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The degradation of poly-adenosine tails of messenger RNAs (mRNAs) in the eukaryotic cells is a determining step in controlling the level of gene expression. The highly conserved Ccr4-Not complex was identified as the major deadenylation complex in all eukaryotic organisms. Plenty of biochemical studies have shown that this complex is also involved in many aspects of the mRNA metabolism, but we are still lacking the detailed structural information about its overall architecture and conformational states that could help to elucidate its multifunction and the way it is coordinated in the cells. Such information can also provide a basis to finding a possible way of intervention since the complex is also involved in some diseases such as cancer and cardiovascular disorders in humans. Meanwhile, the single particle Cryo-EM method has been through a “resolution revolution” recently due to the use of the newly developed direct electron detectors and has since resolved the high-resolution structures of many macromolecular protein complexes in their near-native state. Therefore, it was employed as a suitable method for studying the Ccr4-Not complex here. In this work, the Falcon 3EC direct detector mounted on the 300kV Titan Krios G3i Cryo-EM was evaluated for its practical performance at obtaining high-quality Cryo-EM data from protein samples of different molecular sizes. This served as a proof of principle for this detector’s capabilities and as a data collection guidance for studying the macromolecular complexes, such as the Ccr4-Not, when using an advanced high-performance microscope system. Next, the endogenous yeast Ccr4-Not complex was also purified via the immunoaffinity purification method and evaluated using negative staining EM to assess the conditions of the complex before proceeding to sample preparation for Cryo-EM. This has shown that the complex had an unexpected inherently dynamic property in vitro and extra optimisation procedures were needed to stabilise the complex during the purification and sample preparation. In addition, by using the label-free quantitative Mass spectrometry to examine the coimmunoprecipitated complex via different tagged subunits, it was deduced that two of the subunits (Not3/Not5) that shared some sequence similarity might compete for association with the scaffold subunit of the complex. An uncharacterised protein was also identified coimmunoprecipitating with the Caf130 subunit of the yeast complex. Cryo-EM data from the purified complex provided a low-resolution map that represents a surprisingly smaller partial complex as compared to 3D structures from previous studies, although gel electrophoresis and Mass spectrometry data have identified all of the nine subunits of the Ccr4-Not core complex in the sample. It was concluded that due to the presence of many predicted unstructured regions VI in the subunits and their dynamic composition in solution, the native complex could have been spontaneously denatured at the air/water interface during the sample preparation thus limiting the resolution of the Cryo-EM reconstruction. The purified complex was also examined for its deadenylase and ubiquitin ligase activity by in vitro assays. It was shown that the native complex has a different rate of activity and possibly also a different mode of action compared to the recombinant complexes from other species under similar reaction conditions. The Not4 E3 ligase was also shown to be active in the complex and was likely auto-ubiquitinated in the absence of a substrate. Both types of assays have also shown that the conformational flexibility does not seem to affect the enzymatic reactions when using a chemically crosslinked form of the complex for the assay, which implies that there can be other underlying mechanisms coordinating its structural and functional relationship. The findings from this work have therefore moved our understanding of the Ccr4-Not complex forward by looking at the different structural and functional behaviours of the endogenous complex, especially highlighting the obstacles in sample preparation for the native complex in high-resolution Cryo-EM. This would serve as foundation for future studies on the mechanism of this complex’s catalytic functions and also for optimising the Cryo-EM sample to generate better data that could eventually resolve the structure to a high-resolution.
The ubiquitination of proteins serves as molecular signal to control an enormous number of physiological processes and its dysregulation is connected to human diseases like cancer. The versatility of this signal stems from the diverse ways by which ubiquitin can be attached to its targets. Thus, specificity and tight regulation of the ubiquitination are pivotal requirements of ubiquitin signaling. Ubiquitin-conjugating enzymes (E2s) act at the heart of the ubiquitination cascade, transferring ubiquitin from a ubiquitin-activating enzyme (E1) to a ubiquitin ligase (E3) or substrate. When cooperating with a RING-type E3, ubiquitin-conjugating enzymes can determine linkage specificity in ubiquitin chain formation. Our understanding of the regulation of E2 activities is still limited at a structural level.
The work described here identifies two regulation mechanisms in UBE2S, a cognate E2 of the human RING-type E3 anaphase-promoting complex/cyclosome (APC/C). UBE2S elongates ubiquitin chains on APC/C substrates in a Lys11 linkage-specific manner, thereby targeting these substrates for degradation and driving mitotic progression. In addition, UBE2S was found to have a role in DNA repair by enhancing non-homologous end-joining (NHEJ) and causing transcriptional arrest at DNA damage sites in homologous recombination (HR). Furthermore, UBE2S overexpression is a characteristic feature of many cancer types and is connected to poor prognosis and diminished response to therapy.
The first regulatory mechanism uncovered in this thesis involves the intramolecular auto-ubiquitination of a particular lysine residue (Lys+5) close to the active site cysteine, presumably through conformational flexibility of the active site region. The Lys+5-linked ubiquitin molecule adopts a donor-like, ‘closed’ orientation towards UBE2S, thereby conferring auto-inhibition. Notably, Lys+5 is a major physiological ubiquitination site in ~25% of the human E2 enzymes, thus providing regulatory opportunities beyond UBE2S. Besides the active, monomeric state and the auto-inhibited state caused by auto-ubiquitination, I discovered that UBE2S can adopt a dimeric state. The latter also provides an auto-inhibited state, in which ubiquitin transfer is blocked via the obstruction of donor binding. UBE2S dimerization is promoted by its unique C-terminal extension, suppresses auto-ubiquitination and thereby the proteasomal degradation of UBE2S.
Taken together, the data provided in this thesis illustrate the intricate ways by which UBE2S activity is fine-tuned and the notion that structurally diverse mechanisms have evolved to restrict the first step in the catalytic cycle of E2 enzymes.
Alveolar echinococcosis, which is caused by the metacestode stage of the small fox tapeworm Echinococcus multilocularis, is a severe zoonotic disease with limited treatment options. For a better understanding of cestode biology the genome of E. multilocularis, together with other cestode genomes, was sequenced previously. While a few studies were undertaken to explore the E. multilocularis transcriptome, a comprehensive exploration of global transcription profiles throughout life cycle stages is lacking. This work represents the so far most comprehensive analysis of the E. multilocularis transcriptome. Using RNA-Seq information from different life cycle stages and experimental conditions in three biological replicates, transcriptional differences were qualitatively and quantitatively explored. The analyzed datasets are based on samples of metacestodes cultivated under aerobic and anaerobic conditions as well as metacestodes obtained directly from infected jirds. Other samples are stem cell cultures at three different time points of development as well as non-activated and activated protoscoleces, the larval stage that can develop into adult worms. In addition, two datasets of metacestodes under experimental conditions suitable for the detection of genes that are expressed in stem cells, the so-called germinative cells, and one dataset from a siRNA experiment were analyzed. Analysis of these datasets led to expression profiles for all annotated genes, including genes that are expressed in the tegument of metacestodes and play a role in host-parasite interactions and modulation of the host's immune response. Gene expression profiles provide also further information about genes that might be responsible for the infiltrative growth of the parasite in the liver.
Furthermore, germinative cell-specific genes were identified. Germinative cells are the only proliferating cells in E. multilocularis and therefore of utmost importance for the development and growth of the parasite. Using a combination of germinative cell depletion and enrichment methods, genes with specific expression in germinative cells were identified. As expected, many of these genes are involved in translation, cell cycle regulation or DNA replication and repair. Also identified were transcription factors, many of which are involved in cell fate commitment. As an example, the gene encoding the telomerase reverse transcriptase (TERT) was studied further. Expression of E. multilocularis tert in germinative cells was confirmed experimentally. Cell culture experiments indicate that TERT is required for proliferation and development of the parasite, which makes TERT a potentially interesting drug target for chemotherapy of alveolar echinococcosis.
Germinative cell specific genes in E. multilocularis also include genes of densoviral origin. More than 20 individual densovirus loci with information for non-structural and structural densovirus proteins were identified in the E. multilocularis genome. Densoviral elements were also detected in many other cestode genomes. Genomic integration of these elements suggests that densovirus-based vectors might be suitable tools for genetic manipulation of tapeworms. Interestingly, only three of more than 20 densovirus loci in the E. multilocularis genome are expressed. Since the canonical piRNA pathway is lacking in cestodes, this raises the question about potential silencing mechanisms. Exploration of RNA-Seq information indicated natural antisense transcripts as a potential gene regulation mechanism in E. multilocularis. Preliminary experiments further suggest DNA-methylation, which was previously shown to occur in platyhelminthes, as an interesting avenue to explore in future.
The transcriptome datasets also contain information about genes that are expressed in differentiated cells, for example the serotonin transporter gene that is expressed in nerve cells. Cell culture experiments indicate that serotonin and serotonin transport play an important role in E. multilocularis proliferation, development and survival.
Overall, this work provides a comprehensive transcription data atlas throughout the E. multilocularis life cycle. Identification of germinative cell-specific genes and genes important for host-parasite interactions will greatly facilitate future research. A global overview of gene expression profiles will also aide in the detection of suitable drug targets and the development of new chemotherapeutics against alveolar echinococcosis.
Chlamydia trachomatis, an obligate intracellular human pathogen, is the world’s leading cause of infection related blindness and the most common, bacterial sexually transmitted disease. In order to establish an optimal replicative niche, the pathogen extensively interferes with the physiology of the host cell. Chlamydia switches in its complex developmental cycle between the infectious non-replicative elementary bodies (EBs) and the non-infectious replicative reticulate bodies (RBs). The transformation to RBs, shortly after entering a host cell, is a crucial process in infection to start chlamydial replication. Currently it is unknown how the transition from EBs to RBs is initiated. In this thesis, we could show that, in an axenic media approach, L glutamine uptake by the pathogen is crucial to initiate the EB to RB transition. L-glutamine is converted to amino acids which are used by the bacteria to synthesize peptidoglycan. Peptidoglycan inturn is believed to function in separating dividing Chlamydia. The glutamine metabolism is reprogrammed in infected cells in a c-Myc-dependent manner, in order to accomplish the increased requirement for L-glutamine. Upon a chlamydial infection, the proto-oncogene c-Myc gets upregulated to promote host cell glutaminolysis via glutaminase GLS1 and the L-glutamine transporter SLC1A5/ASCT2. Interference with this metabolic reprogramming leads to limited growth of C. trachomatis. Besides the active infection, Chlamydia can persist over a long period of time within the host cell whereby chronic and recurrent infections establish. C. trachomatis acquire a persistent state during an immune attack in response to elevated interferon-γ (IFN-γ) levels. It has been shown that IFN-γ activates the catabolic depletion of L-tryptophan via indoleamine 2,3-dioxygenase (IDO), resulting in the formation of non-infectious atypical chlamydial forms. In this thesis, we could show that IFN-γ depletes the key metabolic regulator c-Myc, which has been demonstrated to be a prerequisite for chlamydial development and growth, in a STAT1-dependent manner. Moreover, metabolic analyses revealed that the pathogen de routs the host cell TCA cycle to enrich pyrimidine biosynthesis. Supplementing pyrimidines or a-ketoglutarate helps the bacteria to partially overcome the persistent state. Together, the results indicate a central role of c-Myc induced host glutamine metabolism reprogramming and L-glutamine for the development of C. trachomatis, which may provide a basis for anti-infectious strategies. Furthermore, they challenge the longstanding hypothesis of L-tryptophan shortage as the sole reason for IFN-γ induced persistence and suggest a pivotal role of c-Myc in the control of the C. trachomatis dormancy.
Articular cartilage is an exceptional connective tissue which by a network of fibrillar collagen and glycosaminoglycan (GAG) molecules allows both low- friction articulation and distribution of loads to the subchondral bone (Armiento et al., 2018, Ulrich-Vinther et al., 2003). Because of its very limited ability to self-repair, chondral defects following traumatic injury increase the risk for secondary osteoarthritis (OA) (Muthuri et al., 2011). Still, current OA treatments such as common nonsteroidal anti-inflammatory drugs (NSAIDs) and joint replacement primarily address end-stage symptoms (Tonge et al., 2014). As low-grade inflammation plays a pivotal role in the pathogenesis of OA (Robinson et al., 2016), there is a strong demand for novel therapeutic concepts, such as integrating application of anti-inflammatory agents into cartilage cell- based therapies in order to effectively treat OA affected joints in early disease stages. The polyphenolic phytoalexin resveratrol (RSV), found in the skin of red grapes, berries, and peanuts, has been shown to have effective anti-inflammatory properties (Shen et al., 2012). However, its long-term effects on 3D chondrocyte constructs cultured in an inflammatory environment with regard to tissue quality have remained unexplored so far. Therefore, in this study, pellets made from expanded porcine articular chondrocytes were cultured for 14 days with either the pro-inflammatory cytokine interleukin-1β (IL-1β) (1 - 10 ng/ml) or RSV (50 μM) alone, or a co-treatment with both agents. Constructs treated with chondrocyte medium only served as control. Treatment with IL-1β at 10 ng/ml resulted in a significantly smaller pellet size and reduced DNA content. However, RSV counteracted the IL-1β-induced decrease and significantly enhanced diameter and DNA content. Also, in terms of GAG deposition, treatment with IL-1β at 10 ng/ml resulted in a tremendous depletion of absolute GAG content and GAG/DNA. Again, RSV co-treatment counteracted the inflammatory stimulus and led to a partial recovery of GAG content. Histological analysis utilizing safranin-O staining confirmed these findings. Marked expression of the cartilage-degrading enzyme matrix metalloproteinase 13 (MMP13) was detected in IL-1β-treated pellets, but none upon RSV co- treatment. Moreover, co-treatment of IL-1β-challenged constructs with RSV significantly increased absolute collagen content. However, under non- inflammatory conditions, RSV induced gene expression and protein accumulation of collagen type X, a marker for undesirable hypertrophy. Taken together, in the present thesis, RSV was demonstrated to elicit marked beneficial effects on the extracellular matrix composition of 3D cartilaginous constructs in long-term inflammatory culture in vitro, but also induced hypertrophy under non-inflammatory conditions. Based on these findings, further experiments examining multiple concentrations of RSV under various inflammatory conditions appear desirable concerning potential therapeutic applicability in OA.
Hematopoietic cell transplantation (HCT) is a curative therapy for the treatment of malignant and non-malignant bone marrow diseases. The major complication of this treatment is a highly inflammatory reaction called Graft-versus-Host Disease (GvHD). Here, transplanted donor T cells cause massive tissue destruction and inflammation in the main target organs liver, skin and the intestine. Currently, this inflammatory reaction can be treated successfully using strong immunosuppressive agents. One efficient group of immunosuppressants are calcineurin inhibitors such as Cyclosporin A (CsA) and Tacrolimus (FK506). These treatment strategies target all T lymphocytes subsets equally and do not separate GvH from the desirable Graft-versus-Leukemia (GvL) effect. Therefore, we aimed to find immunological targets on alloreactive T cells in order to develop novel treatment strategies, which selectively modulates alloreactive T cells without impairing the GvL effect or hematopoietic immune reconstitution.
The aim of this thesis was to develop a predictive marker panel to track alloreactive T cells in the peripheral blood (PB) of murine allo-HCT recipients. In clinically relevant model of aGvHD we demonstrated that alloreactive T cells have a distinct surface marker expression profile and can be detected in the PB before aGvHD manifestation. Based on our data, we propose a combinatory panel consisting of 4 surface markers (a4b7 integrin, CD162E, CD162P und CD62L) on circulating CD8+ T cells to identify the risk of aGvHD after allo-HCT.
Since tumor necrosis factor receptor superfamily (TNFR SF) members are involved in several immunological processes, we did extensive surface marker expression analysis of several TNFR superfamily members and other immunomodulatory molecules on conventional and regulatory T cells (Tcons vs. Tregs) on different time points during aGvHD progression. The aim of this study was to find subset-specific immunomodulatory molecules on recently activated Tcons and Tregs. We found that GITR, 4-1BB and CD27 were highly expressed on alloreactive and naïve Tregs. In contrast, PD1 expression was highly upregulated on recently activated alloreactive Tcons. The data of this study serves as basis for future approaches, which aim to develop T cell subset specific therapeutic antibody fusion proteins.
a4b7 integrin and CD162P (P-Selectin ligand) are highly upregulated on alloreactive T cells and mediate the infiltration of these cells into GvHD target organs. We developed recombinant (antibody) fusion proteins to target these two homing molecules and could show that antibody-based fusion proteins are superior to ligand-based fusion proteins regarding production efficiency and binding affinity. Therefore, we propose for future studies to focus on the described antibody-based fusion proteins for the selective targeting of T cells.
Since the widely used calcineurin inhibitors are impairing the desirable GvL effect, we investigated if selective NFATc1 inhibition might be a novel strategy to prevent or reduce alloreactivity, while hopefully maintaining the GvL effect. In particular, we addressed the role of the isoform NFATc1 and inhibited its posttranslational modification by SUMO (Small Ubiquitin-related Modifier). Indeed, inhibition of NFATc1 SUMOylation resulted in reduced inflammation and increased Treg frequencies in a murine MHC major mismatch aGvHD model.
Conclusively, we showed that alloreactive T cells can be identified by their surface profile in the PB of allo-HCT recipients before aGvHD symptoms appeared. Furthermore, we introduced a approach to selectively target alloreactive T cells by antibody fusion proteins, which might serve as a novel strategy to separate GvH from GvL. Additionally, we demonstrated that averted posttranslational modification of NFATc1 by SUMOylation serves as potential target to reduce alloreactivity of T cells.
As a non-destructive testing method, X-ray imaging has proved to be suitable for the examination of a variety of objects. The measurement principle is based on the attenuation of X-rays caused by these objects. This attenuation can be recorded as shades of intensity using X-ray detectors and thus contains information about the inner structure of the investigated object. Since X-rays are electromagnetic waves, they also experience a change of phase in addition to their attenuation while penetrating an object. In general, imaging methods based on this effect are referred to as phase contrast imaging techniques. In the laboratory, the two mainly used methods are the propagation based phase contrast or in-line phase contrast and the grating interferometry.
While in-line phase contrast - under certain conditions - shows edge enhancement at interfaces due to interference, phase contrast in the grating interferometry is only indirectly measurable by the use of several gratings. In addition to phase contrast, grating interferometry provides access to the so-called dark-field imaging contrast, which measures the scattering of X-rays caused by an object.
These two imaging techniques, together with a novel concept of laboratory X-ray sources, the liquid-metal-jet, form the main part of this work. Compared to conventional X-ray sources, the liquid-metal-jet source offers higher brightness. The term brightness is defined by the number of X-ray photons per second, emitting area (area of the X-ray spot) and solid angle at which they are emitted.
On the basis of this source, a high resolution in-line phase contrast setup was partially developed in the scope of this work. Several computed tomographies show the feasibility of in-line phase contrast and the improvement of image quality by applying phase retrieval algorithms.
Moreover, the determination of optimized sample positions for in-line phase contrast imaging is treated at which the edge enhancement is maximized. Based on primitive fiber objects, this optimization has proven to be a good approximation.
With its high brightness in combination with a high spatial coherence, the liquid-metal-jet source is also interesting for grating interferometry. The development of such a setup is also part of this work. The overall concept and the characterization of the setup is presented as well as the applicability and its limits for the investigation of various objects.
Due to the very unique concept of this grating interferometer it was possible to realize a modified interferometer system by using a single grating only. Its concept and results are also presented in this work.
Furthermore, a grating interferometer based on a microfocus X-ray tube was tested regarding its performance. Thereby, parameters like the anode material, acquisition geometry and gratings were altered in order to find the advantages and disadvantages of each configuration.
Bismuth Amides Mediate Facile and Highly Selective Pn–Pn Radical‐Coupling Reactions (Pn=N, P, As)
(2021)
The controlled release of well‐defined radical species under mild conditions for subsequent use in selective reactions is an important and challenging task in synthetic chemistry. We show here that simple bismuth amide species [Bi(NAr\(_2\))\(_3\)] readily release aminyl radicals [NAr\(_2\)]. at ambient temperature in solution. These reactions yield the corresponding hydrazines, Ar\(_2\)N−NAr\(_2\), as a result of highly selective N−N coupling. The exploitation of facile homolytic Bi−Pn bond cleavage for Pn−Pn bond formation was extended to higher homologues of the pnictogens (Pn=N–As): homoleptic bismuth amides mediate the highly selective dehydrocoupling of HPnR\(_2\) to give R\(_2\)Pn−PnR\(_2\). Analyses by NMR and EPR spectroscopy, single‐crystal X‐ray diffraction, and DFT calculations reveal low Bi−N homolytic bond‐dissociation energies, suggest radical coupling in the coordination sphere of bismuth, and reveal electronic and steric parameters as effective tools to control these reactions.
Clearly, in nature, but also in technological applications, complex systems built in an entirely ordered and regular fashion are the exception rather than the rule. In this thesis we explore how critical phenomena are influenced by quenched spatial randomness. Specifically, we consider physical systems undergoing a continuous phase transition in the presence of topological disorder, where the underlying structure, on which the system evolves, is given by a non-regular, discrete lattice. We therefore endeavour to achieve a thorough understanding of the interplay between collective dynamics and quenched randomness.
According to the intriguing concept of universality, certain laws emerge from collectively behaving many-body systems at criticality, almost regardless of the precise microscopic realization of interactions in those systems. As a consequence, vastly different phenomena show striking similarities at their respective phase transitions. In this dissertation we pursue the question of whether the universal properties of critical phenomena are preserved when the system is subjected to topological perturbations. For this purpose, we perform numerical simulations of several prototypical systems of statistical physics which show a continuous phase transition. In particular, the equilibrium spin-1/2 Ising model and its generalizations represent -- among other applications -- fairly natural approaches to model magnetism in solids, whereas the non-equilibrium contact process serves as a toy model for percolation in porous media and epidemic spreading. Finally, the Manna sandpile model is strongly related to the concept of self-organized criticality, where a complex dynamic system reaches a critical state without fine-tuning of external variables.
Our results reveal that the prevailing understanding of the influence of topological randomness on critical phenomena is insufficient. In particular, by considering very specific and newly developed lattice structures, we are able to show that -- contrary to the popular opinion -- spatial correlations in the number of interacting neighbours are not a key measure for predicting whether disorder ultimately alters the behaviour of a given critical system.
Temporal development of communities with a focus on insects, in time series of one to four decades
(2021)
Changes and development are fundamental principles in biocenoses and can affect a multitude of ecological processes. In insect communities phenological and density changes, changes in species richness and community composition, as well as interactions between those changes, are the most important macro processes. However, climate change and other factors like habitat degradation and loss alter these processes leading to shifts and general biodiversity declines. Even though knowledge about insect decline in central Europe increased during the last decades, there are significant knowledge gaps about the development of insect communities in certain habitats and taxa. For example, insect communities in small lentic as well as in forested habitats are under-sampled and reported to be less endangered than communities in other habitats. Furthermore, the changes within habitats and taxa are additionally influenced by certain traits, like host or feeding specialization. To disentangle these influences and to increase the knowledge about the general long-term development of insect communities, comprehensive long-term monitoring studies are needed. In addition, long-term effects of conservation strategies should also be evaluated on large time scales in order to be able to decide on a scientific base which strategies are effective in promoting possibly declining taxa. Hence, this thesis also tackles the effects of an integrative conservation strategy on wood dependent beetle and fungi, beside the development of water beetle and macro moth communities over multiple decades. In Chapter 2 I present a study on the development of water beetle communities (Dytiscidae, Haliplidae, Noteridae) in 33 water bodies in Southern Germany from 1991 to 2018. Time-standardized capture per waterbody was used during three periods: between 1991 and 1995, 2007 and 2008, and 2017 and 2018. Results showed annual declines in both species number (ca. -1%) and abundance (ca. -2%). In addition, community composition shifted over time in part due to changing pH values. Hence, the recorded changes during the 28-year study period partly reflect natural succession processes. However, since also moor-related beetle species decreased significantly, it is likely that water beetles in southern Germany are also threatened by non-successional factors, including desiccation, increased nitrogen input and/or mineralization, as well as the loss of specific habitats. The results suggest, that in small to midsize lentic waterbodies, current development should aim for constant creation of new water bodies and protection of moor waterbodies in order to protect water beetle communities on a landscape scale. In Chapter 3 I present an analysis of the development of nocturnal macro moth species richness, abundance and biomass over four decades in forests of southern Germany. Two local scale data sets featuring a coppiced oak forest as well as an oak high forest were analysed separately from a regional data set representing all forest types in the temperate zone of Central Europe. At the regional scale species richness, abundance and biomass showed annual declines of ca. 1 %, 1.3 % and 1.4 %, respectively. These declines were more pronounced in plant host specialists and in dark coloured species. In contrast, species richness increased by ca. 1.5 % annually in the coppiced forest, while no significant trends were found in the high forest. In contrast to past assumptions, insect decline apparently affects also hyper diverse insect groups in forests. Since host specialists and dark coloured species were affected more heavily by the decline than other groups, habitat loss and climate change seem to be potential drivers of the observed trends. However, the positive development of species richness in the coppiced oak forest indicates that maintaining complex and diverse forest ecosystems through active management might compensate for negative trends in biodiversity. Chapter 4 features a study specifically aiming to investigate the long-term effect of deadwood enrichment as an integrative conservation strategy on saproxylic beetles and fungi in a central European beech forest at a landscape scale. A before–after control–impact design, was used to compare assemblages and gamma diversities of saproxylic organisms (beetles and fungi) in strictly protected old-growth forest areas (reserves) and previously moderately and intensively managed forest areas. Forests were sampled one year before and a decade after starting a landscape-wide strategy of dead-wood enrichment. Ten years after the start of the dead-wood enrichment, neither gamma diversities of saproxylic organisms nor species composition of beetles did reflect the previous management types anymore. However, fungal species composition still mirrored the previous management gradient. The results demonstrated that intentional enrichment of dead wood at the landscape scale can effectively restore communities of saproxylic organisms and may thus be a suitable strategy in addition to permanent strict reserves in order to protect wood dependent organisms in Europe. In this thesis I showed, that in contrast to what was assumed and partly reported so far, also water beetles in lentic water bodies and macro moths in forests decreased in species richness, abundance and biomass during the last three to four decades. In line with earlier studies, especially dark coloured species and specialists decreased more than light-coloured species and generalists. The reasons for these declines could partly be attributed to natural processes and pollution and possibly to climate change. However, further studies, especially experimental ones, will be needed to achieve a better understanding of the reasons for insect decline. Furthermore, analyses of time series data should be interpreted cautiously especially if the number of sampling years is smaller than ten years. In addition, validation techniques such as left- and right- censoring and cross validation should be used in order to proof the robustness of the analyses. However, the lack of knowledge, we are still facing today, should not prevent scientists and practitioners from applying conservation measures. In order to prove the effectiveness of such measures, long-term monitoring is crucial. Such control of success is essential for evidence based and thus adapted conservation strategies of threatened organisms.
Pertussis is a highly contagious acute respiratory disease of humans which is mainly caused by the gram-negative obligate human pathogen Bordetella pertussis. Despite the availability and extensive use of vaccines, the disease persists and has shown periodic re-emergence resulting in an estimated 640,000 deaths worldwide in 2014. The pathogen expresses various virulence factors that enable it to modulate the host immune response, allowing it to colonise the ciliated airway mucosa. Many of these factors also directly interfere with host signal transduction systems, causing damage to the ciliated airway mucosa and increase mucous production. Of the many virulence factors of B. pertussis, only the tracheal cytotoxin (TCT) is able to recapitulate the pathophysiology of ciliated cell extrusion and blebbing in animal models and in human nasal biopsies. Furthermore, due to the lack of appropriate human models and donor materials, the role of bacterial virulence factors has been extrapolated from studies using animal models infected with either B. pertussis or with the closely related species B. bronchiseptica which naturally causes respiratory infections in these animals and produces many similar virulence factors. Thus, in the present work, in vitro airway mucosa models developed by co-culturing human airway epithelia cells and fibroblasts from the conduction zone of the respiratory tract on a decellularized porcine small intestine submucosa scaffold (SISser®) were used, since these models have a high correlation to native human conducting zone respiratory epithelia. The major aim was to use the engineered airway mucosa models to elucidate the contribution of B. pertussis TCT in the pathophysiology of the disease as well as the virulence mechanism of B. pertussis in general. TCT and lipopolysaccharide (LPS) either alone or in combination were observed to induce epithelial cell blebbing and necrosis in the in vitro airway mucosa model. Additionally, the toxins induced viscous hyper-mucous secretion and significantly disrupted barrier properties of the in vitro airway mucosa models. This work also sought to assess the invasion and intracellular survival of B. pertussis in the polarised epithelia, which has been critically discussed for many years in the literature. Infection of the models with B. pertussis showed that the bacteria can adhere to the models and invade the epithelial cells as early as 6 hours post inoculation. Invasion and intracellular survival assays indicated the bacteria could invade and persist intracellularly in the epithelial cells for up to 3 days. Due to the novelty of the in vitro airway mucosa models, this work also intended to establish a method for isolating individual cells for scRNA-seq after infection with B. pertussis. Cold dissociation with Bacillus licheniformis subtilisin A was found to be capable of dissociating the cells without inducing a strong fragmentation, a problem which occurs when collagenase and trypsin/EDTA are used. In summary, the present work showed that TCT acts possibly in conjunction with LPS to disrupt the human airway mucosa much like previously shown in the hamster tracheal ring models and thus appears to play an important role during the natural B. pertussis infection. Furthermore, we established a method for infecting and isolating infected cells from the airway mucosa models in order to further investigate the effect of B. pertussis infection on the different cell populations in the airway by single cell analytics in the future.
Clinical practice in CMR with respect to cardiovascular disease is currently focused on tissue characterization, and cardiac function, in particular. In recent years MRI based diffusion tensor imaging (DTI) has been shown to enable the assessment of microstructure based on the analysis of Brownian motion of water molecules in anisotropic tissue, such as the myocardium. With respect to both functional and structural imaging, 7T MRI may increase SNR, providing access to information beyond the reach of clinically applied field strengths. To date, cardiac 7T MRI is still a research modality that is only starting to develop towards clinical application.
In this thesis we primarily aimed to advance methods of ultrahigh field CMR using the latest 7T technology and its application towards the functional and structural characterization of the myocardium.
Regarding the assessment of myocardial microstructure at 7T, feasibility of ex vivo DTI of large animal hearts was demonstrated. In such hearts a custom sequence implemented for in vivo DTI was evaluated and fixation induced alterations of derived diffusion metrics and tissue properties were assessed. Results enable comparison of prior and future ex vivo DTI studies and provide information on measurement parameters at 7T.
Translating developed methodology to preclinical studies of mouse hearts, ex vivo DTI provided highly sensitive surrogates for microstructural remodeling in response to subendocardial damage. In such cases echocardiography measurements revealed mild diastolic dysfunction and impaired longitudinal deformation, linking disease induced structural and functional alterations. Complementary DTI and echocardiography data also improved our understanding of structure-function interactions in cases of loss of contractile myofiber tracts, replacement fibrosis, and LV systolic failure.
Regarding the functional characterization of the myocardium at 7T, sequence protocols were expanded towards a dedicated 7T routine protocol, encompassing accurate cardiac planning and the assessment of cardiac function via cine imaging in humans.
This assessment requires segmentation of myocardial contours. For that, artificial intelligence (AI) was developed and trained, enabling rapid automatic generation of cardiac segmentation in clinical data. Using transfer learning, AI models were adapted to cine data acquired using the latest generation 7T system. Methodology for AI based segmentation was translated to cardiac pathology, where automatic segmentation of scar tissue, edema and healthy myocardium was achieved.
Developed radiofrequency hardware facilitates translational studies at 7T, providing controlled conditions for future method development towards cardiac 7T MRI in humans.
In this thesis the latest 7T technology, cardiac DTI, and AI were used to advance methods of ultrahigh field CMR. In the long run, obtained results contribute to diagnostic methods that may facilitate early detection and risk stratification in cardiovascular disease.
The outcome of the innate immune response to biomaterials mainly determines whether the material will be incorporated in the body to fulfill its desired function or, when it gets encapsulated, will be rejected in the worst case. Macrophages are key players in this process, and their polarization state with either pro- (M1), anti-inflammatory (M2), or intermediate characteristics is crucial for deciding on the biomaterial’s fate. While a transient initial pro-inflammatory state is helpful, a prolonged inflammation deteriorates the proper healing and subsequent regeneration. Therefore, biomaterial-based polarization may aid in driving macrophages in the desired direction. However, the in vivo process is highly complex, and a mono-culture of macrophages in vitro displays only one part of the cellular system, but, to this date, there is a lack of established co-cultures to assess the immune response to biomaterials. Thus, this thesis aimed to establish a functional co-culture system of human macrophages and human mesenchymal stromal cells (hMSCs) to improve the assessment of the immune response to biomaterials in vitro. Together with macrophages, hMSCs are involved in tissue regeneration and inflammatory reactions and can modulate the immune response. In particular, endogenously derived hMSCs considerably contribute to the successful engrafting of biomaterials. This thesis focused on poly(ε-caprolactone) (PCL) fiber-based scaffolds produced by the technique of melt electrowriting (MEW) as biomaterial constructs. Via this fabrication technique, uniform, precisely ordered scaffolds varying in geometry and pore size have been created in-house.
To determine the impact of scaffold geometries and pore sizes on macrophages, mono-cultures incubated on scaffolds were conducted. As a pre-requisite to achieve a functional co-culture system on scaffolds, setups for direct and indirect systems in 2D have initially been established. These setups were analyzed for the capability of cell-cell communication. In parallel, a co-culture medium suitable for both cell types was defined, prior to the establishment of a step-by-step procedure for the co-cultivation of human macrophages and hMSCs on fiber-based scaffolds.
Regarding the scaffold morphologies tested within this thesis to improve M2-like polarization, box-shaped scaffolds outperformed triangular-, round- or disordered-shaped ones. Upon further investigation of scaffolds with box-shaped pores and precise inter-fiber spacing from 100 µm down to only 40 µm, decreasing pore sizes facilitated primary human macrophage elongation accompanied by their differentiation towards the M2 type, which was most pronounced for the smallest pore size of 40 µm. To the best of my knowledge, this was the first time that the elongation of human macrophages in a 3D environment has been correlated to their M2-like polarization. Thus, these results may set the stage for the design, the assessment, and the selection of new biomaterials, which can positively affect the tissue regeneration.
The cell communication of both cell types, detected via mitochondria exchange in direct and indirect co-cultures systems, took place in both directions, i.e., from hMSCs to macrophages and vice versa. Thereby, in direct co-culture, tunneling nanotubes enabled the transfer from one cell type to the respective other, while in indirect co-culture, a non-directional transfer through extracellular vesicles (EVs) released into the medium seemed likely. Moreover, the phagocytic activity of macrophages after 2D co-cultivation and hence immunomodulation by hMSCs increased with the highest phagocytic rate after 48 h being most pronounced in direct co-cultivation.
As the commonly used serum supplements for macrophages and hMSCs, i.e., human serum (hS) and fetal calf serum (FCS), respectively, failed to support the respective other cell type during prolonged cultivation, these sera were replaced by human platelet lysate (hPL), which has been proven to be the optimal supplement for the co-cultivation of human macrophages with hMSCs within this thesis. Thereby, the phenotype of both cell types, the distribution of both cell populations, the phagocytic activity of macrophages, and the gene expression profiles were maintained and comparable to the respective standard mono-culture conditions. This was even true when hPL was applied without the anticoagulant heparin in all cultures with macrophages, and therefore, heparin was omitted for further experiments comprising hPL and macrophages.
Accordingly, a step-by-step operating procedure for the co-cultivation on fiber-based scaffolds has been established comprising the setup for 3D cultivation as well as the description of methods for the analysis of phenotypical and molecular changes upon contact with the biomaterial. The evaluation of the macrophage response depending on the cultivation with or without hMSCs and either on scaffolds or on plastic surfaces has been successfully achieved and confirmed the functionality of the suggested procedures.
In conclusion, the functional co-culture system of human macrophages and hMSCs established here can now be employed to assess biomaterials in terms of the immune response in a more in vivo-related way. Moreover, specifically designed scaffolds used within the present thesis showed auspicious design criteria positively influencing the macrophage polarization towards the anti-inflammatory, pro-healing type and might be adaptable to other biomaterials in future approaches.
Hence, follow-up experiments should focus on the evaluation of the co-culture outcome on promising scaffolds, and the suggested operating procedures should be adjusted to further kinds of biomaterials, such as cements or hydrogels.
Functions of bounded variation are most important in many fields of mathematics. This thesis investigates spaces of functions of bounded variation with one variable of various types, compares them to other classical function spaces and reveals natural “habitats” of BV-functions. New and almost comprehensive results concerning mapping properties like surjectivity and injectivity, several kinds of continuity and compactness of both linear and nonlinear operators between such spaces are given. A new theory about different types of convergence of sequences of such operators is presented in full detail and applied to a new proof for the continuity of the composition operator in the classical BV-space. The abstract results serve as ingredients to solve Hammerstein and Volterra integral equations using fixed point theory. Many criteria guaranteeing the existence and uniqueness of solutions in BV-type spaces are given and later applied to solve boundary and initial value problems in a nonclassical setting.
A big emphasis is put on a clear and detailed discussion. Many pictures and synoptic tables help to visualize and summarize the most important ideas. Over 160 examples and counterexamples illustrate the many abstract results and how delicate some of them are.
Aims
Ischaemic stroke (IS) might induce alterations of cardiac function. Prospective data on frequency of cardiac dysfunction and heart failure (HF) after IS are lacking. We assessed prevalence and determinants of diastolic dysfunction (DD), systolic dysfunction (SD), and HF in patients with acute IS.
Methods and results
The Stroke‐Induced Cardiac FAILure in mice and men (SICFAIL) study is a prospective, hospital‐based cohort study. Patients with IS underwent a comprehensive assessment of cardiac function in the acute phase (median 4 days after IS) including clinical examination, standardized transthoracic echocardiography by expert sonographers, and determination of blood‐based biomarkers. Information on demographics, lifestyle, risk factors, symptoms suggestive of HF, and medical history was collected by a standardized personal interview. Applying current guidelines, cardiac dysfunction was classified based on echocardiographic criteria into SD (left ventricular ejection fraction < 52% in men or <54% in women) and DD (≥3 signs of DD in patients without SD). Clinically overt HF was classified into HF with reduced, mid‐range, or preserved ejection fraction. Between January 2014 and February 2017, 696 IS patients were enrolled. Of them, patients with sufficient echocardiographic data on SD were included in the analyses {n = 644 patients [median age 71 years (interquartile range 60–78), 61.5% male]}. In these patients, full assessment of DD was feasible in 549 patients without SD (94%). Prevalence of cardiac dysfunction and HF was as follows: SD 9.6% [95% confidence interval (CI) 7.6–12.2%]; DD in patients without SD 23.3% (95% CI 20.0–27.0%); and clinically overt HF 5.4% (95% CI 3.9–7.5%) with subcategories of HF with preserved ejection fraction 4.35%, HF with mid‐range ejection fraction 0.31%, and HF with reduced ejection fraction 0.78%. In multivariable analysis, SD and fulfilment of HF criteria were associated with history of coronary heart disease [SD: odds ratio (OR) 3.87, 95% CI 1.93–7.75, P = 0.0001; HF: OR 2.29, 95% CI 1.04–5.05, P = 0.0406] and high‐sensitive troponin T at baseline (SD: OR 1.78, 95% CI 1.31–2.42, P = 0.0003; HF: OR 1.66, 95% CI 1.17–2.33, P = 0.004); DD was associated with older age (OR 1.08, 95% CI 1.05–1.11, P < 0.0001) and treated hypertension vs. no hypertension (OR 2.84, 95% CI 1.23–6.54, P = 0.0405).
Conclusions
A substantial proportion of the study population exhibited subclinical and clinical cardiac dysfunction. SICFAIL provides reliable data on prevalence and determinants of SD, DD, and clinically overt HF in patients with acute IS according to current guidelines, enabling further clarification of its aetiological and prognostic role.
Objectives: We compared the effect of different didactic formats - e - learning and role-playing - on medical students' knowledge and counselling skills in smoking cessation training.
Methods: At a German medical school, 145 third-year students were randomly allocated to attend an online course with video examples or an attendance course with role-playing. Students were trained in smoking cessation counselling according to the 5A's (ask, advise, assess, assist, arrange) for approximately 90 minutes. Practical skills were measured in an objective structured clinical examination (OSCE) and represent the primary endpoint of this prospective comparative study. Additionally, changes in theoretic knowledge were assessed by pre - and post - interventional questionnaires and a final written exam.
Results: In the OSCE, overall scores were higher in the attendance group (Mdn=70.8 % vs. 62.8 %; U=119; p=.087, n=36), but a statistical advantage was only found in one single counselling sequence (“Assist”: Mdn=66.7 % vs. 51.4 %; p = .049) and the rating of the standardised patients (M=4.7 vs. 4.2 out of 5 points, t(27.836)=2.0, p=.028). Students’ results (n=130) from self-assessment and written exams suggest that both approaches are equally well suited to increase theoretical knowledge. The online course was more time efficient (90 vs. 73 minutes).
Conclusions: Seminar and web-based training seem equally well suited for transferring knowledge and skills on tobacco cessation counselling. Considering their particular strengths, these two teaching approaches could be combined.
Background
Landscape composition is known to affect both beneficial insect and pest communities on crop fields. Landscape composition therefore can impact ecosystem (dis)services provided by insects to crops. Though landscape effects on ecosystem service providers have been studied in large-scale agriculture in temperate regions, there is a lack of representation of tropical smallholder agriculture within this field of study, especially in sub-Sahara Africa. Legume crops can provide important food security and soil improvement benefits to vulnerable agriculturalists. However, legumes are dependent on pollinating insects, particularly bees (Hymenoptera: Apiformes) for production and are vulnerable to pests. We selected 10 pigeon pea (Fabaceae: Cajunus cajan (L.)) fields in Malawi with varying proportions of semi-natural habitat and agricultural area within a 1 km radius to study: (1) how the proportion of semi-natural habitat and agricultural area affects the abundance and richness of bees and abundance of florivorous blister beetles (Coleoptera: Melloidae), (2) if the proportion of flowers damaged and fruit set difference between open and bagged flowers are correlated with the proportion of semi-natural habitat or agricultural area and (3) if pigeon pea fruit set difference between open and bagged flowers in these landscapes was constrained by pest damage or improved by bee visitation.
Methods
We performed three, ten-minute, 15 m, transects per field to assess blister beetle abundance and bee abundance and richness. Bees were captured and identified to (morpho)species. We assessed the proportion of flowers damaged by beetles during the flowering period. We performed a pollinator and pest exclusion experiment on 15 plants per field to assess whether fruit set was pollinator limited or constrained by pests.
Results
In our study, bee abundance was higher in areas with proportionally more agricultural area surrounding the fields. This effect was mostly driven by an increase in honeybees. Bee richness and beetle abundances were not affected by landscape characteristics, nor was flower damage or fruit set difference between bagged and open flowers. We did not observe a positive effect of bee density or richness, nor a negative effect of florivory, on fruit set difference.
Discussion
In our study area, pigeon pea flowers relatively late—well into the dry season. This could explain why we observe higher densities of bees in areas dominated by agriculture rather than in areas with more semi-natural habitat where resources for bees during this time of the year are scarce. Therefore, late flowering legumes may be an important food resource for bees during a period of scarcity in the seasonal tropics. The differences in patterns between our study and those conducted in temperate regions highlight the need for landscape-scale studies in areas outside the temperate region.
Two series of organic–inorganic composite materials were synthesized through solvothermal imine condensation between diketopyrrolopyrrole dialdehyde DPP-1 and 5,10,15,20-tetrakis(4-aminophenyl)porphyrin (TAPP) in the presence of varying amounts of either amino- or carboxy-functionalized superparamagnetic iron oxide nanoparticles (FeO). Whereas high FeO loading induced cross-linking of the inorganic nanoparticles by amorphous imine polymers, a lower FeO content resulted in the formation of crystalline covalent organic framework domains. All hybrid materials were analyzed by magnetization measurements, powder X-ray diffraction, electron microscopy, IR, and UV/Vis absorption spectroscopy. Crystallinity, chromophore stacking, and visible absorption features are directly correlated to the mass fraction of the components, thus allowing for a fine-tuning of materials properties.
Many species synchronize reproductive behavior with a particular phase of the lunar cycle to increase reproductive success. In humans, a lunar influence on reproductive behavior remains controversial, although the human menstrual cycle has a period close to that of the lunar cycle. Here, we analyzed long-term menstrual recordings of individual women with distinct methods for biological rhythm analysis. We show that women’s menstrual cycles with a period longer than 27 days were intermittently synchronous with the Moon’s luminance and/or gravimetric cycles. With age and upon exposure to artificial nocturnal light, menstrual cycles shortened and lost this synchrony. We hypothesize that in ancient times, human reproductive behavior was synchronous with the Moon but that our modern lifestyles have changed reproductive physiology and behavior.
High attrition-rates entailed by drug testing in 2D cell culture and animal models stress the need for improved modeling of human tumor tissues. In previous studies our 3D models on a decellularized tissue matrix have shown better predictivity and higher chemoresistance. A single porcine intestine yields material for 150 3D models of breast, lung, colorectal cancer (CRC) or leukemia. The uniquely preserved structure of the basement membrane enables physiological anchorage of endothelial cells and epithelial-derived carcinoma cells. The matrix provides different niches for cell growth: on top as monolayer, in crypts as aggregates and within deeper layers. Dynamic culture in bioreactors enhances cell growth. Comparing gene expression between 2D and 3D cultures, we observed changes related to proliferation, apoptosis and stemness. For drug target predictions, we utilize tumor-specific sequencing data in our in silico model finding an additive effect of metformin and gefitinib treatment for lung cancer in silico, validated in vitro. To analyze mode-of-action, immune therapies such as trispecific T-cell engagers in leukemia, as well as toxicity on non-cancer cells, the model can be modularly enriched with human endothelial cells (hECs), immune cells and fibroblasts. Upon addition of hECs, transmigration of immune cells through the endothelial barrier can be investigated. In an allogenic CRC model we observe a lower basic apoptosis rate after applying PBMCs in 3D compared to 2D, which offers new options to mirror antigen-specific immunotherapies in vitro. In conclusion, we present modular human 3D tumor models with tissue-like features for preclinical testing to reduce animal experiments.