@phdthesis{Kerner2021, author = {Kerner, Florian Tobias}, title = {Reactions of rhodium(I) with diynes and studies of the photophysical behavior of the luminescent products}, doi = {10.25972/OPUS-20910}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-209107}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Chapter 1 deals with the reaction of [Rh(acac)(PMe3)2] with para-substituted 1,4-diphenylbuta-1,3-diynes at room temperature, in which a complex containing a bidentate organic fulvene moiety, composed of two diynes, σ-bound to the rhodium center is formed in an all-carbon [3+2] type cyclization reaction. In addition, a complex containing an organic indene moiety, composed of three diynes, attached to the rhodium center in a bis-σ-manner is formed in a [3+2+3] cyclization process. Reactions at 100 °C reveal that the third diyne inserts between the rhodium center and the bis-σ-bound organic fulvene moiety. Furthermore, the formation of a 2,5- and a 2,4-bis(arylethynyl)rhodacyclopentadiene is observed. The unique [3+2] cyclization product was used for the synthesis of a highly conjugated organic molecule, which is hard to access or even inaccessible by conventional methods. Thus, at elevated temperatures, reaction of the [3+2] product with para-tolyl isocyanate led to the formation of a purple organic compound containing the organic fulvene structure and one equivalent of para-tolyl isocyanate. The blue and green [3+2+3] complexes show an unusually broad absorption from 500 - 1000 nm with extinction coefficients ε of up to 11000 M-1 cm-1. The purple organic molecule shows an absorption spectrum similar to those of known diketopyrrolopyrroles. Additionally, the reaction of [Rh(acac)(PMe3)2] with para-tolyl isocyanate was investigated. A cis-phosphine complex of the form cis-[Rh(acac)(PMe3)2(isocyanate)2] with an isocyanate dimer bound to the rhodium center by one carbon and one oxygen atom was isolated. Replacing the trimethylphosphine ligands in [Rh(acac)(PMe3)2] with the stronger σ-donating NHC ligand Me2Im (1,3-dimethylimidazolin-2-ylidene), again, drastically alters the reaction. Similar [3+2] and [3+2+3] products to those discussed above could not be unambiguously assigned, but cis- and trans-π-complexes, which are in an equilibrium with the two starting materials, were formed. Chapters 2 is about the influence of the backbone of the α,ω-diynes on the formation and photophysical properties of 2,5-bis(aryl)rhodacyclopentadienes. Therefore, different α,ω-diynes were reacted with [Rh(acac)(PMe3)2] and [Rh(acac)(P(p-tolyl)3)2] in equimolar amounts. In general, a faster consumption of the rhodium(I) starting material is observed while using preorganized α,ω-diynes with electron withdrawing substituents in the backbone. The isolated PMe3-substituted rhodacyclopentadienes exhibit fluorescence, despite the presence of the heavy atom rhodium, with lifetimes τF of < 1 ns and photoluminescence quantum yields Φ of < 0.01 as in previously reported P(p-tolyl)-substituted 2,5-bis(arylethynyl)rhodacyclopentadienes. However, an isolated P(p-tolyl)-substituted 2,5-bis(aryl)rhodacyclopentadiene shows multiple lifetimes and different absorption and excitation spectra leading to the conclusion that different species may be present. Reaction of [Rh(acac)(Me2Im)2] with dimethyl 4,4'-(naphthalene-1,8-diylbis(ethyne-2,1-diyl))dibenzoate, results in the formation of a mixture trans- and cis-NHC-substituted 2,5-bis(aryl)rhodacyclopentadienes. In chapter 3 the reaction of various acac- and diethyldithiocarbamate-substituted rhodium(I) catalysts bearing (chelating)phosphines with α,ω-bis(arylethynyl)alkanes (α,ω-diynes), yielding luminescent dimers and trimers, is described. The photophysical properties of dimers and trimers of the α,ω-diynes were investigated and compared to para-terphenyl, showing a lower quantum yield and a larger apparent Stokes shift. Furthermore, a bimetallic rhodium(I) complex of the form [Rh2(ox)(P(p-tolyl)3)4] (ox: oxalate) was reacted with a CO2Me-substituted α,ω-tetrayne forming a complex in which only one rhodium(I) center reacts with the α,ω-tetrayne. The photophysical properties of this mixed rhodium(I)/(III) species shows only negligible differences compared to the P(p-tolyl)- and CO2Me-substituted 2,5-bis(arylethynyl)rhodacyclopentadiene, previously synthesized by Marder and co-workers.}, subject = {{\"U}bergangsmetallkomplexe}, language = {en} } @phdthesis{Yang2021, author = {Yang, Tao}, title = {Functional insights into the role of a bacterial virulence factor and a host factor in Neisseria gonorrhoeae infection}, doi = {10.25972/OPUS-20895}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-208959}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Neisseria gonorrhoeae (GC) is a human specific pathogenic bacterium. Currently, N. gonorrhoeae developed resistance to virtually all the available antibiotics used for treatment. N. gonorrhoeae starts infection by colonizing the cell surface, followed by invasion of the host cell, intracellular persistence, transcytosis and exit into the subepithelial space. Subepithelial bacteria can reach the bloodstream and disseminate to other tissues causing systemic infections, which leads to serious conditions such as arthritis and pneumonia. A number of studies have well established the host-pathogen interactions during the initial adherence and invasion steps. However, the mechanism of intracellular survival and traversal is poorly understood so far. Hence, identification of novel bacterial virulence factors and host factors involved in the host-pathogen interaction is a crucial step in understanding disease development and uncovering novel therapeutic approaches. Besides, most of the previous studies about N. gonorrhoeae were performed in the conventional cell culture. Although they have provided insights into host-pathogen interactions, much information about the native infection microenvironment, such as cell polarization and barrier function, is still missing. This work focused on determining the function of novel bacterial virulence factor NGFG_01605 and host factor (FLCN) in gonococcal infection. NGFG_01605 was identified by Tn5 transposon library screening. It is a putative U32 protease. Unlike other proteins in this family, it is not secreted and has no ex vivo protease activity. NGFG_01605 knockout decreases gonococcal survival in the epithelial cell. 3D models based on T84 cell was developed for the bacterial transmigration assay. NGFG_01605 knockout does not affect gonococcal transmigration. The novel host factor FLCN was identified by shRNA library screening in search for factors that affected gonococcal adherence and/or internalization. We discovered that FLCN did not affect N. gonorrhoeae adherence and invasion but was essential for bacterial survival. Since programmed cell death is a host defence mechanism against intracellular pathogens, we further explored apoptosis and autophagy upon gonococcal infection and determined that FLCN did not affect apoptosis but inhibited autophagy. Moreover, we found that FLCN inhibited the expression of E-cadherin. Knockdown of E- cadherin decreased the autophagy flux and supported N. gonorrhoeae survival. Both non-polarized and polarized cells are present in the cervix, and additionally, E-cadherin represents different polarization properties on these different cells. Therefore, we established 3-D models to better understand the functions of FLCN. We discovered that FLCN was critical for N. gonorrhoeae survival in the 3-D environment as well, but not through inhibiting autophagy. Furthermore, FLCN inhibits the E-cadherin expression and disturbs its polarization in the 3-D models. Since N. gonorrhoeae can cross the epithelial cell barriers through both cell-cell junctions and transcellular migration, we further explored the roles FLCN and E-cadherin played in transmigration. FLCN delayed N. gonorrhoeae transmigration, whereas the knockdown of E-cadherin increased N. gonorrhoeae transmigration. In summary, we revealed roles of the NGFG_01605 and FLCN-E-cadherin axis play in N. gonorrhoeae infection, particularly in relation to intracellular survival and transmigration. This is also the first study that connects FLCN and human-specific pathogen infection.}, language = {en} } @phdthesis{Klein2021, author = {Klein, Thomas}, title = {Establishing an in vitro disease model for Fabry Disease using patient specific induced pluripotent stem cell-derived sensory neurons}, doi = {10.25972/OPUS-19970}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-199705}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Fabry disease (FD) is an X-linked lysosomal storage disorder caused by deficiency of the α-galactosidase A (GLA), leading to intracellular accumulations of globotriaosylceramide (Gb3). Acral burning pain, which can be triggered by heat, fever or physical activity is an early hallmark of FD and greatly reduces patients' quality of life. The pathophysiology of FD pain is unknown and research is hindered by the limited in vivo availability of suitable human biomaterial. To overcome this obstacle, we generated induced pluripotent stem cells (iPSC) from one female and two male patients with a differing pain phenotype, and developed a refined differentiation protocol for sensory neurons to increase reliability and survival of these neurons, serving as an in vitro disease model. Neurons were characterized for the correct neuronal subtype using immunocytochemistry, gene expression analysis, and for their functionality using electrophysiological measurements. iPSC and sensory neurons from the male patients showed Gb3 accumulations mimicking the disease phenotype, whereas no Gb3 depositions were detected in sensory neurons derived from the female cell line, likely caused by a skewed X-chromosomal inactivation in favor of healthy GLA. Using super-resolution imaging techniques we showed that Gb3 is localized in neuronal lysosomes of male patients and in a first experiment using dSTORM microscopy we were able to visualize the neuronal membrane in great detail. To test our disease model, we treated the neurons with enzyme replacement therapy (ERT) and analyzed its effect on the cellular Gb3 load, which was reduced in the male FD-lines, compared to non-treated cells. We also identified time-dependent differences of Gb3 accumulations, of which some seemed to be resistant to ERT. We also used confocal Ca2+ imaging to investigate spontaneous neuronal network activity, but analysis of the dataset proofed to be difficult, nonetheless showing a high potential for further investigations. We revealed that neurons from a patient with pain pain are more easily excitable, compared to cells from a patient without pain and a healthy control. We provide evidence for the potential of patient-specific iPSC to generate a neuronal in vitro disease model, showing the typical molecular FD phenotype, responding to treatment, and pointing towards underlying electrophysiological mechanisms causing different pain phenotypes. Our sensory neurons are suitable for state-of-the-art microscopy techniques, opening new possibilities for an in-depth analysis of cellular changes, caused by pathological Gb3 accumulations. Taken together, our system can easily be used to investigate the effect of the different mutations of GLA on a functional and a molecular level in affected neurons.}, subject = {Induzierte pluripotente Stammzelle}, language = {en} } @phdthesis{Vollmuth2021, author = {Vollmuth, Nadine}, title = {Role of the proto-oncogene c-Myc in the development of Chlamydia trachomatis}, doi = {10.25972/OPUS-20365}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-203655}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {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.}, language = {en} } @phdthesis{Mayer2021, author = {Mayer, Alexander E.}, title = {Protein kinase D3 signaling in the regulation of liver metabolism}, doi = {10.25972/OPUS-20797}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-207978}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The liver plays a pivotal role in maintaining energy homeostasis. Hepatic carbohydrate and lipid metabolism are tightly regulated in order to adapt quickly to changes in nutrient availability. Postprandially, the liver lowers the blood glucose levels and stores nutrients in form of glycogen and triglycerides (TG). In contrast, upon fasting, the liver provides glucose, TG, and ketone bodies. However, obesity resulting from a discrepancy in food intake and energy expenditure leads to abnormal fat accumulation in the liver, which is associated with the development of hepatic insulin resistance, non-alcoholic fatty liver disease, and diabetes. In this context, hepatic insulin resistance is directly linked to the accumulation of diacylglycerol (DAG) in the liver. Besides being an intermediate product of TG synthesis, DAG serves as second messenger in response to G-protein coupled receptor signaling. Protein kinase D (PKD) family members are DAG effectors that integrate multiple metabolic inputs. However, the impact of PKD signaling on liver physiology has not been studied so far. In this thesis, PKD3 was identified as the predominantly expressed isoform in liver. Stimulation of primary hepatocytes with DAG as well as high-fat diet (HFD) feeding of mice led to an activation of PKD3, indicating its relevance during obesity. HFD-fed mice lacking PKD3 specifically in hepatocytes displayed significantly improved glucose tolerance and insulin sensitivity. However, at the same time, hepatic deletion of PKD3 in mice resulted in elevated liver weight as a consequence of increased hepatic lipid accumulation. Lack of PKD3 in hepatocytes promoted sterol regulatory element-binding protein (SREBP)-mediated de novo lipogenesis in vitro and in vivo, and thus increased hepatic triglyceride and cholesterol content. Furthermore, PKD3 suppressed the activation of SREBP by impairing the activity of the insulin effectors protein kinase B (AKT) and mechanistic target of rapamycin complexes (mTORC) 1 and 2. In contrast, liver-specific overexpression of constitutive active PKD3 promoted glucose intolerance and insulin resistance. Taken together, lack of PKD3 improves hepatic insulin sensitivity but promotes hepatic lipid accumulation. For this reason, manipulating PKD3 signaling might be a valid strategy to improve hepatic lipid content or insulin sensitivity. However, the exact molecular mechanism by which PKD3 regulates hepatocytes metabolism remains unclear. Unbiased proteomic approaches were performed in order to identify PKD3 phosphorylation targets. In this process, numerous potential targets of PKD3 were detected, which are implicated in different aspects of cellular metabolism. Among other hits, phenylalanine hydroxylase (PAH) was identified as a target of PKD3 in hepatocytes. PAH is the enzyme that is responsible for the conversion of phenylalanine to tyrosine. In fact, manipulation of PKD3 activity using genetic tools confirmed that PKD3 promotes PAH-dependent conversion of phenylalanine to tyrosine. Therefore, the data in this thesis suggests that PKD3 coordinates lipid and amino acid metabolism in the liver and contributes to the development of hepatic dysfunction.}, subject = {Metabolismus}, language = {en} } @phdthesis{Herz2021, author = {Herz, Michaela}, title = {Genome wide expression profiling of Echinococcus multilocularis}, doi = {10.25972/OPUS-20380}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-203802}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {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.}, subject = {Fuchsbandwurm}, language = {en} } @phdthesis{LiessneeEller2021, author = {Liess [n{\´e}e Eller], Anna Katharina Luise}, title = {Understanding the regulation of the ubiquitin-conjugating enzyme UBE2S}, doi = {10.25972/OPUS-20419}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-204190}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {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.}, subject = {E2}, language = {en} } @phdthesis{Dannhaeuser2021, author = {Dannh{\"a}user, Sven}, title = {Function of the Drosophila adhesion-GPCR Latrophilin/CIRL in nociception and neuropathy}, doi = {10.25972/OPUS-20158}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-201580}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Touch sensation is the ability to perceive mechanical cues which is required for essential behaviors. These encompass the avoidance of tissue damage, environmental perception, and social interaction but also proprioception and hearing. Therefore research on receptors that convert mechanical stimuli into electrical signals in sensory neurons remains a topical research focus. However, the underlying molecular mechanisms for mechano-metabotropic signal transduction are largely unknown, despite the vital role of mechanosensation in all corners of physiology. Being a large family with over 30 mammalian members, adhesion-type G protein-coupled receptors (aGPCRs) operate in a vast range of physiological processes. Correspondingly, diverse human diseases, such as developmental disorders, defects of the nervous system, allergies and cancer are associated with these receptor family. Several aGPCRs have recently been linked to mechanosensitive functions suggesting, that processing of mechanical stimuli may be a common feature of this receptor family - not only in classical mechanosensory structures. This project employed Drosophila melanogaster as the candidate to analyze the aGPCR Latrophilin/dCIRL function in mechanical nociception in vivo. To this end, we focused on larval sensory neurons and investigated molecular mechanisms of dCIRL activity using noxious mechanical stimuli in combination with optogenetic tools to manipulate second messenger pathways. In addition, we made use of a neuropathy model to test for an involvement of aGPCR signaling in the malfunctioning peripheral nervous system. To do so, this study investigated and characterized nocifensive behavior in dCirl null mutants (dCirlKO) and employed genetically targeted RNA-interference (RNAi) to cell-specifically manipulate nociceptive function. The results revealed that dCirl is transcribed in type II class IV peripheral sensory neurons - a cell type that is structurally similar to mammalian nociceptors and detects different nociceptive sensory modalities. Furthermore, dCirlKO larvae showed increased nocifensive behavior which can be rescued in cell specific reexpression experiments. Expression of bPAC (bacterial photoactivatable adenylate cyclase) in these nociceptive neurons enabled us to investigate an intracellular signaling cascade of dCIRL function provoked by light-induced elevation of cAMP. Here, the findings demonstrated that dCIRL operates as a down-regulator of nocifensive behavior by modulating nociceptive neurons. Given the clinical relevance of this results, dCirl function was tested in a chemically induced neuropathy model where it was shown that cell specific overexpression of dCirl rescued nocifensive behavior but not nociceptor morphology.}, subject = {Drosophila}, language = {en} } @phdthesis{Gruendl2021, author = {Gr{\"u}ndl, Marco}, title = {Biochemical characterization of the MMB-Hippo crosstalk and its physiological relevance for heart development}, doi = {10.25972/OPUS-21332}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213328}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The Myb-MuvB (MMB) complex plays an essential role in the time-dependent transcriptional activation of mitotic genes. Recently, our laboratory identified a novel crosstalk between the MMB-complex and YAP, the transcriptional coactivator of the Hippo pathway, to coregulate a subset of mitotic genes (Pattschull et al., 2019). Several genetic studies have shown that the Hippo-YAP pathway is essential to drive cardiomyocyte proliferation during cardiac development (von Gise et al., 2012; Heallen et al., 2011; Xin et al., 2011). However, the exact mechanisms of how YAP activates proliferation of cardiomyocytes is not known. This doctoral thesis addresses the physiological role of the MMB-Hippo crosstalk within the heart and characterizes the YAP-B-MYB interaction with the overall aim to identify a potent inhibitor of YAP. The results reported in this thesis indicate that complete loss of the MMB scaffold protein LIN9 in heart progenitor cells results in thinning of ventricular walls, reduced cardiomyocyte proliferation and early embryonic lethality. Moreover, genetic experiments using mice deficient in SAV1, a core component of the Hippo pathway, and LIN9-deficient mice revealed that the correct function of the MMB complex is critical for proliferation of cardiomyocytes due to Hippo-deficiency. Whole genome transcriptome profiling as well as genome wide binding studies identified a subset of Hippo-regulated cell cycle genes as direct targets of MMB. By proximity ligation assay (PLA), YAP and B-MYB were discovered to interact in embryonal cardiomyocytes. Biochemical approaches, such as co-immunoprecipitation assays, GST-pulldown assays, and µSPOT-based peptide arrays were employed to characterize the YAP-B-MYB interaction. Here, a PY motif within the N-terminus of B-MYB was found to directly interact with the YAP WW-domains. Consequently, the YAP WW-domains were important for the ability of YAP to drive proliferation in cardiomyocytes and to activate MMB target genes in differentiated C2C12 cells. The biochemical information obtained from the interaction studies was utilized to develop a novel competitive inhibitor of YAP called MY-COMP (Myb-YAP competition). In MY-COMP, the protein fragment of B-MYB containing the YAP binding domain is fused to a nuclear localization signal. Co-immunoprecipitation studies as well as PLA revealed that the YAP-B-MYB interaction is robustly blocked by expression of MY-COMP. Adenoviral overexpression of MY-COMP in embryonal cardiomyocytes suppressed entry into mitosis and blocked the pro-proliferative function of YAP. Strikingly, characterization of the cellular phenotype showed that ectopic expression of MY-COMP led to growth defects, nuclear abnormalities and polyploidization in HeLa cells. Taken together, the results of this thesis reveal the mechanism of the crosstalk between the Hippo signaling pathway and the MMB complex in the heart and form the basis for interference with the oncogenic activity of the Hippo coactivator YAP.}, subject = {Zellzyklus}, language = {en} } @phdthesis{vonMeyer2021, author = {von Meyer, Katharina}, title = {Molecular characterization of defensin-like proteins in the fertilization process of \(Nicotiana\) \(tabacum\)}, doi = {10.25972/OPUS-19214}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-192141}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Flowering plants or angiosperms have developed a fertilization mechanism that involves a female egg and central cell, as well as two male sperm cells. A male gametophyte carries the two non-mobile sperm cells, as they need to be delivered to the female gametophyte, the embryo sac. This transport is initiated by a pollen grain that is transmitted onto the stigma of the angiosperm flower. Here it hydrates, germinates, and forms a pollen tube, which navigates through the female plant tissue towards the ovary. The pollen tube grows into an ovule through the funiculus and into one of the two synergid cells. There, growth arrests and the pollen tube bursts, releasing the two sperm cells. One of the sperm cells fuses with the egg cell, giving rise to the embryo, the other one fuses with the central cell, developing into the endosperm, which nourishes the embryo during its development. After a successful fertilization, each ovule develops into a seed and a fruit is formed. This usually consists of several fertilized ovules. The directional growth of the pollen tube through the maternal tissues towards the ovule, as well as sperm cell release, requires a complex communication between the male and the female gametophyte to achieve reproductive success. Over the last years many studies have been performed, contributing to the understanding of cell-cell communication events between the two gametophytes, nevertheless still many aspects remain to be elucidated. This work focused on two topics: i.) Analysis of biological processes affected by pollination and fertilization in the Nicotiana tabacum flower and identification of cysteine rich proteins (CRPs) expressed via isolating and sequencing RNA from the tissue and analyzing the resulting data. ii.) Identification of the defensin-like protein (DEFL) responsible for pollen tube attraction towards the ovule in tobacco. First, tissue samples of pollen tubes and mature ovules were taken at different stages of the fertilization process (unpollinated ovules, after pollination, and after fertilization of the flower). RNA was then isolated and a transcriptome was created. The resulting reads were assembled and transcriptome data analysis was performed. Results showed that pollen tubes and mature ovules differ severely from each other, only sharing about 23 \% of the transcripts, indicating that different biological processes are dominant in the two gametophytes. A MapMan analysis revealed that in the pollen tube the most relevant biological processes are related to the cell wall, signaling, and transport, which supports the fact that the pollen tube grows fast to reach the ovule. On the other hand, in the ovule the values of highest significance were obtained for processes related to protein synthesis and regulation. Upon comparing the transcripts in the ovule before and after pollination, as well as after fertilization, it showed that pollination of the flower causes a bigger alteration in the ovule on the transcriptomic level compared to the step from pollination to fertilization. A total of 953 CRPs were identified in Nicotiana tabacum, including 116 DEFLs. Among those, the peptide responsible for pollen tube attraction towards the ovule should be found. Based on in-silico analysis four candidate peptides were chosen for further analysis, two of which had increased expression levels upon pollination and fertilization and the other two displayed an opposite expression. Quantitative real time PCR experiments were performed for the candidates, confirming the in-silico data in vivo. The candidate transcripts were then expressed in a cell free system and applied to pollen tubes in order to test their effect on the growing cells. Positive controls were used, where pollen tubes grew towards freshly dissected ovules. The four candidates did not provoke a pollen tube attraction towards the peptide, leaving open the chance to work on the 112 remaining DEFLs in the future.}, subject = {Samenpflanzen}, language = {en} } @phdthesis{Becker2021, author = {Becker, Isabelle Carlotta}, title = {The role of megakaryocytes and platelets in vascular and osteogenic development}, doi = {10.25972/OPUS-21024}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-210241}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Platelets, small anucleate cell fragments in the blood stream, derive from large precursor cells, so-called megakaryocytes (MK) residing in the bone marrow (BM). In addition to their role in wound healing, platelets have been shown to play a significant role during inflammatory bleeding. Above all, the immunoreceptor tyrosine-based activation motif (ITAM) receptors GPVI as well as CLEC-2 have been identified as main regulators of vascular integrity. In addition to ITAM-bearing receptors, our group identified GPV as another potent regulator of hemostasis and thrombosis. Surprisingly, concomitant lack of GPV and CLEC-2 deteriorated blood-lymphatic misconnections observed in Clec2-/- mice resulting in severe edema formation and intestinal inflammation. Analysis of lymphatic and vascular development in embryonic mesenteries revealed severely defective blood-lymph-vessel separation, which translated into thrombocytopenia and increased vascular permeability due to reduced tight junction density in mesenteric blood vessels and consequent leakage of blood into the peritoneal cavity. Recently, platelet granule release has been proposed to ameliorate the progression of retinopathy of prematurity (ROP), a fatal disease in newborns leading to retinal degradation. The mechanisms governing platelet activation in this process remained elusive nonetheless, which prompted us to investigate a possible role of ITAM signaling. In the second part of this thesis, granule release during ROP was shown to be GPVI- and partly CLEC-2-triggered since blockade or loss of these receptors markedly deteriorated ROP progression. Proplatelet formation from MKs is highly dependent on a functional microtubule and actin cytoskeleton, the latter of which is regulated by several actin-monomer binding proteins including Cofilin1 and Twinfilin1 that have been associated with actin-severing at pointed ends. In the present study, a redundancy between both proteins especially important for the guided release of proplatelets into the bloodstream was identified, since deficiency in both proteins markedly impaired MK functionality mainly due to altered actin-microtubule crosstalk. Besides ITAM-triggered activation, platelets and MKs are dependent on inhibitory receptors, which prevent overshooting activation. We here identified macrothrombocytopenic mice with a mutation within Mpig6b encoding the ITIM-bearing receptor G6b-B. G6b-B-mutant mice developed a severe myelofibrosis associated with sex-specific bone remodeling defects resulting in osteosclerosis and -porosis in female mice. Moreover, G6b-B was shown to be indispensable for MK maturation as verified by a significant reduction in MK-specific gene expression in G6b-B-mutant MKs due to reduced GATA-1 activity.}, subject = {Megakaryozyt}, language = {en} } @phdthesis{Weigand2021, author = {Weigand, Isabel}, title = {Consequences of Protein Kinase A mutations in adrenocortical cells and tumours}, doi = {10.25972/OPUS-16064}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-160646}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Adrenal Cushing's Syndrome (CS) is a rare but life-threatening disease and therefore it is of great importance to understand the pathogenesis leading to adrenal CS. It is well accepted that Protein Kinase A (PKA) signalling mediates steroid secretion in adrenocortical cells. PKA is an inactive heterotetramer, consisting of two catalytic and two regulatory subunits. Upon cAMP binding to the regulatory subunits, the catalytic subunits are released and are able to phosphorylate their target proteins. Recently, activating somatic mutations affecting the catalytic subunit a of PKA have been identified in a sub-population of cortisol-producing adenomas (CPAs) associated with overt CS. Interestingly, the PKA regulatory subunit IIb has long been known to have significantly lower protein levels in a sub-group of CPAs compared to other adrenocortical tumours. Yet, it is unknown, why these CPAs lack the regulatory subunit IIb, neither are any functional consequences nor are the underlying regulation mechanisms leading to reduced RIIb levels known. The results obtained in this thesis show a clear connection between Ca mutations and reduced RIIb protein levels in CPAs but not in other adrenocortical tumours. Furthermore, a specific pattern of PKA subunit expression in the different zones of the normal adrenal gland is demonstrated. In addition, a Ca L206R mutation-mediated degradation of RIIb was observed in adrenocortical cells in vitro. RIIb degradation was found to be mediated by caspases and by performing mutagenesis experiments of the regulatory subunits IIb and Ia, S114 phosphorylation of RIIb was identified to make RIIb susceptible for degradation. LC-MS/MS revealed RIIb interaction partners to differ in the presence of either Ca WT and Ca L206R. These newly identified interaction partners are possibly involved in targeting RIIb to subcellular compartments or bringing it into spatial proximity of degrading enzymes. Furthermore, reducing RIIb protein levels in an in vitro system were shown to correlate with increased cortisol secretion also in the absence of PRKACA mutations. The inhibiting role of RIIb in cortisol secretion demonstrates a new function of this regulatory PKA subunit, improving the understanding of the complex regulation of PKA as key regulator in many cells.}, subject = {Cushing-Syndrom}, language = {en} } @phdthesis{Thomas2021, author = {Thomas, Sarah Katharina}, title = {Design of novel IL-4 antagonists employing site-specific chemical and biosynthetic glycosylation}, doi = {10.25972/OPUS-17517}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-175172}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The cytokines interleukin 4 (IL-4) and IL-13 are important mediators in the humoral immune response and play a crucial role in the pathogenesis of chronic inflammatory diseases, such as asthma, allergies, and atopic dermatitis. Hence, IL-4 and IL-13 are key targets for treatment of such atopic diseases. For cell signalling IL-4 can use two transmembrane receptor assemblies, the type I receptor consisting of receptors IL-4R and γc, and type II receptor consisting of receptors IL-4R and IL-13R1. The type II receptor is also the functional receptor of IL-13, receptor sharing being the molecular basis for the partially overlapping effects of IL-4 and IL-13. Since both cytokines require the IL-4R receptor for signal transduction, this allows the dual inhibition of both IL-4 and IL-13 by specifically blocking the receptor IL-4R. This study describes the design and synthesis of novel antagonistic variants of human IL-4. Chemical modification was used to target positions localized in IL-4 binding sites for γc and IL-13R1 but outside of the binding epitope for IL-4R. In contrast to existing studies, which used synthetic chemical compounds like polyethylene glycol for modification of IL-4, we employed glycan molecules as a natural alternative. Since glycosylation can improve important pharmacological parameters of protein therapeutics, such as immunogenicity and serum half-life, the introduced glycan molecules thus would not only confer a steric hindrance based inhibitory effect but simultaneously might improve the pharmacokinetic profile of the IL-4 antagonist. For chemical conjugation of glycan molecules, IL-4 variants containing additional cysteine residues were produced employing prokaryotic, as well as eukaryotic expression systems. The thiol-groups of the engineered cysteines thereby allow highly specific modification. Different strategies were developed enabling site-directed coupling of amine- or thiol- functionalized monosaccharides to introduced cysteine residues in IL-4. A linker-based coupling procedure and an approach requiring phenylselenyl bromide activation of IL-4 thiol-groups were hampered by several drawbacks, limiting their feasibility. Surprisingly, a third strategy, which involved refolding of IL-4 cysteine variants in the presence of thiol- glycans, readily allowed synthesis of IL-4 glycoconjugates in form of mixed disulphides in milligram amount. This approach, therefore, has the potential for large-scale synthesis of IL-4 antagonists with highly defined glycosylation. Obtaining a homogenous glycoconjugate with exactly defined glycan pattern would allow using the attached glycan structures for fine-tuning of pharmacokinetic properties of the IL-4 antagonist, such as absorption and metabolic stability. The IL-4 glycoconjugates generated in this work proved to be highly effective antagonists inhibiting IL-4 and/or IL-13 dependent responses in cell-based experiments and in in vitro binding studies. Glycoengineered IL-4 antagonists thus present valuable alternatives to IL-4 inhibitors used for treatment of atopic diseases such as the neutralizing anti-IL-4R antibody Dupilumab.}, subject = {Glykosylierung}, language = {en} } @phdthesis{Ruedenauer2021, author = {R{\"u}denauer, Fabian}, title = {Nutrition facts of pollen: nutritional quality and how it affects reception and perception in bees}, doi = {10.25972/OPUS-21254}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212548}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Nutrients belong to the key elements enabling life and influencing an organism's fitness. The intake of nutrients in the right amounts and ratios can increase fitness; strong deviations from the optimal intake target can decrease fitness. Hence, the ability to assess the nutritional profile of food would benefit animals. To achieve this, they need the according nutrient receptors, the ability to interpret the receptor information via perceptive mechanisms, and the ability to adjust their foraging behavior accordingly. Additionally, eventually existing correlations between the nutrient groups and single nutrient compounds in food could help them to achieve this adjustment. A prominent interaction between food and consumer is the interaction between flowering plants (angiosperms) and animal pollinators. Usually both of the interacting partners benefit from this mutualistic interaction. Plants are pollinated while pollinators get a (most of the times) nutritional reward in form of nectar and/or pollen. As similar interactions between plants and animals seem to have existed even before the emergence of angiosperms, these interactions between insects and angiosperms very likely have co-evolved right from their evolutionary origin. Therefore, insect pollinators with the ability to assess the nutritional profile may have shaped the nutritional profile of plant species depending on them for their reproduction via selection pressure. In Chapter I of this thesis the pollen nutritional profile of many plant species was analyzed in the context of their phylogeny and their dependence on insect pollinators. In addition, correlations between the nutrients were investigated. While the impact of phylogeny on the pollen protein content was little, the mutual outcome of both of the studies included in this chapter is that protein content of pollen is mostly influenced by the plant's dependence on insect pollinators. Several correlations found between nutrients within and between the nutrient groups could additionally help the pollinators to assess the nutrient profile of pollen. An important prerequisite for this assessment would be that the pollinators are able to differentiate between pollen of different plant species. Therefore, in Chapter II it was investigated whether bees have this ability. Specifically, it was investigated whether honeybees are able to differentiate between pollen of two different, but closely related plant species and whether bumblebees prefer one out of three pollen mixes, when they were fed with only one of them as larvae. Honeybees indeed were able to differentiate between the pollen species and bumblebees preferred one of the pollen mixes to the pollen mix they were fed as larvae, possibly due to its nutritional content. Therefore, the basis for pollen nutrient assessment is given in bees. However, there also was a slight preference for the pollen fed as larvae compared to another non-preferred pollen mix, at least hinting at the retention of larval memory in adult bumblebees. Chapter III looks into nutrient perception of bumblebees more in detail. Here it was shown that they are principally able to perceive amino acids and differentiate between them as well as different concentrations of the same amino acid. However, they do not seem to be able to assess the amino acid content in pollen or do not focus on it, but instead seem to focus on fatty acids, for which they could not only perceive concentration differences, but also were able to differentiate between. These findings were supported by feeding experiments in which the bumblebees did not prefer any of the pollen diets containing less or more amino acids but preferred pollen with less fatty acids. In no choice feeding experiments, bumblebees receiving a diet with high fatty acid content accepted undereating other nutrients instead of overeating fat, leading to increased mortality and the inability to reproduce. Hence, the importance of fat in pollen needs to be looked into further. In conclusion, this thesis shows that the co-evolution of flowering plants and pollinating insects could be even more pronounced than thought before. Insects do not only pressure the plants to produce high quality nectar, but also pressure those plants depending on insect pollination to produce high quality pollen. The reason could be the insects' ability to receive and perceive certain nutrients, which enables them to forage selectively leading to a higher reproductive success of plants with a pollinator-suitable nutritional pollen profile.}, subject = {Pollen}, language = {en} } @phdthesis{Krimmer2021, author = {Krimmer, Elena}, title = {Agri-environment schemes and ecosystem services: The influence of different sown flower field characteristics on pollination, natural pest control and crop yield}, doi = {10.25972/OPUS-20657}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-206577}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Insects are responsible for the major part of the ecosystem services pollination and natural pest control. If insects decline, these ecosystem services can not longer be reliably delivered. Agricultural intensification and the subsequent loss and fragmentation of habitats has among others been identified to cause insect decline. Ecological intensification aims to promote alternative and sustainable management practices in agricultural farming, for example to decrease the use of external inputs such as pesticides. Agri-environment schemes make amends for farmers if they integrate ecologically beneficial measures into their farming regime and can therefore promote ecological intensification. There is a wide variety of agri-environment schemes, but the implementation of sown flower fields on crop fields is often included. Flower fields offer foraging resources as well as nesting sites for many different insect species and should be able to support insect populations as well as to increase ecosystem services to adjacent fields. However, the potential of flower fields to exhibit these effects is depending on many factors. Among others, the age and size of the flower field can influence if and how different insects profit from the measure. Additionally, the complexity of the surrounding landscape and therefore the existing biodiversity is influencing the potential of flower fields to increase ecosystem services locally. The goal of this study is to disentangle to which degree these factors influence the ecosystem services pollination and natural pest control and if these factors interact with each other. Furthermore, it will be examined if and how flower fields and ecosystem services influence crop yield. Additional factors examined in this study are distance decay and pesticide use. The abundance of beneficial insects can decrease strongly with increasing distance to suitable habitats. Pesticide use in turn could abrogate positive effects of flower fields on beneficial insects. To examine these different aspects and to be able to make recommendations for flower field implementation, field experiments were conducted on differently composed sown flower fields and adjacent oilseed rape fields. Flower fields differed in their age and continuity as well as in their size. Additionally, flower and oilseed rape fields were chosen in landscapes with different amounts of semi-natural habitat. Oilseed rape fields adjacent to calcareous grasslands and conventional crop fields served as controls. Pollinator observations and pollen beetle and parasitism surveys were conducted in the oilseed rape fields. Additionally, different yield parameters of the oilseed rape plants were recorded. Observations were conducted and samples taken in increasing distance to the flower fields to examine distance decay functions. Spray windows were established to inspect the influence of pesticides on ecosystem services and crop yields. Linear mixed models were used for statistical analysis. The results show, that newly established flower fields with high amounts of flower cover are very attractive for pollinators. If the flower fields reached a certain size (> 1.5ha), the pollinators tended to stay in these fields and did not distribute into the surroundings. High amounts of semi-natural habitat in the surrounding landscape increased the value of small flower fields as starting points for pollinators and their subsequent spillover into crop fields. Additionally, high amounts of semi-natural habitat decreased the decay of pollinators with increasing distance to the flower fields. Based on these results, it can be recommended to establish many small flower fields in landscapes with high amounts of semi-natural habitat and large flower fields in landscapes with low amounts of semi-natural habitat. However, it is mentionable that flower fields are no substitute for perennial semi-natural habitats. These still must be actively conserved to increase pollination to crop fields. Furthermore, the lowest amount of pollen beetle infestation was found on oilseed rape fields adjacent to continuous flower fields aged older than 6 years. Flower fields and calcareous grasslands in general increased pollen beetle parasitism in adjacent oilseed rape fields compared to conventional crop fields. The threshold for effective natural pest control could only be reached in the pesticide free areas in the oilseed rape fields adjacent to continuous flower fields and calcareous grasslands. Parasitism and superparasitism declined with increasing distance to the adjacent fields in pesticide treated areas of the oilseed rape fields. However, they remained on a similar level in spray windows without pesticides. Large flower fields increased parasitism and superparasitism more than small flower fields. Flower fields generally have the potential to increase pollen beetle parasitism rates, but pesticides can abrogate these positive effects of flower fields on natural pest control. Last but not least, effects of flower fields and ecosystem services on oilseed rape yield were examined. No positive effects of pollination on oilseed rape yield could be found. Old and continuous flower fields increased natural pest control in oilseed rape fields, which in turn increased seed set and total seed weight of oilseed rape plants. The pesticide treatment had negative effects on natural pest control, but positive effects on crop yield. Pollination and natural pest control decreased with increasing distance to the field edge, but fruit set slightly increased. The quality of the field in terms of soil and climatic conditions did not influence the yield parameters examined in this study. Yield formation in oilseed rape plants is a complex process with many factors involved, and it is difficult to disentangle indirect effects of flower fields on yield. However, perennial flower fields can promote ecological intensification by increasing crop yield via natural pest control. This study contributes to a better understanding of the effects of differently composed flower fields on pollination, natural pest control and oilseed rape yield.}, subject = {{\"O}kologie}, language = {en} } @phdthesis{RuedtvonCollenberg2021, author = {R{\"u}dt von Collenberg, Cora Freifrau}, title = {The role of Ciliary Neurotrophic Factor in hippocampal synaptic plasticity and learning}, doi = {10.25972/OPUS-20664}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-206646}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Ciliary neurotrophic factor (Cntf) acts as a differentiation and survival factor for different types of neurons and glial cells. It is expressed by peripheral Schwann cells and astrocytes in the central nervous system and mediates its effects via a receptor complex involving CntfRα, LifRß and gp130, leading to downstream activation of Stat3. Recent studies by our group have shown that Cntf modulates neuronal microtubule dynamics via Stat3/stathmin interaction. In a mouse model for motor neuron disease, i.e. pmn, Cntf is able to rescue axonal degeneration through Stat3/stathmin signaling. While these findings suggest a role of Cntf in controlling axonal functions in the neuromuscular system, additional data indicate that Cntf might also play a role in synaptic plasticity in the hippocampus. Electrophysiological recordings in hippocampal organotypic cultures and acute slices revealed a deficit in long-term potentiation (LTP) in Cntf -/- mice. This deficit was rescued by 24 h stimulation with Cntf, combined with an acute application of Cntf during LTP-measurements indicating that Cntf is both necessary and sufficient for hippocampal LTP, and possibly synaptic plasticity. Therefore, Cntf knockout mice were investigated to elucidate this possible role of Cntf in hippocampal LTP and synaptic plasticity. First, we validated the presence of Cntf in the target tissue: in the hippocampus, Cntf was localized in Gfap-positive astrocytes surrounding small blood vessels in the fissure and in meningeal areas close to the dentate gyrus. Laser micro-dissection and qPCR analysis showed a similar distribution of Cntf-coding mRNA validating the obtained immunofluorescent results. Despite the strong LTP deficit in organotypic cultures, in vivo behavior of Cntf -/- mice regarding hippocampus-dependent learning and anxiety-related paradigms was largely inconspicuous. However, western blot analysis of hippocampal organotypic cultures revealed a significant reduction of pStat3 levels in Cntf -/- cultures under baseline conditions, which in turn were elevated upon Cntf stimulation. In order to resolve and examine synaptic structures we turned to in vitro analysis of cultured hippocampal neurons which indicated that pStat3 is predominantly located in the presynapse. In line with these findings, presynapses of Cntf -/- cultures were reduced in size and when in contact to astrocytes, contained less pStat3 immunoreactivity compared to presynapses in wildtype cultures. In conclusion, our findings hypothesize that despite of a largely inconspicuous behavioral phenotype of Cntf -/- mice, Cntf appears to have an influence on pStat3 levels at hippocampal synapses. In a next step these two key questions need to be addressed experimentally: 1) is there a compensatory mechanism by members of the Cntf family, possibly downstream of pStat3, which explains the in vivo behavioral results of Cntf -/- mice and can likewise account for the largely inconspicuous phenotype in CNTF-deficient humans? 2) How exactly does Cntf influence LTP through Stat3 signaling? To unravel the underlying mechanism further experiments should therefore investigate whether microtubule dynamics downstream of Stat3 and stathmin signaling are involved in the Cntf-induced modulation of hippocampal synaptic plasticity, similar to as it was shown in motoneurons.}, subject = {Hippocampus}, language = {en} } @phdthesis{Schuster2021, author = {Schuster, Sarah}, title = {Analysis of \(Trypanosoma\) \(brucei\) motility and the infection process in the tsetse fly vector}, doi = {10.25972/OPUS-19269}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-192691}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {African trypanosomes are protist pathogens that are infective for a wide spectrum of mammalian hosts. Motility has been shown to be essential for their survival and represents an important virulence factor. Trypanosoma brucei is transmitted by the bite of the bloodsucking tsetse fly, the only vector for these parasites. The voyage through the fly is complex and requires several migration, proliferation and differentiation steps, which take place in a defined order and in specific fly tissues. The first part of this doctoral thesis deals with the establishment of the trypanosome tsetse system as a new model for microswimmer analysis. There is an increasing interdisciplinary interest in microbial motility, but a lack of accessible model systems. Therefore, this work introduces the first enclosed in vivo host parasite system that is suitable for analysis of diverse microswimmer types in specific microenvironments. Several methods were used and adapted to gain unprecedented insights into trypanosome motion, the fly´s interior architecture and the physical interaction between host and parasite. This work provides a detailed overview on trypanosome motile behavior as a function of development in diverse host surroundings. In additional, the potential use of artificial environments is shown. This can be used to partly abstract the complex fly architecture and analyze trypanosome motion in defined nature inspired geometries. In the second part of the thesis, the infection of the tsetse fly is under investigation. Two different trypanosome forms exist in the blood: proliferative slender cells and cell cycle arrested stumpy cells. Previous literature states that stumpy cells are pre adapted to survive inside the fly, whereas slender cells die shortly after ingestion. However, infection experiments in our laboratory showed that slender cells were also potentially infective. During this work, infections were set up so as to minimize the possibility of stumpy cells being ingested, corroborating the observation that slender cells are able to infect flies. Using live cell microscopy and fluorescent reporter cell lines, a comparative analysis of the early development following infection with either slender or stumpy cells was performed. The experiments showed, for the first time, the survival of slender trypanosomes and their direct differentiation to the procyclic midgut stage, contradicting the current view in the field of research. Therefore, we can shift perspectives in trypanosome biology by proposing a revised life cycle model of T. brucei, where both bloodstream stages are infective for the vector.}, subject = {Motilit{\"a}t}, language = {en} } @phdthesis{Heiby2021, author = {Heiby, Julia}, title = {Insight into molecular mechanisms of folding and self-association of spider silk protein domains}, doi = {10.25972/OPUS-19345}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-193455}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Spider silk is a biomaterial of extraordinary toughness paired with elasticity. The assembly of silk proteins, so-called spidroins (from "spider" and "fibroin"), generates the silk threads we typically see in our garden or the corners of our houses. Although spider webs from different species vary considerably in geometry and size, many sections of spidroin sequences are conserved. Highly conserved regions, found in all spidroins, relate to the terminal domains of the protein, i.e., the N-terminal (NTD) and C-terminal domains (CTD). Both have an essential function in the silk fibre association and polymerisation. The NTD is a 14 kDa five-helix bundle, which self-associates via a pH-driven mechanism. This process is critical for starting the polymerisation of the fibre. However, detailed insights into how conserved this mechanism is in different species and the quantitative thermodynamic comparison between homologous NTDs was missing. For this reason, four homologous NTDs of the major ampullate gland (MaSp) from spider species Euprosthenops australis, Nephila clavipes, Latrodectus hesperus, and Latrodectus geometricus were investigated. I analysed and quantified equilibrium thermodynamics, kinetics of folding, and self-association. Methods involved dynamic light scattering (MALS), stopped-flow fluorescence and circular dichroism spectroscopy in combination with thermal and chemical denaturation experiments. The results showed conserved, cooperative two-state folding on a sub-millisecond time scale. All homologous NTDs showed a similarly fast association in the order of 10^9 M^-1 s^-1, while the resulting equilibrium dissociation constants were in the low nanomolar range. Electrostatic forces were found to be of great importance for protein association. Monomeric protein stability increased with salt concentration while enhancing its folding speed. However, due to Debye-H{\"u}ckel effects, we found intermolecular electrostatics to be shielded, which reduced the NTDs association capacity significantly at high ionic strength. Altogether, the energetics and kinetics of the NTD dimerisation was conserved for all analysed homologs. Comparable to the NTD, the spider silks CTD is also a α-helix bundle, which covalently links two spidroins. The orientation of the domains predetermines the future fibre geometry. Here again, the detailed quantitative characterisation of the folding and dimerisation was missing. Therefore, the CTD from the E. australis was analysed in-depth. The protein folded via a three-state mechanism and was placed in the family of knotted proteins. By analysing the amino acid composition of the NTD of the MaSp1 of the Euprosthenops australis, we found an unusually high content of methionine residues (Met). To elucidate why this protein exhibits so many Met residues, I mutated all core Mets simultaneously to leucine (Leu). Results revealed a dramatically stabilised NTD, which now folded 50 times faster. After solving the tertiary structure of the mutant by NMR (nuclear magnetic resonance) spectroscopy, the structure of the monomeric mutant was found to be identical with the wild-type protein. However, when probing the dimerisation of the NTD, I could show that the association capacity was substantially impaired for the mutant. Our findings lead to the conclusion that Met provides the NTD with enhanced conformational dynamics and thus mobilises the protein, which results in tightly associated dimers. In additional experiments, I first re-introduced new Met residues into the Met-depleted protein at sequence positions containing native Leu. Hence, the mutated NTD protein was provided with the same number of Leu, which were previously removed by mutation. However, the protein did not regain wild-type characteristics. The functionality was not restored, but its stability was decreased as expected. To probe our hypothesis gained from the MaSp NTD, I transferred the experiment to another protein, namely the Hsp90 chaperone. Therefore, I incorporated methionine residues in the protein, which resulted in a slight improvement of its function. Finally, trial experiments were performed aiming at the synthesis of shortened spidroin constructs containing less repetitive middle-segments than the wild-type protein. The objective was to study the findings of the terminal domains in the context of an intact spidroin. The synthesis of these engineered spidroins was challenging. Nevertheless, preliminary results encourage the assumption that the characteristics observed in the isolated domains hold true in the context of a full-length spidroin.}, subject = {Spinnenseide}, language = {en} } @phdthesis{Markert2021, author = {Markert, Sebastian Matthias}, title = {Enriching the understanding of synaptic architecture from single synapses to networks with advanced imaging techniques}, doi = {10.25972/OPUS-18993}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189935}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Because of its complexity and intricacy, studying the nervous system is often challenging. Fortunately, the small nematode roundworm Caenorhabditis elegans is well established as a model system for basic neurobiological research. The C. elegans model is also the only organism with a supposedly complete connectome, an organism-wide map of synaptic connectivity resolved by electron microscopy, which provides some understanding of how the nervous system works as a whole. However, the number of available data-sets is small and the connectome contains errors and gaps. One example of this concerns electrical synapses. Electrical synapses are formed by gap junctions and difficult to map due to their often ambiguous morphology in electron micrographs, leading to misclassification or omission. On the other hand, chemical synapses are more easily mapped, but many aspects of their mode of operation remain elusive and their role in the C. elegans connectome is oversimplified. A comprehensive understanding of signal transduction of neurons between each other and other cells will be indispensable for a comprehensive understanding of the nervous system. In this thesis, I approach these challenges with a combination of advanced light and electron microscopy techniques. First, this thesis describes a strategy to increase synaptic specificity in connectomics. Specifically, I classify gap junctions with a high degree of confidence. To achieve this, I utilized array tomography (AT). In this thesis, AT is adapted for high-pressure freezing to optimize for structure preservation and for super-resolution light microscopy; in this manner, I aim to bridge the gap between light and electron microscopy resolutions. I call this adaptation super-resolution array tomography (srAT). The srAT approach made it possible to clearly identify and map gap junctions with high precision and accuracy. The results from this study showcased the feasibility of incorporating electrical synapses into connectomes in a systematic manner, and subsequent studies have used srAT for other models and questions. As mentioned above, the C. elegans connectomic model suffers from a shortage of datasets. For most larval stages, including the special dauer larval stage, connectome data is completely missing up to now. To obtain the first partial connectome data-set of the C. elegans dauer larva, we used focused ion-beam scanning electron microscopy (FIB-SEM). This technique offers an excellent axial resolution and is useful for acquiring large volumes for connectomics. Together with our collaborators, I acquired several data-sets which enable the analysis of dauer stage-specific "re-wiring" of the nervous system and thus offer valuable insights into connectome plasticity/variability. While chemical synapses are easy to map relative to electrical synapses, signal transduction via chemical transmitters requires a large number of different proteins and molecular processes acting in conjunction in a highly constricted space. Because of the small spatial scale of the synapse, investigating protein function requires very high resolution, which electron tomography provides. I analyzed electron tomograms of a worm-line with a mutant synaptic protein, the serine/threonine kinase SAD-1, and found remarkable alterations in several architectural features. My results confirm and re-contextualize previous findings and provide new insight into the functions of this protein at the chemical synapse. Finally, I investigated the effectiveness of our methods on "malfunctioning," synapses, using an amyotrophic lateral sclerosis (ALS) model. In the putative synaptopathy ALS, the mechanisms of motor neuron death are mostly unknown. However, mutations in the gene FUS (Fused in Sarcoma) are one known cause of the disease. The expression of the mutated human FUS in C. elegans was recently shown to produce an ALS-like phenotype in the worms, rendering C. elegans an attractive disease model for ALS. Together with our collaboration partners, I applied both srAT and electron tomography methods to "ALS worms" and found effects on vesicle docking. These findings help to explain electrophysiological recordings that revealed a decrease in frequency of mini excitatory synaptic currents, but not amplitudes, in ALS worms compared to controls. In addition, synaptic endosomes appeared larger and contained electron-dense filaments in our tomograms. These results substantiate the idea that mutated FUS impairs vesicle docking and also offer new insights into further molecular mechanisms of disease development in FUS-dependent ALS. Furthermore, we demonstrated the broader applicability of our methods by successfully using them on cultured mouse motor neurons. Overall, using the C. elegans model and a combination of light and electron microscopy methods, this thesis helps to elucidate the structure and function of neuronal synapses, towards the aim of obtaining a comprehensive model of the nervous system.}, subject = {Caenorhabditis elegans}, language = {en} } @phdthesis{BergmannBueno2021, author = {Bergmann Bueno, Amauri}, title = {Ecophysiological adaptations of cuticular water permeability of plants to hot arid biomes}, doi = {10.25972/OPUS-16783}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167832}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Arid environments cover almost one-third of the land over the world. Plant life in hot arid regions is prone to the water shortage and associated high temperatures. Drought-stressed plants close the stomata to reduce water loss. Under such conditions, the remaining water loss exclusively happens across the plant cuticle. The cuticular water permeability equals the minimum and inevitable water loss from the epidermal cells to the atmosphere under maximally stomatal closure. Thus, low cuticular water permeability is primordial for plant survival and viability under limited water source. The assumption that non-succulent xerophytes retard water loss due to the secretion of a heavier cuticle is often found in the literature. Intuitively, this seems to be plausible, but few studies have been conducted to evaluate the cuticular permeability of xerophilous plants. In chapter one, we investigated whether the cuticular permeability of Quercus coccifera L. grown in the aridest Mediterranean-subtype climate is indeed lower than that of individuals grown under temperate climate conditions. Also, the cuticular wax chemical compositions of plants grown in both habitats were qualitatively and quantitatively analysed by gas-chromatography. In few words, our findings showed that although the cuticular wax deposition increased in plants under Mediterranean climate, the cuticular permeability remained unaltered, regardless of habitat. The associated high temperatures in arid regions can drastically increase the cuticular water permeability. Thereby, the thermal stability of the cuticular transpirational barrier is decisive for safeguarding non-succulent xerophytes against desiccation. The successful adaptation of plants to hot deserts might be based on finding different solutions to cope with water and heat stresses. Water-saver plants close the stomata before the leaf water potential drastically changes in order to prevent damage, whereas water-spender plants reduce the leaf water potential by opening the stomata, which allow them to extract water from the deep soil to compensate the high water loss by stomatal transpiration. In chapter two, we compare the thermal stability of the cuticular transpiration barrier of the desert water-saver Phoenix dactylifera L. and the water-spender Citrullus colocynthis (L.) Schrad. In short, the temperature-dependent increase of the cuticular permeability of P. dactylifera was linear over the whole temperature range (25-50°C), while that of C. colocynthis was biphasic with a steep increase at temperatures ≥ 40°C. This drastic increase of cuticular permeability indicates a thermally induced breakdown of the C. colocynthis cuticular transpiration barrier, which does not occur in P. dactylifera. We further discussed how the specific chemical composition of the cutin and cuticular waxes might contribute to the pronounced thermal resistance of the P. dactylifera cuticular transpiration barrier. A multitude of morpho and physiological modifications, including photosynthetic thermal tolerance and traits related to water balance, led to the successful plant colonisation of hot arid regions over the globe. High evaporative demand and elevated temperatures very often go along together, thereby constraining the plant life in arid environments. In chapter 3, we surveyed cuticular permeability, leaf thermal tolerance, and cuticular wax chemical composition of 14 non-succulent plant species native from some of the hottest and driest biomes in South-America, Europe, and Asia. Our findings showed that xerophilous flowering plants present high variability for cuticular permeability and leaf thermal tolerance, but both physiological features could not be associated with the species original habitat. We also provide substantial evidence that non-succulent xerophytes with more efficient cuticular transpirational barrier have higher leaf thermal tolerance, which might indicate a potential coevolution of these features in hot arid biomes. We further discussed the efficiency of the cuticular transpiration barrier in function to the cuticular wax chemical composition in the general discussion section.}, subject = {Plant cuticle}, language = {en} } @phdthesis{Schoenwetter2021, author = {Sch{\"o}nwetter, Elisabeth Sofie}, title = {Towards an understanding of the intricate interaction network of TFIIH}, doi = {10.25972/OPUS-16892}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168926}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The integrity of its DNA is fundamental for every living cell. However, DNA is constantly threatened by exogenous and endogenous damaging agents that can cause a variety of different DNA lesions. The severe consequences of an accumulation of DNA lesions are reflected in cancerogenesis and aging. Several DNA repair mechanisms ensure the repair of DNA lesions and thus maintain DNA integrity. One of these DNA repair mechanisms is nucleotide excision repair (NER), which is famous for its ability to address a large variety of structurally unrelated DNA lesions. A key component of eukaryotic NER is the transcription factor II H (TFIIH) complex, which is not only essential for DNA repair but also for transcription. The TFIIH complex is composed of ten subunits. How these subunits work together during NER to unwind the DNA around the lesion is, however, not yet fully understood. High-resolution structural data and biochemical insights into the function of every subunit are thus indispensable to understand the functional networks within TFIIH. The importance of an intact TFIIH complex is reflected in the severe consequences of patient mutations in the TFIIH subunits XPB, XPD or p8 leading to the hallmark diseases xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. Defects in the NER pathway are further associated with several types of cancer including skin cancer. The herein described work focused on five TFIIH subunits derived from the thermophilic fungus Chaetomium thermophilum, the p34/p44 pair and the ternary XPB/p52/p8 complex. The interaction between p34 and p44 was characterized based on a high-resolution structure of the p34_vWA/p44_RING minimal complex. Biochemical studies of the p34/p44 interaction led to the disclosure of an additional interaction between the p34 and p44 subunits, which had not been characterized so far. The p34/p44 interaction was shown to be central to TFIIH, which justifies the presence of several redundant interfaces to safeguard the interaction between the two proteins and might explain why so far, no patient mutations in these subunits have been identified. The p52 subunit of TFIIH was known to be crucial to stimulate the ATPase activity of XPB, which is required during NER. This work presents the first entire atomic resolution structural characterization of p52, which was derived of several crystal structures of p52 variants and a p52/p8 variant thereby demonstrating the interaction between p52 and p8. The precise structural model of p52 offered the possibility to investigate interactions with other TFIIH subunits in more detail. The middle domain 2 of p52 and the N-terminal domain of XPB were shown to mediate the main interaction between the two subunits. An analysis of the p52 crystal structures within recently published cryo-electron microscopy structures of TFIIH provides a model of how p52 and p8 stimulate the ATPase activity of XPB, which is essential for NER and transcription. The structural and biochemical findings of this work provide an additional building block towards the uncovering of the architecture and function of this essential transcription factor.}, subject = {DNS-Reparatur}, language = {en} } @phdthesis{Brosi2021, author = {Brosi, Cornelia}, title = {Functional characterization of the TTF complex and its role in neurodevelopmental disorders}, doi = {10.25972/OPUS-15778}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157783}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The eukaryotic gene expression requires extensive regulations to enable the homeostasis of the cell and to allow dynamic responses due to external stimuli. Although many regulatory mechanisms involve the transcription as the first step of the gene expression, intensive regulation occurs also in the post-transcriptional mRNA metabolism. Thereby, the particular composition of the mRNPs plays a central role as the components associated with the mRNA form a specific "mRNP code" which determines the fate of the mRNA. Many proteins which are involved in this regulation and the mRNA metabolism are affected in diseases and especially neurological disorders often result from an aberrant mRNP code which leads to changes in the regulation and expression of mRNPs. The focus of this work was on a trimeric protein complex which is termed TTF complex based on its subunits TDRD3, TOP3β and FMRP. Biochemical investigations revealed that the three components of the TTF complex are nucleo-cytosolic shuttle proteins which localize in the cytoplasm at the steady-state, associate with mRNPs and are presumably connected to the translation. Upon cellular stress conditions, the TTF components concentrate in stress granules. Thus, the TTF complex is part of the mRNP code, however its target RNAs and function are still completely unknown. Since the loss of functional FMRP results in the fragile X syndrome and TOP3β is associated with schizophrenia and intellectual disability, the TTF complex connects these phenotypically related neuro-psychiatric disorders with each other on a molecular level. Therefore, the aim of this work was to biochemically characterize the TTF complex and to define its function in the mRNA metabolism. In this work, evidence was provided that TDRD3 acts as the central unit of the TTF complex and directly binds to FMRP as well as to TOP3β. Thereby, the interaction of TDRD3 and TOP3β is very stable, whereas FMRP is a dynamic component. Interestingly, the TTF complex is not bound directly to mRNA, but is recruited via the exon junction complex (EJC) to mRNPs. This interaction is mediated by a specific binding motif of TDRD3, the EBM. Upon biochemical and biological investigations, it was possible to identify the interactome of the TTF complex and to define the role in the mRNA metabolism. The data revealed that the TTF complex is mainly associated with "early" mRNPs and is probably involved in the pioneer round of translation. Furthermore, TOP3β was found to bind directly to the ribosome and thus, establishes a connection between the EJC and the translation machinery. A reduction of the TTF components resulted in selective changes in the proteome in cultured cells, whereby individual protein subsets seem to be regulated rather than the global protein expression. Moreover, the enzymatic analysis of TOP3β indicated that TOP3β is a type IA topoisomerase which can catalytically attack not only DNA but also RNA. This aspect is particularly interesting with regard to the connection between early mRNPs and the translation which has been revealed in this work. The data obtained in this work suggest that the TTF complex plays a role in regulating the metabolism of an early mRNP subset possibly in the course of the pioneer round of translation. Until now, the link between an RNA topoisomerase and the mRNA metabolism is thereby unique and thus provides a completely new perspective on the steps in the post-transcriptional gene expression and its regulation.}, subject = {Messenger-RNP}, language = {en} } @phdthesis{Auer2021, author = {Auer, Daniela}, title = {Impact of the chlamydial deubiquitinase ChlaDUB1 on host cell defense}, doi = {10.25972/OPUS-17846}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178462}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The human pathogen Chlamydia trachomatis is the main cause of sexually transmitted infections worldwide. The obligate intracellular bacteria are the causative agent of several diseases that reach from conjunctivitis causing trachoma and blindness as well as salpingitis and urethritis which can lead to infertility if left untreated. In order to gain genetically engineered Chlamydia that inducible knock down specific gene expression, the CRISPRi system was established in C. trachomatis. In a proof of principle experiment it was shown that C. trachomatis pCRISPRi:gCdu1III target ChlaDUB1 expression and reduce the protein amount up to 50 \%. Knock-down of the DUB did not influence protein levels of anti-apoptotic Mcl-1 and did not make cells susceptible for apoptosis. However, reduced dCas9 protein size, bacterial growth impairment and off target effects interfering with the GFP signal, form obstacles in CRISPRi system in Chlamydia. For routinely use of the CRISPRi method in C. trachomatis further investigation is needed. Since the bacterial life cycle includes two morphological and functional distinct forms, it is essential for chlamydial spread to complete the development cycle and form infectious progeny. Therefore, Chlamydia has evolved strategies to evade the host immune system in order to stay undetected throughout the developmental cycle. The bacteria prevent host cell apoptosis via stabilization of anti-apoptotic proteins like Mcl-1, Survivin and HIF-1α and activate pro-survival pathways, inhibiting invasion of immune cells to the site of infection. The host cell itself can destroy intruders via cell specific defense systems that involve autophagy and recruitment of professional immune cells. In this thesis the role of the chlamydial deubiuqitinase ChlaDUB1 upon immune evasion was elucidated. With the mutant strain Ctr Tn-cdu1 that encodes for a truncated DUB due to transposon insertion, it was possible to identify ChlaDUB1 as a potent opponent of the autophagic system. Mutant inclusions were targeted by K48 and K63 chain ubiquitination. Subsequently the inclusion was recognized by autophagic receptors like p62, NBR1 and NDP52 that was reversed again by complementation with the active DUB. Xenophagy was promoted so far as LC3 positive phagosomes formed around the inclusion of Ctr Tn-cdu1, which did not fuse with the lysosome. The detected growth defect in human primary cells of Chlamydia missing the active DUB was not traced back to autophagy, but was due to impaired development and replication. It was possible to identify Ankib1, the E3 ligase, that ubiquitinates the chlamydial inclusion in a siRNA based screen. The activating enzyme Ube1 and the conjugating enzyme Ube2L3 are also essential in this process. Chlamydia have a reduced genome and depend on lipids and nutrients that are translocated from the host cell to the inclusion to proliferate. Recruitment of fragmented Golgi stacks to the inclusion surface was prevented when ChlaDUB1 was inactive, probably causing diminished bacterial growth. Additionally, the modification of the inclusion by Ankib1 and subsequent decoration by autophagic markers was not only present in human but also murine cells. Comparison of other Chlamydia strains and species revealed Ankib1 to be located at the proximity of the inclusion in C. trachomatis strains only but not in C. muridarum or C. pneumoniae, indicating that Ankib1 is specifically the E3 ligase of C. trachomatis. Moreover, the role of ChlaDUB1 in infected tissue was of interest, since ChlaDUB1 protein was also found in early EB stage and so might get in contact with invading immune cells after cell lysis. While bacteria spread and infect new host cells, Chlamydia can also infect immune cells. Infection of human neutrophils with Ctr Tn-cdu1 shows less bacterial survival and affirms the importance of the DUB for bacterial fitness in these cells.}, subject = {Chlamydia}, language = {en} } @phdthesis{KimbadiLombe2021, author = {Kimbadi Lombe, Blaise}, title = {Novel-Type Dimeric Naphthylisoquinoline Alkaloids from Congolese Ancistrocladus Lianas: Isolation, Structural Elucidation, and Antiprotozoal and Anti-Tumoral Activities}, doi = {10.25972/OPUS-19178}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191789}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Herein described is the discovery of three novel types of dimeric naphthylisoquinoline alkaloids, named mbandakamines, cyclombandakamines, and spirombandakamines. They were found in the leaves of a botanically as yet unidentified, potentially new Ancistrocladus species, collected in the rainforest of the Democratic Republic of the Congo (DRC). Mbandakamines showed an exceptional 6′,1′′-coupling, in the peri-position neighboring one of the outer axes, leading to an extremely high steric hindrance at the central axis, and to U-turn-like molecular shape, which - different from all other dimeric NIQs, whose basic structures are all quite linear - brings three of the four bicyclic ring systems in close proximity to each other. This created an unprecedented follow-up chemistry, involving ring closure reactions, leading to two further, structurally even more intriguing subclasses, the cyclo- and the spirombandakamines, displaying eight stereogenic elements (the highest total number ever found in naphthylisoquinoline alkaloids). The metabolites exhibited pronounced antiplasmodial and antitrypanosomal activities. Likewise reported in this doctoral thesis are the isolation and structural elucidation of naphthylisoquinoline alkaloids from two further potentially new Ancistrocladus species from DRC. Some of these metabolites have shown pronounced antiausterity activities against human pancreatic cancer PANC-1 cells.}, subject = {Naphthylisochinolinalkaloide}, language = {en} } @phdthesis{Spieler2021, author = {Spieler, Valerie}, title = {Bioinspired drug delivery of interleukin-4}, doi = {10.25972/OPUS-19359}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-193590}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Chronic inflammatory diseases such as rheumatoid arthritis, type 2 diabetes and cardiovascular diseases, are associated with the homeostatic imbalance of one of several physiological systems combined with the lack of spontaneous remission, which causes the disease to persevere throughout patients' lives. The inflammatory response relies mainly on tissue-resident, pro-inflammatory M1 type macrophages and, consequently, a chance for therapeutic intervention lies in driving macrophage polarization towards the anti-inflammatory M2 phenotype. Therefore, anti-inflammatory cytokines that promote M2 polarization, including interleukin-4 (IL4), have promising therapeutic potential. Unfortunately, their systemic use is hampered by a short serum half-life and dose-limiting toxicity. On the way towards cytokine therapies with superior safety and efficacy, this thesis is focused on designing bioresponsive delivery systems for the anti-inflammatory cytokine IL4. Chapter 1 describes how anti-inflammatory cytokines are tightly regulated in chronic, systemic inflammation as in rheumatoid arthritis but also in acute, local inflammation as in myocardial infarction. Both diseases show a characteristic progression during which anti-inflammatory cytokine delivery is of variable benefit. A conventional, passive drug delivery system is unlikely to release the cytokines such that the delivery matches the dynamic course of the (patho-)physiological progress. This chapter presents a blueprint for active drug delivery systems equipped with a 24/7 inflammation detector that continuously senses for matrix metalloproteinases (MMP) as surrogate markers of the disease progress and responds by releasing cytokines into the affected tissues at the right time and place. Because they are silent during phases of low disease activity, bioresponsive depots could be used to treat patients in asymptomatic states, as a preventive measure. The drug delivery system only gets activated during flares of inflammation, which are then immediately suppressed by the released cytokine drug and could prevent the steady damage of subclinical chronic inflammation, and therefore reduce hospitalization rates. In a first proof of concept study on controlled cytokine delivery (chapter 2), we developed IL4-decorated particles aiming at sustained and localized cytokine activity. Genetic code expansion was deployed to generate muteins with the IL4's lysine 42 replaced by two different unnatural amino acids bearing a side chain suitable for click chemistry modification. The new IL4 muteins were thoroughly characterized to ensure proper folding and full bioactivity. Both muteins showed cell-stimulating ability and binding affinity to IL4 receptor alpha similar to those of wild type IL4. Copper-catalyzed (CuAAC) and strain-promoted (SPAAC) azide-alkyne cycloadditions were used to site-selectively anchor IL4 to agarose particles. These particles had sustained IL4 activity, as demonstrated by the induction of TF-1 cell proliferation and anti-inflammatory M2 polarization of M-CSF-generated human macrophages. This approach of site-directed IL4 anchoring on particles demonstrates that cytokine-functionalized particles can provide sustained and spatially controlled immune-modulating stimuli. The idea of a 24/7 sensing, MMP driven cytokine delivery system, as described in the introductory chapter, was applied in chapter 3. There, we simulated the natural process of cytokine storage in the extracellular matrix (ECM) by using an injectable solution of IL4 for depot formation by enzyme-catalyzed covalent attachment to ECM components such as fibronectin. The immobilized construct is meant to be cleaved from the ECM by matrix-metalloproteinases (MMPs) which are upregulated during flares of inflammation. These two functionalities are facilitated by a peptide containing two sequences: a protease-sensitive peptide linker (PSL) for MMP cleavage and a sequence for covalent attachment by activated human transglutaminase FXIIIa (TGase) included in the injection mix for co-administration. This peptide was site-selectively conjugated to the unnatural amino acid at IL4 position 42 allowing to preserve wild type bioactivity of IL4. In vitro experiments confirmed the anticipated MMP response towards the PSL and TGase-mediated construct attachment to fibronectin of the ECM. Furthermore, the IL4-peptide conjugates were able to reduce inflammation and protect non-load bearing cartilage along with the anterior cruciate ligament from degradation in an osteoarthritis model in rabbits. This represents the first step towards a minimally invasive treatment option using bioresponsive cytokine depots with potential clinical value for inflammatory conditions. One of the challenges with this approach was the production of the cytokine conjugate, with incorporation of the unnatural amino acid into IL4 being the main bottleneck. Therefore, in chapter 4, we designed a simplified version of this depot system by genetically fusing the bifunctional peptide via a flexible peptide spacer to murine IL4. While human IL4 loses its activity upon C-terminal elongation, murine IL4 is not affected by this modification. The produced murine IL4 fusion protein could be effectively bound to in vitro grown extracellular matrix in presence of TGase. Moreover, the protease-sensitive linker was selectively recognized and cleaved by MMPs, liberating intact and active IL4, although at a slower rate than expected. Murine IL4 offers the advantage to evaluate the bioresponsive cytokine depot in many available mouse models, which was so far not possible with human IL4 due to species selectivity. For murine IL4, the approach was further extended to systemic delivery in chapter 5. To increase the half-life and specifically target disease sites, we engineered a murine IL4 variant conjugated with a folate-bearing PEG chain for targeting of activated macrophages. The bioactive IL4 conjugate had a high serum stability and the PEGylation increased the half-life to 4 h in vivo. Surprisingly, the folate moiety did not improve targeting in an antigen-induced arthritis (AIA) mouse model. IL4-PEG performed better in targeting the inflamed joint, while IL4-PEG-folate showed stronger accumulation in the liver. Fortunately, the modular nature of the IL4 conjugate facilitates convenient adaption of PEG chain length and the targeting moiety to further improve the half-life and localization of the cytokine. In summary, this thesis describes a platform technology for the controlled release of cytokines in response to inflammation. By restricting the release of the therapeutic to the site of inflammation, the benefit-risk ratio of this potent class of biologics can be positively influenced. Future research will help to deepen our understanding of how to perfectly combine cytokine, protease-sensitive linker and immobilization tag or targeting moiety to tackle different diseases.}, subject = {Targeted drug delivery}, language = {en} } @phdthesis{daCruzGueerisoli2021, author = {da Cruz G{\"u}erisoli, Irene Maria}, title = {Investigating the murine meiotic telomere complex TERB1-TERB2-MAJIN: spatial organization and evolutionary history}, doi = {10.25972/OPUS-21056}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-210562}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Einess der faszinierenden Merkmale der meiotischen Prophase I sind die hochkonservierten kr{\"a}ftigen Bewegungen homologer Chromosomen. Diese Bewegungen sind entscheidend f{\"u}r den Erfolg von Schl{\"u}sselereignissen wie die Ausrichtung, Paarung und Rekombination der homologen Chromosomen. Mehrere bisher untersuchte Organismen, darunter S{\"a}ugetiere, W{\"u}rmer, Hefen und Pflanzen, erreichen diese Bewegungen, indem sie die Chromosomenenden an spezialisierten Stellen in der Kernh{\"u}lle verankern. Diese Verankerung erfordert Telomer-Adapterproteine, die bisher in der Spalthefe und der Maus identifiziert wurden. Die meiosespezifischen Telomer-Adapterproteine der Maus, TERB1, TERB2 und MAJIN, sind an der Verankerung des ubiquit{\"a}ren Telomer-Shelterin-protein an den LINC-Komplex beteiligt, mit einem analogen Mechanismus, wie er die Spalthefe beschrieben wird. Obgleich die meiose-spezifischen TelomerAdapterproteine eine wesentliche Rolle spielen, ist der genaue Mechanismus der Verankerung der Telomere an die Kernh{\"u}lle sowie ihre evolution{\"a}re Geschichte bisher noch wenig verstanden. Das Hauptziel dieser Arbeit ist daher die Untersuchung der Organisation des meiosespezifischen TelomerAdapterkomplexes TERB1-TERB2-MAJIN der Maus und dessen Evolutionsgeschichte. Im ersten Teil dieser Arbeit wurde die Organisation des TERB1-TERB2-MAJIN Komplexes mittels hochaufl{\"o}sender Mikroskopie (SIM), an Mausspermatozyten untersucht, sowie die Lokalisation in Bezug auf TRF1 des Telomer-ShelterinKomplexes und die telomerische DNA analysiert. In den Stadien Zygot{\"a}n und Pachyt{\"a}n zeigten die Fluoreszenzsignale eine starke {\"U}berlappung der Verteilung der meiotischen Telomer-Komplex-Proteine, wobei die Organisation von TERB2 an den Chromosomenenden heterogener war als die von TERB1 und MAJIN. Außerdem konnte die TRF1-Lokalisation an den Enden der Lateralelemente (LEs) mit einer griffartigen Anordnung um die TERB1- und MAJIN-Signale im Zygot{\"a}n- und Pachyt{\"a}n-Stadium gezeigt werden. Interessanterweise erwies sich die telomerische DNA als lateral verteilt und teilweise {\"u}berlappend mit der zentralen Verteilung der meiotischen Telomer-Komplex-Proteine an den Enden der LEs. Die Kombination dieser Ergebnisse erlaubte die Beschreibung eines alternativen Modells der Verankerung der Telomer an die Kernh{\"u}lle w{\"a}hrend der meiotischen Prophase I. Der zweite Teil dieser Arbeit analysiert die Evolutionsgeschichte der Mausproteine von TERB1, TERB2 und MAJIN. Die fehlende {\"U}bereinstimmung zwischen den Meiose-spezifische Telomer-Adapteproteinen der Maus und der Spalthefe hat die Frage nach dem evolutionsbedingten Ursprung dieses spezifischen Komplexes aufgeworfen. Um vermeintliche Orthologen der Mausproteinevon TERB1, TERB2 und MAJIN {\"u}ber Metazoen hinweg zu identifizieren, wurden computergest{\"u}tzte Verfahren und phylogenetische Analysen durchgef{\"u}hrt. Dar{\"u}ber hinaus wurden Expressionsstudien implementiert, um ihre potenzielle Funktion w{\"a}hrend der Meiose zu testen. Die Analysen haben ergeben, dass der Meiose-spezifische Telomer-Komplex der Maus sehr alt ist, da er bereits in den Eumetazoen entstand, was auf einen einzigen Ursprung hindeutet. Das Fehlen jeglicher Homologen des meiosespezifischen Telomerkomplexes in Nematoden und die einigen wenigen in Arthropoden nachgewiesenen Kandidaten, deuten darauf hin, dass die Telomer-Adapterproteine in diesen Abstammungslinien verloren/ersetzt oder stark diversifiziert worden sind. Bemerkenswerterweise zeigten Proteindom{\"a}nen von TERB1, TERB2 und MAJIN, die an der Bildung des Komplexes sowie an der Interaktion mit dem Telomer-Shelterin-Protein und den LINC-Komplexen beteiligt sind, eine hohe Sequenz{\"a}hnlichkeit {\"u}ber alle Kladen hinweg. Abschließend lieferte die Genexpression im Nesseltier Hydra vulgaris den Beweis, dass der TERB1-TERB2-MAJIN-Komplex selektiv in der Keimbahn exprimiert wird, was auf die Konservierung meiotischer Funktionen {\"u}ber die gesamte Metazoen-Evolution hinweg hindeutet. Zusammenfassend bietet diese Arbeit bedeutende neue Erkenntnisse hinsichtlich des Meiose-spezifischen Telomer-Adapterkomplex, seines Mechanismus zur Verankerung der Telomer an die Kernh{\"u}lle und die Entschl{\"u}sselung seines Ursprungs in den Metazoen.}, language = {en} } @phdthesis{MezaChincha2021, author = {Meza Chincha, Ana Lucia}, title = {Catalytic Water Oxidation with Functionalized Ruthenium Macrocycles}, doi = {10.25972/OPUS-20962}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-209620}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {In light of the rapidly increasing global demand of energy and the negative effects of climate change, innovative solutions that allow an efficient transition to a carbon-neutral economy are urgently needed. In this context, artificial photosynthesis is emerging as a promising technology to enable the storage of the fluctuating energy of sunlight in chemical bonds of transportable "solar fuels". Thus, in recent years much efforts have been devoted to the development of robust water oxidation catalysts (WOCs) leading to the discovery of the highly reactive Ru(bda) (bda: 2,2'-bipyridine-6,6'-dicarboxylic acid) catalyst family. The aim of this thesis was the study of chemical and photocatalytic water oxidation with functionalized Ruthenium macrocycles to explore the impact of substituents on molecular properties and catalytic activities of trinuclear macrocyclic Ru(bda) catalysts. A further objective of this thesis comprises the elucidation of factors that influence the light-driven water oxidation process with this novel class of supramolecular WOCs.}, subject = {Rutheniumkomplexe}, language = {en} } @phdthesis{Hock2021, author = {Hock, Andreas}, title = {NHC-stabilized Alanes and Gallanes}, doi = {10.25972/OPUS-21252}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212525}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {This thesis describes the synthesis and reactivity of NHC-stabilized Lewis-acid/Lewis-base adducts of alanes and gallanes (NHC = Me2ImMe, iPr2Im, iPr2ImMe, Dipp2Im, Dipp2ImH). As this field of research has developed tremendously, especially in the last five years, the first chapter provides an overview of the current state of knowledge. The influence of electronegative π-donor-substituents on the stability of the NHC alane adducts is examined in chapter 2. For this purpose, the carbene stabilized alanes (NHC)∙AlH3 (NHC = iPr2Im, Dipp2Im) were reacted with secondary amines of different steric demand and with phenols. The π-donor substituents saturate the Lewis acidic aluminium center and coordination of a second NHC-ligand was not observed. The strongly electronegative N and O substituents increase the Lewis acidity of the aluminium atom, which leads to stronger Al-CNHC as well as Al-H bonds, which inhibits the insertion of the carbene into the Al-H bond. In Chapter 3 the development of the synthesis and reactivity of carbene-stabilized gallanes is presented. The synthesis of NHC gallane adducts (NHC)∙GaH3, (NHC)∙GaH2Cl and (NHC)∙GaHCl2 and their reactivity towards NHCs and cAACMe were investigated in detail. The reaction of the mono- and dichlorogallanes (NHC)∙GaH2Cl and (NHC)∙GaHCl2 (NHC = iPr2ImMe, Dipp2Im) with cAACMe led to insertion of the cAACMe with formation of chiral and achiral compounds depending on the sterically demand of the used NHC. Furthermore, the formation of bis-alkylgallanes was observed for the insertion of two equivalents of cAACMe with release of the NHC ligand. Chapter 4 describes investigations concerning the synthesis and reactivity of NHC-stabilized iodoalanes and iodogallanes, which are suitable for the formation of cationic aluminium and gallium dihydrides. The reaction of (NHC)∙EH2I (E = Al, Ga) stabilized by the sterically less demanding NHCs (NHC = Me2ImMe, iPr2Im, iPr2ImMe) with an additional equivalent of the NHC led to the formation of the cationic bis-NHC aluminium and gallium dihydrides [(NHC)2∙AlH2]+I- and [(NHC)2∙GaH2]+I-. Furthermore, the influence of the steric demand of the used NHC was investigated. The adduct (Dipp2Im)∙GaH2I was reacted with an additional equivalent of Dipp2Im. Due to the bulk of the NHC used, rearrangement of one of the NHC ligands from normal to abnormal coordination occurred and the cationic gallium dihydride [(Dipp2Im)∙GaH2(aDipp2Im)] was isolated. Chapter 5 of this thesis reports investigations concerning the reduction of cyclopentadienyl-substituted alanes and gallanes with singlet carbenes. NHC stabilized pentamethylcyclopentadienyl aluminium and gallium dihydrides (NHC)∙Cp*MH2 (E = Al, Ga) were prepared by the reaction of (AlH2Cp*)3 with the corresponding NHCs or by the salt elimination of (NHC)∙GaH2I with KCp*. The gallane adducts decompose at higher temperatures with reductive elimination of Cp*H and formation of Cp*GaI. . The reductive elimination is preferred for sterically demanding NHCs (Dipp2Im > iPr2ImMe > Me2ImMe). In addition, NHC ring expansion of the backbone saturated carbene Dipp2ImH was observed for the reaction of the NHC with (AlH2Cp*)3, which led to (RER-Dipp2ImHH2)AlCp*. Furthermore, the reactivity of the adducts (NHC)∙Cp*EH2 (E = Al, Ga) towards cAACMe was investigated. The reaction of the alane adducts stabilized by the sterically more demanding NHCs iPr2ImMe and Dipp2Im afforded the exceptionally stable insertion product (cAACMeH)Cp*AlH V-10 with liberation of the NHC. The reaction of the gallium hydrides (NHC)∙Cp*GaH2 with cAACMe led to the reductive elimination of cAACMeH2 and formation of Cp*GaI. A variety of neutral and cationic carbene-stabilized alanes and gallanes are presented in this work. The introduction of electronegative π-donor substituents (Cl-, I-, OR-, NR2-) and the investigations on the thermal stability of these compounds led to the conclusion that the stability of alanes and gallanes increased significantly by such a substitution. Investigations on the reactivity of the NHC adducts towards cAACMe resulted in various insertion products of the carbene into the Al-H or Ga-H bonds and the first cAACMe stabilized dichlorogallane was isolated. Furthermore, a first proof was provided that carbenes can be used specifically for the (formal) reduction of group 13 hydrides of the higher homologues. Thus, the synthesis of Cp*GaI from the reaction of (NHC)∙Cp*GaH2 with cAACMe was developed. In the future, this reaction pathway could be of interest for the preparation of other low-valent compounds of aluminium and gallium.}, subject = {Aluminiumhydridderivate}, language = {en} } @phdthesis{PeethambaranNairSyamala2021, author = {Peethambaran Nair Syamala, Pradeep}, title = {Bolaamphiphilic Rylene Bisimides: Thermodynamics of Self-assembly and Stimuli-responsive Properties in Water}, doi = {10.25972/OPUS-21342}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213424}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The present thesis demonstrates how different thermodynamic aspects of self-assembly and stimuli-responsive properties in water can be encoded on the structure of π-amphiphiles, consisting of perylene or naphthalene bisimide cores. Initially, quantitative thermodynamic insights into the entropically-driven self-assembly was studied for a series of naphthalene bisimides with UV/Vis and ITC measurements, which demonstrated that their thermodynamic profile of aggregation is heavily influenced by the OEG side chains. Subsequently, a control over the bifurcated thermal response of entropically driven and commonly observed enthalpically driven self-assembly was achieved by the modulation of glycol chain orientation. Finally, Lower Critical Solution Temperature (LCST) phenomenon observed for these dyes was investigated as a precise control of this behavior is quintessential for self-assembly studies as well as to generate 'smart' materials. It could be shown that the onset of phase separation for these molecules can be encoded in their imide substituents, and they are primarily determined by the supramolecular packing, rather than the hydrophobicity of individual monomers.}, subject = {Supramolekulare Chemie}, language = {en} } @phdthesis{Wehner2021, author = {Wehner, Marius}, title = {Supramolecular Polymorphism in Homo- and Heterochiral Supramolecular Polymerizations}, doi = {10.25972/OPUS-21151}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-211519}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The aim of the first part of this thesis was to investigate (R,R)-PBI as a model system for polymorphism at its origin by a supramolecular approach. The pathway complexity of (R,R)-PBI was fine-tuned by experimental parameters such as solvent, temperature and concentration to make several supramolecular polymorphs accessible. Mechanistic and quantum chemical studies on the kinetics and thermodynamics of the supramolecular polymerization of (R,R)-PBI were conducted to shed light on the initial stages of polymorphism. The second part of this work deals with mechanistic investigations on the supramolecular polymerization of the racemic mixture of (R,R)- and (S,S)-PBI with regard to homochiral and heterochiral aggregation leading to conglomerates and a racemic supramolecular polymer, respectively.}, subject = {Supramolekulare Chemie}, language = {en} } @phdthesis{Tylek2021, author = {Tylek, Tina}, title = {Establishment of a Co-culture System of human Macrophages and hMSCs to Evaluate the Immunomodulatory Properties of Biomaterials}, doi = {10.25972/OPUS-20357}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-203570}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {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.}, subject = {Makrophage}, language = {en} } @phdthesis{Joshi2021, author = {Joshi, Hemant Kumar}, title = {Function of IRAK2 in macrophages and HECTD1 in B cells}, doi = {10.25972/OPUS-15084}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150846}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The Immune system exerts its response against invading pathogens via a cumulative, sequential cooperation of immune cells coordinated by their secreted products. Immune cells, such as macrophages and dendritic cells (DCs), express toll-like receptors (TLRs) to sense the presence of pathogens through pathogen-associated molecular patterns (PAMPs). The interaction of PAMPs with TLRs elicits a cytosolic signaling cascade that enhances the expression of genes to stimulate inflammation. Interleukin 1 receptor-associated kinase 2 (IRAK2) is a component of the TLR signaling pathway. IRAK2 transduces the TLR signal via a direct interaction with TNF receptor-associated factor 6 (TRAF6) and subsequent enhancement of its ubiquitination. During my PhD thesis, I determined that a 55-amino acid long stretch at the C-terminal end of IRAK2 is important for TLR signaling. Overexpression of C-terminal truncated IRAK2 (IRAK2Δ55) in the murine macrophage cell line RAW 264.7 led to impaired CD40 expression after TLR4 stimulation by Lipopolysaccharide (LPS). I observed attenuated competency of IRAK2Δ55 in restoring a full TLR signaling response i.e. IL-6 secretion, NO production and CD40 expression in IRAK2-deficient RAW cells generated via CRISPR-Cas9 approach. Additionally, diminished TLR4 induced activation of nuclear factor κB (NF-κB) and extracellular signal related kinase (ERK) was observed with IRAK2Δ55 reconstituted RAW cells as compared to cell reconstituted with wildtype IRAK2. IRAK2Δ55 reconstituted RAW cells also exhibited reduced TLR4-induced cell death and phosphorylation of receptor interacting protein kinase 3 (RIP3). Co-immunoprecipitation experiments in HEK 293T cells showed that IRAK2Δ55 was still able to bind to TRAF6 alike IRAK2 but failed to induce ubiquitination of TRAF6. In conclusion, the results suggest that the IRAK2 TRAF6 interaction is not sufficient to sustain full TLR signaling. An C-terminus-dependent unknown molecular mechanism is also involved. Through my PhD work, I also analyzed a B cell lineage-specific HECTD1 knock-out mice. HECTD1 is an E3 ubiquitin ligase for various substrate proteins, such as heat shock protein 90 (HSP90), adenomatous polyposis coli and phosphatidylinositol phosphate kinase type 1 γ. Hsp90 regulates a variety of signaling molecules in NF-κB activation pathways which are essential for an optimal B cell response. HECTD1-deficient pro-B cells developed normally into mature B cells. However, TLR4 stimulated HECTD1-deficient B cells displayed reduced immunoglobulin (Ig) production in in vitro cultures. In addition, mice with HECTD1-deficient B cells showed a diminished Ig response after nitrophenylacetyl-keyhole limpet hemocyanin immunization. Thus, HECTD1 is necessary for efficient Ig secretion.}, subject = {Toll-like-Rezeptoren}, language = {en} } @phdthesis{Blum2021, author = {Blum, Carina}, title = {A first step to an integral biointerface design for the early phase of regeneration}, doi = {10.25972/OPUS-21211}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-212117}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The implantation of any foreign material into the body automatically starts an immune reaction that serves as the first, mandatory step to regenerate tissue. The course of this initial immune reaction decides on the fate of the implant: either the biomaterial will be integrated into the host tissue to subsequently fulfill its intended function (e.g., tissue regeneration), or it will be repelled by fibrous encapsulation that determines the implant failure. Especially neutrophils and macrophages play major roles during this inflammatory response and hence mainly decide on the biomaterial's fate. For clinically relevant tissue engineering approaches, biomaterials may be designed in shape and morphology as well as in their surface functionality to improve the healing outcome, but also to trigger stem cell responses during the subsequent tissue regeneration phase. The main focus of this thesis was to unravel the influence of scaffold characteristics, including scaffold morphology and surface functionality, on primary human innate immune cells (neutrophils and macrophages) and human mesenchymal stromal cells (hMSCs) to assess their in vitro immune response and tissue regeneration capacity, respectively. The fiber-based constructs were produced either via melt electrowriting (MEW), when the precise control over scaffold morphology was required, or via solution electrospinning (ES), when the scaffold design could be neglected. All the fiber-based scaffolds used throughout this thesis were composed of the polymer poly(ε caprolactone) (PCL). A novel strategy to model and alleviate the first direct cell contact of the immune system with a peptide-bioactived fibrous material was presented in chapter 3 by treating the material with human neutrophil elastase (HNE) to imitate the neutrophil attack. The main focus of this study was put on the effect of HNE towards an RGDS-based peptide that was immobilized on the surface of a fibrous material to improve subsequent L929 cell adhesion. The elastase efficiently degraded the peptide-functionality, as evidenced by a decreased L929 cell adhesion, since the peptide integrated a specific HNE-cleavage site (AAPV-motif). A sacrificial hydrogel coating based on primary oxidized hyaluronic acid (proxHA), which dissolved within a few days after the neutrophil attack, provided an optimal protection of the peptide-bioactivated fibrous mesh, i.e, the hydrogel alleviated the neutrophil attack and largely ensured the biomaterial's integrity. Thus, according to these results, a means to protect the biomaterial is required to overcome the neutrophil attack. Chapter 4 was based on the advancement of melt electrowriting (MEW) to improve the printing resolution of MEW scaffolds in terms of minimal inter-fiber distances and a concomitant high stacking precision. Initially, to gain a better MEW understanding, the influence of several parameters, including spinneret diameter, applied pressure, and collector velocity on mechanical properties, crystallinity, fiber diameter and fiber surface morphology was analyzed. Afterward, innovative MEW designs (e.g., box-, triangle-, round , and wall-shaped scaffolds) have been established by pushing the printing parameters to their physical limits. Further, the inter-fiber distance within a standardized box-structured scaffold was successfully reduced to 40 µm, while simultaneously a high stacking precision was maintained. In collaboration with a co-worker of my department (Tina Tylek, who performed all cell-based experiments in this study), these novel MEW scaffolds have been proven to facilitate human monocyte-derived macrophage polarization towards the regenerative M2 type in an elongation-driven manner with a more pronounced effect with decreasing pore sizes. Finally, a pro-adipogenic platform for hMSCs was developed in chapter 5 using MEW scaffolds with immobilized, complex ECM proteins (e.g., human decellularized adipose tissue (DAT), laminin (LN), and fibronectin (FN)) to test for the adipogenic differentiation potential in vitro. Within this thesis, a special short-term adipogenic induction regime enabled to more thoroughly assess the intrinsic pro-adipogenic capacity of the composite biomaterials and prevented any possible masking by the commonly used long-term application of adipogenic differentiation reagents. The scaffolds with incorporated DAT consistently showed the highest adipogenic outcome and hence provided an adipo-inductive microenvironment for hMSCs, which holds great promise for applications in soft tissue regeneration. Future studies should combine all three addressed projects in a more in vivo-related manner, comprising a co-cultivation setup of neutrophils, macrophages, and MSCs. The MEW-scaffold, particularly due to its ability to combine surface functionality and adjustable morphology, has been proven to be a successful approach for wound healing and paves the way for subsequent tissue regeneration.}, subject = {Scaffold }, language = {en} } @phdthesis{ScheideNoeth2021, author = {Scheide-N{\"o}th, Jan-Philipp}, title = {Activation of the Interleukin-5 receptor and its inhibition by cyclic peptides}, doi = {10.25972/OPUS-18250}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-182504}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The cytokine interleukin-5 (IL-5) is part of the TH2-mediated immune response. As a key regulator of eosinophilic granulocytes (eosinophils), IL-5 controls multiple aspects of eosinophil life. Eosinophils play a pathogenic role in the onset and progression of atopic diseases as well as hypereosinophilic syndrome (HES). Here, cytotoxic proteins and pro-inflammatory mediators stored in intracellular vesicles termed granula are released upon activation thereby causing local inflammation to fight the pathogen. However, if such inflammation persists, tissue damage and organ failure can occur. Due to the close relationship between eosinophils and IL-5 this cytokine has become a major pharmaceutical target for the treatment of atopic diseases or HES. As observed with other cytokines, IL-5 signals by assembling a heterodimeric receptor complex at the cell surface in a stepwise mechanism. In the first step IL-5 binds to its receptor IL-5Rα (CD125). This membrane-located complex then recruits the so-called common beta chain βc (CD131) into a ternary ligand receptor complex, which leads to activation of intracellular signaling cascades. Based on this mechanism various strategies targeting either IL-5 or IL-5Rα have been developed allowing to specifically abrogate IL-5 signaling. In addition to the classical approach of employing neutralizing antibodies against IL 5/IL-5Rα or antagonistic IL-5 variants, two groups comprising small 18 to 30mer peptides have been discovered, that bind to and block IL-5Rα from binding its activating ligand IL-5. Structure-function studies have provided detailed insights into the architecture and interaction of IL-5IL-5Rα and βc. However, structural information for the ternary IL-5 complex as well as IL-5 inhibiting peptides is still lacking. In this thesis three areas were investigated. Firstly, to obtain insights into the second receptor activation step, i.e. formation of the ternary ligand-receptor complex IL-5•IL-5Rα•βc, a high-yield production for the extracellular domain of βc was established to facilitate structure determination of the ternary ligand receptor assembly by either X-ray crystallography or cryo-electron microscopy. In a second project structure analysis of the ectodomain of IL-5Rα in its unbound conformation was attempted. Data on IL-5Rα in its ligand-free state would provide important information as to whether the wrench-like shaped ectodomain of IL-5Rα adopts a fixed preformed conformation or whether it is flexible to adapt to its ligand binding partner upon interaction. While crystallization of free IL-5Rα failed, as the crystals obtained did not diffract X rays to high resolution, functional analysis strongly points towards a selection fit binding mechanism for IL-5Rα instead of a rigid and fixed IL-5Rα structure. Hence IL-5 possibly binds to a partially open architecture, which then closes to the known wrench-like architecture. The latter is then stabilized by interactions within the D1-D2 interface resulting in the tight binding of IL-5. In a third project X-ray structure analysis of a complex of the IL-5 inhibitory peptide AF17121 bound to the ectodomain of IL-5Rα was performed. This novel structure shows how the small cyclic 18mer peptide tightly binds into the wrench-like cleft formed by domains D1 and D2 of IL-5Rα. Due to the partial overlap of its binding site at IL-5Rα with the epitope for IL-5 binding, the peptide blocks IL-5 from access to key residues for binding explaining how the small peptide can effectively compete with the rather large ligand IL-5. While AF17121 and IL-5 seemingly bind to the same site at IL-5Rα, functional studies however showed that recognition and binding of both ligands differ. With the structure for the peptide-receptor complex at hand, peptide design and engineering could be performed to generate AF17121 analogies with enhanced receptor affinity. Several promising positions in the peptide AF17121 could be identified, which could improve inhibition capacity and might serve as a starting point for AF17121-based peptidomimetics that can yield either superior peptide based IL-5 antagonists or small-molecule-based pharmacophores for future therapies of atopic diseases or the hypereosinophilic syndrome.}, subject = {Interleukin 5}, language = {en} } @phdthesis{Tian2021, author = {Tian, Yaming}, title = {Selective C-X and C-H Borylation by N-Heterocyclic Carbene Nickel(0) Complex}, doi = {10.25972/OPUS-21300}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213004}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Organoboron compounds are important building blocks in organic synthesis, materials science, and drug discovery. The development of practical and convenient ways to synthesize boronate esters attracted significant interest. Photoinduced borylations originated with stoichiometric reactions of arenes and alkanes with well-defined metal-boryl complexes. Now photoredox-initiated borylations, catalyzed either by transition-metal or organic photocatalysts, and photochemical borylations with high efficiency have become a burgeoning area of research. In this chapter, we summarize research in the field of photocatalytic C-X borylation, especially emphasizing recent developments and trends, based on transition-metal catalysis, metal-free organocatalysis and direct photochemical activation. We focus on reaction mechanisms involving single electron transfer (SET), triplet energy transfer (TET), and other radical processes. We developed a highly selective photocatalytic C-F borylation method that employs a rhodium biphenyl complex as a triplet sensitizer and the nickel catalyst [Ni(IMes)2] (IMes = 1,3-dimesitylimidazolin-2-ylidene) for the C-F bond activation and defluoroborylation process. This tandem catalyst system operates with visible (400 nm) light and achieves borylation of a wide range of fluoroarenes with B2pin2 at room temperature in excellent yields and with high selectivity. Direct irradiation of the intermediary C-F bond oxidative addition product trans-[NiF(ArF)(IMes)2] leads to fast decomposition when B2pin2 is present. This destructive pathway can be bypassed by indirect excitation of the triplet states of the nickel(II) complex via the photoexcited rhodium biphenyl complex. Mechanistic studies suggest that the exceptionally long-lived triplet excited state of the Rh biphenyl complex used as the photosensitizer allows for efficient triplet energy transfer to trans-[NiF(ArF)(IMes)2], which leads to dissociation of one of the NHC ligands. This contrasts with the majority of current photocatalytic transformations, which employ transition metals as excited state single electron transfer agents. We have previously reported that C(arene)-F bond activation with [Ni(IMes)2] is facile at room temperature, but that the transmetalation step with B2pin2 is associated with a high energy barrier. Thus, this triplet energy transfer ultimately leads to a greatly enhanced rate constant for the transmetalation step and thus for the whole borylation process. While addition of a fluoride source such as CsF enhances the yield, it is not absolutely required. We attribute this yield-enhancing effect to (i) formation of an anionic adduct of B2pin2, i.e. FB2pin2-, as an efficient, much more nucleophilic {Bpin-} transfer reagent for the borylation/transmetalation process, and/or (ii) trapping of the Lewis acidic side product FBpin by formation of [F2Bpin]- to avoid the formation of a significant amount of NHC-FBpin and consequently of decomposition of {Ni(NHC)2} species in the reaction mixture. We reported a highly selective and general photo-induced C-Cl borylation protocol that employs [Ni(IMes)2] (IMes = 1,3-dimesitylimidazoline-2-ylidene) for the radical borylation of chloroarenes. This photo-induced system operates with visible light (400 nm) and achieves borylation of a wide range of chloroarenes with B2pin2 at room temperature in excellent yields and with high selectivity, thereby demonstrating its broad utility and functional group tolerance. Mechanistic investigations suggest that the borylation reactions proceed via a radical process. EPR studies demonstrate that [Ni(IMes)2] undergoes very fast chlorine atom abstraction from aryl chlorides to give [NiI(IMes)2Cl] and aryl radicals. Control experiments indicate that light promotes the reaction of [NiI(IMes)2Cl] with aryl chlorides generating additional aryl radicals and [NiII(IMes)2Cl2]. The aryl radicals react with an anionic sp2-sp3 diborane [B2pin2(OMe)]- formed from B2pin2 and KOMe to yield the corresponding borylation product and the [Bpin(OMe)]•- radical anion, which reduces [NiII(IMes)2Cl2] under irradiation to regenerate [NiI(IMes)2Cl] and [Ni(IMes)2] for the next catalytic cycle. A highly efficient and general protocol for traceless, directed C3-selective C-H borylation of indoles with [Ni(IMes)2] as the catalyst was achieved. Activation and borylation of N-H bonds by [Ni(IMes)2] is essential to install a Bpin moiety at the N-position as a traceless directing group, which enables the C3-selective borylation of C-H bonds. The N-Bpin group which is formed is easily converted in situ back to an N-H group by the oxidiative addition product of [Ni(IMes)2] and in situ-generated HBpin. The catalytic reactions are operationally simple, allowing borylation of of a variety of substituted indoles with B2pin2 in excellent yields and with high selectivity. The C-H borylation can be followed by Suzuki-Miyaura cross-coupling of the C-borylated indoles in an overall two-step, one-pot process providing an efficient method for synthesizing C3-functionalized heteroarenes.}, subject = {Borylierung}, language = {en} } @phdthesis{Miesler2021, author = {Miesler, Tobias Hans-Herbert}, title = {Development of diagnostic systems targeting the human tongue as a 24/7 available detector}, doi = {10.25972/OPUS-21449}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214490}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {To diagnose diseases correctly requires not only trained and skilled personnel, but also cost-intensive and complex equipment. Rapid tests can help with the initial evaluation, but result generation can also take up to several hours, depending on the test system. At this point, novel bioresponsive diagnostic systems are used, responding to the disease related shift of biological processes. They monitor changes in the biological environment and can react to them e.g. with the release of substances. This can be used in drug delivery formulations but can also help to diagnose diseases occurring in the oral cavity and inform patients of their state of health. The tongue is herein used as a 24/7 available detector. In section I of this work, the foundation for the development of these diagnostic systems was laid. A suitable flavoring agent was found, which is stable, can be coupled to the N-terminus of peptides and has a strongly conceivable taste. For the optimization of the protease-sensitive linker (PSL), an analytical system was established (PICS assay), which determines protease-specific cleavable amino acid sequences. In order to replace the PMMA particles previously required, an acetyl protecting group was introduced N-terminally as it protects peptides and proteins in the human body from degradation by human aminopeptidase. The new synthesized flavor was examined with a NIH cell line for cytotoxicity and with an electronic tongue setup for its bitterness. Section II deals with the structure of a system which detects severe inflammations in the oral cavity, e.g. PA. The established PICS assay was used to confirm the previously used PSL sequence in its application. Using solid phase peptide synthesis, 3 linkers were synthesized which respond to the elevated MMP concentrations present in inflammation. The resulting peptides were acetylated and coupled with HATU/DIPEA to the modified denatonium. Cutting experiments with MMPs over different concentration and time ranges confirmed the response of the diagnostic sensor to these enzymes. The obtained construct was examined for cell toxicity by WST assay. The masked bitterness of the sensors was confirmed by an electronic tongue setup. To address non-human proteases (and thereby infections), section III focuses on the establishment of detection system of a cysteine protease SpeB expressed by Streptococcus pyogenes. The in-house expression of SpeB using E. coli cells was established for this purpose. An analysis of the SpeB cleavage sites was performed using a PICS assay setup. Four constructs with different PSL were synthesized analogous to section II. Cleavage experiments with the expressed and purified SpeB showed a response of two constructs to the protease. In addition, a system was established to quantify the concentration of SpeB in human saliva using western blot technique with subsequent quantification. In section IV a compound was synthesized which can now be coupled to a flavor. The final coupled construct is able to detect present NA activity specifically from influenza A and B. The market for existing influenza diagnostics was explored to determine the need for such a system. A neuraminic acid was modified in positions 4 and 7 and protected in such a way that subsequent coupling via the hydroxy-group in position 2 was selectively possible. In summary, this results in a diagnostic platform that can be used anywhere, by anyone and at any time. This represents a new dimension in the rapid diagnosis of inflammations and bacterial or viral infections.}, subject = {Diagnostik}, language = {en} } @phdthesis{Pernitzsch2021, author = {Pernitzsch, Sandy Ramona}, title = {Functional Characterization of the abundant and conserved small regulatory RNA RepG in Helicobacter pylori}, doi = {10.25972/OPUS-12268}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-122686}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Bacterial small non-coding RNAs (sRNAs) play fundamental roles in controlling and finetuning gene expression in a wide variety of cellular processes, including stress responses, environmental signaling and virulence in pathogens. Despite the identification of hundreds of sRNA candidates in diverse bacteria by genomics approaches, the mechanisms and regulatory capabilities of these posttranscriptional regulators have most intensively been studied in Gram-negative Gammaproteobacteria such as Escherichia coli and Salmonella. So far, almost nothing is known about sRNA-mediated regulation (riboregulation) in Epsilonproteobacteria, including the major human pathogen Helicobacter pylori. H. pylori was even thought to be deficient for riboregulation as none of the sRNAs known from enterobacteria are conserved in Helicobacter and since it lacks the major RNA chaperone Hfq, which is crucial for sRNA function as well as stability in many bacteria. Nonetheless, more than 60 cis- and trans-acting sRNA candidates were recently identified in H. pylori by a global RNA sequencing approach, indicating that this pathogen, in principle, has the capability to use riboregulation for its gene expression control. However, the functions and underlying mechanisms of H. pylori sRNAs remained unclear. This thesis focused on the first functional characterization and target gene identification of a trans-acting sRNA, RepG (Regulator of polymeric G-repeats), in H. pylori. Using in-vitro and in-vivo approaches, RepG was shown to directly base-pair with its C/Urich terminator loop to a variable homopolymeric G-repeat in the 5' untranslated region (UTR) of the tlpB mRNA, thereby regulating expression of the chemotaxis receptor TlpB. While the RepG sRNA is highly conserved, the length of the G-repeat in the tlpB mRNA leader varies among different H. pylori isolates, resulting in a strain-specific tlpB regulation. The modification of the number of guanines within the G-stretch in H. pylori strain 26695 demonstrated that the length of the homopolymeric G-repeat determines the outcome of posttranscriptional control (repression or activation) of tlpB by RepG. This lengthdependent targeting of a simple sequence repeat by a trans-acting sRNA represents a new twist in sRNA-mediated regulation and a novel mechanism of gene expression control, since it uniquely links phase variation by simple sequence repeats to posttranscriptional regulation. In almost all sequenced H. pylori strains, tlpB is encoded in a two gene operon upstream of HP0102, a gene of previously unknown function. This study provided evidence that HP0102 encodes a glycosyltransferase involved in LPS O-chain and Lewis x antigen production. Accordingly, this glycosyltransferase was shown to be essential for mice colonization by H. pylori. The coordinated posttranscriptional regulation of the tlpB-HP0102 operon by antisense base-pairing of RepG to the phase-variable G-repeat in the 5' UTR of the tlpB mRNA allows for a gradual, rather than ON/OFF, control of HP0102 expression, thereby affecting LPS biosynthesis in H. pylori. This fine-tuning of O-chain and Lewis x antigen expression modulates H. pylori antibiotics sensitivity and thus, might be advantageous for Helicobacter colonization and persistence. Whole transcriptome analysis based on microarray and RNA sequencing was used to identify additional RepG target mRNAs and uncover the physiological role of this riboregulator in H. pylori. Altogether, repG deletion affected expression of more than 40 target gene candidates involved various cellular processes, including membrane transport and adhesion, LPS modification, amino acid metabolism, oxidative and nitrosative stress, and nucleic acid modification. The presence of homopolymeric G-repeats/G-rich sequences in almost all target mRNA candidates indicated that RepG hijacks a conserved motif to recognize and regulate multiple target mRNAs in H. pylori. Overall, this study demonstrates that H. pylori employs riboregulation in stress response and virulence control. In addition, this thesis has successfully established Helicobacter as a new model organism for investigating general concepts of gene expression control by Hfq-independent sRNAs and sRNAs in bacterial pathogens.}, subject = {Small RNA}, language = {en} } @phdthesis{Adenugba2021, author = {Adenugba, Akinbami Raphael}, title = {Functional analysis of the gene organization of the pneumoviral attachment protein G}, doi = {10.25972/OPUS-12814}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-128146}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The putative attachment protein G of pneumonia virus of mice (PVM), a member of the Pneumoviruses, is an important virulence factor with so far ambiguous function in a virus-cell as well as in virus-host context. The sequence of the corresponding G gene is characterized by significant heterogeneity between and even within strains, affecting the gene and possibly the protein structure. This accounts in particular for the PVM strain J3666 for which two differing G gene organizations have been described: a polymorphism in nucleotide 65 of the G gene results in the presence of an upstream open reading frame (uORF) that precedes the main ORF in frame (GJ366665A) or extension of the major G ORF for 18 codons (GJ366665U). Therefore, this study was designed to analyse the impact of the sequence variations in the respective G genes of PVM strains J3666 and the reference strain 15 on protein expression, replication and virulence. First, the controversy regarding the consensus sequence of PVM J3666 was resolved. The analysis of 45 distinct cloned fragments showed that the strain separated into two distinct virus populations defined by the sequence and structure of the G gene. This division was further supported by nucleotide polymorphisms in the neighbouring M and SH genes. Sequential passage of this mixed strain in the cell line standardly used for propagation of virus stocks resulted in selection for the GJ366665A-containing population in one of two experiments pointing towards a moderate replicative advantage. The replacement of the G gene of the recombinant PVM 15 with GJ366665A or GJ366665U, respectively, using a reverse genetic approach indicated that the presence of uORF within the GJ366665A significantly reduced the expression of the main G ORF on translational level while the potential extension of the ORF in GJ366665U increased G protein expression. In comparison, the effect of the G gene-structure on virus replication was inconsistent and dependent on cell line and type. While the presence of uORF correlated with a replication advantage in the standardly used BHK-21 cells and primary murine embryonic fibroblasts, replication in the murine macrophage cell line RAW 264.7 did not. In comparison, the GJ366665U variant was not associated with any effect on replication in cultured cells at all. Nonetheless, in-vivo analysis of the recombinant viruses associated the GJ366665U gene variant, and hence an increased G expression, with higher virulence whereas the GJ366665A gene, and therefore an impaired G expression, conferred an attenuated phenotype to the virus. To extend the study to other G gene organizations, a recombinant PVM expressing a G protein without the cytoplasmic domain and for comparison a G-deletion mutant, both known to be attenuated in vivo, were studied. Not noticed before, this structure of the G gene was associated with a 75\% reduction in G protein expression and a significant attenuation of replication in macrophage-like cells. This attenuation was even more prominent for the virus lacking G. Taking into consideration the higher reduction in G protein levels compared to the GJ366665A variant indicates that a threshold amount of G is required for efficient replication in these cells. In conclusion, the results gathered indicated that the expression levels of the G protein were modulated by the sequence of the 5' untranslated region of the gene. At the same time the G protein levels modulated the virulence of PVM.}, subject = {G glycoprotein}, language = {en} } @phdthesis{Hecht2021, author = {Hecht, Markus}, title = {Liquid-Crystalline Perylene Bisimide and Diketopyrrolopyrrole Assemblies}, doi = {10.25972/OPUS-21698}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-216987}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The research presented in this thesis illustrates that self-assembly of organic molecules guided by intermolecular forces is a versatile bottom-up approach towards functional materials. Through the specific design of the monomers, supramolecular architectures with distinct spatial arrangement of the individual building blocks can be realized. Particularly intriguing materials can be achieved when applying the supramolecular approach to molecules forming liquid-crystalline phases as these arrange in ordered, yet mobile structures. Therefore, they exhibit anisotropic properties on a macroscopic level. It is pivotal to precisely control the interchromophoric arrangement as functions originate in the complex structures that are formed upon self-assembly. Consequently, the aim of this thesis was the synthesis and characterization of liquid-crystalline phases with defined supramolecular arrangements as well as the investigation of the structure-property relationship. For this purpose, perylene bisimide and diketopyrrolopyrrole chromophores were used as they constitute ideal building blocks towards functional supramolecular materials due to their thermal stability, lightfastness, as well as excellent optical and electronic features desirable for the application in, e.g., organic electronics.}, subject = {Selbstorganisation}, language = {en} } @phdthesis{Simon2021, author = {Simon, Camilla}, title = {Financial Market Effects of Macroeconomic Policies}, doi = {10.25972/OPUS-21765}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-217654}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Within three self-contained studies, this dissertation studies the impact and interactions between different macroeconomic policy measures in the context of financial markets empirically and quantitatively. The first study of this dissertation sheds light on the financial market effects of unconventional central bank asset purchase programs in the Eurozone, in particular sovereign bond asset purchase programs. The second study quantifies the direct implications of unconventional monetary policy on decisions by German public debt management regarding the maturity structure of gross issuance. The third study provides novel evidence on the role of private credit markets in the propagation of public spending toward private consumption in the U.S. economy. Across these three studies a set of different time-series econometric methods is applied including error correction models and event study frameworks to analyze contemporaneous interactions in financial and macroeconomic data in the context of unconventional monetary policy, as well as vector auto regressions (VARs) and local projections to trace the dynamic consequences of macroeconomic policies over time.}, subject = {Geldpolitik}, language = {en} } @phdthesis{HafergebZailer2021, author = {Hafer [geb. Zailer], Elina}, title = {Tagging - Development of new qNMR methods}, doi = {10.25972/OPUS-21958}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-219583}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {High-resolution nuclear magnetic resonance (NMR) spectroscopy is used in structure elucidation and qualitative as well as quantitative examination of product components. Despite the worldwide development of numerous innovative NMR spectroscopic methods, several official methods that analyze specific substances and do not represent a holistic analysis, are still in use for the quality control of drugs, food and chemicals. Thus, counterfeit or contaminated products of inferior quality can be brought onto the market and distributed despite previous quality controls. To prevent this, three NMR spectroscopic methods have been developed within the scope of this work (1) to study the peroxide value in vegetable and animal oils, (2) for the qualitative and quantitative analysis of metal cations and (3) to determine the enantiomeric excess in chiral alcohols. In oil analysis, titration methods are used to determine the bulk quality parameters such as peroxide value, which represents the concentration of peroxides. Titrations show several drawbacks, such as the need of a large amount of sample and solvents, cross reactions and the low robustness. Thus, an alternative NMR spectroscopic method was developed to improve the peroxide analysis by using triphenylphosphine as a derivatization reagent, which reacts with peroxides in a stoichiometric ratio of 1:1 forming triphenylphosphine oxide. In the 1H-31P decoupled NMR spectrum, the signals of the unreacted triphenylphosphine and the reacted triphenylphosphine oxide are detected at 7.4 ppm and 7.8 ppm, respectively. The ratio of the two signals is used for the calculation of the peroxide concentration. 108 oil samples with a peroxide value between 1 meq/kg and 150 meq/kg were examined using the developed method. Oils with a very low peroxide value of less than 3 meq/kg showed a relative standard deviation of 4.9\%, highly oxidized oils with a peroxide value of 150 meq/kg of 0.2\%. The NMR method was demonstrated as a powerful technique for the analysis of vegetable and krill oils. Another 1H NMR spectroscopic method was developed for the qualitative determination of Be2+, Sr2+ and Cd2+, and for the qualitative and quantitative determination of Ca2+, Mg2+, Hg2+, Sn2+, Pb2+ and Zn2+ by using ethylenediamine tetraacetate (EDTA) as complexing agent. EDTA is a hexadentate ligand that forms stable chelate complexes with divalent cations. The known amount of added EDTA and the signal ratio of free and complexed EDTA are used to calculate the concentrations of the divalent cations, which makes the use of an internal standard obsolete. The use of EDTA with Be2+, Sr2+, Cd2+, Ca2+, Mg2+, Hg2+, Sn2+, Pb2+ and Zn2+ result in complexes whose signals are pH-independent, showing cation-specific chemical shifts and couplings in the 1H NMR spectrum that are used for identification and quantification. In the presented NMR method, the limit of quantification of the cations Ca2+, Mg2+, Hg2+, Sn2+, Pb2+, and Zn2+ was determined with 5-22 μg/mL. This method is applicable in the food and drug sectors. The third NMR spectroscopic method introduced an alternative determination of the enantiomer excess (ee) of the chiral alcohols menthol, borneol, 1-phenylethanol and linalool using phosgene as a derivatizing reagent. Phosgene reacts with a chiral alcohol to form carboxylic acid diesters, made of two identical (RR, SS) or two different enantiomers (RS, SR). These two different types of diastereomers can be examined by the difference of their chemical shifts. In the presented method, the integration values of the carbonyl signals in the 13C NMR spectrum are used for the determination of the enantiomer excess. The limit of quantification depends, among others, on the sample and on the non-labelled or 13C-labelled phosgene used for the analysis. In the case of menthol, a quantification limit of ee=99.1\% was determined using non-labelled phosgene and ee=99.9\% using 13C-labelled phosgene. The 13C NMR method was also applied for the quality control of the enantiomeric purity of borneol, 1-phenylethanol and linalool. The developed 13C NMR method represents a powerful alternative to Mosher's reagent for investigating the enantiomeric excess in chiral alcohols. This work demonstrates the variety of possibilities of applications for the quantitative nuclear magnetic resonance spectroscopy in the chemical analysis of drugs, food and chemicals using tagging reactions such as derivatizations and complexations. The nuclear resonance spectroscopic methods developed in this research work represent powerful alternatives to the previously used quality control techniques.}, subject = {NMR Spektroskopie}, language = {en} } @phdthesis{Oberdoerfer2021, author = {Oberd{\"o}rfer, Sebastian}, title = {Better Learning with Gaming: Knowledge Encoding and Knowledge Learning Using Gamification}, doi = {10.25972/OPUS-21970}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-219707}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Computer games are highly immersive, engaging, and motivating learning environments. By providing a tutorial at the start of a new game, players learn the basics of the game's underlying principles as well as practice how to successfully play the game. During the actual gameplay, players repetitively apply this knowledge, thus improving it due to repetition. Computer games also challenge players with a constant stream of new challenges which increase in difficulty over time. As a result, computer games even require players to transfer their knowledge to master these new challenges. A computer game consists of several game mechanics. Game mechanics are the rules of a computer game and encode the game's underlying principles. They create the virtual environments, generate a game's challenges and allow players to interact with the game. Game mechanics also can encode real world knowledge. This knowledge may be acquired by players via gameplay. However, the actual process of knowledge encoding and knowledge learning using game mechanics has not been thoroughly defined, yet. This thesis therefore proposes a theoretical model to define the knowledge learning using game mechanics: the Gamified Knowledge Encoding. The model is applied to design a serious game for affine transformations, i.e., GEtiT, and to predict the learning outcome of playing a computer game that encodes orbital mechanics in its game mechanics, i.e., Kerbal Space Program. To assess the effects of different visualization technologies on the overall learning outcome, GEtiT visualizes the gameplay in desktop-3D and immersive virtual reality. The model's applicability for effective game design as well as GEtiT's overall design are evaluated in a usability study. The learning outcome of playing GEtiT and Kerbal Space Program is assessed in four additional user studies. The studies' results validate the use of the Gamified Knowledge Encoding for the purpose of developing effective serious games and to predict the learning outcome of existing serious games. GEtiT and Kerbal Space Program yield a similar training effect but a higher motivation to tackle the assignments in comparison to a traditional learning method. In conclusion, this thesis expands the understanding of using game mechanics for an effective learning of knowledge. The presented results are of high importance for researches, educators, and developers as they also provide guidelines for the development of effective serious games.}, subject = {Serious game}, language = {en} } @phdthesis{Eissler2021, author = {Eißler, Christoph Marcel}, title = {Assessment of the left ventricular systolic and diastolic function in rats using electrocardiogram-gated cardiac positron emission tomography}, doi = {10.25972/OPUS-21976}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-219765}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {DD is a cardiac disturbance, which has gained increasing importance in recent years due to its important role in different cardiac disease and cardiomyopathies including ischemic cardiomyopathy, arterial hypertension and diabetic cardiomyopathy. ECG-gated 18F-FDG PET is an imaging technique, that can distinguish between districts of myocardial viability and myocardial scars and further provides information of great interest on the efficacy of experimental approaches designed to improve the cardiac function and/or myocardial metabolism in experimental small animal models. However, ECG-gated 18F-FDG PET is a technique whose feasibility in the assessment of the LV diastolic function in small animals has not been a subject of study. In this thesis, the ability of the ECG-gated 18F-FDG PET for the assessment of both the systolic and diastolic function in eight control rats and in seven ZDF rats, which are an experimental animal model mimicking T2DM conditions and diabetic related complications in humans including DCM, has been investigated The ECG-gated 18F-FDG PET imaging was performed under hyperinsulinemic-euglycemic clamping and the data were stored in list mode files and retrospectively reconstructed. The systolic and diastolic parameters were achieved from the time/volume and the time/filling curve calculated from the software HFV. Additionally, the influence of the number of gates per cardiac cycle on the LV volumes and function parameters has been studied. Hyperinsulinemic-euglycemic clamp procedure and blood glucose measurement did confirm the development of a manifest diabetes in the ZDF rats at the timepoint of the experiments. Regarding the systolic parameters, no significant difference could be detected between the ZDF and ZL rats. The values for the CO were similar in both groups, which demonstrates a similar LV systolic function in the ZDF and the ZL rats at the age of 13 weeks. Values for the systolic parameters are in good line with previous PET, MRI and cardiac catheterization-based studies in diabetic rats. The main finding of this study was that by using in vivo ECG-gated 18F-FDG PET and the software HFV, reliable diastolic parameters could be calculated. Moreover, it was possible to detect the presence of a mild impaired diastolic filling in the ZDF rats in absence of any systolic alteration. This impaired diastolic function in an early stage of diabetes could also be detected by other investigators, who used echocardiography or cardiac catheterization. Therefore, this is the first study showing, that the assessment of the diastolic function in rats can be carried out by ECG-gated 18F-FDG PET imaging. In conclusion, additionally to calculating LV volumes and LV EF, ECG-gated 18F-FDG PET can evaluate the diastolic function of healthy and diabetic rats and is able to detect a DD in ZDF rats.}, subject = {Positronen-Emissions-Tomografie}, language = {en} } @phdthesis{Saedtler2021, author = {Saedtler, Marco}, title = {Pharmaceutical formulation strategies for novel antibiotic substances utilizing salt formation and two- and three-dimensional printing techniques}, doi = {10.25972/OPUS-21978}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-219784}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Salt formation is a routinely used strategy for poorly water-soluble drugs and traditionally performed with small inorganic counterions. High energy crystal lattices as well as effects on the local pH within the aqueous boundary layer during dissolution drive the increased dissolution rate and apparent solubility. Ionic liquids however, by definition low melting ionic salts with often large organic counterions, combine an increased dissolution rate with solubilization of the drug by the counterion itself. Long lasting supersaturation profiles of increased kinetic solubility were reported for several drugs formulated as ionic liquids increasing their overall bioavailability. Furthermore, aggregation and micellization between highly lipophilic compounds and amphiphilic bile acids was described before, demonstrating the capabilities of the human body itself to utilize solubilization of poorly water-soluble compounds. Development of novel counterions not only tailoring the desired physicochemical properties e.g. dissolution rate of the parent drug but adding - in a best-case scenario synergistic - pharmacological activity has been driven forward in the last years. However, salt formation can only be applied for ionizable i.e. acidic or basic compounds. While co-crystals can be used as a nonionized alternative, their formation is not always successful leading to an urgent need for other formulation strategies. In these lines, development of 2D and 3D printing techniques has been ongoing for the last decades and their pharmaceutical application has been demonstrated. The versatile nature and commercial availability allow a decentralized production further elaborating this technique for a highly flexible and patient-oriented supply with medication. This thesis focuses on the theoretical background and potential application of salt formation in the pharmaceutical development of a drug candidate. The first section presents the current knowledge and state of the art in preparation of low melting ionic liquids i.e. salts and is translated to the in vitro investigation of molecular interaction between the poorly water-soluble drug imatinib and components of the human intestinal fluid in the second section. Development of novel antibiotic counterions and assessment of their potential use in pharmaceutical formulations with fluoroquinolones is described in the last two sections. Chapter I describes the application of low melting ionic liquids in pharmaceutical formulation and details their development in the last two decades from versatile organic solvents in chemical synthesis towards amorphous strategies for drug delivery. The chapter gives a general overview on molecular structure and physicochemical properties of several drug containing ionic liquids and details the mechanisms which attribute to a typically fast dissolution, increased aqueous solubility as well as enhanced permeation which was reported in several publications. Chapter II translates the increased aqueous solubility of drugs by an organic counterion to the human gastrointestinal tract with taurocholate and lecithin as main drivers for the solubilization of highly lipophilic and poorly water-soluble drugs. Investigation of the interaction of imatinib - a poorly water-soluble weak base - with fasted- and fed state simulated intestinal fluids revealed a complex interplay between the components of the intestinal fluid and the drug. Mixed vesicles and micelles were observed in concentration dependent aggregation assays and revealed differences in their size, molecular arrangement as well as composition, depending on the tested drug concentration. Overall, the study outlines the effective interaction of weakly basic drugs with taurocholate and lecithin to minimize recrystallization during intestine passage finally leading to favorable supersaturation profiles. Chapter III focuses on the development of novel antibiotic counterions which potentially move the evolution of ionic liquids from a pharmaceutical salt with tailored physicochemical properties to a synergistic combination of two active pharmaceutical ingredients. The natural occurring anacardic acid derived from the cashew nut shell inspired a series of antibacterial active acidic compounds with increasing alkyl chain length. Their physicochemical properties, antibacterial activity, bacterial biofilm inhibition and cytotoxicity were detailed and in vivo activity in a Galleria mellonella model was assessed. This group of anacardic acid derivatives is synthetically accessible, easily modifiable and yielded two compounds with favorable activity and physicochemical profile for further drug development. Chapter IV outlines the potential application of anacardic acid derivatives in pharmaceutical formulations by salt formation with fluoroquinolone antibiotics as well as novel techniques such as 2D/3D printing for preparation of drug imprinted products. Despite anacardic acid derivatives demonstrated promising physicochemical properties, salt formation with fluoroquinolone antibiotics was not feasible. However, 2D/3D printed samples with anacardic acid derivative alone or in combination with ciprofloxacin demonstrated physical compatibility between drug and matrix as well as antibacterial activity against three S. aureus strains in an agar diffusion assay. Conclusively, drug printing can be applied for the herein tested compounds, but further process development is necessary. In summary, preparation of low melting ionic liquids, salts or co-crystals is an appropriate strategy to increase the aqueous solubility of poorly water-soluble drugs and tailor physicochemical properties. The counterion itself solubilizes the drug and furthermore potentially interferes with the complex micellar environment in the human intestine. However, salt formation as routinely used formulation strategy is not feasible in every case and development of alternative techniques is crucial to hurdle challenges related to unfavorable physicochemical properties. The outlined techniques for 2D/3D drug printing provide versatile production of drug products while extending the design space for novel drug development.}, subject = {L{\"o}slichkeit}, language = {en} } @phdthesis{Bauer2021, author = {Bauer, Andr{\´e}}, title = {Automated Hybrid Time Series Forecasting: Design, Benchmarking, and Use Cases}, doi = {10.25972/OPUS-22025}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-220255}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {These days, we are living in a digitalized world. Both our professional and private lives are pervaded by various IT services, which are typically operated using distributed computing systems (e.g., cloud environments). Due to the high level of digitalization, the operators of such systems are confronted with fast-paced and changing requirements. In particular, cloud environments have to cope with load fluctuations and respective rapid and unexpected changes in the computing resource demands. To face this challenge, so-called auto-scalers, such as the threshold-based mechanism in Amazon Web Services EC2, can be employed to enable elastic scaling of the computing resources. However, despite this opportunity, business-critical applications are still run with highly overprovisioned resources to guarantee a stable and reliable service operation. This strategy is pursued due to the lack of trust in auto-scalers and the concern that inaccurate or delayed adaptations may result in financial losses. To adapt the resource capacity in time, the future resource demands must be "foreseen", as reacting to changes once they are observed introduces an inherent delay. In other words, accurate forecasting methods are required to adapt systems proactively. A powerful approach in this context is time series forecasting, which is also applied in many other domains. The core idea is to examine past values and predict how these values will evolve as time progresses. According to the "No-Free-Lunch Theorem", there is no algorithm that performs best for all scenarios. Therefore, selecting a suitable forecasting method for a given use case is a crucial task. Simply put, each method has its benefits and drawbacks, depending on the specific use case. The choice of the forecasting method is usually based on expert knowledge, which cannot be fully automated, or on trial-and-error. In both cases, this is expensive and prone to error. Although auto-scaling and time series forecasting are established research fields, existing approaches cannot fully address the mentioned challenges: (i) In our survey on time series forecasting, we found that publications on time series forecasting typically consider only a small set of (mostly related) methods and evaluate their performance on a small number of time series with only a few error measures while providing no information on the execution time of the studied methods. Therefore, such articles cannot be used to guide the choice of an appropriate method for a particular use case; (ii) Existing open-source hybrid forecasting methods that take advantage of at least two methods to tackle the "No-Free-Lunch Theorem" are computationally intensive, poorly automated, designed for a particular data set, or they lack a predictable time-to-result. Methods exhibiting a high variance in the time-to-result cannot be applied for time-critical scenarios (e.g., auto-scaling), while methods tailored to a specific data set introduce restrictions on the possible use cases (e.g., forecasting only annual time series); (iii) Auto-scalers typically scale an application either proactively or reactively. Even though some hybrid auto-scalers exist, they lack sophisticated solutions to combine reactive and proactive scaling. For instance, resources are only released proactively while resource allocation is entirely done in a reactive manner (inherently delayed); (iv) The majority of existing mechanisms do not take the provider's pricing scheme into account while scaling an application in a public cloud environment, which often results in excessive charged costs. Even though some cost-aware auto-scalers have been proposed, they only consider the current resource demands, neglecting their development over time. For example, resources are often shut down prematurely, even though they might be required again soon. To address the mentioned challenges and the shortcomings of existing work, this thesis presents three contributions: (i) The first contribution-a forecasting benchmark-addresses the problem of limited comparability between existing forecasting methods; (ii) The second contribution-Telescope-provides an automated hybrid time series forecasting method addressing the challenge posed by the "No-Free-Lunch Theorem"; (iii) The third contribution-Chamulteon-provides a novel hybrid auto-scaler for coordinated scaling of applications comprising multiple services, leveraging Telescope to forecast the workload intensity as a basis for proactive resource provisioning. In the following, the three contributions of the thesis are summarized: Contribution I - Forecasting Benchmark To establish a level playing field for evaluating the performance of forecasting methods in a broad setting, we propose a novel benchmark that automatically evaluates and ranks forecasting methods based on their performance in a diverse set of evaluation scenarios. The benchmark comprises four different use cases, each covering 100 heterogeneous time series taken from different domains. The data set was assembled from publicly available time series and was designed to exhibit much higher diversity than existing forecasting competitions. Besides proposing a new data set, we introduce two new measures that describe different aspects of a forecast. We applied the developed benchmark to evaluate Telescope. Contribution II - Telescope To provide a generic forecasting method, we introduce a novel machine learning-based forecasting approach that automatically retrieves relevant information from a given time series. More precisely, Telescope automatically extracts intrinsic time series features and then decomposes the time series into components, building a forecasting model for each of them. Each component is forecast by applying a different method and then the final forecast is assembled from the forecast components by employing a regression-based machine learning algorithm. In more than 1300 hours of experiments benchmarking 15 competing methods (including approaches from Uber and Facebook) on 400 time series, Telescope outperformed all methods, exhibiting the best forecast accuracy coupled with a low and reliable time-to-result. Compared to the competing methods that exhibited, on average, a forecast error (more precisely, the symmetric mean absolute forecast error) of 29\%, Telescope exhibited an error of 20\% while being 2556 times faster. In particular, the methods from Uber and Facebook exhibited an error of 48\% and 36\%, and were 7334 and 19 times slower than Telescope, respectively. Contribution III - Chamulteon To enable reliable auto-scaling, we present a hybrid auto-scaler that combines proactive and reactive techniques to scale distributed cloud applications comprising multiple services in a coordinated and cost-effective manner. More precisely, proactive adaptations are planned based on forecasts of Telescope, while reactive adaptations are triggered based on actual observations of the monitored load intensity. To solve occurring conflicts between reactive and proactive adaptations, a complex conflict resolution algorithm is implemented. Moreover, when deployed in public cloud environments, Chamulteon reviews adaptations with respect to the cloud provider's pricing scheme in order to minimize the charged costs. In more than 400 hours of experiments evaluating five competing auto-scaling mechanisms in scenarios covering five different workloads, four different applications, and three different cloud environments, Chamulteon exhibited the best auto-scaling performance and reliability while at the same time reducing the charged costs. The competing methods provided insufficient resources for (on average) 31\% of the experimental time; in contrast, Chamulteon cut this time to 8\% and the SLO (service level objective) violations from 18\% to 6\% while using up to 15\% less resources and reducing the charged costs by up to 45\%. The contributions of this thesis can be seen as major milestones in the domain of time series forecasting and cloud resource management. (i) This thesis is the first to present a forecasting benchmark that covers a variety of different domains with a high diversity between the analyzed time series. Based on the provided data set and the automatic evaluation procedure, the proposed benchmark contributes to enhance the comparability of forecasting methods. The benchmarking results for different forecasting methods enable the selection of the most appropriate forecasting method for a given use case. (ii) Telescope provides the first generic and fully automated time series forecasting approach that delivers both accurate and reliable forecasts while making no assumptions about the analyzed time series. Hence, it eliminates the need for expensive, time-consuming, and error-prone procedures, such as trial-and-error searches or consulting an expert. This opens up new possibilities especially in time-critical scenarios, where Telescope can provide accurate forecasts with a short and reliable time-to-result. Although Telescope was applied for this thesis in the field of cloud computing, there is absolutely no limitation regarding the applicability of Telescope in other domains, as demonstrated in the evaluation. Moreover, Telescope, which was made available on GitHub, is already used in a number of interdisciplinary data science projects, for instance, predictive maintenance in an Industry 4.0 context, heart failure prediction in medicine, or as a component of predictive models of beehive development. (iii) In the context of cloud resource management, Chamulteon is a major milestone for increasing the trust in cloud auto-scalers. The complex resolution algorithm enables reliable and accurate scaling behavior that reduces losses caused by excessive resource allocation or SLO violations. In other words, Chamulteon provides reliable online adaptations minimizing charged costs while at the same time maximizing user experience.}, subject = {Zeitreihenanalyse}, language = {en} } @phdthesis{Boettcher2021, author = {B{\"o}ttcher, Jan Frederic}, title = {Fate of Topological States of Matter in the Presence of External Magnetic Fields}, doi = {10.25972/OPUS-22045}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-220451}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The quantum Hall (QH) effect, which can be induced in a two-dimensional (2D) electron gas by an external magnetic field, paved the way for topological concepts in condensed matter physics. While the QH effect can for that reason not exist without Landau levels, there is a plethora of topological phases of matter that can exist even in the absence of a magnetic field. For instance, the quantum spin Hall (QSH), the quantum anomalous Hall (QAH), and the three-dimensional (3D) topological insulator (TI) phase are insulating phases of matter that owe their nontrivial topology to an inverted band structure. The latter results from a strong spin-orbit interaction or, generally, from strong relativistic corrections. The main objective of this thesis is to explore the fate of these preexisting topological states of matter, when they are subjected to an external magnetic field, and analyze their connection to quantum anomalies. In particular, the realization of the parity anomaly in solid state systems is discussed. Furthermore, band structure engineering, i.e., changing the quantum well thickness, the strain, and the material composition, is employed to manipulate and investigate various topological properties of the prototype TI HgTe. Like the QH phase, the QAH phase exhibits unidirectionally propagating metallic edge channels. But in contrast to the QH phase, it can exist without Landau levels. As such, the QAH phase is a condensed matter analog of the parity anomaly. We demonstrate that this connection facilitates a distinction between QH and QAH states in the presence of a magnetic field. We debunk therefore the widespread belief that these two topological phases of matter cannot be distinguished, since they are both described by a \$\mathbb{Z}\$ topological invariant. To be more precise, we demonstrate that the QAH topology remains encoded in a peculiar topological quantity, the spectral asymmetry, which quantifies the differences in the number of states between the conduction and valence band. Deriving the effective action of QAH insulators in magnetic fields, we show that the spectral asymmetry is thereby linked to a unique Chern-Simons term which contains the information about the QAH edge states. As a consequence, we reveal that counterpropagating QH and QAH edge states can emerge when a QAH insulator is subjected to an external magnetic field. These helical-like states exhibit exotic properties which make it possible to disentangle QH and QAH phases. Our findings are of particular importance for paramagnetic TIs in which an external magnetic field is required to induce the QAH phase. A byproduct of the band inversion is the formation of additional extrema in the valence band dispersion at large momenta (the `camelback'). We develop a numerical implementation of the \$8 \times 8\$ Kane model to investigate signatures of the camelback in (Hg,Mn)Te quantum wells. Varying the quantum well thickness, as well as the Mn-concentration, we show that the class of topologically nontrivial quantum wells can be subdivided into direct gap and indirect gap TIs. In direct gap TIs, we show that, in the bulk \$p\$-regime, pinning of the chemical potential to the camelback can cause an onset to QH plateaus at exceptionally low magnetic fields (tens of mT). In contrast, in indirect gap TIs, the camelback prevents the observation of QH plateaus in the bulk \$p\$-regime up to large magnetic fields (a few tesla). These findings allowed us to attribute recent experimental observations in (Hg,Mn)Te quantum wells to the camelback. Although our discussion focuses on (Hg,Mn)Te, our model should likewise apply to other topological materials which exhibit a camelback feature in their valence band dispersion. Furthermore, we employ the numerical implementation of the \$8\times 8\$ Kane model to explore the crossover from a 2D QSH to a 3D TI phase in strained HgTe quantum wells. The latter exhibit 2D topological surface states at their interfaces which, as we demonstrate, are very sensitive to the local symmetry of the crystal lattice and electrostatic gating. We determine the classical cyclotron frequency of surface electrons and compare our findings with experiments on strained HgTe.}, subject = {Topologie}, language = {en} } @phdthesis{Aurbach2021, author = {Aurbach, Katja}, title = {Studies on the role of the cytoskeleton in platelet production}, doi = {10.25972/OPUS-23466}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-234669}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Platelets are small anucleated cell fragments that originate from megakaryocytes (MKs), which are large cells located in the bone marrow (BM). MKs extend long cytoplasmic protrusions, a process which is called proplatelet formation, into the lumen of the sinusoidal vessels where platelets are sized by the bloodstream. During the process of platelet biogenesis, segments of the MK penetrate the endothelium and, through cytoskeletal remodeling inside the MK, proplatelet fragments are released. Rho GTPases, such as RhoA and RhoB, are critically involved in cytoskeletal rearrangements of both the actin and the tubulin cytoskeleton. The first part of this thesis concentrated on the protein RhoB and its involvement in cytoskeletal organization in MKs and platelets. Single knockout (KO) mice lacking RhoB had a minor microthrombocytopenia, which means a smaller platelet size and reduced platelet number, accompanied by defects in the microtubule cytoskeleton in both MKs and platelets. In particular, tubulin organization and stability, which is regulated by posttranslational modifications of α-tubulin, were disturbed in RhoB-/- platelets. In contrast, RhoB-/- MKs produced abnormally shaped proplatelets but had unaltered posttranslational modifications of α-tubulin. The second part focused on the influence of RhoA and RhoB on MK localization and platelet biogenesis in murine BM. Many intact RhoA-/- MKs are able to transmigrate through the endothelial layer and stay attached to the vessel wall, whereas only 1\% of wildtype (wt) MKs are detectable in the intrasinusoidal space. Concomitant deficiency of RhoA and RhoB reverts this transmigration and results in macrothrombocytopenia, MK clusters around the vessel in the BM and defective MK development. The underlying mechanism that governs MKs to distinct localizations in the BM is poorly understood, thus this thesis suggests that this process may be dependent on RhoB protein levels, as RhoA deficiency is coincided with increased RhoB levels in MKs and platelets. The third part of this thesis targeted the protein PDK1, a downstream effector of Rho GTPases, in regard to MK maturation and polarization throughout thrombopoiesis. MK- and platelet-specific KO in mice led to a significant macrothrombocytopenia, impaired actin cytoskeletal reorganization during MK spreading and proplatelet formation, with defective MK maturation. This was associated with decreased PAK activity and, subsequently, phosphorylation of its substrates LIMK and Cofilin. Together, the observations of this thesis highlight the importance of Rho GTPases and their downstream effectors on the regulation of the MK and platelet cytoskeleton.}, subject = {Megakaryozyt}, language = {en} } @phdthesis{Wang2021, author = {Wang, Zhenjiu}, title = {Numerical simulations of continuum field theories and exotic quantum phase transitions}, doi = {10.25972/OPUS-23800}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-238001}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {In this thesis, we investigate several topics pertaining to emergent collective quantum phenomena in the domain of correlated fermions, using the quantum Monte Carlo method. They display exotic low temperature phases as well as phase transitions which are beyond the Landau-Ginzburg theory. The interplay between three key points is crucial for us: fermion statistics, many body effects and topology. We highlight the following several achievements: 1. Successful modeling of continuum field theories with lattice Hamiltonians, 2. their sign-problem-free Monte Carlo simulations of these models, 3. and numerical results beyond mean field descriptions. First, we consider a model of Dirac fermions with a spin rotational invariant inter- action term that dynamically generates a quantum spin Hall insulator. Surprisingly, an s-wave superconducting phase emerges due to the condensation of topological de- fects of the spin Hall order parameter. When particle-hole symmetry is present, the phase transition between the topological insulator and the superconducting phase is an example of a deconfined quantum critical point(DQCP). Although its low energy effec- tive field theory is purely bosonic, the exact conservation law of the skyrmion number operator rules out the possibility of realizing this critical point in lattice boson models. This work is published in Ref. [1]. Second, we dope the dynamically generated quantum spin Hall insulator mentioned above. Hence it is described by a field theory without Lorentz invariance due to the lack of particle-hole symmetry. This sheds light on the extremely hot topic of twisted bilayergraphene: Why is superconductivity generated when the repulsive Coulomb interaction is much stronger than the electron-phonon coupling energy scale? In our case, Cooper pairs come from the topological skyrmion defects of the spin current order parameter, which are charged. Remarkably, the nature of the phase transition is highly non-mean-field-like: one is not allowed to simply view pairs of electrons as single bosons in a superfluid-Mott insulator transition, since the spin-current order parameter can not be ignored. Again, due to the aforementioned skyrmions, the two order parameters are intertwined: One phase transition occurs between the two symmetry breaking states. This work is summarized in Ref. [2]. Third, we investigate the 2 + 1 dimensional O(5) nonlinear sigma model with a topological Wess-Zumino-Witten term. Remarkably, we are able to perform Monte Carlo calculations with a UV cutoff given by the Dirac Landau level quantization. It is a successful example of simulating a continuous field theory without lattice regularization which leads to an additional symmetry breaking. The Dirac background and the five anti-commuting Dirac mass terms naturally introduce the picture of a non-trivial Berry phase contribution in the parameter space of the five component order parameter. Using the finite size scaling method given by the flux quantization, we find a stable critical phase in the low stiffness region of the sigma model. This is a candidate ground state of DQCP when the O(5) symmetry breaking terms are irrelevant at the critical point. Again, it has a bosonic low energy field theory which is seemingly unable to be realized in pure boson Hamiltonians. This work is summarized in Ref. [3].}, subject = {Quanten-Monte-Carlo-Methode}, language = {en} } @phdthesis{Kasper2021, author = {Kasper, Christian Andreas}, title = {Engineering of Highly Coherent Silicon Vacancy Defects in Silicon Carbide}, doi = {10.25972/OPUS-23779}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-237797}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {In this work the creation of silicon vacancy spin defects in silicon carbide with predictable properties is demonstrated. Neutron and electron irradiation was used to create silicon vacancy ensembles and proton beam writing to create isolated vacancies at a desired position. The coherence properties of the created silicon vacancies as a function of the emitter density were investigated and a power-law function established. Sample annealing was implemented to increase the coherence properties of existing silicon vacancies. Further, spectral hole burning was used to implement absolute dc-magnetometry.}, subject = {St{\"o}rstelle}, language = {en} } @phdthesis{Poehner2021, author = {P{\"o}hner, Nicolai}, title = {Educational robotics competitions as out-of-school learning setting for STEM education: An empirical study on students' learning of problem solving skills through participation in the World Robot Olympiad}, doi = {10.25972/OPUS-24317}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-243179}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Educational robotics is an innovative approach to teaching and learning a variety of different concepts and skills as well as motivating students in the field of Science, Technology, Engineering, and Mathematics (STEM) education. This especially applies to educational robotics competitions such as, for example, the FIRST LEGO League, the RoboCup Junior, or the World Robot Olympiad as out-of-school and goal-oriented approach to educational robotics. These competitions have gained greatly in popularity in recent years and thousands of students participate in these competitions worldwide each year. Moreover, the corresponding technology became more accessible for teachers and students to use it in their classrooms and has arguably a high potential to impact the nature of science education at all levels. One skill, which is said to be benefitting from educational robotics, is problem solving. This thesis understands problem solving skills as engineering design skills (in contrast to scientific inquiry). Problem solving skills count as important skills as demanded by industry leaders and policy makers in the context of 21st century skills, which are relevant for students to be well-prepared for their future working life in today's world, shaped by an ongoing process of automation, globalization, and digitalization. The overall aim of this thesis is to try to answer the question if educational robotics competitions such as the World Robot Olympiad (WRO) have a positive impact on students' learning in terms of their problem solving skills (as part of 21st century skills). In detail, this thesis focuses on a) if students can improve their problem solving skills through participation in educational robotics competitions, b) how this skill development is accomplished, and c) the teachers' support of their students during their learning process in the competition. The corresponding empirical studies were conducted throughout the seasons of 2018 and 2019 of the WRO in Germany. The results show overall positive effects of the participation in the WRO on students' learning of problem solving skills. They display an increase of students' problem solving skills, which is not moderated by other variables such as the competition's category or age group, the students' gender or experience, or the success of the teams at the competition. Moreover, the results indicate that students develop their problem solving skills by using a systematic engineering design process and sophisticated problem solving strategies. Lastly, the teacher's role in the educational robotics competitions as manager and guide (in terms of the constructionist learning theory) of the students' learning process (especially regarding the affective level) is underlined by the results of this thesis. All in all, this thesis contributes to the research gap concerning the lack of systematic evaluation of educational robotics to promote students' learning by providing more (methodologically) sophisticated research on this topic. Thereby, this thesis follows the call for more rigorous (quantitative) research by the educational robotics community, which is necessary to validate the impact of educational robotics.}, subject = {Fachdidaktik}, language = {en} }