@phdthesis{Karama2021, author = {Karama, Alphonse}, title = {East African Seasonal Rainfall prediction using multiple linear regression and regression with ARIMA errors models}, doi = {10.25972/OPUS-25183}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251831}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The detrimental impacts of climate variability on water, agriculture, and food resources in East Africa underscore the importance of reliable seasonal climate prediction. To overcome this difficulty RARIMAE method were evolved. Applications RARIMAE in the literature shows that amalgamating different methods can be an efficient and effective way to improve the forecasts of time series under consideration. With these motivations, attempt have been made to develop a multiple linear regression model (MLR) and a RARIMAE models for forecasting seasonal rainfall in east Africa under the following objectives: 1. To develop MLR model for seasonal rainfall prediction in East Africa. 2. To develop a RARIMAE model for seasonal rainfall prediction in East Africa. 3. Comparison of model's efficiency under consideration In order to achieve the above objectives, the monthly precipitation data covering the period from 1949 to 2000 was obtained from Climate Research Unit (CRU). Next to that, the first differenced climate indices were used as predictors. In the first part of this study, the analyses of the rainfall fluctuation in whole Central- East Africa region which span over a longitude of 15 degrees East to 55 degrees East and a latitude of 15 degrees South to 15 degrees North was done by the help of maps. For models' comparison, the R-squared values for the MLR model are subtracted from the R-squared values of RARIMAE model. The results show positive values which indicates that R-squared is improved by RARIMAE model. On the other side, the root mean square errors (RMSE) values of the RARIMAE model are subtracted from the RMSE values of the MLR model and the results show negative value which indicates that RMSE is reduced by RARIMAE model for training and testing datasets. For the second part of this study, the area which is considered covers a longitude of 31.5 degrees East to 41 degrees East and a latitude of 3.5 degrees South to 0.5 degrees South. This region covers Central-East of the Democratic Republic of Congo (DRC), north of Burundi, south of Uganda, Rwanda, north of Tanzania and south of Kenya. Considering a model constructed based on the average rainfall time series in this region, the long rainfall season counts the nine months lead of the first principal component of Indian sea level pressure (SLP_PC19) and the nine months lead of Dipole Mode Index (DMI_LR9) as selected predictors for both statistical and predictive model. On the other side, the short rainfall season counts the three months lead of the first principal component of Indian sea surface temperature (SST_PC13) and the three months lead of Southern Oscillation Index (SOI_SR3) as predictors for predictive model. For short rainfall season statistical model SAOD current time series (SAOD_SR0) was added on the two predictors in predictive model. By applying a MLR model it is shown that the forecast can explain 27.4\% of the total variation and has a RMSE of 74.2mm/season for long rainfall season while for the RARIMAE the forecast explains 53.6\% of the total variation and has a RMSE of 59.4mm/season. By applying a MLR model it is shown that the forecast can explain 22.8\% of the total variation and has a RMSE of 106.1 mm/season for short rainfall season predictive model while for the RARIMAE the forecast explains 55.1\% of the total variation and has a RMSE of 81.1 mm/season. From such comparison, a significant rise in R-squared, a decrease of RMSE values were observed in RARIMAE models for both short rainfall and long rainfall season averaged time series. In terms of reliability, RARIMAE outperformed its MLR counterparts with better efficiency and accuracy. Therefore, whenever the data suffer from autocorrelation, we can go for MLR with ARIMA error, the ARIMA error part is more to correct the autocorrelation thereby improving the variance and productiveness of the model.}, subject = {Regression}, language = {en} } @phdthesis{Orth2021, author = {Orth, Barbara}, title = {Identification of an atypical peptide binding mode of the BTB domain of the transcription factor MIZ1 with a HUWE1-derived peptide}, doi = {10.25972/OPUS-25044}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-250447}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Ubiquitination is a posttranslational modification with immense impact on a wide range of cellular processes, including proteasomal degradation, membrane dynamics, transcription, translation, cell cycle, apoptosis, DNA repair and immunity. These diverse functions stem from the various ubiquitin chain types, topologies, and attachment sites on substrate proteins. Substrate recruitment and modification on lysine, serine or threonine residues is catalyzed by ubiquitin ligases (E3s). An important E3 that decides about the fate of numerous substrates is the HECT-type ubiquitin ligase HUWE1. Depending on the substrate, HUWE1 is involved in different processes, such as cell proliferation and differentiation, DNA repair, and transcription. One of the transcription factors that is ubiquitinated by HUWE1 is the MYC interacting zinc finger protein 1 (MIZ1). MIZ1 is a BTB/POZ (Bric-{\`a}-brac, Tramtrack and Broad-Complex/Pox virus and zinc finger) zinc finger (ZF) protein that binds to DNA through its 13 C2H2-type zinc fingers and either activates or represses the transcription of target genes, including genes involved in cell cycle arrest, such as P21CIP1 (CDKN1A). The precise functions of MIZ1 depend on its interactions with the MYC-MAX heterodimer, but also its heterodimerization with other BTB-ZF proteins, such as BCL6 or NAC1. How MIZ1 interacts with HUWE1 has not been studied and, as a consequence, it has not been possible to rationally develop tools to manipulate this interaction with specificity in order to better understand the effects of the interaction on the transcriptional function of MIZ1 on target genes or processes downstream. One aspect of my research, therefore, aimed at characterizing the MIZ1-HUWE1 interaction at a structural level. I determined a crystal structure of the MIZ1-BTB-domain in complex with a peptide, referred to as ASC, derived from a C terminal region of HUWE1, previously named 'activation segment'. The binding mode observed in this crystal structure could be validated by binding and activity assays in vitro and by cell-based co-IP experiments in the context of N-terminally truncated HUWE1 constructs. I was not able to provide unambiguous evidence for the identified binding mode in the context of full-length HUWE1, indicating that MIZ1 recognition by HUWE1 requires yet unknown regions in the cell. While the structural details of the MIZ1-HUWE1 interaction remains to be elucidated in the context of the full-length proteins, the binding mode between MIZ1BTB and ASC revealed an interesting, atypical structural feature of the BTB domain of MIZ1 that, to my knowledge, has not been described for other BTB-ZF proteins: The B3 region in MIZ1BTB is conformationally malleable, which allows for a HUWE1-ASC-peptide-mediated β-sheet extension of the upper B1/B2-strands, resulting in a mixed, 3 stranded β-sheet. Such β-sheet extension does not appear to occur in other homo- or heterodimeric BTB-ZF proteins, including MIZ1-heterodimers, since these proteins typically possess a pre-formed B3-strand in at least one subunit. Instead, BCL6 co repressor-derived peptides (SMRT and BCOR) were found to extend the lower β-sheet in BCL6BTB by binding to an adjacent 'lateral groove'. This interaction follows a 1:1 stoichiometry, whereas the MIZ1BTB-ASC-complex shows a 2:1 stoichiometry. The crystal structure of the MIZ1BTB-ASC-complex I determined, along with comparative binding studies of ASC with monomeric, homodimeric, and heterodimeric MIZ1BTB variants, respectively, suggests that ASC selects for MIZ1BTB homodimers. The structural data I generated may serve as an entry point for the prediction of additional interaction partners of MIZ1 that also have the ability to extend the upper β-sheet of MIZ1BTB. If successful, such interaction partners and structures thereof might aid the design of peptidomimetics or small-molecule inhibitors of MIZ1 signaling. Proof-of-principle for such a structure-guided approach targeting BTB domains has been provided by small-molecule inhibitors of BCL6BTB co-repressors interactions. If a similar approach led to molecules that interfere with specific interactions of MIZ1, they would provide intriguing probes to study MIZ1 biology and may eventually allow for the development of MIZ1-directed cancer therapeutics.}, subject = {Ubiquitin}, language = {en} } @phdthesis{Gentzsch2021, author = {Gentzsch, Christian}, title = {Molecular Imaging of Opioid Receptors and Butyrylcholinesterase with Selective, Tailored Probes Using Positron Emission Tomography and Fluorescence Microscopy}, doi = {10.25972/OPUS-24752}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247529}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The present thesis concerns the molecular imaging of opioid receptors and human butyrylcholinesterase with the aid of tailored probes, which are suitable for the respective applied imaging techniques. The first part focusses on imaging of opioid receptors with selective probes using total internal reflection- and single molecule fluorescence microscopy. Design and synthesis of the ligands are presented and their pharmacological characterization and application in microscopy experiments are shown. The second part of this thesis focused on the development of 18F-labeled, selective radiotracers for imaging of butyrylcholinesterase via positron emission tomography. The design and synthesis of each a reversible and pseudoirreversible 18F-labeled tracer are presented. After evaluation of the binding properties of each tracer, their initial application in ex vivo autoradiography- and preliminary in vivo microPET studies is described and analyzed.}, subject = {Fluoreszenzmikroskopie}, language = {en} } @phdthesis{Kraus2021, author = {Kraus, Amelie Johanna}, title = {H2A.Z - a molecular guardian of RNA polymerase II transcription in African trypanosomes}, doi = {10.25972/OPUS-25056}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-250568}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {In eukaryotes, the enormously long DNA molecules need to be packaged together with histone proteins into nucleosomes and further into compact chromatin structures to fit it into the nucleus. This nuclear organisation interferes with all phases of transcription that require the polymerase to bind to DNA. During transcription - the process in which the hereditary information stored in DNA is transferred to many transportable RNA molecules - nucleosomes form a physical obstacle for polymerase progression. Thus, transcription is usually accompanied by processes mediating nucleosome destabilisation, including post-translational histone modifications (PTMs) or exchange of canonical histones by their variant forms. To the best of our knowledge, acetylation of histones has the highest capability to induce chromatin opening. The lysine modification can destabilise histone-DNA interactions within a nucleosome and can serve as a binding site for various chromatin remodelers that can modify the nucleosome composition. For example, H4 acetylation can impede chromatin folding and can stimulate the exchange of canonical H2A histone by its variant form H2A.Z at transcription start sites (TSSs) in many eukaryotes, including humans. As histone H4, H2A.Z can be post-translationally acetylated and as acetylated H4, acetylated H2A.Z is enriched at TSSs suggested to be critical for transcription. However, thus far, it has been difficult to study the cause and consequence of H2A.Z acetylation. Even though, genome-wide chromatin profiling studies such as ChIP-seq have already revealed the genomic localisation of many histone PTMs and variant proteins, they can only be used to study individual chromatin marks and not to identify all factors important for establishing a distinct chromatin structure. This would require a comprehensive understanding of all marks associated to a specific genomic locus. However, thus far, such analyses of locus-specific chromatin have only been successful for repetitive regions, such as telomeres. In my doctoral thesis, I used the unicellular parasite Trypanosoma brucei as a model system for chromatin biology and took advantage of its chromatin landscape with TSSs comprising already 7\% of the total T. brucei genome (humans: 0.00000156\%). Atypical for a eukaryote, the protein-coding genes are arranged in long polycistronic transcription units (PTUs). Each PTU is controlled by its own ~10 kb-wide TSS, that lies upstream of the PTU. As observed in other eukaryotes, TSSs are enriched with nucleosomes containing acetylated histones and the histone variant H2A.Z. This is why I used T. brucei to particularly investigate the TSS-specific chromatin structures and to identify factors involved in H2A.Z deposition and transcription regulation in eukaryotes. To this end, I established an approach for locus-specific chromatin isolation that would allow me to identify the TSSs- and non-TSS-specific chromatin marks. Later, combining the approach with a method for quantifying lysine-specific histone acetylation levels, I found H2A.Z and H4 acetylation enriched in TSSs-nucleosomes and mediated by the histone acetyltransferases HAT1 and HAT2. Depletion of HAT2 reduced the levels of TSS-specific H4 acetylation, affected targeted H2A.Z deposition and shifted the sites of transcription initiation. Whereas HAT1 depletion had only a minor effect on H2A.Z deposition, it had a strong effect on H2A.Z acetylation and transcription levels. My findings demonstrate a clear link between histone acetylation, H2A.Z deposition and transcription initiation in the early diverged unicellular parasite T. brucei, which was thus far not possible to determine in other eukaryotes. Overall, my study highlights the usefulness of T. brucei as a model system for studying chromatin biology. My findings allow the conclusion that H2A.Z regardless of its modification state defines sites of transcription initiation, whereas H2A.Z acetylation is essential co-factor for transcription initiation. Altogether, my data suggest that TSS-specific chromatin establishment is one of the earliest developed mechanisms to control transcription initiation in eukaryotes.}, subject = {Chromatin}, language = {en} } @phdthesis{Hirsch2021, author = {Hirsch, Florian}, title = {IR/UV Double-Resonance Spectroscopy of Reactive Hydrocarbon Species and their Reaction Products in Cold Molecular Jets}, doi = {10.25972/OPUS-25175}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251755}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Reactive hydrocarbon species are important in a multitude of different scientific areas. In this thesis, the vibrational spectra of hydrocarbon radicals, biradicals and their reaction product have been studied in a gas-phase environment. The specific molecules investigated here, are of particular importance in the field of combustion and astrochemistry. They were produced from suitable precursors in a pyrolytically heated micro-reactor and subsequently seeded in an appropriate carrier gas. As methodology, IR/UV ion dip spectroscopy has been utilized, which delivers massselected gas-phase IR spectra of all ionizable species detectable in the molecular beam. These, with the help of DFT calculations, allow for determination of the fingerprint IR spectra, identification of mass carriers and formulation of potential reaction mechanisms. All studies have been conducted in collaboration with the group of Prof. Dr. Anouk M. Rjis and the necessary potent IR radiation has been provided by the free-electron laser FELIX. Thus, the IR/UV measurements have been executed at the FELIX Laboratory of the Radboud University in Nijmegen. The first study presented in this thesis is the investigation of ortho-benzyne in Chapter 3.1. This molecule is of particular interest due to its uncommon electronic structure and its role in high-temperature reactions. Although, the infrared spectrum of o-C6H4 was not accessible, a number of reaction products were identified via their fingerprint spectra. Masses in the range from 78 - 228 were assigned to their respective carrier. The identified species include typical PAHs like naphthalene, phenanthrene, up to triphenylene. The identified masses further suggest a PAH growth heavily influenced by diradical 1,4-cycloaddition followed by fragmentation, as well as by classical HACA- and PAC-like mechanisms. These results were augmented by threshold photoionization measurements from Engelbert Reusch, who identified lighter reaction products, which have insufficient IR absorption or unsuitable ionization characteristics to be identified in the IR/UV experiment. An interesting observation is the identification of m/z = 152. This carrier has been assigned differently by the IR and TPES experiments. Whereas the IR spectrum clearly identifies the species as 2-ethynylnaphthalene, the TPES evidently is in great agreement with biphenylene. This is a good example how different experimental methodologies can benefit from each other to gain a deeper insight into the actual science of a particular system. Probably, the prime example for an aromatically resonance stabilized radical is benzyl. This radical is of high importance for many combustion studies, as it represents the primary high-temperature decomposition product of toluene. The goal of the study was the identification of the benzyl self reaction products and the results are discussed in Section 3.2. The radical was pyrolytically produced by its respective nitrite precursor. The mass spectrum showed that the benzyl self reaction formed two products with C11 and three with C14 constitution. All mass peaks were evenly spaced by two mass units, respectively, which suggests a close relation in formation. Indeed, the C11 products were identified as diphenylmethane and fluorene, which are simply connected via cyclization. The heaviest product was identified as phenanthrene, which is formed via the cyclization of bibenzyl to 9,10-dihydrophenanthrene and subsequent elimination of hydrogen. This result was quiet interesting as the intermediate of this reaction was often assumed to be stilbene, which was not observed in the study. Hence, the reaction seems to undergo cyclization first before phenanthrene is finally formed via hydrogen elimination. Expanding the molecular frame of benzyl by an additional methyl group leads to the xylyl radicals and its decomposition product the xylylenes. Also important in combustion research, xylyl radicals represent the preferred decomposition products of xylene, a frequently used anti-knock agent in modern gasoline blends. After further hydrogen elimination the xylyl radicals can then form their respective xylylenes. The results of the xylyl experiments are discussed in Section 3.3. Here the gas-phase vibrational spectrum in the fingerprint region for all three isomers has been recorded for the first time in isolation. Although, all isomers have a very similar structure and symmetry, and consequently similar vibrational bands, the resolution of the experimental data was exceedingly sufficient for a clear assignment. Additionally, the dimerization products of meta- and para-xylyl could also be identified. A similar approach was taken to determine the fingerprint spectra for the xylylenes. Here, only para-xylylene could be unambiguously identified as the carrier of mass 104. For both ortho- and meta-xylylene precursors, only isomerization products were observed as the carriers of mass 104; benzocyclobutene and styrene, respectively. A possible explanation is elaborated upon in the troubleshooting Sec- tion 3.4.3.5. In the final experimental section a study on the decomposition of phthalide is presented. The objective of this experiment was mainly focused around the formation of C7 species, particularly the fulvenallenyl radical C7H5. In fact, the first experimental fingerprint spectrum of isolated C7H5 in the gas-phase was measured and is displayed in Fig. 3.45. Furthermore, the experiment demonstrates that the pyrolysis products of phthalide are excellent soot precursors, as many heavier reaction products have been identified. These include typical PAH species like naphthalene and phenanthrene as well as their methylated isomers. A large number of molecules with terminal ethynyl moieties indicate a strong influence of HACA growth in the experimental environment. However, many formation pathways of products have been discussed, which are formed involving experiment specific species, like C5H5 and C7H5, and often include expansion steps from 5- to 6-membered rings.}, subject = {Infrarotspektroskopie}, language = {en} } @phdthesis{Bachmann2021, author = {Bachmann, Julia}, title = {Role of Adipose-Derived Stromal/Stem Cells in Cell-Assisted Lipotransfer - Characterization of their Secretory Capacity under Ischemia-Like Stress Conditions and Establishment of a 3D Adipose Tissue-ASC Co-Culture}, doi = {10.25972/OPUS-25178}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251786}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The use of human adipose-derived mesenchymal stem cells (ASCs) for cell-based therapeutic approaches, in terms of repair and regeneration of various tissues and organs, offers an alternative therapeutic tool in the field of regenerative medicine. The ability of ASCs to differentiate along mesenchymal lineages is not the only property that makes these cells particularly attractive for therapeutic purposes. Their promising functions in promoting angiogenesis, reducing inflammation as well as in functional tissue restoration are largely related to the trophic effects of a broad panel of secreted cytokines and growth factors. However, in cell-based approaches, the cell-loaded construct often is exposed to an ischemic microenvironment characterized by severe oxidative and nutritional stress after transplantation due to the initial lack of vascular connection, resulting in reduced cell viability and altered cell behaviour. Therefore, the effective use of ASCs in regenerative medicine first requires a comprehensive characterization of the cells in terms of their viability, differentiation capacity and especially their secretory capabilities under ischemia-mimicking conditions in order to better understand their beneficial role. Accordingly, in the first part of this work, ASCs were investigated under different ischemic conditions, in which cells were exposed to both glucose and oxygen deprivation, with respect to viability and secretory function. Using mRNA gene expression analysis, significantly higher expression of selected angiogenic, anti-apoptotic and immunomodulatory factors (IL-6, VEGF, STC-1) could be demonstrated under harsh ischemic conditions. These results were reflected at the protein expression level by a significantly increased secretion of these factors. For stanniocalcin-1 (STC-1), a factor not yet described in ASCs, a particularly high expression with significant secreted amounts of the protein could be demonstrated under harsh ischemic conditions. Thus, the first part of this work, in addition to the characterization of the viability, provided first insights into the secretory response of ASCs under ischemic conditions. The response of ASCs to glucose deficiency in combination with severe hypoxia has been little explored to date. Thus, the focus of the second part of this work was on a more detailed investigation of the secretory response of ASCs under glucose and oxygen deprivation. For a more comprehensive analysis of the secretion profile, a cytokine antibody array was performed, which allowed the detection of a broad panel of secreted angiogenic factors (IL-8, ANG), matrix-regulating proteins (TIMP-1, TIMP-2), chemokines (MCP-1/CCL2, IP-10/CXCL 10) and other factors under ischemic conditions. To verify these results, selected factors were examined using ELISA. The analysis revealed that the secretion of individual factors (e.g., STC-1, VEGF) was significantly upregulated by the combination of glucose and oxygen deprivation compared to oxygen deprivation alone. In order to investigate the impact of the secretome of ischemic ASCs on cell types involved in tissue regeneration, the effect of conditioned medium of ischemia-challenged ASCs on both endothelial cells and fibroblasts was investigated in subsequent experiments. Significantly increased viability and tube formation of endothelial cells as well as activated migration of fibroblasts by the secreted factors of ischemic ASCs could be demonstrated. A direct correlation of these effects to STC-1, which was significantly upregulated under ischemic conditions and has been described as a regulator of key cellular functions, could not be verified. The particular secretory capacity of ASCs provides a valuable tool for cell-based therapies, such as cell-assisted lipotransfer (CAL), where by enriching fat grafts with isolated ASCs, a significantly improved survival rate of the transplanted construct is achieved with less resorption of the fat tissue as well as a reduction in adverse implications, such as fibrosis and cyst formation. In order to better understand the function of ASCs in CAL, an autologous transwell-based lipograft-ASC co-culture was established in the last part of this work, in which first investigations showed a markedly increased secretion of VEGF compared to lipografts without added ASCs. As the stability rate of the fat tissue and thus the success of CAL is presumably also dependent on the preparation of the tissue before transplantation, the conventional preparation method of fat tissue for vocal fold augmentation in laryngoplasty was additionally evaluated in vitro in a pilot experiment. By analyzing the viability and tissue structure of the clinically prepared injection material, a large number of dead cells and a clearly damaged tissue structure with necrotic areas could be demonstrated. In comparison, the preparation method of the fat tissue established in this work as small tissue fragments was able to provide a clearly intact, vital, and vascularized tissue structure. This type of adipose tissue preparation represents a promising alternative for clinical vocal fold augmentation. In conclusion, the results of this work contribute to a comprehensive characterization of ASCs under ischemic conditions, such as those prevalent at the transplantation site or in tissue regeneration. The results obtained, especially on the secretory capacity of ASCs, provide new insights into how ASCs mediate regenerative effects in an ischemic milieu and why their use for therapeutic purposes is highly attractive and promising.}, subject = {Adipose}, language = {en} } @phdthesis{Loeblein2021, author = {L{\"o}blein, Jochen}, title = {Development of Dynamic Self-Initiated Photografting and Photopolymerization}, doi = {10.25972/OPUS-25182}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251828}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {After examining suitable parameters for a newly designed system, dynamic SIPGP could be developed. For the first time, SIPGP was performed while applying a constant flow of monomer solution through the reaction system. This added a new parameter: the flow rate (rfl). Accordingly, this parameter was examined, comparing dynamic to static SIPGP. It could be shown, that by applying higher rfl to the system, the contact angle increases, which indicates a slower coating. The flow patterns inside the reactor were then modelled and calculated. These calculations indicated, that, due to higher flow velocities, the contact angle on the coated samples would be lower on the sides of the sample and higher in the middle. This finding was verified by contact angle measurements. The influence of dynamic SIPGP on the temperature inside the reaction chamber during the reaction was examined by temperature sensors inside the reactor. This showed, that the constant flow of monomer solution can be utilized to decrease the warming of the reaction solution during the reaction. Finally it was shown, that dynamic SIPGP can decrease the formation of bulk polymer on the sample, which is forming during the reaction. This enables SIPGP to fabricate more homogeneous coatings by applying a constant monomer flow.}, subject = {Hydrogel}, language = {en} } @phdthesis{Schmidt2021, author = {Schmidt, Stefanie}, title = {Cartilage Tissue Engineering - Comparison of Articular Cartilage Progenitor Cells and Mesenchymal Stromal Cells in Agarose and Hyaluronic Acid-Based Hydrogels}, doi = {10.25972/OPUS-25171}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251719}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Articular cartilage damage caused by sports accidents, trauma or gradual wear and tear can lead to degeneration and the development of osteoarthritis because cartilage tissue has only limited capacity for intrinsic healing. Osteoarthritis causes reduction of mobility and chronic pain and is one of the leading causes of disability in the elderly population. Current clinical treatment options can reduce pain and restore mobility for some time, but the formed repair tissue has mostly inferior functionality compared to healthy articular cartilage and does not last long-term. Articular cartilage tissue engineering is a promising approach for the improvement of the quality of cartilage repair tissue and regeneration. In this thesis, a promising new cell type for articular cartilage tissue engineering, the so-called articular cartilage progenitor cell (ACPC), was investigated for the first time in the two different hydrogels agarose and HA-SH/P(AGE-co-G) in comparison to mesenchymal stromal cells (MSCs). In agarose, ACPCs´ and MSCs´ chondrogenic capacity was investigated under normoxic (21 \% oxygen) and hypoxic (2 \% oxygen) conditions in monoculture constructs and in zonally layered co-culture constructs with ACPCs in the upper layer and MSCs in the lower layer. In the newly developed hyaluronic acid (HA)-based hydrogel HA-SH/P(AGE-co-G), chondrogenesis of ACPCs and MSCs was also evaluated in monoculture constructs and in zonally layered co-culture constructs like in agarose hydrogel. Additionally, the contribution of the bioactive molecule hyaluronic acid to chondrogenic gene expression of MSCs was investigated in 2D monolayer, 3D pellet and HA-SH hydrogel culture. It was shown that both ACPCs and MSCs could chondrogenically differentiate in agarose and HA-SH/P(AGE-co-G) hydrogels. In agarose hydrogel, ACPCs produced a more articular cartilage-like tissue than MSCs that contained more glycosaminoglycan (GAG), less type I collagen and only little alkaline phosphatase (ALP) activity. Hypoxic conditions did not increase extracellular matrix (ECM) production of ACPCs and MSCs significantly but improved the quality of the neo-cartilage tissue produced by MSCs. The creation of zonal agarose constructs with ACPCs in the upper layer and MSCs in the lower layer led to an ECM production in zonal hydrogels that lay in general in between the ECM production of non-zonal ACPC and MSC hydrogels. Even though zonal co-culture of ACPCs and MSCs did not increase ECM production, the two cell types influenced each other and, for example, modulated the staining intensities of type II and type I collagen in comparison to non-zonal constructs under normoxic and hypoxic conditions. In HA-SH/P(AGE-co-G) hydrogel, MSCs produced more ECM than ACPCs, but the ECM was limited to the pericellular region for both cell types. Zonal HASH/P(AGE-co-G) hydrogels resulted in a native-like zonal distribution of ECM as MSCs in the lower zone produced more ECM than ACPCs in the upper zone. It appeared that chondrogenesis of ACPCs was supported by hydrogels without biological attachment sites such as agarose, and that chondrogenesis of MSCs benefited from hydrogels with biological cues like HA. As HA is an attractive material for cartilage tissue engineering, and the HA-based hydrogel HA-SH/P(AGE-co-G) appeared to be beneficial for MSC chondrogenic differentiation, the contribution of HA to chondrogenic gene expression of MSCs was investigated. An upregulation of chondrogenic gene expression was found in 2D monolayer and 3D pellet culture of MSCs in response to HA supplementation, while gene expression of osteogenic and adipogenic transcription factors was not upregulated. MSCs, encapsulated in a HA-based hydrogel, showed upregulation of gene expression for chondrogenic, osteogenic and adipogenic differentiation markers as well as for stemness markers. In a 3D bioprinting process, using the HA-based hydrogel, gene expression levels of MSCs mostly did not change. Nevertheless, expression of three tested genes (COL2A1, SOX2, CD168) was downregulated in printed in comparison to cast constructs, underscoring the importance of closely monitoring cellular behaviour during and after the printing process. In summary, it was confirmed that ACPCs are a promising cell source for articular cartilage engineering with advantages over MSCs when they were cultured in a suitable hydrogel like agarose. The performance of the cells was strongly dependent on the hydrogel environment they were cultured in. The different chondrogenic performance of ACPCs and MSCs in agarose and HA-SH/P(AGE-co-G) hydrogels highlighted the importance of choosing suitable hydrogels for the different cell types used in articular cartilage tissue engineering. Hydrogels with high polymer content, such as the investigated HA-SH/P(AGE-co-G) hydrogels, can limit ECM distribution to the pericellular area and should be developed further towards less polymer content, leading to more homogenous ECM distribution of the cultured cells. The influence of HA on chondrogenic gene expression and on the balance between differentiation and maintenance of stemness in MSCs was demonstrated. More studies should be performed in the future to further elucidate the signalling functions of HA and the effects of 3D bioprinting in HA-based hydrogels. Taken together, the results of this thesis expand the knowledge in the area of articular cartilage engineering with regard to the rational combination of cell types and hydrogel materials and open up new possible approaches to the regeneration of articular cartilage tissue.}, subject = {Hyaliner Knorpel}, language = {en} } @phdthesis{Babu2021, author = {Babu, Dinesh Kumar}, title = {Efficient Data Fusion Approaches for Remote Sensing Time Series Generation}, doi = {10.25972/OPUS-25180}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251808}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Fernerkundungszeitreihen beschreiben die Erfassung von zeitlich gleichm{\"a}ßig verteilten Fernerkundungsdaten in einem festgelegten Zeitraum entweder global oder f{\"u}r ein vordefiniertes Gebiet. F{\"u}r die {\"U}berwachung der Landwirtschaft, die Erkennung von Ver{\"a}nderungen der Ph{\"a}nologie oder f{\"u}r das Umwelt-Monitoring werden nahezu t{\"a}gliche Daten mit hoher r{\"a}umlicher Aufl{\"o}sung ben{\"o}tigt. Bei vielen verschiedenen fernerkundlichen Anwendungen h{\"a}ngt die Genauigkeit von der dichte und der Verl{\"a}sslichkeit der fernerkundlichen Datenreihe ab. Die verschiedenen Fernerkundungssatellitenkonstellationen sind immer noch nicht in der Lage, fast t{\"a}glich oder t{\"a}glich Bilder mit hoher r{\"a}umlicher Aufl{\"o}sung zu liefern, um die Bed{\"u}rfnisse der oben erw{\"a}hnten Fernerkundungsanwendungen zu erf{\"u}llen. Einschr{\"a}nkungen bei den Sensoren, hohe Entwicklungskosten, hohe Betriebskosten der Satelliten und das Vorhandensein von Wolken, die die Sicht auf das Beobachtungsgebiet blockieren, sind einige der Gr{\"u}nde, die es sehr schwierig machen, fast t{\"a}gliche oder t{\"a}gliche optische Fernerkundungsdaten mit hoher r{\"a}umlicher Aufl{\"o}sung zu erhalten. Mit Entwicklungen bei den optischen Sensorsystemen und gut geplanten Fernerkundungssatellitenkonstellationen kann dieser Zustand verbessert werden, doch ist dies mit Kosten verbunden. Selbst dann wird das Problem nicht vollst{\"a}ndig gel{\"o}st sein, so dass der wachsende Bedarf an zeitlich und r{\"a}umlich hochaufl{\"o}senden Daten nicht vollst{\"a}ndig gedeckt werden kann. Da der Datenerfassungsprozess sich auf Satelliten st{\"u}tzt, die physische Systeme sind, k{\"o}nnen diese aus verschiedenen Gr{\"u}nden unvorhersehbar ausfallen und einen vollst{\"a}ndigen Verlust der Beobachtung f{\"u}r einen bestimmten Zeitraum verursachen, wodurch eine L{\"u}cke in der Zeitreihe entsteht. Um den langfristigen Trend der ph{\"a}nologischen Ver{\"a}nderungen aufgrund der sich schnell {\"a}ndernden Umweltbedingungen zu beobachten, sind die Fernerkundungsdaten aus der gegenw{\"a}rtig nicht ausreichend. Hierzu werden auch Daten aus der Vergangenheit ben{\"o}tigt. Eine bessere Alternativl{\"o}sung f{\"u}r dieses Problem kann die Erstellung von Fernerkundungszeitreihen durch die Fusion von Daten mehrerer Fernerkundungssatelliten mit unterschiedlichen r{\"a}umlichen und zeitlichen Aufl{\"o}sungen sein. Dieser Ansatz soll effektiv und effizient sein. Bei dieser Methode kann ein zeitlich und r{\"a}umlich hoch aufgel{\"o}stes Bild von einem Satelliten, wie Sentinel-2 mit einem zeitlich und r{\"a}umlich niedrig aufgel{\"o}sten Bild von einem Satelliten, wie Sentinel-3 fusioniert werden, um synthetische Daten mit hoher zeitlicher und r{\"a}umlicher Aufl{\"o}sung zu erzeugen. Die Erzeugung von Fernerkundungszeitreihen durch Datenfusionsmethoden kann sowohl auf die gegenw{\"a}rtig erfassten Satellitenbilder als auch auf die in der Vergangenheit von den Satelliten aufgenommenen Bilder angewandt werden. Dies wird die dringend ben{\"o}tigten zeitlich und r{\"a}umlich hochaufl{\"o}senden Bilder f{\"u}r Fernerkundungsanwendungen liefern. Dieser vereinfachte Ansatz ist kosteneffektiv und bietet den Forschern die M{\"o}glichkeit, aus der begrenzten Datenquelle, die ihnen zur Verf{\"u}gung steht, die f{\"u}r ihre Anwendung ben{\"o}tigten Daten selbst zu generieren. Ein effizienter Datenfusionsansatz in Kombination mit einer gut geplanten Satellitenkonstellation kann ein L{\"o}sungsansatz sein, um eine nahezu t{\"a}gliche Zeitreihen von Fernerkundungsdaten l{\"u}ckenlos gew{\"a}hrleistet. Ziel dieser Forschungsarbeit ist die Entwicklung eines effizienten Datenfusionsansatzes, um dichte Fernerkundungszeitreihen zu erhalten.}, language = {en} } @phdthesis{Pieper2021, author = {Pieper, Sabrina H.}, title = {Temporal information transfer by electrical stimulation in auditory implants}, doi = {10.25972/OPUS-22388}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-223887}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {In deafness, which is caused by the malfunctioning of the inner ear, an implantation of a cochlear implant (CI) is able to restore hearing. The CI is a neural prosthesis that is located within the cochlea. It replaces the function of the inner hair cells by direct electrical stimulation of the auditory nerve fibers. The CI enables many deaf or severe hearing-impaired people to achieve a good speech perception. Nevertheless, there is a lot of potential for further improvements. Compared to normal-hearing listeners rate pitch discrimination is much worse. Rate pitch discrimination is the ability to distinguish the pitch of two stimuli with two different pulse rates. This ability is important for enjoying music as well as speech perception (in noise). Further, the small dynamic range in electrical hearing (compared to normal-hearing listeners) and therefore the small intensity resolution limits the performance of CI users. Both, rate pitch coding and dynamic range were investigated in this doctoral thesis. For the first issue, a pitch discrimination task was designed to determine the just-noticeable-difference (JND) in pitch with 200 and 400 pps as reference. Additionally to the default biphasic pulse (single pulse) the experiment was performed with double pulses. The double pulse consists out of two biphasic pulses directly after each other and a small interpulse interval (IPI) in between. Three different IPIs (15, 50, and 150 µs) were tested. The statistical analysis of JNDs revealed no significant effects between stimulation with single-pulse or double-pulse trains. A follow-up study investigated an alternating pulse train consisting of single and double pulses. To investigate if the 400 pps alternating pulse train is comparable in pitch with the 400 pps single-pulse train, a pairwise pitch comparison test was conducted. The alternating pulse train was compared with single-pulse trains at 200, 300 and 400 pps. The results showed that the alternating pulse train is for most subjects similar in pitch with the 200 pps single-pulse train. Therefore, pitch perception seemed to be dominated by the double pulses within the pulse train. Accordingly, double pulses with different amplitudes were tested. Based on the facilitation effect, a larger neuronal response was expected by stimulating with two pulses with a short IPI within the temporal facilitation range. In other studies, this effect was shown to be maximal in CIs of the manufacturer Cochlear, with first pulse amplitudes set at or slightly below the electrically evoked compound action potential (ECAP) threshold. The second pulse amplitude did not influence the facilitation effect and therefore could be choose at will. Similarly, this effect was tested in this thesis with CIs of the manufacturer MED-EL. Nevertheless, to achieve a proper signal-to-noise ratio, technical issues had to be addressed like a high noise floor, resulting in incorrect determination of the ECAP threshold. After solving this issues, the maximum facilitation effect was around the ECAP threshold as in the previous study with Cochlear. For future studies this effect could be used in a modified double pulse rate pitch experiment with the first pulse amplitude at ECAP threshold and the second pulse amplitude variable to set the most comfortable loudness level (MCL). The last study within this thesis investigated the loudness perception at two different loudness levels and the resulting dynamic range for different interphase-gaps (IPG). A larger IPG can reduce the amplitude at same loudness level to save battery power. However, it was unknown if the IPG has an influence on the dynamic range. Different IPGs (10 and 30 µs) were compared with the default IPG (2.1 µs) in a loudness matching experiment. The experiment was performed at the most comfortable loudness level (MCL) of the subject and the amplitude of half the dynamic range (50\%-ADR). An upper dynamic range was calculated from the results of MCL and 50\%-ADR (therefore not the whole dynamic range was covered). As expected from previous studies a larger IPG resulted in smaller amplitudes. However, the observed effect was larger at MCL than at 50\%-ADR which resulted in a smaller upper dynamic range. This is the first time a decrease of this dynamic range was shown.}, subject = {Cochlear-Implantat}, 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{Zetzl2021, author = {Zetzl, Teresa Margarete}, title = {Cancer-related fatigue intervention}, doi = {10.25972/OPUS-25166}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251662}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The incidence of cancer cases is rising steadily, while improved early detection and new cancer-specific therapies are reducing the mortality rate. In addition to curing cancer or prolonging life, increasing the quality of life is thus an important goal of oncology, which is why the burdens of cancer and treatment are becoming more important. A common side effect of cancer and its therapy is cancer-related fatigue, a tiredness that manifests itself on physical, emotional and cognitive levels and is not in proportion to previous physical efforts. Since the etiology of fatigue has not yet been fully clarified, symptom-oriented therapy is preferable to cause-specific therapy. In addition to activity management, sleep hygiene, and cognitive behavioral therapy, mind-body interventions such as yoga are recommended for reducing fatigue. Previous studies with small sample sizes were able to examine the efficacy of yoga regarding fatigue predominantly in patients with breast cancer. Long-term effects of yoga have rarely been studied and there have been no attempts to increase long-term effects through interventions such as reminder e-mails. This dissertation takes a closer look at these mentioned aspects of the study sample and long-term effects. An 8-week randomized controlled yoga intervention was conducted, including patients with different cancer types reporting mild to severe fatigue. Following the 8-week yoga therapy, a randomized group of participants received weekly reminder e-mails for 6 months for regular yoga practice, whereas the control group did not receive reminder e-mails. The first paper is a protocol article, which addresses the design and planned implementation of the research project this dissertation is based upon. This serves to ensure better replicability and comparability with other yoga studies. Due to a very low consent rate of patients in the pilot phase, it was necessary to deviate from the protocol article in the actual implementation and the planned inclusion criterion of fatigue >5 was reduced to fatigue >1. The second paper examines the efficacy of the eight-week yoga intervention. Patients in the intervention group who participated in the yoga classes seven times or more showed a significantly greater reduction in general and physical fatigue than those who participated less often. The efficacy of yoga was related to the number of attended yoga sessions. Women with breast cancer who participated in yoga reported greater reductions in fatigue than women with other cancer types. There was also an improvement for depression and quality of life after eight weeks of yoga therapy compared to no yoga therapy. These results imply that yoga is helpful in reducing depression and cancer-related fatigue, especially in terms of physical aspects and improving quality of life. The third paper focuses on the efficacy of reminder e-mails in terms of fatigue and practice frequency. Patients who received reminder e-mails reported greater reductions in general and emotional fatigue, as well as significant increases in practice frequency, compared to patients who did not receive reminder e-mails. Compared to fatigue scores before yoga, significantly lower fatigue and depression scores and higher quality of life were reported after yoga therapy and at follow-up six months later. Weekly e-mail reminders after yoga therapy may have positive effects on general and emotional fatigue and help cancer patients with fatigue establish a regular yoga practice at home. However, higher practice frequency did not lead to higher improvement in physical fatigue as found in Paper 2. This may indicate other factors that influence the efficacy of yoga practice on physical fatigue, such as mindfulness or side effects of therapy. This research project provides insight into the efficacy of yoga therapy for oncology patients with fatigue. It is important that such interventions be offered early, while fatigue symptoms are not too severe. Regular guided yoga practice can reduce physical fatigue, but subsequent yoga practice at home does not further reduce physical fatigue. Reminder emails after completed yoga therapy could only reduce patients' emotional fatigue. It may be that physical fatigue was reduced as much as possible by the previous yoga therapy and that there was a floor effect, or it may be that reminder emails are not suitable as an intervention to reduce physical fatigue at all. Further research is needed to examine the mechanisms of the different interventions in more detail and to find appropriate interventions that reduce all levels of fatigue equally.}, subject = {Erm{\"u}dungssyndrom}, language = {en} } @phdthesis{Flederer2021, author = {Flederer, Frank}, title = {CORFU - An Extended Model-Driven Framework for Small Satellite Software with Code Feedback}, doi = {10.25972/OPUS-24981}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249817}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Corfu is a framework for satellite software, not only for the onboard part but also for the ground. Developing software with Corfu follows an iterative model-driven approach. The basis of the process is an engineering model. Engineers formally describe the basic structure of the onboard software in configuration files, which build the engineering model. In the first step, Corfu verifies the model at different levels. Not only syntactically and semantically but also on a higher level such as the scheduling. Based on the model, Corfu generates a software scaffold, which follows an application-centric approach. Software images onboard consist of a list of applications connected through communication channels called topics. Corfu's generic and generated code covers this fundamental communication, telecommand, and telemetry handling. All users have to do is inheriting from a generated class and implement the behavior in overridden methods. For each application, the generator creates an abstract class with pure virtual methods. Those methods are callback functions, e.g., for handling telecommands or executing code in threads. However, from the model, one can not foresee the software implementation by users. Therefore, as an innovation compared to other frameworks, Corfu introduces feedback from the user code back to the model. In this way, we extend the engineering model with information about functions/methods, their invocations, their stack usage, and information about events and telemetry emission. Indeed, it would be possible to add further information extraction for additional use cases. We extract the information in two ways: assembly and source code analysis. The assembly analysis collects information about the stack usage of functions and methods. On the one side, Corfu uses the gathered information to accomplished additional verification steps, e.g., checking if stack usages exceed stack sizes of threads. On the other side, we use the gathered information to improve the performance of onboard software. In a use case, we show how the compiled binary and bandwidth towards the ground is reducible by exploiting source code information at run-time.}, subject = {FRAMEWORK }, language = {en} } @phdthesis{Balakrishnan2021, author = {Balakrishnan, Ashwin}, title = {Fast molecular mobility of β\(_2\)-adrenergic receptor revealed by time-resolved fluorescence spectroscopy}, doi = {10.25972/OPUS-25085}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-250856}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {G-protein- coupled receptors (GPCRs) are the largest family of membrane confined receptors and they transduce ligand binding to downstream effects. Almost 40\% of the drugs in the world target GPCRs due to their function, albeit knowing less about their activation. Understanding their dynamic behaviour in basal and activated state could prove key to drug development in the future. GPCRs are known to exhibit complex molecular mobility patterns. A plethora of studies have been and are being conducted to understand the mobility of GPCRs. Due to limitations of imaging and spectroscopic techniques commonly used, the relevant timescales are hard to access. The most commonly used techniques are electron paramagnetic resonance or double electronelectron resonance, nuclear magnetic resonance, time-resolved fluorescence, single particle tracking and fluorescence recovery after photobleaching. Among these techniques only fluorescence has the potential to probe live cells. In this thesis, I use different time-resolved fluorescence spectroscopic techniques to quantify diffusion dynamics / molecular mobility of β2-adrenergic receptor (β2-AR) in live cells. The thesis shows that β2-AR exhibits mobility over an exceptionally broad temporal range (nanosecond to second) that can be linked to its respective physiological scenario. I explain how β2-AR possesses surprisingly fast lateral mobility (~10 μm²/s) associated with vesicular transport in contrast to the prior reports of it originating from fluorophore photophysics and free fluorophores in the cytosol. In addition, β2-AR has rotational mobility (~100 μs) that makes it conform to the Saffman-Delbr{\"u}ck model of membrane diffusion unlike earlier studies. These contrasts are due to the limitations of the methodologies used. The limitations are overcome in this thesis by using different time-resolved fluorescence techniques of fluorescence correlation spectroscopy (FCS), time-resolved anisotropy (TRA) and polarisation resolved fullFCS (fullFCS). FCS is limited to microsecond to the second range and TRA is limited to the nanosecond range. fullFCS complements the two techniques by covering the blind spot of FCS and TRA in the microsecond range. Finally, I show how ligand stimulation causes a decrease in lateral mobility which could be a hint at cluster formation due to internalisation and how β2-AR possesses a basal oligomerisation that does not change on activation. Thus, through this thesis, I show how different complementary fluorescence techniques are necessary to overcome limitations of each technique and to thereby elucidate functional dynamics of GPCR activation and how it orchestrates downstream signalling.}, language = {en} } @phdthesis{Shamburger2021, author = {Shamburger, William}, title = {Total Synthesis of Mono- and Dimeric Naphthylisoquinoline Alkaloids and Related Analogs}, doi = {10.25972/OPUS-25061}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-250612}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Our research group focusses on the isolation, structural elucidation, and synthesis of bioactive natural products, among others, the naphthylisoquinoline alkaloids from tropical lianas. This intriguing class of compounds comprises representatives with activities against, e.g. P. falciparum, the cause of Malaria tropica, against the neglected disease leishmaniasis, and, as discovered more recently, against different types of cancer cells. Based on the high potency of theses extraordinary secondary metabolites, this thesis was devoted to the total synthesis of bioactive natural products and closely related analogs.}, subject = {Naphthylisochinolinalkaloide}, language = {en} } @phdthesis{Breunig2021, author = {Breunig, Daniel Manfred}, title = {Transport properties and proximity effect of topological hybrid structures}, doi = {10.25972/OPUS-25054}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-250546}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Over the last two decades, accompanied by their prediction and ensuing realization, topological non-trivial materials like topological insulators, Dirac semimetals, and Weyl semimetals have been in the focus of mesoscopic condensed matter research. While hosting a plethora of intriguing physical phenomena all on their own, even more fascinating features emerge when superconducting order is included. Their intrinsically pronounced spin-orbit coupling leads to peculiar, time-reversal symmetry protected surface states, unconventional superconductivity, and even to the emergence of exotic bound states in appropriate setups. This Thesis explores various junctions built from - or incorporating - topological materials in contact with superconducting order, placing particular emphasis on the transport properties and the proximity effect. We begin with the analysis of Josephson junctions where planar samples of mercury telluride are sandwiched between conventional superconducting contacts. The surprising observation of pronounced excess currents in experiments, which can be well described by the Blonder-Tinkham-Klapwijk theory, has long been an ambiguous issue in this field, since the necessary presumptions are seemingly not met. We propose a resolution to this predicament by demonstrating that the interface properties in hybrid nanostructures of distinctly different materials yet corroborate these assumptions and explain the outcome. An experimental realization is feasible by gating the contacts. We then proceed with NSN junctions based on time-reversal symmetry broken Weyl semimetals and including superconducting order. Due to the anisotropy of the electron band structure, both the transport properties as well as the proximity effect depend substantially on the orientation of the interfaces between the materials. Moreover, an imbalance can be induced in the electron population between Weyl nodes of opposite chirality, resulting in a non-vanishing spin polarization of the Cooper pairs leaking into the normal contacts. We show that such a system features a tunable dipole character with possible applications in spintronics. Finally, we consider partially superconducting surface states of three-dimensional topological insulators. Tuning such a system into the so-called bipolar setup, this results in the formation of equal-spin Cooper pairs inside the superconductor, while simultaneously acting as a filter for non-local singlet pairing. The creation and manipulation of these spin-polarized Cooper pairs can be achieved by mere electronic switching processes and in the absence of any magnetic order, rendering such a nanostructure an interesting system for superconducting spintronics. The inherent spin-orbit coupling of the surface state is crucial for this observation, as is the bipolar setup which strongly promotes non-local Andreev processes.}, subject = {Supraleitung}, language = {en} } @phdthesis{MonyNair2021, author = {Mony Nair, Rahul}, title = {Elucidating ubiquitin recognition by the HECT-type ubiquitin ligase HUWE1}, doi = {10.25972/OPUS-22103}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221030}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The small protein modifier ubiquitin is at the heart of an immensely versatile posttranslational modification system that orchestrates countless physiological and disease-associated cellular processes. Key to this versatility are the manifold modifications that can be assembled from ubiquitin "building blocks" and are associated with specific functional outcomes for the modified substrates. In particular, ubiquitin molecules can form polymeric chains of distinct lengths and linkage types that give rise to distinct chain conformations, thereby providing recognition sites for specific signaling receptors/effectors. The class of E3 enzymes (ubiquitin ligases) provides critical specificity determinants in ubiquitin linkage formation; it is therefore crucial to unravel precisely how E3 enzymes operate in order to understand the structural basis of ubiquitin signaling and exploit these insights for therapeutic benefit. Overexpression and deregulation of the HECT-type ubiquitin ligase HUWE1 is implicated in several different cancer types and neurodegenerative disorders. It is largely unknown which factors control the ubiquitin modifications formed by HUWE1, how the catalytic HECT domain interacts with functionally distinct ubiquitin molecules (donor, acceptor and regulatory ubiquitin molecules) and which conformational transitions enable these interactions during ubiquitin chain formation. One aim of this study was to structurally elucidate the recognition of donor ubiquitin by the HECT domain of HUWE1. To this end I utilized a ubiquitin activity-based probe to reconstitute a proxy for a donor ubiquitin-linked conjugate of the HECT domain of HUWE1 and determined its structure by X-ray crystallography. This structure reveals that the donor ubiquitin binds to the C-lobe of HUWE1 in the same way as NEDD4-type ligases, corroborating the idea that HECT ligases utilize a conserved mode of donor ubiquitin recognition. independent of their linkage and substrate specificities. With the help of biochemical analyses, I also validated specific features of the structure, in particular the positioning of the C-terminal tail of the ligase, which was known to be critical for activity. In the newly determined structure, which reflects an "L-shaped", active state of the HECT domain, this tail is fully resolved and coordinated at the N-lobe-C-lobe interface. I defined residues that are critical for this coordination and showed that they are also essential for the activity of HUWE1, including auto-ubiquitination, free ubiquitin chain formation, and substrate ubiquitination. Furthermore, I discovered that the N-lobe of HUWE1 harbors a ubiquitin-binding exosite similar to NEDD4-type ligases and E6AP. My in-vitro activity and binding assays show that HUWE1 uses the exosite for isopeptide bond formation, but that it is dispensable for thioester bond formation. The binding assays further show that the donor ubiquitin loaded HECT domain binds an additional ubiquitin molecule at the exosite more tightly than the apo HECT domain, which possibly suggests allosteric communication between the two sites. Finally, I showed that the ubiquitin activity-based probe (ubiquitin-propargylamine) can label the catalytic cysteine of HUWE1 and NEDD4-type with close to quantitative turn- over, while it does not react with the HECT domain of the evolutionarily more divergent E6AP. The determinants underlying these differential reactivities remain to be explored. Taken, together my results significantly enhance our mechanistic understanding of the catalytic domain of HUWE1 and pinpoint linchpins for therapeutic interventions with the activity of this disease-relevant enzyme.}, language = {en} } @phdthesis{Eiring2021, author = {Eiring, Patrick}, title = {Super-resolution microscopy of plasma membrane receptors}, doi = {10.25972/OPUS-25004}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-250048}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Plasma membrane receptors are the most crucial and most commonly studied components of cells, since they not only ensure communication between the extracellular space and cells, but are also responsible for the regulation of cell cycle and cell division. The composition of the surface receptors, the so-called "Receptome", differs and is characteristic for certain cell types. Due to their significance, receptors have been important target structures for diagnostic and therapy in cancer medicine and often show aberrant expression patterns in various cancers compared to healthy cells. However, these aberrations can also be exploited and targeted by different medical approaches, as in the case of personalized immunotherapy. In addition, advances in modern fluorescence microscopy by so-called single molecule techniques allow for unprecedented sensitive visualization and quantification of molecules with an attainable spatial resolution of 10-20 nm, allowing for the detection of both stoichiometric and expression density differences. In this work, the single molecule sensitive method dSTORM was applied to quantify the receptor composition of various cell lines as well as in primary samples obtained from patients with hematologic malignancies. The focus of this work lies on artefact free quantification, stoichiometric analyses of oligomerization states and co localization analyses of membrane receptors. Basic requirements for the quantification of receptors are dyes with good photoswitching properties and labels that specifically mark the target structure without generating background through non-specific binding. To ensure this, antibodies with a predefined DOL (degree of labeling) were used, which are also standard in flow cytometry. First background reduction protocols were established on cell lines prior analyses in primary patient samples. Quantitative analyses showed clear expression differences between the cell lines and the patient cells, but also between individual patients. An important component of this work is the ability to detect the oligomerization states of receptors, which enables a more accurate quantification of membrane receptor densities compared to standard flow cytometry. It also provides information about the activation of a certain receptor, for example of FLT3, a tyrosine kinase, dimerizing upon activation. For this purpose, different well-known monomers and dimers were compared to distinguish the typical localization statistics of single bound antibodies from two or more antibodies that are in proximity. Further experiments as well as co localization analyses proved that antibodies can bind to closely adjacent epitopes despite their size. These analytical methods were subsequently applied for quantification and visualization of receptors in two clinically relevant examples. Firstly, various therapeutically relevant receptors such as CD38, BCMA and SLAMF7 for multiple myeloma, a malignant disease of plasma cells, were analyzed and quantified on patient cells. Furthermore, the influence of TP53 and KRAS mutations on receptor expression levels was investigated using the multiple myeloma cell lines OPM2 and AMO1, showing clear differences in certain receptor quantities. Secondly, FLT3 which is a therapeutic target receptor for acute myeloid leukemia, was quantified and stoichiometrically analyzed on both cell lines and patient cells. In addition, cells that have developed resistance against midostaurin were compared with cells that still respond to this type I tyrosine-kinase-inhibitor for their FLT3 receptor expression and oligomerization state.}, subject = {Fluoreszenzmikroskopie}, 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{Habenstein2021, author = {Habenstein, Jens}, title = {Neuropeptides in the brain of \(Cataglyphis\) \(nodus\) ants and their role as potential modulators of behavior}, doi = {10.25972/OPUS-24961}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249618}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {An adequate task allocation among colony members is of particular importance in large insect societies. Some species exhibit distinct polymorphic worker classes which are responsible for a specific range of tasks. However, much more often the behavior of the workers is related to the age of the individual. Ants of the genus Cataglyphis (Foerster 1850) undergo a marked age-related polyethism with three distinct behavioral stages. Newly emerged ants (callows) remain more or less motionless in the nest for the first day. The ants subsequently fulfill different tasks inside the darkness of the nest for up to four weeks (interior workers) before they finally leave the nest to collect food for the colony (foragers). This thesis focuses on the neuronal substrate underlying the temporal polyethism in Cataglyphis nodus ants by addressing following major objectives: (1) Investigating the structures and neuronal circuitries of the Cataglyphis brain to understand potential effects of neuromodulators in specific brain neuropils. (2) Identification and localization of neuropeptides in the Cataglyphis brain. (3) Examining the expression of suitable neuropeptide candidates during behavioral maturation of Cataglyphis workers. The brain provides the fundament for the control of the behavioral output of an insect. Although the importance of the central nervous system is known beyond doubt, the functional significance of large areas of the insect brain are not completely understood. In Cataglyphis ants, previous studies focused almost exclusively on major neuropils while large proportions of the central protocerebrum have been often disregarded due to the lack of clear boundaries. Therefore, I reconstructed a three-dimensional Cataglyphis brain employing confocal laser scanning microscopy. To visualize synapsin-rich neuropils and fiber tracts, a combination of fluorescently labeled antibodies, phalloidin (a cyclic peptide binding to filamentous actin) and anterograde tracers was used. Based on the unified nomenclature for insect brains, I defined traceable criteria for the demarcation of individual neuropils. The resulting three-dimensional brain atlas provides information about 33 distinct synapse-rich neuropils and 30 fiber tracts, including a comprehensive description of the olfactory and visual tracts in the Cataglyphis brain. This three-dimensional brain atlas further allows to assign present neuromodulators to individual brain neuropils. Neuropeptides represent the largest group of neuromodulators in the central nervous system of insects. They regulate important physiological and behavioral processes and have therefore recently been associated with the regulation of the temporal polyethism in social insects. To date, the knowledge of neuropeptides in Cataglyphis ants has been mainly derived from neuropeptidomic data of Camponotus floridanus ants and only a few neuropeptides have been characterized in Cataglyphis. Therefore, I performed a comprehensive transcriptome analysis in Cataglyphis nodus ants and identified peptides by using Q-Exactive Orbitrap mass spectrometry (MS) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. This resulted in the characterization of 71 peptides encoded on 49 prepropeptide genes, including a novel neuropeptide-like gene (fliktin). In addition, high-resolution MALDI-TOF MS imaging (MALDI-MSI) was applied for the first time in an ant brain to localize peptides on thin brain cryosections. Employing MALDI-MSI, I was able to visualize the spatial distribution of 35 peptides encoded on 16 genes. To investigate the role of neuropeptides during behavioral maturation, I selected suitable neuropeptide candidates and analyzed their spatial distributions and expression levels following major behavioral transitions. Based on recent studies, I suggested the neuropeptides allatostatin-A (Ast-A), corazonin (Crz) and tachykinin (TK) as potential regulators of the temporal polyethism. The peptidergic neurons were visualized in the brain of C. nodus ants using immunohistochemistry. Independent of the behavioral stages, numerous Ast-A- and TK-immunoreactive (-ir) neurons innervate important high-order integration centers and sensory input regions with cell bodies dispersed all across the cell body rind. In contrast, only four corazonergic neurons per hemisphere were found in the Cataglyphis brain. Their somata are localized in the pars lateralis with axons projecting to the medial protocerebrum and the retrocerebral complex. Number and branching patterns of the Crz-ir neurons were similar across behavioral stages, however, the volume of the cell bodies was significantly larger in foragers than in the preceding behavioral stages. In addition, quantitative PCR analyses displayed increased Crz and Ast-A mRNA levels in foragers, suggesting a concomitant increase of the peptide levels. The task-specific expression of Crz and Ast-A along with the presence in important sensory input regions, high-order integration center, and the neurohormonal organs indicate a sustaining role of the neuropeptides during behavioral maturation of Cataglyphis workers. The present thesis contains a comprehensive reference work for the brain anatomy and the neuropeptidome of Cataglyphis ants. I further demonstrated that neuropeptides are suitable modulators for the temporal polyethism of Cataglyphis workers. The complete dataset provides a solid framework for future neuroethological studies in Cataglyphis ants as well as for comparative studies on insects. This may help to improve our understanding of the functionality of individual brain neuropils and the role of neuropeptides, particularly during behavioral maturation in social insects.}, subject = {Cataglyphis}, language = {en} } @phdthesis{Krueger2021, author = {Kr{\"u}ger, S{\"o}ren}, title = {Unterschiedliche Einfl{\"u}sse von Komplement auf Reaktionen neutrophiler Granulozyten auf die Infektion mit \(Neisseria\) \(meningitidis\)}, doi = {10.25972/OPUS-24969}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249697}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The gram-negative diplococcus Neisseria meningitidis (Nme) is a frequent human-specific, commensal bacterium of the upper respiratory tract. Under certain conditions especially in infants, meningococci can translocate into the bloodstream and cause invasive meningococcal disease (IMD) manifesting as meningitis or sepsis or a combination of both. IMD is feared for its rapid progression and high fatality rate if it remains untreated. IMD affects up to one million people annually causing substantial morbidity and mortality worldwide. It is well-established that the complement system is an important protective factor in meningococcal disease through opsonization of bacteria with C3b and the lytic activity of the membrane attack complex although the inflammatory C5a/C5aR1 axis can aggravate IMD. The role of neutrophil granulocytes in meningococcal infection is less clear despite their abundant recruitment throughout the course of disease. This study aimed to characterize neutrophil responses to Nme in vitro and the influence of complement on these responses. In infection assays with whole blood and isolated PMNs, effective binding, internalization and killing of Nme by neutrophils was demonstrated. A significant complement-dependence of neutrophil phagocytosis and oxidative burst was observed. The opsonizing and lytic pathway of the complement cascade were found to be most relevant for these responses since blockade of C3 using inhibitor Compstatin Cp20 reduced phagocytosis and oxidative burst significantly more than the blockade of the inflammatory branch with C5aR1-antagonist PMX53. Opsonization with specific antibodies could not replicate the effect of complement activation indicating that engagement of neutrophil complement receptors, particularly complement receptor 3, is involved. Other neutrophil effector functions such as degranulation and IL-8 release were activated in a complement-independent manner implying activation by other inflammatory signals. Considering existing evidence on the overall protective effect of PMNs, further studies investigating the contribution of each neutrophil effector function to infection survival in vivo are required. Ideally, this should be studied in a murine meningitis or sepsis model in the context of complement activation.}, subject = {Neisseria meningitidis}, 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{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{Wagner2021, author = {Wagner, Rabea Marie}, title = {The Bacterial Exo- and Endo-Cytoskeleton Spatially Confines Functional Membrane Microdomain Dynamics in \(Bacillus\) \(subtilis\)}, doi = {10.25972/OPUS-21745}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-217458}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Cellular membranes form a boundary to shield the inside of a cell from the outside. This is of special importance for bacteria, unicellular organisms whose membranes are in direct contact with the environment. The membrane needs to allow the reception of information about beneficial and harmful environmental conditions for the cell to evoke an appropriate response. Information gathering is mediated by proteins that need to be correctly organized in the membrane to be able to transmit information. Several principles of membrane organization are known that show a heterogeneous distribution of membrane lipids and proteins. One of them is functional membrane microdomains (FMM) which are platforms with a distinct lipid and protein composition. FMM move within the membrane and their integrity is important for several cellular processes like signal transduction, membrane trafficking and cellular differentiation. FMM harbor the marker proteins flotillins which are scaffolding proteins that act as chaperones in tethering protein cargo to FMM. This enhances the efficiency of cargo protein oligomerization or complex formation which in turn is important for their functionality. The bacterium Bacillus subtilis contains two flotillin proteins, FloA and FloT. They form different FMM assemblies which are structurally similar, but differ in the protein cargo and thus in the specific function. In this work, the mobility of FloA and FloT assemblies in the membrane was dissected using live-cell fluorescence microscopy techniques coupled to genetic, biochemical and molecular biological methods. A characteristic mobility pattern was observed which revealed that the mobility of both flotillins was spatially restricted. Restrictions were bigger for FloT resulting in a decreased diffusion coefficient compared to FloA. Flotillin mobility depends on the interplay of several factors. Firstly, the intrinsic properties of flotillins determine the binding of different protein interaction partners. These proteins directly affect the mobility of flotillins. Additionally, binding of interaction partners determines the assembly size of FloA and FloT. This indirectly affects the mobility, as the endo-cytoskeleton spatially restricts flotillin mobility in a size-dependent manner. Furthermore, the extracellular cell wall plays a dual role in flotillin mobility: its synthesis stimulates flotillin mobility, while at the same time its presence restricts flotillin mobility. As the intracellular flotillins do not have spatial access to the exo-cytoskeleton, this connection is likely mediated indirectly by their cell wall-associated protein interaction partners. Together the exo- and the endo-cytoskeleton restrict the mobility of FloA and FloT. Similar structural restrictions of flotillin mobility have been reported for plant cells as well, where the actin cytoskeleton and the cell wall restrict flotillin mobility. These similarities between eukaryotic and prokaryotic cells indicate that the restriction of flotillin mobility might be a conserved mechanism.}, subject = {Heubacillus}, language = {en} } @phdthesis{Endres2021, author = {Endres, Theresa}, title = {PAF1 complex and MYC couple transcription elongation with double-strand break repair}, doi = {10.25972/OPUS-24955}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249557}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The oncogene MYC is deregulated and overexpressed in a high variety of human cancers and is considered an important driver in tumorigenesis. The MYC protein binds to virtually all active promoters of genes which are also bound by the RNA Polymerase II (RNAPII). This results in the assumption that MYC is a transcription factor regulating gene expression. The effects of gene expression are weak and often differ depending on the tumor entities or MYC levels. These observations could argue that the oncogene MYC has additional functions independent of altering gene expression. In relation to this, the high diversity of interaction partners might be important. One of them is the RNAPII associated Factor I complex (PAF1c). In this study, direct interaction between PAF1c and MYC was confirmed in an in-vitro pulldown assay. ChIP sequencing analyses revealed that knockdown of PAF1c components resulted in reduced MYC occupancy at active promoters. Depletion or activation as well as overexpression of MYC led to reduced or enhanced global occupancy of PAF1c in the body of active genes, arguing that MYC and PAF1c bind cooperatively to chromatin. Upon PAF1c knockdown cell proliferation was reduced and additionally resulted in an attenuation of activation or repression of MYC-regulated genes. Interestingly, knockdown of PAF1c components caused an accumulation in S-phase of cells bearing oncogenic MYC levels. Remarkably, enhanced DNA damage, measured by elevated gH2AX and pKAP1 protein levels, was observed in those cells and this DNA damage occurs specifically during DNA synthesis. Strikingly, MYC is involved in double strand break repair in a PAF1c-dependent manner at oncogenic MYC levels. Collectively the data show that the transfer of PAF1c from MYC onto the RNAPII couples the transcriptional elongation with double strand break repair to maintain the genomic integrity in MYC-driven tumor cells.}, language = {en} } @phdthesis{Schiemenz2021, author = {Schiemenz, Fabian}, title = {Covariance and Uncertainty Realism for Low Earth Orbiting Satellites via Quantification of Dominant Force Model Uncertainties}, doi = {10.25972/OPUS-24947}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249474}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The safety of future spaceflight depends on space surveillance and space traffic management, as the density of objects in Earth orbit has reached a level that requires collision avoidance maneuvers to be performed on a regular basis to avoid a mission or, in the context of human space flight, life-endangering threat. Driven by enhanced sensor systems capable of detecting centimeter-sized debris, megaconstellations and satellite miniaturization, the space debris problem has revealed many parallels to the plastic waste in our oceans, however with much less visibility to the eye. Future catalog sizes are expected to increase drastically, making it even more important to detect potentially dangerous encounters as early as possible. Due to the limited number of monitoring sensors, continuous observation of all objects is impossible, resulting in the need to predict the orbital paths and their uncertainty via models to perform collision risk assessment and space object catalog maintenance. For many years the uncertainty models used for orbit determination neglected any uncertainty in the astrodynamic force models, thereby implicitly assuming them to be flawless descriptions of the true space environment. This assumption is known to result in overly optimistic uncertainty estimates, which in turn complicate collision risk analysis. The keynote of this doctoral thesis is to establish uncertainty realism for low Earth orbiting satellites via a physically connected quantification of the dominant force model uncertainties, particularly multiple sources of atmospheric density uncertainty and orbital gravity uncertainty. The resulting process noise models are subsequently integrated into classical and state of the art orbit determination algorithms. Their positive impact is demonstrated via numerical orbit determination simulations and a collision risk assessment study using all non-restricted objects in the official United States space catalogs. It is shown that the consideration of atmospheric density uncertainty and gravity uncertainty significantly improves the quality of the orbit determination and thus makes a contribution to future spaceflight safety by increasing the reliability of the uncertainty estimates used for collision risk assessment.}, subject = {Space Debris}, language = {en} } @phdthesis{Blank2021, author = {Blank, Felix}, title = {The use of the Hypercube Queueing Model for the location optimization decision of Emergency Medical Service systems}, doi = {10.25972/OPUS-24909}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249093}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Die strategische Planung von medizinischen Notfallsystemen steht in einem unmittelbaren Zusammenhang mit der {\"U}berlebenswahrscheinlichkeit von betroffenen Patienten. Die Forschung hat zahlreiche Kenngr{\"o}ßen und Evaluationsparameter entwickelt, die zur Bewertung verwendet werden k{\"o}nnen. Darunter fallen beispielsweise die Reaktionszeit, die Systemauslastung, diverse Wartezeitenparameter sowie der Anteil der Nachfrage, der nicht unmittelbar bedient werden kann. Dabei ist das Hypercube Queueing Modell eines der am h{\"a}ufigsten verwendeten Modelle. Aufgrund seines theoretischen Hintergrundes und der damit verbundenen hohen notwendigen Rechenzeiten wurde das Hypercube Queueing Modell erst in der j{\"u}ngeren Vergangenheit h{\"a}ufiger zur Optimierung von medizinischen Notfallsystemen verwendet. Gleichermaßen wurden nur wenige Systemparameter mit Hilfe des Modelles berechnet und das volle Potenzial demnach noch nicht ausgesch{\"o}pft. Die meisten der bereits vorhandenen Studien im Bereich der Optimierung unter Zuhilfenahme eines Hypercube Queueing Modells nutzen die zu erwartende Reaktionszeit des Systems als Zielparameter. Obwohl die Verwendung von diesem eine zumeist ausgeglichene Systemkonfiguration zur Folge hat, wurden andere Zielparameter identifziert. Die Verwendung des Hypercube Queueing Modells in den Modellen der robusten Optimierung sowie des robusten Goal Programmings haben versucht einen ganzheitlicheren Blick, durch die Verwendung von unterschiedlichen Tageszeiten, zu offerieren. Dabei hat sich gezeigt, dass das Verhalten von medizinischen Notfallsystemen sowie die Parameter stark von diesen abh{\"a}ngen. Daher sollte die Analyse und gegebenenfalls Optimierung dieser Systeme unterschiedliche Verteilungen der Nachfrage, in Abh{\"a}ngigkeit ihrer Menge und r{\"a}umlichen Verteilung, unbedingt ber{\"u}cksichtigen um eine m{\"o}glichst ganzheitliche Entscheidungsgrundlage zu garantieren.}, subject = {Warteschlangentheorie}, language = {en} } @phdthesis{Volpato2021, author = {Volpato, Daniela}, title = {Bitopic Ligands and their molecular fragments for the study of the M1 Muscarinic Receptor}, doi = {10.25972/OPUS-24881}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-248815}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The past decades have witnessed the development of new pharmaceutical compounds that modulate receptor function by targeting allosteric sites. Allosteric sites are, by definition, domains topographically distinct from the orthosteric binding pocket where the natural ligand binds. Exploring the possibilities of linking orthosteric and allosteric pharmacophores in one compound to yield 'bitopic' compounds is a strategy derived from the "message-address" concept by Schwyzer , first applied to GPCRs by Portoghese et al. This concept explicitly underlines the orthosteric/allosteric combination, in opposite to the more general umbrella term bivalent. The broad possibilities of bitopic ligands in the pharmaceutical field are under continuous study. Bitopic compounds are promising pharmaceutical tools for taking advantage of the allosteric binding to achieve subtype selectivity while preserving high affinity at the receptor. The development of bitopic ligands, based on the idea of combining high affinity (via orthosteric sites) with high selectivity (via allosteric sites), have led to the development of highly selective bivalent ligands for GPCRs , such as for the opioid receptors , muscarinic acetylcholine receptors (mAChRs), serotonin receptors, cannabinoid receptors, and gonadotropin-releasing hormone receptors. This concept has even been extended to other receptors, for examples nicotinic receptors and other proteins, such as acetylcholinesterases and the tyrosine kinase receptors TrkA and TrkC. The reasons to pursue a bitopic ligand approach are various. An improved affinity for the target GPCR and/or an improved selectivity either at the level of receptor subtype, or at the level of signaling pathway. Another advantage of bitopic ligands over purely allosteric ligands is that the former rely on the appropriate presence of endogenous agonist tone to mediate their effects, whereas a bitopic ligand would engage the orthosteric site irrespective of the presence or absence of endogenous tone. By way of introduction to the hybrid approach, a review of the concept of hybrids compounds targeting the cholinergic system is presented in section A of this thesis. Recent updates in hybrid molecule design as a strategy for selectively addressing multiple target proteins involved in Alzheimer's disease (AD) is here reported . This represents the potential and the growing interest in hybrid compound as pharmacological tools to achieve receptor subtype selectivity and/or, to study the overall functional activity of the receptor. Until now, muscarinic acetylcholine receptors (mAChRs) have proved to be a particularly fruitful receptor model for the development and characterization of bitopic ligands. In this thesis, several examples of new muscarinic bitopic approach are reported in the results section. A study of bipharmacophoric ligands composed of the muscarinic positive allosteric modulators (BQCAderived compounds) linked with chain of various lengths to different orthosteric building blocks is reported in the result part 1. Synthesis and examination of the potential pharmacological characteristic of Oxotremorine-BQCAd compounds and Xanomeline-BQCAd hybrid derivatives are described in results parts 2 and 4, respectively. Moreover, the bitopic concept has even been extended to other proteins, such as acetylcholinesterase. In the result part 5 an overview of the new Tacrine-Xanomeline hybrids aiming to improve the inhibitory potency of the acetylcholinesterase and simultaneously to increase the cholinergic tone, via the xanomelinic portion acting on the M1 receptor is given. A new trivalent approach is presented for the first time to deepen the study of the M1 muscarinic receptor in the result part 6. Moreover, the synthesis of a new series of iperoxo-derived alkane, bis(ammonio)alkane-type and rigidified chain ligands is given in the result part 7 together with some prospects for further research.}, subject = {Ligand }, language = {en} } @phdthesis{Bartsch2021, author = {Bartsch, Jan}, title = {Theoretical and numerical investigation of optimal control problems governed by kinetic models}, doi = {10.25972/OPUS-24906}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249066}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {This thesis is devoted to the numerical and theoretical analysis of ensemble optimal control problems governed by kinetic models. The formulation and study of these problems have been put forward in recent years by R.W. Brockett with the motivation that ensemble control may provide a more general and robust control framework for dynamical systems. Following this formulation, a Liouville (or continuity) equation with an unbounded drift function is considered together with a class of cost functionals that include tracking of ensembles of trajectories of dynamical systems and different control costs. Specifically, \$L^2\$, \$H^1\$ and \$L^1\$ control costs are taken into account which leads to non--smooth optimization problems. For the theoretical investigation of the resulting optimal control problems, a well--posedness theory in weighted Sobolev spaces is presented for Liouville and related transport equations. Specifically, existence and uniqueness results for these equations and energy estimates in suitable norms are provided; in particular norms in weighted Sobolev spaces. Then, non--smooth optimal control problems governed by the Liouville equation are formulated with a control mechanism in the drift function. Further, box--constraints on the control are imposed. The control--to--state map is introduced, that associates to any control the unique solution of the corresponding Liouville equation. Important properties of this map are investigated, specifically, that it is well--defined, continuous and Frechet differentiable. Using the first two properties, the existence of solutions to the optimal control problems is shown. While proving the differentiability, a loss of regularity is encountered, that is natural to hyperbolic equations. This leads to the need of the investigation of the control--to--state map in the topology of weighted Sobolev spaces. Exploiting the Frechet differentiability, it is possible to characterize solutions to the optimal control problem as solutions to an optimality system. This system consists of the Liouville equation, its optimization adjoint in the form of a transport equation, and a gradient inequality. Numerical methodologies for solving Liouville and transport equations are presented that are based on a non--smooth Lagrange optimization framework. For this purpose, approximation and solution schemes for such equations are developed and analyzed. For the approximation of the Liouville model and its optimization adjoint, a combination of a Kurganov--Tadmor method, a Runge--Kutta scheme, and a Strang splitting method are discussed. Stability and second--order accuracy of these resulting schemes are proven in the discrete \$L^1\$ norm. In addition, conservation of mass and positivity preservation are confirmed for the solution method of the Liouville model. As numerical optimization strategy, an adapted Krylow--Newton method is applied. Since the control is considered to be an element of \$H^1\$ and to obey certain box--constraints, a method for calculating a \$H^1\$ projection is presented. Since the optimal control problem is non-smooth, a semi-smooth adaption of Newton's method is taken into account. Results of numerical experiments are presented that successfully validate the proposed deterministic framework. After the discussion of deterministic schemes, the linear space--homogeneous Keilson--Storer master equation is investigated. This equation was originally developed for the modelling of Brownian motion of particles immersed in a fluid and is a representative model of the class of linear Boltzmann equations. The well--posedness of the Keilson--Storer master equation is investigated and energy estimates in different topologies are derived. To solve this equation numerically, Monte Carlo methods are considered. Such methods take advantage of the kinetic formulation of the Liouville equation and directly implement the behaviour of the system of particles under consideration. This includes the probabilistic behaviour of the collisions between particles. Optimal control problems are formulated with an objective that is constituted of certain expected values in velocity space and the \$L^2\$ and \$H^1\$ costs of the control. The problems are governed by the Keilson--Storer master equation and the control mechanism is considered to be within the collision kernel. The objective of the optimal control of this model is to drive an ensemble of particles to acquire a desired mean velocity and to achieve a desired final velocity configuration. Existence of solutions of the optimal control problem is proven and a Keilson--Storer optimality system characterizing the solution of the proposed optimal control problem is obtained. The optimality system is used to construct a gradient--based optimization strategy in the framework of Monte--Carlo methods. This task requires to accommodate the resulting adjoint Keilson--Storer model in a form that is consistent with the kinetic formulation. For this reason, we derive an adjoint Keilson--Storer collision kernel and an additional source term. A similar approach is presented in the case of a linear space--inhomogeneous kinetic model with external forces and with Keilson--Storer collision term. In this framework, a control mechanism in the form of an external space--dependent force is investigated. The purpose of this control is to steer the multi--particle system to follow a desired mean velocity and position and to reach a desired final configuration in phase space. An optimal control problem using the formulation of ensemble controls is stated with an objective that is constituted of expected values in phase space and \$H^1\$ costs of the control. For solving the optimal control problems, a gradient--based computational strategy in the framework of Monte Carlo methods is developed. Part of this is the denoising of the distribution functions calculated by Monte Carlo algorithms using methods of the realm of partial differential equations. A standalone C++ code is presented that implements the developed non--linear conjugated gradient strategy. Results of numerical experiments confirm the ability of the designed probabilistic control framework to operate as desired. An outlook section about optimal control problems governed by non--linear space--inhomogeneous kinetic models completes this thesis.}, subject = {Optimale Kontrolle}, 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{Andreska2021, author = {Andreska, Thomas}, title = {Effects of dopamine on BDNF / TrkB mediated signaling and plasticity on cortico-striatal synapses}, doi = {10.25972/OPUS-17431}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-174317}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Progressive loss of voluntary movement control is the central symptom of Parkinson's disease (PD). Even today, we are not yet able to cure PD. This is mainly due to a lack of understanding the mechanisms of movement control, network activity and plasticity in motor circuits, in particular between the cerebral cortex and the striatum. Brain-derived neurotrophic factor (BDNF) has emerged as one of the most important factors for the development and survival of neurons, as well as for synaptic plasticity. It is thus an important target for the development of new therapeutic strategies against neurodegenerative diseases. Together with its receptor, the Tropomyosin receptor kinase B (TrkB), it is critically involved in development and function of the striatum. Nevertheless, little is known about the localization of BDNF within presynaptic terminals in the striatum, as well as the types of neurons that produce BDNF in the cerebral cortex. Furthermore, the influence of midbrain derived dopamine on the control of BDNF / TrkB interaction in striatal medium spiny neurons (MSNs) remains elusive so far. Dopamine, however, appears to play an important role, as its absence leads to drastic changes in striatal synaptic plasticity. This suggests that dopamine could regulate synaptic activity in the striatum via modulation of BDNF / TrkB function. To answer these questions, we have developed a sensitive and reliable protocol for the immunohistochemical detection of endogenous BDNF. We find that the majority of striatal BDNF is provided by glutamatergic, cortex derived afferents and not dopaminergic inputs from the midbrain. In fact, we found BDNF in cell bodies of neurons in layers II-III and V of the primary and secondary motor cortex as well as layer V of the somatosensory cortex. These are the brain areas that send dense projections to the dorsolateral striatum for control of voluntary movement. Furthermore, we could show that these projection neurons significantly downregulate the expression of BDNF during the juvenile development of mice between 3 and 12 weeks. In parallel, we found a modulatory effect of dopamine on the translocation of TrkB to the cell surface in postsynaptic striatal Medium Spiny Neurons (MSNs). In MSNs of the direct pathway (dMSNs), which express dopamine receptor 1 (DRD1), we observed the formation of TrkB aggregates in the 6-hydroxydopamine (6-OHDA) model of PD. This suggests that DRD1 activity controls TrkB surface expression in these neurons. In contrast, we found that DRD2 activation has opposite effects in MSNs of the indirect pathway (iMSNs). Activation of DRD2 promotes a rapid decrease in TrkB surface expression which was reversible and depended on cAMP. In parallel, stimulation of DRD2 led to induction of phospho-TrkB (pTrkB). This effect was significantly slower than the effect on TrkB surface expression and indicates that TrkB is transactivated by DRD2. Together, our data provide evidence that dopamine triggers dual modes of plasticity on striatal MSNs by acting on TrkB surface expression in DRD1 and DRD2 expressing MSNs. This surface expression of the receptor is crucial for the binding of BDNF, which is released from corticostriatal afferents. This leads to the induction of TrkB-mediated downstream signal transduction cascades and long-term potentiation (LTP). Therefore, the dopamine-mediated translocation of TrkB could be a mediator that modulates the balance between dopaminergic and glutamatergic signaling to allow synaptic plasticity in a spatiotemporal manner. This information and the fact that TrkB is segregated to persistent aggregates in PD could help to improve our understanding of voluntary movement control and to develop new therapeutic strategies beyond those focusing on dopaminergic supply.}, subject = {Brain-derived neurotrophic factor}, language = {en} } @phdthesis{Kalb2021, author = {Kalb, Jacqueline}, title = {The role of BRCA1 and DCP1A in the coordination of transcription and replication in neuroblastoma}, doi = {10.25972/OPUS-24871}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-248711}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The deregulation of the MYC oncoprotein family plays a major role in tumorigenesis and tumour maintenance of many human tumours. Because of their structure and nuclear localisation, they are defined as undruggable targets which makes it difficult to find direct therapeutic approaches. An alternative approach for targeting MYC-driven tumours is the identification and targeting of partner proteins which score as essential in a synthetic lethality screen. Neuroblastoma, an aggressive entity of MYCN-driven tumours coming along with a bad prognosis, are dependent on the tumour suppressor protein BRCA1 as synthetic lethal data showed. BRCA1 is recruited to promoter regions in a MYCN-dependent manner. The aim of this study was to characterise the role of BRCA1 in neuroblastoma with molecular biological methods. BRCA1 prevents the accumulation of RNA Polymerase II (RNAPII) at the promoter region. Its absence results in the formation of DNA/RNA-hybrids, so called R-loops, and DNA damage. To prevent the accumulation of RNAPII, the cell uses DCP1A, a decapping factor known for its cytoplasmatic and nuclear role in mRNA decay. It is the priming factor in the removal of the protective 5'CAP of mRNA, which leads to degradation by exonucleases. BRCA1 is necessary for the chromatin recruitment of DCP1A and its proximity to RNAPII. Cells showed upon acute activation of MYCN a higher dependency on DCP1A. Its activity prevents the deregulation of transcription and leads to proper coordination of transcription and replication. The deregulation of transcription in the absence of DCP1A results in replication fork stalling and leads to activation of the Ataxia telangiectasia and Rad3 related (ATR) kinase. The result is a disturbed cell proliferation to the point of increased apoptosis. The activation of the ATR kinase pathway in the situation where DCP1A is knocked down and MYCN is activated, makes those cells more vulnerable for the treatment with ATR inhibitors. In summary, the tumour suppressor protein BRCA1 and the decapping factor DCP1A, mainly known for its function in the cytoplasm, have a new nuclear role in a MYCN-dependent context. This study shows their essentiality in the coordination of transcription and replication which leads to an unrestrained growth of tumour cells if uncontrolled.}, subject = {Neuroblastom}, language = {en} } @phdthesis{Maistrenko2021, author = {Maistrenko, Oleksandr}, title = {Pangenome analysis of bacteria and its application in metagenomics}, doi = {10.25972/OPUS-21499}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-214996}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The biosphere harbors a large quantity and diversity of microbial organisms that can thrive in all environments. Estimates of the total number of microbial species reach up to 1012, of which less than 15,000 have been characterized to date. It has been challenging to delineate phenotypically, evolutionary and ecologically meaningful lineages such as for example, species, subspecies and strains. Even within recognized species, gene content can vary considerably between sublineages (for example strains), a problem that can be addressed by analyzing pangenomes, defined as the non-redundant set of genes within a phylogenetic clade, as evolutionary units. Species considered to be ecologically and evolutionary coherent units, however to date it is still not fully understood what are primary habitats and ecological niches of many prokaryotic species and how environmental preferences drive their genomic diversity. Majority of comparative genomics studies focused on a single prokaryotic species in context of clinical relevance and ecology. With accumulation of sequencing data due to genomics and metagenomics, it is now possible to investigate trends across many species, which will facilitate understanding of pangenome evolution, species and subspecies delineation. The major aims of this thesis were 1) to annotate habitat preferences of prokaryotic species and strains; 2) investigate to what extent these environmental preferences drive genomic diversity of prokaryotes and to what extent phylogenetic constraints limit this diversification; 3) explore natural nucleotide identity thresholds to delineate species in bacteria in metagenomics gene catalogs; 4) explore species delineation for applications in subspecies and strain delineation in metagenomics. The first part of the thesis describes methods to infer environmental preferences of microbial species. This data is a prerequisite for the analyses performed in the second part of the thesis which explores how the structure of bacterial pangenomes is predetermined by past evolutionary history and how is it linked to environmental preferences of the species. The main finding in this subchapter that habitat preferences explained up to 49\% of the variance for pangenome structure, compared to 18\% by phylogenetic inertia. In general, this trend indicates that phylogenetic inertia does not limit evolution of pangenome size and diversity, but that convergent evolution may overcome phylogenetic constraints. In this project we show that core genome size is associated with higher environmental ubiquity of species. It is likely this is due to the fact that species need to have more versatile genomes and most necessary genes need to be present in majority of genomes of that species to be highly prevalent. Taken together these findings may be useful for future predictive analyses of ecological niches in newly discovered species. The third part of the thesis explores data-driven, operational species boundaries. I show that homologous genes from the same species from different genomes tend to share at least 95\% of nucleotide identity, while different species within the same genus have lower nucleotide identity. This is in line with other studies showing that genome-wide natural species boundary might be in range of 90-95\% of nucleotide identity. Finally, the fourth part of the thesis discusses how challenges in species delineation are relevant for the identification of meaningful within-species groups, followed by a discussion on how advancements in species delineation can be applied for classification of within-species genomic diversity in the age of metagenomics.}, subject = {Pangenom}, language = {en} } @phdthesis{EliasdosSantos2021, author = {Elias dos Santos, Graciely}, title = {Spin-Orbit Torques and Galvanomagnetic Effects Generated by the 3D Topological Insulator HgTe}, doi = {10.25972/OPUS-24797}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247971}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {In meiner Dissertation besch{\"a}ftigte ich mich mit der Frage, ob der 3D topologische Isolator Quecksilbertellurid (3D TI HgTe) ein geeignetes Material f{\"u}r Spintronik-Anwendungen ist. Wir untersuchten Spin-Bahn-Drehmomente, die auf Elektronen beim Tunneln zwischen HgTe und einem angrenzenden Ferromagneten (Permalloy) einwirken. Zun{\"a}chst setzten wir die Methode der Ferromagnetresonanz (SOT-FMR) f{\"u}r diese Untersuchungen ein. Im ersten Teil der Dissertation werden die Leser in die mathematische Beschreibung von Spin- Bahn-Drehmomenten in einem Hybridsystem bestehend aus topologischem Isolator (TI) und Ferromagnet (FM) eingef{\"u}hrt. Des Weiteren werden die Probenherstellung und der Messaufbau f{\"u}r SOT-FMR Messungen besprochen. Unsere SOT-FMR Messungen ergaben, dass bei tiefen Temperaturen (T = 4.2 K) die Normalkomponente (bezogen auf der TI-Oberfl{\"a}che) des Drehmoments groß war. Bei Raumtemperatur konnten im Signal beide Komponenten (parallel und normal zur TI-Oberfl{\"a}che) beobachtet werden. Aus der Symmetrie der Mixing-Spannung (Abbildungen 3.14 und 3.15) schlossen wir, dass 3D TI HgTe ein Spin-Bahn-Drehmoment auf das Elektronensystem des Permalloys {\"u}bertr{\"a}gt. Unsere Untersuchungen zeigten dar{\"u}ber hinaus, dass die Effizienz dieser {\"U}bertragung mit der anderer vorhandener topologischen Isolatoren vergleichbar ist (siehe Abb. 3.17). Abschließend wurden parasit{\"a}re Effekte bei der Absch{\"a}tzung des Spin-Bahn-Drehmoments bzw. andere Interpretationen des Messsignals und seiner Komponenten (z.B., Thermospannungen) ausf{\"u}hrlich diskutiert. Obwohl die hier gezeigten Ergebnisse vermehrt darauf hinweisen, dass der 3D TI HgTe m{\"o}glicherweise effizient f{\"u}r die Anwendung von Spin-Drehmomenten in angrezenden Ferromagneten ist [1], wird dem Leser weiderholt klargemacht, dass parasit{\"a}re Effekte eventuelle das korrekte Schreiben und Lesen der Information in Ferromagneten verunreignigt. Diese sollten auch bei der Interpretation von publizierten Resultaten besonders hohen Spin-Bahn-Drehmoment{\"u}bertragungen in der Literatur ber{\"u}cksichtigt werden [1-3]. Die Nachteile der SOT-FMR-Messmethode f{\"u}hrten zu einerWeiterentwicklung unseres Messkonzepts, bei dem der Ferromagnet durch eine Spin-Valve-Struktur ersetzt wurde. In dieser Messanordnung ist der Stromfluss durch den 3D TI im Gegensatz zu den vorangegangenen Messungen bekannt und die Widerstands{\"a}nderung der Spin-Valve-Struktur kann durch den GMR-Effekt ausgelesen werden. Die Ausrichtung der Magnetisierung des Ferromagneten in den SOT-FMR-Experimenten erforderte es, ein magnetisches Feld von bis zu 300 mT parallel zur TI-Oberfl{\"a}che anzulegen. Motiviert durch diesen Umstand, untersuchten wir den Einfluss eines parallelen Magnetfelds auf den Magnetowiderstand in 3D TI HgTe. Die {\"u}berraschenden Resultate dieser Messungen werden im zweiten Teil der Dissertation beschrieben. Obwohl nichtmagnetisches Quecksilbertellurid untersucht wurde, oszillierte der transversale Magnetowiderstand (Rxy) mit dem Winkel � zwischen der Magnetfeldrichtung (parallel zur Oberfl{\"a}che) und der elektrischen Stromflussrichtung im topologischen Isolator. Dieser Effekt ist eine typische Eigenschaft von ferromagnetischen Materialien und wird planarer Hall-Effekt (PHE) genannt[4, 5]. Magnetowiderstands- (MR-)Oszillationen wurden ebenfalls sowohl im L{\"a}ngswiderstand (Rxx) und im transversalen Widerstand (Rxy) {\"u}ber einen weiten Bereich von magnetischen Feldst{\"a}rken und Ladungstr{\"a}gerdichten des topologischen Isolators beobachtet. Der PHE wurde bereits zuvor in einem anderen TI-Material (Bi2-xSbxTe3) beschrieben [6]. Als physikalischer Mechanismus wurde von den Autoren Elektronenstreuung an magnetisch polarisierten Streuzentren vorgeschlagen. Wir diskutierten sowohl diesen Erkl{\"a}rungsansatz als auch andere Theorievorschl{\"a}ge in der Literatur [7, 8] kritisch. In dieser Doktorarbeit haben wir versucht, der PHE des 3D TI HgTe durch die Asymmetrie in der Bandstruktur dieses Materials zu erkl{\"a}ren. In k.p Bandstrukturrechnungen mit einer 6-Orbital-Basis zeigten wir, dass das Zwischenspiel von Rashba- und Dresselhaus-Spin-Bahn- Wechselwirkung mit dem magnetischen Feld parallel zur TI-Oberfl{\"a}che zu einer Verformung der Fermikontur des Valenzbands von 3D TI-HgTe f{\"u}hrt, welche ihrerseits eine Anisotropie des Leitf{\"a}higkeit bedingt. Die ben{\"o}tigten Magnetfeldst{\"a}rken in diesem Modell waren mit bis zu 40 T jedoch etwa eine Gr{\"o}ßenordnung gr{\"o}ßer als jene in unseren Experimenten. Des Weiteren lieferte eine direkte Berechnung der Zustandsdichten f{\"u}r Bin k I und Bin ? I bisher keine klaren Resultate. Die komplizierte Abh{\"a}ngigkeit der Rashba-Spin-Bahn-Kopplung f{\"u}r p-leitendes HgTe [9] machte es außerdem schwierig, diesen Term in die Bandstrukturrechnung zu inkludieren. Trotz umfangreicher Bem{\"u}hungen, den Ursprung der galvanomagnetischen Effekte im 3D TI HgTe zu verstehen, konnte in dieser Arbeit der Mechanismus des PHE und der MR-Oszillationen nicht eindeutig bestimmt werden. Es gelang jedoch, einige aus der Literatur bekannte Theorien f{\"u}r den PHE und die MR-Oszillationseffekte in topologischen Isolatoren auszuschließen. Die Herausforderung, eine vollst{\"a}ndige theoretische Beschreibung zu entwickeln, die allen experimentellen Aspekten (PHE, Gatespannungsabh{\"a}ngigkeit und MR-Oszillationen) gerecht wird, bleibt weiter bestehen. Abschließend m{\"o}chte die Autorin ihre Hoffnung ausdr{\"u}cken, den Lesern die Komplexit{\"a}t der Fragestellung n{\"a}her gebracht zu haben und sie in die Kunst elektrischer Messungen an topologischen Isolatoren bei angelegtem parallelem Magnetfeld initiiert zu haben.}, language = {en} } @phdthesis{Klett2021, author = {Klett, Michael}, title = {Auxiliary particle approach for strongly correlated electrons : How interaction shapes order}, doi = {10.25972/OPUS-24812}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-248121}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Since the genesis of condensed matter physics, strongly correlated fermionic systems have shown a variety of fascinating properties and remain a vital topic in the field. Such systems arise through electronic interaction, and despite decades of intensive research, no holistic approach to solving this problem has been found. During that time, physicists have compiled a wealth of individual experimental and theoretical results, which together give an invaluable insight into these materials, and, in some instances, can explain correlated phenomena. However, there are several systems that stubbornly refuse to fall completely in line with current theoretical descriptions, among them the high-\( T_c{}\) cuprates and heavy fermion compounds. Although the two material classes have been around for the better part of the last 50 years, large portions of their respective phase diagram are still under intensive debate. Recent experiments in several electron-doped cuprates compounds, e.g. neodymium cerium copper oxide (Nd\(_{2x}\)Ce\(_x\)CuO\(_4\)), reveal a charge ordering about an antiferromagnetic ground state. So far, it has not been conclusively clarified how this intertwining of charge and spin polarization comes about and how it can be reconciled with a rigorous theoretical description. The heavy-fermion semimetals, on the other hand, have enjoyed renewed scientific interest with the discovery of topological Kondo insulators, a new material class offering a unique interface of topology, symmetry breaking, and correlated phenomena. In this context, samarium hexaboride (SmB\(_6\)) has emerged as a prototypical system, which may feature a topological ground state. In this thesis, we present a spin rotational invariant auxiliary particle approach to investigate the propensities of interacting electrons towards forming new states of order. In particular, we study the onset of spin and charge order in high-\( T_c{}\) cuprate systems and Kondo lattices, as well as the interplay of magnetism and topology. To that end, we use a sophisticated mean-field approximation of bosonic auxiliary particles augmented by a stability analysis of the saddle point via Gaussian fluctuations. The latter enables the derivation of dynamic susceptibilities, which describe the response of the system under external fields and offer a direct comparison to experiments. Both the mean-field and fluctuation formalisms require a numerical tool that is capable of extremizing the saddle point equations, on the one hand, and reliably solving a loop integral of the susceptibility-type, on the other. A full, from scratch derivation of the formalism tailored towards a software implementation, is provided and pedagogically reviewed. The auxiliary particle method allows for a rigorous description of incommensurate magnetic order and compares well to other established numerical and analytical techniques. Within our analysis, we employ the two-dimensional one-band Hubbard as well as the periodic Anderson model as minimal Hamiltonians for the high-\( T_c{}\) cuprates and Kondo systems, respectively. For the former, we observe a regime of intertwined charge- and spin-order in the electron-doped regime, which matches recent experimental observations in the cuprate material Nd\(_{2x}\)Ce\(_x\)CuO\(_4\). Furthermore, we localize the emergence of a Kondo regime in the periodic Anderson model and establish the magnetic phase diagram of the two-band model for topological Kondo insulators. The emerging antiferromagnetic ground state can be characterized by its topological properties and shows, for a non-trivial phase, topologically protected hinge modes.}, subject = {Festk{\"o}rpertheorie}, language = {en} } @phdthesis{Hrynevich2021, author = {Hrynevich, Andrei}, title = {Enhancement of geometric complexity and predictability of melt electrowriting for biomedical applications}, doi = {10.25972/OPUS-24764}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247642}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {This thesis encompasses the development of the additive manufacturing technology melt electrowriting, in order to achieve the improved applicability in biomedical applications and design of scaffolds. Melt electrowriting is a process capable of producing highly resolved structures from microscale fibres. Nevertheless, there are parameters influencing the process and it has not been clear how they affect the printing result. In this thesis the influence of the processing and environmental parameters is investigated with the impact on their effect on the jet speed, fibre diameter and scaffold morphology, which has not been reported in the literature to date and significantly influences the printing quality. It was demonstrated that at higher ambient printing temperatures the fibres can be hampered to the extent that the individual fibres are completely molten together and increased air humidity intensifies this effect. It was also shown how such parameters as applied voltage, collector distance, feed pressure and polymer temperature influence the fibre diameter and critical translation speed. Based on these results, a detailed investigation of the fibre diameter control and printing of scaffolds with novel architectures was made. As an example, a 20-fold diameter ratio is obtained within one scaffold by changing the collector speed and the feed pressure during the printing process. Although the pressure change caused fibre diameter oscillations, different diameter fibres were successfully integrated into two scaffold designs, which were tested for mesenchymal stromal cell suspension and adipose tissue spheroid seeding. Further design and manufacturing aspects are discussed while jet attraction to the printed structures is illuminated in connection with the fibre positioning control of the multilayer scaffolds. The artefacts that appear with the increasing scaffold height of sinusoidal laydown patterns are counteracted by layer-by-layer path adjustment. For the prediction of a printing error of the first deposited layer, an algorithm is developed, that utilizes an empirical jet lag equation and the speed of fibre deposition. This model was able to predict the position of the printing fibre with up to ten times smaller error than the of the programmed path. The same model allows to qualitatively assess the fibre diameter change along the nonlinear pattern as well as to indicate the areas of the greatest pattern deformation with the growing scaffold height. Those results will be used in the later chapters for printing of the novel MEW structures for biomedical applications. In the final chapter the concept of multimodal scaffold was combined with the suspended fibre printing, for the manufacturing of the MEW scaffolds with controlled pore interconnectivity in three dimensions. Those scaffolds were proven to be a promising substate for the control of the neurite spreading of the chick DRG neurons.}, subject = {Elektrospinnen}, language = {en} } @phdthesis{Siewert2021, author = {Siewert, Aaron}, title = {Nucleotide analogs as rigid spin labels for DNA and RNA}, doi = {10.25972/OPUS-24765}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247657}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Nucleic acids are one of the important classes of biomolecules together with carbohydrates, proteins and lipids. Both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are most well known for their respective roles in the storage and expression of genetic information. Over the course of the last decades, nucleic acids with a variety of other functions have been discovered in biological organisms or created artificially. Examples of these functional nucleic acids are riboswitches, aptamers and ribozymes. In order to gain information regarding their function, several analytical methods can be used. Electron paramagnetic resonance (EPR) spectroscopy is one of several techniques which can be used to study nucleic acid structure and dynamics. However, EPR spectroscopy requires unpaired electrons and because nucleic acids themselves are not paramagnetic, the incorporation of spin labels which carry a radical is necessary. Here, three new spin labels for the analysis of nucleic acids by EPR spectroscopy are presented. All of them share two important design features. First, the paramagnetic center is located at a nitroxide, flanked by ethyl groups to prevent nitroxide degradation, for example during solid phase synthesis. Furthermore, they were designed with rigidity as an important quality, in order to be useful for applications like pulsed electron double resonance (PELDOR) spectroscopy, where independent motion of the spin labels relative to the macromolecule has a noticeable negative effect on the precision of the measurements. Benzi-spin is a spin label which differs from most previous examples of rigid spin labels in that rather than being based on a canonical nucleoside, with a specific base pairing partner, it is supposed to be a universal nucleoside which is sufficiently rigid for EPR measurements when placed opposite to a number of different nucleosides. Benzi-spin was successfully incorporated into a 20 nt oligonucleotide and its base pairing behavior with seven different nucleosides was examined by UV/VIS thermal denaturation and continuous wave (CW) EPR experiments. The results show only minor differences between the different nucleosides, thus confirming the ability of benzi-spin to act as a universally applicable spin label. Lumi-spin is derived from lumichrome. It features a rigid scaffold, as well as a free 2'-hydroxy group, which should make it well suited for PELDOR experiments once it is incorporated into RNA oligonucleotides. E{\c{C}}r is based on the {\c{C}} family of spin labels, which contains the most well known rigid spin labels for nucleic acids to this day. It is essentially a version of E{\c{C}}m with a free 2'-hydroxy group. It was converted to triphosphate E{\c{C}}rTP and used for primer extension experiments to test the viability of enzymatic incorporation of rigid spin labels into oligonucleotides as an alternative to solid-phase synthesis. Incorporation into DNA by Therminator III DNA polymerase in both single-nucleotide and full-length primer extensions was achieved. All three of these spin labels represent further additions to the expanding toolbox of EPR spectroscopy on nucleic acids and might prove valuable for future research.}, subject = {Nucleins{\"a}uren}, language = {en} } @phdthesis{Sarma2021, author = {Sarma, Bhavishya}, title = {Merkel Cell Carcinoma: Investigations on its carcinogenesis and new therapeutic approaches}, doi = {10.25972/OPUS-24740}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247402}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Merkel cell carcinoma (MCC) is a rare and aggressive skin cancer with an increasing incidence. The majority of MCC cases (approximately 80\%) are associated with the Merkel cell polyomavirus (MCPyV). This virus encodes for the MCPyV T antigens (small T (sT) and large T (LT)), which are oncoproteins that drive MCC carcinogenesis. However, the precise cells of the skin that are transformed by the T antigens are not known i.e., the cells of origin of MCC are yet to be discovered. Therefore, the first part of this study involved the generation and evaluation of a vector system that could be used to study MCC oncogenesis. To this end, a set of lentiviral vectors was cloned that allows independent, inducible expression of potential key factors in MCC oncogenesis. In addition, a CRISPR/Cas9 knock in was established that allows the coding sequence for a fluorescent protein to be placed under the control of the promoter of KRT20, one of the most crucial markers of MCC. The functionality of this KRT20 reporter was proven in the MCPyV-positive MCC cell line, WaGa. The different inducible vector systems (doxycycline-inducible MCPyV T antigens or MCPyV sT, RheoSwitch-inducible ATOH1 and IPTG-inducible dnMAML1 and GLI1) were found to have different efficacies in various cellular systems and in particular, a considerable reduction in efficiency was observed at times upon the interaction of several vectors in one cell. In the second and more important part of this study, the role of the well-established anti-malarial drug, artesunate, which possesses additional anti-tumor and anti-viral activity, in the treatment of MCPyV-positive MCC was analyzed. In our study, artesunate was found to be cytotoxic towards MCPyV-positive MCC cell lines in vitro and repressed tumor growth in vivo in a mouse model. Artesunate was also found to downregulate T antigen expression, which is critical for the proliferation of MCPyV-positive MCC cells. The repression of T antigen expression, however, was not the sole mechanism of artesunate's cytotoxic action; instead, the MCPyV-positive MCC cell line, WaGa, was found to be even less sensitive to artesunate after shRNA knockdown of the T antigens. Since loss of membrane integrity occurred more rapidly than degradation/loss of genomic DNA under the influence of artesunate in four of five MCPyV-positive MCC cell lines examined, apoptosis, although widely described as a modus operandi for artesunate, did not appear to be a determinant of the cytotoxicity of artesunate against MCPyV-positive MCC cells. Instead, we were able to demonstrate that artesunate induced the recently described iron-dependent and lipid peroxide-associated form of cell death known as "ferroptosis". This was achieved primarily through the use of inhibitors that can suppress specific individual steps of the ferroptotic process. Thus, artesunate-induced cell death of MCPyV-positive MCC cells could be suppressed by iron chelators and by the inhibition of lipid peroxidation and lysosomal transport. Surprising results were obtained from the analysis of two proteins associated with the ferroptotic process, namely, ferroptosis suppressor protein 1 (FSP1) and tumor suppressor protein p53. Here, we showed that ectopically- 2 expressed FSP1 cannot suppress artesunate-induced ferroptosis in MCPyV-positive MCC cells and that p53 does not play a pro-ferroptotic role in artesunate-induced cell death of MCPyV-positive MCCs. Since artesunate did not suppress the interferon-γ-induced expression of immune-related molecules such as HLA and PD-L1 on the surface of MCPyV-positive MCCs, our study also provided the first positive evidence for its use in combinatorial immunotherapy. Overall, this study showed that artesunate appears to be an effective drug for the treatment of MCPyV-positive MCC and might also be considered for its use in combinatorial MCC immunotherapy in the future.}, language = {en} } @phdthesis{Solger2021, author = {Solger, Franziska}, title = {Central role of sphingolipids on the intracellular survival of \(Neisseria\) \(gonorrhoeae\) in epithelial cells}, doi = {10.25972/OPUS-24753}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247534}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Neisseria gonorrhoeae are Gram-negative bacteria with diplococcal shape. As an obligate human pathogen, it is the causative agent of gonorrhoea, a sexually transmitted disease. Gonococci colonize a variety of mucosal tissues, mainly the urogenital tract in men and women. Occasionally N. gonorrhoeae invades the bloodstream, leading to disseminated gonococcal infection. These bacteria possess a repertoire of virulence factors, which expression patterns can be adapted to the environmental conditions of the host. Through the accumulation of antibiotic resistances and in absence of vaccines, some neisserial strains have the potential to spread globally and represent a major public health threat. Therefore, it is necessary to understand the exact molecular mechanisms underlying the successful infection and progression of gonococci within their host. This deeper understanding of neisserial infection and survival mechanisms is needed for the development of new therapeutic agents. In this work, the role of host-cell sphingolipids on the intracellular survival of N. gonorrhoeae was investigated. It was shown that different classes of sphingolipids strongly interact with invasive gonococci in epithelial cells. Therefore, novel and highly specific clickable sphingolipid analogues were applied to study these interactions with this pathogen. The formation of intra- and extracellular sphingosine vesicles, which were able to target gonococci, was observed. This direct interaction led to the uptake and incorporation of sphingosine into the neisserial membrane. Together with in vitro results, sphingosine was identified as a potential bactericidal reagent as part of the host cell defence. By using different classes of sphingolipids and their clickable analogues, essential structural features, which seem to trigger the bacterial uptake, were detected. Furthermore, effects of key enzymes of the sphingolipid signalling pathway were tested in a neutrophil infection model. In conclusion, the combination of click chemistry and infection biology made it possible to shed some light on the dynamic interplay between cellular sphingosine and N. gonorrhoeae. Thereby, a possible "catch-and-kill" mechanism could have been observed.}, subject = {Neisseria gonorrhoeae}, language = {en} } @phdthesis{RiechelmannverhSteinbacher2021, author = {Riechelmann [verh. Steinbacher], Eva Katharina}, title = {Gaze interaction: Cognitive mechanisms of oculomotor action control}, doi = {10.25972/OPUS-21527}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-215279}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Humans use their eyes not only as visual input devices to perceive the environment, but also as an action tool in order to generate intended effects in their environment. For instance, glances are used to direct someone else's attention to a place of interest, indicating that gaze control is an important part of social communication. Previous research on gaze control in a social context mainly focused on the gaze recipient by asking how humans respond to perceived gaze (gaze cueing). So far, this perspective has hardly considered the actor's point of view by neglecting to investigate what mental processes are involved when actors decide to perform an eye movement to trigger a gaze response in another person. Furthermore, eye movements are also used to affect the non-social environment, for instance when unlocking the smartphone with the help of the eyes. This and other observations demonstrate the necessity to consider gaze control in contexts other than social communication whilst at the same time focusing on commonalities and differences inherent to the nature of a social (vs. non-social) action context. Thus, the present work explores the cognitive mechanisms that control such goal-oriented eye movements in both social and non-social contexts. The experiments presented throughout this work are built on pre-established paradigms from both the oculomotor research domain and from basic cognitive psychology. These paradigms are based on the principle of ideomotor action control, which provides an explanatory framework for understanding how goal-oriented, intentional actions come into being. The ideomotor idea suggests that humans acquire associations between their actions and the resulting effects, which can be accessed in a bi-directional manner: Actions can trigger anticipations of their effects, but the anticipated resulting effects can also trigger the associated actions. According to ideomotor theory, action generation involves the mental anticipation of the intended effect (i.e., the action goal) to activate the associated motor pattern. The present experiments involve situations where participants control the gaze of a virtual face via their eye movements. The triggered gaze responses of the virtual face are consistent to the participant's eye movements, representing visual action effects. Experimental situations are varied with respect to determinants of action-effect learning (e.g., contingency, contiguity, action mode during acquisition) in order to unravel the underlying dynamics of oculomotor control in these situations. In addition to faces, conditions involving changes in non-social objects were included to address the question of whether mechanisms underlying gaze control differ for social versus non-social context situations. The results of the present work can be summarized into three major findings. 1. My data suggest that humans indeed acquire bi-directional associations between their eye movements and the subsequently perceived gaze response of another person, which in turn affect oculomotor action control via the anticipation of the intended effects. The observed results show for the first time that eye movements in a gaze-interaction scenario are represented in terms of their gaze response in others. This observation is in line with the ideomotor theory of action control. 2. The present series of experiments confirms and extends pioneering results of Huestegge and Kreutzfeldt (2012) with respect to the significant influence of action effects in gaze control. I have shown that the results of Huestegge and Kreutzfeldt (2012) can be replicated across different contexts with different stimulus material given that the perceived action effects were sufficiently salient. 3. Furthermore, I could show that mechanisms of gaze control in a social gaze-interaction context do not appear to be qualitatively different from those in a non-social context. All in all, the results support recent theoretical claims emphasizing the role of anticipation-based action control in social interaction. Moreover, my results suggest that anticipation-based gaze control in a social context is based on the same general psychological mechanisms as ideomotor gaze control, and thus should be considered as an integral part rather than as a special form of ideomotor gaze control.}, subject = {Verhaltenskontrolle}, language = {en} } @phdthesis{Karimi2021, author = {Karimi, Sohail Mehmood}, title = {A Comparative Study on Guard Cell Function of the Glycophyte \(Arabidopsis\) \(thaliana\) and the Halophyte \(Thellungiella\) \(salsuginea\) Under Saline Growth Conditions}, doi = {10.25972/OPUS-19094}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-190942}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The greatest problems faced during the 21st century is climate change which is a big threat to food security due to increasing number of people. The increase in extreme weather events, such as drought and heat, makes it difficult to cultivate conventional crops that are not stress tolerant. As a result, increasing irrigation of arable land leads to additional salinization of soils with plant-toxic sodium and chloride ions. Knowledge about the adaptation strategies of salt-tolerant plants to salt stress as well as detailed knowledge about the control of transpiration water loss of these plants are therefore important to guarantee productive agriculture in the future. In the present study, I have characterized salt sensitive and salt tolerant plant species at physiological, phenotypic and transcriptomic level under short (1x salt) and long-time (3x) saline growth conditions. Two approaches used for long-time saline growth conditions (i.e increasing saline conditions (3x salt) and constant high saline conditions (3x 200 mM salt) were successfully developed in the natural plant growth medium i.e soil. Salt sensitive plants, A. thaliana, were able to survive and successfully set seeds at the toxic concentrations on the increasing saline growth mediums, with minor changes in the phenotype. However, under constant high saline conditions they could not survive. This was due to keeping low potassium, and high salt ions (sodium and chloride) in the photosynthetic tissue i.e leaf. Similarly, high potassium and low salt ions in salt tolerant T. salsuginea on both saline environments were the key for survival of this plant species. Being salt tolerant, T. salsuginea always kept high potassium levels and low sodium (during 1x) and chloride levels (during both 1x and 3x) in the leaf tissue. A strict control over transpirational water loss via stomata (formed by pair of guard cells) is important to maintain plant water balance. Aperture size of the stomata is regulated by the turgidity of the guard cells. More turgid the guard cells, bigger the apertures are and hence more transpiration. Under osmotic stress, the water loss is reduced which was evident in the salt sensitive A. thaliana plants under both short and long-time saline growth conditions. As the osmotic stress was only increased during long time saline growth conditions in T. salsuginea therefore, water loss was also decreased only under these saline conditions. Environmental CO2 assimilation also takes place via stomata in plants which then is used for photosynthesis. Stomatal apertures also influence CO2 assimilation. As the light absorbing photosynthetic pigments were more affected in A. thaliana, therefore photosynthetic activity of the whole plant was also reduced. Similarly, both short and long-time saline growth conditions also reduced the effective quantum yield of A. thaliana guard cells. Growth of the plant is dependent on energy which comes from photosynthesis. Reduced environmental CO2 assimilation would affect photosynthesis and hence growth, which was clearly observed in A. thaliana guard cells under long-time saline growth conditions. Major differences in both guard cells types were observed in their chloride and potassium levels. Energy Dispersive X-Ray Analysis (EDXA) suggested strict control of chloride accumulation in T. salsuginea guard cells as the levels remain unchanged under all conditions. Similarly, use of sodium in place of potassium for osmotic adjustments seems to be dependent on Na+/K+ rations in both guard cell types. Increased salt ions and reduced potassium levels in A. thaliana guard cells posed negative effect on photochemistry which in turn increased ROS metabolism and reduced energy related pathways at transcriptomic level in this plant species. Moreover, photosynthesis was strongly affected in A. thaliana guard cells both at transcriptomic and physiological levels. Similarly, global phytohormones induced changes were more evident in A. thaliana guard cells especially on 3x salt medium. Among all phytohormones, genes under the control of auxin were more differentially expressed in A. thaliana guard cells which suggests wide changes in growth and development in this plant species under salinity. Phytohormone, ABA is vital for closing the stomata under abiotic stress conditions. Increased levels of ABA during saline conditions led to efflux of potassium and counter anions (chloride, malate, nitrate) from the guard cells which caused the outward flow of water and hence reduction in turgor pressure. Reduced turgor pressure led to reduced water loss and CO2 assimilation especially in A. thaliana. Guard cells of both plant species synthesized ABA during saline conditions which was reflected from transcriptomic data and ABA quantification in the guard cells. ABA induced signaling in both plant species varied at the ABA receptor (PYL/PYR) levels where totally contrasting responses were observed. PYL2, PYL8 and PYL9 were specific to A. thaliana, furthermore, PYL2 was found to be differentially expressed only under 3x salt growth conditions thus suggesting its role during long term salt stress in this plant species. Protein phosphatases, which negatively regulate ABA signaling on one hand and act as ABA sensor on the other hand were found to be more differentially expressed in A. thaliana than T. salsuginea guard cells, which suggests their diverse role in both plant species under saline conditions. Differential expression of more ABA signaling players in long time saline conditions was prominent which could be because of darkness, as it is well known that rapid closure of stomata under dark conditions require ABA signaling. Moreover, representation of these components in dark also suggests that plants become more sensitive to dark under saline conditions which is also evident from the transpiration rates. Altogether, increased salt ions in A. thaliana guard cells and leaves led to pigment degradation and ABA induced reduction in transpiration which in turn influenced its growth. In contrast, T. salsuginea is the salt excluder and therefore keeps low levels of salt ions especially the chloride both in leaves and guard cells which mildly affects its growth. Guard cells of A. thaliana encounter severe energy problems at physiological and transcriptomic level. Main differences in the ABA signalling between both plant species were observed at the ABA receptor level.}, language = {en} } @phdthesis{Kehrberger2021, author = {Kehrberger, Sandra}, title = {Effects of climate warming on the timing of flowering and emergence in a tritrophic relationship: plants - bees - parasitoids}, doi = {10.25972/OPUS-21393}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213932}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The right timing of phenological events is crucial for species fitness. Species should be highly synchronized with mutualists, but desynchronized with antagonists. With climate warming phenological events advance in many species. However, often species do not respond uniformly to warming temperatures. Species-specific responses to climate warming can lead to asynchrony or even temporal mismatch of interacting species. A temporal mismatch between mutualists, which benefit from each other, can have negative consequences for both interaction partners. For host-parasitoid interactions temporal asynchrony can benefit the host species, if it can temporally escape its parasitoid, with negative consequences for the parasitoid species, but benefit the parasitoid species if it increases synchrony with its host, which can negatively affect the host species. Knowledge about the drivers of phenology and the species-specific responses to these drivers are important to predict future effects of climate change on trophic interactions. In this dissertation I investigated how different drivers act on early flowering phenology and how climate warming affects the tritrophic relationship of two spring bees (Osmia cornuta \& Osmia bicornis), an early spring plant (Pulsatilla vulgaris), which is one of the major food plants of the spring bees, and three main parasitoids of the spring bees (Cacoxenus indagator, Anthrax anthrax, Monodontomerus). In Chapter II I present a study in which I investigated how different drivers and their change over the season affect the reproductive success of an early spring plant. For that I recorded on eight calcareous grasslands around W{\"u}rzburg, Germany the intra-seasonal changes in pollinator availability, number of co-flowering plants and weather conditions and studied how they affect flower visitation rates, floral longevity and seed set of the early spring plant P. vulgaris. I show that bee abundances and the number of hours, which allowed pollinator foraging, were low at the beginning of the season, but increased over time. However, flower visitation rates and estimated total number of bee visits were higher on early flowers of P. vulgaris than later flowers. Flower visitation rates were also positively related to seed set. Over time and with increasing competition for pollinators by increasing numbers of co-flowering plants flower visitation rates decreased. My data shows that a major driver for early flowering dates seems to be low interspecific competition for pollinators, but not low pollinator abundances and unfavourable weather conditions. Chapter III presents a study in which I investigated the effects of temperature on solitary bee emergence and on the flowering of their food plant and of co-flowering plants in the field. Therefore I placed bee cocoons of two spring bees (O. cornuta \& O. bicornis) on eleven calcareous grasslands which differed in mean site temperature. On seven of these grasslands the early spring plant P. vulgaris occurred. I show that warmer temperatures advanced mean emergence in O. cornuta males. However, O. bicornis males and females of both species did not shift their emergence. Compared to the bees P. vulgaris advanced its flowering phenology more strongly with warmer temperatures. Co-flowering plants did not shift flowering onset. I suggest that with climate warming the first flowers of P. vulgaris face an increased risk of pollinator limitation whereas for bees a shift in floral resources may occur. In Chapter IV I present a study in which I investigated the effects of climate warming on host-parasitoid relationships. I studied how temperature and photoperiod affect emergence phenology in two spring bees (O. cornuta \& O. bicornis) and three of their main parasitoids (C. indagator, A. anthrax, Monodontomerus). In a climate chamber experiment with a crossed design I exposed cocoons within nest cavities and cocoons outside of nest cavities to two different temperature regimes (long-term mean of W{\"u}rzburg, Germany and long-term mean of W{\"u}rzburg + 4 °C) and three photoperiods (W{\"u}rzburg vs. Sn{\aa}sa, Norway vs. constant darkness) and recorded the time of bee and parasitoid emergence. I show that warmer temperatures advanced emergence in all studied species, but bees advanced less strongly than parasitoids. Consequently, the time period between female bee emergence and parasitoid emergence decreased in the warm temperature treatment compared to the cold one. Photoperiod influenced the time of emergence only in cocoons outside of nest cavities (except O. bicornis male emergence). The data also shows that the effect of photoperiod compared to the effect of temperature on emergence phenology was much weaker. I suggest that with climate warming the synchrony of emergence phenologies of bees and their parasitoids will amplify. Therefore, parasitism rates in solitary bees might increase which can negatively affect reproductive success and population size. In this dissertation I show that for early flowering spring plants low interspecific competition for pollinators with co-flowering plants is a major driver of flowering phenology, whereas other drivers, like low pollinator abundances and unfavourable weather conditions are only of minor importance. With climate warming the strength of different drivers, which act on the timing of phenological events, can change, like temperature. I show that warmer temperatures advance early spring plant flowering more strongly than bee emergence and flowering phenology of later co-flowering plants. Furthermore, I show that warmer temperatures advance parasitoid emergence more strongly than bee emergence. Whereas temperature changes can lead to non-uniform temporal shifts, I demonstrate that geographic range shifts and with that altered photoperiods will not change emergence phenology in bees and their parasitoids. In the tritrophic system I investigated in this dissertation climate warming may negatively affect the reproductive success of the early spring plant and the spring bees but not of the parasitoids, which may even benefit from warming temperatures.}, subject = {Biene }, language = {en} } @phdthesis{Anton2021, author = {Anton, Selma}, title = {Characterization of cAMP nanodomains surrounding the human Glucagon-like peptide 1 receptor using FRET-based reporters}, doi = {10.25972/OPUS-19069}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-190695}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Cyclic adenosine monophosphate (cAMP), the ubiquitous second messenger produced upon stimulation of GPCRs which couple to the stimulatory GS protein, orchestrates an array of physiological processes including cardiac function, neuronal plasticity, immune responses, cellular proliferation and apoptosis. By interacting with various effector proteins, among others protein kinase A (PKA) and exchange proteins directly activated by cAMP (Epac), it triggers signaling cascades for the cellular response. Although the functional outcomes of GSPCR-activation are very diverse depending on the extracellular stimulus, they are all mediated exclusively by this single second messenger. Thus, the question arises how specificity in such responses may be attained. A hypothesis to explain signaling specificity is that cellular signaling architecture, and thus precise operation of cAMP in space and time would appear to be essential to achieve signaling specificity. Compartments with elevated cAMP levels would allow specific signal relay from receptors to effectors within a micro- or nanometer range, setting the molecular basis for signaling specificity. Although the paradigm of signaling compartmentation gains continuous recognition and is thoroughly being investigated, the molecular composition of such compartments and how they are maintained remains to be elucidated. In addition, such compartments would require very restricted diffusion of cAMP, but all direct measurements have indicated that it can diffuse in cells almost freely. In this work, we present the identification and characterize of a cAMP signaling compartment at a GSPCR. We created a F{\"o}rster resonance energy transfer (FRET)-based receptor-sensor conjugate, allowing us to study cAMP dynamics in direct vicinity of the human glucagone-like peptide 1 receptor (hGLP1R). Additional targeting of analogous sensors to the plasma membrane and the cytosol enables assessment of cAMP dynamics in different subcellular regions. We compare both basal and stimulated cAMP levels and study cAMP crosstalk of different receptors. With the design of novel receptor nanorulers up to 60nm in length, which allow mapping cAMP levels in nanometer distance from the hGLP1R, we identify a cAMP nanodomain surrounding it. Further, we show that phosphodiesterases (PDEs), the only enzymes known to degrade cAMP, are decisive in constraining cAMP diffusion into the cytosol thereby maintaining a cAMP gradient. Following the discovery of this nanodomain, we sought to investigate whether downstream effectors such as PKA are present and active within the domain, additionally studying the role of A-kinase anchoring proteins (AKAPs) in targeting PKA to the receptor compartment. We demonstrate that GLP1-produced cAMP signals translate into local nanodomain-restricted PKA phosphorylation and determine that AKAP-tethering is essential for nanodomain PKA. Taken together, our results provide evidence for the existence of a dynamic, receptor associated cAMP nanodomain and give prospect for which key proteins are likely to be involved in its formation. These conditions would allow cAMP to exert its function in a spatially and temporally restricted manner, setting the basis for a cell to achieve signaling specificity. Understanding the molecular mechanism of cAMP signaling would allow modulation and thus regulation of GPCR signaling, taking advantage of it for pharmacological treatment.}, language = {en} } @phdthesis{Busch2021, author = {Busch, Albert Franz Jakob}, title = {Modification of angiogenesis to abrogate abdominal aortic aneurysm growth}, doi = {10.25972/OPUS-24135}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-241356}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Introduction: Abdominal aortic aneurysm (AAA) is a pathological saccular enlargement most often of the infrarenal aorta. Eventual rupture is fatal, making preemptive surgical therapy upon a diameter threshold of >50mm the treatment of choice. The pathophysiology, especially the initial trigger aortic remodeling is still largely unknown. However, some characteristic features involved in aneurysm growth have been established, such as medial angiogenesis, low-grade inflammation, vascular smooth muscle cell (VSMC) phenotype switch, extracellular remodeling, altered hemodynamics and an eventual humoral immune answer. Currently, no medical treatment options are available. RNA therapeutics and drug repurposing offer new possibilities to overcome this shortage. Using such to target angiogenesis in the aneurysm wall and investigate their potential mechanisms is the aim of this thesis. Material and Methods: We test our hypothesis by targeting the long non-coding RNA H19 and re-use the anti-cancer drug Lenvatinib in two murine inducible AAA models and one preclinical large animal model in the LDLR-/- pig. Furthermore, a H19-/- mouse is included to verify the results. AAA and control samples from a human biobank along with a primary human cell culture are used to verify results ex vivo by qPCR, WesternBlot, live cell imaging, histo- and immunohistochemistry along with gene array analysis, RNA knockdown, pull-down- and promotor assays. Results: H19 is significantly upregulated in AAA mice models and its knockdown limited aneurysm growth. It is well known that H19 interacts with several transcription factors. We found that cytoplasmic interaction between H19 and hypoxia-inducible factor 1-alpha (HIF1α) increased apoptosis in cultured SMCs associated with sequential p53 stabilization. In contrast, the knockdown of H19 was associated with markedly decreased apoptotic cell rates. Our data underline that HIF1α was essential in mediating the pro-apoptotic effects of H19. Secondly, Lenvatinib was applied both systemically and locally by endovascular means in mice with an established AAA. The drug significantly halted aneurysm growth and array analysis revealed myosin heavy chain 11 (MYH11) as the most differentially regulated target. This was shown to be up regulated after Lenvatinib treatment of primary AAA smooth muscle cells suggesting a salvage mechanism to obtain a contractile phenotype based on gene expression and immunohistochemistry. The same results were shown upon a local endovascular Lenvatinib-coated balloon angioplasty in the established aneurysmatic lesion of a novel atherosclerotic LDLR-/- Yucatan minipig model. Decreased phosphorylation of extracellular-signal regulated kinases 1-2 (ERK1-2) is the downstream effect of Lenvatinib-specific blockage of the vascular endothelial growth factor receptor (VEGFR2). Conclusion: Taking into account the heterogeneity of the disease, inhibition of VSMC phenotype switch, extracellular remodeling and angiogenesis seem promising targets in some if not all AAA patients. Together with surveillance and surgical therapy, these new non-invasive treatment strategies would allow for a more personalized approach to treat this disease.}, subject = {Aortenaneurysma}, language = {en} } @phdthesis{Renner2021, author = {Renner, Rebecca}, title = {Aggregation, Chirality and Reduction of Nonplanar Polycyclic Aromatic Hydrocarbons}, doi = {10.25972/OPUS-24700}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247000}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Within this thesis the interactions between novel corannulene derivatives in solution as well as in the solid state by changing the imide residue of a literature known extended corannulene dicarboximide were investigated, in order to obtain a better understanding of the packing and possible charge transport in potential applications. Accordingly, the goal of the work was to synthesize and investigate an electron-poor corannulene bis(dicarboximide) based on previously published work but with higher solubility and less steric encumbrance in imide position to enable self-assembly in solution. To obtain further insights into the conformational stability, structure and chiroptical properties of heavily twisted PBIs another aim of this thesis was the design, synthesis, and optoelectronic investigation of various fourfold directly arylated PBIs by substitution in bay position with smaller hydrocarbons with different steric demand, i.e., benzene, naphthalene and pyrene, which should be separable by chiral high performance liquid chromatography (HPLC). As of yet, no concise study concerning the optical and electronic properties of differently core-substituted PBIs in the neutral as well as the mono- and dianionic state in solution is available, which also elucidates the origin of the different optical transitions observed in the absorption and emission spectra. Thus, in this thesis, the investigation of five PBI derivatives with different frontier energetic levels to produce a reference work of reduced PBIs was tackled.}, subject = {Corannulene}, 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{Jansch2021, author = {Jansch, Charline}, title = {Effects of SLC2A3 copy number variants on neurodevelopment and glucose metabolism in ADHD patient-specific neurons}, doi = {10.25972/OPUS-21620}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-216201}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Neuropsychiatric disorders, such as attention-deficit/hyperactivity disorder (ADHD), represent a burden which deeply impair the patient's life. Neurobiological research has therefore increasingly focused on the examination of brain neurotransmitter systems, such as the serotonin (5-HT) system, since a dysfunction has been repeatedly implicated in the pathology of these diseases. However, investigation of functional human neurons in vitro has been restricted by technical limitations for a long time until the discovery of human induced pluripotent stem cells (iPSCs) revolutionized the field of experimental disease models. Since the pathogenesis of neuropsychiatric disorders involves a complex genetic component, genome-wide association studies (GWAS) revealed numerous risk genes that are associated with an increased risk for ADHD. For instance, the novel ADHD candidate gene SLC2A3 which encodes the glucose transporter-3 (GLUT3), facilitates the transport of glucose across plasma membranes and is essential for the high energy demand of several cell types, such as stem cells and neurons. Specifically, copy number variants (CNVs) of SLC2A3 might therefore impact cerebral glucose metabolism as well as the assembly of synaptic proteins in human neurons which might contribute to the pathogenesis of ADHD. We hypothesized that an altered SLC2A3 gene dosage in human neurons can exert diverse protective or detrimental effects on neurodevelopmental processes as well as the coping of glucometabolic stress events, such as hypo- and hyperglycaemic conditions. The generation of specific iPSC lines from ADHD patients and healthy probands served as basis to efficiently differentiate stem cells into 5-HT specific neurons. Using this neuronal culture, we were able to examine effects of SLC2A3 CNVs on the basal expression of SCL2A3 and GLUT3 in human neurons. Furthermore, the focus was on potentially altered coping of the cells with glucose deprivation and the treatment with specific high- and low glycaemic media. High-resolution fluorescence imaging in combination with electrophysiological and molecular biological techniques showed that: 1) The generated human iPSCs are fully reprogrammed human stem cells showing typical characteristics of embryonic stem cell-like morphology, growth behaviour, the ability to differentiate into different cell types of the human body and the expression of pluripotency-specific markers. 2) The neuronal subtype derived from our stem cells display typical characteristics of 5-HT specific median and dorsal neurons and forms synapses reflected by the expression of pre- and postsynaptic proteins. 3) Even if SLC2A3 CNVs influence SLC2A3 and GLUT3 basal expression, no significant alterations in gene and protein expression caused by hyper- and hypoglycaemic conditions, nor in the assembly of proteins associated with synapse formation could be observed in human iPSC-derived neurons.}, subject = {Stammzelle}, language = {en} } @phdthesis{vonWardenburg2021, author = {von Wardenburg, Niels Oliver}, title = {Investigations into the Pathogenic Antibody-Antigen-Interference of Glycine Receptor Autoantibodies}, doi = {10.25972/OPUS-24721}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247217}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Anti-glycine receptor (GlyR) autoantibodies belong to the novel group of autoantibodies that target neuronal cell-surface antigens (NCS), which are accompanied with various neurologic and neuropsychiatric conditions. The inhibitory ionotropic GlyR is one of the major inhibitory neurotransmitter receptors and therefore involved in maintaining homeostasis of neuronal excitation levels at brain stem and spinal cord. Anti-GlyR autoantibodies are associated with progressive encephalomyelitis with rigidity and myoclonus or stiff person syndrome. These neuromotor disorders are characterized by exaggerated startle, muscle stiffness, and painful spasms, leading to immobility and fatal outcome in some cases. It was hypothesized that imbalance of motoneuronal inhibition by functional impairment of GlyR and receptor internalization are direct consequences of antibody-antigen interference. Here, serum samples of four patients were tested for anti-GlyR autoantibodies and were used for the analysis of the functional impact on the electrophysiological properties of recombinant GlyRs, transiently expressed in HEK293 cells. Furthermore, the recognition pattern of anti- GlyR autoantibodies to human, zebrafish and chimeric GlyRα1 located the epitope to the far N-terminal region. The pathogenicity of anti-GlyR autoantibodies and thereby the autoimmunologic etiology of the disease was confirmed by passive transfer of patient serum to zebrafish (Danio rerio) larvae, that yielded an abnormal escape response - a brain stem reflex that corresponds to the exaggerated startle of afflicted patients. The phenotype was accompanied by profound reduction of GlyR clusters in spinal cord cryosections of treated zebrafish larvae. Together, these novel insights into the pathogenicity of GlyR autoantibodies confirm the concept of a novel neurologic autoimmune disease and might contribute to the development of innovative therapeutic strategies.}, language = {en} } @phdthesis{GamachegebRupp2021, author = {Gamache [geb. Rupp], Mira Theresa}, title = {Ligand Design for Ru(II) Photosensitizers in Photocatalytic Hydrogen Evolution}, doi = {10.25972/OPUS-24676}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-246766}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {This thesis investigates different ligand designs for Ru(II) complexes and the activity of the complexes as photosensitizer (PS) in photocatalytic hydrogen evolution. The catalytic system typically contains a catalyst, a sacrificial electron donor (SED) and a PS, which needs to exhibit strong absorption and luminescence, as well as reversible redox behavior. Electron-withdrawing pyridine substituents on the terpyridine metal ion receptor result in an increase of excited-state lifetime and quantum yield (Φ = 74*10-5; τ = 3.8 ns) and lead to complex III-C1 exhibiting activity as PS. While the turn-over frequency (TOFmax) and turn-over number (TON) are relatively low (TOFmax = 57 mmolH2 molPS-1 min-1; TON(44 h) = 134 mmolH2 molPS-1), the catalytic system is long-lived, losing only 20\% of its activity over the course of 12 days. Interestingly, the heteroleptic design in III-C1 proves to be beneficial for the performance as PS, despite III-C1 having comparable photophysical and electrochemical properties as the homoleptic complex IV-C2 (TOFmax = 35 mmolH2 molPS-1 min-1; TON(24 h) = 14 mmolH2 molPS-1). Reductive quenching of the excited PS by the SED is identified as rate-limiting step in both cases. Hence, the ligands are designed to be more electron-accepting either via N-methylation of the peripheral pyridine substituents or introduction of a pyrimidine ring in the metal ion receptor, leading to increased excited-state lifetimes (τ = 9-40 ns) and luminescence quantum yields (Φ = 40-400*10-5). However, the more electron-accepting character of the ligands also results in anodically shifted reduction potentials, leading to a lack of driving force for the electron transfer from the reduced PS to the catalyst. Hence, this electron transfer step is found to be a limiting factor to the overall performance of the PS. While higher TOFmax in hydrogen evolution experiments are observed for pyrimidine-containing PS (TOFmax = 300-715 mmolH2 molPS-1 min-1), the longevity for these systems is reduced with half-life times of 2-6 h. Expansion of the pyrimidine-containing ligands to dinuclear complexes yields a stronger absorptivity (ε = 100-135*103 L mol-1 cm-1), increased luminescence (τ = 90-125 ns, Φ = 210-350*10-5) and can also result in higher TOFmax given sufficient driving force for electron transfer to the catalyst (TOFmax = 1500 mmolH2 molPS-1 min-1). When comparing complexes with similar driving forces, stronger luminescence is reflected in a higher TOFmax. Besides thermodynamic considerations, kinetic effects and electron transfer efficiency are assumed to impact the observed activity in hydrogen evolution. In summary, this work shows that targeted ligand design can make the previously disregarded group of Ru(II) complexes with tridentate ligands attractive candidates for use as PS in photocatalytic hydrogen evolution.}, subject = {Fotokatalyse}, language = {en} } @phdthesis{Baumhoer2021, author = {Baumhoer, Celia Am{\´e}lie}, title = {Glacier Front Dynamics of Antarctica - Analysing Changes in Glacier and Ice Shelf Front Position based on SAR Time Series}, doi = {10.25972/OPUS-24581}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-245814}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The Antarctic Ice Sheet stores ~91\% of the global ice volume which is equivalent to a sea-level rise of 58.3 meters. Recent disintegration events of ice shelves and retreating glaciers along the Antarctic Peninsula and West Antarctica indicate the current vulnerable state of the Antarctic Ice Sheet. Glacier tongues and ice shelves create a safety band around Antarctica with buttressing effects on ice discharge. Current decreases in glacier and ice shelf extent reduce the effective buttressing forces and increase ice discharge of grounded ice. The consequence is a higher contribution to sea-level rise from the Antarctic Ice Sheet. So far, it is unresolved which proportion of Antarctic glacier retreat can be attributed to climate change and which part to the natural cycle of growth and decay in the lifetime of a glacier. The quantitative assessment of the magnitude, spatial extent, distribution, and dynamics of circum-Antarctic glacier and ice shelf retreat is of utmost importance to monitor Antarctica's weakening safety band. In remote areas like Antarctica, earth observation provides optimal properties for large-scale mapping and monitoring of glaciers and ice shelves. Nowadays, the variety of available satellite sensors, technical advancements regarding spatial resolution and revisit times, as well as open satellite data archives create an ideal basis for monitoring calving front change. A systematic review conducted within this thesis revealed major gaps in the availability of glacier and ice shelf front position measurements despite the improved satellite data availability. The previously limited availability of satellite imagery and the time-consuming manual delineation of calving fronts did neither allow a circum-Antarctic assessment of glacier retreat nor the assessment of intra-annual changes in glacier front position. To advance the understanding of Antarctic glacier front change, this thesis presents a novel automated approach for calving front extraction and explores drivers of glacier retreat. A comprehensive review of existing methods for glacier front extraction ascertained the lack of a fully automatic approach for large-scale monitoring of Antarctic calving fronts using radar imagery. Similar backscatter characteristics of different ice types, seasonally changing backscatter values, multi-year sea ice, and m{\´e}lange made it challenging to implement an automated approach with traditional image processing techniques. Therefore, the present abundance of satellite data is best exploited by integrating recent developments in big data and artificial intelligence (AI) research to derive circum-Antarctic calving front dynamics. In the context of this thesis, the novel AI-based framework "AntarcticLINES" (Antarctic Glacier and Ice Shelf Front Time Series) was created which provides a fully automated processing chain for calving front extraction from Sentinel-1 imagery. Open access Sentinel-1 radar imagery is an ideal data source for monitoring current and future changes in the Antarctic coastline with revisit times of less than six days and all-weather imaging capabilities. The developed processing chain includes the pre-processing of dual-polarized Sentinel-1 imagery for machine learning applications. 38 Sentinel-1 scenes were used to train the deep learning architecture U-Net for image segmentation. The trained weights of the neural network can be used to segment Sentinel-1 scenes into land ice and ocean. Additional post-processing ensures even more accurate results by including morphological filtering before extracting the final coastline. A comprehensive accuracy assessment has proven the correct extraction of the coastline. On average, the automatically extracted coastline deviates by 2-3 pixels (93 m) from a manual delineation. This accuracy is in range with deviations between manually delineated coastlines from different experts. For the first time, the fully automated framework AntarcticLINES enabled the extraction of intra-annual glacier front fluctuations to assess seasonal variations in calving front change. Thereby, for example, an increased calving frequency of Pine Island Glacier and a beginning disintegration of Glenzer Glacier were revealed. Besides, the extraction of the entire Antarctic coastline for 2018 highlighted the large-scale applicability of the developed approach. Accurate results for entire Antarctica were derived except for the Western Antarctic Peninsula where training imagery was not sufficient and should be included in future studies. Furthermore, this dissertation presents an unprecedented record of circum-Antarctic calving front change over the last two decades. The newly extracted coastline for 2018 was compared to previous coastline products from 2009 and 1997. This revealed that the Antarctic Ice Sheet shrank 29,618±1193 km2 in extent between 1997-2008 and gained an area of 7,108±1029 km2 between 2009-2018. Glacier retreat concentrated along the Antarctic Peninsula and West Antarctica. The only East Antarctic coastal sector primarily experiencing calving front retreat was Wilkes Land in 2009-2018. Finally, potential drivers of circum-Antarctic glacier retreat were identified by combining data on glacier front change with changes in climate variables. It was found that strengthening westerlies, snowmelt, rising sea surface temperatures, and decreasing sea ice cover forced glacier retreat over the last two decades. Relative changes in mean air temperature could not be identified as a driver for glacier retreat and further investigations on extreme events in air temperature are necessary to assess the effect of atmospheric forcing on frontal retreat. The strengthening of all identified drivers was closely connected to positive phases of the Southern Annular Mode (SAM). With increasing greenhouse gases and ozone depletion, positive phases of SAM will occur more often and force glacier retreat even further in the future. Within this thesis, a comprehensive review on existing Antarctic glacier and ice shelf front studies was conducted revealing major gaps in Antarctic calving front records. Therefore, a fully automated processing chain for glacier and ice shelf front extraction was implemented to track circum-Antarctic calving front fluctuations on an intra-annual basis. The large-scale applicability was certified by presenting two decades of circum-Antarctic calving front change. In combination with climate variables, drivers of recent glacier retreat were identified. In the future, the presented framework AntarcticLINES will greatly contribute to the constant monitoring of the Antarctic coastline under the pressure of a changing climate.}, language = {en} }