melanomentwicklung relevant ist. Diesbezüglich wurde auch die Rolle der miR-101-3p zunächst mit dem Fokus auf Seneszenz funktionell untersucht. Wir bestätigten, dass die langfristige Hemmung der miR-101-3p in normalen Melanozyten zu einem verzögerten Eintritt in die Seneszenz führt und die Zellen somit vor dem Altern schützt. In Melanomzellen induzierte die Re-Expression von miR-101-3p jedoch keine Seneszenz, sondern Apoptose. Mittels RNA-Sequenzierung und differenzieller Genexpressionsanalysen nach Re-Expression der miR-101-3p wurden unsere Ergebnisse und die Bedeutung des Verlusts der miR-101-3p für die Melanomprogression außerdem bestätigt. Unsere Resultate zeigten, dass die Re-Expression der miR-101-3p die genomische Instabilität erhöht, irreversiblen DNA-Schaden verursacht und die Apoptose auslöst. Die Daten sind somit hinweisgebend, dass der Verlust der miR-101-3p in Melanomen ein frühes Ereignis in der Melanomprogression ist. Dort beeinflusst er die genomische Integrität und trägt zur Aufrechterhaltung des erhöhten bioenergetischen Bedarfs bei. Der Zusammenhang der funktionellen Analysen wird in Abbildung 1 veranschaulicht dargestellt. In dieser Doktorarbeit konnte somit der Verlust der miR-101-3p als wichtiger Prozess für die Melanomentstehung, sowie der weiteren Tumorprogression herausgearbeitet werden.
  • Doctoral thesis
    Open Access
    CHEMO-SENSORY CHARACTERIZATION OF ODOR-ACTIVE CONSTITUENTS IN NATIVE WOODS AND THEIR STRUCTURE-ODOR RELATIONSHIPS
    (2024) Ghadiriasli, Rahil; Büttner, Andrea
    The living tree and its obtained wood have played a prominent role in human everyday life in the form of building material and furniture, or in products of daily use. The aroma components emanating from wood-based products have a powerful influence on human Psychophysiological activity and have been used for mental, spiritual and physical healing. The wood aroma can be used in the indoor environment to foster relaxation and stress release effects. The current study was conducted to determine the individual wood odor and its constituents in two diverse types of woods, namely Oak wood and cembran pine wood. Oak wood has been used since long during the maturation and aging process imparting aroma and flavor in alcoholic beverages and vinegar as by-products that have been either fermented or aged in oak barrels. Several investigations targeted the aroma composition of modified and heat-treated oak wood, but only little information about aroma-active compounds constituting the native and raw oak wood is available. The Cembran pine wood (Pinus cembra L.), also known as Arolla pine, Swiss pine, or Stone pine, has a prominent and long-lasting aroma that has been reported to relieve stress and that is widely used in aromatherapy. However, the odorants responsible for this distinctive aroma are not yet comprehensively revealed. Therefore, the main objective of this thesis was to characterize the impacting odorants and to deepen the knowledge about native oak wood and unique Cembran pine wood odor by applying a combinatory chemo-analytical approach based on human-sensory evaluations and multi-dimensional gas chromatographic and mass spectrometric techniques. Furthermore, it was tried in this thesis to gain deeper insights into formation pathways and odor sources in these two types of wood and their applications. Most of these odorants comprised aldehydes, acids, lactones, a series of terpenes, mostly mono- and sesquiterpenes, and several odor-active compounds containing a phenolic core moiety. The odor profiles of all wood samples were compared, the potent odorants were determined, and selected odorants of both types of wood samples (oak and Cembran wood samples) were quantified by application of stable isotope dilution assays (SIDA). Odor activity values (OAVs) were calculated based on the odor threshold (OTs) determined in water. The second part of this thesis dealt with the investigation of the effects of different geographical regions and pedoclimatic conditions on the odor of different wood samples. This study focused on elucidating the smell profiles of several natural oak samples from Germany, Austria, and Hungary. Particular consideration is given to view the current challenges associated with climate change on the forestry sector, and thus concerning the respective regional conditions, and underwent statistical interpretation. In the case of Cembran wood, the influence of different geographical forest regions in Austria and Italy was determined and evaluated by means of principal component analysis (PCA) and statistical interpretation of obtained data. Recombination experiments by mixing the dominant odor-active compounds in their naturally occurring concentrations revealed a good agreement of the model mixtures with the overall smell of the respective native wood samples. In addition, the structure odor relationships in representative substance classes of wood were elucidated. Specifically, the smell impressions of guaiacol and selected structurally related odorants such as alkylated, alkenylated, methoxylated and halogenated guaiacol derivatives were studied. All investigated compounds elicited characteristic smoky, vanilla-like, and /or clove-like smell impressions. Smoky smells, primarily comprising guaiacols, phenols and cresols, are enjoyed in diverse foods and beverages such as wine, whiskey, smoked ham, cheese, or baked goods such as pizza. Furthermore, the studies indicated that the odor properties of alkylated and halogenated guaiacols and phenols demonstrated the smoky smells are not the same for everyone and can be differently perceived in individual humans. Overall, the odor threshold investigation of guaiacol and its alkylated, alkenylated, and methoxylated derivatives showed that no specific substituent caused a significant and universal effect on OT. However, the positioning of the substituents to the hydroxyl function seems to have an impact on OT. Obtained data could be used to identification and analysis of the investigated compounds. Furthermore, the results can also be avail in understanding the structure and the odor correlation of compounds, which is still not fully resolved. Finally, to investigate the wine off-odors, barrel-aged wine samples were analyzed by gas chromatography-olfactometry (GC-O), with regards to the presence of the typical earthy-smelling off-odor. The 2-methylisoborneol (2-MIB) was detected in these wines, although the wine samples were seven years old and all the previous studies showed that this substance is unstable in wine and must. Degradation products of 2-MIB were synthesised, and with regard to their odor, these dehydration products were found to be odorless. To investigate this paradoxical situation, 2-MIB stability was analyzed in wine and model solutions, starting with an elevated initial concentration. Therefore it was concluded that although 2-MIB concentration greatly decreased with time it still can be detected in old wines and can induce the earthy off-odor.
  • Doctoral thesis
    Open Access
    β2-Mikroglobulin induziert die NLRP3-Inflammasom-Aktivierung in Myelom-assoziierten Makrophagen und fördert das Zellwachstum beim Multiplen Myelom
    (2024) Hofbauer-Stache, Daniel; Burkovski, Andreas
    Das MM (Multiples Myelom, Multiple myeloma) ist eine bisher unheilbare hämatologische B-Zellerkrankung, die durch die monoklonale Proliferation und Akkumulation maligner Plasma-zellen im KM (Knochenmark) gekennzeichnet ist. Hierbei stellt die inflammatorische Tumor-mikroumgebung, die mit den malignen Plasmazellen wechselwirkt, eine Schlüsselkomponente des MM dar. Diese trägt zur Aufrechterhaltung des Wachstums maligner MM-Zellen bei und wirkt sich sowohl auf die Bildung osteolytischer Läsionen als auch auf das gesamte Immun-system aus. Zwar ist bisher unklar, welchem physiologischen Ursprung das inflammatorische Tumormikromilieu bei MM-Patient:innen zugrunde liegt. Dennoch wir vermutet, dass proin-flammatorische MAMs (Myelom-assoziierte Makrophagen, Myeloma-associated macropha-ges) das KM-Tumorstroma infiltrieren und durch die Freisetzung von Wachstumsfaktoren und den proinflammatorischen Zytokinen IL-(Interleukin, Interleukin)-1β und IL-18 eine inflammato-rische Tumormikroumgebung induzieren. Diese stellen einen ungünstigen prognostischen Faktor dar und begünstigen die MM-Pathogenese. Aus diesem Grund wurde in der vorliegen-den Arbeit geklärt, welcher Zusammenhang zwischen einem in MAMs aktiven NLRP-(Nucleotide-binding oligomerization, leucine-rich repeat and pyrin domain-containing)-3-Inflammasom, das zelluläre Entzündungsreaktionen reguliert, der Entstehung einer inflamma-torischen Tumormikroumgebung und dem MM-Zellwachstum besteht. Zahlreiche Ergebnisse sprechen dafür, dass das aktive NLRP3-Inflammasom die MM-Pathogenese im KM von MM-Patient:innen maßgeblich beeinflusst. Dies wurde unter Verwendung des spezifischen NLRP3-Inflammasom-Inhibitors MCC950 bestätigt, der NLRP3-assoziierte Effekte signifikant reduzierte. Darüber hinaus wurde neben IL-1β insbesondere IL-18 als Wachstumsfaktor identi-fiziert, der den Rezeptor IL-18Rα auf der MM-Zelloberfläche stimuliert und somit eine ent-scheidende Rolle für das MM-Zellwachstum spielt. Hierbei wurde geklärt, welche Bedeutung β2m (β2-Mikroglobulin, β2-microglobulin), einer Komponente des MHC-(Haupthistokompatibilitätskomplex, Major histocompatibility complex)-I-Komplexes, zukommt. Frühere Studien sprechen dafür, dass eine hohe β2m-Konzentration mit der MM-Tumorlast, einer schlechten Prognose und dem Nichtansprechen von MM-Patient:innen auf eine Therapie korreliert. Außerdem synthetisieren MM-Zellen größere β2m-Mengen und setzen diese frei. Bisher ist jedoch wenig über die biologische Wirkung und das immunregulatorische Potential von β2m bekannt. Eine frühere Studie deutet darauf hin, dass β2m eine proinflammatorische Immunantwort in myeloischen Zellen induziert. Aus diesem Grund wurde weiterhin geklärt, ob β2m die Entstehung eines inflammatorischen Tumormikromilieus beeinflusst und das MM-Zellwachstum fördert. Zahlreiche Ergebnisse der vorliegenden Arbeit identifizierten β2m als endogenes DAMP (Schaden-assoziiertes molekulares Muster, Damage-associated molecular pattern), das das aktive NLRP3-Inflammasom in humanen Makrophagen induzierte und die Sekretion der proinflammatorischen Zytokine IL-1β und IL-18 begünstigte. Nachdem humane Makrophagen β2m phagozytierten, befand sich β2m im reifen Lysosom, das einen niedrigen pH-(Potentia hydrogenii)-Wert zwischen 4,5 und 5 aufweist. Da freies β2m die einzigartige Eigenschaft besitzt, unter einem in den Lysosomen vorherrschenden pH-Wert zu aggregieren, bildeten sich Amyloidfibrillen. Die Akkumulation der Amyloidfibrillen rief eine lysosomale Schädigung hervor, wodurch lysosomale Proteasen freigesetzt wurden, die das aktive NLRP3-Inflammasom und die daraus resultierende IL-1β- und IL-18-Sekretion induzierten. Hierbei stellen die β2m-Phagozytose sowie die lysosomale β2m-Aggregation die zellulären und molekularen Schlüsselereignisse dar. Diese Ergebnisse konnten unter Verwendung der β2m-Mutation W60G bestätigt werden. W60G weist im Vergleich zu β2m eine niedrigere Ag-gregationstendenz auf und war daher nicht in der Lage, ein aktives NLRP3-Inflammasom zu induzieren. Darüber hinaus lassen zahlreiche Ergebnisse vermuten, dass β2m das aktive NLRP3-Inflammasom in MAMs induzierte. Dadurch konnte das inflammatorische Tumormik-romilieu aufrechterhalten und sowohl das MM-Zellwachstum als auch die MM-Pathogenese entscheidend beeinflusst werden. Der Fokus richtete sich insbesondere auf das proinflamma-torische Zytokin IL-18, das das MM-Zellwachstum entscheidend begünstigte. Zukünftige präk-linische und klinische Studien sollten jedoch klären, ob IL-18 als universeller Wachstumsfaktor fungiert. Die Ergebnisse der vorliegenden Arbeit könnten den Weg für die Entwicklung neuar-tiger Wirkstoffe ebnen, sodass zukünftige therapeutische Ansätze optimiert und individuelle Behandlungen dieser schweren Erkrankung ermöglicht werden (Abbildung 2-1).
  • Doctoral thesis
    Open Access
    Highly Reactive Aluminyl Anions and Monomeric Alumoxanes
    (2024) Grams, Samuel; Harder, Sjoerd
    Dissertationsschrift zur Erlangung des Doktorgrades Dr. rer. nat.
  • Doctoral thesis
    Open Access
    Consistency, Robustness and Sparsity for Learning Algorithms
    (2024) Roith, Tim; Burger, Martin
    This thesis is concerned with consistency, robustness and sparsity of supervised and semi-supervised learning algorithms. For the latter, we consider the so-called Lipschitz learning task (Nadler, Boaz, Nathan Srebro, and Xueyuan Zhou. "Statistical analysis of semi-supervised learning: The limit of infinite unlabelled data." Advances in neural information processing systems 22 (2009)) for which we prove Gamma convergence and convergence rates for discrete solutions to their continuum counterpart in the infinite data limit. In the supervised regime, we deal with input-robustness w.r.t. adversarial attacks and resolution changes. For the multi-resolution setting, we analyze the role of Fourier neural operators (Li, Zongyi, et al. "Fourier neural operator for parametric partial differential equations." arXiv preprint arXiv:2010.08895 (2020).) and their connection to standard convolutional neural layers. Concerning the computational complexity of neural network training, we propose an algorithm based on Bregman iterations (Osher, Stanley, et al. "An iterative regularization method for total variation-based image restoration." Multiscale Modeling & Simulation 4.2 (2005)) that allows for sparse weight matrices throughout the training. We also provide the convergence analysis for the stochastic adaption of the original Bregman iterations.
  • Doctoral thesis
    Open Access
    X-ray Observations of Accreting Compact Objects
    (2024) König, Ole; Wilms, Jörn
    In meiner Dissertation untersuche ich die Physik akkretierender kompakter Objekte in Doppelsternsystemen. Die Akkretion von Materie eines Begleitsterns führt zu der Bildung einer turbulenten Scheibe um das kompakte Objekt, die effizient gravitative potenzielle Energie in Strahlung umwandelt. In Schwarzlochdoppelsternen kann stark variable Röntgenstrahlung mit weltraumbasierten Teleskopen detektiert werden. Sie entsteht durch Comptonisierung in direkter Nähe des Schwarzen Lochs. Die genaue Geometrie dieser Region ist jedoch umstritten. Bereits kurz nach der Entdeckung des ersten Schwarzen Lochs, Cygnus X-1, wurde erkannt, dass die Variabilität im harten Röntgenwellenlängenbereich genutzt werden kann um Aussagen über die Struktur der innersten Region des Systems zu treffen. Wie sich jedoch die Variabilität der Akkretionsscheibe auf das generelle Verhalten der Quelle auswirkt, kann nur zuverlässig in der weichen Röntgenstrahlung betrachtet werden. Diese Studien sind in den letzten Jahren durch eine neue Röntgenmission möglich geworden. Cygnus X-1 zeigt Übergänge zwischen einem spektral harten Zustand, der von comptonisierter Emission dominiert ist, und einem weichen Zustand, in dem die Strahlung der Akkretionscheibe dominiert. In meiner Arbeit untersuche ich zum ersten Mal die Variabilität von Cygnus X-1 bei Energien <1keV in diesen Zuständen anhand der Neutron Star Interior Composition Explorer (NICER) Beobachtungskampagne. Ich untersuche die Verbindung der Variabilität zwischen niedrigen und hohen Energien, welche sehr kohärent im harten Spektralzustand ist. Die hohe Kohärenz zeigt, dass es einen Prozess gibt, der die Variabilität verbindet, was stark vermuten lässt, dass es einen kausalen physikalischen Zusammenhang zwischen den Fluktuationen der Akkretionsscheibe und der Variabilität in der comptonisierenden Region gibt. Ich zeige, dass sich dieser Prozess im weichen Spektralzustand fundamental ändert, da die Variabilität inkohärent wird. Im harten Spektralzustand können zwei etablierte Variabilitätskomponenten identifiziert werden. Ich zeige, dass diese Komponenten vermutlich individuellen physikalischen Prozessen in der Akkretionsscheibe und der comptonisierenden Region zugeordnet werden können. Ich entdecke ein neues Variabilitätsphänomen, das klar zwischen diesen beiden Variabilitätskomponenten lokalisiert und nur bei niedrigen Energien zu sehen ist. Es kann charakterisiert werden durch eine abrupte Änderung in den Ankunftszeiten der harten (>2keV) und weichen (<1,5keV) Photonen, zusammen mit einer Reduktion der Kohärenz. Das Phänomen ist fundamental mit den Variabilitätskomponenten verbunden und folgt ihrer wohlbekannten Verschiebung zu höheren Frequenzen wenn Cygnus X-1 weicher wird. Ich zeige, dass das Phänomen nicht nur eine Eigenschaft von Cygnus X-1 ist, sondern auch im harten Spektralzustand von transienten Röntgendoppelsternen zu sehen ist, was die Entdeckung einer neuen generellen Eigenschaft akkretierender Schwarzer Löcher in Doppelsternsystemen suggeriert. Im zweiten Teil meiner Dissertation betrachte ich einen Nova Ausbruch eines akkretierenden Weißen Zwerges. In Doppelsternsystemen mit einem Spenderstern sammelt sich wasserstoffreiche Materie in einer Hülle auf der Oberfläche des Weißen Zwerges. Sobald die Hülle eine kritische Masse erreicht hat, startet eine instabile thermonukleare Explosion, wodurch die Hülle abrupt expandiert und ihre meiste Masse verliert. Dieser Ausbruch wird Nova genannt. Seit über 30 Jahren sagt die Novatheorie die Existenz einer "Feuerball" Phase voraus, die direkt der Kettenreaktion folgt. Diese Phase sollte als weicher, heller und kurzer Röntgenblitz zu sehen sein, bevor die Nova im optischen Licht sichtbar wird. Der Blitz ist jedoch schwierig zu detektieren, da Novae normalerweise durch ihren Helligkeitsanstieg im sichtbaren Licht entdeckt werden. Zu diesem Zeitpunkt ist der Röntgenblitz schon vorbei. Ich präsentiere die klare Detektion eines extrem hellen und sehr weichen Röntgenblitzes von der klassischen galaktischen Nova YZ Reticuli, beobachtet mit dem extended ROentgen Survey with an Imaging Telescope Array (eROSITA) Weltraumteleskop. Der Blitz fand 11 Stunden vor dem 9 Magnituden starken Anstieg im optischen Licht statt und hatte eine maximale Helligkeit von 3,7 Magnituden. Auf der Südhalbkugel war die Quelle für etwa fünf Tage mit dem bloßen Auge sichtbar. Vier Stunden vor und nach dem Ereignis wurde keine Röntgenquelle detektiert, wodurch die Dauer des Blitzes auf unter acht Stunden begrenzt werden konnte. Diese Detektion kann eindeutig der Feuerballphase von YZ Reticuli zugeordnet werden. Die Hauptherausforderung der Analyse ist die extreme Helligkeit der Quelle, die zu schwerwiegender Übersättigung im Detektor führte. Ein detailliertes Verständnis der physikalischen Prozesse im Halbleitermaterial ist notwendig, um die resultierenden Verzerrungen des Spektrums zu verstehen. Der Simulator SIXTE ist in der Lage, diese komplexen Detektoreffekte zu modellieren. Mithilfe eines simulationsbasierten Minimierungsprozesses kann ich so die physikalischen Parameter der Quelle rekonstruieren, insbesondere die Temperatur, Leuchtkraft und Absorption der Photosphäre. In Übereinstimmung mit theoretischen Vorhersagen kann das Spektrum der Quelle mit einem Schwarzkörper einer Temperatur von 3,27+0,11-0,33 x 105 K (28,2+0,9-2,8 eV), oder eines Atmosphärenmodells, modelliert werden. Die Photosphäre emittiert mit der Eddington-Leuchtkraft und ist nur etwas größer als ein Weißer Zwerg. Diese Detektion einer expandierenden Photosphäre eines Weißen Zwergs vor der Abstoßung der Hülle bildet das letzte Verbindungsstück des vorhergesagten photosphärischen Lichtkurvenverlaufs und eröffnet neue Möglichkeiten, um die gesamte Energetik der Nova zu vermessen.
  • Doctoral thesis
    Open Access
    Investigation of micro-macro models for reactive transport in elastically deformable perforated media
    (2024) Knoch, Jonas; Neuss-Radu, Maria
    In this work we deal with mathematical models for transport processes in elastically deformable perforated media, which are motivated, for example, by biomedical applications concerning the transport of nutrients or drugs through deformable biological tissues, like pulmonary or cardiac tissue. The models are needed to provide practically relevant insights into the underlying mechanisms through numerical simulations. In this context, the heterogeneity of the tissue, caused by its cellular structure, as well as a strong coupling of all processes pose challenges for the analytical and numerical treatment. Starting from a microscopic description, where the transport equation is formulated on the deformed domain, we first derive a novel effective micro-macro model in the _Lagrangian_ framework. For this purpose, we transform the transport problem to the reference domain and use asymptotic expansions to formally arrive at the effective model. The information about the heterogeneity and deformation of the underlying medium is now contained in so-called effective coefficients and the derived model is much easier to handle numerically, since the perforations no longer have to be resolved explicitly. We then analytically investigate a unidirectionally coupled version of the effective micro-macro model in which the elastic properties of the medium do not depend on the concentration. Assuming a smallness condition on the data of the elasticity problem, as well as sufficient regularity of all data and the domains, we can prove global existence in time and uniqueness of solutions. To simulate the derived effective micro-macro model, we develop and investigate a numerical scheme that we implement based on the finite element software library _deal.II_. After validating our scheme through grid convergence studies and visualizing numerically computed solutions, we use it to numerically verify the convergence of the microscopic solutions to the effective solutions as the scale parameter $\varepsilon$ approaches zero. Furthermore, we compare the effective micro-macro model with alternative, simpler effective descriptions of transport in elastic perforated media. A numerical sensitivity analysis emphasizes the effects of deformation and microstructure on the transport of diffusing substances through the medium. In addition, we compare different alternative strategies to the efficient and accurate calculation of the effective coefficients based on cell solutions. Here, the approximation of the effective coefficients using a feedforward neural network is superior in terms of time saving and accuracy. Finally, we formulate a mathematical description of key components of energy metabolism in deformable tissues within the framework of the derived effective micro-macro model and reproduce in the simulations key features of the energy metabolism, in particular the metabolic reprogramming under hypoxic conditions that plays a role in various diseases such as sepsis, cancer or Covid-19.
  • Doctoral thesis
    Open Access
    Quantum Optical Nonlinearity of a Single Molecule Strongly Coupled to a Microcavity
    (2024-03) Pscherer, André; Sandoghdar, Vahid
    Achieving near-deterministic photon-emitter and photon-photon interactions is one of the main challenges in constructing large-scale quantum networks. Because of the finite scattering cross-section and branching ratio of emitters existing up to date, it is not possible to achieve this goal without the fabrication of photonic structures around the emitter. In this work, we employ a tunable Fabry-Pérot microcavity with a finesse as high as $\mathcal{F} = 24000$, which selectively enhances the coherent 0-0 zero-phonon line (00ZPL) of a single dibenzoterrylene (DBT) molecule in an anthracene crystal. Due to the small cavity mode volume of only $V = 4.4 \, \lambda^3$, we achieve high coupling rates up to $2g = 2\pi \cdot 1.54 \, \text{GHz}$ between single cavity photons and molecular excitations. This exceeds both the cavity loss rate ($\kappa = 2\pi \cdot 1.3 \, \text{GHz}$) and the free-space emission rate of the molecule ($\gamma = 2\pi \cdot 0.04 \, \text{GHz}$). We report the first spectroscopic observation of a single molecule strongly coupled to a cavity and find a cooperativity of $C = 45$. The transmission spectrum of the coupled system shows two polariton peaks separated by a dip with transmission $T < 1 \, \%$. We furthermore perform ringdown measurements which elucidate the dynamics of the energy transfer between cavity and molecule. This marks the first measurement of a single molecule undergoing single-photon Rabi oscillations. As photon-emitter interactions are highly efficient in this system, we utilize its nonlinearity to mediate photon-photon interactions. Saturating the molecule increases the transmission through the common resonance, reaching $T = 50 \, \%$ with a mean photon number as low as $\bar{n} = 0.40$ in the cavity. In a pump-probe configuration, we benchmark the performance of our system as a high-contrast all-optical switch at the level of single photons. As this nonlinearity is quantum in origin, we inspect the photon statistics of the transmitted light and find an intensity autocorrelation value of $g^{(2)}(0) = 252$ due to the strong selective suppression of single photons. In addition, we show that symmetric two-frequency excitation leads to four- and even six-wave-mixing sidebands in the emitted spectrum. Lastly, we present spectrally tailored dichroic cavity mirrors with a finesse of $\mathcal{F} = 10000$, which transmit Stokes-shifted fluorescence of the molecule. The detected rate of fluorescence light is proportional to the excited state population of the molecule. This additional information enables several new experiments, three of which we evaluate the feasibility of: Firstly, the direct access to the excited-state population can be used to test the prediction that a two-level system, our molecule, can exhibit steady-state inversion when coupled to a high-finesse cavity. Secondly, it is possible to detect cavity-mediated coupling between two molecules by exciting a two-photon transition at the average resonance frequency of the molecules. This gives rise to a resonance which can be observed in the excited-state population, but not in the cavity transmission. Thirdly, we estimate the cavity parameters necessary to resolve the quantization of the AC Stark shift. This would allow us to detect the photon statistics inside the cavity. The results in this thesis benchmark the ability of single molecules to mediate interactions between single photons. This represents a major step towards the realization of a network of quantum emitters connected via a quantum photonic channel.
  • Doctoral thesis
    Open Access
    Interleukin 3 receptor signaling alters the biomechanical and migratory properties of regulatory CD4+ T cells and counteracts intestinal inflammation
    (2024-03-25) Ullrich, Karen Anne-Marie; Zundler, Sebastian; Neurath, Markus
    Inflammatory bowel diseases (IBD) with the most frequent subtypes being ulcerative colitis and Crohn’s disease, are relapsing-remitting inflammatory disorders of the gastrointestinal tract with the highest prevalence in industrialized countries. The main symptoms of IBD are abdominal pain, cramps and diarrhea, which heavily impact the patients’ general well-being. Moreover, due to the chronic nature of the diseases and the risk for serious complications, life-long therapy is often required and affected patients frequently experience substantial constraints in social participation. However, the pathogenesis of IBD is still not fully elucidated and therapeutic options are only effective in subgroups of patients. Thus, more detailed insights into the immunologic mechanisms driving IBD to develop novel treatment options for these diseases are necessary. Despite the fact that an important role of interleukin 3 (IL-3) has been shown in the context of several other immune-mediated diseases such as arthritis, myocarditis or sepsis, its role in IBD is still unknown. Therefore, the aim of this work was to uncover the role of IL-3 for the T cell-dependent pathogenesis of chronic intestinal inflammation by profiling its expression in mice and humans, by addressing its effects on cytoskeleton and mechanobiology, by determining its role for T cell migration in vitro and in vivo and by evaluating its impact on experimental colitis. In the inflamed human and mouse gut tissue an upregulation of IL-3 was observed. Additionally, Il3 and Il3ra deficiency in mice aggravated T cell dependent experimental colitis, which was attributable to alteration of actin cytoskeleton dynamics resulting in higher elasticity of regulatory T cells (Tregs). This led to increased Treg egress from the inflamed gut resulting in an overweight of pro-inflammatory effector T cells. Consistently, IL-3 had similar impact on mechanobiology and migration in human T cells and its expression correlated with the abundance of Tregs in the gut of patients with IBD. Taken together, this study shows for the first time that IL-3 receptor signaling controls T cell trafficking by inducing changes in the actin cytoskeleton leading to modulation of the mechanobiology and, thus, to an altered migratory behavior of regulatory T cells. Therefore, IL-3 seems to be a promising candidate for future therapeutic approaches in IBD.
  • Doctoral thesis
    Open Access
    Synthesis and Reactivity of Low Oxidation State Alkaline-Earth Metal Complexes
    (2024-03-30) Mai, Jonathan; Harder, Sjoerd
    This work describes synthesis and reactivity of low oxidation state alkaline-earth metal complexes.