@phdthesis{Masota2023,
  author    = {Masota, Nelson Enos},
  title     = {The Search for Novel Effective Agents Against Multidrug-Resistant Enterobacteriaceae},
  doi       = {10.25972/OPUS-30263},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-302632},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {This thesis aimed at searching for new effective agents against Multidrug-Resistant Enterobacteriaceae. This is necessitated by the urgent need for new and innovative antibacterial agents addressing the critical priority pathogens prescribed by the World Health Organization (WHO). Among the available means for antibiotics discovery and development, nature has long remained a proven, innovative, and highly reliable gateway to successful antibacterial agents. Nevertheless, numerous challenges surrounding this valuable source of antibiotics among other drugs are limiting the complete realization of its potential. These include the availability of good quality data on the highly potential natural sources, limitations in methods to prepare and screen crude extracts, bottlenecks in reproducing biological potentials observed in natural sources, as well as hurdles in isolation, purification, and characterization of natural compounds with diverse structural complexities. Through an extensive review of the literature, it was possible to prepare libraries of plant species and phytochemicals with reported high potentials against Escherichia coli and Klebsiella pneumnoniae. The libraries were profiled to highlight the existing patterns and relationships between the reported antibacterial activities and studied plants' families and parts, the type of the extracting solvent, as well as phytochemicals' classes, drug-likeness and selected parameters for enhanced accumulation within the Gram-negative bacteria. In addition, motivations, objectives, the role of traditional practices and other crucial experimental aspects in the screening of plant extracts for antibacterial activities were identified and discussed. Based on the implemented strict inclusion criteria, the created libraries grant speedy access to well-evaluated plant species and phytochemicals with potential antibacterial activities. This way, further studies in yet unexplored directions can be pursued from the indicated or related species and compounds. Moreover, the availability of compound libraries focusing on related bacterial species serves a great role in the ongoing efforts to develop the rules of antibiotics penetrability and accumulation, particularly among Gram-negative bacteria. Here, in addition to hunting for potential scaffolds from such libraries, detailed evaluations of large pool compounds with related antibacterial potential can grant a better understanding of structural features crucial for their penetration and accumulation. Based on the scarcity of compounds with broad structural diversity and activity against Gram-negative bacteria, the creation and updating of such libraries remain a laborious but important undertaking. A Pressurized Microwave Assisted Extraction (PMAE) method over a short duration and low-temperature conditions was developed and compared to the conventional cold maceration over a prolonged duration. This method aimed at addressing the key challenges associated with conventional extraction methods which require long extraction durations, and use more energy and solvents, in addition to larger quantities of plant materials. Furthermore, the method was intended to replace the common use of high temperatures in most of the current MAE applications. Interestingly, the yields of 16 of 18 plant samples under PMAE over 30 minutes were found to be within 91-139\% of those obtained from the 24h extraction by maceration. Additionally, different levels of selectivity were observed upon an analytical comparison of the extracts obtained from the two methods. Although each method indicated selective extraction of higher quantities or additional types of certain phytochemicals, a slightly larger number of additional compounds were observed under maceration. The use of this method allows efficient extraction of a large number of samples while sparing heat-sensitive compounds and minimizing chances for cross-reactions between phytochemicals. Moreover, findings from another investigation highlighted the low likelihood of reproducing antibacterial activities previously reported among various plant species, identified the key drivers of poor reproducibility, and proposed possible measures to mitigate the challenge. The majority of extracts showed no activities up to the highest tested concentration of 1024 µg/mL. In the case of identical plant species, some activities were observed only in 15\% of the extracts, in which the Minimum Inhibitory Concentrations (MICs) were 4 - 16-fold higher than those in previous reports. Evaluation of related plant species indicated better outcomes, whereby about 18\% of the extracts showed activities in a range of 128-512 μg/mL, some of the activities being superior to those previously reported in related species. Furthermore, solubilizing plant crude extracts during the preparation of test solutions for Antibacterial Susceptibility Testing (AST) assays was outlined as a key challenge. In trying to address this challenge, some studies have used bacteria-toxic solvents or generally unacceptable concentrations of common solubilizing agents. Both approaches are liable to give false positive results. In line with this challenge, this study has underscored the suitability of acetone in the solubilization of crude plant extracts. Using acetone, better solubility profiles of crude plant extracts were observed compared to dimethyl sulfoxide (DMSO) at up to 10 \%v/v. Based on lacking toxicity against many bacteria species at up to 25 \%v/v, its use in the solubilization of poorly water-soluble extracts, particularly those from less polar solvents is advocated. In a subsequent study, four galloylglucoses were isolated from the leaves of Paeonia officinalis L., whereby the isolation of three of them from this source was reported for the first time. The isolation and characterization of these compounds were driven by the crucial need to continually fill the pre-clinical antibiotics pipeline using all available means. Application of the bioautography-guided isolation and a matrix of extractive, chromatographic, spectroscopic, and spectrometric techniques enabled the isolation of the compounds at high purity levels and the ascertainment of their chemical structures. Further, the compounds exhibited the Minimum Inhibitory Concentrations (MIC) in a range of 2-256 µg/mL against Multidrug-Resistant (MDR) strains of E. coli and K. pneumonia exhibiting diverse MDR phenotypes. In that, the antibacterial activities of three of the isolated compounds were reported for the first time. The observed in vitro activities of the compounds resonated with their in vivo potentials as determined using the Galleria mellonella larvae model. Additionally, the susceptibility of the MDR bacteria to the galloylglucoses was noted to vary depending on the nature of the resistance enzymes expressed by the MDR bacteria. In that, the bacteria expressing enzymes with higher content of aromatic amino acids and zero or positive net charges were generally more susceptible. Following these findings, a plausible hypothesis for the observed patterns was put forward. The generally challenging pharmacokinetic properties of galloylglucoses limit their further development into therapeutic agents. However, the compounds can replace or reduce the use of antibiotics in livestock keeping as well as in the treatment of septic wounds and topical or oral cavity infections, among other potential uses. Using nature-inspired approaches, a series of glucovanillin derivatives were prepared following feasible synthetic pathways which in most cases ensured good yields and high purity levels. Some of the prepared compounds showed MIC values in a range of 128 - 512 μg/mL against susceptible and MDR strains of Klebsiella pneumoniae, Methicillin-Resistant Staphylococcus aureus (MRSA) and Vancomycin-Resistant Enterococcus faecium (VRE). These findings emphasize the previously reported essence of small molecular size, the presence of protonatable amino groups and halogen atoms, as well as an amphiphilic character, as crucial features for potential antibacterial agents. Due to the experienced limited success in the search for new antibacterial agents using purely synthetic means, pursuing semi-synthetic approaches as employed in this study are highly encouraged. This way, it is possible to explore broader chemical spaces around natural scaffolds while addressing their inherent limitations such as solubility, toxicity, and poor pharmacokinetic profiles.},
  subject      = {Enterobacteriaceae},
  language  = {en}
}
@phdthesis{Ganskih2023,
  author    = {Ganskih, Sabina},
  title     = {Dissecting the functional interplay between SARS-CoV-2 viral RNAs and the host proteome},
  doi       = {10.25972/OPUS-34648},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346486},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The recent pandemic has reminded the public that basic research in virology is pivotal for human health. Understanding the mechanisms of successful viral replication and the role of host factors can help to combat viral infections and prevent future pandemics. Our lab has published the first SARS-CoV-2 RNA-protein interaction atlas, laying the foundation to investigate the interplay between viral RNA and host RNA binding proteins (RBP). Based on this, my project created the largest collection of binding profiles of host and viral RBPs on SARS-CoV-2 RNA to date. This revealed the host protein SND1 as the first human RBP that specifically binds negative sense viral RNA at the 5´ end, a region associated with viral transcription initiation. The binding profile shares similarities with the viral RBP nsp9, which binds the 5´ ends of positive and negative sense SARS-CoV-2 RNA. Depletion of SND1 shows reduced levels of viral RNA revealing it as a proviral host factor. To decode the underlying molecular mechanism, I characterized the protein-protein interactions of SND1 in SARS-CoV-2 infected and uninfected cells. Infection remodels the protein interactors of SND1 from general RNA biology to membrane association and viral RNA synthesis. Upon infection, SND1 specifically interacts with nsp9, the RBP that shares the same binding region on the negative strand of SARS-CoV-2 RNA. Recent work demonstrates that nsp9 is NMPylated in vitro suggesting a functional role of nsp9 in priming of viral RNA synthesis. I was able to show that nsp9 is covalently linked to the 5´ ends of SARS-CoV-2 RNA during infection of human cells. Analysing the covalent bond of nsp9 with the viral RNA on nucleotide level shows close proximity to the initiation sites of viral RNA synthesis, suggesting that nsp9 acts as a protein-primer of SARS-CoV-2 RNA synthesis. SND1 modulates the distribution of nsp9 on the viral RNA, since depletion of SND1 results in imbalanced occupancy of nsp9 at the 5´ends of viral RNA. This study is the first to provide evidence for the priming mechanism of SARS-CoV-2 in authentic viral replication and further reveals how this mechanism is modulated by the host RBP SND1. Detailed knowledge about priming of viral RNA synthesis can help to find targeted antivirals that could be used to fight coronaviral infections.},
  subject      = {SARS-CoV-2},
  language  = {en}
}
@phdthesis{Bauer2023,
  author    = {Bauer, Christian},
  title     = {Towards ecological and efficient electrochemical energy storage in supercapacitors and sodium ion batteries using onion-like carbon},
  doi       = {10.25972/OPUS-31795},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-317956},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {In this thesis, the usage of onion-like carbon (OLC) for energy storage applications was researched regarding sustainability, performance and processability. This work targets to increase the scientific understanding regarding the role of OLC in electrodes and to facilitate a large-scale production, which is the foundation for commercial application. Research was devoted to increase the knowledge in the particular field, to yield synergistic approaches and a shared value regarding sustainability and performance.},
  subject      = {Elektrochemie},
  language  = {en}
}
@phdthesis{Sun2023,
  author    = {Sun, Aili},
  title     = {Effect of Tjap1 knock-down on blood-brain barrier properties under normal and hypoxic conditions},
  doi       = {10.25972/OPUS-34645},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346450},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Stroke is one of the leading causes of mortality and disability worldwide. The blood-brain barrier (BBB) plays an important role in maintaining brain homeostasis by tightly regulating the exchange of substances between circulating blood and brain parenchyma. BBB disruption is a common pathologic feature of stroke and traumatic brain injury. Understanding the cellular and molecular events that affect the BBB after ischaemic brain injury is important to improve patient prognosis. We have previously shown that microRNA-212/132 is elevated in hypoxic brain microvascular endothelial cells and acts through suppressing the expression of direct microRNA-212/132 target genes with function at the BBB: claudin-1, junctional adhesion molecule 3 (Jam3) and tight-junction associated protein 1 (Tjap1). While the role of claudin-1 and Jam3 at the BBB is well known, the role of Tjap1 is still unclear. The aim of this work was therefore to characterize the role of Tjap1 in brain endothelial cells using a knock-down (KD) approach in established murine in vitro BBB models cEND and cerebEND. Tjap1 KD was established by stable transfection of a plasmid expressing shRNA against Tjap1. The successful downregulation of Tjap1 mRNA and protein was demonstrated by qPCR and Western blot. Tjap1 KD resulted in impaired barrier properties of endothelial cells as shown by lower TEER values and higher paracellular permeability. Interestingly, the Tjap1 KD cells showed lower cell viability and proliferation but migrated faster in a wound healing assay. In the tube formation assay, Tjap1 KD cell lines showed a lower angiogenic potential due to a significantly lower tube length and number as well as a lower amount of branching points in formed capillaries. Tjap1 KD cells showed changes in gene and protein expression. The TJ proteins claudin-5, Jam3 and ZO-1 were significantly increased in Tjap1 KD cell lines, while occludin was strongly decreased. In addition, efflux pump P-glycoprotein was downregulated in Tjap1 KD cells. Oxygen-glucose deprivation (OGD) is a method to mimic stroke in vitro. Brain endothelial cell lines treated with OGD showed lower barrier properties compared to cells cultured under normal condition. These effects were more severe in Tjap1 KD cells, indicating active Tjap1 involvement in the OGD response in brain microvascular endothelial cells. We thus have shown that Tjap1 contributes to a tight barrier of the BBB, regulates cell viability and proliferation of endothelial cells, suppresses their migration and promotes new vessel formation. This means that Tjap1 function is important for mature BBB structure in health and disease.},
  subject      = {Schlaganfall},
  language  = {en}
}
@phdthesis{Gralke2023,
  author    = {Gralke, Verena Maria},
  title     = {The Impact of Media Literacy in Adolescence and Young Adulthood. - Correlative and Experimental Investigations on the Influence of Media Literacy on Cognitive and Political Variables, and on Knowledge Acquisition from Media -},
  doi       = {10.25972/OPUS-34601},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346018},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {This thesis consists of three studies investigating the influence media literacy has on political variables, cognitive variables, and learning. Adolescents from 13 years of age and young adults are included in the studies. This thesis is divided into three chapters. Study I and II are one comprehensive study, but will be presented separately for better readability. Chapter I provides the reader with background knowledge for the original studies presented in chapter II includes information about media use, different conceptualizations of media literacy and its development over the lifetime, as well as media literacy's impact on cognitive and political variables. Additionally, current literature on the comparison of the learning outcomes of different kinds of texts (written, auditory, and audiovisual) is presented, with a differentiation between text-based information and inferences. In chapter II, the original studies are placed in the current state of research and presented in detail. In chapter III, a critical discussion of the studies is conducted, and a general model of the influence media literacy has on the investigated cognitive and political factors is presented, followed by a conclusion of the research. The theoretical foundation of this thesis is three models of media literacy proposed by Groeben (2002, 2004), Hobbs (1997), and Potter (1998, 2016). These three models are similar in that they define media literacy as a multifactorial construct with skills that develop further in the course of life. Their ideas are integrated and developed further, leading to our own model of media literacy. It encompasses five scales: media sign literacy, distinction between reality and fiction, knowledge of media law, knowledge of media effects, and production skills. Thereupon, the assessment tool W{\"u}rzburg Media Literacy Test (WMK; W{\"u}rzburger Medienkompetenztest) is designed. There is evidence that media use and media literacy influence socio-political factors. Young adults name the internet as the main source of information on political topics (see Pasek et al., 2006), and knowledge demonstrably fosters political participation (Delli Carpini \& Keeter, 1996). However, the kind of participation activity regarded is important (Quintelier \& Vissers, 2008), as sometimes real-life participation is supplemented by online activities (Quan-Haase \& Wellman, 2002). Media literacy is the key to evaluating the quality of information from media. Whether or not a direct link between media literacy and political interest exists has, as far as I know, not yet been investigated. Several studies have shown that precursors and subcomponents of media literacy have the capacity to influence cognitive variables. For instance, children with higher media sign literacy possess better reading proficiency (Nieding et al., 2017) and are better at collecting information and drawing inferences from hypermedia and films (Diergarten et al., 2017) as compared to children with low literacy. These precursors and subcomponents are more efficient in processing medial sign systems, reducing cognitive load, and consequently, liberating cognitive capacity for other mental tasks (Sweller, 1988). Paino and Renzulli (2012) showed that highly computer-proficient adolescents exhibit better mathematics and reading abilities. Different types of media influence the learning process differently, and the learning process can be enhanced by combining these different types of media, if the material is prepared according to the research findings and Mayer's (2002) cognitive theory of multimedia learning. Similarly, a reduction in cognitive load takes place and more resources can be invested in the learning process itself (Mayer \& Moreno, 2003; Sweller, 1988). It is not easy to answer the question of whether one medium is superior for learning to another. Generally, adults learn best from written texts (e.g., Byrne \& Curtis, 2000), and audiovisual and auditory texts are comparable (e.g., Hayes et al., 1986); however, there is little research regarding the comparison of the latter two. Study I examined whether media literacy has a positive impact on interest in politics and the political self-concept. A sample of 101 13-to 20-year-olds was drawn. The control variables were intelligence, socio-economic status (SES), openness to experiences, perspective-taking, age, and sex. Additionally, an evaluation of the WMK was conducted, which indicated good construct validity and excellent overall reliability. Media literacy was positively associated with interest in politics, political self-concept, and perspective-taking but not with openness. In hierarchical regressions and path analysis, a direct influence of media literacy and openness on interest in politics could be found. Political self-concept was solely influenced by interest in politics. Although media literacy had no direct influence on political self-concept, it influenced its precursor interest in politics and was thus expected to have distal influence. The results of the first study confirm previous findings (e.g., Vecchione \& Caprara, 2009), where political self-concept is regarded as a precursor of political participation. In conclusion, the findings of study I suggested that by stimulating political interest, media literacy could, mediated through political self-concept, foster political participation. Study II (which was conducted on the same sample as study I) was concerned with the question of whether highly media-literate adolescent and young adult participants exhibit better academic skills (mathematics; reading) and academic achievement (grades) compared to less media-literate participants. Additionally, to obtain information about potential development during adolescence, a group of 50 13-year-olds was compared with a group of 51 19-year-olds in terms of their media literacy. The control variables were intelligence, SES, sex, and age. The results showed that a significant development of media literacy took place during adolescence (∆M = .17), agreeing with Potter's (1998, 2013) development theory of media literacy. Media literacy was significantly correlated with reading skills and school grades. Regarding adults, media literacy was also significantly correlated with mathematical skills; the association was greater than that with reading skills. However, no connection with mathematical skills was found for adolescents. To control for the influence of age and intelligence, which were both associated with media literacy, hierarchical regressions and path analyses were conducted. The results revealed that media literacy had a greater impact on grades and academic abilities than intelligence. These results are in line with those obtained by Paino and Renzulli (2012). Study III investigated whether media literacy helps young adults to better learn from three kinds of media, a written, an auditory, and an audio-visual text, and which medium achieves the best learning results. Three groups of 91 young adults were compared (written, auditory, and audio-visual text) in terms of their learning outcomes. These outcomes were conceptualized as directly stated information in the text (assessed by text-based questions) and inferential learning (inference questions). A computer-based short version of the WMK was applied to assess media literacy, which should be optimized in the future. The control variables were intelligence, verbal ability, media usage, prior knowledge, and SES. In hierarchical regression, media literacy turned out to be a significant predictor of text inferences, even when other relevant variables, such as intelligence, were controlled for. Inferences foster the building of the situation model, which is believed by many authors to be true comprehension of a text (Zwaan \& Radvansky, 1998). The outcomes of study III support Ohler's (1994) assumption that media literacy fosters the creation of a more elaborated situational model. Text-based questions were only influenced by prior knowledge. As assumed by Potter (1998, 2016), the media literacy of young adults in the Western world suffices to extract relevant facts from educational learning material. Both subjects were best in the written text condition for text-based and inference question results. Audiovisual and auditory texts showed no significant differences. The written text condition did not excel in the auditory text condition for inferences. The results accord with those obtained by, for instance, Byrne and Curtis (2000). Taken together, these studies show that media literacy can influence several cognitive and political variables. It stimulates political interest, reading comprehension, school grades, and mathematical abilities in young adults, as well as drawing inferences from different kinds of texts. Additionally, media literacy develops further during adolescence.},
  subject      = {Media Literacy},
  language  = {en}
}
@phdthesis{Philipp2023,
  author    = {Philipp, Marius Balthasar},
  title     = {Quantifying the Effects of Permafrost Degradation in Arctic Coastal Environments via Satellite Earth Observation},
  doi       = {10.25972/OPUS-34563},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345634},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Permafrost degradation is observed all over the world as a consequence of climate change and the associated Arctic amplification, which has severe implications for the environment. Landslides, increased rates of surface deformation, rising likelihood of infrastructure damage, amplified coastal erosion rates, and the potential turnover of permafrost from a carbon sink to a carbon source are thereby exemplary implications linked to the thawing of frozen ground material. In this context, satellite earth observation is a potent tool for the identification and continuous monitoring of relevant processes and features on a cheap, long-term, spatially explicit, and operational basis as well as up to a circumpolar scale. A total of 325 articles published in 30 different international journals during the past two decades were investigated on the basis of studied environmental foci, remote sensing platforms, sensor combinations, applied spatio-temporal resolutions, and study locations in an extensive review on past achievements, current trends, as well as future potentials and challenges of satellite earth observation for permafrost related analyses. The development of analysed environmental subjects, utilized sensors and platforms, and the number of annually published articles over time are addressed in detail. Studies linked to atmospheric features and processes, such as the release of greenhouse gas emissions, appear to be strongly under-represented. Investigations on the spatial distribution of study locations revealed distinct study clusters across the Arctic. At the same time, large sections of the continuous permafrost domain are only poorly covered and remain to be investigated in detail. A general trend towards increasing attention in satellite earth observation of permafrost and related processes and features was observed. The overall amount of published articles hereby more than doubled since the year 2015. New sources of satellite data, such as the Sentinel satellites and the Methane Remote Sensing LiDAR Mission (Merlin), as well as novel methodological approaches, such as data fusion and deep learning, will thereby likely improve our understanding of the thermal state and distribution of permafrost, and the effects of its degradation. Furthermore, cloud-based big data processing platforms (e.g. Google Earth Engine (GEE)) will further enable sophisticated and long-term analyses on increasingly larger scales and at high spatial resolutions. In this thesis, a specific focus was put on Arctic permafrost coasts, which feature increasing vulnerability to environmental parameters, such as the thawing of frozen ground, and are therefore associated with amplified erosion rates. In particular, a novel monitoring framework for quantifying Arctic coastal erosion rates within the permafrost domain at high spatial resolution and on a circum-Arctic scale is presented within this thesis. Challenging illumination conditions and frequent cloud cover restrict the applicability of optical satellite imagery in Arctic regions. In order to overcome these limitations, Synthetic Aperture RADAR (SAR) data derived from Sentinel-1 (S1), which is largely independent from sun illumination and weather conditions, was utilized. Annual SAR composites covering the months June-September were combined with a Deep Learning (DL) framework and a Change Vector Analysis (CVA) approach to generate both a high-quality and circum-Arctic coastline product as well as a coastal change product that highlights areas of erosion and build-up. Annual composites in the form of standard deviation (sd) and median backscatter were computed and used as inputs for both the DL framework and the CVA coastal change quantification. The final DL-based coastline product covered a total of 161,600 km of Arctic coastline and featured a median accuracy of ±6.3 m to the manually digitized reference data. Annual coastal change quantification between 2017-2021 indicated erosion rates of up to 67 m per year for some areas based on 400 m coastal segments. In total, 12.24\% of the investigated coastline featured an average erosion rate of 3.8 m per year, which corresponds to 17.83 km2 of annually eroded land area. Multiple quality layers associated to both products, the generated DL-coastline and the coastal change rates, are provided on a pixel basis to further assess the accuracy and applicability of the proposed data, methods, and products. Lastly, the extracted circum-Arctic erosion rates were utilized as a basis in an experimental framework for estimating the amount of permafrost and carbon loss as a result of eroding permafrost coastlines. Information on permafrost fraction, Active Layer Thickness (ALT), soil carbon content, and surface elevation were thereby combined with the aforementioned erosion rates. While the proposed experimental framework provides a valuable outline for quantifying the volume loss of frozen ground and carbon release, extensive validation of the utilized environmental products and resulting volume loss numbers based on 200 m segments are necessary. Furthermore, data of higher spatial resolution and information of carbon content for deeper soil depths are required for more accurate estimates.},
  subject      = {Dauerfrostboden},
  language  = {en}
}
@phdthesis{Muth2023,
  author    = {Muth, Felicitas Vanessa},
  title     = {Step by step: Sense of agency for complex action-event sequences},
  doi       = {10.25972/OPUS-30756},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-307569},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {From simply ringing a bell to preparing a five-course menu, human behavior commonly causes changes in the environment. Such episodes where an agent acts, thereby causing changes in their environment constitute the sense of agency. In this thesis four series of experi-ments elucidate how the sense of agency is represented in complex action-event sequences, thereby bridging a gap between basic cognitive research and real-life practice. It builds upon extensive research on the sense of agency in unequivocal sequences consisting of single ac-tions and distinct, predominantly auditory, outcomes. Employing implicit as well as explicit measures, the scope is opened up to multi-step sequences. The experiments show that it is worthwhile devoting more research to complex action-event sequences. With a newly introduced auditory measure (Chapter II), common phenomena such as temporal binding and a decrease in agency ratings following distorted feedback were replicated in multi-step sequences. However, diverging results between traditional implicit and explicit measures call for further inspection. Multisensory integration appears to gain more weight when multiple actions have to be performed to attain a goal leading to more accurate representations of the own actions (Chapter III). Additionally, freedom of choice (Chapter III) as well as early spatial ambiguity altered the perceived timing of outcomes, while late spatial ambi-guity (Chapter IV) and the outcome's self-relevance did not (Chapter V). The data suggests that the cognitive system is capable of representing multi-step action-event sequences implicitly and explicitly. Actions and sensory events show a temporal attraction stemming from a bias in the perception of outcomes. Explicit knowledge about causing an event-sequence facilitates neither feelings of control nor taking authorship. The results corroborate current theorizing on the un-derpinnings of temporal binding and the divergence between traditional implicit and explicit measures of the sense of agency. Promising avenues for further research include structured analyses of how much inferred causality contributes to implicit and explicit measures of agency as well as finding alternative measures to capture conceptual as well as non-conceptual facets of the agency experience with one method.},
  subject      = {Psychologie},
  language  = {en}
}
@phdthesis{Meiser2023,
  author    = {Meiser, Elisabeth},
  title     = {Single-molecule dynamics at a bottleneck: a systematic study of the narrow escape problem in a disc},
  doi       = {10.25972/OPUS-31965},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-319650},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Diffusion facilitates numerous reactions within the biological context of a cell. It is remarkable how the cost-efficient random process of Brownian motion promotes fast reactions. From the narrow escape theory, it is possible to determine the mean first passage time of such processes based on their reaction space and diffusion coefficient. The narrow escape theory of Brownian particles is characterized by a confining domain with reflective boundaries and a small reaction site. In this thesis, the mean first passage time was systematically tested in a disc as a function of the escape opening size in vitro and in silico. For the in vitro experiments, a model system of patterned supported-lipid bilayers (SLB) was established. Such a model is prepared by a combined colloid metalization approach, where a gold scaffold on glass facilitates assembly of SLB patches of distinct sizes through vesicle fusion. The model setup was evaluated and found to match all necessary requirements to test the nar- row escape problem in vitro. In particular, the reflectivity of the boundaries, the unhindered, free diffusion of the tracer lipids, and the distinct area were assessed. Observed results of the mean first passage time agreed with the theory of the narrow escape problem. There was excellent agreement in both absolute values and across a range of small escape opening sizes. Additionally, I developed a straightforward method, a correction factor, to calculate the mean first passage time from incomplete experimental traces. By re-scaling the mean first passage time to the fraction of particles that escaped, I was able to overcome the lifetime limitations of fluorescent probes. Previously inaccessible measurements of the mean first passage time relying on fluorescent probes will be made possible through this approach. The in vitro experiments were complemented with various in silico experiments. The latter were based on random walk simulations in discs, mimicking the in vitro situation with its uncertainties. The lifetime of single particles was either set sufficiently long to allow all particles to escape, or was adjusted to meet the lifetime limitations observed in the in vitro experiments. A comparison of the mean first passage time from lifetime-unlimited particles to the corrected, lifetime-limited particles did support the use of the correction factor. In agreement with the narrow escape theory, it was experimentally found that the mean first passage time is independent of the start point of the particle within the domain. This is when the particle adheres to a minimum distance to the escape site. In general, the presented random walk simulations do accurately represent the in vitro experiments in this study. The required hardware for the establishment of an astigmatism-based 3D system was installed in the existing microscope. The first attempts to analyze the obtained 3D imaging data gave insight into the potential of the method to investigate molecule dynamics in living trypanosome cells. The full functionality will be realized with the ongoing improvement of image analysis outside of this thesis.},
  subject      = {Freies Molek{\"u}l},
  language  = {en}
}
@phdthesis{Majumder2023,
  author    = {Majumder, Snigdha},
  title     = {Selective inhibition of NFAT in mouse and human T cells by CRISPR/Cas9 to ameliorate acute Graft-versus-Host Disease while preserving Graft-versus-Leukemia effect},
  doi       = {10.25972/OPUS-29325},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-293256},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Allogenic hematopoietic stem cell transplantation (allo-HCT) is a curative therapy for the treatment of malignant and non-malignant bone marrow diseases. The major complication of this treatment is a highly inflammatory reaction known as Graft-versus-Host Disease (GvHD). Cyclosporin A (CsA) and tacrolimus are used to treat GvHD which limits inflammation but also interferes with the anticipated Graft-versus-Leukemia (GvL) effect. These drugs repress conventional T cells (Tcon) along with regulatory T cells (Treg), which are important for both limiting GvHD and supporting GvL. Both of these drugs inhibit calcineurin (CN), which dephosphorylates and activates the nuclear factor of activated T-cells (NFAT) family of transcription factors. Here, we make use of our Cd4cre.Cas9+ mice and developed a highly efficient non-viral CRISPR/Cas9 gene editing method by gRNA-only nucleofection. Utilizing this technique, we demonstrated that unstimulated mouse T cells upon NFATc1 or NFATc2 ablation ameliorated GvHD in a major mismatch mouse model. However, in vitro pre-stimulated mouse T cells could not achieve long-term protection from GvHD upon NFAT single-deficiency. This highlights the necessity of gene editing and transferring unstimulated human T cells during allo-HCT. Indeed, we established a highly efficient ribonucleoprotein (RNP)-mediated CRISPR/Cas9 gene editing for NFATC1 and/or NFATC2 in pre-stimulated as well as unstimulated primary human T cells. In contrast to mouse T cells, not NFATC1 but NFATC2 deficiency in human T cells predominantly affected proinflammatory cytokine production. However, either NFAT single-knockout kept cytotoxicity of human CD3+ T cells untouched against tumor cells in vitro. Furthermore, mouse and human Treg were unaffected upon the loss of a single NFAT member. Lastly, NFATC1 or NFATC2-deficient anti-CD19 CAR T cells, generated with our non-viral 'one-step nucleofection' method validated our observations in mouse and human T cells. Proinflammatory cytokine production was majorly dependent on NFATC2 expression, whereas, in vitro cytotoxicity against CD19+ tumor cells was undisturbed in the absence of either of the NFAT members. Our findings emphasize that NFAT single-deficiency in donor T cells is superior to CN-inhibitors as therapy during allo-HCT to prevent GvHD while preserving GvL in patients.},
  subject      = {CRISPR/Cas-Methode},
  language  = {en}
}
@phdthesis{Obid2023,
  author    = {Obid, Nada},
  title     = {EMG activity of masticatory muscles of patients with different bruxism grades during tasks with submaximal controlled force},
  doi       = {10.25972/OPUS-34588},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345883},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The main objective of this study was to test whether subjects with different degrees of bruxism differ regarding EMG parameters and whether CES intervention affects those parameters. The hypothesis was that CES influences EMG parameters and after its' cessation, all EMG parameters return to baseline (exposure-response relationship). For this purpose, forty subjects were examined, 16 men and 24 women, matched for age and gender and assigned randomly in the intervention (N=20) and control group (N=20). The procedure was as follows: 1-week inactive GC (N=40), 2 weeks inactive/active GC (N=20/N=20), 2 weeks inactive GC (N=40). Each interval was followed by a surface EMG recording from eight muscle parts (right and left anterior -, medial -, and posterior masseter and right and left anterior temporalis) under force-controlled feedback (BiteFork®) with three submaximal bite forces. The resulting EMG activity is expressed as RMS \% MVC and RMS at MVC. The statistics is performed with t-test, one-way rmANOVA, and Friedman rmANOVA on ranks, according to the distribution of the data. The significance level was set at p≤0.05. The results generated from the within-groups and between-groups comparison were mostly not statistically significant and could therefore not offer clinically relevant conclu-sions. However, it cannot be excluded that a higher submaximal bite force and an extended intervention interval would have rendered different outcomes. The insufficient study sample resulted in a low observed power which makes the findings prone to Type II er-ror. It can be concluded that this study did not find any substantiating differences be-tween the EMG values of participants with various bruxism activity and that CES could not influence the studied EMG parameters in the two weeks intervention time. Our hypothesis which supposes that subjects with high and low bruxism activity differ in RMS \% MVC could not be verified. However, with the gained knowledge, it is recom-mended to further elaborate a definite bruxism diagnosis by using portable EMG devices.},
  subject      = {Bruxismus},
  language  = {en}
}
@phdthesis{Hauptstein2023,
  author    = {Hauptstein, Niklas},
  title     = {Site directed molecular design and performances of Interferon-α2a and Interleukin-4 bioconjugates with PEG alternative polymers},
  doi       = {10.25972/OPUS-29691},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-296911},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Serum half-life elongation as well as the immobilization of small proteins like cytokines is still one of the key challenges for biologics. This accounts also for cytokines, which often have a molecular weight between 5 and 40 kDa and are therefore prone to elimination by renal filtration and sinusoidal lining cells. To solve this problem biologics are often conjugated to poly(ethylene glycol) (PEG), which is the gold standard for the so called PEGylation. PEG is a synthetic, non-biodegradable polymer for increasing the hydrodynamic radius of the conjugated protein to modulate their pharmacokinetic performance and prolong their therapeutic outcome. Though the benefits of PEGylation are significant, they also come with a prize, which is a loss in bioactivity due to steric hindrance and most often the usage of heterogeneous bioconjugation chemistries. While PEG is a safe excipient in most cases, an increasing number of PEG related side-effects, such as immunological responses like hypersensitivity and accelerated blood clearance upon repetitive exposure occur, which highlights the need for PEG alternative polymers, that can replace PEG in such cases. Another promising method to significantly prolong the residence time of biologics is to immobilize them at a desired location. To achieve this, the transglutaminase (TG) Factor XIIIa (FXIIIa), which is an important human enzyme during blood coagulation can be used. FXIIIa can recognize specific peptide sequences that contain a lysine as substrates and link them covalently to another peptide sequence, that contains a glutamine, forming an isopeptide bond. This mechanism can be used to link modified proteins, which have a N- or C-terminal incorporated signal peptide by mutation, to the extracellular matrix (ECM) of tissues. Additionally, both above-described methods can be combined. By artificially introducing a TG recognition sequence, it is possible to attach an azide group containing peptide site-specifically to the TG, recognition sequence. This allows the creation of a site-selective reactive site at the proteins N- or C-terminus, which can then be targeted by cyclooctyne functionalized polymers, just like amber codon functionalized proteins. This thesis has focused on the two cytokines human Interferon-α2a (IFN-α2a) and human, as well as murine Interleukin-4 (IL-4) as model proteins to investigate the above-described challenges. IFN-α2a has been chosen as a model protein because it is an approved drug since 1986 in systemic applications against some viral infections, as well as several types of cancer. Furthermore, IFN-α2 is also approved in three PEGylated forms, which have different molecular weights and use different conjugation techniques for polymer attachment. This turns it into an ideal candidate to compare new polymers against the gold standard PEG. Interleukin-4 (IL-4) has been chosen as the second model protein due to its similar size and biopotency. This allows to compare found trends from IFN-α2a with another bioconjugate platform and distinguish between IFN-α2a specific, or general trends. Furthermore, IL-4 is a promising candidate for clinical applications as it is a potent anti-inflammatory protein, which polarizes macrophages from the pro-inflammatory M1 state into the anti-inflammatory M2 state.},
  subject      = {Cytokine},
  language  = {en}
}
@phdthesis{Mahlmeister2023,
  author    = {Mahlmeister, Bernhard},
  title     = {Twisted Rylene Bisimides for Organic Solar Cells and Strong Chiroptical Response in the Near Infrared},
  doi       = {10.25972/OPUS-34610},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-346106},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The chirality of the interlocked bay-arylated perylene motif is investigated upon its material prospect and the enhancement of its chiroptical response to the NIR spectral region. A considerable molecular library of inherently chiral perylene bisimides (PBIs) was utilized as acceptors in organic solar cells to provide decent device performances and insights into the structure-property relationship of PBI materials within a polymer blend. For the first time in the family of core-twisted PBIs, the effects of enantiopurity on the device performance was thoroughly investigated. The extraordinary structural sensitivity of CD spectroscopy served as crucial analytical tool to bridge the highly challenging gap between molecular properties and device analytics by proving the excitonic chirality of a helical PBI dimer. The chirality of this perylene motif could be further enhanced on a molecular level by both the expansion and the enhanced twisting of the π-scaffold to achieve a desirable strong chiroptical NIR response introducing a new family of twisted QBI-based nanoribbons. These achievements could be substantially further developed by expanding this molecular concept to a supramolecular level. The geometrically demanding supramolecular arrangement necessary for the efficient excitonic coupling was carefully encoded into the molecular design. Accordingly, the QBIs could form the first J-type aggregate constituting a fourfold-stranded superhelix of a rylene bisimide with strong excitonic chirality. Therefore, this thesis has highlighted the mutual corroboration of experimental and theoretical data from the molecular to the supramolecular level. It has demonstrated that for rylene bisimide dyes, the excitonic contribution to the overall chiroptical response can be designed and rationalized. This can help to pave the way for new organic functional materials to be used for chiral sensing or chiral organic light-emitting devices.},
  subject      = {Molek{\"u}l},
  language  = {en}
}
@phdthesis{Fuchs2023,
  author    = {Fuchs, Manuela},
  title     = {Global discovery and functional characterization of Hfq-associated sRNA-target networks in \(C.\) \(difficile\)},
  doi       = {10.25972/OPUS-34598},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345982},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {In this work, dRNA-seq (differential RNA sequencing) and RNAtag-seq were applied to first define the global transcriptome architecture of C. difficile, followed by Hfq RIP-seq (RNA immunoprecipitation followed by RNA-seq) and RIL-seq (RNA interaction by ligation and sequencing) to characterize the Hfq-mediated sRNA interactome on a transcriptome-wide scale. These approaches resulted in the annotation of > 60 novel sRNAs. Notably, it not only revealed 50 Hfq-bound sRNAs, but also > 1000 mRNA-sRNA interactions, confirming Hfq as a global RNA matchmaker in C. difficile. Similar to its function in Gram-negative species, deletion of Hfq resulted in decreased sRNA half-lives, providing evidence that Hfq affects sRNA stability in C. difficile. Finally, several sRNAs and their function in various infection relevant conditions were characterized. The sRNA nc085 directly interacts with the two-component response regulator eutV, resulting in regulation of ethanolamine utilization, an abundant intestinal carbon and nitrogen source known to impact C. difficile pathogenicity. Meanwhile, SpoY and SpoX regulate translation of the master regulator of sporulation spo0A in vivo, thereby affecting sporulation initiation. Furthermore, SpoY and SpoX deletion significantly impacts C. difficile gut colonization and spore burden in a mouse model of C. difficile infection.},
  subject      = {Clostridium difficile},
  language  = {en}
}
@phdthesis{Fusi2023,
  author    = {Fusi, Lorenza},
  title     = {Crosstalk between the MEK5/ERK5 and PKB/FoxO pathways: underlying mechanism and its relevance for vasoprotection and tumorigenesis},
  doi       = {10.25972/OPUS-29676},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-296769},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Forkhead box O transcription factors are a family of proteins involved in cellular processes downstream of the Insulin-PI3K-PKB pathway. In response to extra- or intracellular stresses, for example starvation or oxidative stress, FoxOs are required to direct cell cycle progression and apoptosis. In endothelial cells, they induce apoptosis, and their deregulation is linked to diseases involving the insulin pathway, such as diabetes. FoxOs also exhibit a complex role in tumour transformation: here their main function is to suppress tumorigenesis. In both physiological and cancer contexts, FoxO activation leads to the transcription of some general targets, such as p27kip1 or IGFBP1. The FoxOs can also induce tissue-specific genes, as ANGPT2 and BIM in the endothelium. In endothelial cells, another pathway with a pivotal function is the MEK5/ERK5 MAPK signalling way. Its activation promotes cell survival and proliferation in stressful conditions, e.g., when blood vessels are exposed to the shear forces exerted by the blood stream. Furthermore, recent data described ERK5 as a kinase directing tumour resistance upon therapy-induced stress. Comparing their reported roles in various tumours and in the endothelium, FoxO proteins and the MEK5/ERK5 MAPK cascade appear to exert opposite functions. First non-published data confirmed the hypothesis that FoxO factors are subject to a negative modulation by the MEK5/ERK5 pathway. Hence, one goal of this PhD project was to further characterise this crosstalk at molecular level. The major mechanism of FoxO regulation is the balance among several post translational modifications, such as phosphorylation, acetylation, and ubiquitination. Most importantly, the PKB dependent phosphorylation of FoxOs negatively controls their activity, and it is critical for their subcellular localization. Therefore, the regulation of FoxO localization as mechanism of ERK5 dependent suppression was studied, but the results presented in this thesis argue against this hypothesis. However, additional experiments are required to explore the impact of ERK5 activity on FoxO post-translational modifications. FoxO activity can also be modulated by the interaction with other proteins, which in turn could explain general- and tissue-specific gene expression. Thus, another objective of this work was to investigate FoxO3-interactome in endothelial cells and the impact of MEK5/ERK5 activation on it. As published in (Fusi et al. 2022) and presented here, this analysis unveiled TRRAP as new FoxO bound protein in several cell types. Moreover, the interaction did not rely on the capacity of the FoxOs to bind their consensus DNA sequences at the promoter of target genes. Functional data demonstrated that TRRAP is required for FoxO-dependent gene transcription in endothelial and osteosarcoma cells. In addition, TRRAP expression in the endothelium is important for FoxO induced apoptosis. In summary, the interaction between FoxO factors and TRRAP revealed a new regulatory mechanism of FoxO-dependent gene transcription. It remains to be analysed whether the MEK5/ERK5 cascade may exert its suppressive effect on FoxO activity by interfering with their binding to TRRAP and whether such a mechanism may be relevant for tumorigenesis.},
  subject      = {Endothel},
  language  = {en}
}
@phdthesis{Steinfatt2023,
  author    = {Steinfatt, Tim Alexander},
  title     = {Modulation of regulatory T cells for the immunotherapy of inflammatory diseases and cancer},
  doi       = {10.25972/OPUS-19260},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-192600},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Regulatory T cells (Tregs) are the masters of immune regulation controlling inflammation and tolerance, tissue repair and homeostasis. Multiple immunological diseases result from altered Treg frequencies and Treg dysfunction. We hypothesized that augmenting Treg function and numbers would prevent inflammatory disease whereas inhibiting or depleting Tregs would improve cancer immunotherapy. In the first part of this thesis, we explored whether in vivo activation and expansion of Tregs would impair acute graft-versus-host disease (aGvHD). In this inflammatory disease, Tregs are highly pathophysiological relevant and their adoptive transfer proved beneficial on disease outcome in preclinical models and clinical studies. IL-2 has been recognized as a key cytokine for Treg function. Yet, attempts in translating Treg expansion via IL-2 have remained challenging, due to IL-2s extremely broad action on other cell types including effector T cells, NK cells, eosinophils and vascular leakage syndrome, and importantly, due to poor pharmacokinetics in vivo. We addressed the latter issue using an IL-2-IgG-fusion protein (irrIgG-IL-2) with improved serum retention and demonstrated profound Treg expansion in vivo in FoxP3-luciferase reporter mice. Further, we augmented Treg numbers and function via the selective-TNF based agonists of TNFR2 (STAR2). Subsequently, we tested a next-generation TNFR2 agonist, termed NewSTAR, which proved even more effective. TNFR2 stimulation augmented Treg numbers and function and was as good as or even superior to the IL-2 strategy. Finally, in a mouse model of aGvHD we proved the clinical relevance of Treg expansion and activation with irrIgG-IL-2, STAR2 and NewSTAR. Notably, the TNFR2 stimulating constructs were outstanding as we observed not the IL-2 prototypic effects on other cell populations and no severe side effects. In the second part of this thesis, we explored Tregs in pancreatic ductal adenocarcinoma (PDAC) and developed targeting strategies. Among several tumor entities in which Tregs impact survival, preclinical and clinical data demonstrated their negative role on PDAC. In our studies we employed the orthotopic syngeneic Panc02 model in immunocompetent mice. Based on flow cytometric analysis of the tumor microenvironment we propose TIGIT and TNFRSF members as novel therapeutic targets. Surprisingly, we found that blocking TNFR2 did not interfere with intratumoral Treg accumulation. However, we decreased the highly abundant intratumoral Tregs when we disrupted the tumor extracellular matrix. In PDAC, Treg manipulation alone did not lead to tumor regression and we propose that an additional immune boost may be necessary for efficient tumor immune surveillance and cancer clearance. This contrasts with aGvHD, in which Treg manipulation alone was sufficient to improve disease outcome. Conclusively, we demonstrated the enormous medical benefit of Treg manipulation. Our promising data obtained with our newly developed powerful tools highlight the potential to translate our findings into clinical practice to therapeutically target human Tregs in patients. With novel TNFR2 agonists (STAR2, NewSTAR) we augmented Treg numbers and function as (or even more) effectively than with IL-2, without causing adverse side effects. Importantly, exogenous in vivo Treg expansion protected mice from aGvHD. For the therapy of PDAC, we identified novel targets on Tregs, notably TIGIT and members of the TNFRSF. We demonstrated that altering the extracellular tumor matrix can efficiently disrupt the Treg abundance in tumors. These novel targeting strategies appear as attractive new treatment options and they may benefit patients suffering from inflammatory disease and cancer in the future.},
  language  = {en}
}
@phdthesis{Reuter2023,
  author    = {Reuter, Christian Steffen},
  title     = {Development of a tissue-engineered primary human skin infection model to study the pathogenesis of tsetse fly-transmitted African trypanosomes in mammalian skin},
  doi       = {10.25972/OPUS-25114},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251147},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Many arthropods such as mosquitoes, ticks, bugs, and flies are vectors for the transmission of pathogenic parasites, bacteria, and viruses. Among these, the unicellular parasite Trypanosoma brucei (T. brucei) causes human and animal African trypanosomiases and is transmitted to the vertebrate host by the tsetse fly. In the fly, the parasite goes through a complex developmental cycle in the alimentary tract and salivary glands ending with the cellular differentiation into the metacyclic life cycle stage. An infection in the mammalian host begins when the fly takes a bloodmeal, thereby depositing the metacyclic form into the dermal skin layer. Within the dermis, the cell cycle-arrested metacyclic forms are activated, re-enter the cell cycle, and differentiate into proliferative trypanosomes, prior to dissemination throughout the host. Although T. brucei has been studied for decades, very little is known about the early events in the skin prior to systemic dissemination. The precise timing and the mechanisms controlling differentiation of the parasite in the skin continue to be elusive, as does the characterization of the proliferative skin-residing trypanosomes. Understanding the first steps of an infection is crucial for developing novel strategies to prevent disease establishment and its progression. A major shortcoming in the study of human African trypanosomiasis is the lack of suitable infection models that authentically mimic disease progression. In addition, the production of infectious metacyclic parasites requires tsetse flies, which are challenging to keep. Thus, although animal models - typically murine - have produced many insights into the pathogenicity of trypanosomes in the mammalian host, they were usually infected by needle injection into the peritoneal cavity or tail vein, bypassing the skin as the first entry point. Furthermore, animal models are not always predictive for the infection outcome in human patients. In addition, the relatively small number of metacyclic parasites deposited by the tsetse flies makes them difficult to trace, isolate, and study in animal hosts. The focus of this thesis was to develop and validate a reconstructed human skin equivalent as an infection model to study the development of naturally-transmitted metacyclic parasites of T. brucei in mammalian skin. The first part of this work describes the development and characterization of a primary human skin equivalent with improved mechanical properties. To achieve this, a computer-assisted compression system was designed and established. This system allowed the improvement of the mechanical stability of twelve collagen-based dermal equivalents in parallel through plastic compression, as evaluated by rheology. The improved dermal equivalents provided the basis for the generation of the skin equivalents and reduced their contraction and weight loss during tissue formation, achieving a high degree of standardization and reproducibility. The skin equivalents were characterized using immunohistochemical and histological techniques and recapitulated key anatomical, cellular, and functional aspects of native human skin. Furthermore, their cellular heterogeneity was examined using single-cell RNA sequencing - an approach which led to the identification of a remarkable repertoire of extracellular matrix-associated genes expressed by different cell subpopulations in the artificial skin. In addition, experimental conditions were established to allow tsetse flies to naturally infect the skin equivalents with trypanosomes. In the second part of the project, the development of the trypanosomes in the artificial skin was investigated in detail. This included the establishment of methods to successfully isolate skin-dwelling trypanosomes to determine their protein synthesis rate, cell cycle and metabolic status, morphology, and transcriptome. Microscopy techniques to study trypanosome motility and migration in the skin were also optimized. Upon deposition in the artificial skin by feeding tsetse, the metacyclic parasites were rapidly activated and established a proliferative population within one day. This process was accompanied by: (I) reactivation of protein synthesis; (II) re-entry into the cell cycle; (III) change in morphology; (IV) increased motility. Furthermore, these observations were linked to potentially underlying developmental mechanisms by applying single-cell parasite RNA sequencing at five different timepoints post-infection. After the initial proliferative phase, the tsetse-transmitted trypanosomes appeared to enter a reversible quiescence program in the skin. These quiescent skin-residing trypanosomes were characterized by very slow replication, a strongly reduced metabolism, and a transcriptome markedly different from that of the deposited metacyclic forms and the early proliferative trypanosomes. By mimicking the migration from the skin to the bloodstream, the quiescent phenotype could be reversed and the parasites returned to an active proliferating state. Given that previous work has identified the skin as an anatomical reservoir for T. brucei during disease, it is reasonable to assume that the quiescence program is an authentic facet of the parasite's behavior in an infected host. In summary, this work demonstrates that primary human skin equivalents offer a new and promising way to study vector-borne parasites under close-to-natural conditions as an alternative to animal experimentation. By choosing the natural transmission route - the bite of an infected tsetse fly - the early events of trypanosome infection have been detailed with unprecedented resolution. In addition, the evidence here for a quiescent, skin-residing trypanosome population may explain the persistence of T. brucei in the skin of aparasitemic and asymptomatic individuals. This could play an important role in maintaining an infection over long time periods.},
  subject      = {Trypanosoma brucei},
  language  = {en}
}
@phdthesis{Gotthard2023,
  author    = {Gotthard, Hannes},
  title     = {Targeting Colorectal Cancer Stem Cells with Hemibodies},
  doi       = {10.25972/OPUS-30309},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-303090},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The cancer stem cell hypothesis is a cancer development model which elicited great interest in the last decades stating that cancer heterogeneity arises from a stem cell through asymmetrical division. The Cancer Stem Cell subset is described as the only population to be tumorigenic and having the potential to renew. Conventional therapy often fails to eradicate CSC resulting in tumor relapse. Consequently, it is of great inter-est to eliminate this subset of cells to provide the best patient outcome. In the last years several approaches to target CSC were developed, one of them being immunotherapeu-tic targeting with antibodies. Since markers associated with CSC are also expressed on normal stem cells or healthy adjacent tissue in colorectal cancer, dual targeting strate-gies are preferred over targeting only a single antigen. Subsequently, the idea of dual targeting two CSC markers in parallel by a newly developed split T cell-engaging anti-body format termed as Hemibodies emerged. In a preliminary single cell RNA sequenc-ing analysis of colorectal cancer cells CD133, CD24, CD166 and CEA were identified as suitable targets for the combinatorial targeting strategy. Therefore, this study focused on trispecific and trivalent Hemibodies comprising a split binding moiety against CD3 and a binding moiety against either CD133, CD24, CD166 or CEA to overcome the occurrence of resistance and to efficiently eradicate all tumor cells including the CSC compartment. The study showed that the Hemibody combinations CD133xCD24, CD133xCD166 and CD133xCEA are able to eliminate double positive CHO cells with high efficacy while having a high specificity indicated by no killing of single antigen positive cells. A thera-peutic window ranging between one to two log levels could be achieved for all combina-tions mentioned above. The combinations CD133xCD24 and CD133xCD166 further-more proved its efficacy and specificity on established colorectal cancer cell lines. Be-sides the evaluation of specificity and efficacy the already introduced 1st generation of Hemibodies could be improved into a 2nd generation Hemibody format with increased half-life, stability and production yield. In future experiments the applicability of above-mentioned Hemibodies will be proven on patient-derived micro tumors to also include variables like tumor microenvironment and infiltration.},
  subject      = {Monoklonaler bispezifischer Antik{\"o}rper},
  language  = {en}
}
@phdthesis{Schlauersbach2023,
  author    = {Schlauersbach, Jonas},
  title     = {The bile-drug-excipient interplay},
  doi       = {10.25972/OPUS-29653},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-296537},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The bile system in vertebrates is an evolutionary conserved endogenous solubilization system for hydrophobic fats and poorly water-soluble vitamins. Bile pours out from the gallbladder through the common bile duct into the duodenum triggered by cholecystokinin. Cholecystokinin is released from enteroendocrine cells after food intake. The small intestine is also the absorption site of many orally administered drugs. Most emerging drug candidates belong to the class of poorly water-soluble drugs (PWSDs). Like hydrophobic vitamins, these PWSDs might as well be solubilized by bile. Therefore, this natural system is of high interest for drug formulation strategies. Simulated intestinal fluids containing bile salts (e.g., taurocholate TC) and phospholipids (e.g., lecithin L) have been widely applied over the last decade to approximate the behavior of PWSDs in the intestine. Solubilization by bile can enhance the oral absorption of PWSDs being at least in part responsible for the positive "food effect". The dissolution rate of PWSDs can be also enhanced by the presence of bile. Furthermore, some PWSDs profit from supersaturation stabilization by bile salts. Some excipients solubilizing PWSDs seemed to be promising candidates for drug formulation when investigated in vitro without bile. When tested in vivo, these excipients reduced the bioavailability of drugs. However, these observations have been hardly examined on a molecular level and general links between bile interaction in vitro and bioavailability are still missing. This thesis investigated the interplay of bile, PWSDs, and excipients on a molecular level, providing formulation scientists a blueprint for rational formulation design taking bile/PWSD/excipient/ interaction into account. The first chapter focus on an in silico 1H nuclear magnetic resonance (NMR) spectroscopy-based algorithm for bile/drug interaction prediction. Chapter II to IV report the impact of excipients on bioavailability of PWSDs interacting with bile. At last, we summarized helpful in vitro methods for drug formulation excipient choice harnessing biopharmaceutic solubilization in chapter V. Chapter I applies 1H NMR studies with bile and drugs on a large scale for quantitative structure-property relationship analysis. 141 drugs were tested in simulated intestinal media by 1H NMR. Drug aryl-proton signal shifts were correlated to in silico calculated molecular 2D descriptors. The probability of a drug interacting with bile was dependent on its polarizability and lipophilicity, whereas interaction with lipids in simulated intestinal media components was dependent on molecular symmetry, lipophilicity, hydrogen bond acceptor capability, and aromaticity. The probability of a drug to interact with bile was predictive for a positive food effect. This algorithm might help in the future to identify a bile and lipid interacting drug a priori. Chapter II investigates the impact of excipients on bile and free drug fraction. Three different interaction patterns for excipients were observed. The first pattern defined excipients that interacted with bile and irreversibly bound bile. Therefore, the free drug fraction of bile interacting drugs increased. The second pattern categorized excipients that formed new colloidal entities with bile which had a high affinity to bile interacting drugs. These colloids trapped the drug and decreased the free drug fraction. The last excipient pattern described excipients that formed supramolecular structures in coexistence with bile and had no impact on the free drug fraction. These effects were only observed for drugs interacting with bile (Perphenazine and Imatinib). Metoprolol's free drug fraction, a compound not interacting with bile, was unaffected by bile or bile/excipient interaction. We hypothesized that bile/excipient interactions may reduce the bioavailability of bile interacting drugs. Chapter III addresses the hypothesis from chapter II. A pharmacokinetic study in rats revealed that the absorption of Perphenazine was reduced by bile interacting excipients due to bile/excipient interaction. The simultaneous administration of excipient patterns I and II did not further reduce or enhance Perphenazine absorption. Conversely, the absorption of Metoprolol was not impacted by excipients. This reinforced the hypothesis, that drugs interacting with bile should not be formulated with excipients also interacting with bile. Chapter IV further elaborates which in vitro methods using simulated intestinal fluids are predictive for a drug's pharmacokinetic profile. The PWSD Naporafenib was analyzed in vitro with simulated intestinal fluids and in presence of excipients regarding solubility, supersaturation, and free drug fraction. Naporafenib showed a strong interaction with TC/L from simulated bile. Assays with TC/L, but not without identified one excipient as possibly bioavailability reducing, one as supersaturation destabilizing, and the last as bile not interacting and supersaturation stabilizing excipient. A pharmacokinetic study in beagle dogs outlined and confirmed the in vitro predictions. The Appendix summarizes in vivo predictive methods as presented in chapter I to IV and rationalizes experimental design paving the way towards a biopharmaceutic excipient screening. The first presented preliminary decision tree is transformed into a step-by-step instruction. The presented decision matrix might serve as a blueprint for processes in early phase drug formulation development. In summary, this thesis describes how a drug can be defined as bile interacting or non-interacting and gives a guide as well how to rate the impact of excipients on bile. We showed in two in vivo studies that bile/excipient interaction reduced the bioavailability of bile interacting drugs, while bile non-interacting drugs were not affected. We pointed out that the bile solubilization system must be incorporated during drug formulation design. Simulated gastrointestinal fluids offer a well-established platform studying the fate of drugs and excipients in vivo. Therefore, rational implementation of biopharmaceutic drug and excipient screening steers towards efficacy of oral PWSD formulation design.},
  subject      = {Solubilisation},
  language  = {en}
}
@phdthesis{Landwehr2023,
  author    = {Landwehr, Laura-Sophie},
  title     = {Steroid Hormones and Cancer Immunity - learning from Adrenocortical Carcinoma},
  doi       = {10.25972/OPUS-25189},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-251895},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Adrenocortical carcinoma (ACC) is a rare, but highly aggressive endocrine malignancy. Tumor-related hypercortisolism is present in 60 \% of patients and associated with worse outcome. While cancer immunotherapies have revolutionized the treatment of many cancer entities, the results of initial studies of different immune checkpoint inhibitors in ACC were heterogeneous. Up to now, five small clinical trials with a total of 121 patients have been published and demonstrated an objective response in only 17 patients. However, one of the studies, by Raj et al., reported a clinically meaningful disease control rate of 52 \% and a median overall survival of almost 25 months suggesting that a subgroup of ACC patients may benefit from immunotherapeutic approaches. Following the hypothesis that some ACCs are characterized by a glucocorticoid-induced T lymphocytes depletion, several studies were performed as part of the presented thesis. First, the immune cell infiltration in a large cohort of 146 ACC specimens was investigated. It was demonstrated for the first time, and against the common assumption, that ACCs were infiltrated not only by FoxP3+ regulatory T cells (49.3 \%), but also that a vast majority of tumor samples was infiltrated by CD4+ TH cells (74 \%) and CD8+ cytotoxic T cells (84.3 \%), albeit the immune cell number varied heterogeneously and was rather low (median: 7.7 CD3+ T cells / high power field, range: 0.1-376). Moreover, the presence of CD3+-, CD4+- and CD8+ ACC-infiltrating lymphocytes was associated with an improved recurrence-free (HR: 0.31 95 \% CI 0.11-0.82) and overall survival (HR: 0.47 96 \% CI 0.25-0.87). Particularly, patients with tumor-infiltrating CD4+ TH cells without glucocorticoid excess had a significantly longer overall survival compared to patients with T cell-depleted ACC and hypercortisolism (121 vs. 27 months, p = 0.004). Hence, the impact of glucocorticoids might to some extent be responsible for the modest immunogenicity in ACC as hypercortisolism was reversely correlated with the number of CD4+ TH cells. Accordingly, CD3+ T cells co-cultured with steroidogenic NCI-H295R ACC cells demonstrated in vitro an enhanced anti-tumoral cytotoxicity by secreting 747.96 ±225.53 pg/ml IFN-γ in a therapeutically hormone-depleted microenvironment (by incubation with metyrapone), versus only 276.02 ±117.46 pg/ml IFN-γ in a standard environment with glucocorticoid excess. Other potential biomarkers to predict response to immunotherapies are the immunomodulatory checkpoint molecules, programmed cell death 1 (PD-1) and its ligand PD-L1, since both are targets of antibodies used therapeutically in different cancer entities. In a subcohort of 129 ACCs, expressions of both molecules were heterogeneous (PD-1 17.4 \%, range 1-15; PD-L1 24.4 \%, range 1 - 90) and rather low. Interestingly, PD-1 expression significantly influenced ACC patients´ overall (HR: 0.21 95 \% CI 0.53-0.84) and progression- free survival (HR: 0.30 95 \% CI 0.13-0.72) independently of established factors, like ENSAT tumor stage, resection status, Ki67 proliferation index and glucocorticoid excess, while PD-L1 had no impact. In conclusion, this study provides several potential explanations for the heterogeneous results of the immune checkpoint therapy in advanced ACC. In addition, the establishment of PD-1 as prognostic marker can be easily applied in routine clinical care, because it is nowadays anyway part of a detailed histo-pathological work-up. Furthermore, these results provide the rationale and will pave the way towards a combination therapy using immune checkpoint inhibitors as well as glucocorticoid blockers. This will increase the likelihood of re-activating the immunological anti-tumor potential in ACC. However, this will have to be demonstrated by additional preclinical in vivo experiments and finally in clinical trials with patients.},
  subject      = {Steroidhormon},
  language  = {en}
}
@phdthesis{Weinmann2023,
  author    = {Weinmann, Joshua},
  title     = {Chemical Modifications of Quinolone Amides Against African Trypanosomiasis: Balancing Solubility, Bioactivity, and Cytotoxicity},
  doi       = {10.25972/OPUS-29659},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-296599},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The human African trypanosomiasis is a neglected tropical disease, which is caused by the protozoan Trypanosoma brucei and transmitted by the bite of the tsetse fly. An untreated infection leads to death. However, only a few drugs with significant drawbacks are currently available for treatment. In this thesis, quinolone amides with an antitrypanosomal activity were synthesized and their biological and physicochemical properties were measured. New structure-activity relationships and a promising lead structure were discovered.},
  subject      = {Trypanosomiase},
  language  = {en}
}
@phdthesis{SchliermanngebStratmann2023,
  author    = {Schliermann [geb. Stratmann], Anna Theresa},
  title     = {The Role of FGF Receptor 2 in GDF5 mediated Signal Transduction},
  doi       = {10.25972/OPUS-19288},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-192889},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Bone morphogenetic proteins (BMPs) are involved in various aspects of cell-cell communication in complex life forms. They act as morphogens, help differentiate different cell types from different progenitor cells in development, and are involved in many instances of intercellular communication, from forming a body axis to healing bone fractures, from sugar metabolism to angiogenesis. If the same protein or protein family carries out many functions, there is a demand to regulate and fine-tune their biological activities, and BMPs are highly regulated to generate cell- and context-dependent outcomes. Not all such instances can be explained yet. Growth/differentiation factor (GDF)5 (or BMP14) synergizes with BMP2 on chondrogenic ATDC5 cells, but antagonizes BMP2 on myoblastic C2C12 cells. Known regulators of BMP2/GDF5 signal transduction failed to explain this context-dependent difference, so a microarray was performed to identify new, cell-specific regulatory components. One identified candidate, the fibroblast growth factor receptor (FGFR)2, was analyzed as a potential new co-receptor to BMP ligands such as GDF5: It was shown that FGFR2 directly binds BMP2, GDF5, and other BMP ligands in vitro, and FGFR2 was able to positively influence BMP2/GDF5-mediated signaling outcome in cell-based assays. This effect was independent of FGFR2s kinase activity, and independent of the downstream mediators SMAD1/5/8, p42/p44, Akt, and p38. The elevated colocalization of BMP receptor type IA and FGFR2 in the presence of BMP2 or GDF5 suggests a signaling complex containing both receptors, akin to other known co-receptors of BMP ligands such as repulsive guidance molecules. This unexpected direct interaction between FGF receptor and BMP ligands potentially opens a new category of BMP signal transduction regulation, as FGFR2 is the second receptor tyrosine kinase to be identified as BMP co-receptor, and more may follow. The integration of cell surface interactions between members of the FGF and BMP family especially may widen the knowledge of such cellular communication mechanisms which involve both growth factor families, including morphogen gradients and osteogenesis, and may in consequence help to improve treatment options in osteochodnral diseases.},
  subject      = {Molekularbiologie},
  language  = {en}
}
@phdthesis{Alzheimer2023,
  author    = {Alzheimer, Mona},
  title     = {Development of tissue-engineered three-dimensional infection models to study pathogenesis of \(Campylobacter\) \(jejuni\)},
  doi       = {10.25972/OPUS-19344},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-193440},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Infectious diseases caused by pathogenic microorganisms are one of the largest socioeconomic burdens today. Although infectious diseases have been studied for decades, in numerous cases, the precise mechanisms involved in the multifaceted interaction between pathogen and host continue to be elusive. Thus, it still remains a challenge for researchers worldwide to develop novel strategies to investigate the molecular context of infectious diseases in order to devise preventive or at least anti-infective measures. One of the major drawbacks in trying to obtain in-depth knowledge of how bacterial pathogens elicit disease is the lack of suitable infection models to authentically mimic the disease progression in humans. Numerous studies rely on animal models to emulate the complex temporal interactions between host and pathogen occurring in humans. While they have greatly contributed to shed light on these interactions, they require high maintenance costs, are afflicted with ethical drawbacks, and are not always predictive for the infection outcome in human patients. Alternatively, in-vitro two-dimensional (2D) cell culture systems have served for decades as representatives of human host environments to study infectious diseases. These cell line-based models have been essential in uncovering virulence-determining factors of diverse pathogens as well as host defense mechanisms upon infection. However, they lack the morphological and cellular complexity of intact human tissues, limiting the insights than can be gained from studying host-pathogen interactions in these systems. The focus of this thesis was to establish and innovate intestinal human cell culture models to obtain in-vitro reconstructed three-dimensional (3D) tissue that can faithfully mimic pathogenesis-determining processes of the zoonotic bacterium Campylobacter jejuni (C. jejuni). Generally employed for reconstructive medicine, the field of tissue engineering provides excellent tools to generate organ-specific cell culture models in vitro, realistically recapitulating the distinctive architecture of human tissues. The models employed in this thesis are based on decellularized extracellular matrix (ECM) scaffolds of porcine intestinal origin. Reseeded with intestinal human cells, application of dynamic culture conditions promoted the formation of a highly polarized mucosal epithelium maintained by functional tight and adherens junctions. While most other in-vitro infection systems are limited to a flat monolayer, the tissue models developed in this thesis can display the characteristic 3D villi and crypt structure of human small intestine. First, experimental conditions were established for infection of a previously developed, statically cultivated intestinal tissue model with C. jejuni. This included successful isolation of bacterial colony forming units (CFUs), measurement of epithelial barrier function, as well as immunohistochemical and histological staining techniques. In this way, it became possible to follow the number of viable bacteria during the infection process as well as their translocation over the polarized epithelium of the tissue model. Upon infection with C. jejuni, disruption of tight and adherens junctions could be observed via confocal microscopy and permeability measurements of the epithelial barrier. Moreover, C. jejuni wildtype-specific colonization and barrier disruption became apparent in addition to niche-dependent bacterial localization within the 3D microarchitecture of the tissue model. Pathogenesis-related phenotypes of C. jejuni mutant strains in the 3D host environment deviated from those obtained with conventional in-vitro 2D monolayers but mimicked observations made in vivo. Furthermore, a genome-wide screen of a C. jejuni mutant library revealed significant differences for bacterial factors required or dispensable for interactions with unpolarized host cells or the highly prismatic epithelium provided by the intestinal tissue model. Elucidating the role of several previously uncharacterized factors specifically important for efficient colonization of a 3D human environment, promises to be an intriguing task for future research. At the frontline of the defense against invading pathogens is the protective, viscoelastic mucus layer overlying mucosal surfaces along the human gastrointestinal tract (GIT). The development of a mucus-producing 3D tissue model in this thesis was a vital step towards gaining a deeper understanding of the interdependency between bacterial pathogens and host-site specific mucins. The presence of a mucus layer conferred C. jejuni wildtype-specific protection against epithelial barrier disruption by the pathogen and prevented a high bacterial burden during the course of infection. Moreover, results obtained in this thesis provide evidence in vitro that the characteristic corkscrew morphology of C. jejuni indeed grants a distinct advantage in colonizing mucous surfaces. Overall, the results obtained within this thesis highlight the strength of the tissue models to combine crucial features of native human intestine into accessible in-vitro infection models. Translation of these systems into infection research demonstrated their ability to expose in-vivo like infection outcomes. While displaying complex organotypic architecture and highly prismatic cellular morphology, these tissue models still represent an imperfect reflection of human tissue. Future advancements towards inclusion of human primary and immune cells will strive for even more comprehensive model systems exhibiting intricate multicellular networks of in-vivo tissue. Nevertheless, the work presented in this thesis emphasizes the necessity to investigate host-pathogen interactions in infection models authentically mimicking the natural host environment, as they remain among the most vital parts in understanding and counteracting infectious diseases.},
  subject      = {Campylobacter jejuni},
  language  = {en}
}
@phdthesis{Schmidt2023,
  author    = {Schmidt, Sebastian},
  title     = {A closer look at long-established drugs: enantioselective protein binding and stability studies},
  doi       = {10.25972/OPUS-34594},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345945},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The aim of this work was to investigate older, established drugs. The extent of the protein binding of chiral ephedra alkaloids to AGP and of ketamine to albumin was determined. Since enantiomers of these drugs are individual available, the focus was on possible enantioselective binding and structural moieties involved in the binding. Previously published work suggested that ephedrine and pseudoephedrine can bind stereoselectively to proteins other than albumin in serum. For the determination of the extent of protein binding, the established ultrafiltration with subsequent chiral CE analysis was used. To determine the influence of basicity on binding, the drugs methylephedrine and norephedrine were also analyzed. Drug binding to AGP increased with increasing basicity as follows: norephedrine < methylephedrine < ephedrine < pseudoephedrine. pKaff was determined both graphically using the Klotz plot and mathematical indicating a low affinity of the ephedra alkaloids to AGP. Using STD-NMR spectroscopy experiments the aromatic protons and the C-CH3 side chain were shown to be most strongly involved in binding, which could be confirmed by molecular docking experiments in more detail. For all drugs, van der Waals-, π π , cationic interactions, hydrogen bonds, and a formation of a salt bridge were observed. The individual enantiomers showed no significant differences and thus the binding of ephedra alkaloids to AGP is not significant. In contrast to the ephedra alkaloids, the possible enantioselective binding to albumin was investigated for R and S ketamine. Again, ultrafiltration followed by CE analysis was performed. The binding of ketamine to one main binding site could be identified. A non-linear fit was used for the determination of pKaff. Using the NMR methods STD-NMR, waterLOGSY-NMR, and CPMG-NMRspectroscopy: the aromatic protons as well as the protons of the NCH3 methyl group showed the largest signal intensity changes, while the cyclohexanone protons showed the smallest changes. pKaff was also determined by the change in the chemical shift at different drug-protein ratios. These obtained values confirm the values obtained from ultrafiltration. Based on this, ketamine is classified as a low-affinity ligand to albumin. There were no significant differences between the individual enantiomers and thus the binding of ketamine to albumin is not a stereoselective process. Using statistical design of experiments an efficient chiral CE method for determining the extent of protein binding of R and S ketamine to albumin was developed and validated according to ICH Q2 (R1) guideline. The stability of ketamine was also investigated because a yellowish discoloration of an aqueous solution of ketamine developed under heat. XRPD investigations showed the same crystal structure for all batches examined. An untargeted screening using LC HRMS as well as LC UV measurements showed no degradation of ketamine or the presence of impurities in stress and non-stressed ketamine solutions, confirming the stability of ketamine under the stress conditions investigated. The lower the quality of the water used in the stress tests, the more intense the yellow discoloration occurred. The impurity or the mechanism that causes the yellow discoloration could not be identified.},
  subject      = {Proteinbindung},
  language  = {en}
}
@phdthesis{Spitzel2023,
  author    = {Spitzel, Marlene},
  title     = {The impact of inflammation, hypoxia, and vasculopathy on pain development in the α-galactosidase A mouse model of Morbus Fabry},
  doi       = {10.25972/OPUS-34579},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345794},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Fabry disease (FD), an X-linked lysosomal storage disorder, is caused by variants in the gene α-galactosidase A (GLA). As a consequence, the encoded homonymous enzyme GLA is not produced in sufficient amount or does not function properly. Subsequently, globotriaosylceradmide (Gb3), the target substrate of GLA, starts accumulating in several cell types, especially neurons and endothelial cells. FD patients suffer from multiorgan symptoms including cardiomyopathy, nephropathy, stroke, and acral burning pain. It is suggested that the impact of pathological Gb3 accumulation, inflammatory and hypoxic processes, and vasculopathy are contributing to the specific FD pain phenotype. Thus, we investigated the role of inflammation, hypoxia, and vasculopathy on molecular level in dorsal root ganglia (DRG) of the GLA knockout (KO) mouse model. Further, we investigated pain-like characteristics of GLA KO mice at baseline (BS), after capsaicin administration, and after repeated enzyme replacement therapy (ERT) administration for a period of 1.5 years. Acquired data showed disturbances in immune response markers represented by downregulated inflammation-associated genes and lower numbers of CD206+ macrophages in DRG of GLA KO mice. Hypoxic mechanisms were active in DRG of GLA KO mice reflected by increased gene expression of hypoxia- and DNA damage-associated targets, higher numbers of hypoxia-inducible factor 1α-positive (HIF1α+) and carbonic anhydrase 9-positive (CA9+) neurons in DRG of GLA KO mice, and DRG neuronal HIF1α cytosolic-nuclear translocation in GLA KO mice. Vascularization in DRG of GLA KO mice was reduced including lower numbers of blood vessel branches and reduced total blood vessel length. Pain-like behavior of the GLA KO mouse model revealed no mechanical hypersensitivity at BS but age-dependent heat hyposensitivity, which developed also age-matched wild type (WT) mice. Capsaicin administration under isoflurane anesthesia did not elicit the development of nocifensive behavior in GLA KO mice after mechanical or heat stimulation. Repeated ERT administration did not show a clear effect in GLA KO mice in terms of restored heat hyposensitivity to BS paw withdrawal latencies. In summary, we demonstrated the impact of disturbed immune response markers, active hypoxic mechanisms, and reduced vascularization on molecular FD pathophysiology.},
  subject      = {Fabry-Krankheit},
  language  = {en}
}
@phdthesis{Ruettger2023,
  author    = {R{\"u}ttger, Lennart},
  title     = {Regulatory T cells limit antiviral CD8 T cell responses through IL-2 competition},
  doi       = {10.25972/OPUS-29674},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-296747},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Regulatory T cells (Treg) are critical immune cells to ensure immune homeostasis. Treg do so by establishing tolerance to self-antigens as well as food-derived antigens. Additionally, they fine-tune immune responses to limit the damage caused by inevitable inflammation during the resolution of an ongoing infection or anti-tumor response. Despite countless efforts to gain a detailed understanding of the mechanisms Treg utilize to regulate adaptive immune responses, in vivo evidence is rather limited. We were interested in the cell-cell interactions of Treg and their spatio-temporal dynamics during a viral infection. We sought to address Interleukin-2 (IL-2) competition as a viable mechanism to control anti-viral CD8 T cell responses. We used intra-vital 2-photon imaging to analyze the interactions between Treg and activated T cells during viral infection. Additionally, we performed multiple loss- and gain-of-function experiments, addressing the IL-2 active signaling of CD8, CD4, and regulatory T cells to understand the competitive sensing of IL-2. Finally, we performed single-cell RNA sequencing to understand the cell-intrinsic differences in Treg caused by infection. We found that IL-2 competition by Treg limits the CD8 T cell response and can alter the differentiation of CD8 T cells. Furthermore, we show that Treg do not arrest in proximity to CD8 T cells for prolonged periods and therefore are unlikely to regulate CD8 T cells via contact-dependent mechanisms previously proposed. Our data support an area control model in which Treg scavenge IL-2 while actively migrating through the LN, constantly limiting access to IL-2. Establishing CD4 T cells as the major source of IL-2 during the later phases of infection, we provide direct evidence that Treg compete with CD8 T cells for CD4-derived IL-2. Finally, we show that IL-2 limitation is in correlation with CD25 expression levels and has an impact on the differentiation of CD8 T cells. Altering the differentiation of CD8 T cells to increase effector or memory functions has huge implications in clinical treatments, e.g 'checkpoint immunotherapy'. Especially in scenarios like checkpoint immunotherapy, where an efficient expansion of CD8 T cells is vital to the success of the treatment, it is invaluable to understand the spatio-temporal dynamics of Treg. Not only can the expansion phase be optimized, but also side effects can be better controlled by ensuring the adequate timing of treatments and boosting the anti-inflammatory response after the initial establishment of CD8 T cells. On top of this, the gained understanding of the regulatory mechanism of Treg can help to enhance the efficacy of autoimmune disorder treatments. Overall, this study addressed highly relevant questions in the Treg field and answered aspects of Treg regulation, refining their mode of action and the spatio-temporal dynamics during viral infection, providing evidence for IL-2 competition as a major regulatory mechanism controlling antiviral CD8 T cell responses.},
  subject      = {Regulatorischer T-Lymphozyt},
  language  = {en}
}
@phdthesis{Kowalski2023,
  author    = {Kowalski, Alexander Anton},
  title     = {Multi-orbital quantum phenomena: from magnetic impurities to lattice models with strong Hund's coupling},
  doi       = {10.25972/OPUS-34587},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-345878},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Strong correlations caused by interaction in systems of electrons can bring about unusual physical phenomena due to many-body quantum effects that cannot properly be captured by standard electronic structure methods like density functional theory. In this thesis, we apply the state-of-the-art continuous-time quantum Monte Carlo algorithm in hybridization expansion (CT-HYB) for the strongly correlated multi-orbital Anderson impurity model (AIM) to the solution of models of magnetic impurities on metallic surfaces and, via dynamical mean-field theory (DMFT), to the solution of a lattice model, the multi-orbital Hubbard model with Hund's coupling. A concise introduction to the theoretical background focuses on information directly relevant to the understanding of applied models, methods, and the interpretation of results. It starts with a discussion of the AIM with its parameters and its solution in the path integral formalism, the basis of the CT-HYB algorithm. We consider its derivation and implementation in some detail before reviewing the DMFT approach to correlated lattice models and the interpretation of the single-particle Green's function. We review two algorithmic developments for the CT-HYB algorithm that help to increase the performance of calculations especially in case of a complex structure of the interaction matrix and allow the precise calculation of self-energies and vertex functions also at intermediate and higher frequencies. Our comparative analysis of Kondo screening in the cobalt on copper impurity system points out the importance of an accurate interaction matrix for qualitatively correct Kondo temperatures and the relevance of all d-orbitals in that case. Theoretical modeling of cobalt impurities in copper "atomic wires" fails to reproduce variations and partial absence of Kondo resonances depending on the wire size. We analyze the dependence of results on parameters and consider possible reasons for the discrepancy. Different Kondo temperatures of iron adatoms adsorbed on clean or oxygen-reconstructed niobium in the normal state are qualitatively reproduced, with the adsorption distance identified as major factor and implications for the superconducting state pointed out. Moving on to lattice problems, we demonstrate the connection between Hund's coupling, shown to cause first-order character of the interaction-driven Mott transition at half-filling in the two-orbital Hubbard model, and a phase separation zone ending in a quantum critical point at finite doping. We touch on similarities in realistic models of iron-pnictide superconductors. We analyze the manifestation of the compressibility divergence at the finite-temperature critical points away from half-filling in the eigenbasis of the two-particle generalized susceptibility. A threshold for impurity susceptibility eigenvalues that indicates divergence of the DMFT lattice compressibility and distinguishes thermodynamic stability and instability of DMFT solutions is determined.},
  subject      = {Starke Kopplung},
  language  = {en}
}
@phdthesis{Brown2023,
  author    = {Brown, Helena Charlotte},
  title     = {Investigating the role of the platelet receptor C-type lectin-like receptor 2 in models of thrombosis},
  doi       = {10.25972/OPUS-29310},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-293108},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Platelets have a key physiological role in haemostasis however, inappropriate thrombus formation can lead to cardiovascular diseases such as myocardial infarction or stroke. Although, such diseases are common worldwide there are comparatively few anti-platelet drugs, and these are associated with an increased risk of bleeding. Platelets also have roles in thrombo-inflammation, immuno-thrombosis and cancer, in part via C-type lectin-like receptor 2 (CLEC-2) and its ligand podoplanin. Although CLEC-2 contributes to these diseases in mice, as well as to thrombus stability, it is unclear whether CLEC-2 has similar roles in humans, particularly as human CLEC-2 (hCLEC-2) cannot be investigated experimentally in vivo. To investigate hCLEC-2 in vivo, we generated a humanised CLEC-2 mouse (hCLEC-2KI) model, as well as a novel monoclonal antibody, HEL1, that binds to a different site than an existing antibody, AYP1. Using these antibodies, we have provided proof of principle for the use of hCLEC-2KI mice to test potential therapeutics targeting hCLEC-2, and shown for the first time that hCLEC-2 can be immunodepleted, with little effect on haemostasis. However, our results have also suggested that there are species differences in the role of CLEC-2 in arterial thrombosis. We further confirmed this using human blood where blocking CLEC-2 ligand binding had no effect on thrombosis, whereas we confirmed a minor role for mouse CLEC-2 in thrombus stability. We also investigated the effect of blocking CLEC-2 signalling using the Bruton's tyrosine kinase inhibitor PRN473 on CLEC-2 mediated immuno-thrombosis in a Salmonella typhimurium infection model. However, no effect on thrombosis was observed suggesting that CLEC-2 signalling is not involved. Overall, our results suggest that there may be differences in the role of human and mouse CLEC-2, at least in arterial thrombosis, which could limit the potential of CLEC-2 as an anti-thrombotic target. However, it appears that the interaction between CLEC-2 and podoplanin is conserved and therefore CLEC-2 could still be a therapeutic target in immuno-thrombosis, thrombo-inflammation and cancer. Furthermore, any potential human specific therapeutics could be investigated in vivo using hCLEC-2KI mice.},
  subject      = {Thrombozyt},
  language  = {en}
}
@phdthesis{Rudloff2023,
  author    = {Rudloff, Jan Philipp},
  title     = {Post-Truth Epistemic Beliefs Rooted in the Dark Factor of Personality Predict Irrational Cognition and Behavior},
  doi       = {10.25972/OPUS-34478},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-344782},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Conspiracy theories and fake news are receiving wide media coverage and their proliferation has motivated academic research on the driving factors irrational cognition and behavior. This dissertation focuses on individuals' beliefs about knowledge and knowing, which are commonly referred to as epistemic beliefs. The term post-truth epistemic beliefs is proposed and defined as a strong trust in one's intuition, a low need to align opinions with evidence, and the strong conviction that truth is a matter of power. Across six online studies, a mediation model is proposed and tested. It includes the core of all dark traits, the Dark Factor of Personality (D), as an antecedent of post-truth epistemic beliefs, and irrational cognition and behavior as consequences. Manuscript \#1 comprises four studies showing that post-truth epistemic beliefs are rooted in D and predict increased endorsement of COVID-19 conspiracy theories as well as less engagement in health-protective behavior against COVID-19. Manuscript \#2 includes a US nationally representative study suggesting that post-truth epistemic beliefs and D predict a lower probability of having been vaccinated against COVID-19. Manuscript \#3 presents a repeated measures experiment indicating that the nexus of D and post-truth epistemic beliefs also predicts less discernment between fake and accurate news. These findings highlight a major insight and a serious challenge for rational communication: Some individuals deliberately disregard (scientific) evidence and rational decision-making. Against this background, the need to foster the epistemological development of students and educators is emphasized.},
  subject      = {Verschw{\"o}rungstheorie},
  language  = {en}
}
@phdthesis{Li2023,
  author    = {Li, Kunkun},
  title     = {Dissecting the interconnection of Ca\(^{2+}\) and pH signaling in plants with a novel biosensor for dual imaging},
  doi       = {10.25972/OPUS-24973},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-249736},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Calcium ion (Ca2+) and protons (H+) are both regarded as second messengers, participating in plant growth and stress mechanisms. However, H+ signals in plant physiology are less well investigated compared to Ca2+ signals. If interconnections between these two second messengers exist remains to be uncovered because appropriate imaging tools to monitor Ca2+ and H+ simultaneously in the same cell as well as accurate bioinformatics analysis remain to be developed. To overcome this problem and unravel the role and possible interconnection of Ca2+ and H+ in plants, a new biosensor named CapHensor was developed and optimized to visualize intracellular Ca2+ and H+ changes simultaneously and ratiometrically in the same cell. The CapHensor consisted of an optimized green fluorescent pH sensor (PRpHluorin) and an established red fluorescent Ca2+ sensor (R-GECO1) that were combined in one construct via a P2A sequence. A P2A self-cleavage site between the two sensors allowed to express equal amounts but spatially separated sensors, which enabled artifact-free and ratiometric imaging of cellular Ca2+ and pH side-by-side. The function of the CapHensor was verified in pollen tubes, since they possess standing Ca2+ and pH gradients. We found better imaging quality and the signal-to-noise ratio to be enhanced in live-cell imaging when two R-GECO1 proteins were fused in tandem within the CapHensor construct. To guarantee exclusive subcellular localization and avoid mixed signals from different compartments, Nuclear Export Sequence (NES) and Nuclear Localization Sequence (NLS) were used to target PRpHluorin and R-GECO1 to distinct compartments. After optimization and verification its function, CapHensor was successfully expressed in different cell types to investigate the role of Ca2+ and H+ signals to control polar growth of pollen tube, stomatal movement or leaf defense signaling. Results obtained in the past indicated both Ca2+ gradients and pH gradients in pollen tubes play roles in polar growth. However, the role and temporal relationship between the growth process and changes in Ca2+ and pH have not been conclusively resolved. Using CapHensor, I found cytosolic acidification at the tip could promote and alkalization to suppress growth velocity in N. tabacum pollen tubes, indicating that cytosolic H+ concentrations ([H+]cyt) play an important role in regulation pollen tubes growth despite the accompanied changes in cytosolic Ca2+ concentrations ([Ca2+]cyt). Moreover, growth correlated much better with the tip [H+]cyt regime than with the course of the tip [Ca2+]cyt regime. However, surprisingly, tip-focused [Ca2+]cyt andII [H+]cyt oscillations both lagged behind growth oscillations approximately 33 s and 18 s, respectively, asking for a re-evaluation of the role that tip [Ca2+]cyt may play in pollen tube growth. Live-cell CapHensor imaging combined with electrophysiology uncovered that oscillatory membrane depolarization correlated better with tip [H+]cyt oscillations than with tip [Ca2+]cyt oscillations, indicative for a prominent role of [H+]cyt to also control electrogenic membrane transport. Using CapHensor, reading out cellular movement at the same time enabled to provide a precise temporal and spatial resolution of ion signaling events, pointing out a prominent role of [H+]cyt in pollen tube tip growth. For leaf cells, a special CapHensor construct design had to be developed, containing additional NES localization sequences to avoid overlapping of fluorescense signals from the nucleus and the cytosol. Once this was achieved, the role of Ca2+ and pH changes in guard cells, another typical single-cell system was investigated. Cytosolic pH changes have been described in stomatal movement, but the physiological role of pH and the interaction with changing Ca2+ signals were still unexplored. Combining CapHensor with the here developed technique to monitor stomatal movement in parallel, the role of Ca2+ and H+ in stomatal movement was studied in detail and novel aspects were identified. The phytohormone ABA and the bacterial elicitor flagellin (flg22) are typical abiotic and biotic stresses, respectively, to trigger stomatal closure. What kind of Ca2+ and H+ signals by ABA and flg22 are set-off in guard cells and what their temporal relationship and role for stomatal movement is were unknown. Similar [Ca2+]cyt increases were observed upon ABA and flg22 triggered stomatal closure, but [H+]cyt dynamics differed fundamentally. ABA triggered pronounced cytosolic alkalization preceded the [Ca2+]cyt responses significantly by 57 s while stomata started to close ca. 205 s after phytohormone application. With flg22, stomatal closure was accompanied only with a mild cytosolic alkalization but the [Ca2+]cyt response was much more pronounced compared to the ABA effects. Where the cytosolic alkalization originates from was unclear but the vacuole was speculated to contribute in the past. In this thesis, vacuolar pH changes were visualized by the dye BCECF over time, basically displaying exactly the opposite course of the concentration shift in the vacuole than observed in the cytosol. This is indicative for the vacuolar pH dynamics to be coupled strongly to the cytosolic pH changes. In stomatal closure signalling, reactive oxygen species (ROS) were proposed to play a major role, however, only very high concentration of H2O2 (> 200 µM), which resulted in the loss of membrane integrity, induced stomatal closure. Unexpectedly, physiological concentrations of ROS led to cytosolic acidificationIII which was associated with stomatal opening, but not stomatal closure. To study the role of [H+]cyt to steer stomatal movement in detail, extracellular and intracellular pH variations were evoked in N. tabacum guard cells and their behaviour was followed. The results demonstrated cytosolic acidification stimulated stomatal opening while cytosolic alkalization triggered stomatal closure accompanied by [Ca2+]cyt elevations. This demonstrated pH regulation to be an important aspect in stomatal movement and to feed-back on the Ca2+-dynamics. It was remarkable that cytosolic alkalization but not [Ca2+]cyt increase seemed to play a crucial role in stomatal closure, because more pronounced cytosolic alkalization, evoked stronger stomatal closure despite similar [Ca2+]cyt increases. Increases in [Ca2+]cyt, which are discussed as an early stomatal closure signal in the past, could not trigger stomatal closure alone in my experiments, even when extremely strong [Ca2+]cyt signals were triggered. Regarding the interaction between the two second messengers, [Ca2+]cyt and [H+]cyt were negatively correlated most of the times, which was different from pollen tubes showing positive correlation of [Ca2+]cyt and [H+]cyt regimes. [Ca2+]cyt elevations were always associated with a cytosolic alkalization and this relationship could be blocked by the presence of vanadate, a plasma membrane H+-pump blocker, indicating plasma membrane H+-ATPases to contribute to the negative correlation of [Ca2+]cyt and [H+]cyt. To compare with guard cells, cytosolic and nuclear versions of CapHensor were expressed in N. benthamiana mesophyll cells, a multicellular system I investigated. Mesophyll cell responses to the same stimuli as tested in guard cells demonstrated that ABA and H2O2 did not induce any [Ca2+]cyt and [H+]cyt changes while flg22 induced an increase in [Ca2+]cyt and [H+]cyt, which is different from the response in guard cells. I could thus unequivocally demonstrate that guard cells and mesophyll cells do respond differently with [Ca2+]cyt and [H+]cyt changes to the same stimuli, a concept that has been proposed before, but never demonstrated in such detail for plants. Spontaneous Ca2+ oscillations have been observed for a long time in guard cells, but the function or cause is still poorly understood. Two populations of oscillatory guard cells were identified according to their [Ca2+]cyt and [H+]cyt phase relationship in my study. In approximately half of the oscillatory cells, [H+]cyt oscillations preceded [Ca2+]cyt oscillations whereas [Ca2+]cyt was the leading signal in the other half of the guard cells population. Strikingly, natural [H+]cyt oscillations were dampened by ABA but not by flg22. This effect could be well explained by dampening of vacuolar H+ oscillations in the presence of ABA, but not through flg22. Vacuolar pH contributes to spontaneous [H+]cyt oscillations and ABA but not flg22 can block the interdependence of naturalIV [Ca2+]cyt and [H+]cyt signals. To study the role of [Ca2+]cyt oscillations in stomatal movement, solutions containing high and low KCl concentrations were applied aiming to trigger [Ca2+]cyt oscillations. The triggering of [Ca2+]cyt oscillations by this method was established two decades ago leading to the dogma that [Ca2+]cyt increases are the crucial signal for stomatal closure. However, I found stomatal movement by this method was mainly due to osmotic effects rather than [Ca2+]cyt increases. Fortunately, through this methodology, I found a strong correlation between cytosolic pH and the transport of potassium across the plasma membrane and vacuole existed. The plasma membrane H+-ATPases and H+-coupled K+ transporters were identified as the cause of [H+]cyt changes, both very important aspects in stomata physiology that were not visualized experimentally before. Na+ transport is also important for stomatal regulation and leaves generally since salt can be transported from the root to the shoot. Unlike well-described Ca2+- dependent mechanisms in roots, how leaves process salt stress is not at all understood. I applied salt on protoplasts from leaves, mesophyll cells and guard cells and combined live-cell imaging with Vm recordings to understand the transport and signaling for leaf cells to cope with salt stress. In both, mesophyll and guard cells, NaCl did not trigger Ca2+-signals as described for roots but rather triggered Ca2+ peaks when washing salt out. However, membrane depolarization and pronounced alkalinization were very reliably triggered by NaCl, which could presumably act as a signal for detoxification of high salt concentrations. In line with this, I found the vacuolar cation/H+ antiporter NHX1 to play a role in sodium transport, [H+]cyt homeostasis and the control of membrane potential. Overexpression of AtNHX1 enabled to diminish [H+]cyt changes and resulted in a smaller depolarization responses druing NaCl stress. My results thus demonstrated in contrast to roots, leaf cells do not use Ca2+-dependent signalling cascades to deal with salt stress. I could show Na+ and K+ induced [H+]cyt and Vm responses and Cl- transport to only have a minor impact. Summing all my results up briefly, I uncovered pH signals to play important roles to control pollen tube growth, stomatal movement and leaf detoxification upon salt. My results strongly suggested pH changes might be a more important signal than previously thought to steer diverse processes in plants. Using CapHensor in combination with electrophysiology and bioinformatics tools, I discovered distinct interconnections between [Ca2+]cyt and [H+]cyt in different cell types and distinct [Ca2+]cyt and [H+]cyt signals are initiated through diverse stimuli and environmental cues. The CapHensor will be very useful in the future to further investigate the coordinated role of Ca2+ and pH changes in controlling plant physiology.},
  subject      = {Pflanzen},
  language  = {en}
}
@phdthesis{Baumgaertner2023,
  author    = {Baumg{\"a}rtner, Kiana Jasmin},
  title     = {Spectroscopic Investigation of the Transient Interplay at Hybrid Molecule-Substrate Interfaces after Photoexcitation: Ultrafast Electronic and Atomic Rearrangements},
  doi       = {10.25972/OPUS-33053},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-330531},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {This thesis is aimed at establishing modalities of time-resolved photoelectron spectroscopy (tr-PES) conducted at a free-electron laser (FEL) source and at a high harmonic generation (HHG) source for imaging the motion of atoms, charge and energy at photoexcited hybrid organic/inorganic interfaces. Transfer of charge and energy across interfaces lies at the heart of surface science and device physics and involves a complex interplay between the motion of electrons and atoms. At hybrid organic/inorganic interfaces involving planar molecules, such as pentacene and copper(II)-phthalocyanine (CuPc), atomic motions in out-of-plane direction are particularly apparent. Such hybrid interfaces are of importance to, e.g., next-generation functional devices, smart catalytic surfaces and molecular machines. In this work, two hybrid interfaces - pentacene atop Ag(110) and copper(II)-phthalocyanine (CuPc) atop titanium disulfide (1T-TiSe2) - are characterized by means of modalities of tr-PES. The experiments were conducted at a HHG source and at the FEL source FLASH at Deutsches Elektronen-Synchrotron DESY (Hamburg, Germany). Both sources provide photon pulses with temporal widths of ∼ 100 fs and thus allow for resolving the non-equilibrium dynamics at hybrid interfaces involving both electronic and atomic motion on their intrinsic time scales. While the photon energy at this HHG source is limited to the UV-range, photon energies can be tuned from the UV-range to the soft x-ray-range at FLASH. With this increased energy range, not only macroscopic electronic information can be accessed from the sample's valence and conduction states, but also site-specific structural and chemical information encoded in the core-level signatures becomes accessible. Here, the combined information from the valence band and core-level dynamics is obtained by performing time- and angle-resolved photoelectron spectroscopy (tr-ARPES) in the UV-range and subsequently performing time-resolved x-ray photoelectron spectroscopy (tr-XPS) and time-resolved photoelectron diffraction (tr-XPD) in the soft x-ray regime in the same experimental setup. The sample's bandstructure in energy-momentum space and time is captured by a time-of-flight momentum microscope with femtosecond temporal and sub-{\AA}ngstr{\"o}m spatial resolutions. In the investigated systems, out-of-equilibrium dynamics are traced that are connected to the transfer of charge and energy across the hybrid interfaces. While energetic shifts and complementary population dynamics are observed for molecular and substrate states, the shapes of involved molecular orbitals change in energy-momentum space on a subpicosecond time scale. In combination with theory support, these changes are attributed to iiiatomic reorganizations at the interface and transient molecular structures are reconstructed with sub-{\AA}ngstr{\"o}m precision. Unique to the material combination of CuPc/TiSe2, a structural rearrangement on the macroscopic scale is traced simultaneously: ∼ 60 \% of the molecules undergo a concerted, unidirectional in-plane rotation. This surprising observation and its origin are detailed in this thesis and connected to a particularly efficient charge transfer across the CuPc/TiSe2 interface, resulting in a charging of ∼ 45 \% of CuPc molecules.},
  subject      = {ARPES},
  language  = {en}
}
@phdthesis{Luettig2023,
  author    = {L{\"u}ttig, Julian Konstantin},
  title     = {Coherent Higher-Order Spectroscopy: Investigating Multi-Exciton Interaction},
  doi       = {10.25972/OPUS-29318},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-293182},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The goal of this thesis was the development and application of higher-order spectroscopic techniques. In contrast to ordinary pump-probe (PP) and two-dimensional (2D) spectroscopy, higher-order coherently detected spectroscopic methods measure a polarization that has an order of nonlinearity higher than three. The key idea of the techniques in this thesis is to isolate the higher-order signals from the lower-order signals either by their excitation frequency or by their excitation intensity dependence. Due to the increased number of interactions in higher-order spectroscopy, highly excited states can be probed. For excitonic systems such as aggregates and polymers, the fifth-order signal allows one to directly measure exciton-exciton annihilation (EEA). In polymers and aggregates, the exciton transport is not connected to a change of the absorption and can therefore not be investigated with conventional third-order techniques. In contrast, EEA can be used as a probe to study exciton diffusion in these isonergetic systems. As a part of this thesis, anisotropy in fifth-order 2D spectroscopy was investigated and was used to study geometric properties in polymers. In 2D spectroscopy, the multi-quantum signals are separated from each other by their spectral position along the excitation axis. This concept can be extended systematically to higher signals. Another approach to isolate multi-quantum signals in PP spectroscopy utilizes the excitation intensity. The PP signal is measured at specific excitation intensities and linear combinations of these measurements result in different signal contributions. However, these signals do not correspond to clean nonlinear signals because the higher-order signals contaminate the lower-order multi-quantum signals. In this thesis, a correction protocol was derived that uses the isolated multiquantum signals, both from 2D spectroscopy and from PP spectroscopy, to remove the contamination of higher-order signals resulting in clean nonlinear signals. Using the correction on the third-order signal allows one to obtain annihilation-free signals at high excitation intensities, i.e., with high signal-to-noise ratio. Isolation and correction in PP and 2D spectroscopy were directly compared by measuring the clean third-order signals of squaraine oligomers at high excitation intensities. Furthermore, higher-order PP spectroscopy was used to isolate up to the 13th nonlinear order of squaraine polymers. The demonstrated spectroscopic techniques represent general procedures to isolate clean signals in terms of perturbation theory. The technique of higher-order PP spectroscopy needs only small modifications of ordinary PP setups which opens the field of higher-order spectroscopy to the broad scientific community. The technique to obtain clean nonlinear signals allows one to systematically increase the number of interacting (quasi)particles in a system and to characterize their interaction energies and dynamics.},
  subject      = {Coherent Multidimensional Spectroscopy},
  language  = {en}
}
@phdthesis{Ye2023,
  author    = {Ye, Liqing},
  title     = {RNA-RNA interactions in viral genome packaging},
  doi       = {10.25972/OPUS-29636},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-296361},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {RNA is one of the most abundant macromolecules and plays essential roles in numerous biological processes. This doctoral thesis consists of two projects focusing on RNA structure and RNA-RNA interactions in viral genome packaging. In the first project I developed a method called Functional Analysis of RNA Structure (FARS-seq) to investigate structural features regulating genome dimerization within the HIV-1 5'UTR. Genome dimerization is a conserved feature of retroviral replication and is thought to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. It also plays a role in genome integrity and evolution through recombination, and is linked to a structural switch that may regulate genome packaging and translation within cells. Despite its importance for HIV-1 replication, the RNA signals regulating genome dimerization, and the molecular mechanism leading to the selection of the genome dimer over the monomer for packaging are incompletely understood. The FARS-seq method combines RNA structural information obtained by chemical probing with single nucleotide resolution profiles of RNA function obtained by mutational interference. In this way, we found nucleotides that were critical for dimerization, especially within the well-characterized dimerization motif within stem-loop 1 (SL1). We also found stretches of nucleotides that enhanced genome dimerization upon mutation, suggesting their role in negatively regulating dimerization. A structural analysis identified distinct structural signatures within monomeric and dimeric RNA. The dimeric conformation displayed the canonical transactivation response (TAR), PolyA, primer binding site (PBS), and SL1-SL3 stem-loops, and contained a long range U5-AUG interaction. Unexpectedly, in monomeric RNA, SL1 was reconfigured into long- and short-range base-pairings with PolyA and PBS, respectively. Intriguingly, these base pairings concealed the palindromic sequence needed for dimerization and disrupted the internal loop in SL1 previously shown to contain the major packaging motif for Pr55Gag. We therefore rationally introduced mutations into PolyA and PBS, and showed how these regions regulate genome dimerization, and the binding of Pr55Gag in vitro, as well as genome packaging into virions. These findings give insights into late stages of the HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging. In the second project, I developed a proximity ligation and high-throughput sequencing-based method, RNA-RNA seq, which can measure direct (RNA-RNA) and indirect (protein-mediated) interactions. In contrast to existing methods, RNA-RNA seq is not limited by specific protein or RNA baits, nor to a particular crosslinking reagent. The genome of influenza A virus contains eight segments, which assemble into a "7+1" supramolecular complex. However, the molecular details of genome assembly are poorly understood. Our goal is to use RNA-RNA seq to identify the sites of interaction between the eight genomic RNAs of influenza, and to use this information to define the quaternary RNA architecture of the genome. We showed that RNA-RNA seq worked on model substrates, like the HIV-1 Dimerization Initiation Site (DIS) RNA and purified ribosome, as well as influenza A virus infected cells.},
  subject      = {RNS-Viren},
  language  = {en}
}
@phdthesis{Kohl2023,
  author    = {Kohl, Patrick Laurenz},
  title     = {The buzz beyond the beehive: population demography, parasite burden and limiting factors of wild-living honeybee colonies in Germany},
  doi       = {10.25972/OPUS-33032},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-330327},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The western honeybee (Apis mellifera) is widely known as the honey producer and pollinator managed by beekeepers but neglected as a wild bee species. Central European honeybee populations have been anthropogenically disturbed since about 1850 through introgression and moderate artificial selection but have never been truly domesticated due to a lack of mating control. While their decline in the wild was historically attributed to the scarcity of nesting cavities, a contemporary view considers the invasion of the parasitic mite Varroa destructor in the 1970s as the major driver. However, there are no longitudinal population data available that could substantiate either claim. Based on the insight that introduced European honeybees form viable wild populations in eastern North America and reports on the occurrence of wild-living colonies from various European countries, we systematically studied the ecology of wild-living honeybees in Germany. First, we investigated whether wild-living honeybees colonising German forests form a self-sustaining population. Second, we asked how the parasite burden of wild-living colonies relates to that of managed colonies. And third, we explored whether the winter mortality of wild-living colonies is associated with parasite burden, nest depredation, or the lack of resources on the landscape scale. Between 2017 and 2021, we monitored listed trees with black woodpecker cavities for honeybees in the managed forests of three study regions (Swabian Alb, counties Coburg and Lichtenfels, county Weilheim-Schongau). Continuity of occupation was determined using microsatellite genetic markers. Wild-living colonies predictably colonised forests in summer, when about 10\% of all cavities were occupied. The annual colony survival rate and colony lifespan (based on N=112 colonies) were 10.6\% and 0.6 years, with 90\% of colonies surviving summer (July-September), 16\% surviving winter (September-April), and 72\% surviving spring (April-July). The average maximum and minimum colony densities were 0.23 (July) and 0.02 (April) colonies per km^2. During the (re-)colonisation of forests in spring, swarms preferred cavities that had already been occupied by other honeybee colonies. We estimate the net reproductive rate of the population to be R0= 0.318, meaning that it is currently not self-sustaining but maintained by the annual immigration of swarms from managed hives. The wild-living colonies are feral in a behavioural sense. We compared the occurrence of 18 microparasites among feral colonies (N=64) and managed colonies (N=74) using qPCR. Samples were collected in four regions (the three regions mentioned above and the city of Munich) in July 2020; they consisted of 20 workers per colony captured at flight entrances. We distinguished five colony types representing differences in colony age and management histories. Besides strong regional variation, feral colonies consistently hosted fewer microparasite taxa (median: 5, range 1-8) than managed colonies (median: 6, range 4-9) and had different parasite communities. Microparasites that were notably less prevalent among feral colonies were Trypanosomatidae, Chronic bee paralysis virus, and Deformed wing viruses A and B. In the comparison of five colony types, parasite burden was lowest in newly founded feral colonies, intermediate in overwintered feral colonies and managed nucleus colonies, and highest in overwintered managed colonies and hived swarms. This suggests that the natural mode of colony reproduction by swarming, which creates pauses in brood production, and well-dispersed nests, which reduce horizontal transmission, explain the reduced parasite burden in feral compared to managed colonies. To explore the roles of three potential drivers of feral colony winter mortality, we combined colony observations gathered during the monitoring study with data on colony-level parasite burden, observations and experiments on nest depredation, and landscape analyses. There was no evidence for an effect of summertime parasite burden on subsequent winter mortality: colonies that died (N=57) did not have a higher parasite burden than colonies that survived (N=10). Camera traps (N=15) installed on cavity trees revealed that honeybee nests are visited by a range of vertebrate species throughout the winter at rates of up to 10 visits per week. Four woodpecker species, great tits, and pine martens acted as true nest depredators. The winter survival rate of colonies whose nest entrances were protected by screens of wire mesh (N=32) was 50\% higher than that of colonies with unmanipulated entrances (N=40). Analyses of land cover maps revealed that the landscapes surrounding surviving colonies (N=19) contained on average 6.4 percentage points more resource-rich cropland than landscapes surrounding dying colonies (N=94). We estimate that tens of thousands of swarms escape from apiaries each year to occupy black woodpecker cavities and other hollow spaces in Germany and that feral colonies make up about 5\% of the regional honeybee populations. They are unlikely to contribute disproportionately to the spread of bee diseases. Instead, by spatially complementing managed colonies, they contribute to the pollination of wild plants in forests. Honeybees occupying tree cavities likely have various effects on forest communities by acting as nest site competitors or prey, and by accumulating biomass in tree holes. Nest depredation (a consequence of a lack of well-protected nest sites) and food resource limitation seem to be more important than parasites in hampering feral colony survival. The outstanding question is how environmental and intrinsic factors interact in preventing population establishment. Nest boxes with movable frames could be used to better study the environmental drivers of feral colonies' mortality. Pairs of wild (self-sustaining) and managed populations known to exist outside Europe could provide answers to whether modern apiculture creates honeybee populations maladapted to life in the wild. In Europe, large continuous forests might represent evolutionary refuges for wild honeybees.},
  subject      = {Biene <Gattung>},
  language  = {en}
}
@phdthesis{Dhillon2023,
  author    = {Dhillon, Maninder Singh},
  title     = {Potential of Remote Sensing in Modeling Long-Term Crop Yields},
  doi       = {10.25972/OPUS-33052},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-330529},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Accurate crop monitoring in response to climate change at a regional or field scale plays a significant role in developing agricultural policies, improving food security, forecasting, and analysing global trade trends. Climate change is expected to significantly impact agriculture, with shifts in temperature, precipitation patterns, and extreme weather events negatively affecting crop yields, soil fertility, water availability, biodiversity, and crop growing conditions. Remote sensing (RS) can provide valuable information combined with crop growth models (CGMs) for yield assessment by monitoring crop development, detecting crop changes, and assessing the impact of climate change on crop yields. This dissertation aims to investigate the potential of RS data on modelling long-term crop yields of winter wheat (WW) and oil seed rape (OSR) for the Free State of Bavaria (70,550 km2), Germany. The first chapter of the dissertation describes the reasons favouring the importance of accurate crop yield predictions for achieving sustainability in agriculture. Chapter second explores the accuracy assessment of the synthetic RS data by fusing NDVIs of two high spatial resolution data (high pair) (Landsat (30 m, 16-days; L) and Sentinel-2 (10 m, 5-6 days; S), with four low spatial resolution data (low pair) (MOD13Q1 (250 m, 16-days), MCD43A4 (500 m, one day), MOD09GQ (250 m, one-day), and MOD09Q1 (250 m, 8-days)) using the spatial and temporal adaptive reflectance fusion model (STARFM), which fills regions' cloud or shadow gaps without losing spatial information. The chapter finds that both L-MOD13Q1 (R2 = 0.62, RMSE = 0.11) and S-MOD13Q1 (R2 = 0.68, RMSE = 0.13) are more suitable for agricultural monitoring than the other synthetic products fused. Chapter third explores the ability of the synthetic spatiotemporal datasets (obtained in chapter 2) to accurately map and monitor crop yields of WW and OSR at a regional scale. The chapter investigates and discusses the optimal spatial (10 m, 30 m, or 250 m), temporal (8 or 16-day) and CGMs (World Food Studies (WOFOST), and the semi-empiric light use efficiency approach (LUE)) for accurate crop yield estimations of both crop types. Chapter third observes that the observations of high temporal resolution (8-day) products of both S-MOD13Q1 and L-MOD13Q1 play a significant role in accurately measuring the yield of WW and OSR. The chapter investigates that the simple light use efficiency (LUE) model (R2 = 0.77 and relative RMSE (RRMSE) = 8.17\%) that required fewer input parameters to simulate crop yield is highly accurate, reliable, and more precise than the complex WOFOST model (R2 = 0.66 and RRMSE = 11.35\%) with higher input parameters. Chapter four researches the relationship of spatiotemporal fusion modelling using STRAFM on crop yield prediction for WW and OSR using the LUE model for Bavaria from 2001 to 2019. The chapter states the high positive correlation coefficient (R) = 0.81 and R = 0.77 between the yearly R2 of synthetic accuracy and modelled yield accuracy for WW and OSR from 2001 to 2019, respectively. The chapter analyses the impact of climate variables on crop yield predictions by observing an increase in R2 (0.79 (WW)/0.86 (OSR)) and a decrease in RMSE (4.51/2.57 dt/ha) when the climate effect is included in the model. The fifth chapter suggests that the coupling of the LUE model to the random forest (RF) model can further reduce the relative root mean square error (RRMSE) from -8\% (WW) and -1.6\% (OSR) and increase the R2 by 14.3\% (for both WW and OSR), compared to results just relying on LUE. The same chapter concludes that satellite-based crop biomass, solar radiation, and temperature are the most influential variables in the yield prediction of both crop types. Chapter six attempts to discuss both pros and cons of RS technology while analysing the impact of land use diversity on crop-modelled biomass of WW and OSR. The chapter finds that the modelled biomass of both crops is positively impacted by land use diversity to the radius of 450 (Shannon Diversity Index ~0.75) and 1050 m (~0.75), respectively. The chapter also discusses the future implications by stating that including some dependent factors (such as the management practices used, soil health, pest management, and pollinators) could improve the relationship of RS-modelled crop yields with biodiversity. Lastly, chapter seven discusses testing the scope of new sensors such as unmanned aerial vehicles, hyperspectral sensors, or Sentinel-1 SAR in RS for achieving accurate crop yield predictions for precision farming. In addition, the chapter highlights the significance of artificial intelligence (AI) or deep learning (DL) in obtaining higher crop yield accuracies.},
  subject      = {Ernteertrag},
  language  = {en}
}
@phdthesis{Scheitl2023,
  author    = {Scheitl, Carolin P. M.},
  title     = {In vitro selected ribozymes for RNA methylation and labeling},
  doi       = {10.25972/OPUS-33004},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-330049},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The focus of this work was the development and application of highly efficient RNA catalysts for the site-specific modification of RNA with special focus on methylation. In the course of this thesis, the first methyltransferase ribozyme (MTR1), which uses m6G as the methyl group donor was developed and further characterized. The RNA product was identified as the natural modification m1A. X-Ray crystallography was used to solve the 3D structure of the ribozyme, which directly suggested a plausible reaction meachnism. The MTR1 ribozyme was also successfully repurposed for a nucleobase transformation reaction of a purine nucleoside. This resulted in a formyl-imidazole moiety directly on the intact RNA, which was directly used for further bioconjugation reactions. Finally, additional selections and reselections led to the identification of highly active alkyltransferase ribozymes that can be used for the labeling of various RNA targets},
  subject      = {Methylierung},
  language  = {en}
}
@phdthesis{Grundke2023,
  author    = {Grundke, Andrea},
  title     = {Head and Heart: On the Acceptability of Sophisticated Robots Based on an Enhancement of the Mind Perception Dichotomy and the Uncanny Valley of Mind},
  doi       = {10.25972/OPUS-33015},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-330152},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {With the continuous development of artificial intelligence, there is an effort to let the expressed mind of robots resemble more and more human-like minds. However, just as the human-like appearance of robots can lead to feelings of aversion to such robots, recent research has shown that the apparent mind expressed by machines can also be responsible for their negative evaluations. This work strives to explore facets of aversion evoked by machines with human-like mind (uncanny valley of mind) within three empirical projects from a psychological point of view in different contexts, including the resulting consequences. In Manuscript \#1, the perspective of previous work in the research area is reversed and thus shows that humans feel eeriness in response to robots that can read human minds, a capability unknown from human-human interaction. In Manuscript \#2, it is explored whether empathy for a robot being harmed by a human is a way to alleviate the uncanny valley of mind. A result of this work worth highlighting is that aversion in this study did not arise from the manipulation of the robot's mental capabilities but from its attributed incompetence and failure. The results of Manuscript \#3 highlight that status threat is revealed if humans perform worse than machines in a work-relevant task requiring human-like mental capabilities, while higher status threat is linked with a higher willingness to interact, due to the machine's perceived usefulness. In sum, if explanatory variables and concrete scenarios are considered, people will react fairly positively to machines with human-like mental capabilities. As long as the machine's usefulness is palpable to people, but machines are not fully autonomous, people seem willing to interact with them, accepting aversion in favor of the expected benefits.},
  subject      = {Humanoider Roboter},
  language  = {en}
}
@phdthesis{Franz2023,
  author    = {Franz, Anemone},
  title     = {Determining the prevalence and morbidity of \(Schistosoma\), soil-transmitted-helminths and intestinal protozoa in orphans and street children in Mwanza city, Northern Tanzania},
  doi       = {10.25972/OPUS-32948},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-329487},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The present study investigates the infection rates of parasites, morbidity, and the living conditions of street children and orphans in Mwanza city, northern Tanzania. A high percentage of orphans and street children in Mwanza city is infected with one or more parasites. A significantly higher rate of infections with S. mansoni in street children as compared with orphans could be observed. The prevalence of S. mansoni determined by POC CCA test was 65.9\% for orphans and 94.5\% for street children. 19.2\% of the orphans tested positive for S. mansoni in Kato Katz. Of the street children, 77.1\% showed positive test results in Kato-Katz. Only 1.3\% of the orphans stated in the questionnaire that they use the lake to wash, whereas 91.1\% of the street children named the lake as at least one of their options for washing. Protozoal infections used as a marker for hygiene were at a comparable level for both groups. Microscopy showed positive results for G. intestinalis in 8.2\% and for E. histolytica/dispar in 23\% of orphans and 8.1\% for G. intestinalis, and 23.8\% for E. histolytica/dispar in street children. Through ultrasonography, we observed no signs of severe PPF and only a few mild PPF patterns. Most street children use the lake to wash and often do not have access to adequate sanitation. However, everyone in the study group indicated having access to safe drinking water. Overall, we found the general hygienic conditions for both groups to be inadequate. With the help of simple public health measures, like improve sanitation and regular mass drug administration, the overall situation would likely be considerably improved.},
  subject      = {Schistosomiasis},
  language  = {en}
}
@phdthesis{Riemens2023,
  author    = {Riemens, Renzo J. M.},
  title     = {Neuroepigenomics in Alzheimer's disease: The single cell ADds},
  isbn      = {978-94-6423-524-1},
  doi       = {10.25972/OPUS-25457},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-254574},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Die Forschung, die in dieser Arbeit zusammengestellt wird, kann in zwei Teile geteilt werden. Der erste Teil, bestehend aus vier Kapiteln, konzentriert sich auf die Rolle der epigenetischen Dysregulation in der {\"A}tiopathophysiologie der sporadischen Alzheimer-Krankheit (sAD). Neben Einblicken in die neuesten Entwicklungen in neuroepigenomischen Studien zu dieser Krankheit geht der erste Teil der Arbeit auch auf verbleibende Herausforderungen ein und gibt einen Ausblick auf m{\"o}gliche Entwicklungen auf diesem Gebiet. Der zweite Teil, der drei weitere Kapitel umfasst, konzentriert sich auf die Anwendung von auf induzierten pluripotenten Stammzellen (iPSC) basierenden Krankheitsmodellen f{\"u}r das Studium der AD, einschließlich, aber nicht beschr{\"a}nkt auf mechanistische Studien zur epigenetischen Dysregulation unter Verwendung dieser Plattform. Neben der Skizzierung der bisherigen Forschung mit iPSC-basierten Modellen f{\"u}r sAD gibt der zweite Teil der Arbeit auch Einblicke in die Gewinnung krankheitsrelevanter Nervenkulturen auf Basis der gezielten Differenzierung von iPSCs und beinhaltet dar{\"u}ber hinaus einen experimentellen Ansatz f{\"u}r den Aufbau eines solchen Modellsystems.},
  subject      = {Epigenetik},
  language  = {en}
}
@phdthesis{Gruener2023,
  author    = {Gr{\"u}ner, Julia},
  title     = {Pathogenesis of anti-paranodal autoantibodies in peripheral neuropathies},
  doi       = {10.25972/OPUS-24865},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-248655},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Autoantibodies against proteins of the node of Ranvier have been identified in a subset of patients with chronic inflammatory demyelinating polyradiculoneuropathy (CIDP). Main antigens targeted by autoantibodies are the paranodal proteins contactin 1 (CNTN1), neurofascin (NF) 155 or contactin associated protein (Caspr) as well as the nodal NF186. Several studies investigated the role of anti-paranodal autoantibodies in the pathophysiology of CIDP leading to the current knowledge that immunoglobulin G (IgG)4 deposition leads to detachment of myelin from the axon at the paranodes. However, many questions remain unsolved. Thus, autoantibodies against NF155 have been well studied and their pathogenicity has been proven in an animal model in vivo. However, in some patients, autoantibodies against all isoforms of NF are detectable. These anti-pan-NF autoantibodies occur more rarely and lead to a very severe clinical phenotype. As the pathogenesis of patient-derived autoantibodies against pan-NF has never been investigated in vivo before, we used an animal model to study the effect of acute exposure to anti-pan-NF IgG3 by intraneural injections to the rat sciatic nerve. In addition, we used anti-NF155 IgG4 from a seropositive patient. Behavioral testings as well as nerve conduction studies did not re- veal any deficits after injected neither for anti-NF155 nor for anti-pan-NF autoantibodies. This leads to the suspicion that the disease is more likely induced by a chronic process. A common symptom in patients with anti-CNTN1 associated neuropathy is sensory ataxia and therefore, an involvement of dorsal root ganglia (DRGs) is hypothesized. We show that sera from anti-CNTN1 positive patients specifically bind to DRG neurons in vitro and reduce surface expression of CNTN1. This is most probably due to internalization mediated by coexisting IgG3 although IgG4 is the predominant subclass of autoantibodies. As it is known that CNTN1 interacts with the β1 subunit of specific sodium channels we analyzed channel expression and sodium currents of DRG neurons after incubation with anti-CNTN1 positive patients' sera. We identified reduced sodium currents after long-term treatment with patients' material although surface channel expression remained stable. We therefore concluded that CNTN1 might influence channel properties indirectly through auxiliary β1 subunits. Moreover, we suggest an involvement of DRG neurons in the pathogenesis of anti-CNTN1 associated CIDP as medium-large size neurons are more affected than small neurons. However, the exact mechanism of how anti-CNTN1 autoantibodies influence sodium channels should be subject of further studies. Furthermore, preliminary results indicate that the epitope for anti-CNTN1 autoantibodies from seropositive patients might be associated with distinct clinical features. We could show that autoantibodies might be either directed against a conformational epitope as binding is prevented after deletion of the first immunoglobulin (Ig) domain of CNTN1 or against the fibronectin type III (FnIII) domains. Strikingly, both patients with FnIII do- main specificity had very high titers of anti-CNTN1 autoantibodies and a chronic disease progression, whereas patients binding to a conformational epitope or to the Ig domains are related to a relapsing-remitting or even monophasic disease course. However, these results need to be further confirmed before a clear statement can be made. In conclusion, the present study contributes to elucidate the pathogenesis of peripheral neuropathies associated with anti-paranodal autoantibodies. However, further studies are required including a higher number of patients as well as considering effects on structures like DRGs besides the node of Ranvier to fully understand the disease mechanisms.},
  subject      = {Autoantik{\"o}rper},
  language  = {en}
}
@phdthesis{Gerlach2023,
  author    = {Gerlach, Marius David},
  title     = {Spectroscopy of fulminic acid HCNO with VUV- and soft X-ray radiation},
  doi       = {10.25972/OPUS-32972},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-329722},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Die Fulmins{\"a}ure HCNO wurde zum ersten Mal im Jahre 1800 synthetisiert und wurde seitdem immer wieder verwendet, um neue chemische Konzepte und Theorien zu entwickeln. Durch die erstmalige Entdeckung der Fulmins{\"a}ure im Weltall im Jahr 2009 ist die Fulmins{\"a}ure heutzutage vor allem im Bereich der Astrochemie interessant. In dieser Doktorarbeit haben wir die Interaktion von Fulmins{\"a}ure mit interstellar Strahlung, genauer mit VUV- sowie weicher R{\"o}ntgenstrahlung untersucht. In Zuge der Messung mit VUV-Strahlung konnten wir das Photoelektronenspektrum von HCNO mit hoher Aufl{\"o}sung aufnehmen und den Renner-Teller verzerrten Grundzustand des Kations mit Hilfe von Wellenpaketdynamiksimulationen beschreiben. Außerdem konnten wir den Mechanismus der dissoziativen Photoionisation bis zu einer Bindungsenergie von 15.3 eV aufkl{\"a}ren. Mit weicher R{\"o}ntgenstrahlung ist es m{\"o}glich die 1s Elektronen des HCNO zu ionisieren oder anzuregen. Der erzeugte Zustand zerf{\"a}llt anschließend durch einen Auger-Meitner Prozess, bei dem ein Auger-Elektron erzeugt wird. Im Zuge der Auger-Elektronenspektroskopie haben wir die kinetische Energie dieser Elektronen gemessen und konnten mittels quantenchemischer Rechnung die beobachten Signale analysieren. Wir untersuchten außerdem, wie das durch den Auger-Meitner Prozess erzeugte Ion zerf{\"a}llt. Hier konnten wir eine Selektivit{\"a}t des Zerfalls beobachten, je nachdem welches der 1s Elektronen im ersten Schritt angeregt oder ionisiert wurde. Diese Beobachtung konnten wir durch ein einfaches thermodynamisches Argument erkl{\"a}ren. Diese Arbeit gibt also ein vollst{\"a}ndiges Bild {\"u}ber die Interaktion von HCNO mit ionisierender Strahlung. Die erhaltenen Daten k{\"o}nnten f{\"u}r die Beschreibung von HCNO im interstellaren Raum Bedeutung haben.},
  subject      = {Chemie},
  language  = {en}
}
@phdthesis{Helbig2023,
  author    = {Helbig, Tobias Thimo},
  title     = {Theory of eigenstate thermalization},
  doi       = {10.25972/OPUS-32996},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-329968},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Next to the emergence of nearly isolated quantum systems such as ultracold atoms with unprecedented experimental tunability, the conceptualization of the eigenstate thermalization hypothesis (ETH) by Deutsch and Srednicki in the late 20th century has sparked exceptional interest in the mechanism of quantum thermalization. The ETH conjectures that the expectation value of a local observable within the quantum state of an isolated, interacting quantum system converges to the thermal equilibrium value at large times caused by a loss of phase coherence, referred to as dephasing. The thermal behavior within the quantum expectation value is traced back to the level of individual eigenstates, who locally act as a thermal bath to subsystems of the full quantum system and are hence locally indistinguishable to thermal states. The ETH has important implications for the understanding of the foundations of statistical mechanics, the quantum-to-classical transition, and the nature of quantum entanglement. Irrespective of its theoretical success, a rigorous proof has remained elusive so far. \$\$ \ \$\$ An alternative approach to explain thermalization of quantum states is given by the concept of typicality. Typicality deals with typical states \(\Psi\) chosen from a subspace of Hilbert space with energy \(E\) and small fluctuations \(\delta\) around it. It assumes that the possible microstates of this subspace of Hilbert space are uniformly distributed random vectors. This is inspired by the microcanonical ensemble in classical statistical mechanics, which assumes equal weights for all accessible microstates with energy \(E\) within an energy allowance \(\delta\). It follows from the ergodic hypothesis, which states that the time spent in each part of phase space is proportional to its volume leading to large time averages being equated to ensemble averages. In typicality, the Hilbert space of quantum mechanics is hence treated as an analogue of classical phase space where statistical and thermodynamic properties can be defined. Since typicality merely shifts assumptions of statistical mechanics to the quantum realm, it does not provide a complete understanding of the emergence of thermalization on a fundamental microscopic level. \$\$ \ \$\$ To gain insights on quantum thermalization and derive it from a microscopic approach, we exclusively consider the fundamental laws of quantum mechanics. In the joint work with T. Hofmann, R. Thomale and M. Greiter, on which this thesis reports, we explore the ETH in generic local Hamiltonians in a two-dimensional spin-\(1/2\) lattice with random nearest neighbor spin-spin interactions and random on-site magnetic fields. This isolated quantum system is divided into a small subsystem weakly coupled to the remaining part, which is assumed to be large and which we refer to as bath. Eigenstates of the full quantum system as well as the action of local operators on those can then be decomposed in terms of a product basis of eigenstates of the small subsystem and the bath. Central to our analysis is the fact that the coupling between the subsystem and the bath, represented in terms of the uncoupled product eigenbasis, is given by an energy dependent random band matrix, which is obtained from both analytical and numerical considerations. \$\$ \ \$\$ Utilizing the methods of Dyson-Brownian random matrix theory for random band matrices, we analytically show that the overlaps of eigenstates of the full quantum system with the uncoupled product eigenbasis are described by Cauchy-Lorentz distributions close to their respective peaks. The result is supported by an extensive numerical study using exact diagonalization, where the numerical parameters for the overlap curve agree with the theoretical calculation. The information on the decomposition of the eigenstates of the full quantum system enables us to derive the reduced density matrix within the small subsystem given the pure density matrix of a single eigenstate. We show that in the large bath limit the reduced density matrix converges to a thermal density matrix with canonical Boltzmann probabilities determined by renormalized energies of the small subsystem which are shifted from their bare values due the influence of the coupling to the bath. The behavior of the reduced density matrix is confirmed through a finite size scaling analysis of the numerical data. Within our calculation, we make use of the pivotal result, that the density of states of a local random Hamiltonian is given by a Gaussian distribution under very general circumstances. As a consequence of our analysis, the quantum expectation value of any local observable in the subsystem agrees with its thermal expectation value, which proves the validity of the ETH in the equilibrium phase for the considered class of random local Hamiltonians and elevates it from hypothesis to theory. \$\$ \ \$\$ Our analysis of quantum thermalization solely relies on the application of quantum mechanics to large systems, locality and the absence of integrability. With the self-averaging property of large random matrices, random matrix theory does not entail a statistical assumption, but is rather applied as a mathematical tool to extract information about the behavior of large quantum systems. The canonical distribution of statistical mechanics is derived without resorting to statistical assumptions such as the concepts of ergodicity or maximal entropy, nor assuming any characteristics of quantum states such as in typicality. In future research, with this microscopic approach it may become possible to exactly pinpoint the origin of failure of quantum thermalization, e.g. in systems that exhibit many body localization or many body quantum scars. The theory further enables the systematic investigation of equilibration, i.e. to study the time scales on which thermalization takes place.},
  subject      = {Thermalisierung},
  language  = {en}
}
@phdthesis{Marquardt2023,
  author    = {Marquardt, Andr{\´e}},
  title     = {Machine-Learning-Based Identification of Tumor Entities, Tumor Subgroups, and Therapy Options},
  doi       = {10.25972/OPUS-32954},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-329548},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Molecular genetic analyses, such as mutation analyses, are becoming increasingly important in the tumor field, especially in the context of therapy stratification. The identification of the underlying tumor entity is crucial, but can sometimes be difficult, for example in the case of metastases or the so-called Cancer of Unknown Primary (CUP) syndrome. In recent years, methylome and transcriptome utilizing machine learning (ML) approaches have been developed to enable fast and reliable tumor and tumor subtype identification. However, so far only methylome analysis have become widely used in routine diagnostics. The present work addresses the utility of publicly available RNA-sequencing data to determine the underlying tumor entity, possible subgroups, and potential therapy options. Identification of these by ML - in particular random forest (RF) models - was the first task. The results with test accuracies of up to 99\% provided new, previously unknown insights into the trained models and the corresponding entity prediction. Reducing the input data to the top 100 mRNA transcripts resulted in a minimal loss of prediction quality and could potentially enable application in clinical or real-world settings. By introducing the ratios of these top 100 genes to each other as a new database for RF models, a novel method was developed enabling the use of trained RF models on data from other sources. Further analysis of the transcriptomic differences of metastatic samples by visual clustering showed that there were no differences specific for the site of metastasis. Similarly, no distinct clusters were detectable when investigating primary tumors and metastases of cutaneous skin melanoma (SKCM). Subsequently, more than half of the validation datasets had a prediction accuracy of at least 80\%, with many datasets even achieving a prediction accuracy of - or close to - 100\%. To investigate the applicability of the used methods for subgroup identification, the TCGA-KIPAN dataset, consisting of the three major kidney cancer subgroups, was used. The results revealed a new, previously unknown subgroup consisting of all histopathological groups with clinically relevant characteristics, such as significantly different survival. Based on significant differences in gene expression, potential therapeutic options of the identified subgroup could be proposed. Concludingly, in exploring the potential applicability of RNA-sequencing data as a basis for therapy prediction, it was shown that this type of data is suitable to predict entities as well as subgroups with high accuracy. Clinical relevance was also demonstrated for a novel subgroup in renal cell carcinoma. The reduction of the number of genes required for entity prediction to 100 genes, enables panel sequencing and thus demonstrates potential applicability in a real-life setting.},
  subject      = {Maschinelles Lernen},
  language  = {en}
}
@phdthesis{Hugo2023,
  author    = {Hugo, Julian},
  title     = {'Signal-close-to-noise' calcium activity reflects neuronal excitability},
  doi       = {10.25972/OPUS-29260},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-292605},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Chronic pain conditions are a major reason for the utilization of the health care system. Inflammatory pain states can persist facilitated by peripheral sensitization of nociceptors. The voltage-gated sodium channel 1.9 (NaV1.9) is an important regulator of neuronal excitability and is involved in inflammation-induced pain hypersensitivity. Recently, oxidized 1-palmitoyl-2-arachidonoyl-sn-glycerol-3-phosphatidylcholine (OxPAPC) was identified as a mediator of acute inflammatory pain and persistent hyperalgesia, suggesting an involvement in proalgesic cascades and peripheral sensitization. Peripheral sensitization implies an increase in neuronal excitability. This thesis aims to characterize spontaneous calcium activity in neuronal compartments as a proxy to investigate neuronal excitability, making use of the computational tool Neural Activity Cubic (NA3). NA3 allows automated calcium activity event detection of signal-close-to-noise calcium activity and evaluation of neuronal activity states. Additionally, the influence of OxPAPC and NaV1.9 on the excitability of murine dorsal root ganglion (DRG) neurons and the effect of OxPAPC on the response of DRG neurons towards other inflammatory mediators (prostaglandin E2, histamine, and bradykinin) is investigated. Using calcium imaging, the presence of spontaneous calcium activity in murine DRG neurons was established. NA3 was used to quantify this spontaneous calcium activity, which revealed decreased activity counts in axons and somata of NaV1.9 knockout (KO) neurons compared to wildtype (WT). Incubation of WT DRG neurons with OxPAPC before calcium imaging did not show altered activity counts compared to controls. OxPAPC incubation also did not modify the response of DRG neurons treated with inflammatory mediators. However, the variance ratio computed by NA3 conclusively allowed to determine neuronal activity states. In conclusion, my findings indicate an important function of NaV1.9 in determining the neuronal excitability of DRG neurons in resting states. OxPAPC exposition does not influence neuronal excitability nor sensitizes neurons for other inflammatory mediators. This evidence reduces the primary mechanism of OxPAPC-induced hyperalgesia to acute effects. Importantly, it was possible to establish an approach for unbiased excitability quantification of DRG neurons by calcium activity event detection and calcium trace variance analysis by NA3. It was possible to show that signal-close-to-noise calcium activity reflects neuronal excitability states.},
  subject      = {Entz{\"u}ndung},
  language  = {en}
}
@phdthesis{BergmannBorges2023,
  author    = {Bergmann Borges, Alyssa},
  title     = {The endo-lysosomal system of \(Trypanosoma\) \(brucei\): insights from a protist cell model},
  doi       = {10.25972/OPUS-32924},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-329248},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Most of the studies in cell biology primarily focus on models from the opisthokont group of eukaryotes. However, opisthokonts do not encompass the full diversity of eukaryotes. Thus, it is necessary to broaden the research focus to other organisms to gain a comprehensive understanding of basic cellular processes shared across the tree of life. In this sense, Trypanosoma brucei, a unicellular eukaryote, emerges as a viable alternative. The collaborative efforts in genome sequencing and protein tagging over the past two decades have significantly expanded our knowledge on this organism and have provided valuable tools to facilitate a more detailed analysis of this parasite. Nevertheless, numerous questions still remain. The survival of T. brucei within the mammalian host is intricately linked to the endo-lysosomal system, which plays a critical role in surface glycoprotein recycling, antibody clearance, and plasma membrane homeostasis. However, the dynamics of the duplication of the endo-lysosomal system during T. brucei proliferation and its potential relationship with plasma membrane growth remain poorly understood. Thus, as the primary objective, this thesis explores the endo-lysosomal system of T. brucei in the context of the cell cycle, providing insights on cell surface growth, endosome duplication, and clathrin recruitment. In addition, the study revisits ferritin endocytosis to provide quantitative data on the involvement of TbRab proteins (TbRab5A, TbRab7, and TbRab11) and the different endosomal subpopulations (early, late, and recycling endosomes, respectively) in the transport of this fluid-phase marker. Notably, while these subpopulations function as distinct compartments, different TbRabs can be found within the same region or structure, suggesting a potential physical connection between the endosomal subpopulations. The potential physical connection of endosomes is further explored within the context of the cell cycle and, finally, the duplication and morphological plasticity of the lysosome are also investigated. Overall, these findings provide insights into the dynamics of plasma membrane growth and the coordinated duplication of the endo-lysosomal system during T. brucei proliferation. The early duplication of endosomes suggests their potential involvement in plasma membrane growth, while the late duplication of the lysosome indicates a reduced role in this process. The recruitment of clathrin and TbRab GTPases to the site of endosome formation supports the assumption that the newly formed endosomal system is active during cell division and, consequently, indicates its potential role in plasma membrane homeostasis. Furthermore, considering the vast diversity within the Trypanosoma genus, which includes ~500 described species, the macroevolution of the group was investigated using the combined information of the 18S rRNA gene sequence and structure. The sequence-structure analysis of T. brucei and other 42 trypanosome species was conducted in the context of the diversity of Trypanosomatida, the order in which trypanosomes are placed. An additional analysis focused on Trypanosoma highlighted key aspects of the group's macroevolution. To explore these aspects further, additional trypanosome species were included, and the changes in the Trypanosoma tree topology were analyzed. The sequence-structure phylogeny confirmed the independent evolutionary history of the human pathogens T. brucei and Trypanosoma cruzi, while also providing insights into the evolution of the Aquatic clade, paraphyly of groups, and species classification into subgenera.},
  subject      = {Endocytose},
  language  = {en}
}
@phdthesis{Bleier2023,
  author    = {Bleier, Michael},
  title     = {Underwater Laser Scanning - Refractive Calibration, Self-calibration and Mapping for 3D Reconstruction},
  isbn      = {978-3-945459-45-4},
  doi       = {10.25972/OPUS-32269},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-322693},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {There is great interest in affordable, precise and reliable metrology underwater: Archaeologists want to document artifacts in situ with high detail. In marine research, biologists require the tools to monitor coral growth and geologists need recordings to model sediment transport. Furthermore, for offshore construction projects, maintenance and inspection millimeter-accurate measurements of defects and offshore structures are essential. While the process of digitizing individual objects and complete sites on land is well understood and standard methods, such as Structure from Motion or terrestrial laser scanning, are regularly applied, precise underwater surveying with high resolution is still a complex and difficult task. Applying optical scanning techniques in water is challenging due to reduced visibility caused by turbidity and light absorption. However, optical underwater scanners provide significant advantages in terms of achievable resolution and accuracy compared to acoustic systems. This thesis proposes an underwater laser scanning system and the algorithms for creating dense and accurate 3D scans in water. It is based on laser triangulation and the main optical components are an underwater camera and a cross-line laser projector. The prototype is configured with a motorized yaw axis for capturing scans from a tripod. Alternatively, it is mounted to a moving platform for mobile mapping. The main focus lies on the refractive calibration of the underwater camera and laser projector, the image processing and 3D reconstruction. For highest accuracy, the refraction at the individual media interfaces must be taken into account. This is addressed by an optimization-based calibration framework using a physical-geometric camera model derived from an analytical formulation of a ray-tracing projection model. In addition to scanning underwater structures, this work presents the 3D acquisition of semi-submerged structures and the correction of refraction effects. As in-situ calibration in water is complex and time-consuming, the challenge of transferring an in-air scanner calibration to water without re-calibration is investigated, as well as self-calibration techniques for structured light. The system was successfully deployed in various configurations for both static scanning and mobile mapping. An evaluation of the calibration and 3D reconstruction using reference objects and a comparison of free-form surfaces in clear water demonstrate the high accuracy potential in the range of one millimeter to less than one centimeter, depending on the measurement distance. Mobile underwater mapping and motion compensation based on visual-inertial odometry is demonstrated using a new optical underwater scanner based on fringe projection. Continuous registration of individual scans allows the acquisition of 3D models from an underwater vehicle. RGB images captured in parallel are used to create 3D point clouds of underwater scenes in full color. 3D maps are useful to the operator during the remote control of underwater vehicles and provide the building blocks to enable offshore inspection and surveying tasks. The advancing automation of the measurement technology will allow non-experts to use it, significantly reduce acquisition time and increase accuracy, making underwater metrology more cost-effective.},
  subject      = {Selbstkalibrierung},
  language  = {en}
}
@phdthesis{Mott2023,
  author    = {Mott, Kristina},
  title     = {Regulation of platelet biogenesis in the native and myeloablated bone marrow niche},
  doi       = {10.25972/OPUS-28963},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-289630},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Megakaryocytes (MKs) are the largest cells of the hematopoietic system and the precursor cells of platelets. During proplatelet formation (PPF) bone marrow (BM) MKs extent large cytoplasmic protrusions into the lumen of sinusoidal blood vessels. Under homeostatic conditions PPF occurs exclusively in the direction of the sinusoid, while platelet generation into the marrow cavity is prevented. So far, the mechanisms regulating this process in vivo are still not completely understood, especially when PPF is deregulated during disease. This thesis investigated the mechanisms of PPF in native BM and after myeloablation by total body irradiation (TBI). First, we have identified a specialized type of BM stromal cells, so called CXCL12-abundant reticular (CAR) cells, as novel possible regulators of PPF. By using complementary high-resolution microscopy techniques, we have studied the morphogenetic events at the MK/vessel wall interface in new detail, demonstrating that PPF formation preferentially occurs at CAR cell-free sites at the endothelium. In the second part of this thesis, we analyzed the processes leading to BM remodeling in response to myeloablation by TBI. We used confocal laser scanning microscopy (CLSM) to study the kinetic of radiation-triggered vasodilation and mapped extracellular matrix (ECM) proteins after TBI. We could demonstrate that collagen type IV and laminin α5 are specifically degraded at BM sinusoids. At the radiation-injured vessel wall we observed ectopic release of platelet-like particles into the marrow cavity concomitantly to aberrant CAR cell morphology, suggesting that the balance of factors regulating PPF is disturbed after TBI. ECM proteolysis is predominantly mediated by the matrix metalloproteinase MMP9, as revealed by gelatin-zymography and by a newly established BM in situ zymography technique. In transgenic mice lacking MMP9 vascular recovery was delayed, hinting towards a role of MMP9 in vessel reconstitution after myeloablation. In a third series of experiments, we studied the irradiated BM in the context of hematopoietic stem cell transplantation (HSCT). By using mice as BM donors that ubiquitously express the fluorescent reporter protein dsRed we tracked engraftment of donor cells and especially MKs in the recipient BM. We found a distinct engraftment pattern and cluster formation for MKs, which is different from other blood cell lineages. Finally, we assessed platelet function after TBI and HSCT and were the first to demonstrate that platelets become massively hyporeactive, particularly upon stimulation of the collagen receptor GPVI. In summary, our findings shed light on the processes of PPF during health and disease which will help to develop treatments for aberrant thrombopoiesis.},
  subject      = {Knochenmark},
  language  = {en}
}
@phdthesis{Bauer2023,
  author    = {Bauer, Carsten},
  title     = {Learning Curve Effects in Hospitals as Highly Specialized Expert Organizations},
  doi       = {10.25972/OPUS-32871},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328717},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The collection at hand is concerned with learning curve effects in hospitals as highly specialized expert organizations and comprises four papers, each focusing on a different aspect of the topic. Three papers are concerned with surgeons, and one is concerned with the staff of the emergency room in a conservative treatment. The preface compactly addresses the steadily increasing health care costs and economic pressure, the hospital landscape in Germany as well as its development. Furthermore, the DRG lump-sum compensation and the characteristics of the health sector, which is strongly regulated by the state and in which ethical aspects must be omnipresent, are outlined. Besides, the benefit of knowing about learning curve effects in order to cut costs and to keep quality stable or even improve it, is addressed. The first paper of the collection investigates the learning effects in a hospital which has specialized on endoprosthetics (total hip and knee replacement). Doing so, the specialized as well as the non-specialized interventions are studied. Costs are not investigated directly, but cost indicators. The indicator of costs in the short term are operating room times. The one of medium- to long-term costs is quality. It is operationalized by complications in the post-anesthesia care unit. The study estimates regression models (OLS and logit). The results indicate that the specialization comes along with advantages due to learning effects in terms of shorter operating room times and lower complication rates in endoprosthetic interventions. For the non-specialized interventions, the results are the same. There are no possibly negative effects of specialization on non-specialized surgeries, but advantageous spillover effects. Altogether, the specialization can be regarded as reasonable, as it cuts costs of all surgeries in the short, medium, and long term. The authors are Carsten Bauer, Nele M{\"o}bs, Oliver Unger, Andrea Szczesny, and Christian Ernst. In the second paper surgeons' learning curves effects in a teamwork vs. an individual work setting are in the focus of interest. Thus, the study combines learning curve effects with teamwork in health care, an issue increasingly discussed in recent literature. The investigated interventions are tonsillectomies (surgical excision of the palatine tonsils), a standard intervention. The indicator of costs in the short and medium to long term are again operating room times and complications as a proxy for quality respectively. Complications are secondary bleedings, which usually occur a few days after surgery. The study estimates regression models (OLS and logit). The results show that operating room times decrease with increasing surgeon's experience. Surgeons who also operate in teams learn faster than the ones always operating on their own. Thus, operating room times are shorter for surgeons who also take part in team interventions. As a special feature, the data set contains the costs per case. This enables assuring that the assumed cost indicators are valid. The findings recommend team surgeries especially for resident physicians. The authors are Carsten Bauer, Oliver Unger, and Martin Holderried. The third paper is dedicated to stapes surgery, a therapy for conductive hearing loss caused by otosclerosis (overflow bone growth). It is conceptually simple, but technically difficult. Therefore, it is regarded as the optimum to study learning curve effects in surgery. The paper seeks a comprehensive investigation. Thus, operating room times are employed as short-term cost indicator and quality as the medium to long term one. To measure quality, the postoperative difference between air and bone conduction threshold as well as a combination of this difference and the absence of complications. This paper also estimates different regression models (OLS and logit). Besides investigating the effects on department level, the study also considers the individual level, this means operating room times and quality are investigated for individual surgeons. This improves the comparison of learning curves, as the surgeons worked under widely identical conditions. It becomes apparent that the operating room times initially decrease with increasing experience. The marginal effect of additional experience gets smaller until the direction of the effect changes and the operating room times increase with increasing experience, probably caused by the allocation of difficult cases to the most experienced surgeons. Regarding quality, no learning curve effects are observed. The authors are Carsten Bauer, Johannes Taeger, and Kristen Rak. The fourth paper is a systematic literature review on learning effects in the treatment of ischemic strokes. In case of stroke, every minute counts. Therefore, there is the inherent need to reduce the time from symptom onset to treatment. The article is concerned with the reduction of the time from arrival at the hospital to thrombolysis treatment, the so-called "door-to-needle time". In the literature, there are studies on learning in a broader sense caused by a quality improvement program as well as learning in a narrower sense, in which learning curve effects are evaluated. Besides, studies on the time differences between low-volume and high-volume hospitals are considered, as the differences are probably the result of learning and economies of scale. Virtually all the 165 evaluated articles report improvements regarding the time to treatment. Furthermore, the clinical results substantiate the common association of shorter times from arrival to treatment with improved clinical outcomes. The review additionally discusses the economic implications of the results. The author is Carsten Bauer. The preface brings forward that after the measurement of learning curve effects, further efforts are necessary for using them in order to increase efficiency, as the issue does not admit of easy, standardized solutions. Furthermore, the postface emphasizes the importance of multiperspectivity in research for the patient outcome, the health care system, and society.},
  subject      = {Lernkurve},
  language  = {en}
}
@phdthesis{Lan2023,
  author    = {Lan, Yangyang},
  title     = {Bamboo-branch Songs (\({zhuzhici}\)) of Shandong Province: Lyrical Records of Local Life, Traveling and Local History},
  doi       = {10.25972/OPUS-32868},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328687},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {This dissertation presents a comprehensive exploration of the bamboo branch song (zhuzhici 竹枝詞), a classical Chinese poetry genre. One of the defining features of the bamboo branch song genre is its emphasis on all aspects of local culture. As a result, these poems typically have a specific focus on a particular place. This dissertation takes the bamboo branch songs of Shandong Province as its primary subject. The dissertation is divided into two parts. The first section focuses on a cultural study of the bamboo branch song genre. By examining the genre, this dissertation concludes that the bamboo branch song is a genre of vernacular poetry in imperial China. The language has a vernacular style, and the content has a clear focus on local affairs. The subsequent section delves into the Bamboo Branch Songs of Shandong Province, with almost 2,000 poems collected from different sources. From everyday routines to customs, travel culture, and historical episodes, the poems cover a wide range of topics, offering a detailed glimpse into the various facets of the region's society. Women play a significant role in the poems about social life in Bamboo Branch Songs of Shandong Province. They were often the central figures in the ceremonies of festivals, and their behaviour was given special attention. The bamboo branch song genre has an internal character as a form of travel writing. The poems were usually written by authors who had made observations on their journeys. This dissertation delves into the travel culture of the capital Ji'nan, through the lens of bamboo branch songs, providing valuable insights into the region. Another common motif of bamboo branch songs is history. Some nostalgic poems deal with local historical sites, events, legends and personalities. This dissertation finds that these poems contain unique historical information with a microcosmic and individual perspective.},
  language  = {en}
}
@phdthesis{Hoffmann2023,
  author    = {Hoffmann, Jan Vincent},
  title     = {Small-animal SPECT with Two Stationary Detectors: Performance Evaluation and Image Quality Assessment of Multi-pinhole Collimators},
  doi       = {10.25972/OPUS-32819},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328195},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {SPECT as a representative of molecular imaging allows visualization of metabolic processes in vivo. In clinical practice, single photon emission imaging is an established modality for myocardial perfusion imaging or the diagnosis of adrenal or neuroendocrine tumors, to name a few. With technical advances in scanner design and data processing leading to improved spatial resolution and image quality, SPECT has become a serious contender in small animal preclinical imaging. With multi-pinhole collimation, submillimeter spatial resolutions are achieved without limiting sensitivity, which has led to a significant increase of interest in SPECT for preclinical research in recent years. In this dissertation, the potential of a two-detector system through an analysis of three dedicated mouse collimators with multi-pinhole configurations was demonstrated. For this, sensitivity, spatial resolution, and uniformity as key parameters were determined. In the second part of the present work, an evaluation of the image quality at different activity concentrations to allow prediction of the system performance related to in vivo studies was performed. Therefore, a visual evaluation, as well as a calculation of the contrastto-noise ratio, was performed using mini Derenzo phantoms for the respective three mouse collimators. To better classify the results, the study was extended by a comparison with the predecessor system. Due to the absence of the third bottom detector, sensitivity and uniformity are slightly compromised. All three collimators were able to achieve a spatial resolution in the submillimeter range, XUHR-M offers a peak resolution of up to 0.35 mm. In terms of resolution, both evaluated systems performed on an equal level. Visual assessment of image quality indicates a slight advantage of the new two-detector system, and the contrast-to-noise ratio seems to benefit from the improved SROSEM algorithm. However, the differences between the two systems are marginal. The U-SPECT5/CT E-Class is proven to be state-of-the-art for small animal imaging and is a powerful instrument for preclinical molecular imaging research. Improvements in system design compensate well for the reduction in the detection area, allowing excellent imaging even with low activity concentrations.},
  subject      = {SPECT},
  language  = {en}
}
@phdthesis{Janssen2023,
  author    = {Janßen, Jan Paul},
  title     = {Capabilities of a multi-pinhole SPECT system with two stationary detectors for in vivo imaging in rodents},
  doi       = {10.25972/OPUS-32860},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328608},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Molecular imaging of rats is of great importance for basic and translational research. As a powerful tool in nuclear medicine, SPECT can be used to visualize specific functional processes in the body, such as myocardial perfusion or bone metabolism. Typical applications in laboratory animals are imaging diagnostics or the development of new tracers for clinical use. Innovations have enabled resolutions of up to a quarter of a millimeter with acceptable sensitivity. These advances have recently led to significantly more interest in SPECT both clinically and preclinically. The objective of this thesis was to evaluate the performance of the new U-SPECT5/CT E-Class by MILabs with a dedicated ultra-high resolution multi-pinhole collimator for rats and its potential for in vivo imaging of rats. The unique features of the U-SPECT are the large stationary detectors and the new iterative reconstruction algorithm. In addition, compared to the conventional system, the "E-Class" uses only two detectors instead of three. First, the sensitivity, maximum resolution, and uniformity were determined as performance parameters. Thereafter, CNRs for different activity levels comparable to those of typical in vivo activities were examined. Finally, two example protocols were carried out for imaging with 99mTc-MIBI and 99mTc-HMDP in healthy rats to evaluate the in vivo capabilities. For this purpose, CNR calculations and an image quality assessment were performed. The focus was on image quality as a function of scan time and post-reconstruction filter across a wide range of realistically achievable in vivo conditions. Performance was reasonable compared to other systems in the literature, with a sensitivity of 567 cps/MBq, a maximum resolution of 1.20 mm, and a uniformity of 55.5\%. At the lower activities, resolution in phantom studies decreased to ≥1.80 mm while maintaining good image quality. High-quality bone and myocardial perfusion SPECTs were obtained in rats with a resolution of ≥1.80 mm and ≥2.20 mm, respectively. Although limited sensitivity remains a weakness of SPECT, the U-SPECT5/CT E-Class with the UHR-RM collimator can achieve in vivo results of the highest standard despite the missing third detector. Currently, it is one of the best options for high-resolution radionuclide imaging in rats.},
  subject      = {SPECT},
  language  = {en}
}