@phdthesis{Schardt2023, author = {Schardt, Simon}, title = {Agent-based modeling of cell differentiation in mouse ICM organoids}, doi = {10.25972/OPUS-30194}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-301940}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {Mammalian embryonic development is subject to complex biological relationships that need to be understood. However, before the whole structure of development can be put together, the individual building blocks must first be understood in more detail. One of these building blocks is the second cell fate decision and describes the differentiation of cells of the inner cell mass of the embryo into epiblast and primitive endoderm cells. These cells then spatially segregate and form the subsequent bases for the embryo and yolk sac, respectively. In organoids of the inner cell mass, these two types of progenitor cells are also observed to form, and to some extent to spatially separate. This work has been devoted to these phenomena over the past three years. Plenty of studies already provide some insights into the basic mechanics of this cell differentiation, such that the first signs of epiblast and primitive endoderm differentiation, are the expression levels of transcription factors NANOG and GATA6. Here, cells with low expression of GATA6 and high expression of NANOG adopt the epiblast fate. If the expressions are reversed, a primitive endoderm cell is formed. Regarding the spatial segregation of the two cell types, it is not yet clear what mechanism leads to this. A common hypothesis suggests the differential adhesion of cell as the cause for the spatial rearrangement of cells. In this thesis however, the possibility of a global cell-cell communication is investigated. The approach chosen to study these phenomena follows the motto "mathematics is biology's next microscope". Mathematical modeling is used to transform the central gene regulatory network at the heart of this work into a system of equations that allows us to describe the temporal evolution of NANOG and GATA6 under the influence of an external signal. Special attention is paid to the derivation of new models using methods of statistical mechanics, as well as the comparison with existing models. After a detailed stability analysis the advantages of the derived model become clear by the fact that an exact relationship of the model parameters and the formation of heterogeneous mixtures of two cell types was found. Thus, the model can be easily controlled and the proportions of the resulting cell types can be estimated in advance. This mathematical model is also combined with a mechanism for global cell-cell communication, as well as a model for the growth of an organoid. It is shown that the global cell-cell communication is able to unify the formation of checkerboard patterns as well as engulfing patterns based on differently propagating signals. In addition, the influence of cell division and thus organoid growth on pattern formation is studied in detail. It is shown that this is able to contribute to the formation of clusters and, as a consequence, to breathe some randomness into otherwise perfectly sorted patterns.}, subject = {Mathematische Modellierung}, language = {en} } @phdthesis{Krimmer2021, author = {Krimmer, Elena}, title = {Agri-environment schemes and ecosystem services: The influence of different sown flower field characteristics on pollination, natural pest control and crop yield}, doi = {10.25972/OPUS-20657}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-206577}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Insects are responsible for the major part of the ecosystem services pollination and natural pest control. If insects decline, these ecosystem services can not longer be reliably delivered. Agricultural intensification and the subsequent loss and fragmentation of habitats has among others been identified to cause insect decline. Ecological intensification aims to promote alternative and sustainable management practices in agricultural farming, for example to decrease the use of external inputs such as pesticides. Agri-environment schemes make amends for farmers if they integrate ecologically beneficial measures into their farming regime and can therefore promote ecological intensification. There is a wide variety of agri-environment schemes, but the implementation of sown flower fields on crop fields is often included. Flower fields offer foraging resources as well as nesting sites for many different insect species and should be able to support insect populations as well as to increase ecosystem services to adjacent fields. However, the potential of flower fields to exhibit these effects is depending on many factors. Among others, the age and size of the flower field can influence if and how different insects profit from the measure. Additionally, the complexity of the surrounding landscape and therefore the existing biodiversity is influencing the potential of flower fields to increase ecosystem services locally. The goal of this study is to disentangle to which degree these factors influence the ecosystem services pollination and natural pest control and if these factors interact with each other. Furthermore, it will be examined if and how flower fields and ecosystem services influence crop yield. Additional factors examined in this study are distance decay and pesticide use. The abundance of beneficial insects can decrease strongly with increasing distance to suitable habitats. Pesticide use in turn could abrogate positive effects of flower fields on beneficial insects. To examine these different aspects and to be able to make recommendations for flower field implementation, field experiments were conducted on differently composed sown flower fields and adjacent oilseed rape fields. Flower fields differed in their age and continuity as well as in their size. Additionally, flower and oilseed rape fields were chosen in landscapes with different amounts of semi-natural habitat. Oilseed rape fields adjacent to calcareous grasslands and conventional crop fields served as controls. Pollinator observations and pollen beetle and parasitism surveys were conducted in the oilseed rape fields. Additionally, different yield parameters of the oilseed rape plants were recorded. Observations were conducted and samples taken in increasing distance to the flower fields to examine distance decay functions. Spray windows were established to inspect the influence of pesticides on ecosystem services and crop yields. Linear mixed models were used for statistical analysis. The results show, that newly established flower fields with high amounts of flower cover are very attractive for pollinators. If the flower fields reached a certain size (> 1.5ha), the pollinators tended to stay in these fields and did not distribute into the surroundings. High amounts of semi-natural habitat in the surrounding landscape increased the value of small flower fields as starting points for pollinators and their subsequent spillover into crop fields. Additionally, high amounts of semi-natural habitat decreased the decay of pollinators with increasing distance to the flower fields. Based on these results, it can be recommended to establish many small flower fields in landscapes with high amounts of semi-natural habitat and large flower fields in landscapes with low amounts of semi-natural habitat. However, it is mentionable that flower fields are no substitute for perennial semi-natural habitats. These still must be actively conserved to increase pollination to crop fields. Furthermore, the lowest amount of pollen beetle infestation was found on oilseed rape fields adjacent to continuous flower fields aged older than 6 years. Flower fields and calcareous grasslands in general increased pollen beetle parasitism in adjacent oilseed rape fields compared to conventional crop fields. The threshold for effective natural pest control could only be reached in the pesticide free areas in the oilseed rape fields adjacent to continuous flower fields and calcareous grasslands. Parasitism and superparasitism declined with increasing distance to the adjacent fields in pesticide treated areas of the oilseed rape fields. However, they remained on a similar level in spray windows without pesticides. Large flower fields increased parasitism and superparasitism more than small flower fields. Flower fields generally have the potential to increase pollen beetle parasitism rates, but pesticides can abrogate these positive effects of flower fields on natural pest control. Last but not least, effects of flower fields and ecosystem services on oilseed rape yield were examined. No positive effects of pollination on oilseed rape yield could be found. Old and continuous flower fields increased natural pest control in oilseed rape fields, which in turn increased seed set and total seed weight of oilseed rape plants. The pesticide treatment had negative effects on natural pest control, but positive effects on crop yield. Pollination and natural pest control decreased with increasing distance to the field edge, but fruit set slightly increased. The quality of the field in terms of soil and climatic conditions did not influence the yield parameters examined in this study. Yield formation in oilseed rape plants is a complex process with many factors involved, and it is difficult to disentangle indirect effects of flower fields on yield. However, perennial flower fields can promote ecological intensification by increasing crop yield via natural pest control. This study contributes to a better understanding of the effects of differently composed flower fields on pollination, natural pest control and oilseed rape yield.}, subject = {{\"O}kologie}, language = {en} } @phdthesis{Lampert2001, author = {Lampert, Kathrin P.}, title = {Alternative life history strategies in the West African reed frog, Hyperolius nitidulus}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1677}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2001}, abstract = {Distinct juvenile behaviour differences, changes in adult sizes and reproductive capacity and a long reproductive period triggered the working hypothesis of two alternative life-cycle strategies favouring aestivation or immediate reproduction. The hypothesis for the life-cycles of Hyperolius nitidulus that differed from the commonly assumed reproductive strategy for this species was confirmed by the results of this study. Aestivated juveniles start to mature at the beginning of the rainy season and reproduce subsequently. Their tadpoles grow until metamorphosis and either reproduce in this same season, in which case their offspring aestivates (one year - two generations), or they delay reproduction to the following year and aestivate themselves (one year - one generation). Juveniles trying to reproduce as fast as possible will invest in growth and differentiation and show no costly adaptations to aestivation, while juveniles delaying reproduction to the following rainy season will be well adapted to dry season conditions. Indirect evidence for the existence of a second generation was found in all three investigation years: adult size decreased abruptly towards the end of the rainy season, mainly due to the arrival of very small individuals, and clutch size decreased abruptly. Also at the end of the rainy season juveniles had two behavioural types: one hiding on the ground and clearly avoiding direct sunlight and another sitting freely above ground showing higher tolerance towards dry season conditions (high air temperatures and low humidity). Skin morphology differed between the types showing many more purine crystals in a higher order in the dry-season adapted juveniles. The final proof for the existence of a second generation came with the recapture of individuals marked as juveniles when they left the pond. The 45 recaptured frogs definitely came back to the pond to reproduce during the same season in 1999. Second generation frogs (males and females) were significantly smaller than the rest of all adults and egg diameter was reduced. Clutch size did not differ significantly. It was found that females did not discriminate against second generation males when coming to the ponds to reproduce. Second generation males had a similar chance to be found in amplexus as first generation males. Indirect and direct evidence for a second generation matched very well. The sudden size decrease in adults occurred just at the time when the first marked frogs returned. The observation that freshly metamorphosed froglets were able to sit in the sun directly after leaving the water led to the assumption that the decision whether to aestivate or to reproduce already happens during the frogs' larval period. Water chemistry and the influence of light was investigated to look for the factors triggering the decision, but only contaminated water increased the number of juveniles ready for aestivation. Whether the life history polymorphism observed in Hyperolius nitidulus is due to phenotypic plasticity or genetic polymorphism is still not known. Despite this uncertainty, there is no doubt that the optimal combination of different life histories is profitable and may be a reason for the wide range and high local abundance of Hyperolius nitidulus.}, subject = {Westafrika}, language = {en} } @phdthesis{Glos2006, author = {Glos, Julian}, title = {Amphibian communities of the dry forest of Western Madagascar : taxonomy, ecology and conservation}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-18146}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {In meiner Arbeit habe ich taxonomische, gemeinschafts{\"o}kologische und aut{\"o}kologische Aspekte im westmadagassischen Trockenwald untersucht. Ziel dieser Arbeit war es Antworten auf die Fragen zu geben wie die einzelnen Arten die Habitate in Raum und Zeit nutzen, welchen Einfluss abiotische Parameter, Austrocknungsrisiko der Laichgew{\"a}sser und Mikrohabitat haben und wie Pr{\"a}datoren die Gemeinschaft und das Verhalten einzelner Arten beeinflussen. Somit tr{\"a}gt diese Arbeit dazu bei die grundlegenden Mechanismen zu verstehen, die die Zusammensetzung einer Lebensgemeinschaft bestimmen. Im Einzelnen untersuchte ich hierzu folgende Fragestellungen: Aus welchen Arten bestehen die Anurengemeinschaften des westmadagassischen Trockenwaldes, und wie lassen sich diese Arten morphologisch voneinander abgrenzen? Welche Unterschiede finden sich zwischen den Arten bez{\"u}glich ihres Paarungssystems, ihrer life-history und ihrer Habitatwahl bzw. den Anpassungen an ihr Habitat? Gibt es spezifische Kaulquappengemeinschaften, die sich anhand biotischer und abiotischer Umweltvariablen vorhersagen lassen? Unterscheiden sich die Muster der Vorhersagbarkeit von Gemeinschaften zwischen unterschiedlichen Habitattypen innerhalb eines lokalen r{\"a}umlichen Skalenniveaus? Wie beeinflusst das Vorkommen von Raubfeinden die Verteilung von Kaulquappen und deren Verhalten auf der r{\"a}umlichen Skalenebene einzelner Laichgew{\"a}sser? Anhand welcher Umweltvariablen l{\"a}sst sich die Laichplatzwahl von Anuren in diesem Habitat vorhersagen? Wie lassen sich die Ergebnisse nutzen, um Empfehlungen zum Schutz bedrohter Arten auszusprechen? In dieser Arbeit beschreibe ich eine Froschart wissenschaftlich neu. Diese Art, Scaphiophryne menabensis, ist die seltenste Froschart in ihrem Verbreitungsgebiet, und aus meiner Arbeit resultiert die dringende Empfehlung, sie in ein bestehendes Schutzkonzept f{\"u}r den Kirindy-Wald und seine Umgebung mit einzubeziehen. Weiterhin beschreibe ich wissenschaftlich erstmalig in dieser Arbeit f{\"u}nf Kaulquappenarten und pr{\"a}sentiere Daten zu {\"O}kologie, life-history und Verhalten dieser Arten. Die wissenschaftliche Beschreibung weiterer Frosch- und Kaulquappenarten ist Gegenstand noch andauernder Studien (Scaphiophryne sp., Heterixalus carbonei und H. tricolor; Revision der Kaulquappen von Scaphiophryne). Die Ergebnisse dieser Arbeit stellen damit die Basis f{\"u}r alle weiteren {\"o}kologischen Studien an Fr{\"o}schen und Kaulquappen dieses {\"O}kosystems dar. FAZIT Die Amphibienfauna Madagaskars ist einzigartig, und sie stellt ein aufregendes Feld f{\"u}r {\"o}kologische Fragestellungen dar, sowohl als eigenst{\"a}ndiges System betrachtet als auch als Modell f{\"u}r andere Systeme. Umso mehr verwundert es, dass bislang kaum detaillierte {\"o}kologische Studien an diesem System durchgef{\"u}hrt wurden. Die vorliegende Arbeit schafft zun{\"a}chst mit der taxonomischen Beschreibung der vorkommenden Arten die Basis f{\"u}r {\"o}kologische Fragestellungen und zeigt dann auf den Ebenen sowohl der Gemeinschaft als auch einzelner Arten, wie verschiedene Umweltfaktoren die Verteilung von Anuren in Raum und Zeit beeinflussen. Es zeigt sich, dass sowohl statische Eigenschaften der Gew{\"a}sser als auch dynamische Faktoren wie Raubfeinde oder das Vorhandensein anderer Kaulquappen die Verteilung der Arten auf verschiedenen r{\"a}umlichen Skalenebenen sowie deren Verhalten beeinflussen. Somit tragen die Ergebnisse dieser Arbeit dazu bei, die grundlegenden Mechanismen zu verstehen, die die Zusammensetzung der Lebensgemeinschaften in diesem {\"O}kosystem bestimmen. Nicht zuletzt erm{\"o}glichen diese Erkenntnisse, geeignete, artenorientierte Schutzkonzepte f{\"u}r diese in ihrer Existenz stark bedrohte Anurengemeinschaft zu entwickeln und die Effekte von Habitatzerst{\"o}rung auf diese Gemeinschaft aufzuzeigen.}, subject = {Lurche}, language = {en} } @phdthesis{Brembs2000, author = {Brembs, Bj{\"o}rn}, title = {An Analysis of Associative Learning in Drosophila at the Flight Simulator}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1039}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2000}, abstract = {Most natural learning situations are of a complex nature and consist of a tight conjunction of the animal's behavior (B) with the perceived stimuli. According to the behavior of the animal in response to these stimuli, they are classified as being either biologically neutral (conditioned stimuli, CS) or important (unconditioned stimuli, US or reinforcer). A typical learning situation is thus identified by a three term contingency of B, CS and US. A functional characterization of the single associations during conditioning in such a three term contingency has so far hardly been possible. Therefore, the operational distinction between classical conditioning as a behavior-independent learning process (CS-US associations) and operant conditioning as essentially behavior-dependent learning (B-US associations) has proven very valuable. However, most learning experiments described so far have not been successful in fully separating operant from classical conditioning into single-association tasks. The Drosophila flight simulator in which the relevant behavior is a single motor variable (yaw torque), allows for the first time to completely separate the operant (B-US, B-CS) and the classical (CS-US) components of a complex learning situation and to examine their interactions. In this thesis the contributions of the single associations (CS-US, B-US and B-CS) to memory formation are studied. Moreover, for the first time a particularly prominent single association (CS-US) is characterized extensively in a three term contingency. A yoked control shows that classical (CS-US) pattern learning requires more training than operant pattern learning. Additionally, it can be demonstrated that an operantly trained stimulus can be successfully transferred from the behavior used during training to a new behavior in a subsequent test phase. This result shows unambiguously that during operant conditioning classical (CS-US) associations can be formed. In an extension to this insight, it emerges that such a classical association blocks the formation of an operant association, which would have been formed without the operant control of the learned stimuli. Instead the operant component seems to develop less markedly and is probably merged into a complex three-way association. This three-way association could either be implemented as a sequential B-CS-US or as a hierarchical (B-CS)-US association. The comparison of a simple classical (CS-US) with a composite operant (B, CS and US) learning situation and of a simple operant (B-US) with another composite operant (B, CS and US) learning situation, suggests a hierarchy of predictors of reinforcement. Operant behavior occurring during composite operant conditioning is hardly conditioned at all. The associability of classical stimuli that bear no relation to the behavior of the animal is of an intermediate value, as is operant behavior alone. Stimuli that are controlled by operant behavior accrue associative strength most easily. If several stimuli are available as potential predictors, again the question arises which CS-US associations are formed? A number of different studies in vertebrates yielded amazingly congruent results. These results inspired to examine and compare the properties of the CS-US association in a complex learning situation at the flight simulator with these vertebrate results. It is shown for the first time that Drosophila can learn compound stimuli and recall the individual components independently and in similar proportions. The attempt to obtain second-order conditioning with these stimuli, yielded a relatively small effect. In comparison with vertebrate data, blocking and sensory preconditioning experiments produced conforming as well as dissenting results. While no blocking could be found, a sound sensory preconditioning effect was obtained. Possible reasons for the failure to find blocking are discussed and further experiments are suggested. The sensory preconditioning effect found in this study is revealed using simultaneous stimulus presentation and depends on the amount of preconditioning. It is argued that this effect is a case of 'incidental learning', where two stimuli are associated without the need of reinforcement. Finally, the implications of the results obtained in this study for the general understanding of memory formation in complex learning situations are discussed.}, subject = {Taufliege}, language = {en} } @phdthesis{Bucher2008, author = {Bucher, Daniel}, title = {An Electrophysiological Analysis of Synaptic Transmission at the Drosophila Larval Neuromuscular Junction}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-27784}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {In this thesis, synaptic transmission was studied electrophysiologically at an invertebrate model synapse, the neuromuscular junction of the Drosophila 3rd instar wandering larvae. In the first part, synaptic function is characterized at the neuromuscular junction in fly lines which are null mutants for the synaptic proteins "the synapse associated protein of 47 kDa" (Sap-47156), Synapsin (Syn97), the corresponding double mutant (Sap-47156, Syn97), a null mutant for an as yet uncharacterized Drosophila SR protein kinase, the Serine-Arginine protein kinase 3 (SRPK3), and the L{\"o}chrig (Loe) mutant which shows a strong neurodegenerative phenotype. Intracellular voltage recordings from larval body wall muscles 6 and 7 were performed to measure amplitude and frequency of spontaneous single vesicle fusion events (miniature excitatory junction potentials or mEJPs). Evoked excitatory junction potentials (eEJPs) at different frequencies and calcium concentrations were also measured to see if synaptic transmission was altered in mutants which lacked these synaptic proteins. In addition, structure and morphology of presynaptic boutons at the larval neuromuscular junction were examined immunohistochemically using monoclonal antibodies against different synaptic vesicle proteins (SAP-47, CSP, and Synapsin) as well as the active zone protein Bruchpilot. Synaptic physiology and morphology was found to be similar in all null mutant lines. However, L{\"o}chrig mutants displayed an elongated bouton morphology, a significant shift towards larger events in mEJP amplitude frequency histograms, and increased synaptic facilitation during a 10 Hz tetanus. These deficits suggest that Loe mutants may have a defect in some aspect of synaptic vesicle recycling. The second part of this thesis involved the electrophysiological characterization of heterologously expressed light activated proteins at the Drosophila neuromuscular junction. Channelrhodopsin-2 (ChR2), a light gated ion channel, and a photoactivated adenylate cyclase (PAC) were expressed in larval motor neurons using the UAS-Gal4 system. Single EJPs could be recorded from muscles 15, 16, and 17 when larva expressing ChR2 were illuminated with short (100 ms) light pulses, whereas long light pulses (10 seconds) resulted in trains of EJPs with a frequency of around 25 Hz. Larva expressing PAC in preparations where motor neurons were cut from the ventral ganglion displayed a significant increase in mEJP frequency after a 1 minute exposure to blue light. Evoked responses in low (.2 mM) calcium were also significantly increased when PAC was stimulated with blue light. When motor nerves were left intact, PAC stimulation resulted in light evoked EJPs in muscles 6 and 7 in a manner consistent with RP3 motor neuron activity. ChR2 and PAC are therefore useful and reliable tools for manipulating neuronal activity in vivo.}, subject = {Drosophila}, language = {en} } @phdthesis{Nilla2012, author = {Nilla, Jaya Santosh Chakravarthy}, title = {An Integrated Knowledgebase and Network Analysis Applied on Platelets and Other Cell Types}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-85730}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Systems biology looks for emergent system effects from large scale assemblies of molecules and data, for instance in the human platelets. However, the computational efforts in all steps before such insights are possible can hardly be under estimated. In practice this involves numerous programming tasks, the establishment of new database systems but as well their maintenance, curation and data validation. Furthermore, network insights are only possible if strong algorithms decipher the interactions, decoding the hidden system effects. This thesis and my work are all about these challenges. To answer this requirement, an integrated platelet network, PlateletWeb, was assembled from different sources and further analyzed for signaling in a systems biological manner including multilevel data integration and visualization. PlateletWeb is an integrated network database and was established by combining the data from recent platelet proteome and transcriptome (SAGE) studies. The information on protein-protein interactions and kinase-substrate relationships extracted from bioinformatical databases as well as published literature were added to this resource. Moreover, the mass spectrometry-based platelet phosphoproteome was combined with site-specific phosphorylation/ dephosphorylation information and then enhanced with data from Phosphosite and complemented by bioinformatical sequence analysis for site-specific kinase predictions. The number of catalogued platelet proteins was increased by over 80\% as compared to the previous version. The integration of annotations on kinases, protein domains, transmembrane regions, Gene Ontology, disease associations and drug targets provides ample functional tools for platelet signaling analysis. The PlateletWeb resource provides a novel systems biological workbench for the analysis of platelet signaling in the functional context of protein networks. By comprehensive exploration, over 15000 phosphorylation sites were found, out of which 2500 have the corresponding kinase associations. The network motifs were also investigated in this anucleate cell and characterize signaling modules based on integrated information on phosphorylation and protein-protein interactions. Furthermore, many algorithmic approaches have been introduced, including an exact approach (heinz) based on integer linear programming. At the same time, the concept of semantic similarities between two genes using Gene Ontology (GO) annotations has become an important basis for many analytical approaches in bioinformatics. Assuming that a higher number of semantically similar gene functional annotations reflect biologically more relevant interactions, an edge score was devised for functional network analysis. Bringing these two approaches together, the edge score, based on the GO similarity, and the node score, based on the expression of the proteins in the analyzed cell type (e.g. data from proteomic studies), the functional module as a maximum-scoring sub network in large protein-protein interaction networks was identified. This method was applied to various proteome datasets (different types of blood cells, embryonic stem cells) to identify protein modules that functionally characterize the respective cell type. This scalable method allows a smooth integration of data from various sources and retrieves biologically relevant signaling modules.}, subject = {Systembiologie}, language = {en} } @phdthesis{Wawrowsky2007, author = {Wawrowsky, Kolja Alexander}, title = {Analysis and Visualization in Multidimensional Microscopy}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-23867}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2007}, abstract = {The live sciences currently undergo a paradigm shift to computer aided discoveries. Discoveries in the live sciences were historically made by either direct observation or as a result of chemical assays. Today we see a growing shift toward computer aided analysis and visualization. This gradual process happens in microscopy. Multidimensional laser scanning microscopy can acquire very complex multichannel data from fixed or live specimen. New probes such as visible fluorescent proteins let us observe the expression of genes and track protein localization. Ion sensitive dyes change intensity with the concentration of ions in the cell. The laser scanning confocal allows us to record these processes in three dimensions over time. This work demonstrates the application of software analysis to multidimensional microscopy data. We introduce methods for volume investigation, ion flux analysis and molecular modeling. The visualization methods are based on a multidimensional data model to accommodate complex datasets. The software uses vector processing and multiple processors to accelerate volume rendering and achieve interactive rendering. The algorithms are based on human visual perception and allow the observer a wide range of mixed render modes. The software was used to reconstruct the pituitary development in zebrafish and observe the degeneration of neurons after injury in a mouse model. Calicum indicator dyes have long been used to study calcium fluxes. We optimized the imaging method to minimize impact on the cell. Live cells were imaged continuously for 45 minutes and subjected to increasing does of a drug. We correlated the amplitude of calcium oscillations to increasing doses of a drug and obtain single cell dose response curves. Because this method is very sensitive and measures single cell responses it has potential in drug discovery and characterization. Microtubules form a dynamic cytoskeleton, which is responsible for cell shape, intracellular transport and has an integral role in mitosis. A hallmark of microtubule organization is lateral interactions. Microtubules are bundles by proteins into dense structures. To estimate the contribution of this bundling process, we created a fractal model of microtubule organization. This model demonstrates that morphology of complex microtubule arrays can be explained by bundling alone. In summary we showed that advances in software for visualization, data analysis and modeling lead to new discoveries.}, subject = {Konfokale Mikroskopie}, language = {en} } @phdthesis{Schuster2021, author = {Schuster, Sarah}, title = {Analysis of \(Trypanosoma\) \(brucei\) motility and the infection process in the tsetse fly vector}, doi = {10.25972/OPUS-19269}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-192691}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {African trypanosomes are protist pathogens that are infective for a wide spectrum of mammalian hosts. Motility has been shown to be essential for their survival and represents an important virulence factor. Trypanosoma brucei is transmitted by the bite of the bloodsucking tsetse fly, the only vector for these parasites. The voyage through the fly is complex and requires several migration, proliferation and differentiation steps, which take place in a defined order and in specific fly tissues. The first part of this doctoral thesis deals with the establishment of the trypanosome tsetse system as a new model for microswimmer analysis. There is an increasing interdisciplinary interest in microbial motility, but a lack of accessible model systems. Therefore, this work introduces the first enclosed in vivo host parasite system that is suitable for analysis of diverse microswimmer types in specific microenvironments. Several methods were used and adapted to gain unprecedented insights into trypanosome motion, the fly´s interior architecture and the physical interaction between host and parasite. This work provides a detailed overview on trypanosome motile behavior as a function of development in diverse host surroundings. In additional, the potential use of artificial environments is shown. This can be used to partly abstract the complex fly architecture and analyze trypanosome motion in defined nature inspired geometries. In the second part of the thesis, the infection of the tsetse fly is under investigation. Two different trypanosome forms exist in the blood: proliferative slender cells and cell cycle arrested stumpy cells. Previous literature states that stumpy cells are pre adapted to survive inside the fly, whereas slender cells die shortly after ingestion. However, infection experiments in our laboratory showed that slender cells were also potentially infective. During this work, infections were set up so as to minimize the possibility of stumpy cells being ingested, corroborating the observation that slender cells are able to infect flies. Using live cell microscopy and fluorescent reporter cell lines, a comparative analysis of the early development following infection with either slender or stumpy cells was performed. The experiments showed, for the first time, the survival of slender trypanosomes and their direct differentiation to the procyclic midgut stage, contradicting the current view in the field of research. Therefore, we can shift perspectives in trypanosome biology by proposing a revised life cycle model of T. brucei, where both bloodstream stages are infective for the vector.}, subject = {Motilit{\"a}t}, language = {en} } @phdthesis{FernandezMora2005, author = {Fern{\´a}ndez-Mora, Eugenia}, title = {Analysis of the maturation of Rhodococcus equi-containing vacuoles in macrophages}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-14049}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2005}, abstract = {Rhodococcus equi is a Gram-positive intracellular pathogen which can cause severe bronchopneumonia in foals. In recent years, the role of this bacterium as human pathogen has been noted, as R.equi infections in humans have increase in frequency. This increase is associated with the rise in immunosupressed individuals, specially AIDS patients, where infection leads to symptoms and pathology similar to those seen in foals with a high mortality rate. Due to its capability to survive and multiply in murine and equine macrophages, R.equi has been classified as a facultative intracellular bacterium. R.equi is found frequently in macrophages in alveolar infiltrate from infected animals. The pathogenicity of R.equi depends on its ability to exist and multiply inside macrophages and has been associated with the presence of virulence plasmids. It has been observed that, inside foal alveolar macrophages, R.equi-containing vacuoles (RCVs) do not mature into phagolysosomes. However, most of the intracellular events during R.equi infection have not been investigated in detail. The aim of this study was to elucidate the intracellular compartmentation of R.equi and the mechanism by which the bacteria avoid destruction in host macrophages. The importance of the virulence-associated plasmids of R.equi for the establishment of RCVs was also evaluated. Furthermore, the intracellular fate of viable and non-viable R.equi was compared in order to study whether viability of R.equi influeciantes the establishment of RCVs. In this study, the RCV was characterized by using a variety of endocytic markers to follow the path of the bacteria trhough murine macropages. Transmission electron microscopy-base analysis showed that R.equi was found equally frequently in phagosomes with loosely or thightly apposed membranes, and RCV often contains numerous membranous vesicles. Laser scanning microscopy of infected macrophages showed that the majority of phagosomes containing R.equi acquired transiently the early endosomal markers Rab5, Ptlns3P, and EEA-1, suggesting initially undisturbed phagosome maturation. Although the RCV acquired some late endosomal markers, such as Rab7, LAMP-1, and Lamp-2, they did not acquired vATPase, did not interact with pre-labeled lysosomes, and failed to acidify. These data clearly suggest that the RCV is a compartment which has left vacuoles that resemble multivesicular body compartments (MVB), which are transport intermediates between early and late endosomes and display internal vesicles very similar to the ones observed within RCVs. Analyisis of several R.equi strains containing either VapA- or VapB-expressing plasmids or neither demonstrated that the possession of the virulence-associated plasmids does not affect phagosome trafficking over a two hour period of infection. The finding that non-viable R.equi was still able to inhibit phagosome maturation (although not to the same extent as viable R.equi did) suggests that heat-insensitive factors, such as cell periphery lipids, may play a major role in inhibition of phagosome maturation, although heat-sensitive factors may also be involved.}, subject = {Rhodococcus equi}, language = {en} } @phdthesis{Dinev2001, author = {Dinev, Dragomir}, title = {Analysis of the role of extracellular signal regulated kinase (ERK5) in the differentiation of muscle cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-1180481}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2001}, abstract = {The MEK5/ ERK5 kinase module is a relatively new discovered mitogen-activated protein kinase (MAPK) signalling pathway with a poorly defined physiological function. Since ERK5 and its upstream activator MEK5 are abundant in skeletal muscle a function of the cascade during muscle differentiation was examined. ERK5 becomes activated upon induction of differentiation in mouse myoblasts. The selective activation of the pathway results in promoter activation of differentiation-specific genes, such as the cdk-inhibitor p21 gene, the myosin light chain (MLC1A) gene, or an E-box containing promoter element, where myogenic basic-helix-loop-helix proteins such as MyoD or myogenin bind. Moreover, myogenic differentiation is completely blocked, when ERK5 expression is inhibited by antisense RNA. The effect can be detected also on the expression level of myogenic determination and differentiation markers such as p21, MyoD and myogenin. Another new finding is that stable expression of ERK5 in C2C12 leads to differentiation like phenotype and to increased p21 expression levels under growth conditions. These results provide first evidence that the MEK5/ERK5 MAP kinase cascade is critical for early steps of muscle cell differentiation.}, subject = {Muskelzelle}, language = {en} } @phdthesis{Zimmermann2020, author = {Zimmermann, Henriette}, title = {Antigenic variation and stumpy development in \(Trypanosoma\) \(brucei\)}, doi = {10.25972/OPUS-14690}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146902}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2020}, abstract = {The eukaryotic parasite Trypanosoma brucei has evolved sophisticated strategies to persist within its mammalian host. Trypanosomes evade the hosts' immune system by antigenic variation of their surface coat, consisting of variant surface glycoproteins (VSGs). Out of a repertoire of thousands of VSG genes, only one is expressed at any given time from one of the 15 telomeric expression sites (ES). The VSG is stochastically exchanged either by a transcriptional switch of the active ES (in situ switch) or by a recombinational exchange of the VSG within the active ES. However, for infections to persist, the parasite burden has to be limited. The slender (sl) bloodstream form secretes the stumpy induction factor (SIF), which accumulates with rising parasitemia. SIF induces the irreversible developmental transition from the proliferative sl to the cell cycle-arrested but fly-infective stumpy (st) stage once a concentration threshold is reached. Thus, antigenic variation and st development ensure persistent infections and transmissibility. A previous study in monomorphic cells indicated that the attenuation of the active ES could be relevant for the development of trypanosomes. The present thesis investigated this hypothesis using the inducible overexpression of an ectopic VSG in pleomorphic trypanosomes, which possess full developmental competence. These studies revealed a surprising phenotypic plasticity: while the endogenous VSG was always down-regulated upon induction, the ESactivity determined whether the VSG overexpressors arrested in growth or kept proliferating. Full ES-attenuation induced the differentiation of bona fide st parasites independent of the cell density and thus represents the sole natural SIF-independent differentiation trigger to date. A milder decrease of the ES-activity did not induce phenotypic changes, but appeared to prime the parasites for SIF-induced differentiation. These results demonstrate that antigenic variation and development are linked and indicated that the ES and the VSG are independently regulated. Therefore, I investigated in the second part of my thesis how ES-attenuation and VSG-silencing can be mediated. Integration of reporters with a functional or defective VSG 3'UTR into different genomic loci showed that the maintenance of the active state of the ES depends on a conserved motif within the VSG 3'UTR. In situ switching was only triggered when the telomere-proximal motif was partially deleted, suggesting that it serves as a DNA-binding motif for a telomere-associated protein. The VSG levels seem to be additionally regulated in trans based on the VSG 3'UTR independent of the genomic context, which was reinforced by the regulation of a constitutively expressed reporter with VSG 3' UTR upon ectopic VSG overexpression.}, subject = {Trypanosoma brucei}, language = {en} } @phdthesis{Ernst2006, author = {Ernst, Raffael}, title = {Anuran communities on the cutting edge : Analysing patterns and processes in anthropogenically altered tropical forests - Studies from the Guiana Shield and West Africa}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-18373}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {Summary Timber harvesting is currently the most common commercial utilisation activity in tropical forests. Assessing the effects of logging on different aspects of biodiversity and general ecosystem properties is hence of prime importance if the few remaining areas of intact tropical forest are to be protected effectively and efficiently. Tropical amphibian communities are an appropriate model system for studies on the impacts of human-induced environmental changes on the dynamics of complex biological systems. This thesis elaborates on patterns of diversity changes in tropical forest amphibian communities facing habitat alterations associated with selective logging in two globally important eco-regions (C{\^o}te d'Ivoire, Upper Guinea, West Africa and Guyana, the Guiana Shield, northern South America). The thesis is organised along two main themes. After a general introduction, a section on general methodology and an introduction to the model systems studied, the first theme moves from general patterns to underlying processes. A second theme running through both chapters carries from undisturbed systems to disturbed systems. A final section integrates findings and addresses implications for conservation management of anthropogenically altered tropical forests. Several case studies at the species- population and community level are being presented and data on the direct and indirect impacts of anthropogenic habitat alteration on respective organizational levels are provided. A key statement that is stressed on throughout the studies is the fact that common measures of diversity, such as species richness and species-diversity only inadequately reflect processes of diversity change following anthropogenic disturbance. They also fail to describe actual impacts on the dynamics of complex biological systems. It is argued that commonly used measures produce an incoherent and insufficient picture of diversity patterns and the underlying processes that shape these patterns. Thus, an understanding of higher levels of diversity, such as \&\#946;-diversity and functional diversity (and hence compositional patterns) appears to be the key to effectively mitigating the impacts of human-induced disturbance on amphibian communities. It is shown that the predictability of amphibian community composition depends on the respective level of anthropogenic disturbance imposed on a particular habitat. Hence, human activities that lead to changes in the structure of a forest, such as logging, not only alter simple system descriptors, such as the number of species in a given community, but rather alter the dynamics of the entire system. In this context, functional diversity is shown to be an important aspect underlying the actual mechanism that leads to the observed change of predictability patterns. Functional differences between species, rather than number of species per se appear to be the decisive factor in sustaining desirable ecosystem states and thus in maintaining important ecosystem services. Because biological diversity appears to play a substantial role in ecosystem resilience required to safeguard essential ecosystem functions in the face of environmental change, the thesis calls for a critical revision of common diversity assessments approaches. The studies advocate the reconsideration of the uncritical use of widespread measures and descriptors of biodiversity on grounds of inconsistent patterns found throughout numerous studies, including those presented herein.}, subject = {Tropischer Regenwald}, language = {en} } @phdthesis{Borst2017, author = {Borst, Andreas}, title = {Apoptosis \& senescence: cell fate determination in inhibitor-treated melanoma cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-155085}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {Neoplasms of the skin represent the most frequent tumors worldwide; fortunately, most of them are benign or semi-malignant and well treatable. However, the two most aggressive and deadly forms of malignant skin-neoplasms are melanoma and Merkel cell carcinoma (MCC), being responsible for more than 90\% of skin-cancer related deaths. The last decade has yielded enormous progress in melanoma therapy with the advent of targeted therapies, like BRAF or MEK inhibitors, and immune-stimulating therapies, using checkpoint antibodies targeting CTLA- 4, PD-1 or PD-L1. Very recent studies suggest that also MCC patients benefit from a treatment with checkpoint antibodies. Nevertheless, in an advanced metastatic stage, a cure for both of these aggressive malignancies is still hard to achieve: while only a subset of patients experience durable benefit from the immune-based therapies, the widely applicable targeted therapies struggle with development of resistances that inevitably occur in most patients, and finally lead to their death. The four articles included in this thesis addressed current questions concerning therapy and carcinogenesis of melanoma and MCC. Moreover, they are discussed in the light of the up-to-date research regarding targeted and immune-based therapies. In article I we demonstrated that besides apoptosis, MAPK pathway inhibition in BRAF-mutated melanoma cells also induces senescence, a permanent cell cycle arrest. These cells may provide a source for relapse, as even permanently arrested cancer cells can contribute to a pro-tumorigenic milieu. To identify molecular factors determining the differential response, we established M14 melanoma cell line derived single cell clones that either undergo cell death or arrest when treated with BRAF/MEK inhibitors. Using these single cell clones, we demonstrated in article IV that downregulation of the pro-apoptotic BH3-only protein BIK via epigenetic silencing is involved in apoptosis deficiency, which can be overcome by HDAC inhibitors. These observations provide a possible explanation for the lack of a complete and durable response to MAPK inhibitor treatment in melanoma patients, and suggest the application of HDAC inhibitors as a complimentary therapy to MAPK pathway inhibition. Concerning MCC, we scrutinized the interactions between the Merkel cell polyomavirus' (MCV) T antigens (TA) and the tumor suppressors p53 and Rb in article II and III, respectively. In article III, we demonstrated that the cell cycle master regulator Rb is the crucial target of MCV large T (LT), while it - in contrast to other polyomavirus LTs - exhibits much lower affinity to the related proteins p107 and p130. Knockdown of MCV LT led to proliferation arrest in MCC cells, which can be rescued by knockdown of Rb, but not by knockdown of p107 and p130. Contrary to Rb, restriction of p53 in MCC seems to be independent of the MCV TAs, as we demonstrated in article II. In conclusion, the presented thesis has revealed new molecular details, regarding the response of melanoma cells towards an important treatment modality and the mechanisms of viral carcinogenesis in MCC.}, subject = {Melanom}, language = {en} } @phdthesis{Jovcic2002, author = {Jovcic, Alexander}, title = {Applications of aerobic and anaerobic bacteria in the fields of biological degradation of contaminants and biological wastewater treatment}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-6702}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {In the work here presented four distinctly different problems were investigated. The first problem was an investigation into the degradation of Dichloroethylene (DCE) and 1,1-bis (p-Chlorophenyl)-2-dichloroethylene (DDE) utilising pure bacterial cultures. The second investigation dealt with the degradation of DDE and polychlorinated Biphenyl's (PCB's) utilising anaerobic sediments and soils from New Zealand. The third investigation worked on the Granulation of anaerobic River-sediments in Upflow Anaerobic Sludge Blanket (UASB) Reactors. The last investigation describes the commissioning of an industrial aerobic Wastewater Treatment Plant and the Implementation of biological Nitrogen- and Phosphate removal in this Wastewater Treatment Plant. Since the chemical Structure of DCE and DDE have certain similarities, Bacteria that were capable of degrading DCE, were tested here, whether they would also be able to degrade DDE utilising a co-metabolic pathway. In the experiments the aerobic bacteria Methylosinus trichosporium and Mycobacterium vaccae and the anaerobic bacteria Acetobacterium woodii and Clostridium butyricum were used. Approximately 60\% of the added DCE was degraded by M. vaccae, while M. trichosporium degraded approximately 50\%. A. woodii and C. butyricum degraded 40\% and 30\% respectively of the added DCE. Further experiments with these cultures and DDE lead to a microbial degradation of DDE to an extent of 34.6\% for M. vaccae, 14.1\% for C. butyricum, 2.2\% for A. woodii and 10.5\% for M. trichosporium. Additional experiments, utilising [14C]-DDE, showed that the DDE had not been degraded but were attached to the bacterial cells. The second investigation utilised anaerobic soils and sediments from New Zealand to study the anaerobic co-metabolic degradation of DDE and PCB's. The soils and sediments originated from the River Waikato, from Wastewater Ponds in Kinleith, Marine-Sediments from Mapua, and a variety of soils comtaminated with Pentachlorophenyl (PCP). The cultures from these soils and sediments were raised on a variety of Carbon- and Energy-sources. Beside DDE, Aroclor 1260, and a mix of four pure PCB-Congeneres (one Tetra-, one Hexa, one Hepta- and one Deca-Chlorobiphenyl) were used to test for the reductive dechlorination. The cultivation process of the baceria lasted six months. Samples of the cultures were taken after zero, three and six months. These samples were tested for the increase of cell-protein, the degradation of carbon- and energy-sources, and the removal of the added polychlorinated chemicals. The organochlorines were analysed using reversed phase HPLC and FID-GC. When a change in the Chromatogram was detected the respective cultures were further analysed using ECD-GC and GC-MS. The results showed that the culutres grew under these conditions, but no degradation of DDE and the PCB-Mix could be detected, and only small changes in the composition/chromatograms of Aroclor 1260 were found. The third investigation worked on the Granulation of River-Sediments in UASB-Reactors. Sediments from the River Waikato in New Zealand and the River Saale in Germany were used. In both cases the Granulation process was successful, which was demonstrated by microscopic comparisons of the Sediments and the resulting Granules. The two main bacterial cultures detected were Methanosarcina- and Methanothrix-like cultures. The main carbon- and energy-source was Lactic Acid, which was used at a concentration of 21,8 g COD/L. The Granulation-Process was a combination of using high a COD-Concentration combined with a low Volumetric Loading-Rate. Comparisons of the specific degradation-rates of a variety of carbon- and energy-sources between the Sediments and the Granules, showed no increased degradation rates in regard to the same cell-mass, but the increased bio-mass in the Granules allowed for higher degradation-rates within the UASB-reactors. The fourth investigation describes the commissioning of an industrial Wastewater Treatment Plant for a Dairy-Site in Edendale, Southland, New Zealand. This Plant consists of a DAF-Unit (Dissolved Air Flotation), two Extended Aeration Lagoons with Activated Sludge and two Clarifiers, one for the Activated Sludge and the second for the dosing of Aluminium-Sulphate and the removal of Phosphat-Sulphate. Biological processes for the removal of carbon- and energy-sources were optimised and biological processes for the reduction of Nitrogen- and Phosphate-Concentrations within the wastewater were implemented and optimised. Bilogical removal rates for COD of 95\% and above, for Nitrogen of 85-92\% and Phosphate of 64-83\% were achieved.}, subject = {Biologische Abwasserreinigung}, language = {en} } @phdthesis{Vainshtein2010, author = {Vainshtein, Yevhen}, title = {Applying microarray-based techniques to study gene expression patterns: a bio-computational approach}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51967}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {The regulation and maintenance of iron homeostasis is critical to human health. As a constituent of hemoglobin, iron is essential for oxygen transport and significant iron deficiency leads to anemia. Eukaryotic cells require iron for survival and proliferation. Iron is part of hemoproteins, iron-sulfur (Fe-S) proteins, and other proteins with functional groups that require iron as a cofactor. At the cellular level, iron uptake, utilization, storage, and export are regulated at different molecular levels (transcriptional, mRNA stability, translational, and posttranslational). Iron regulatory proteins (IRPs) 1 and 2 post-transcriptionally control mammalian iron homeostasis by binding to iron-responsive elements (IREs), conserved RNA stem-loop structures located in the 5'- or 3'- untranslated regions of genes involved in iron metabolism (e.g. FTH1, FTL, and TFRC). To identify novel IRE-containing mRNAs, we integrated biochemical, biocomputational, and microarray-based experimental approaches. Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Methods In this project response to the iron treatment was examined under different conditions using bioinformatical methods. This would improve our understanding of an iron regulatory network. For these purposes we used microarray gene expression data. To identify novel IRE-containing mRNAs biochemical, biocomputational, and microarray-based experimental approaches were integrated. IRP/IRE messenger ribonucleoproteins were immunoselected and their mRNA composition was analysed using an IronChip microarray enriched for genes predicted computationally to contain IRE-like motifs. Analysis of IronChip microarray data requires specialized tool which can use all advantages of a customized microarray platform. Novel decision-tree based algorithm was implemented using Perl in IronChip Evaluation Package (ICEP). Results IRE-like motifs were identified from genomic nucleic acid databases by an algorithm combining primary nucleic acid sequence and RNA structural criteria. Depending on the choice of constraining criteria, such computational screens tend to generate a large number of false positives. To refine the search and reduce the number of false positive hits, additional constraints were introduced. The refined screen yielded 15 IRE-like motifs. A second approach made use of a reported list of 230 IRE-like sequences obtained from screening UTR databases. We selected 6 out of these 230 entries based on the ability of the lower IRE stem to form at least 6 out of 7 bp. Corresponding ESTs were spotted onto the human or mouse versions of the IronChip and the results were analysed using ICEP. Our data show that the immunoselection/microarray strategy is a feasible approach for screening bioinformatically predicted IRE genes and the detection of novel IRE-containing mRNAs. In addition, we identified a novel IRE-containing gene CDC14A (Sanchez M, et al. 2006). The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip, but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls (Vainshtein Y, et al., 2010).}, subject = {Microarray}, language = {en} } @phdthesis{KuklovskyformerFinke2024, author = {Kuklovsky [former Finke], Valerie}, title = {Are some bees smarter than others? An examination of consistent individual differences in the cognitive abilities of honey bees}, doi = {10.25972/OPUS-32301}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-323012}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {Cognition refers to the ability to of animals to acquire, process, store and use vital information from the environment. Cognitive processes are necessary to predict the future and reduce the uncertainty of the ever-changing environment. Classically, research on animal cognition focuses on decisive cognitive tests to determine the capacity of a species by the testing the ability of a few individuals. This approach views variability between these tested key individuals as unwanted noise and is thus often neglected. However, inter-individual variability provides important insights to behavioral plasticity, cognitive specialization and brain modularity. Honey bees Apis mellifera are a robust and traditional model for the study of learning, memory and cognition due to their impressive capabilities and rich behavioral repertoire. In this thesis I have applied a novel view on the learning abilities of honey bees by looking explicitly at individual differences in a variety of learning tasks. Are some individual bees consistently smarter than some of her sisters? If so, will a smart individual always perform good independent of the time, the context and the cognitive requirements or do bees show distinct isolated 'cognitive modules'? My thesis presents the first comprehensive investigation of consistent individual differences in the cognitive abilities of honey bees. To speak of an individual as behaving consistently, a crucial step is to test the individual multiple times to examine the repeatability of a behavior. I show that free-flying bees remain consistent in a visual discrimination task for three consecutive days. Successively, I explored individual consistency in cognitive proficiency across tasks involving different sensory modalities, contexts and cognitive requirements. I found that free-flying bees show a cognitive specialization between visual and olfactory learning but remained consistent across a simple discrimination task and a complex concept learning task. I wished to further explore individual consistency with respect to tasks of different cognitive complexity, a question that has never been tackled before in an insect. I thus performed a series of four experiments using either visual or olfactory stimuli and a different training context (free-flying and restrained) and tested bees in a discrimination task, reversal learning and negative patterning. Intriguingly, across all these experiments I evidenced the same results: The bees' performances were consistent across the discrimination task and reversal learning and negative patterning respectively. No association was evidenced between reversal learning and negative patterning. After establishing the existence of consistent individual differences in the cognitive proficiency of honey bees I wished to determine factors which could underlie these differences. Since genetic components are known to underlie inter-individual variability in learning abilities, I studied the effects of genetics on consistency in cognitive proficiency by contrasting bees originating from either from a hive with a single patriline (low genetic diversity) or with multiple patrilines (high genetic diversity). These two groups of bees showed differences in the patterns of individually correlated performances, indicating a genetic component accounts for consistent cognitive individuality. Another major factor underlying variability in learning performances is the individual responsiveness to sucrose solution and to visual stimuli, as evidenced by many studies on restrained bees showing a positive correlation between responsiveness to task relevant stimuli and learning performances. I thus tested whether these relationships between sucrose/visual responsiveness and learning performances are applicable for free-flying bees. Free-flying bees were again subjected to reversal learning and negative patterning and subsequently tested in the laboratory for their responsiveness to sucrose and to light. There was no evidence of a positive relationship between sucrose/visual responsiveness and neither performances of free-flying bees in an elemental discrimination, reversal learning and negative patterning. These findings indicate that relationships established between responsiveness to task relevant stimuli and learning proficiency established in the laboratory with restrained bees might not hold true for a completely different behavioral context i.e. for free-flying bees in their natural environment. These results show that the honey bee is an excellent insect model to study consistency in cognitive proficiency and to identify the underlying factors. I mainly discuss the results with respect to the question of brain modularity in insects and the adaptive significance of individuality in cognitive abilities for honey bee colonies. I also provide a proposition of research questions which tie in this theme of consistent cognitive proficiency and could provide fruitful areas for future research.}, subject = {Lernen}, language = {en} } @phdthesis{Muenz2015, author = {M{\"u}nz, Thomas Sebastian}, title = {Aspects of neuronal plasticity in the mushroom body calyx during adult maturation in the honeybee Apis mellifera}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-111611}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {Division of labor represents a major advantage of social insect communities that accounts for their enormous ecological success. In colonies of the honeybee, Apis mellifera, division of labor comprises different tasks of fertile queens and drones (males) and, in general, sterile female workers. Division of labor also occurs among workers in form of an age-related polyethism. This helps them to deal with the great variety of tasks within the colony. After adult eclosion, workers spend around three weeks with various duties inside the hive such as tending the brood or cleaning and building cells. After this period workers switch to outdoor tasks and become foragers collecting nectar, pollen and water. With this behavioral transition, workers face tremendous changes in their sensory environment. In particular, visual sensory stimuli become important, but also the olfactory world changes. Foragers have to perform a completely new behavioral repertoire ranging from long distance navigation based on landmark orientation and polarized-skylight information to learning and memory tasks associated with finding profitable food sources. However, behavioral maturation is not a purely age-related internal program associated with a change, for example, in juvenile hormone titers. External factors such as primer pheromones like the brood pheromone or queen mandibular pheromone can modulate the timing of this transition. In this way colonies are able to flexibly adjust their work force distribution between indoor and outdoor tasks depending on the actual needs of the colony. Besides certain physiological changes, mainly affecting glandular tissue, the transition from indoor to outdoor tasks requires significant adaptations in sensory and higher-order integration centers of the brain. The mushroom bodies integrate olfactory, visual, gustatory and mechanosensory information. Furthermore, they play important roles in learning and memory processes. It is therefore not surprising that the mushroom bodies, in particular their main input region, the calyx, undergo volumetric neuronal plasticity. Similar to behavioral maturation, plastic changes of the mushroom bodies are associated with age, but are also to be affected by modulating factors such as task and experience. In my thesis, I analyzed in detail the neuronal processes underlying volumetric plasticity in the mushroom body. Immunohistochemical labeling of synaptic proteins combined with quantitative 3D confocal imaging revealed that the volume increase of the mushroom body calyx is largely caused by the growth of the Kenyon cell dendritic network. This outgrowth is accompanied by changes in the synaptic architecture of the mushroom body calyx, which is organized in a distinct pattern of synaptic complexes, so called microglomeruli. During the first week of natural adult maturation microglomeruli remain constant in total number. With subsequent behavioral transition from indoor duties to foraging, microglomeruli are pruned while the Kenyon cell dendritic network is still growing. As a result of these processes, the mushroom body calyx neuropil volume enlarges while the total number of microgloumeruli becomes reduced in foragers compared to indoor workers. In the visual subcompartments (calyx collar) this process is induced by visual sensory stimuli as the beginning of pruning correlates with the time window when workers start their first orientation flights. The high level of analysis of cellular and subcellular process underlying structural plasticity of the mushroom body calyx during natural maturation will serve as a framework for future investigations of behavioral plasticity in the honeybee. The transition to foraging is not purely age-dependent, but gets modulated, for example, by the presence of foragers. Ethyl oleate, a primer pheromone that is present only in foragers, was shown to delay the onset of foraging in nurse bees. Using artificial application of additional ethyl oleate in triple cohort colonies, I tested whether it directly affects adult neuronal plasticity in the visual input region of the mushroom body calyx. As the pheromonal treatment failed to induce a clear behavioral phenotype (delayed onset of foraging) it was not possible to show a direct link between the exposure to additional ethyl oleate and neuronal plasticity in mushroom body calyx. However, the general results on synaptic maturation confirmed my data of natural maturation processes in the mushroom body calyx. Given the result that dendritic plasticity is a major contributor to neuronal plasticity in the mushroom body calyx associated with division of labor, the question arose which proteins could be involved in mediating these effects. Calcium/calmodulin-dependent protein kinase II (CaMKII) especially in mammals, but also in insects (Drosophila, Cockroach), was shown to be involved in facilitating learning and memory processes like long-term synaptic potentiation. In addition to presynaptic effects, the protein was also revealed to directly interact with cytoskeleton elements in the postsynapse. It therefore is a likely candidate to mediate structural synaptic plasticity. As part of my thesis, the presence and distribution of CaMKII was analyzed, and the results showed that the protein is highly concentrated in a distinct subpopulation of the mushroom body intrinsic neurons, the noncompact Kenyon cells. The dendritic network of this population arborizes in two calyx subregions: one receiving mainly olfactory input - the lip - and the collar receiving visual input. This distribution pattern did not change with age or task. The high concentration of CaMKII in dendritic spines and its overlap with f-actin indicates that CaMKII could be a key player inducing structural neuronal plasticity associated with learning and memory formation and/or behavioral transitions related to division of labor. Interestingly CaMKII immunoreactivity was absent in the basal ring, another subregion of the mushroom body calyx formed almost exclusively by the inner compact Kenyon cells and known to receive combined visual and olfactory input. This indicates differences of this mushroom body subregion regarding the molecular mechanisms controlling plastic changes in corresponding Kenyon cells. How is timing of behavioral and neuronal plasticity regulated? The primer pheromone ethyl oleate was found in high concentrations on foragers and was shown to influence behavioral maturation by delaying the onset of foraging when artificially applied in elevated concentrations. But how is ethyl oleate transferred and how does it shift the work force distribution between indoor and outdoor tasks? Previous work showed that ethyl oleate concentrations are highest in the honeycrop of foragers and suggested that it is transferred and communicated inside the colony via trophallaxis. The results of this thesis however clearly show, that ethyl oleate was not present inside the honey crop or the regurgitate, but rather in the surrounding tissue of the honey crop. As additionally the second highest concentration of ethyl oleate was measured on the surface of the cuticle of forgers, trophallaxis was ruled out as a mode of transmission. Neurophysiological measurements at the level of the antennae (electroantennogram recordings) and the first olfactory neuropil (calcium imaging of activity in the antennal lobe) revealed that the primer pheromone ethyl oleate is received and processed as an olfactory stimulus. Appetitive olfactory conditioning using the proboscis extension response as a behavioral paradigm showed that ethyl oleate can be associated with a sugar reward. This indicates that workers are able to perceive, learn and memorize the presence of this pheromone. As ethyl oleate had to be presented by a heated stimulation device at close range, it can be concluded that this primer pheromone acts via close range/contact chemoreception through the olfactory system. This is also supported by previous behavioral observations. Taken together, the findings presented in this thesis revealed structural changes in the synaptic architecture of the mushroom body calyx associated with division of labor. For the primer pheromone ethyl oleate, which modulates the transition from nursing to foraging, the results clearly showed that it is received via the olfactory system and presumably acts via this pathway. However, manipulation experiments did not indicate a direct effect of ethyl oleate on synaptic plasticity. At the molecular level, CaMKII is a prime candidate to mediate structural synaptic plasticity in the mushroom body calyx. Future combined structural and functional experiments are needed to finally link the activity of primer pheromones like ethyl oleate to the molecular pathways mediating behavioral and synaptic plasticity associated with division of labor in Apis mellifera. The here identified underlying processes will serve as excellent models for a general understanding of fundamental mechanisms promoting behavioral plasticity.}, subject = {Biene}, language = {en} } @phdthesis{Yarali2008, author = {Yarali, Ayse}, title = {Aspects of predictive learning in the fruit fly}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-28741}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {Past experience contributes to behavioural organization mainly via learning: Animals learn otherwise ordinary cues as predictors for biologically significant events. This thesis studies such predictive, associative learning, using the fruit fly Drosophila melanogaster. I ask two main questions, which complement each other: One deals with the processing of those cues that are to be learned as predictors for an important event; the other one deals with the processing of the important event itself, which is to be predicted. Do fruit flies learn about combinations of olfactory and visual cues? I probe larval as well as adult fruit flies for the learning about combinations of olfactory and visual cues, using a so called 'biconditional discrimination' task: During training, one odour is paired with reinforcement only in light, but not in darkness; the other odour in turn is reinforced only in darkness, but not in light. Thus, neither the odours nor the visual conditions alone predict reinforcement, only combinations of both do. I find no evidence that either larval or adult fruit flies were to solve such task, speaking against a cross-talk between olfactory and visual modalities. Previous studies however suggest such cross-talk. To reconcile these results, I suggest classifying different kinds of interaction between sensory modalities, according to their site along the sensory-motor continuum: I consider an interaction 'truly' cross-modal, if it is between the specific features of the stimuli. I consider an interaction 'amodal' if it instead engages the behavioural tendencies or 'values' elicited by each stimulus. Such reasoning brings me to conclude that different behavioural tasks require different kinds of interaction between sensory modalities; whether a given kind of interaction will be found depends on the neuronal infrastructure, which is a function of the species and the developmental stage. Predictive learning of pain-relief in fruit flies Fruit flies build two opposing kinds of memory, based on an experience with electric shock: Those odours that precede shock during training are learned as predictors for punishment and are subsequently avoided; those odours that follow shock during training on the other hand are learned as signals for relief and are subsequently approached. I focus on such relief learning. I start with a detailed parametric analysis of relief learning, testing for reproducibility as well as effects of gender, repetition of training, odour identity, odour concentration and shock intensity. I also characterize how relief memories, once formed, decay. In addition, concerning the psychological mechanisms of relief learning, first, I show that relief learning establishes genuinely associative conditioned approach behaviour and second, I report that it is most likely not mediated by context associations. These results enable the following neurobiological analysis of relief learning; further, they will form in the future the basis for a mathematical model; finally, they will guide the researchers aiming at uncovering relief learning in other experimental systems. Next, I embark upon neurogenetic analysis of relief learning. First, I report that fruit flies mutant for the so called white gene build overall more 'negative' memories about an experience with electric shock. That is, in the white mutants, learning about the painful onset of shock is enhanced, whereas learning about the relieving offset of shock is diminished. As they are coherently affected, these two kinds of learning should be in a balance. The molecular mechanism of the effect of white on this balance remains unresolved. Finally, as a first step towards a neuronal circuit analysis of relief learning, I compare it to reward learning and punishment learning. I find that relief learning is distinct from both in terms of the requirement for biogenic amine signaling: Reward and punishment are respectively signalled by octopamine and dopamine, for relief learning, either of these seem dispensible. Further, I find no evidence for roles for two other biogenic amines, tyramine and serotonin in relief learning. Based on these findings I give directions for further research.}, subject = {Lernen}, language = {en} } @phdthesis{Hauff2009, author = {Hauff, Cornelia}, title = {Aspects of the mode of action of bispecific T cell engager (BiTE) antibodies}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48369}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2009}, abstract = {Bispecific T cell engager (BiTE) display a novel design among the class of bispecific antibodies and hold great promise to fight diverse cancers. BiTE molecules consist of two different binding entities derived from two human IgG antibodies connected by a short peptide linker. Their binding arms are directed against the CD3e chain of the T cell receptor on T cells and against an antigen that is specific for (e.g., CD19 for lymphoma in MT103) or over-expressed on (e.g., EpCAM for epithelial cancer in MT110) tumor cells. Without requirement for pre- or co-stimulation, BiTE molecules efficiently redirect CD3+ T cells towards tumor cells expressing the relevant target antigen. Only a BiTE molecule simultaneously bound to both tumor cell and T cell activates the T cell to exert its cytolytic function resulting in tumor cell death. In T cells stimulated with both BiTE and target cells, elevated levels of caspase activation and increased expression of cytotoxic and signaling proteins are observed. These include cytolytic proteins granzyme B and perforin, activation markers CD69 and CD25 and adhesion molecules CD2 and LFA-1. Activated T cells secrete the usual mix of cytokines, among them pro-inflammatory cytokines IFN-g and TNF-a. The membrane of tumor cells expressing the relevant target antigen is perforated during the attack of BiTE-stimulated effector cells as can be concluded from adenylate kinase release from the cytosol of tumor cells. Ca2+-chelator EGTA completely blocked BiTE-mediated activation of caspases and tumor cell lysis. As perforin is strictly Ca2+-dependent, a major role for this pore-forming protein is assumed for the elimination of tumor cells via BiTE-stimulated T cells. Granzyme B and caspases are main players in BiTE-mediated elimination of tumor cells. Inhibitors of granzyme B or caspases reduce or block, respectively the activation of caspases. However, other signals of apoptosis (cleavage of PARP and fragmentation of DNA) were only reduced by granzyme B inhibitor or caspase inhibitor. Most interestingly, the lytic capacity of BiTE molecules was not impaired by granzyme B inhibitor or caspase inhibitor. It seems that there is no requirement for granzyme B and caspases to be present simultaneously. Instead the data presented provide evidence that they can be replaced one at a time by related proteins. Pre-incubation of effector cells with the glucocorticoids dexamethasone or methylprednisolone resulted in markedly decreased secretion of cytokines by T cells yet only a small reduction in the expression of activation markers and adhesion molecules on T cells and specific lysis of tumor cells upon BiTE stimulation. Soluble factors secreted in an undirected manner by BiTE-stimulated T cells do not mediate tumor cell death by themselves. Bystander cells negative for the antigen that is recognized by the BiTE molecule will not be compromised by BiTE activity. The cytokine TGF-b reduced proliferation as well as granzyme B and perforin expression of BiTE-stimulated T cells. Redirected lysis by BiTE-activated T cells was also decreased under the influence of TGF-b, however lysis was still performed at a reasonable rate (72 \% of target cells). TGF-b does not exert a deleterious effect on lytic potential of BiTE-stimulated T cells. The minimal anticipated biological effect level for the BiTE MT110 was determined for the entry of MT110 into phase I clinical studies. Experiments analyzing redirected lysis of tumor cells, expression of activation marker CD25 and cytokine release by T cells revealed a MABEL value of 50 pg/ml for MT110.}, subject = {Antik{\"o}rper}, language = {en} } @phdthesis{Heidbreder2012, author = {Heidbreder, Meike}, title = {Association and Activation of TNF-Receptor I Investigated with Single-Molecule Tracking and Super-Resolution Microscopy in Live Cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-73191}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Cellular responses to outer stimuli are the basis for all biological processes. Signal integration is achieved by protein cascades, recognizing and processing molecules from the environment. Factors released by pathogens or inflammation usually induce an inflammatory response, a signal often transduced by Tumour Necrosis Factor alpha (TNF). TNFα receptors TNF-R1 and TNF-R2 can in turn lead to apoptosis or proliferation via NF-B. These processes are closely regulated by membrane compartimentalization, protein interactions and trafficking. Fluorescence microscopy offers a reliable and non-invasive method to probe these cellular events. However, some processes on a native membrane are not resolvable, as they are well below the diffraction limit of microscopy. The recent development of super-resolution fluorescence microscopy methods enables the observation of these cellular players well below this limit: by localizing, tracking and counting molecules with high spatial and temporal resolution, these new fluorescence microscopy methods offer a previously unknown insight into protein interactions at the near-molecular level. Direct stochastic optical reconstruction microscopy (dSTORM) utilizes the reversible, stochastic blinking events of small commercially available fluorescent dyes, while photoactivated localization microscopy (PALM) utilizes phototransformation of genetically encoded fluorescent proteins. By photoactivating only a small fraction of the present fluorophores in each observation interval, single emitters can be localized with high precision and a super-resolved image can be reconstructed. Quantum Dot Triexciton imaging (QDTI) utilizes the three-photon absorption (triexcitonic) properties of quantum dots (QD) and to achieve a twofold resolution increase using conventional confocal microscopes. In this thesis, experimental approaches were implemented to achieve super-resolution microscopy in fixed and live-cells to study the spatial and temporal dynamics of TNF and other cellular signaling events. We introduce QDTI to study the three-dimensional cellular distribution of biological targets, offering an easy method to achieve resolution enhancement in combination with optical sectioning, allowing the preliminary quantification of labeled proteins. As QDs are electron dense, QDTI can be used for correlative fluorescence and transmission electron microscopy, proving the versatility of QD probes. Utilizing the phototransformation properties of fluorescent proteins, single-receptor tracking on live cells was achieved, applying the concept of single particle tracking PALM (sptPALM) to track the dynamics of a TNF-R1-tdEos chimera on the membrane. Lateral receptor dynamics can be tracked with high precision and the influences of ligand addition or lipid disruption on TNF-R1 mobility was observed. The results reveal complex receptor dynamics, implying internalization processes in response to TNFα stimulation and a role for membrane domains with reduced fluidity, so-called lipid raft domains, in TNF-R1 compartimentalization prior or post ligand induction. Comparisons with previously published FCS data show a good accordance, but stressing the increased data depth available in sptPALM experiments. Additionally, the active transport of NF-κB-tdEos fusions was observed in live neurons under chemical stimulation and/or inhibition. Contrary to phototransformable proteins that need no special buffers to exhibit photoconversion or photoactivation, dSTORM has previously been unsuitable for in vivo applications, as organic dyes relied on introducing the probes via immunostaining in concert with a reductive, oxygen-free medium for proper photoswitching behaviour. ATTO655 had been previously shown to be suitable for live-cell applications, as its switching behavior can be catalyzed by the reductive environment of the cytoplasm. By introducing the cell-permeant organic dye via a chemical tag system, a high specificity and low background was achieved. Here, the labeled histone H2B complex and thus single nucleosome movements in a live cell can be observed over long time periods and with ~20 nm resolution. Implementing these new approaches for imaging biological processes with high temporal and spatial resolution provides new insights into the dynamics and spatial heterogeneities of proteins, further elucidating their function in the organism and revealing properties that are usually only detectable in vitro.  }, subject = {Fluoreszenzmikrosopie}, language = {en} } @phdthesis{Roeschert2021, author = {R{\"o}schert, Isabelle}, title = {Aurora-A prevents transcription-replication conflicts in MYCN-amplified neuroblastoma}, doi = {10.25972/OPUS-24303}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-243037}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Neuroblastoma is the most abundant, solid, extracranial tumor in early childhood and the leading cause of cancer-related childhood deaths worldwide. Patients with high-risk neuroblastoma often show MYCN-amplification and elevated levels of Aurora-A. They have a low overall survival and despite multimodal therapy options a poor therapeutic prognosis. MYCN-amplified neuroblastoma cells depend on Aurora-A functionality. Aurora-A stabilizes MYCN and prevents it from proteasomal degradation by competing with the E3 ligase SCFFBXW7. Interaction between Aurora-A and MYCN can be observed only in S phase of the cell cycle and activation of Aurora-A can be induced by MYCN in vitro. These findings suggest the existence of a profound interconnection between Aurora-A and MYCN in S phase. Nevertheless, the details remain elusive and were investigated in this study. Fractionation experiments show that Aurora-A is recruited to chromatin in S phase in a MYCN-dependent manner. Albeit being unphosphorylated on the activating T288 residue, Aurora-A kinase activity was still present in S phase and several putative, novel targets were identified by phosphoproteomic analysis. Particularly, eight phosphosites dependent on MYCN-activated Aurora-A were identified. Additionally, phosphorylation of serine 10 on histone 3 was verified as a target of this complex in S phase. ChIP-sequencing experiments reveal that Aurora-A regulates transcription elongation as well as histone H3.3 variant incorporation in S phase. 4sU-sequencing as well as immunoblotting demonstrated that Aurora-A activity impacts splicing. PLA measurements between the transcription and replication machinery revealed that Aurora-A prevents the formation of transcription-replication conflicts, which activate of kinase ATR. Aurora-A inhibitors are already used to treat neuroblastoma but display dose-limiting toxicity. To further improve Aurora-A based therapies, we investigated whether low doses of Aurora-A inhibitor combined with ATR inhibitor could increase the efficacy of the treatment albeit reducing toxicity. The study shows that the combination of both drugs leads to a reduction in cell growth as well as an increase in apoptosis in MYCN-amplified neuroblastoma cells, which is not observable in MYCN non-amplified neuroblastoma cells. This new approach was also tested by a collaboration partner in vivo resulting in a decrease in tumor burden, an increase in overall survival and a cure of 25\% of TH-MYCN mice. These findings indicate indeed a therapeutic window for targeting MYCN-amplified neuroblastoma.}, subject = {Neuroblastom}, language = {en} } @phdthesis{Grimm2019, author = {Grimm, Johannes}, title = {Autocrine and paracrine effects of BRAF inhibitor induced senescence in melanoma}, doi = {10.25972/OPUS-18116}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-181161}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2019}, abstract = {The FDA approval of targeted therapy with BRAFV600E inhibitors like vemurafenib and dabrafenib in 2011 has been the first major breakthrough in the treatment of metastatic melanoma since almost three decades. Despite increased progression free survival and elevated overall survival rates, complete responses are scarce due to resistance development approximately six months after the initial drug treatment. It was previously shown in our group that melanoma cells under vemurafenib pressure in vitro and in vivo exhibit features of drug-induced senescence. It is known that some cell types, which undergo this cell cycle arrest, develop a so-called senescence associated secretome and it has been reported that melanoma cell lines also upregulate the expression of different factors after senescence induction. This work describes the effect of the vemurafenib-induced secretome on cells. Conditioned supernatants of vemurafenib-treated cells increased the viability of naive fibroblast and melanoma cell lines. RNA analysis of donor melanoma cells revealed elevated transcriptional levels of FGF1, MMP2 and CCL2 in the majority of tested cell lines under vemurafenib pressure, and I could confirm the secretion of functional proteins. Similar observations were also done after MEK inhibition as well as in a combined BRAF and MEK inhibitor treatment situation. Interestingly, the transcription of other FGF ligands (FGF7, FGF17) was also elevated after MEK/ERK1/2 inhibition. As FGF receptors are therapeutically relevant, I focused on the analysis of FGFR-dependent processes in response to BRAF inhibition. Recombinant FGF1 increased the survival rate of melanoma cells under vemurafenib pressure, while inhibition of the FGFR pathway diminished the viability of melanoma cells in combination with vemurafenib and blocked the stimulatory effect of vemurafenib conditioned medium. The BRAF inhibitor induced secretome is regulated by active PI3K/AKT signaling, and the joint inhibition of mTor and BRAFV600E led to decreased senescence induction and to a diminished induction of the secretome-associated genes. In parallel, combined inhibition of MEK and PI3K also drastically decreased mRNA levels of the relevant secretome components back to basal levels. In summary, I could demonstrate that BRAF inhibitor treated melanoma cell lines acquire a specific PI3K/AKT dependent secretome, which is characterized by FGF1, CCL2 and MMP2. This secretome is able to stimulate other cells such as naive melanoma cells and fibroblasts and contributes to a better survival under drug pressure. These data are therapeutically highly relevant, as they imply the usage of novel drug combinations, especially specific FGFR inhibitors, with BRAF inhibitors in the clinic.}, subject = {Inhibitor}, language = {en} } @phdthesis{Seitz2020, author = {Seitz, Nicola}, title = {Bee demise and bee rise: From honey bee colony losses to finding measures for advancing entire bee communities}, doi = {10.25972/OPUS-18418}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-184180}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2020}, abstract = {My dissertation comprises three studies: (1) an assessment of honey bee colony losses in the USA between 2014 and 2015, (2) an exploration of the potential of reclaimed sand mines as bee habitat, and (3) an evaluation of native and non-native pollinator friendly plants in regard to their attraction to bees. While the first study focuses on honey bees, the latter two studies primarily take wild bees or entire bee communities in focus. The study on honey bee colony losses was conducted within the framework of the Bee Informed Partnership (BIP, beeinformed.org) and aligns with the annual colony loss surveys which have been conducted in the USA since the winter of 2006/2007. It was the fourth year for which summer and annual losses were calculated in addition to winter losses. Among participants, backyard beekeepers were the largest group (n = 5690), although sideline (n = 169) and commercial (n = 78) beekeepers managed the majority (91.7 \%) of the 414 267 surveyed colonies. Overall, 15.1 \% of the estimated 2.74 million managed colonies in the USA were included in the study. Total honey bee colony losses (based on the entirety of included colonies) were higher in summer (25.3 \%) than in winter (22.3 \%) and amounted to 40.6 \% for the entire 2014/2015 beekeeping year. Average colony losses per beekeeper or operation were higher in winter (43.7 \%) than in summer (14.7 \%) and amounted to 49 \% for the entire 2014/2015 beekeeping year. Due to the dominance of backyard beekeepers among participants, average losses per operation (or unweighted loss) stronger reflected this smaller type of beekeeper. Backyard beekeepers mainly named colony management issues (e.g., starvation, weak colony in the fall) as causes for mortality, while sideline and commercial beekeepers stronger emphasized parasites or factors outside their control (e.g., varroa, nosema, queen failure). The second study took place at reclaimed sand mines. Sand mines represent anthropogenically impacted habitats found worldwide, which bear potential for bee conservation. Although floral resources can be limited at these habitats, vegetation free patches of open sandy soils and embankments may offer good nesting possibilities for sand restricted and other bees. We compared bee communities as found in three reclaimed sand mines and at adjacent roadside meadows in Maryland, USA, over two years. Both sand mines and roadsides hosted diverse bee communities with 111 and 88 bee species, respectively. Bee abundances as well as richness and Shannon diversity of bee species were higher in sand mines than at roadsides and negatively correlated with the percentage of vegetational ground cover. Species composition also differed significantly between habitats. Sand mines hosted a higher proportion of ground nesters, more uncommon and more 'sand loving' bees similar to natural sandy areas of Maryland. Despite the destruction of the original pre-mining habitat, sand mines thus appear to represent a unique habitat for wild bees, particularly when natural vegetation and open sand spots are encouraged. Considering habitat loss, the lack of natural disturbance regimes, and ongoing declines of wild bees, sand mines could add promising opportunities for bee conservation which has hitherto mainly focused on agricultural and urban habitats. The third study was an experimental field study on pollinator friendly plants. Bees rely on the pollen and nectar of plants as their food source. Therefore, pollinator friendly plantings are often used for habitat enhancements in bee conservation. Non-native pollinator friendly plants may aid in bee conservation efforts, but have not been tested and compared with native pollinator friendly plants in a common garden experiment. In this study, we seeded mixes of 20 native and 20 non-native pollinator friendly plants in two separate plots at three sites in Maryland, USA. For two years, we recorded flower visitors to the plants throughout the blooming period and additionally sampled bees with pan traps. A total of 3744 bees (120 species) were sampled in the study. Of these, 1708 bees (72 species) were hand netted directly from flowers for comparisons between native and non-native plants. Depending on the season, bee abundance and species richness was either similar or lower (early season and for richness also late season) at native plots compared to non-native plots. Additionally, the overall bee community composition differed significantly between native and non-native plots. Furthermore, native plants were associated with more specialized plant-bee visitation networks compared to non-native plants. In general, visitation networks were more specialized in the early season than the later seasons. Four species (Bombus impatiens, Halictus poeyi/ligatus, Lasioglossum pilosum, and Xylocopa virginica) out of the five most abundant bee species (also including Apis mellifera) foraged more specialized on native than non-native plants. Our study showed that non-native plants were well accepted by a diverse bee community and had a similar to higher attraction for bees compared to native plants. However, we also demonstrated alterations in foraging behavior, bee community assemblage, and visitation networks. As long as used with caution, non-native plants can be a useful addition to native pollinator friendly plantings. This study gives a first example of a direct comparison between native and non-native pollinator friendly plants.}, subject = {Biene}, language = {en} } @phdthesis{Gabel2024, author = {Gabel, Martin Sebastian}, title = {Behavioural resistance to \(Varroa\) \(destructor\) in the Western honeybee \(Apis\) \(mellifera\) - Mechanisms leading to decreased mite reproduction}, doi = {10.25972/OPUS-36053}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-360536}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {The Western Honeybee (Apis mellifera) is among the most versatile species in the world. Its adaptability is rooted in thousands of the differently specialized individuals acting jointly together. Thus, bees that are able to handle a certain task or condition well can back up other individuals less capable to do so on the colony level. Vice versa, the latter individuals might perform better in other situations. This evolutionary recipe for success ensures the survival of colonies despite challenging habitat conditions. In this context, the ectoparasitic mite Varroa destructor reflects the most pronounced biotic challenge to honeybees worldwide. Without proper treatment, infested colonies rapidly dwindle and ultimately die. Nevertheless, resistance behaviours against this parasite have evolved in some populations through natural selection, enabling colonies to survive untreated. In this, different behaviours appear to be adapted to the respective habitat conditions and may complement each other. Yet, the why and how of this behavioural response to the mite remains largely unknown. My thesis focuses on the biological background of Varroa-resistance traits in honeybees and presents important findings for the comprehension of this complex host-parasite interaction. Based on this, I draw implications for both, applied bee breeding and scientific investigations in the field of Varroa-resistance. Specifically, I focus on two traits commonly found in resistant and, to a lower degree, also mite-susceptible colonies: decreased mite reproduction and the uncapping and subsequent recapping of sealed brood cells. Examining failures in the reproductive success of mites as a primary mechanism of Varroa-resistance, I was able to link them to specific bee behaviours and external factors. Since mite reproduction and the brood rearing of bees are inevitably connected, I first investigated the effects of brood interruption on the reproductive success of mites. Brood interruption decreased the reproductive success of mites both immediately and in the long term. By examining the causes of reproductive failure, I could show that this was mainly due to an increased share of infertile mites. Furthermore, I proved that interruption in brood rearing significantly increased the expression of recapping behaviour. These findings consequently showed a dynamic modulation of mite reproduction and recapping, as well as a direct effect of brood interruption on both traits. To further elucidate the plasticity in the expression of both traits, I studied mite reproduction, recapping behaviour and infestation levels over the course of three years. The resulting extensive dataset unveiled a significant seasonal variation in mite reproduction and recapping. In addition, I show that recapping decreases the reproductive success of mites by increasing delayed developing female offspring and cells lacking male offspring. By establishing a novel picture-based brood investigation method, I could furthermore show that both the removal of brood cells and recapping activity specifically target brood ages in which mite offspring would be expected. Recapping, however, did not cause infertility of mites. Considering the findings of my first study, this points towards complementary mechanisms. This underlines the importance of increased recapping behaviour and decreased mite reproduction as resistance traits, while at the same time emphasising the challenges of reliable data acquisition. To pave the way for a practical application of these findings in breeding, we then investigated the heritability (i.e., the share of genotypic variation on the observed phenotypic variation) of the accounted traits. By elaborating comparable test protocols and compiling data from over 4,000 colonies, we could, for the first time, demonstrate that recapping of infested cells and decreased reproductive success of mites are heritable (and thus selectable) traits in managed honeybee populations. My thesis proves the importance of recapping and decreased mite reproduction as resistance traits and therefore valuable goals for breeding efforts. In this regard, I shed light on the underlying mechanisms of both traits, and present clear evidence for their interaction and heritability.}, subject = {Varroa destructor}, language = {en} } @phdthesis{Heidinger2015, author = {Heidinger, Ina M. M.}, title = {Beyond metapopulation theory: Determinants of the dispersal capacity of bush crickets and grasshoppers}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-135068}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {Habitat fragmentation and destruction due to anthropogenic land use are the major causes of the increasing extinction risk of many species and have a detrimental impact on animal populations in numerous ways. The long-term survival and stability of spatially structured populations in fragmented landscapes largely depends on the colonisation of habitat patches and the exchange of individuals and genes between patches. The degree of inter-patch dispersal, in turn, depends on the dispersal ability of a species (i.e. the combination of physiological and morphological factors that facilitate dispersal) and the landscape structure (i.e. the nature of the landscape matrix or the spatial configuration of habitat patches). As fragmentation of landscapes is increasing and the number of species is continuously declining, a thorough understanding of the causes and consequences of dispersal is essential for managing natural populations and developing effective conservation strategies. In the context of animal dispersal, movement behaviour is intensively investigated with capture-mark-recapture studies. For the analysis of such experiments, the influence of marking technique, handling and translocation of marked animals on movement pattern is of crucial importance since it may mask the effects of the main research question. Chapter 2 of this thesis presents a capture-mark-recapture study investigating the effect of translocation on the movement behaviour of the blue-winged grasshopper Oedipoda caerulescens. Transferring individuals of this grasshopper species to suitable but unfamilliar sites has a significant influence on their movement behaviour. Translocated individuals moved longer distances, showed smaller daily turning angles, and thus their movements were more directed than those of resident individuals. The effect of translocation was most pronounced on the first day of the experiment, but may persist for longer. On average, daily moved distances of translocated individuals were about 50 \% longer than that of resident individuals because they have been transferred to an unfamiliar habitat patch. Depending on experiment duration, this leads to considerable differences in net displacement between translocated and resident individuals. In summary, the results presented in chapter 2 clearly point out that translocation effects should not be disregarded in future studies on arthropod movement, respectively dispersal. Studies not controlling for possible translocation effects may result in false predictions of dispersal behaviour, habitat detection capability or habitat preferences. Beside direct field observations via capture-mark-recapture methods, genetic markers can be used to investigate animal dispersal. Chapter 3 presents data on the genetic structure of populations of Metrioptera bicolor, a wing-dimorphic bush cricket, in a spatially structured landscape with patches of suitable habitat distributed within a diverse matrix of different habitat types. Using microsatellite markers, the effects of geographic distance and different matrix types on the genetic differentiation among 24 local populations was assessed. The results of this study clearly indicate that for M. bicolor the isolation of local populations severely depends on the type of surrounding matrix. The presence of forest and a river running through the study area was positively correlated with the extent of genetic differentiation between populations. This indicates that both matrix types severely impede gene flow and the exchange of individuals between local populations of this bush cricket. In addition, for a subsample of populations which were separated only by arable land or settlements, a significant positive correlation between pairwise genetic and geographic distances exists. For the complete data set, this correlation could not be found. This is most probably due to the adverse effect of forest and river on gene flow which dominates the effect of geographic distance in the limited set of patches investigated in this study. The analyses in chapter 3 clearly emphasize the differential resistance of different habitat types on dispersal and the importance of a more detailed view on matrix 'quality' in metapopulation studies. Studies that focus on the specific dispersal resistance of different matrix types may provide much more detailed information on the dispersal capacity of species than a mere analysis of isolation by distance. Such information is needed to improve landscape oriented models for species conservation. In addition to direct effects on realised dispersal (see chapter 3), landscape structure on its own is known to act as an evolutionary selection agent because it determines the costs and benefits of dispersal. Both morphological and behavioural traits of individuals and the degree to which a certain genotype responds to environmental variation have heritable components, and are therefore expected to be able to respond to selection pressures. Chapter 4 analyses the influence of patch size, patch connectivity (isolation of populations) and sand dynamics (stability of habitat) on thorax- and wing length as proxies for dispersal ability of O. caerulescens in coastal grey dunes. This study revealed clear and sex-specific effects of landscape dynamics and patch configuration on dispersal-related morphology. Males of this grasshopper species were smaller and had shorter wings if patches were larger and less connected. In addition, both sexes were larger in habitat patches with high sand dynamics compared to those in patches with lower dynamics. The investments in wing length were only larger in connected populations when sand dynamics were low, indicating that both landscape and patch-related environmental factors are of importance. These results are congruent with theoretical predictions on the evolution of dispersal in metapopulations. They add to the evidence that dispersal-related morphology varies and is selected upon in recently structured populations even at small spatial scales. Dispersal involves different individual fitness costs like increased predation risk, energy expenditure, costs of developing dispersal-related traits, failure to find new suitable habitat as well as reproductive costs. Therefore, the decision to disperse should not be random but depend on the developmental stage or the physiological condition of an individual just as on actual environmental conditions (context-dependent dispersal, e.g. sex- and wing morph-biased dispersal). Biased dispersal is often investigated by comparing the morphology, physiology and behaviour of females and males or sedentary and dispersive individuals. Studies of biased dispersal in terms of capture-mark-recapture experiments, investigating real dispersal and not routine movements, and genetic proofs of biased dispersal are still rare for certain taxa, especially for orthopterans. However, information on biased dispersal is of great importance as for example, undetected biased dispersal may lead to false conclusions from genetic data. In chapter 5 of this thesis, a combined approach of morphological and genetic analyses was used to investigate biased dispersal of M. bicolor. The presented results not only show that macropterous individuals are predestined for dispersal due to their morphology, the genetic data also indicate that macropters are more dispersive than micropters. Furthermore, even within the group of macropterous individuals, males are supposed to be more dispersive than females. To get an idea of the flight ability of M. bicolor, the morphological data were compared with that of Locusta migratoria and Schistocerca gregaria, which are proved to be very good flyers. Based on the morphological data presented here, one can assume a good flight ability for macropters of M. bicolor, although flying individuals of this species are seldom observed in natural populations.}, subject = {Heuschrecken <{\"U}berfamilie>}, language = {en} } @phdthesis{Bertho2016, author = {Bertho, Sylvain}, title = {Biochemical and molecular characterization of an original master sex determining gene in Salmonids}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139130}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Sexual development is a fundamental and versatile process that shapes animal morphology, physiology and behavior. The underlying developmental process is composed of the sex determination and the sex differentiation. Sex determination mechanisms are extremely labile among taxa. The initial triggers of the sex determination process are often genetics called sex determining genes. These genes are expressed in the bipotential gonad and tilt the balance to a developmental program allowing the differentiation of either a testis or an ovary. Fish represent a large and fascinating vertebrate group to study both sex determination and sex differentiation mechanisms. To date, among the known sex determining genes, three gene families namely sox, dmrt and TGF-β factors govern this developmental program. As exception to this rule, sdY "sexually dimorphic on the Y" does not belong to one of these families as it comes from the duplication / evolution of an ancestor gene related to immunity, i.e., the interferon related factor 9, irf9. sdY is the master sex determining gene in salmonids, a group of fishes that include species such as rainbow trout and Atlantic salmon. The present study was aimed to firstly characterize the features of SdY protein. Results indicate that SdY is predominantly localized in the cytoplasm tested in various fish and mammalian cell lines and confirmed by different methods. Predictive in silico analysis revealed that SdY is composed of a β-sandwich core surrounded by three α-helices as well specific characteristics conferring a putative protein-protein interaction site. Secondly, the study was aimed to understand how SdY could trigger testicular differentiation. SdY is a truncated divergent version of Irf9 that has a conserved protein-protein domain but lost the DNA interaction domain of its ancestor gene. It was then hypothesized that SdY could initiate testicular differentiation by protein-protein interactions. To evaluate this we first conducted a yeast-two-hybrid screen that revealed a high proportion of transcription factors including fox proteins. Using various biochemical and cellular methods we confirm an interaction between SdY and Foxl2, a major transcription factor involved in ovarian differentiation and identity maintenance. Interestingly, the interaction of SdY with Foxl2 leads to nuclear translocation of SdY from the cytoplasm. Furthermore, this SdY translocation mechanism was found to be specific to fish Foxl2 and to a lesser extend Foxl3 and not other Fox proteins or mammalian FoxL2. In addition, we found that this interaction allows the stabilization of SdY and prevents its degradation. Finally, to better decipher SdY action we used as a model a mutated version of SdY that was identified in XY females of Chinook salmon natural population. Results show that this mutation induces a local conformation defect obviously leading to a misfolded protein and a quick degradation. Moreover, the mutated version compromised the interaction with Foxl2 defining a minimal threshold to induce testicular differentiation. Altogether results from my thesis propose that SdY would trigger testicular differentiation in salmonids by preventing Foxl2 to promote ovarian differentiation. Further research should be now carried out on how this interaction of SdY and Foxl2 acts in-vivo.}, subject = {Lachsartige }, language = {en} } @phdthesis{Fackler2014, author = {Fackler, Marc}, title = {Biochemical characterization of GAS2L3, a target gene of the DREAM complex}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-103394}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {GAS2L3 was identified recently as a target gene of the DREAM complex (Reichert et al., 2010; Wolter et al., 2012). It was shown that GAS2L3 is expressed in a cell cycle specific manner and that depletion of the protein leads to defects in cytokinesis and genomic instability (Wolter et al., 2012). Major aim of this thesis was, to further characterize the biochemical properties and physiological function of GAS2L3. By in vitro co-sedimentation and bundling assays, GAS2L3 was identified as a cytoskeleton associated protein which bundles, binds and crosslinks F-actin and MTs. GST pulldown assays and co-immunoprecipitation experiments revealed that GAS2L3 interacts in vitro and in vivo with the chromosomal passenger complex (CPC), a very important regulator of mitosis and cytokinesis, and that the interaction is mediated by the GAR domain of GAS2L3 and the C-terminal part of Borealin and the N-terminal part of Survivin. Kinase assays showed that GAS2L3 is not a substrate of the CPC but is strongly phosphorylated by CDK1 in vitro. Depletion of GAS2L3 by shRNA influenced protein stability and activity of the CPC. However pharmacological studies showed that the decreased CPC activity is not responsible for the observed cytokinesis defects upon GAS2L3 depletion. Immunofluorescence experiments revealed that GAS2L3 is localized to the constriction zone by the CPC in a GAR dependent manner and that the GAR domain is important for proper protein function. New interacting proteins of GAS2L3 were identified by stable isotope labelling by amino acids in cell culture (SILAC) in combination with tandem affinity purification and subsequent mass spectrometrical analysis. Co-immunoprecipitation experiments further confirmed the obtained mass spectrometrical data. To address the physiological function of GAS2L3 in vivo, a conditional and a non-conditional knockout mouse strain was established. The non-conditional mouse strain showed a highly increased mortality rate before weaning age probably due to heart failure. The physiological function of GAS2L3 in vivo as well as the exact reason for the observed heart phenotype is not known at the moment.}, subject = {Zellzyklus}, language = {en} } @phdthesis{Gruendl2021, author = {Gr{\"u}ndl, Marco}, title = {Biochemical characterization of the MMB-Hippo crosstalk and its physiological relevance for heart development}, doi = {10.25972/OPUS-21332}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213328}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {The Myb-MuvB (MMB) complex plays an essential role in the time-dependent transcriptional activation of mitotic genes. Recently, our laboratory identified a novel crosstalk between the MMB-complex and YAP, the transcriptional coactivator of the Hippo pathway, to coregulate a subset of mitotic genes (Pattschull et al., 2019). Several genetic studies have shown that the Hippo-YAP pathway is essential to drive cardiomyocyte proliferation during cardiac development (von Gise et al., 2012; Heallen et al., 2011; Xin et al., 2011). However, the exact mechanisms of how YAP activates proliferation of cardiomyocytes is not known. This doctoral thesis addresses the physiological role of the MMB-Hippo crosstalk within the heart and characterizes the YAP-B-MYB interaction with the overall aim to identify a potent inhibitor of YAP. The results reported in this thesis indicate that complete loss of the MMB scaffold protein LIN9 in heart progenitor cells results in thinning of ventricular walls, reduced cardiomyocyte proliferation and early embryonic lethality. Moreover, genetic experiments using mice deficient in SAV1, a core component of the Hippo pathway, and LIN9-deficient mice revealed that the correct function of the MMB complex is critical for proliferation of cardiomyocytes due to Hippo-deficiency. Whole genome transcriptome profiling as well as genome wide binding studies identified a subset of Hippo-regulated cell cycle genes as direct targets of MMB. By proximity ligation assay (PLA), YAP and B-MYB were discovered to interact in embryonal cardiomyocytes. Biochemical approaches, such as co-immunoprecipitation assays, GST-pulldown assays, and µSPOT-based peptide arrays were employed to characterize the YAP-B-MYB interaction. Here, a PY motif within the N-terminus of B-MYB was found to directly interact with the YAP WW-domains. Consequently, the YAP WW-domains were important for the ability of YAP to drive proliferation in cardiomyocytes and to activate MMB target genes in differentiated C2C12 cells. The biochemical information obtained from the interaction studies was utilized to develop a novel competitive inhibitor of YAP called MY-COMP (Myb-YAP competition). In MY-COMP, the protein fragment of B-MYB containing the YAP binding domain is fused to a nuclear localization signal. Co-immunoprecipitation studies as well as PLA revealed that the YAP-B-MYB interaction is robustly blocked by expression of MY-COMP. Adenoviral overexpression of MY-COMP in embryonal cardiomyocytes suppressed entry into mitosis and blocked the pro-proliferative function of YAP. Strikingly, characterization of the cellular phenotype showed that ectopic expression of MY-COMP led to growth defects, nuclear abnormalities and polyploidization in HeLa cells. Taken together, the results of this thesis reveal the mechanism of the crosstalk between the Hippo signaling pathway and the MMB complex in the heart and form the basis for interference with the oncogenic activity of the Hippo coactivator YAP.}, subject = {Zellzyklus}, language = {en} } @phdthesis{Kortmann2022, author = {Kortmann, Mareike}, title = {Biodiversity and recreation - Optimizing tourism and forest management in forests affected by bark beetles}, doi = {10.25972/OPUS-24031}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-240317}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2022}, abstract = {Forests are multi-functional system, which have to fulfil different objectives at the same time. The main functions include the production of wood, storage of carbon, the promotion of biological diversity and the provision of recreational space. Yet, global forests are affected by large and intense natural disturbances, like bark beetle infestations. While natural disturbances threaten wood production and are perceived as 'catastrophe' diminishing recreational value, biodiversity can benefit from the disturbance-induced changes in forest structures. This trade-off poses a dilemma to managers of bark beetle affected stands, particularly in protected areas designated to both nature conservation and recreation. Forest landscapes need a sustainable management concept aligning these different objectives. In order to support this goal with scientific knowledge, the aim of this work is to analyse ecological and social effects along a gradient of different disturbance severities. In this context, I studied the effects of a disturbance severity gradient on the diversity of different taxonomic groups including vascular plants, mosses, lichens, fungi, arthropods and birds in five national parks in Central Europe. To analyse the recreational value of the landscape I conducted visitor surveys in the same study areas in which the biodiversity surveys were performed. To analyse possible psychological or demographic effects on preferences for certain disturbance intensities, an additional online survey was carried out.}, subject = {Borkenk{\"a}fer}, language = {en} } @phdthesis{FadlElMola2003, author = {Fadl El Mola, Faisal Mohamed}, title = {Bioinformatic and molecular approaches for the analysis of the retinal pigment epithelium (RPE) transcriptome}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-6877}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2003}, abstract = {There is substantial interest in the identification of genes underlying susceptibility to complex human diseases because of the potential utility of such genes in disease prediction and therapy. The complex age-related macular degeneration (AMD) is a prevalent cause of legal blindness in industrialized countries and predominantly affects the elderly population over 75 years of age. Although vision loss in AMD results from photoreceptor cell death in the central retina, the initial pathogenesis likely involves processes in the retinal pigment epithelium (RPE) (Liang and Godley, 2003). The goal of the current study was to identify and characterize genes specifically or abundantly expressed in the RPE in order to determine more comprehensively the transcriptome of the RPE. In addition, our aim was to assess the role of these genes in AMD pathogenesis. Towards this end, a bovine cDNA library enriched for RPE transcripts was constructed in-house using a PCR-based suppression subtractive hybridization (SSH) technique (Diatchenko et al., 1996, 1999), which normalizes for sequence abundance and achieves high enrichment for differentially expressed genes. CAP3 (Huang and Madan, 1999) was used to assemble the high quality sequences of all the 2379 ESTs into clusters or singletons. 1.2\% of the 2379 RPE-ESTs contains vector sequences and was excluded from further analysis. 5\% of the RPE-ESTs showed homology to multipe chromosomes and were not included in further assembly process. The rest of the ESTs (2245) were assembled into 175 contigs and 509 singletons, which revealed approximately 684 unique genes in the dataset. Out of the 684, 343 bovine RPE transcripts did not align to their human orthologues. A large fraction of clones were shown to include a considerable 3´untranslated regions of the gene that are not conserved between bovine and human. It is the coding regions that can be conserved between bovine and human and not the 3' UTR (Sharma et al., 2002). Therefore, more sequencing from the cDNA library with reclustering of those 343 ESTs together with continuous blasting might reveal their human orthologoues. To handle the large volume of data that the RPE cDNA library project has generated a highly efficient and user-friendly RDBMS was designed. Using RDBMS data storage can be managed efficiently and flexibly. The RDBMS allows displaying the results in query-based form and report format with additional annotations, links and search functions. Out of the 341 known and predicted genes identified in this study, 2 were further analyzed. The RPE or/and retina specificity of these two clones were further confirmed by RT-PCR analysis in adult human tissues. Construction of a single nucleotide polymphism (SNP) map was initiated as a first step in future case/control association studies. SNP genotyping was carried out for one of these two clones (RPE01-D2, now known as RDH12). 12 SNPs were identified from direct sequencing of the 23.4-kb region, of which 5 are of high frequency. In a next step, comparison of allele frequencies between AMD patients and healthy controls is required. Completion of the expression analysis for other predicted genes identified during this study is in progress using real time RT-PCR and will provide additional candidate genes for further analyses. This study is expected to contribute to our understanding of the genetic basis of RPE function and to clarify the role of the RPE-expressed genes in the predisposition to AMD. It may also help reveal the mechanisms and pathways that are involved in the development of AMD or other retinal dystrophies.}, subject = {Senile Makuladegeneration}, language = {en} } @phdthesis{Blenk2007, author = {Blenk, Steffen}, title = {Bioinformatical analysis of B-cell lymphomas}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-27421}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2007}, abstract = {Background: The frequency of the most observed cancer, Non Hodgkin Lymphoma (NHL), is further rising. Diffuse large B-cell lymphoma (DLBCL) is the most common of the NHLs. There are two subgroups of DLBCL with different gene expression patterns: ABC ("Activated B-like DLBCL") and GCB ("Germinal Center B-like DLBCL"). Without therapy the patients often die within a few months, the ABC type exhibits the more aggressive behaviour. A further B-cell lymphoma is the Mantle cell lymphoma (MCL). It is rare and shows very poor prognosis. There is no cure yet. Methods: In this project these B-cell lymphomas were examined with methods from bioinformatics, to find new characteristics or undiscovered events on the molecular level. This would improve understanding and therapy of lymphomas. For this purpose we used survival, gene expression and comparative genomic hybridization (CGH) data. In some clinical studies, you get large data sets, from which one can reveal yet unknown trends. Results (MCL): The published proliferation signature correlates directly with survival. Exploratory analyses of gene expression and CGH data of MCL samples (n=71) revealed a valid grouping according to the median of the proliferation signature values. The second axis of correspondence analysis distinguishes between good and bad prognosis. Statistical testing (moderate t-test, Wilcoxon rank-sum test) showed differences in the cell cycle and delivered a network of kinases, which are responsible for the difference between good and bad prognosis. A set of seven genes (CENPE, CDC20, HPRT1, CDC2, BIRC5, ASPM, IGF2BP3) predicted, similarly well, survival patterns as proliferation signature with 20 genes. Furthermore, some bands could be associated with prognosis in the explorative analysis (chromosome 9: 9p24, 9p23, 9p22, 9p21, 9q33 and 9q34). Results (DLBCL): New normalization of gene expression data of DLBCL patients revealed better separation of risk groups by the 2002 published signature based predictor. We could achieve, similarly well, a separation with six genes. Exploratory analysis of gene expression data could confirm the subgroups ABC and GCB. We recognized a clear difference in early and late cell cycle stages of cell cycle genes, which can separate ABC and GCB. Classical lymphoma and best separating genes form a network, which can classify and explain the ABC and GCB groups. Together with gene sets which identify ABC and GCB we get a network, which can classify and explain the ABC and GCB groups (ASB13, BCL2, BCL6, BCL7A, CCND2, COL3A1, CTGF, FN1, FOXP1, IGHM, IRF4, LMO2, LRMP, MAPK10, MME, MYBL1, NEIL1 and SH3BP5; Altogether these findings are useful for diagnosis, prognosis and therapy (cytostatic drugs).}, subject = {Bioinformatik}, language = {en} } @phdthesis{Zeeshan2012, author = {Zeeshan, Ahmed}, title = {Bioinformatics Software for Metabolic and Health Care Data Management}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-73926}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Computer Science approaches (software, database, management systems) are powerful tools to boost research. Here they are applied to metabolic modelling in infections as well as health care management. Starting from a comparative analysis this thesis shows own steps and examples towards improvement in metabolic modelling software and health data management. In section 2, new experimental data on metabolites and enzymes induce high interest in metabolic modelling including metabolic flux calculations. Data analysis of metabolites, calculation of metabolic fluxes, pathways and their condition-specific strengths is now possible by an advantageous combination of specific software. How can available software for metabolic modelling be improved from a computational point of view? A number of available and well established software solutions are first discussed individually. This includes information on software origin, capabilities, development and used methodology. Performance information is obtained for the compared software using provided example data sets. A feature based comparison shows limitations and advantages of the compared software for specific tasks in metabolic modeling. Often found limitations include third party software dependence, no comprehensive database management and no standard format for data input and output. Graphical visualization can be improved for complex data visualization and at the web based graphical interface. Other areas for development are platform independency, product line architecture, data standardization, open source movement and new methodologies. The comparison shows clearly space for further software application development including steps towards an optimal user friendly graphical user interface, platform independence, database management system and third party independence especially in the case of desktop applications. The found limitations are not limited to the software compared and are of course also actively tackled in some of the most recent developments. Other improvements should aim at generality and standard data input formats, improved visualization of not only the input data set but also analyzed results. We hope, with the implementation of these suggestions, metabolic software applications will become more professional, cheap, reliable and attractive for the user. Nevertheless, keeping these inherent limitations in mind, we are confident that the tools compared can be recommended for metabolic modeling for instance to model metabolic fluxes in bacteria or metabolic data analysis and studies in infection biology. ...}, subject = {Stoffwechsel}, language = {en} } @phdthesis{Kuhlemann2022, author = {Kuhlemann, Alexander}, title = {Bioorthogonal labeling of neuronal proteins using super-resolution fluorescence microscopy}, doi = {10.25972/OPUS-24373}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-243731}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2022}, abstract = {The synaptic cleft is of central importance for synaptic transmission, neuronal plasticity and memory and thus well studied in neurobiology. To target proteins of interest with high specificity and strong signal to noise conventional immunohistochemistry relies on the use of fluorescently labeled antibodies. However, investigations on synaptic receptors remain challenging due to the defined size of the synaptic cleft of ~20 nm between opposing pre- and postsynaptic membranes. At this limited space, antibodies bear unwanted side effects such as crosslinking, accessibility issues and a considerable linkage error between fluorophore and target of ~10 nm. With recent single molecule localization microscopy (SMLM) methods enabling localization precisions of a few nanometers, the demand for labeling approaches with minimal linkage error and reliable recognition of the target molecules rises. Within the scope of this work, different labeling techniques for super-resolution fluorescence microscopy were utilized allowing site-specific labeling of a single amino acid in synaptic proteins like kainate receptors (KARs), transmembrane α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor regulatory proteins (TARPs), γ-aminobutyric acid type A receptors (GABA-ARs) and neuroligin 2 (NL2). The method exploits the incorporation of unnatural amino acids (uAAs) in the protein of interest using genetic code expansion (GCE) via amber suppression technology and subsequent labeling with tetrazine functionalized fluorophores. Implementing this technique, hard-to-target proteins such as KARs, TARPs and GABA-ARs could be labeled successfully, which could only be imaged insufficiently with conventional labeling approaches. Furthermore, functional studies involving electrophysiological characterization, as well as FRAP and FRET experiments validated that incorporation of uAAs maintains the native character of the targeted proteins. Next, the method was transferred into primary hippocampal neurons and in combination with super-resolution microscopy it was possible to resolve the nanoscale organization of γ2 and γ8 TARPs. Cluster analysis of dSTORM localization data verified synaptic accumulation of γ2, while γ8 was homogenously distributed along the neuron. Additionally, GCE and bioorthogonal labeling allowed visualization of clickable GABA-A receptors located at postsynaptic compartments in dissociated hippocampal neurons. Moreover, saturation experiments and FRET imaging of clickable multimeric receptors revealed successful binding of multiple tetrazine functionalized fluorophores to uAA-modified dimeric GABA-AR α2 subunits in close proximity (~5 nm). Further utilization of tetrazine-dyes via super-resolution microscopy methods such as dSTORM and click-ExM will provide insights to subunit arrangement in receptors in the future. This work investigated the nanoscale organization of synaptic proteins with minimal linkage error enabling new insights into receptor assembly, trafficking and recycling, as well as protein-protein interactions at synapses. Ultimately, bioorthogonal labeling can help to understand pathologies such as the limbic encephalitis associated with GABA-AR autoantibodies and is already in application for cancer therapies.}, subject = {microscopy}, language = {en} } @phdthesis{Muellner2004, author = {M{\"u}llner, Antje}, title = {Breeding ecology and related life-history traits of the hoatzin, Opisthocomus hoazin, in a primary rainforest habitat}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13239}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2004}, abstract = {The hoatzin (Opisthocomus hoazin) is an enigmatic bird that lives in the riparian lowlands of northern South America. Among its peculiar attributes are 1) microbial foregut fermentation, unique in birds, to convert plant cellulose in the foliage which it consumes into simple sugars, 2) an ongoing debate about the puzzling taxonomic position, although a relationship to the Cuculiformes appears likely, 3) adaptive wing claws in the young which are used for climbing, and 4) co-operative breeding behaviour. Despite the information available on digestive mode and taxonomy little has been published on its breeding biology and behaviour and until now almost all knowledge was based on a study in the savannah of Venezuela. This is the first detailed study of the hoatzin's nesting ecology in a rainforest habitat. From 1995-1998 and in 2000 I monitored a hoatzin population which consisted of approximately 700 individuals in an Amazonian rainforest in Ecuador situated in the Cuyabeno Wildlife Reserve (between 0°02' N, 76°0' W, 0°03' S, and 76°14' W). The area is composed of various black water lagoons and small rivers, flooded forests and terra firme forest. Primarily, I examined group composition and breeding pattern and success related to traits such as clutch and egg size, offspring sex ratio and the number of parents involved in a common breeding attempt. Apart from standardised observations and monitoring I took blood samples from chicks, which were later used for molecular sexing and for DNA fingerprints. Food plants were collected and determined and a rough habitat mapping was conducted. Since the impacts of boat tourism in the area became apparent I investigated the interactions of adult and young hoatzins with tourists and measured the plasma concentration of the hormone corticosterone in chicks as an indicator of stress. Each chapter has its own introduction to the specific topic and can be read independently. The main findings of this study are: The reproduction of the hoatzin was timed strictly following the bimodal rainy pattern in the area. There was only one breeding attempt per year. Only 18\% of breeding attempts ended successfully with at least one fledgling. Incubation started with the first egg laid and led to hatching asynchrony. In most cases only the A-chick survived and there is evidence for a brood reduction strategy. I observed egg size variation patterns both within the clutches and between the clutches. Approximately 80\% of breeding attempts were carried out with auxiliaries. Units with alloparentals had a higher breeding success than single pairs. The results indicate a trade-off between helping and group size. DNA band-sharing comparisons revealed the existence of joint-nests, where several females laid their eggs in one single nest. The clutches of these joint-nests suffered severe egg loss during all stages of incubation. Breeding success did not differ between single- and joint-nests. The primary offspring sex ratio was biased towards daughters. There was no differential mortality between the sexes until fledging. Individual breeding units employed an adaptive production of offspring of each sex according to their current group size. Rainforest tourism negatively influenced the survival and growth of young, not yet fledged hoatzins. In addition tourist-exposed young showed a stronger hormonal stress response than their conspecifics from undisturbed sites. In contrast, breeding adults appear to have habituated to tourist boats and exposure to observers.}, subject = {Hoatzins}, language = {en} } @phdthesis{Halboth2018, author = {Halboth, Florian}, title = {Building behavior and nest climate control in leaf-cutting ants: How environmental cues affect the building responses of workers of \(Atta\) \(vollenweideri\)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-161701}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {The present work investigates the influence of environmental stimuli on the building behavior of workers of the leaf-cutting ant Atta vollenweideri. It focuses on cues related to the airflow-driven ventilation of their giant underground nests, i.e., air movements and their direction, carbon dioxide concentrations and humidity levels of the nest air. First, it is shown that workers are able to use airflow and its direction as learned orientation cue by performing learning experiments with individual foragers using a classical conditioning paradigm. This ability is expected to allow workers to also navigate inside the nest tunnels using the prevailing airflow directions for orientation, for example during tasks related to nest construction and climate control. Furthermore, the influence of carbon dioxide on the digging behavior of workers is investigated. While elevated CO2 levels hardly affect the digging rate of the ants, workers prefer to excavate at locations with lower concentrations and avoid higher CO2 levels when given a choice. Under natural conditions, shifting their digging activity to soil layers containing lower carbon dioxide levels might help colonies to excavate new or to broaden existing nest openings, if the CO2 concentration in the underground rises. It is also shown that workers preferably transport excavated soil along tunnels containing high CO2 concentrations, when carbon dioxide levels in the underground are elevated as well. In addition, workers prefer to carry soil pellets along outflow tunnels instead of inflow tunnels, at least for high humidity levels of the air. The material transported along tunnels providing outflow of CO2-rich air might be used by workers for the construction of ventilation turrets on top of the nest mound, which is expected to promote the wind-induced ventilation and the removal of carbon dioxide from the underground. The climatic conditions inside the nest tunnels also influence the structural features of the turrets constructed by workers on top the nest. While airflow and humidity have no effect on turret structure, outflow of CO2-rich air from the nest causes workers to construct turrets with additional openings and increased aperture, potentially enhancing the airflow-driven gas exchanges within the nest. Finally, the effect of airflow and ventilation turrets on the gas exchanges in Atta vollenweideri nests is tested experimentally on a physical model of a small nest consisting of a single chamber and two nest tunnels. The carbon dioxide clearance rate from the underground was measured depending on both the presence of airflow in the nest and the structural features of the built turrets. Carbon dioxide is removed faster from the physical nest model when air moves through the nest, confirming the contribution of wind-induced flow inside the nest tunnels to the ventilation of Atta vollenweideri nests. In addition, turrets placed on top of one of the tunnel openings of the nest further enhance the CO2 clearance rate and the effect is positively correlated with turret aperture. Taken together, climatic variables like airflow, carbon dioxide and humidity levels strongly affect the building responses of Atta vollenweideri leaf-cutting ants. Workers use these environmental stimuli as orientation cue in the nest during tasks related to excavation, soil transport and turret construction. Although the effects of these building responses on the microclimatic conditions inside the nest remain elusive so far, the described behaviors are expected to allow ant colonies to restore and maintain a proper nest climate in the underground.}, subject = {Verhalten}, language = {en} } @phdthesis{BollazziSosa2008, author = {Bollazzi Sosa, Leonardo Martin}, title = {Building behaviour and the control of nest climate in Acromyrmex leaf-cutting ants}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-27610}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {This work was aimed at experimentally studying whether climatic variables act as environmental cues for workers' building behaviour in leaf-cutting ants of the genus Acromyrmex, and to what extent building responses account for the maintenance of nest climate in a proper range for the inhabiting colony. Specifically, this work presents independent analysis in different Acromyrmex species with disparate ecology and nesting habits, aimed at understanding to what extent: i) temperature and humidity act as cues for workers' building behaviour, ii) inter- and intraspecific differences in the nesting habits observed in South American Acromyrmex are based on distinct building behaviours and on the variation in regional climate across continent, iii) differences in nest architecture account for the maintenance of nest climate in a proper range for colony members and, iv) climatic variables trigger building responses aimed at controlling short-term changes in nest climate. It is first experimentally shown that soil temperature acts as a cue for workers' digging behaviour. Acromyrmex lundi workers were observed to respond to both soil temperature as well as its changes, and to decide accordingly where to start or whether to stop digging. The soil temperature range preferred by workers to dig, between 20°C and maximally 30.6°C, matches the range at which colony growth is expected to be maximized. Temperature-sensitive digging might therefore lead to the establishment of the fungus chambers in soil layers with a proper range of temperatures for colony growth. Based on that, it was hypothesized that nest depth in Acromyrmex largely depends on the depth at which this temperature range is located across the soil profile, i.e., the higher the temperature in the superficial soil layers, the deeper the nest location, since soil temperature decreases with increasing depth. A bibliographic survey on nesting habits of 21 South American Acromyrmex species confirmed that the warmer the soil temperature at 50 cm depth throughout the South American continent, the higher the number of species presenting subterranean nests, compared with those inhabiting superficial nests. Temperature-sensitive digging in Acromyrmex would therefore explain the geographical distribution of nesting habits observed for this genus in the South American continent, i.e., subterranean in the northern tropical regions, and superficial in the southern temperate ones. In addition, results showed that Acromyrmex colonies from temperate regions indeed achieve thermoregulatory benefits through the determination of nest depth based on thermoregulatory needs. In sympatrically-occurring colonies of the grass-cutting ant A. heyeri, temperature inside superficial thatched nests was higher, and more suitable for colony growth, than that inside subterranean nests. This temperature surplus was even higher in spring, at the time of production of sexual brood, than in winter or summer. It was demonstrated that such temperature surplus was brought about by the low thermal diffusivity of the nest thatch, which prevents diurnal nest overheating by the incoming solar radiation, and avoids losses of the accumulated daily heat into the cold air during night, thus leading to high average nest temperatures. Although highly advantageous for colonies in terms of nest temperature, the determination of nest depth based on thermoregulatory needs may differentially affect nest ventilation and humidity depending on how nest exposition influences the exchange of nest air with the outside air. For instance, colonies with a superficial nesting habit might benefit from improved nest ventilation, but be at risk of desiccation due to their exposition and the consequent humidity losses into the dry outside air. Results demonstrated that in two Acromyrmex species, short-term regulatory building responses triggered and spatially organized by climatic variables occur, and may counteract undesired changes in internal nest humidity. Workers of the thatching grass-cutting ant A. heyeri, for instance, closed a number of nest-thatch openings as a response to desiccation of the outside air, even at a nest temperature that otherwise triggered the response of opening them so as to reduce nest temperature. In the leaf-cutting ant A. ambiguus, the direction of the airflow inside nest tunnels was shown to act as a cue for spatially guiding the building behaviour of plugging nest entrances. However, workers only responded if the humidity content of the circulating air was low, trading therefore nest ventilation for humidity maintenance.}, subject = {Verhaltens{\"o}kologie}, language = {en} } @phdthesis{Scholl2015, author = {Scholl, Christina}, title = {Cellular and molecular mechanisms contributing to behavioral transitions and learning in the honeybee}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-115527}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {The honeybee Apis mellifera is a social insect well known for its complex behavior and the ability to learn tasks associated with central place foraging, such as visual navigation or to learn and remember odor-reward associations. Although its brain is smaller than 1mm² with only 8.2 x 105 neurons compared to ~ 20 x 109 in humans, bees still show amazing social, cognitive and learning skills. They express an age - related division of labor with nurse bees staying inside the hive and performing tasks like caring for the brood or cleaning, and foragers who collect food and water outside the hive. This challenges foragers with new responsibilities like sophisticated navigation skills to find and remember food sources, drastic changes in the sensory environment and to communicate new information to other bees. Associated with this plasticity of the behavior, the brain and especially the mushroom bodies (MBs) - sensory integration and association centers involved in learning and memory formation - undergo massive structural and functional neuronal alterations. Related to this background my thesis on one hand focuses on neuronal plasticity and underlying molecular mechanisms in the MBs that accompany the nurse - forager transition. In the first part I investigated an endogenous and an internal factor that may contribute to the nurse - forager phenotype plasticity and the correlating changes in neuronal network in the MBs: sensory exposure (light) and juvenile hormone (JH). Young bees were precociously exposed to light and subsequently synaptic complexes (microglomeruli, MG) in the MBs or respectively hemolymph juvenile hormone (JH) levels were quantified. The results show that light input indeed triggered a significant decrease in MG density, and mass spectrometry JH detection revealed an increase in JH titer. Interestingly light stimulation in young bees (presumably nurse bees) triggered changes in MG density and JH levels comparable to natural foragers. This indicates that both sensory stimuli as well as the endocrine system may play a part in preparing bees for the behavioral transition to foraging. Considering a connection between the JH levels and synaptic remodeling I used gene knockdown to disturb JH pathways and artificially increase the JH level. Even though the knockdown was successful, the results show that MG densities remained unchanged, showing no direct effect of JH on synaptic restructuring. To find a potential mediator of structural synaptic plasticity I focused on the calcium-calmodulin-dependent protein kinase II (CaMKII) in the second part of my thesis. CaMKII is a protein known to be involved in neuronal and behavioral plasticity and also plays an important part in structural plasticity reorganizing synapses. Therefore it is an interesting candidate for molecular mechanisms underlying MG reorganization in the MBs in the honeybee. Corresponding to the high abundance of CaMKII in the learning center in vertebrates (hippocampus), CaMKII was shown to be enriched in the MBs of the honeybee. Here I first investigated the function of CaMKII in learning and memory formation as from vertebrate work CaMKII is known to be associated with the strengthening of synaptic connections inducing long term potentiation and memory formation. The experimental approach included manipulating CaMKII function using 2 different inhibitors and a specific siRNA to create a CaMKII knockdown phenotype. Afterwards bees were subjected to classical olfactory conditioning which is known to induce stable long-term memory. All bees showed normal learning curves and an intact memory acquisition, short-term and mid-term memory (1 hour retention). However, in all cases long-term memory formation was significantly disrupted (24 and 72 hour retention). These results suggests the necessity of functional CaMKII in the MBs for the induction of both early and late phases of long-term memory in honeybees. The neuronal and molecular bases underlying long-term memory and the resulting plasticity in behavior is key to understanding higher brain function and phenotype plasticity. In this context CaMKII may be an important mediator inducing structural synaptic and neuronal changes in the MB synaptic network.}, subject = {Biene}, language = {en} } @phdthesis{Reinboth2012, author = {Reinboth, Jennifer}, title = {Cellular Factors Contributing to Host Cell Permissiveness in Support of Oncolytic Vaccinia Virus Replication}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-85392}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {In initial experiments, the well characterized VACV strain GLV-1h68 and three wild-type LIVP isolates were utilized to analyze gene expression in a pair of autologous human melanoma cell lines (888-MEL and 1936 MEL) after infection. Microarray analyses, followed by sequential statistical approaches, characterized human genes whose transcription is affected specifically by VACV infection. In accordance with the literature, those genes were involved in broad cellular functions, such as cell death, protein synthesis and folding, as well as DNA replication, recombination, and repair. In parallel to host gene expression, viral gene expression was evaluated with help of customized VACV array platforms to get better insight over the interplay between VACV and its host. Our main focus was to compare host and viral early events, since virus genome replication occurs early after infection. We observed that viral transcripts segregated in a characteristic time-specific pattern, consistent with the three temporal expression classes of VACV genes, including a group of genes which could be classified as early-stage genes. In this work, comparison of VACV early replication and respective early gene transcription led to the identification of seven viral genes whose expression correlated strictly with replication. We considered the early expression of those seven genes to be representative for VACV replication and we therefore referred to them as viral replication indicators (VRIs). To explore the relationship between host cell transcription and viral replication, we correlated viral (VRI) and human early gene expression. Correlation analysis revealed a subset of 114 human transcripts whose early expression tightly correlated with early VRI expression and thus early viral replication. These 114 human molecules represented an involvement in broad cellular functions. We found at least six out of 114 correlates to be involved in protein ubiquitination or proteasomal function. Another molecule of interest was the serine-threonine protein kinase WNK lysine-deficient protein kinase 1 (WNK1). We discovered that WNK1 features differences on several molecular biological levels associated with permissiveness to VACV infection. In addition to that, a set of human genes was identified with possible predictive value for viral replication in an independent dataset. A further objective of this work was to explore baseline molecular biological variances associated with permissiveness which could help identifying cellular components that contribute to the formation of a permissive phenotype. Therefore, in a subsequent approach, we screened a set of 15 melanoma cell lines (15-MEL) regarding their permissiveness to GLV-1h68, evaluated by GFP expression levels, and classified the top four and lowest four cell lines into high and low permissive group, respectively. Baseline gene transcriptional data, comparing low and highly permissive group, suggest that differences between the two groups are at least in part due to variances in global cellular functions, such as cell cycle, cell growth and proliferation, as well as cell death and survival. We also observed differences in the ubiquitination pathway, which is consistent with our previous results and underlines the importance of this pathway in VACV replication and permissiveness. Moreover, baseline microRNA (miRNA) expression between low and highly permissive group was considered to provide valuable information regarding virus-host co-existence. In our data set, we identified six miRNAs that featured varying baseline expression between low and highly permissive group. Finally, copy number variations (CNVs) between low and highly permissive group were evaluated. In this study, when investigating differences in the chromosomal aberration patterns between low and highly permissive group, we observed frequent segmental amplifications within the low permissive group, whereas the same regions were mostly unchanged in the high group. Taken together, our results highlight a probable correlation between viral replication, early gene expression, and the respective host response and thus a possible involvement of human host factors in viral early replication. Furthermore, we revealed the importance of cellular baseline composition for permissiveness to VACV infection on different molecular biological levels, including mRNA expression, miRNA expression, as well as copy number variations. The characterization of human target genes that influence viral replication could help answering the question of host cell response to oncolytic virotherapy and provide important information for the development of novel recombinant vaccinia viruses with improved features to enhance replication rate and hence trigger therapeutic outcome.}, subject = {Vaccinia-Virus}, language = {en} } @phdthesis{Blume2009, author = {Blume, Constanze}, title = {Cellular functions of VASP phosphorylations}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48321}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2009}, abstract = {Members of the enabled/vasodilator-stimulated phosphoprotein (Ena/VASP) family are important regulators of the actin cytoskeleton dynamics. VASP functions as well as its interactions with other proteins are regulated by phosphorylation at three sites - serine157 (S157), serine239 (S239), and threonine278 (T278) in humans. cAMP- and cGMP- dependent protein kinases phosphorylate S157 and S239, respectively. In contrast, the kinase responsible for T278 was as yet unknown and identified in the first part of this thesis. In a screen for T278 phosphorylating kinases using a phospho-specific antibody against phosphorylated T278 AMP-activated protein kinase (AMPK) was identified in endothelial cells. Mutants of AMPK with altered kinase-activity modulate T278-phosphorylation levels in cells. AMPK-driven T278-phosphorylation impaired stress fiber formation and changed cell morphology in living cells. AMPK is a fundamental sensor of cellular and whole body energy homeostasis. Zucker Diabetic Fatty (ZDF) rats, which are an animal model for type II diabetes mellitus, were used to analyze the impact of phosphorylated T278 in vivo. AMPK-activity and T278-phosphorylation were substantially reduced in arterial vessel walls of ZDF rats in comparison to control animals. These findings demonstrate that VASP is a new AMPK substrate, that VASP phosphorylation mediates the effects of metabolic regulation on actin cytoskeleton rearrangements, and that this signaling system becomes down-regulated in diabetic vessel disorders in rats. In the second part of this thesis, a functional analysis of differential VASP phosphorylations was performed. To systematically address VASP phosphorylation patterns, a set of VASP phosphomimetic mutants was cloned. These mutants enable the mimicking of defined phosphorylation patterns and the specific analysis of single kinase-mediated phosphorylations. VASP localization to the cell periphery was increased by S157- phosphorylation and modulated by phosphorylation at S239 and T278. Latter phosphorylations synergistically reduced actin polymerization. In contrast, S157- phosphorylation had no effect on actin-dynamics. Taken together, the results of the second part show that phosphorylation of VASP serves as a fine regulator of localization and actin polymerization activity. In summary, this study revealed the functions of VASP phosphorylations and established novel links between signaling pathways and actin cytoskeleton rearrangement.}, subject = {Vasodilatator-stimuliertes Phosphoprotein}, language = {en} } @phdthesis{Boehme2009, author = {B{\"o}hme, Linda}, title = {Cellular response to double-stranded RNA in Chlamydia trachomatis-infected human host cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-46474}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2009}, abstract = {Chlamydien sind Gram-negative, obligat-intrazellul{\"a}re Bakterien, die f{\"u}r ein weites Spektrum an relevanten Krankheiten verantwortlich sind. Auf Grund ihres zweiphasigen Entwicklungszyklusses sind Chlamydien von einer intakten Wirtszelle abh{\"a}ngig, um sich erfolgreich vermehren und im Organismus ausbreiten zu k{\"o}nnen. Daher haben Chlamydien anspruchsvolle Strategien entwickelt, um das Immunsystem des Wirtes auszuschalten oder den programmierten Zelltod ihrer Wirtszelle zu verhindern. In der vorliegenden Arbeit wurde untersucht, ob eine Infektion mit C. trachomatis einen Einfluss auf die zellul{\"a}re Antwort auf dsRNA nehmen kann. Die Synthese von dsRNA ist ein charakteristisches Merkmal der Replikation von Viren, welche sowohl die Apoptose induzieren als auch das Immunsystem aktivieren kann. Um eine chlamydiale und virale Co-Infektion zu simulieren, wurden Chlamydien-infizierte Epithelzellen mit der synthetischen dsRNA Polyinosin-Polycytidins{\"a}ure (polyI:C) transfiziert. Im ersten Teil der Arbeit wurde untersucht, ob Chlamydien die durch dsRNA eingeleitete Apoptose verhindern k{\"o}nnen. Eine signifikante Reduktion der dsRNA-induzierten Apoptose konnte in infizierten Zellen beobachtet werden. Es zeigte sich, dass die Prozessierung der Initiator-Caspase-8 in infizierten Zellen unterblieb. Dies war von der fr{\"u}hen bakteriellen Proteinsynthese abh{\"a}ngig und f{\"u}r die dsRNA-vermittelte Apoptose spezifisch, da der durch TNFalpha bewirkte Zelltod nicht auf der Ebene der Caspase-8 verhindert werden konnte. Die Aktivierung von zellul{\"a}ren Faktoren, die bei der Apoptoseinduzierung eine wichtige Rolle spielen, beispielsweise PKR und RNase L, war in infizierten Zellen jedoch unver{\"a}ndert. Stattdessen konnte durch RNA Interferenz-vermittelte Depletion gezeigt werden, dass der zellul{\"a}re Caspase-8-Inhibitor cFlip eine entscheidende Rolle bei der chlamydialen Blockierung der dsRNA-vermittelten Apoptose spielt. Mittels Co-Immunopr{\"a}zipitation konnte ein erster Hinweis darauf gefunden werden, dass C. trachomatis eine Anreicherung von cFlip im dsRNA-induzierten Komplex von Caspase-8 und FADD bewirkt. Im zweiten Teil der Arbeit wurde untersucht, ob Chlamydien die Immunantwort auf virale Infektionen beeinflussen, welche vor allem die Expression von Interferonen und Interleukinen beinhaltet. Es stellte sich heraus, dass die Aktivierung des Interferon regulatory factor 3 (IRF-3) und des zur Familie von NF-kappaB Trankriptionsfaktoren geh{\"o}renden p65, zwei zentralen Regulatoren der Immunantwort auf dsRNA, in infizierten Epithelzellen ver{\"a}ndert war. Die Degradation von IkappaB-alpha, des Inhibitors von NF-kappaB, war in infizierten Zellen beschleunigt, begleitet von einer Ver{\"a}nderung der Translokation des Transkriptionsfaktors in den Zellkern. Im Gegensatz dazu wurde die nukle{\"a}re Translokation von IRF-3 durch die Infektion signifikant verhindert. Die hier vorgestellten Daten zeigen erstmals, dass eine Infektion mit C. trachomatis die zellul{\"a}re Antwort auf dsRNA signifikant ver{\"a}ndern kann und implizieren einen Einfluss von chlamydialen Infektionen auf den Ausgang von viralen Superinfektionen.}, subject = {Chlamydia trachomatis}, language = {en} } @phdthesis{Solger2021, author = {Solger, Franziska}, title = {Central role of sphingolipids on the intracellular survival of \(Neisseria\) \(gonorrhoeae\) in epithelial cells}, doi = {10.25972/OPUS-24753}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-247534}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {Neisseria gonorrhoeae are Gram-negative bacteria with diplococcal shape. As an obligate human pathogen, it is the causative agent of gonorrhoea, a sexually transmitted disease. Gonococci colonize a variety of mucosal tissues, mainly the urogenital tract in men and women. Occasionally N. gonorrhoeae invades the bloodstream, leading to disseminated gonococcal infection. These bacteria possess a repertoire of virulence factors, which expression patterns can be adapted to the environmental conditions of the host. Through the accumulation of antibiotic resistances and in absence of vaccines, some neisserial strains have the potential to spread globally and represent a major public health threat. Therefore, it is necessary to understand the exact molecular mechanisms underlying the successful infection and progression of gonococci within their host. This deeper understanding of neisserial infection and survival mechanisms is needed for the development of new therapeutic agents. In this work, the role of host-cell sphingolipids on the intracellular survival of N. gonorrhoeae was investigated. It was shown that different classes of sphingolipids strongly interact with invasive gonococci in epithelial cells. Therefore, novel and highly specific clickable sphingolipid analogues were applied to study these interactions with this pathogen. The formation of intra- and extracellular sphingosine vesicles, which were able to target gonococci, was observed. This direct interaction led to the uptake and incorporation of sphingosine into the neisserial membrane. Together with in vitro results, sphingosine was identified as a potential bactericidal reagent as part of the host cell defence. By using different classes of sphingolipids and their clickable analogues, essential structural features, which seem to trigger the bacterial uptake, were detected. Furthermore, effects of key enzymes of the sphingolipid signalling pathway were tested in a neutrophil infection model. In conclusion, the combination of click chemistry and infection biology made it possible to shed some light on the dynamic interplay between cellular sphingosine and N. gonorrhoeae. Thereby, a possible "catch-and-kill" mechanism could have been observed.}, subject = {Neisseria gonorrhoeae}, language = {en} } @phdthesis{FetivaMora2023, author = {Fetiva Mora, Maria Camila}, title = {Changes in chromatin accessibility by oncogenic YAP and its relevance for regulation of cell cycle gene expression and cell migration}, doi = {10.25972/OPUS-30291}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-302910}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {Various types of cancer involve aberrant cell cycle regulation. Among the pathways responsible for tumor growth, the YAP oncogene, a key downstream effector of the Hippo pathway, is responsible for oncogenic processes including cell proliferation, and metastasis by controlling the expression of cell cycle genes. In turn, the MMB multiprotein complex (which is formed when B-MYB binds to the MuvB core) is a master regulator of mitotic gene expression, which has also been associated with cancer. Previously, our laboratory identified a novel crosstalk between the MMB-complex and YAP. By binding to enhancers of MMB target genes and promoting B-MYB binding to promoters, YAP and MMB co-regulate a set of mitotic and cytokinetic target genes which promote cell proliferation. This doctoral thesis addresses the mechanisms of YAP and MMB mediated transcription, and it characterizes the role of YAP regulated enhancers in transcription of cell cycle genes. The results reported in this thesis indicate that expression of constitutively active, oncogenic YAP5SA leads to widespread changes in chromatin accessibility in untransformed human MCF10A cells. ATAC-seq identified that newly accessible and active regions include YAP-bound enhancers, while the MMB-bound promoters were found to be already accessible and remain open during YAP induction. By means of CRISPR-interference (CRISPRi) and chromatin immuniprecipitation (ChIP), we identified a role of YAP-bound enhancers in recruitment of CDK7 to MMB-regulated promoters and in RNA Pol II driven transcriptional initiation and elongation of G2/M genes. Moreover, by interfering with the YAP-B-MYB protein interaction, we can show that binding of YAP to B-MYB is also critical for the initiation of transcription at MMB-regulated genes. Unexpectedly, overexpression of YAP5SA also leads to less accessible chromatin regions or chromatin closing. Motif analysis revealed that the newly closed regions contain binding motifs for the p53 family of transcription factors. Interestingly, chromatin closing by YAP is linked to the reduced expression and loss of chromatin-binding of the p53 family member Np63. Furthermore, I demonstrate that downregulation of Np63 following expression of YAP is a key step in driving cellular migration. Together, the findings of this thesis provide insights into the role of YAP in the chromatin changes that contribute to the oncogenic activities of YAP. The overexpression of YAP5SA not only leads to the opening of chromatin at YAP-bound enhancers which together with the MMB complex stimulate the expression of G2/M genes, but also promotes the closing of chromatin at ∆Np63 -bound regions in order to lead to cell migration.}, subject = {Chromatin}, language = {en} } @phdthesis{Kronhardt2012, author = {Kronhardt, Angelika}, title = {Channel Formation, Binding and Translocation Properties of Anthrax, CDT and Related Toxins of the AB7 type}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-71559}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {The ability to produce toxins is spread among a huge variety of bacterial strains. A very prominent class of bacterial protein toxins is the family of binary AB toxins sharing a common mode of intoxication. A pore forming component B binds and translocates an enzymatic component A into the cytosol of target cells exhibiting a fatal mode of action. These components are supposed to be not toxic themselves but both required for cell toxicity. Anthrax toxin produced by the Gram-positive bacteria Bacillus anthracis is the best studied binary toxin especially since its use as a biological weapon in the context of the attacks of 9/11 in 2001. In contrast to other binary toxins, Anthrax toxin possesses two different enzymatic components, edema factor (EF), a calcium- and calmodulin-dependent adenylat-cyclase and lethal factor (LF), a zinc-dependent metalloprotease. Protective antigen (PA) is the pore-forming component responsible for binding and translocation. Clostridium botulinum possesses in addition to the well known botulinum toxin (Botox) a variety of other toxins, such as the binary C2 toxin. C2 toxin is composed of the binding and translocation moiety C2II and the enzymatic moiety C2I acting as an actin-ADP-ribosyltransferase. In this study, the mode of translocation and the binding kinetics to the enzymatic component were studied in a biophysical experimental setup. In chapter 2, the binding of the N-terminal fractions EFN and LFN to the PA channel are analyzed in artificial bilayer membranes revealing lower binding affinity compared to full-length EF and LF. Other biophysical properties like voltage-dependency and ionic-strength dependency are not influenced. The results suggest that additional forces are involved in the binding process, than those concerning the N-terminus exclusively, as it was supposed previously. As the treatment of an Anthrax infection with antibiotics is often medicated very late due to the lack of early symptoms, tools to prevent intoxication are required. 4-aminoquinolones like chloroquine are known to block the PA channel, thereby inhibiting intoxication but they also lead to severe side-effects. In chapter 3 new promising agents are described that bind to PA in artificial bilayer systems, elucidating common motives and features which are necessary for binding to PA in general. The possible interaction of Anthrax and C2 toxin is investigated by measuring the binding of one enzymatic component to the respective other toxin's pore (chapter 4). Interestingly, in vitro experiments using the black lipid bilayer assay show that PA is able to bind to C2I resulting in half saturation constants in the nanomolar range. Furthermore, in vivo this combination of toxin components exhibits cell toxicity in human cell lines. This is first-time evidence that a heterologous toxin combination is functional in in vitro and in vivo systems. In contrast, C2II is able to bind to EF as well as to LF in vitro, whereas in in vivo studies almost no toxic effect is detected. In the case of PA, an N-terminal His6-tag attached to the enzymatic subunit increased the binding affinity (chapter 5). A His6-tag attached to not related proteins also led to high binding affinities, providing the possibility to establish PA as a general cargo protein. In chapter 6 a set of different molecules and proteins is summarized, which are either related or not related to binary toxins, PA is able to bind. In first line, the presence of positive charges is found to be responsible for binding to PA which is in accordance to the fact that PA is highly cation selective. Furthermore, we present evidence that different cationic electrolytes serve as a binding partner to the PA channel. In the last decade another toxin has aroused public attention as it was found to be responsible for a rising number of nosocomial infections: Clostridium difficile CDT toxin. The mode of action of the enzymatic subunit CDTa is similar to C2I of C2 toxin, acting as an ADP-ribosylating toxin. The channel forming and binding properties of CDT toxin are studied in artificial bilayer membranes (chapter 7). We found that two different types of channels are formed by the B component CDTb. The first channel is similar to that of iota toxin's Ib of Clostridium perfringens with comparable single channel conductance, selectivity and binding properties to the enzymatic subunit CDTa. The formation of this type of channel is cholesterol-dependent, whereas in the absence of cholesterol another kind of channel is observed. This channel has a single channel conductance which is rather high compared to all other binary toxin channels known so far, it is anion selective and does not show any binding affinity to the enzymatic component CDTa. The results reveal completely new insights in channel formation properties and the flexibility of a pore-forming component. Additionally, these findings suggest further possibilities of toxicity of the pore forming component itself which is not known for any other binary toxin yet. Therefore, the pathogenic role of this feature has to be studied in detail.}, subject = {Bacillus anthracis}, language = {en} } @phdthesis{Huenten2005, author = {H{\"u}nten, Peter}, title = {Channel-forming proteins in the cell wall of amino acid-producing Corynebacteria}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13890}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2005}, abstract = {Corynebacterium glutamicum is together with C. callunae and C. efficiens a member of the diverse group of mycolic-acid containing actinomycetes, the mycolata. These bacteria are potent producer of glutamate, lysine and other amino acids on industrial scale. The cell walls of most actinomycetes contain besides an arabinogalactan-peptidoglycan complex large amounts of mycolic acids. This three-layer envelope is called MAP (mycolyl-arabinogalactan-peptidoglycan) complex and it represents a second permeability barrier beside the cytoplasmic membrane similar to the outer membrane of Gram-negative bacteria. In analogy to the situation in the outer membrane of Gram-negative bacteria, channels are present in the mycolic acid layer of the mycobacterial cell wall for the passage of hydrophilic solutes. Molecular studies have provided far-reaching findings on the amino acid flux and its balance in C. glutamicum in general, but the L-glutamate export still remains unknown. The properties of the outer layers, typical of mycolata, seem to be of major importance in this process, and diffusion seems to play a key role for this part of the cell wall. The major aim of this thesis was to identify and study novel channel-forming proteins of the amino acid producers C. glutamicum, C. callunae and C. efficiens. Cell wall extracts of the organisms were investigated and a novel pore-forming protein, named PorH, that is homologue in all three organisms, was detected and characterized. PorHC.glut was isolated from C. glutamicum cells cultivated in minimal medium. The protein was identified in lipid bilayer experiments and purified to homogeneity by fast-protein liquid chromatography across a HiTrap-Q column. The purified protein forms cation-selective channels with a diameter of about 2.2 nm and an average single-channel conductance of about 2.5 nS in 1 M KCl in the lipid bilayer assay. Organic solvent extracts were used to study the permeability properties of the cell wall of C. callunae and C.efficiens. The cell extracts contained channel-forming activity, the corresponding proteins were purified to homogeneity by fast-protein liquid chromatography across a HiTrap-Q column and named PorHC.call and PorHC.eff. Channels formed by PorHC.call are cation-selective with a diameter of about 2.2 nm and an average single-channel conductance of 3 nS, whereas PorHC.eff forms slightly anion selective channels with an average single-channel conductance of 2.3 nS in 1 M KCl in the lipid bilayer assay. The PorH proteins were partially sequenced and the corresponding genes, which were designated as porH, were identified in the published genome sequence of C. glutamicum and C. efficiens. The chromosome of C. callunae is not sequenced, but PorHC.call shows a high homology to PorHC.eff and PorHC.glut. The proteins have no N-terminal extension, only the inducer methionine, which suggests that secretion of the proteins could be very similar to that of PorAC.glut of C. glutamicum. PorHC.glut is coded in the bacterial chromosome by a gene that is localized in the vincinity of the porAC.glut gene, within a putative operon formed by 13 genes that are encoded by the minus strand. Both porins are cotranscribed and coexist in the cell wall, which was demonstrated in RT-PCR and immunological detection experiments. The arrangement of porHC.glut and porAC.glut on the chromosome is similar to that of porBC.glut and porCC.glut and it was found that PorAC.glut, PorHC.glut, PorBC.glut and PorCC.glut coexist in the cell wall of C. glutamicum. The molecular mass of about 6 kDa of the PorH channel forming proteins is rather small and suggests that the cell wall channels are formed by oligomers. A possibly hexameric form was demonstrated for PorHC.glut in Western blot analysis with anti- PorHC.glut antibodies. Secondary structure predictions for PorHC.glut, PorHC.call and PorHC.eff predict that a stretch of about 42 amino acids of PorHC.glut and 28 amino acids of PorHC.call and PorHC.eff forms amphipathic \&\#61537;-helices with a total length of 6.3 nm and 4.2 nm respectively. This should be sufficient to cross the mycolic acid layer. Another objective of this work was to establish an heterologous expression system for corynebacterial channel-forming proteins, to investigate the channel-forming properties of the up to now only hypothetical porins PorA, PorB, PorC from C. efficiens and PorC from C. glutamicum. We could demonstrate with recombinant expression experiments in E. coli that porBC.eff and porCC.eff encode for channel-forming proteins. They are, like PorBC.glut, anion-selective with a similar single-channel conductance of 1 nS in 1 M KCl.}, subject = {Corynebacterium callunae}, language = {en} } @phdthesis{Laisney2010, author = {Laisney, Juliette Agn{\`e}s Genevi{\`e}ve Claire}, title = {Characterisation and regulation of the Egfr/Egfr ligand system in fish models for melanoma}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51369}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {Fish of the genus Xiphophorus belong to the oldest animal models in cancer research. The oncogene responsible for the generation of spontaneous aggressive melanoma encodes for a mutated epidermal growth factor receptor (Egfr) and is called xmrk for Xiphophorus melanoma receptor kinase. Xmrk constitutive activation mechanisms and subsequent signaling pathways have already been investigated and charaterized but it is still unknown if Egfr ligands may also play a role in Xmrk-driven melanoma formation. To investigate the potential role of Egfr ligands in Xmrk-driven melanoma, I firstly analyzed the evolution of teleost and tetrapod Egfr/Egfr ligand systems. I especially focused on the analysis on the medaka fish, a closely related species to Xiphophorus, for which the whole genome has been sequenced. I could identify all seven Egfr ligands in medaka and could show that the two teleost-specific Egfr copies of medaka display dissimilar expression patterns in adult tissues together with differential expression of Egfr ligand subsets, arguing for subfunctionalization of receptor functions in this fish. Our phylogenetic and synteny analyses supported the hypothesis that only one gene in the chordate ancestor gave rise to the diversity of Egfr ligands found in vertebrate genomes today. I also could show that the Egfr extracellular subdomains implicated in ligand binding are not evolutionary conserved between tetrapods and teleosts, making the use of heterologous ligands in experiments with fish cells debatable. Despite its well understood and straight-forward process, Xmrk-driven melanomagenesis in Xiphophorus is problematic to further investigate in vivo. Our laboratory recently established a new melanoma animal model by generating transgenic mitf::xmrk medaka fishes, a Xiphophorus closely related species offering many more advantages. These fishes express xmrk under the control of the pigment-cell specific Mitf promoter. During my PhD thesis, I participated in the molecular analysis of the stably transgenic medaka and could show that the Xmrk-induced signaling pathways are similar when comparing Xiphophorus with transgenic mitf::xmrk medaka. These data together with additional RNA expression, protein, and histology analyses showed that Xmrk expression under the control of a pigment cell-specific promoter is sufficient to induce melanoma in the transgenic medaka, which develop very stereotyped tumors, including uveal and extracutaneous melanoma, with early onset during larval stages. To further investigate the potential role of Egfr ligands in Xmrk-driven melanoma, I made use of two model systems. One of them was the above mentioned mitf::xmrk medaka, the other was an in-vitro cell culture system, where the EGF-inducible Xmrk chimera HERmrk is stably expressed in murine melanocytes. Here I could show that HERmrk activation strongly induced expression of amphiregulin (Areg) and heparin-binding EGF-like growth factor (Hbegf) in melanocytes. This regulation was dependent on the MAPK and SRC signaling pathways. Moreover, upregulation of Adam10 and Adam17, the two major sheddases of Egfr ligands, was observed. I also could demonstrate the functionality of the growth factors by invitro analyses. Using the mitf::xmrk medaka model I could also show the upregulation of a subset of ligand genes, namely egf, areg, betacellulin (btc) and epigen (epgn) as well as upregulation of medaka egfrb in tumors from fish with metastatic melanoma. All these results converge to support an Xmrk-induced autocrine Egfr ligand loop. Interestingly, my in-vitro experiments with conditioned supernatant from medaka Egf- and Hbegf-producing cells revealed that not only Xiphophorus Egfrb, but also the pre-activated Xmrk could be further stimulated by the ligands. Altogether, I could show with in-vitro and in-vivo experiments that Xmrk is capable of inducing a functional autocrine Egfr ligand loop. These data confirm the importance of autocrine loops in receptor tyrosine kinase (RTK)-dependent cancer development and show the possibility for a constitutively active RTK to strengthen its oncogenic signaling by ligand binding.}, subject = {Schwertk{\"a}rpfling}, language = {en} } @phdthesis{Schneider2011, author = {Schneider, Matthias}, title = {Characterisation of Metalloprotease-mediated EGFR Signal Transactivation after GPCR Stimulation}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-65105}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {In the context of metalloprotease-mediated transactivation of the epidermal growth factor receptor, different monoclonal antibodies against ADAM17 / TACE were characterized for their ability to block the sheddase. Activity of some of them was observed at doses between 2µg/mL and 10µg/mL. Kinetic analyses showed their activity starting at around 30 minutes. In cellular assays performed with the antibodies, especially upon treatment of cells with sphingosine-1-phosphate a reduction in proliferation was observed with some candidates. Moreover this study provides potential new roles for ß-Arrestins. Their involvement in the triple membrane-passing signal pathway of EGFR transactivation was shown. Furthermore, in overexpressing cellular model systems, an interaction between ADAM17 and ß-Arrestin1 could be observed. Detailed analysis discovered that phosphorylation of ß-Arrestin1 is crucial for this interaction. Additionally, the novel mechanism of UV-induced EGFR transactivation was extended to squamous cell carcinoma. The mechanism happens in a dose dependent manner and requires a metalloprotease to shed the proligand Amphiregulin. The involvement of both ADAM9 and ADAM17, being the metalloproteases responsible for this cleavage, was shown for SCC9 cells.}, subject = {Epidermaler Wachstumsfaktor-Rezeptor}, language = {en} } @phdthesis{Hart2004, author = {Hart, Stefan}, title = {Characterisation of the molecular mechanisms of EGFR signal transactivation in human cancer}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-10067}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2004}, abstract = {In a variety of established tumour cell lines, but also in primary mammary epithelial cells metalloprotease-dependent transactivation of the EGFR, and EGFR characteristic downstream signalling events were observed in response to stimulation with physiological concentrations of GPCR agonists such as the mitogens LPA and S1P as well as therapeutically relevant concentrations of cannabinoids. Moreover, this study reveals ADAM17 and HB-EGF as the main effectors of this mechanism in most of the cancer cell lines investigated. However, depending on the cellular context and GPCR agonist, various different members of the ADAM family are selectively recruited for specific ectodomain shedding of proAR and/or proHB-EGF and subsequent EGFR activation. Furthermore, biological responses induced by LPA or S1P such as migration in breast cancer and HNSCC cells, depend on ADAM17 and proHB-EGF/proAR function, respectively, suggesting that highly abundant GPCR ligands may play a role in tumour development and progression. Moreover, EGFR signal transactivation could be identified as the mechanistic link between cannabinoid receptors and the activation of mitogen activated protein kinases (MAPK) ERK1/2 as well as pro-survival Akt/PKB signalling. Depending on the cellular context, cannabinoid-induced signal cross-communication was mediated by shedding of proAmphiregulin and/or proHB-EGF by ADAM17. Most importantly, our data show that concentrations of THC comparable to those detected in the serum of patients after THC administration accelerate proliferation of cancer cells instead of apoptosis and thereby may contribute to cancer progression in patients.}, subject = {Epidermaler Wachstumsfaktor-Rezeptor}, language = {en} } @phdthesis{Gloeckner2001, author = {Gl{\"o}ckner, Herma}, title = {Characterization of a new miniaturized hollow-fiber bioreactor for cultivation of cell lines and primary cells to improve cytostatic drug testing in vitro}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-1181317}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2001}, abstract = {Monolayer or suspension cell cultures are of only limited value as experimental models for human cancer. Therefore, more sophisticated, three-dimensional culture systems like spheroid cultures or histocultures are used, which more closely mimic the tumor in individual patients compared to monolayer or suspension cultures. As tissue culture or tissue engineering requires more sophisticated culture, specialized in vitro techniques may also improve experimental tumor models. In the present work, a new miniaturized hollow-fiber bioreactor system for mammalian cell culture in small volumes (up to 3 ml) is characterized with regard to transport characteristics and growth of leukemic cell lines (chapter 2). Cell and medium compartment are separated by dialysis membranes and oxygenation is accomplished using oxygenation membranes. Due to a transparent housing, cells can be observed by microscopy during culture. The leukemic cell lines CCRF-CEM, HL-60 and REH were cultivated up to densities of 3.5 x 107/ml without medium change or manipulation of the cells. Growth and viability of the cells in the bioreactor were the same or better, and the viable cell count was always higher compared to culture in Transwell{\^a} plates. As shown using CCRF-CEM cells, growth in the bioreactor was strongly influenced and could be controlled by the medium flow rate. As a consequence, consumption of glucose and generation of lactate varied with the flow rate. Influx of low molecular weight substances in the cell compartment could be regulated by variation of the concentration in the medium compartment. Thus, time dependent concentration profiles (e.g. pharmacokinetic profiles of drugs) can be realized as illustrated using glucose as a model compound. Depending on the molecular size cut-off of the membranes used, added growth factors like GM-CSF and IL-3 as well as factors secreted from the cells are retained in the cell compartment for up to one week. Second, a method for monitoring cell proliferation the hollow-fiber bioreactor by use of the Alamar BlueTM dye was developed (chapter 3). Alamar BlueTM is a non-fluorescent compound which yields a fluorescent product after reduction e.g. by living cells. In contrast to the MTT-assay, the Alamar BlueTM-assay does not lead to cell death. However, when not removed from the cells, the Alamar BlueTM dye shows a reversible, time- and concentration-dependent growth inhibition as observed for leukemic cell lines. When applied in the medium compartment of a hollow-fiber bioreactor system, the dye is delivered to the cells across the hollow-fiber membrane, reduced by the cells and released from the cell into the medium compartment back again. Thus, fluorescence intensity can be measured in medium samples reflecting growth of the cells in the cell compartment. This procedure offers several advantages. First, exposure of the cells to the dye can be reduced compared to conventional culture in plates. Second, handling steps are minimized since no sample of the cells needs to be taken for readout. Moreover, for the exchange of medium, a centrifugation step can be avoided and the cells can be cultivated further. Third, the method allows to discriminate between cell densities of 105, 106 and 107 of proliferating HL-60 cells cultivated in the cell compartment of the bioreactor. Measurement of fluorescence in the medium compartment is more sensitive compared to glucose or lactate measurement for cell counts below 106 cells/ml, in particular. In conclusion, the Alamar BlueTM-assay combined with the hollow-fiber bioreactor offers distinct advantages for the non-invasive monitoring of cell viability and proliferation in a closed system. In chapter 4 the use of the hollow-fiber bioreactor as a tool for toxicity testing was investigated, as current models for toxicity as well as efficacy testing of drugs in vitro allow only limited conclusions with regard to the in vivo situation. Examples of the drawbacks of current test systems are the lack of realistic in vitro tumor models and difficulties to model drug pharmacokinetics. The bioreactor proved to be pyrogen free and is steam-sterilizable. Leukemic cell lines like HL-60 and primary cells such as PHA-stimulated lymphocytes can be grown up to high densities of 1-3 x 107 and analyzed during growth in the bioreactor by light-microscopy. The cytostatic drug Ara-C shows a dose-dependent growth inhibition of HL-60 cells and a dose-response curve similar to controls in culture plates. The bioreactor system is highly flexible since several systems can be run in parallel, soluble drugs can be delivered continuously via a perfusion membrane and gaseous compounds via an oxygenation membrane which also allows to control pO2 and pH (via pCO2) during culture in the cell compartment. The modular concept of the bioreactor system allows realization of a variety of different design properties, which may lead to an improved in vitro system for toxicity testing by more closely resembling the in vivo situation. Whereas several distinct advantages of the new system have been demonstrated, more work has to be done to promote in vitro systems in toxicity testing and drug development further and to reduce the need for animal tests.}, subject = {Hohlfaserreaktor}, language = {en} } @phdthesis{Cicova2016, author = {Cicova, Zdenka}, title = {Characterization of a novel putative factor involved in host adaptation in Trypanosoma brucei}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-142462}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Trypanosomes are masters of adaptation to different host environments during their complex life cycle. Large-scale proteomic approaches provide information on changes at the cellular level in a systematic way. However, a detailed work on single components is necessary to understand the adaptation mechanisms on a molecular level. Here we have performed a detailed characterization of a bloodstream form (BSF) stage-specific putative flagellar host adaptation factor (Tb927.11.2400) identified previously in a SILAC-based comparative proteome study. Tb927.11.2400 shares 38\% amino acid identity with TbFlabarin (Tb927.11.2410), a procyclic form (PCF) stage specific flagellar BAR domain protein. We named Tb927.11.2400 TbFlabarin like (TbFlabarinL) and demonstrate that it is a result of a gene duplication event, which occurred in African trypanosomes. TbFlabarinL is not essential for growth of the parasites under cell culture conditions and it is dispensable for developmental differentiation from BSF to the PCF in vitro. We generated a TbFlabarinL-specific antibody and showed that it localizes in the flagellum. The co-immunoprecipitation experiment together with a biochemical cell fractionation indicated a dual association of TbFlabarinL with the flagellar membrane and the components of the paraflagellar rod.}, subject = {Trypanosoma brucei}, language = {en} } @phdthesis{Putz2002, author = {Putz, Gabriele}, title = {Characterization of memories and ignorant (S6KII) mutants in operant conditioning in the heat-box}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-4195}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {Learning and memory processes of operant conditioning in the heat-box were analysed. Age, sex, and larval desity were not critical parameters influencing memory, while low or high activity levels of flies were negatively correlated with their performance. In a search for conditioning parameters leading to high retention scores, intermittent training was shown to give better results than continuous training. As the memory test is the immediate continuation of the conditioning phase just omitting reinforcement, we obtain a memory which consists of two components: a spatial preference for one side of the chamber and a stay-where-you-are effect in which the side preference is contaminated by the persistence of heat avoidance. Intermittent training strengthens the latter. In the next part, memory retention was investigated. Flies were trained in one chamber and tested in a second one after a brief reminder training. With this direct transfer, memory scores reflect an associative learning process in the first chamber. To investigate memory retention after extended time periods, indirect transfer experiments were performed. The fly was transferred to a different environment between training and test phases. With this procedure an after-effect of the training was still observed two hours later. Surprisingly, exposure to the chamber without conditioning also lead to a memory effect in the indirect transfer experiment. This exposure effect revealed a dispositional change that facilitates operant learning during the reminder training. The various memory effects are independent of the mushroom bodies. The transfer experiments and yoked controls proved that the heat-box records an associative memory. Even two hours after the operant conditioning procedure, the fly remembers that its position in the chamber controls temperature. The cAMP signaling cascade is involved in heat-box learning. Thus, amnesiac, rutabaga, and dunce mutants have an impaired learning / memory. Searching for, yet unknown, genes and signaling cascades involved in operant conditioning, a Drosophila melanogaster mutant screen with 1221 viable X-chromosome P-element lines was performed. 29 lines with consistently reduced heat avoidance/ learning or memory scores were isolated. Among those, three lines have the p[lacW] located in the amnesiac ORF, confirming that with the chosen candidate criteria the heat-box is a useful tool to screen for learning and /or memory mutants. The mutant line ignP1 (8522), which is defective in the gene encoding p90 ribosomal S6 kinase (S6KII), was investigated. The P-insertion of line ignP1 is the first Drosophila mutation in the ignorant (S6KII) gene. It has the transposon inserted in the first exon. Mutant males are characterized by low training performance, while females perform well in the standard experiment. Several deletion mutants of the ignorant gene have been generated. In precise jumpouts the phenotype was reverted. Imprecise jumpouts with a partial loss of the coding region were defective in operant conditioning. Surprisingly, null mutants showed wild-type behavior. This might indicate an indirect effect of the mutated ignorant gene on learning processes. In classical odor avoidance conditioning, ignorant null mutants showed a defect in the 3-min, 30-min, and 3-hr memory, while the precise jumpout of the transposon resulted in a reversion of the behavioral phenotype. Deviating results from operant and classical conditioning indicate different roles for S6KII in the two types of learning.}, subject = {Taufliege}, language = {en} } @phdthesis{Bargul2018, author = {Bargul, Joel Ltilitan}, title = {Characterization of motility and erythrocyte adherence as virulence factors in African trypanosomes}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-115053}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {Pathogens causing African animal trypanosomiasis (AAT), the major livestock disease in sub-Saharan Africa, belong to the salivarian group of the African trypanosomes, which are transmitted by the bite of the tsetse fly (Glossina spec.). T. vivax, T. congolense and T. brucei brucei are major pathogens of cattle in particular, causing nagana, with dramatic socio-economic consequences for the affected regions. The parasites additionally have a huge reservoir of other livestock and wild animal hosts. T. brucei, the species which also includes the subspecies pathogenic to humans causing sleeping sickness, has been extensively studied as the cultivatable model trypanosome. But less is known about the other salivarian species, which are not routinely held in culture, if at all possible. A hallmark of trypanosomal lifestyle is the protozoan flagellates incessant motility, which enables them to populate an enormous range of habitats in very diverse hosts. We were now able to characterize, for the first time with high spatiotemporal resolution microscopy, the swimming behaviour and mechanism of the most relevant salivarian species isolated directly from blood. We show the influence of viscosity on the motility of bloodstream form (BSF) cells and simulate their movement between erythrocytes, giving a clear picture of how all analyzed species move under varying environmental conditions. We show that although the basic mechanism of flagellar motility applies to all analyzed species, there are clear morphological differences that produce different reactions to the physical environment. We could define specific conditions for highly increased swimming persistence and speed for compared to the behaviour in standard culture. These results have important implications for the parasites survival strategies in the host, e.g. regarding the capacity for antibody clearance. Although we show all species to effectively remove antibodies from the cell surface, T. congolense differed markedly in its motility behaviour, which gives rise to interesting questions about this species behaviour in the bloodstream. Most of the T. congolense parasites (and to a lesser extent T. vivax) adhere to sheep erythrocytes. Further in vitro studies showed that T. congolense and T. vivax adhered to rabbit, goat, pig and cattle erythrocytes- but binding behaviour was absent in murine blood. Notably, both T. brucei and T. evansi lacked adherence to all studied host erythrocytes. Generally, attachment to blood cells caused reduction of swimming velocities. Judging from its cell architecture, as well as the motility studies in higher media viscosity and in micropillar arrays, T. congolense is not adapted to swim at high speeds in the mammalian bloodstream. Low swimming speeds could allow these purely intravascular parasites to remain bound to the host erythrocytes.}, subject = {Motili{\"a}t}, language = {en} } @phdthesis{Kober2015, author = {Kober, Christina}, title = {Characterization of Murine GL261 Glioma Models for Oncolytic Vaccinia Virus Therapy}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-118556}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2015}, abstract = {Glioblastoma multiforme (GBM) is one of the most frequent and malignant forms of brain cancer in adults. The prognosis is poor with a median survival time of 12-15 months. There is a broad range of alternative treatment options studied in preclinical and clinical trials for GBM. One alternative treatment option is oncolytic virotherapy, defined as the use of replication-competent viruses that selectively infect and destroy cancer cells while leaving, non-transformed cells unharmed. Vaccinia virus (VACV) is one favorable candidate. Although oncolytic viruses can kill tumor cells grown in vitro with high efficiency, they often exhibit reduced replication capacity in vivo suggesting that physiological aspects of the tumor microenvironment decrease the virus' therapeutic potential. The percentage and composition of immune cells varies between cancer types and patients and is investigated as a biomarker in several studies. Making oncolytic virotherapy successful for GBM, it is necessary to understand the individual tumor biology, the interaction with the microenvironment and immune system. It was demonstrated that the attenuated VACV wild-type (wt) isolate LIVP 1.1.1 replicate and lyse the murine GL261 glioma cell line in vitro. In the following, the replication efficacy was characterized in a comparative approach in vivo. Immunocompetent C57BL/6 (wt) mice and immunodeficient mouse strains of different genetic background C57BL/6 athymic and Balb/c athymic mice were used. In addition, subcutaneous and intracranial locations were compared. The results revealed viral replication exclusively in Balb/c athymic mice with subcutaneous tumors but in none of the other models. In the following, the tumor microenvironment of the subcutaneous tumor models at the time of infection was performed. The study showed that implantation of the same tumor cells in different mouse strains resulted in a different tumor microenvironment with a distinct composition of immune cells. Highest differences were detected between immunodeficient and immunocompetent mice. The study showed major differences in the expression of MHCII with strongest expression in C57BL/6 wt and weakest in Balb/c athymic tumors. In the following, the influence of the phenotypic change associated with the upregulation of MHCII on GL261 tumor cells on viral replication was analyzed. Comparison of C57BL/6 wt and C57BL/6 IFN-γ knockout mice revealed endogenous IFN-γ levels to upregulate MHCII on GL261 tumor cells and to reduce viral replication in C57BL/6 wt mice. Analysis of single cell suspensions of tumor homogenates of C57BL/6 and Balb/c athymic mice showed that the IFN-γ-mediated anti-tumor effect was a reversible effect. Furthermore, reasons for inhibition of virus replication in orthotopic glioma models were elucidated. By immunohistochemical analysis it was shown that intratumoral amounts of Iba1+ microglia and GFAP+ astrocytes in Gl261 gliomas was independent from intratumoral VACV injection. Based on these findings virus infection in glioma, microglia and astrocytes was compared and analyzed in cell culture. In contrast to the GL261 glioma cells, replication was barely detectable in BV-2 microglia and IMA2.1 astrocytic cells. Co-culture experiments revealed that microglia compete for virus uptake in cell culture. It was further shown that BV-2 cells showed apoptotic characteristics after VACV infection while GL261 cells showed signs of necrotic cell death. Additionally, in BV-2 cells with M1-phenotype a further reduction of viral replication and inhibition of cell lysis was detected. Infection of IMA 2.1 cells was independent of the M1/M2-phenotype. Application of BV-2 microglia with M1-phenotype onto organotypic slice cultures with implanted GL261 tumors resulted in reduced infection of BV-2 cells with LIVP 1.1.1, whereas GL261 cells were significantly infected. Taken together, the analyzed GL261 tumors were imprinted by the immunologic and genetic background in which they grow. The experimental approach applied in this thesis can be used as suitable model which reflects the principles of personalized medicine In an additional project, based on gene expression data and bioinformatic analyses, the biological role and function of the anti-apoptotic factor AVEN was analyzed with regard to oncolytic VACV therapy. Besides a comparison of the replication efficacy of GLV-1h68 and VACV-mediated cell killing of four human tumor cell lines, it was shown that AVEN was expressed in all analyzed cells. Further, shown for HT-29 and 1936-MEL, the knockdown of AVEN by siRNA in cell culture resulted in an increase of apoptotic characteristics and a decrease of VACV infection. These findings provide essential insights for future virus development.}, subject = {Krebs }, language = {en} } @phdthesis{Keppler2020, author = {Keppler, Sarah}, title = {Characterization of Novel Mutations in Receptor-Tyrosine Kinases in Multiple Myeloma}, doi = {10.25972/OPUS-15572}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-155720}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2020}, abstract = {Multiple myeloma (MM) is a disease of terminally differentiated B-cells which accumulate in the bone marrow leading to bone lesions, hematopoietic insufficiency and hypercalcemia. Genetically, MM is characterized by a great heterogeneity. A recent next-generation sequencing approach resulted in the identification of a signaling network with an accumulation of mutations in receptor-tyrosine kinases (RTKs), adhesion molecules and downstream effectors. A deep-sequencing amplicon approach of the coding DNA sequence of the six RTKs EPHA2, EGFR, ERBB3, IGF1R, NTRK1 and NTRK2 was conducted in a patient cohort (75 MM samples and 68 corresponding normal samples) of the "Deutsche Studiengruppe Multiples Myelom (DSMM)" to further elucidate the role of RTKs in MM. As an initial approach the detected mutations were correlated with cytogenetic abnormalities and clinical data in the course of this thesis. RTK mutations were present in 13\% of MM patients of the DSMM XI trial and accumulated in the ligand-binding and tyrosine-kinase domain. The newly identified mutations were associated with an adverse patient survival, but not with any cytogenetic abnormality common in MM. Especially rare patient-specific SNPs (single nucleotide polymorphism) had a negative impact on patient survival. For a more comprehensive understanding of the role of rare RTK SNPs in MM, a second amplicon sequencing approach was performed in a patient cohort of the DSMM XII trial that included 75 tumor and 184 normal samples. This approach identified a total of 23 different mutations in the six RTKs EPHA2, EGFR, ERBB3, IGF1R, NTRK1 and NTRK2 affecting 24 patients. These mutations could furthermore be divided into 20 rare SNPs and 3 SNVs (single nucleotide variant). In contrast to the first study, the rare SNPs were significantly associated with the adverse prognostic factor del17p. IGF1R was among the most commonly mutated RTKs in the first amplicon sequencing approach and is known to play an important role in diverse cellular processes such as cell proliferation and survival. To study the role of IGF1R mutations in the hard-to-transfect MM cells, stable IGF1R-knockdown MM cell lines were established. One of the knockdown cell lines (L363-C/C9) as well as a IGF1R-WT MM cell line (AMO1) were subsequently used for the stable overexpression of WT IGF1R and mutant IGF1R (N1129S, D1146N). Overall, an impact on the MAPK and PI3K/AKT signaling pathways was observed upon the IGF1R knockdown as well as upon WT and mutant IGF1R overexpression. The resulting signaling pattern, however, differed between different MM cell lines used in this thesis as well as in a parallel performed master thesis which further demonstrates the great heterogeneity described in MM. Taken together, the conducted sequencing and functional studies illustrate the importance of RTKs and especially of IGF1R and its mutants in the pathogenesis of MM. Moreover, the results support the potential role of IGF1R as a therapeutic target for a subset of MM patients with mutated IGF1R and/or IGF1R overexpression.}, subject = {Plasmozytom}, language = {en} } @phdthesis{Nuwal2010, author = {Nuwal, Tulip}, title = {Characterization of Synapsin, Tubulin-Binding Chaperone E-like, And Their Putative Interactions With Synapse Associated Protein Of 47 kDa In Drosophila melanogaster}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51683}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {In this thesis we have used Drosophila melanogaster as a model organism to investigate proteins and their putative interacting partners that are directly or indirectly involved in the release of neurotransmitters at the synapse. We have used molecular techniques to investigate conserved synaptic proteins, synapsin and synapse associated protein of 47 kD (SAP47), and a putative interaction partner of SAP47, tubulin binding chaperone E-like (TBCEL). SAP47 and synapsins are highly conserved synaptic vesicle associated proteins in Drosophila melanogaster. To further investigate the role and function of Sap47 and Syn genes, we had earlier generated the null mutants by P-element mutagenesis (Funk et al., 2004; Godenschwege et al., 2004). Western blots and ELISA of brain homogenates from Sap47156 null mutants showed the presence of up-regulated phospho-synapsin in comparison to wild-type (CS) and the presence of up-regulated phospho-synapsin was partially abolished when a pan-neuronal rescue of SAP47 was performed by the Gal4- UAS technique. Thus, the results suggest a qualitative and quantitative modulation of synapsin by SAP47. At the transcript level, we did not observe any difference in content of Syn transcript in Sap47156 and wild-type CS flies. The question of a direct molecular interaction between SAP47 and synapsin was investigated by co-immunoprecipitation (Co-IP) experiments and we did not find any stable interactions under the several IP conditions we tested. The possibility of Sap47 as a modifier of Syn at the genetic level was investigated by generating and testing homozygous double null mutants of Sap47 and Syn. The Syn97, Sap47156 double mutants are viable but have a reduced life span and decreased locomotion when compared to CS. In 2D-PAGE analysis of synapsins we identified trains of spots corresponding to synapsins, suggesting that synapsin has several isoforms and each one of them is posttranslationally modified. In an analysis by Blue native-SDS-PAGE (BN-SDS-2D- PAGE) and Western blot we observed synapsin and SAP47 signals to be present at 700-900 kDa and 200-250 kDa, respectively, suggesting that they are part of large but different complexes. We also report the possibility of Drosophila synapsin forming homo- and heteromultimers, which has also been reported for synapsins of vertebrates. In parallel to the above experiments, phosphorylation of synapsins in Drosophila was studied by IP techniques followed by 1D-SDS gel electrophoresis and mass spectrometry (in collaboration with S. Heo and G. Lubec). We identified and verified 5 unique phosphorylation sites in Drosophila synapsin from our MS analysis. Apart from phosphorylation modifications we identified several other PTMs which have not been verified. The significance of these phosphorylations and other identified PTMs needs to be investigated further and their implications for synapsin function and Drosophila behavior has to be elucidated by further experiments. In a collaborative project with S. Kneitz and N. Nuwal, we investigated the effects of Sap156 and Syn97 mutations by performing a whole Drosophila transcriptome microarray analysis of the individual null mutants and the double mutants (V2 and V3). We obtained several candidates which were significantly altered in the mutants. These genes need to be investigated further to elucidate their interactions with Sap47 and Syn. In another project, we investigated the role and function of Drosophila tubulin- binding chaperone E-like (Tbcel, CG12214). The TBCEL protein has high homology to vertebrate TBCE-like (or E-like) which has high sequence similarity to tubulin-binding chaperone E (TBCE) (hence the name TBCE-Like). We generated an anti-TBCEL polyclonal antiserum (in collaboration with G. Krohne). According to flybase, the Tbcel gene has only one exon and codes for two different transcripts by alternative transcription start sites. The longer transcript RB is present only in males whereas the shorter transcript RA is present only in females. In order to study the gene function we performed P- element jump-out mutagenesis to generate deletion mutants. We used the NP4786 (NP) stock which has a P(GawB) insertion in the 5' UTR of the Tbcel gene. NP4786 flies are homozygous lethal due to a second-site lethality as the flies are viable over a deficiency (Df) chromosome (a deletion of genomic region spanning the Tbcel gene and other upstream and downstream genes). We performed the P-element mutagenesis twice. In the first trial we obtained only revertants and the second experiment is still in progress. In the second attempt, jump-out was performed over the deficiency chromosome to prevent homologous chromosome mediated double stranded DNA repair. During the second mutagenesis an insertion stock G18151 became available. These flies had a P-element insertion in the open reading frame (ORF) of the Tbcel gene but was homozygous viable. Western blots of fresh tissue homogenates of NP/Df and G18151 flies probed with anti-TBCEL antiserum showed no TBCEL signal, suggesting that these flies are Tbcel null mutants. We used these flies for further immunohistochemical analyses and found that TBCEL is specifically expressed in the cytoplasm of cyst cells of the testes and is associated with the tubulin of spermatid tails in wild-type CS, whereas in NP/Df and G18151 flies the TBCEL staining in the cyst cells was absent and there was a disruption of actin investment cones. We also found enrichment of TBCEL staining around the actin investment cone. These results are also supported by the observation that the enhancer trap expression of the NP4786 line is localised to the cyst cells, similar to TBCEL expression. Also, male fertility of NP/Df and G18151 flies was tested and they were found to be sterile with few escapers. Thus, these results suggest that TBCEL is involved in Drosophila spermatogenesis with a possible role in the spermatid elongation and individualisation process.}, subject = {Taufliege}, language = {en} } @phdthesis{Reis2017, author = {Reis, Helena}, title = {Characterization of telomere protein complexes in Trypanosoma brucei}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151323}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2017}, abstract = {African trypanosomiasis is a disease endemic to sub-Saharan Africa. It affects humans as well as wild and domestic animals. The human form of the disease is known as sleeping sickness and the animal form as nagana, which are usually fatal if left untreated. The cause of African trypanosomiasis is the unicellular parasite Trypanosoma brucei. During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host the parasite multiplies as bloodstream form (BSF) extracellularly in the bloodstream or the lymphatic system. Survival of BSF parasites relies on immune evasion by antigenic variation of surface proteins because its extracellular lifestyle leads to direct exposure to immune responses. At any given time each BSF cell expresses a single type of variant surface glycoprotein (VSG) on its surface from a large repertoire. The active VSG is transcribed from one of 15 specialized subtelomeric domains, termed bloodstream expression sites (BESs). The remaining 14 BESs are silenced. This monoallelic expression and periodic switching of the expressed VSG enables to escape the immune response and to establish a persistent infection in the mammalian host. During developmental differentiation from BSF to the insect vector-resident procyclic form (PCF), the active BES is transcriptionally silenced to stop VSG transcription. Thus, all 15 BESs are inactive in the PCF cells as surface protein expression is developmentally regulated. Previous reports have shown that the telomere complex components TbTRF, TbRAP1 and TbTIF2 are involved in VSG transcriptional regulation. However, the precise nature of their contribution remains unclear. In addition, no information is available about the role of telomeres in the initiation and regulation of developmental BES silencing. To gain insights into the regulatory mechanisms of telomeres on VSG transcription and developmental repression it is therefore essential to identify the complete composition of the trypanosome telomere complex. To this end, we used two complementary biochemical approaches and quantitative label-free interactomics to determine the composition of telomere protein complexes in T. brucei. Firstly, using a telomeric pull-down assay we found 17 potential telomere-binding proteins including the known telomere-binding proteins TbTRF and TbTIF2. Secondly, by performing a co-immunoprecipitation experiment to elucidate TbTRF interactions we co-purified five proteins. All of these five proteins were also enriched with telomeric DNA in the pull-down assay. To validate these data, I characterized one of the proteins found in both experiments (TelBP1). In BSF cells, TelBP1 co-localizes with TbTRF and interacts with already described telomere-binding proteins such as TbTRF, TbTIF2 and TbRAP1 indicating that TelBP1 is a novel component of the telomere complex in trypanosomes. Interestingly, protein interaction studies in PCF cells suggested a different telomere complex composition compared to BSF cells. In contrast to known members of the telomere complex, TelBP1 is dispensable for cell viability indicating that its function might be uncoupled from the known telomere-binding proteins. Overexpression of TelBP1 had also no effect on cell viability, but led to the discovery of two additional shorter isoforms of TelBP1. However, their source and function remained elusive. Although TelBP1 is not essential for cell viability, western blot analysis revealed a 4-fold upregulation of TelBP1 in the BSF stage compared to the PCF stage supporting the concept of a dynamic telomere complex composition. We observed that TelBP1 influences the kinetics of transcriptional BES silencing during developmental transition from BSF to PCF. Deletion of TelBP1 caused faster BES silencing compared to wild-type parasites. Taken together, TelBP1 function illustrates that developmental BES silencing is a fine-tuned process, which involves stage-specific changes in telomere complex formation.}, subject = {Trypanosoma brucei}, language = {en} } @phdthesis{Weisert2024, author = {Weisert, Nadine}, title = {Characterization of telomere-associated proteins in \(Trypanosoma\) \(brucei\)}, doi = {10.25972/OPUS-35273}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-352732}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {The unicellular pathogen Trypanosoma brucei is the causative agent of African trypanosomiasis, an endemic disease prevalent in sub-Saharan Africa. Trypanosoma brucei alternates between a mammalian host and the tsetse fly vector. The extracellular parasite survives in the mammalian bloodstream by periodically exchanging their ˈvariant surface glycoproteinˈ (VSG) coat to evade the host immune response. This antigenic variation is achieved through monoallelic expression of one VSG variant from subtelomeric ˈbloodstream form expression sitesˈ (BES) at a given timepoint. During the differentiation from the bloodstream form (BSF) to the procyclic form (PCF) in the tsetse fly midgut, the stage specific surface protein is transcriptionally silenced and replaced by procyclins. Due to their subtelomeric localization on the chromosomes, VSG transcription and silencing is partly regulated by homologues of the mammalian telomere complex such as TbTRF, TbTIF2 and TbRAP1 as well as by ˈtelomere-associated proteinsˈ (TelAPs) like TelAP1. To gain more insights into transcription regulation of VSG genes, the identification and characterization of other TelAPs is critical and has not yet been achieved. In a previous study, two biochemical approaches were used to identify other novel TelAPs. By using ˈco-immunoprecipitationˈ (co-IP) to enrich possible interaction partners of TbTRF and by affinity chromatography using telomeric repeat oligonucleotides, a listing of TelAP candidates has been conducted. With this approach TelAP1 was identified as a novel component of the telomere complex, involved in the kinetics of transcriptional BES silencing during BSF to PCF differentiation. To gain further insights into the telomere complex composition, other previously enriched proteins were characterized through a screening process using RNA interference to deplete potential candidates. VSG expression profile changes and overall proteomic changes after depletion were analyzed by mass spectrometry. With this method, one can gain insights into the functions of the proteins and their involvement in VSG expression site regulation. To validate the interaction of proteins enriched by co-IP with TbTRF and TelAP1 and to identify novel interaction proteins, I performed reciprocal affinity purifications of the four most promising candidates (TelAP2, TelAP3, PPL2 and PolIE) and additionally confirmed colocalization of two candidates with TbTRF via immunofluorescence (TelAP2, TelAP3). TelAP3 colocalizes with TbTRF and potentially interacts with TbTRF, TbTIF2, TelAP1 and TelAP2, as well as with two translesion polymerases PPL2 and PolIE in BSF. PPL2 and PolIE seem to be in close contact to each other at the telomeric ends and fulfill different roles as only PolIE is involved in VSG regulation while PPL2 is not. TelAP2 was previously characterized to be associated with telomeres by partially colocalizing with TbTRF and cells show a VSG derepression phenotype when the protein was depleted. Here I show that TelAP2 interacts with the telomere-binding proteins TbTRF and TbTIF2 as well as with the telomere-associated protein TelAP1 in BSF and that TelAP2 depletion results in a loss of TelAP1 colocalization with TbTRF in BSF. In conclusion, this study demonstrates that characterizing potential TelAPs is effective in gaining insights into the telomeric complex's composition and its role in VSG regulation in Trypanosoma brucei. Understanding these interactions could potentially lead to new therapeutic targets for combatting African trypanosomiasis.}, subject = {Telomer }, language = {en} } @phdthesis{JimenezPearson2005, author = {Jim{\´e}nez-Pearson, Mar{\´i}a-Antonieta}, title = {Characterization of the mechanisms of two-component signal transduction involved in motility and chemotaxis of Helicobacter pylori}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-15698}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2005}, abstract = {Flagellen-basierte Motilit{\"a}t und Chemotaxis stellen essentielle Pathogenit{\"a}tsfaktoren dar, die f{\"u}r die erfolgreiche Kolonisierung der Magenschleimhaut durch H. pylori notwendig sind. Die Mechanismen der Regulation der Flagellensynthese und das Chemotaxis-System von H. pylori weisen trotz einiger {\"A}hnlichkeiten fundamentale Unterschiede zu den Systemen anderer Bakterien auf. In H. pylori ist die Flagellensynthese durch eine komplex regulierte Kaskade kontrolliert, die Regulatorkomponenten wie das Zweikomponentensystem HP244/FlgR, die Sigma Faktoren 54 und 28 und den Sigma Faktor28-Antagonisten FlgM enth{\"a}lt. Das Signal, welches {\"u}ber die Histidinkinase des Zweikomponentensystems HP244/FlgR die Expression der Sigma Faktor54-abh{\"a}ngigen Klasse 2 Flagellengene reguliert, ist bisher noch nicht bekannt. Allerdings konnte mit HP137 ein Protein identifiziert werden, das im „yeast two-hybrid" System sowohl mit der korrespondierenden Kinase HP244 des Flagellenregulators FlgR, als auch mit der Flagellenkomponente FlgE´ interagiert (Rain et al., 2001). In dieser Arbeit wurde eine m{\"o}gliche Rolle von HP137 in einem R{\"u}ckkopplungsmechanismus untersucht, welcher die Aktivit{\"a}t der Histidinkinase in der Flagellenregulation kontrollieren k{\"o}nnte. Obwohl die Deletion des ORF hp137 zu einer unbeweglichen Mutante f{\"u}hrte, legen die erfolglosen Komplementations Experimente, sowie die Beobachtung, dass HP137 in vitro keinen bedeutenden Effekt auf die Aktivit{\"a}t der Histidinkinase HP244 hat nahe, dass HP137 weder in H. pylori noch im nahe verwandten C. jejuni direkt an der Flagellenregulation beteiligt ist. Das Chemotaxis-System von H. pylori unterscheidet sich vom gutuntersuchten Chemotaxis-System der Enterobakterien in einigen Aspekten. Zus{\"a}tzlich zu dem CheY Response Regulator Protein (CheY1) besitzt H. pylori eine weitere CheY-artige Receiver-Dom{\"a}ne (CheY2) welche C-terminal an die Histidinkinase CheA fusioniert ist. Zus{\"a}tzlich finden sich im Genom von H. pylori Gene, die f{\"u}r drei CheV Proteine kodieren die aus einer N-terminalen Dom{\"a}ne {\"a}hnlich CheW und einer C-terminalen Receiver Dom{\"a}ne bestehen, w{\"a}hrend man keine Orthologen zu den Genen cheB, cheR, and cheZ findet. Um einen Einblick in den Mechanismus zu erhalten, welcher die chemotaktische Reaktion von H. pylori kontrolliert, wurden Phosphotransferreaktionen zwischen den gereinigten Signalmodulen des Zweikomponentensystems in vitro untersucht. Durch in vitro-Phosphorylierungsexperimente wurde eine ATP-abh{\"a}ngige Autophosphorylierung der bifunktionellen Histidinkinase CheAY2 und von CheA´, welches ein verk{\"u}rztes Derivat von ChAY2 ohne Receiver-Dom{\"a}ne darstellt, nachgewiesen. CheA´ zeigt eine f{\"u}r an der Chemotaxis beteiligte Histidinkinasen typische Phosphorylierungskinetik mit einer ausgepr{\"a}gten exponentiellen Phase, w{\"a}hrend die Phosphorylierungskinetik von CheAY2 nur eine kurze exponentielle Phase aufweist, gefolgt von einer Phase in der die Hydrolyse von CheAY2~P {\"u}berwiegt. Es wurde gezeigt, dass die Anwesenheit einer der CheY2 Dom{\"a}ne die Stabilit{\"a}t der phosphorylierten P1 Dom{\"a}ne im CheA Teil des bifunktionellen Proteins beeinflusst. Außerdem wurde gezeigt, dass sowohl CheY1 als auch CheY2 durch CheAY2 phosphoryliert werden und dass die drei CheV Proteine die Histidinkinase CheA´~P dephosphorylieren, wenn auch mit einer im Vergleich zu CheY1 und CheY2 geringeren Affinit{\"a}t. Außerdem ist CheA´ in der Lage seine Phosphatgruppen auf CheY1 aus C. jejuni und CheY aus E. coli zu {\"u}bertragen. Retrophosphorylierungsexperimente weisen darauf hin, dass CheY1~P die Phosphatgruppe zur{\"u}ck auf die Histidinkinase CheAY2 {\"u}bertragen kann und dass die CheY2-Dom{\"a}ne in dem bifunktionellen Protein CheAY2 als „Phosphat Sink" agiert der den Phosphorylierungszustand und damit die Aktivit{\"a}t des frei diffundierbaren Proteins CheY1 reguliert, das vermutlich es mit dem Flagellenmotor interagiert. Es konnte weiterhin gezeigt werden, dass die unabh{\"a}ngige Funktion der beiden Dom{\"a}nen CheA´ und CheY2 f{\"u}r eine normale chemotaktische Signalgebung in vivo nicht ausreicht. In dieser Arbeit wurden also Hinweise auf eine komplexe Kaskade Phosphat{\"u}bertragungsreaktionen im chemotaktischen System von H. pylori gefunden, welches {\"A}hnlichkeiten zu dem Syteme-Chemotaxis von S. meliloti aufweist an denen multiple CheY Proteine beteiligt sind. Die Rolle der CheV Proteine bleibt im Moment unklar, jedoch k{\"o}nnte es sein, dass sie an einer weiteren Feinregulierung der Phosphatgruppen{\"u}bertragungsreaktionen in diesem komplexen chemotaktischen System beteiligt sind}, subject = {Helicobacter pylori}, language = {en} } @phdthesis{Kirchmaier2010, author = {Kirchmaier, Bettina Carmen}, title = {Characterization of the Popeye domain containing gene family in zebrafish}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-49413}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {The Popeye domain containing (Popdc) gene family of membrane proteins is predominantly expressed in striated and smooth muscle tissues and has been shown to act as novel cAMP-binding proteins. In mice, loss of Popdc1 and Popdc2, respectively, affects sinus node function in the postnatal heart in an age and stress-dependent manner. In this thesis, I examined gene expression pattern and function of the Popdc gene family during zebrafish development with an emphasis on popdc2. Expression of the zebrafish popdc2 was exclusively present in cardiac and skeletal muscle during cardiac development, whereas popdc3 was expressed in striated muscle tissue and in distinct regions of the brain. In order to study the function of these genes, an antisense morpholino-based knockdown approach was used. Knockdown of popdc2 resulted in aberrant development of facial and tail musculature. In the heart, popdc2 morphants displayed irregular ventricular contractions with 2:1 and 3:1 ventricular pauses. Recordings of calcium transients using a transgenic indicator line Tg(cmlc2:gCaMP)s878 and selective plane illumination microscopy (SPIM) revealed the presence of an atrioventricular (AV) block in popdc2 morphants as well as a complete heart block. Interestingly, preliminary data revealed that popdc3 morphants developed a similar phenotype. In order to find a morphological correlate for the observed AV conduction defect, I studied the structure of the AV canal in popdc2 morphants using confocal analysis of hearts of the transgenic line Tg(cmlc2:eGFP-ras)s883, which outlines individual cardiac myocytes with the help of membrane-localized GFP. However, no evidence for morphological alterations was obtained. To ensure that the observed arrhythmia phenotype in the popdc2 morphant was based on a myocardial defect and not caused by defective valve development, live imaging was performed revealing properly formed valves. Thus, in agreement with the data obtained in knockout mice, popdc2 and popdc3 genes in zebrafish are involved in the regulation of cardiac electrical activity. However, both genes are not required for cardiac pacemaking, but they play essential roles in AV conduction. In order to elucidate the biological importance of cAMP-binding, wild type Popdc1 as well as mutants with a significant reduction in binding affinity for cAMP in vitro were overexpressed in zebrafish embryos. Expression of wild type Popdc1 led to a cardiac insufficiency phenotype characterized by pericardial edema and venous blood retention. Strikingly, the ability of the Popdc1 mutants to induce a cardiac phenotype correlated with the binding affinity for cAMP. These data suggest that cAMP-binding represents an important biological property of the Popdc protein family.}, subject = {Zebrab{\"a}rbling}, language = {en} } @phdthesis{Romanov2019, author = {Romanov, Natalie}, title = {Characterizing Variation of Protein Complexes and Functional Modules on a Temporal Scale and across Individuals}, doi = {10.25972/OPUS-16813}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168139}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2019}, abstract = {A fundamental question in current biology concerns the translational mechanisms leading from genetic variability to phenotypes. Technologies have evolved to the extent that they can efficiently and economically determine an individual's genomic composition, while at the same time big data on clinical profiles and diagnostics have substantially accumulated. Genome-wide association studies linking genomic loci to certain traits, however, remain limited in their capacity to explain the cellular mechanisms that underlie the given association. For most associations, gene expression has been blamed; yet given that transcript and protein abundance oftentimes do not correlate, that finding does not necessarily decrypt the underlying mechanism. Thus, the integration of further information is crucial to establish a model that could prove more accurate in predicting genotypic effects on the human organism. In this work we describe the so-called proteotype as a feature of the cell that could provide a substantial link between genotype and phenotype. Rather than looking at the proteome as a set of independent molecules, we demonstrate a consistent modular architecture of the proteome that is driven by molecular cooperativity. Functional modules, especially protein complexes, can be further interrogated for differences between individuals and tackled as imprints of genetic and environmental variability. We also show that subtle stoichiometric changes of protein modules could have broader effects on the cellular system, such as the transport of specific molecular cargos. The presented work also delineates to what extent temporal events and processes influence the stoichiometry of protein complexes and functional modules. The re-wiring of the glycolytic pathway for example is illustrated as a potential cause for an increased Warburg effect during the ageing of the human bone marrow. On top of analyzing protein abundances we also interrogate proteome dynamics in terms of stability and solubility transitions during the short temporal progression of the cell cycle. One of our main observations in the thesis encompass the delineation of protein complexes into respective sub-complexes according to distinct stability patterns during the cell cycle. This has never been demonstrated before, and is functionally relevant for our understanding of the dis- and assembly of large protein modules. The insights presented in this work imply that the proteome is more than the sum of its parts, and primarily driven by variability in entire protein ensembles and their cooperative nature. Analyzing protein complexes and functional modules as molecular reflections of genetic and environmental variations could indeed prove to be a stepping stone in closing the gap between genotype and phenotype and customizing clinical treatments in the future.}, subject = {Proteotype}, language = {en} } @phdthesis{Huber2014, author = {Huber, Annette}, title = {Chlamydial deubiquitinase ChlaDUB1 as regulator of host cell apoptosis and new target for anti-chlamydial therapy}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-110013}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {Chlamydia trachomatis is an obligate intracellular pathogen that replicates inside a vacuole, the so-called inclusion. During replication by a biphasic life-cycle Chlamydia secrete via their type 3 secretion system various effector proteins into the inclusion lumen, the inclusion membrane or the host cell cytosol to form their favored replication niche. Chlamydia-infected cells are highly resistant against apoptosis since the replicative form of Chlamydia is non-infectious and premature cell death would cause complete loss of one Chlamydia generation. The bacteria block apoptosis by preventing mitochondrial outer membrane permeabilization. Various proteins with anti-apoptotic function are enriched in Chlamydia-infected cells such as Mcl-1, cIAP2, Survivin or HIF1α. The accumulation of these proteins is a result of increased gene expression and direct protein stabilization. However, the molecular mechanisms and involved bacterial effector proteins are mostly unknown. With this work the molecular mechanisms of Mcl-1 stabilization and the participation of chlamydial factors were investigated. Mcl-1 is a member of the Bcl-2 protein family and has an extremely short half-life causing its permanent ubiquitination and subsequent degradation by the 26S proteasome under normal homeostasis whilst Mcl-1 accumulation results in apoptosis inhibition. It was shown that during C. trachomatis infection Mcl-1 ubiquitination is reduced causing its stabilization albeit no cellular ubiquitin-proteasome-system components are involved in this process. However, C. trachomatis express the two deubiquitinases ChlaDUB1 and ChlaDUB2 which are mostly uncharacterized. With this work the expression profile, subcellular localization, substrates and function of the deubiquitinases were investigated. It was shown that ChlaDUB1 is secreted to the surface of the inclusion where it interacts with Mcl-1 which is accumulated in the proximity of this compartment. By utilization of infection experiments, heterologous expression systems and in vitro experiments a direct interaction of ChlaDUB1 and Mcl-1 was demonstrated. Furthermore, it was shown that Mcl-1 is deubiquitinated by ChlaDUB1 causing its stabilization. During replicative phase of infection, ChlaDUB2 seems to be accumulated in the chlamydial particles. However, ChlaDUB2 substrates could not be identified which would give an indication for the physiological role of ChlaDUB2. Since 2011, a protocol to transform C. trachomatis with artificial plasmid DNA is available. As part of this work the transformation of C. trachomatis with plasmid DNA suitable for the permanent or inducible protein overexpression on a routinely basis was established. In addition, the first targeted homologous recombination into the chlamydial genome to replace the ChlaDUB1 gene by a modified one was performed and validated. The targeted homologous recombination was also used to create a ChlaDUB1 knock-out mutant; however deletion of ChlaDUB1 seems to be lethal for C. trachomatis. Due to the fact that ChlaDUB1-lacking Chlamydia could not be obtained an inhibitor screen was performed and identified CYN312 as a potential ChlaDUB1 inhibitor. Application of CYN312 during infection interfered with chlamydial growth and reduced Mcl-1 quantity in infected cells. Furthermore, CYN312 treated Ctr-infected cells were significantly sensitized for apoptosis. Taken together, C. trachomatis secretes the deubiquitinase ChlaDUB1 to the surface of the inclusion where it deubiquitinates Mcl-1 causing its accumulation in infected cells resulting in apoptosis resistance. Application of the ChlaDUB1 inhibitor CYN312 interferes with Mcl-1 stabilization sensitizing infected cells for apoptosis.}, subject = {Chlamydia trachomatis}, language = {en} } @phdthesis{Goldau2002, author = {Goldau, Rainer}, title = {Clinical evaluation of novel methods to determine dialysis parameters using conductivity cells}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-3125}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {During the last two decades an ongoing discussion about the necessary dose of dialysis brought the result that the urea based Kt/V value is significantly correlated to morbidity of the end stage renal disease (ESRD) patients. Even if it is not completely accepted, it seems to be more and more agreement of the nephrological community that for good dialysis practice Kt/V should be kept above 1.2 to 1.3 in the usual 3X4 hours per week dialysis schedule for patients without own residual clearance to assure long term quality of life, low morbidity and mortality. K is the clearance of urea the dialysis system can apply, t is the treatment time and V is the urea distribution volume of the patient, which is nearly equal to total body water. Kt/V has the unit of a drug dose (ml of drug per ml of patient volume) and therefore sometimes is called dialysis 'dose', even if this is subject of discussion because it implies that the dose can be described with only one urea related number. This work does not participate in this discussion. The premise of this work is more technical: Whatever the final result of the above discussion will be, a patient-friendly, precise cost-neutral and handy technical solution should be given to the hand of the interested nephrologist to continuously supervise the urea based Kt/V that is applied to the patient. Of course this is combined with the hope that the long term mortality can be decreased if a covering online dialysis success control is facilitated. The technical solution that has been chosen is based on the equivalence of the diffusion coefficients of sodium chloride and urea. It is central subject of the investigation if the diffusive behaviour of sodium is equal to that of urea crossing the dialysis filter membrane. The advantage that makes the principle so handy is that sodium can be measured very precise by standard conductivity cells as they are implemented in dialysis machines in large numbers. The only necessary hardware modification is a second conductivity cell downstream the dialyser to be able to measure the mass balance over the filter. This is more complicated with urea that can only be measured undergoing an enzymatic conversion to ammonium ions. The ammonium ions induce a membrane potential, which is measured with very sensitive amplifiers. A cooling chain for the enzyme must be maintained. To find and approve the conductivity based technical solution two in-vivo studies have been conducted. In the first study a conductivity step profile, varying the conductivity in static levels in a baseline - 7 min high - 7min low- baseline shape, was applied that can be utilised to measure the urea clearance very accurate. This principle has been described in 1982 in a patent application. In a sequence of 206 computer recorded dialysis sessions with 22 patients it was found that urea clearance could be electrolytically measured with a mean error+/-standard deviation of -1.46+/-4.75\% , n=494. The measurement of Kt/V according to a single pool model was of similar accuracy: 2.88+/-4.15\% . Although in accordance with other studies these findings at an average confirmed the high correlation of ionic and urea based clearance measurements, an effect was found that was not consistent with the theory that was existent so far. It was found in the first study that the accuracy of the step profile measurements were dependent of the size of the patient, in particular of the urea distribution volume. Moreover it was of relevance which part of the step profile was used: the high-low states, the baseline- low or the baseline-high states. This was a theoretical lack. Careful analysis led to the result that sodium transfer from and into the patient was the reason for the dependence. This led to the enhancement of the theory that seems to correctly describe the nature of the effect. A new demand now was to minimise the sodium transfer. This was limited using static step profiles because in the time it needs to become stable sodium is shifted. In consequence non-stable, dynamic short conductivity boli were developed that allowed to minimise the amount of sodium to be shifted to the limits of the technical resolution of the measurement systems. Also the associated mathematical tools to evaluate the boli had to be suited to the problem. After termination of this process a second study was conducted to approve the new method found. In this study with 10 patients and 93 sessions, 264 step profile measurements and 173 bolus ionic dialysance measurements it was found that the bolus measurements matched their related blood side urea clearance references with the outstanding accuracy of (error+/-SD) 0.06+/-4.76\%. The result was not significantly different (p=0.87) from the reference by student's t-test for paired data. The Kt/V reference according to the single pool variable volume urea kinetic model (sPVVUKM) was found to be matched by the bolus principle with 5.32+/-3.9\% accuracy and a correlation of 0.98. The remaining difference of 5.32\% can be attributed to the neglect of the urea generation rate. Also the step profile was found to be very precise here. The error versus sPVVUKM was 0.05\%+/-5\%, r=0.96. However it did not image the neglect of urea generation correctly. Also a two pool modelling that comprises an internal compartimentation of the fluid pools of the patient was applied to the continuously recorded data. This two pool urea kinetic model (2PUKM) is regarded to be a more precise theoretical approach and now includes the urea generation. It found the bolus principle to deviate -3.04 +/- 14.3\%, n.s., p=0.13. The high standard deviation is due to the complexity of the model. Further from the developed theory a simplified method to roughly measure the sodium distribution volume could be derived. This method was tested in-vitro versus a container with dialysate of known volume and in-vivo versus the urea distribution volume. The in-vitro results were -19.9+/-34\%, r=0.92, n.s, p=0.916. In-vivo they were found to be -7.4+/-23.2\%, r=0.71, n.s., p=0.39. Due to dilution theory the sodium and urea distribution volumes virtually appear to be very similar using this method, although they absolutely differ significantly. Facing the strong simplifications that were made before applying this theory these results seem to be very encouraging that it could be possible to develop a principle to measure not only K but also V electrolytically. This would allow a true Kt/V measurement. The empirical urea distribution volume measurement using anthropometrical formulas has been compared to analytical methods. It has been found that the use Watson's formula with a -13\% correction gives good results. The correction should be applied with great care because it increases Kt/V just on a arithmetical base to the disadvantage of the patient. Also electrolytical plasma sodium measurement was evaluated and can be measured using a mixed analytic-empirical formula with an accuracy of 4.3+/-1.2\%. In summary, conductivity based methods seem to be a convenient method to measure several dialysis parameters of some clinical interest without effort. The results of this work meanwhile are implemented with substantial numbers into commonly available dialysis machines and the experience of the first time shows that the principle is well accepted by the clinicians.}, subject = {H{\"a}modialyse}, language = {en} } @phdthesis{Mao2006, author = {Mao, Zhengrong}, title = {Clonality analysis in B-Cell Chronic Lymphocytic Leukemia (B-CLL) associated with Richter's syndrome}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-20596}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {Die chronische lymphatische Leuk{\"a}mie vom B-Zell-Typ (B-CLL) macht ca. 90\% der chronischen lymphatischen Leuk{\"a}mien aus. Der klinische Verlauf der B-CLL ist heterogen, und bei 3-5\% der Patienten kommt es im Verlauf der Erkrankung zu einer Transformation in ein aggressives Lymphom, meist in ein diffuses großzelliges B-Zell-Lymphom (DLBCL) oder in ein Hodgkin-Lymphom (HL). Eine solche Transformation wird als Richter-Syndrom bezeichnet und ist mit einer ung{\"u}nstigen klinischen Prognose assoziiert. In B-Zell-Lymphomen (B-NHL) erm{\"o}glicht der Mutationsstatus der variablen Anteile der Immunglobulinschwerkettengene (IgVH) eine Aussage {\"u}ber das Entwicklungsstadium der B-Zelle, in dem sich die Transformation zu einem B-Zell-Lymphom ereignet hat. In der B-CLL stellt der Mutationsstatus auch einen bedeutenden prognostischen Faktor dar, wobei die Erkrankung bei Patienten mit unmutierten IgVH Genen meist einen ung{\"u}nstigen klinischen Verlauf zeigt. Die wenigen bisher durchgef{\"u}hrten molekularen Analysen an F{\"a}llen von Richter-Syndromen deuten darauf hin, dass ein Transformationsereignis sowohl bei B-CLL-Patienten mit mutierten als auch mit unmutierten IgVH Genen vorkommen kann, und dass die Tumorzellen des DLBCL oder HL sowohl klonal identisch mit dem B-CLL-Klon sein k{\"o}nnen als auch unabh{\"a}ngig als sekund{\"a}res Lymphom entstehen k{\"o}nnen. Um die klonale Beziehung zwischen DLBCL- bzw. Hodgkin/Reed-Sternberg (HRS)-Zellen und den Zellen der vorbestehenden B-CLL zu analysieren, den Mutationsstatus des IgVH Gens sowie m{\"o}gliche prognostische Faktoren in B-CLL-F{\"a}llen mit Richter-Transformation zu identifizieren, wurde eine gr{\"o}ßere Fallserie mit Hilfe eines PCR-basierten GeneScan Ansatzes mit anschließender Sequenzierung der IgVH-Gene untersucht. In F{\"a}llen mit HRS bzw. HRS-{\"a}hnlichen Zellen wurden die CD30-positiven Tumorzellen mittels Laser-Capture Mikrodissektion (LCM) isoliert. Weiterhin erfolgte eine morphologische und immunhistochemische Analyse der F{\"a}lle. Insgesamt wurden 48 Patientenproben untersucht, darunter 40 F{\"a}lle mit Richter-Syndrom sowie weitere 8 B-CLL-F{\"a}lle mit CD30-positiven HRS-{\"a}hnlichen Zellen. Unter den 40 Proben mit Richter-Syndrom zeigten 34 B-CLL-F{\"a}lle eine Transformation in ein DLBCL, in 6 F{\"a}llen erfolgte eine Transformation in ein HL. In 23 F{\"a}llen mit B-CLL und DLBCL wurde eine Sequenzierung der IgVH Gene durchgef{\"u}hrt. In 18 F{\"a}llen waren B-CLL und DLBCL klonal identisch, in 5 F{\"a}llen war das DLBCL als klonal unabh{\"a}ngige Neoplasie entstanden. Unter den klonal verwandten Paaren zeigten 11 von 15 Paaren unmutierte IgVH-Gene sowohl in der B-CLL als auch im DLBCL, wohingegen 5 von 6 F{\"a}lle mit Transformation einer B-CLL in ein HL mutierte IgVH Gene trugen. HRS-Zellen in 2 F{\"a}llen und HRS-{\"a}hnliche Zellen in einem Fall waren klonal verschieden vom B-CLL-Zellklon. Die VH-Gene VH3-23, VH3-74, VH1-2 und VH3-9 waren {\"u}berproportional h{\"a}ufig in B-CLL F{\"a}llen mit einer sp{\"a}teren Transformation in ein DLBCL vertreten, wohingegen VH4-34 und VH3-48 in mehr als der H{\"a}lfte der F{\"a}lle mit Transformation zu einem HL nachgewiesen werden konnten. Der immunhistochemische Nachweis von ZAP70 zeigte eine signifikante Assoziation mit unmutierten IgVH-Genen in B-CLL mit nachfolgender Richter-Transformation. Bei 24 Patienten konnte der klinische Verlauf eruiert werden. Die mediane {\"U}berlebenszeit von Patienten mit B-CLL mit stattgehabter Transformation in ein DLBCL oder ein HL betrug 7 beziehungsweise 21 Monate. Es fanden sich weder signifikante Unterschiede der {\"U}berlebenszeit zwischen klonal verwandten und nicht verwandten F{\"a}llen, noch zwischen IgVH-mutierten und -unmutierten F{\"a}llen. Zusammenfassend kann festgestellt werden, dass bei der Richter-Transformation einer B-CLL in ein DLBCL dieses einerseits aus dem pr{\"a}existenten B-CLL-Klon entstehen kann, andererseits aber auch als unabh{\"a}ngige, klonal nicht verwandte Neoplasie auftreten kann. In der Mehrzahl der F{\"a}lle (78\% in dieser Serie) sind B-CLL und DLBCL jedoch klonal identisch und nur gelegentlich entsteht ein DLBCL ohne klonale Beziehung zur B-CLL als unabh{\"a}ngige, sekund{\"a}re Neoplasie. Eine klonale Transformation in ein DLBCL tritt vorwiegend bei B-CLL-Patienten mit unmutierten IgVH-Genen auf, wohingegen die Mehrzahl der B-CLL-Patienten mit einer Transformation in ein HL oder CD30-positive HRS-{\"a}hnliche Zellen mutierte IgVH-Gene aufweist. Dieser Befund l{\"a}sst auf unterschiedliche Transformationswege der beiden Subtypen des Richter-Syndroms schließen. Weiterhin existieren vermutlich wesentliche Unterschiede in der Pathogenese zwischen DLBCL-F{\"a}llen, die sich aus einer vorbestehenden B-CLL entwickelt haben, und de novo DLBCL-F{\"a}llen, da de novo DLBCL zumeist durch mutierte IgVH-Gene charakterisiert sind.}, subject = {B-Zell-Leuk{\"a}mie}, language = {en} } @phdthesis{Stojic2005, author = {Stojic, Jelena}, title = {Cloning and functional characterization of novel genes expressed preferentially in the human retina}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-13746}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2005}, abstract = {The human retina is a multi-layered neuronal tissue specialized for the reception and processing of visual information. The retina is composed of a great diversity of neuronal cell types including rod and cone photoreceptors, bipolar cells, ganglion cells, amacrine cells, horizontal cells and M{\"u}ller glia. In response to light, a coordinated series of molecular events, the so-called phototransduction cascade, is triggered in photoreceptor cells and the signals from the photoreceptors are further processed by the bipolar and ganglion cells to the higher centers of the brain. The retina as highly complex system may be greatly susceptible to genetic defects which can lead to a wide range of disease phenotypes. Therefore, isolation and characterisation of the genes active in the human retina will facilitate our deeper understanding of retinal physiology and mechanisms underlying retinal degeneration and provide novel candidates for the retinal disease genes. To identify novel genes that are specifically or predominantly expressed in the human retina, a cDNA library enriched for retina specific transcripts was generated using suppression subtractive hybridization (SSH) technique. In total, 1113 clones were randomly isolated from the retina SSH cDNA library and partially sequenced. On the basis of BLASTN algorithm analysis these clones were classified into four categories including those with I) significant homology to known human genes (766/1113), II) significant homology to partial transcripts and hypothetical gene predictions (162/1113), III) no homology to known mRNAs (149/1113), and IV) vector sequences and clones derived from mitochondrial genes (36/1113). After correcting for redundancy, category I represented 234 known human genes and category II a total of 92unknown transcripts. Clones from category I, were selected for expression analysis by RT-PCR in a great number of human tissues. This resulted in the identification of 16 genes which were expressed exclusively in the retina, 13 which were highly expressed in the retina compared to other tissues, 12 genes which were specifically expressed in neuronal tissues and 48 ubiquitously expressed genes. Thus, our expression analysis resulted in the identification of 29 genes exclusively or abundantly transcribed in the human retina. Of those, retina specific genes L25,L33, L35, L37, L38 and L40 were selected for further analysis. To characterize the complete mRNA sequences of these transcripts a full-length human retina cDNA library was constructed. The analysis of the L25 gene revealed three splicing variants of the ABCC5 gene, consequently named ABCC5_SV1 (SV1), ABCC5_SV2 (SV2) and ABCC5_SV3 (SV3).These isoforms comprise the first five exons of ABCC5 and additional novel exons named 5a, 5b and 5c, generated by differential exon usage. The determined lengths of the three transcripts are 2039 bp, 1962 bp, and 1887 bp in size, respectively. RT-PCR, real-time PCR and Northern blot analysis of ABCC5 as well as the isoforms SV1, SV2 and SV3demonstrated high levels of expression for all transcripts in the retina compared to other tissues. Analysis of their nucleotide sequences revealed that inclusion of exon 5a in splicing variant SV1 produced a frame shift and premature termination codon (PTC). Our data show that this splice variant is the target of nonsense mediated mRNA decay (NMD). This was shown by inhibition of protein synthesis with antibiotics puromycin and anisomycin in human cell lines A-RPE 19 and Y79. Our analysis resulted in an increase of the PTC containing transcript and a decrease of the ABCC5 transcript. Conversely, the amount of both transcripts (SV1 and ABCC5) returned to pre-treatment levels after removal of the inhibitors. Together, our results suggest that alternative splicing of the ubiquitously expressed ABCC5 gene in addition to NMD is involved in retina-specific transcriptional regulation of the mRNA level of ABCC5. In contrast, additional experiments demonstrated that the levels of expression ofSV2 and SV3 isoforms do not appear to influence ABCC5 transcription. Several of the cloned genes were selected for additional genotyping of single nucleotide polymorphisms (SNPs) in order to construct their SNP maps which are going to be used for future association studies of complex disease AMD. Thus, identification of novel retinal genes and their functional characterization will further our elucidation of retinal physiology in general and in the diseased state in particular, by providing candidate retinal disease genes.}, subject = {Netzhaut}, language = {en} } @phdthesis{Kolmer2002, author = {Kolmer, Kerstin}, title = {Co-operation and conflict in societies of the ponerine ant genus Pachycondyla}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-2153}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {A significant relatedness is of fundamental importance for the evolution and maintenance of social life (kin selection theory, Hamilton 1964a,b). Not only kin selection itself, but also more complex evolutionary theories make predictions on the occurrence of conflict and co-operation in animal societies. They all depend on the genetic relationships among individuals. Therefore, the study of unrelated, co-operating individuals provides a unique opportunity to critically test predictions based on these evolutionary theories. Using allozyme electrophoresis, the study species Pachycondyla villosa was found to represent three different species. Young queens in one of these species, provisionally called Pachycondyla cf. inversa, may co-operate during colony founding (pleometrosis). Approximately 50 per cent of all founding colonies collected near Itabuna, Brazil, consisted of two to five founding queens. Queens of P. cf. inversa have to forage for food (semi-claustral founding), and in founding associations only one queen specialised for this risky task. A microsatellite study showed that nestmate queens were typically not related. How can a division of labour be achieved, where one individual performs risky tasks to the favour of another individual to which it is not related? In contrast to the predictions made by group selectionists, this study provided clear evidence that the division of labour among co-foundresses of P. cf. inversa results from social competition: Co-foundresses displayed aggressive interactions and formed dominance hierarchies which predominantly served to force subordinates to forage. The frequency of queen antagonism increased with the duration since food was last added to the foraging arena. The social status was not, or only weakly associated with the reproductive status: As predicted by the reproductive skew theory, all foundresses laid eggs at similar rates, though the subordinate may be harassed during egg laying and occasionally, some of her eggs may be eaten by the dominant. The differential oophagy presumably was also reflected in a microsatellite study of foundress associations, which was conducted shortly after the first workers emerged: Here, the co-foundresses occasionally contributed unequally to the colony's workers. Conflicts among workers or between workers and queens, e.g. over the division of labour or sex ratio, strongly depend on the genetic relationships among members of a colony. The number of two to five co-founding queens in polygynous colonies of P. cf. inversa, and the lack of relatedness among them, should lead to a decrease in the relatedness of workers. However, nestmate workers were closely related. Furthermore, worker relatedness may decrease as several queens were found to be multiply inseminated. Inbreeding coefficients were significantly different from zero in both queens and workers. No evidence for a geographical substructuring of the population was found. The deviation from random mating presumably was probably due to small, localised nuptial flights. Virgin queens do not mate near their natal nest and disperse before founding colonies. The analysis of cuticular hydrocarbons obtained from live queens revealed consistent differences between the patterns of cuticular hydrocarbons of queens with high vs. low rank: only high-ranking queens showed considerable amounts of cuticular pentadecane (n-C15) and heptadecene (n-C17:1). The presence of the two substances apparently was not associated with reproductive status. It is not yet known, if the two substances indeed serve to communicate high social status in P. cf. inversa. In experimentally assembled associations of two founding queens, queens engaged in aggressive interactions which already within one to twenty minutes resulted in stable dominance hierarchies. The queens attacking first usually won the contest and became dominant. Nest ownership at least for a couple of days did not influence the outcome of dominance interactions in the laboratory experiments, whereas queen body size apparently played an important role: In all eight trials, the larger queen became dominant. However, dominant queens from natural foundress associations were on average not larger than subordinates, suggesting that in the field, resident asymmetries might override size asymmetries only after a more prolonged period of nest ownership. Sequencing of the COI/COII region of mitochondrial DNA displayed sufficient variability for the study of the sociogenetic structure of the secondarily polygynous ant Pachycondyla obscuricornis: Six different haplotypes could be distinguished among six workers of different colonies from one study population in Costa Rica. The variability of other methods which were established (RFLPs, microsatellites, allozymes, and multilocus DNA fingerprinting) was too low for a further study on the genetic structure in P. obscuricornis.}, subject = {Pachycondyla}, language = {en} } @phdthesis{Obermaier2000, author = {Obermaier, Elisabeth}, title = {Coexistence and resource use in space and time in a West African tortoise beetle community}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1815}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2000}, abstract = {Tropical rain forests and coral reefs are usually regarded as the epitome of complexity and diversity. The mechanisms, however, that allow so many species to coexist continuously, still need to be unraveled. Earlier equilibrium models explain community organization with a strict niche separation and specialization of the single species, achieved mainly by interspecific competition and consecutive resource partitioning. Recent non-equilibrium or stochastic models see stochastic factors ("intermediate disturbances") as more important. Such systems are characterized by broad niche overlaps and an unpredictable species composition. Mechanisms of coexistence are most interesting where species interactions are strongest and species packing is highest. This is the case within a functional group or guild where species use similar resources. In this project a community of seven closely related leaf beetle species (Chrysomelidae: Cassidinae) was investigated which coexist on a common host plant system (fam. Convovulaceae) in a tropical moist savanna (Ivory Coast, Como{\´e}-Nationalpark). A broad overlap in the seasonal phenology of the leaf beetle species stood in contrast to a distinct spatial niche differentiation. The beetle community could be separated in a savanna-group (host plant: Ipomoea) and in a river side group (host plant: Merremia). According to a correspondence analysis the five species at the river side, using a common host plant, Merremia hederacea, proved to be predictable in their species composition. They showed a small scale niche differentiation along the light gradient (microhabitats). Laboratory studies confirmed differences in the tolerance towards high temperatures (up to 50°C in the field). Physiological trade-offs between phenology, microclimate and food quality seem best to describe patterns of resource use of the beetle species. Further a phylogeny based on mt-DNA sequencing of the beetle community was compared to its ecological resource use and the evolution of host plant use was reconstructed}, subject = {Westafrika}, language = {en} } @phdthesis{Lee1999, author = {Lee, Kyeong-Hee}, title = {Cofilin}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1681}, school = {Universit{\"a}t W{\"u}rzburg}, year = {1999}, abstract = {This study has identified cofilin, an actin binding protein, as a control element in the reorganization of the actin cytoskeleton which is highly relevant for T lymphocyte activation. Cofilin is regulated in its activity by reversible phosphorylation which is inducible by stimulation through accessory receptors such as CD2 and CD28. First it could be demonstrated that accessory receptor triggering induces the transient association of cofilin with the actin cytoskeleton and that only the dephosphorylated form of cofilin possesses the capacity to bind cytoskeletal actin in vivo. PI3-kinase inhibitors block both the dephosphorylation of cofilin and its association with the actin cytoskeleton. Importantly, cofilin, actin, PI3-kinase and one of its substrates, namely phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) which can bind to cofilin, co-localize within CD2-receptor caps. The cofilin/F-actin interaction has been identified as a crucial regulatory element for receptor cap formation and the strength of signal transduction. To this end, appropriately designed cell permeable non-toxic peptides that are homologous to actin binding motifs of the human cofilin sequence were introduced into untransformed human peripheral blood T lymphocytes. These peptides competitively and dose dependently inhibit the activation induced interaction of cofilin with the actin cytoskeleton in vivo. By this approach it was possible to study, for the first time, the functional consequences of this interaction in immunocompetent T cells. The present data demonstrate that inhibition of the actin/cofilin interaction in human T lymphocytes by means of these cofilin derived peptides abolishes receptor cap formation and strongly modulates functional T cell responses such as T cell proliferation, interleukin-2 production, cell surface expression of CD69, gIFN production, and CD95L expression. Importantly, receptor independent activation by PMA and calcium ionophore circumvents these peptide produced inhibitory effects on lymphocyte stimulation and places the cofilin/actin interaction to a proximal step in the cascade of signaling events following T cell activation via surface signals. The present results are novel since as yet no information existed regarding the molecular elements which link cell surface receptor stimulation directly to the resulting reorganization of the actin cytoskeleton.}, subject = {T-Lymphozyt}, language = {en} } @phdthesis{Petrov2023, author = {Petrov, Ivan}, title = {Combinational therapy of tumors in syngeneic mouse tumor models with oncolytic Vaccinia virus strains expressing IL-2 and INF-g. Human adipose tissue-derived stem cell mediated delivery of oncolytic Vaccinia virus}, doi = {10.25972/OPUS-27355}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-273550}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2023}, abstract = {Cancer is one of the leading causes of death worldwide, with currently assessed chances to develop at least one cancer in a lifetime for about 20\%. High cases rates and mortality require the development of new anticancer therapies and treatment strategies. Another important concern is toxicity normally associated with conventional therapy methods, such as chemo- and radiotherapy. Among many proposed antitumoral agents, oncolytic viruses are still one of the promising and fast-developing fields of research with almost a hundred studies published data on over 3000 patients since the beginning of the new millennia. Among all oncolytic viruses, the Vaccinia virus is arguably one of the safest, with an extremely long and prominent history of use, since it was the one and only vaccine used in the Smallpox Eradication Program in the 1970s. Interestingly enough, it was the first oncolytic virus proven to have tumor tropism in vitro and in vivo in laboratory settings, and this year we can celebrate an unofficial 100th anniversary since the publication of the fact. While being highly immunogenic, Vaccinia virus DNA replication takes place in the cytoplasm of the infected cell, and virus genes never integrate into the host genome. Another advantage of using Vaccinia as an oncolytic agent is its high genome capacity, which allows inserting up to 25 kbps of exogenous genes, thus allowing to additionally arm the virus against the tumor. Oncolytic virus action consists of two major parts: direct oncolysis and immune activation against the tumor, with the latter being the key to successful treatment. To this moment, preclinical research data are mostly generated in immunocompromised xenograft models, which have hurdles to be properly translated for clinical use. In the first part of the current study, fourteen different recombinant Vaccinia virus strains were tested in two different murine tumor cell lines and corresponding immunocompetent animal models. We found, that Copenhagen backbone Vaccinia viruses while being extremely effective in cell culture, do not show significant oncolytic efficacy in animals. In contrast, several of the LIVP backbone viruses tested (specifically, IL-2 expressing ones) have little replication ability when compared to the Copenhagen strain, but are able to significantly delay tumor growth and prolong survival of the treated animals. We have also noted cytokine related toxicity of the animals to be mouse strain specific. We have also tested the virus with the highest therapeutic benefit in combination with romidepsin and cyclophosphamide. While the combination with histone deacetylase inhibitor romidepsin did not result in therapeutic benefit in our settings, the addition of cyclophosphamide significantly improved the efficacy of the treatment, at the same time reducing cytokine-associated toxicity of the IL-2 expressing virus. In the second part of the work, we analyzed the ability of adipose-derived mesenchymal stem cells to serve as a carrier for the oncolytic Vaccinia virus. We showed for the first time that the cells can be infected with the virus and can generate virus progeny. They are also able to survive for a substantially long time and, when injected into the bloodstream of tumor-bearing animals, produce the virus that is colonizing the tumor. Analysis of the systemic distribution of the cells after injection revealed that infected and uninfected cells are not distributed in the same manner, possibly suggesting that infected cells are getting recognized and cleared by an impaired immune system of athymic mice faster than non-infected cells. Despite this, injection of virus-loaded adipose-derived mesenchymal stem cells to human A549 tumor-bearing xenograft mice resulted in rapid tumor regression and reduced virus-related side effects of the treatment when compared to injection of the naked virus. In conclusion, we have tested two different approaches to augmenting oncolytic Vaccinia virus therapy. First, the combination of recombinant Vaccinia virus expressing IL-2 and cyclophosphamide showed promising results in a syngeneic mouse model, despite the low permissivity of murine cells to the virus. Second, we loaded the oncolytic Vaccinia virus into mesenchymal stem cells and have proven that they can potentially serve as a vehicle for the virus.}, subject = {Vaccinia-virus}, language = {en} } @phdthesis{Leingaertner2013, author = {Leing{\"a}rtner, Annette}, title = {Combined effects of climate change and extreme events on plants, arthropods and their interactions}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-87758}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2013}, abstract = {I. Global climate change directly and indirectly influences biotic and abiotic components of ecosystems. Changes in abiotic ecosystem components caused by climate change comprise temperature increases, precipitation changes and more frequently occurring extreme events. Mediated by these abiotic changes, biotic ecosystem components including all living organisms will also change. Expected changes of plants and animals are advanced phenologies and range shifts towards higher latitudes and altitudes which presumably induce changes in species interactions and composition. Altitudinal gradients provide an optimal opportunity for climate change studies, because they serve as natural experiments due to fast changing climatic conditions within short distances. In this dissertation two different approaches were conducted to reveal species and community responses to climate change. First, species richness and community trait analyses along an altitudinal gradient in the Bavarian Alps (chapters II, III) and second, climate change manipulation experiments under different climatic contexts (chapters IV, V, IV). II. We performed biodiversity surveys of butterfly and diurnal moth species on 34 grassland sites along an altitudinal gradient in the National Park Berchtesgaden. Additionally, we analysed the dominance structure of life-history traits in butterfly assemblages along altitude. Species richness of butterflies and diurnal moths decreased with increasing altitude. The dominance of certain life-history-traits changed along the altitudinal gradient with a higher proportion of larger-winged species and species with higher egg numbers towards higher altitudes. However, the mean egg maturation time, population density and geographic distribution within butterfly assemblages decreased with increasing altitude. Our results indicate that butterfly assemblages were mainly shaped by environmental filtering. We conclude that butterfly assemblages at higher altitudes will presumably lack adaptive capacity to future climatic conditions, because of specific trait combinations. III. In addition to butterfly and diurnal moth species richness we also studied plant species richness in combination with pollination type analyses along the altitudinal gradient. The management type of the alpine grasslands was also integrated in the analyses to detect combined effects of climate and management on plant diversity and pollination type. Plant species richness was highest at intermediate altitudes, whereby the management type influenced the plant diversity with more plant species at grazed compared to mown or non-managed grasslands. The pollination type was affected by both the changing climate along the gradient and the management type. These results suggest that extensive grazing can maintain high plant diversity along the whole altitudinal gradient. With ongoing climate change the diversity peak of plants may shift upwards, which can cause a decrease in biodiversity due to reduced grassland area but also changes in species composition and adaptive potential of pollination types. IV. We set up manipulation experiments on 15 grassland sites along the altitudinal gradient in order to determine the combined effects of extreme climatic events (extreme drought, advanced and delayed snowmelt) and elevation on the nutritional quality and herbivory rates of alpine plants. The leaf CN (carbon to nitrogen) ratio and the plant damage through herbivores were not significantly affected by the simulated extreme events. However, elevation influenced the CN ratios and herbivory rates of alpine plants with contrasting responses between plant guilds. Furthermore, we found differences in nitrogen concentrations and herbivory rates between grasses, legumes and forbs, whereas legumes had the highest nitrogen concentrations and were damaged most. Additionally, CN ratios and herbivory rates increased during the growing season, indicating a decrease of food plant quality during the growing season. Contrasting altitudinal responses of grasses, legumes and forbs presumably can change the dominance structure among these plant guilds with ongoing climate change. V. In this study we analysed the phenological responses of grassland species to an extreme drought event, advanced and delayed snowmelt along the altitudinal gradient. Advanced snowmelt caused an advanced beginning of flowering, whereas this effect was more pronounced at higher than at lower altitudes. Extreme drought and delayed snowmelt had rather low effects on the flower phenology and the responses did not differ between higher and lower sites. The strongest effect influencing flower phenology was altitude, with a declining effect through the season. The length of flowering duration was not significantly influenced by treatments. Our data suggest that plant species at higher altitudes may be more affected by changes in snowmelt timing in contrast to lowland species, as at higher altitudes more severe changes are expected. However, the risk of extreme drought events on flowering phenology seems to be low. VI. We established soil-emergence traps on the advanced snowmelt and control treatment plots in order to detect possible changes in abundances and emergence phenologies of five arthropod orders due to elevation and treatment. Additionally, we analysed the responses of Coleoptera species richness to elevation and treatment. We found that the abundance and species richness of Coleoptera increased with elevation as well as the abundance of Diptera. However, the abundance of Hemiptera decreased with elevation and the abundances of Araneae and Hymenoptera showed no elevational patterns. The advanced snowmelt treatment increased the abundances of Araneae and Hymenoptera. The emergence of soil-hibernating arthropods was delayed up to seven weeks at higher elevations, whereas advanced snowmelt did not influence the emergence phenology of arthropods immediately after snowmelt. With climate change earlier snowmelt will occur more often, which especially will affect soil-hibernating arthropods in alpine regions and may cause desynchronisations between species interactions. VII. In conclusion, we showed that alpine ecosystems are sensitive towards changing climate conditions and extreme events and that many alpine species in the Bavarian Alps are endangered. Many alpine species could exist under warmer climatic conditions, however they are expected to be outcompeted by more competitive lowland species. Furthermore, host-parasite or predator-prey interactions can be disrupted due to different responses of certain guilds to climate change. Understanding and predicting the complex dynamics and potential risks of future climate change remains a great challenge and therefore further studies analysing species and community responses to climate change are needed.}, subject = {Insekten}, language = {en} } @phdthesis{Schmitt2004, author = {Schmitt, Thomas}, title = {Communication in the hymenoptera : chemistry, ecology and evolution}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-11267}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2004}, abstract = {Insects exhibit complex systems of communication with chemical signalling being the most important mode. Although there are many studies on chemical communication in insects, the evolution of chemical signals is not well understood. Due to the conflict of interests between individuals, different selective pressures might act on sender and receiver. In this thesis I investigate different types of communication where either the sender, the receiver or both parties yield benefits. These studies were conducted with one digger wasp species, honeybees, one chrysidid wasp, and three ant species. Senders might benefit by exploiting existing preferences of receivers. Such sensory exploitation might influence the evolution of male signals that are designed to attract females. The sex pheromone of male European beewolves Philanthus triangulum (Hymenoptera, Crabronidae) might have evolved according to the sensory exploitation hypothesis. A three-step scenario is supported by our studies. First, a major component of the honeybee alarm pheromone, (Z)-11-eicosen-1-ol, is also found on the cuticles and in the air surrounding foraging honeybees. Second, it could be shown, that (Z)-11- eicosen-1-ol plays a crucial role as kairomone for prey identification of honeybees by beewolf females. Third, a reanalysis of the beewolf male sex pheromone shows a remarkable similarity of compounds between the pheromone and the honeybee cuticle, besides the co-occurrence of (Z)-11-eisosen-ol. The majority of the cuticular hydrocarbons of honeybees occur also in the headspace of foraging workers. These results strongly support the hypothesis that beewolf males evolved a pheromone that exploits the females' pre-existing sensory sensitivity. In addition, the male sex pheromone shows a significantly higher similarity among brothers than among non-related individuals, which might enable beewolf females to discriminate against brothers and avoid detrimental effects of breeding. Together with the studies on the possible sensory exploitation this result shows that both, male and female beewolves probably gain more benefits than costs from the pheromone communication and, thus, the communication system as a whole can be regarded as cooperative. To maintain the reproductive division of labour in eusocial colonies, queens have to signal their presence and fecundity. In the ant Camponotus floridanus (Hymenoptera, Formicidae) queens mark their own eggs with a distinctive pattern of cuticular hydrocarbons. Two different hypotheses have been developed. One suggests a form of worker manipulation by the queen. The alternative hypothesis assumes a cooperative signal that provides information on the condition of the queen. The results of our investigation clearly favour the latter hypothesis. Chemical mimicry is a form of non-cooperative communication that benefits predominantly the sender. We provided conclusive evidence that the cockoo wasp, Hedychrum rutilans (Hymenoptera, Chrysididae), the primary brood parasitoid of Philanthus triangulum, evades recognition by beewolf females most probably by chemical mimicry of the odour of its host. Furthermore, the adaptation of the chemical signature in the social ant parasite Protomognathus americanus (Hymenoptera, Formicidae) to its Leptothorax (Hymenoptera, Formicidae) hosts was investigated. Although this parasite is principally adapted to its hosts' cuticular hydrocarbon profile, there are still pronounced differences between the profiles of parasites and hosts. This might be explained by the trade-off, which the parasites faces when confronted locally with two host species with different cuticular hydrocarbon profiles. Non-cooperative communication in the sense that only receivers benefit was discovered in the exploitation of honeybees volatile cuticular hydrocarbons by beewolf females. By using emitted (Z)-11-eicosen-1-ol as a kairomone, the receiver, the beewolf female, yields the benefits and the sender, the honeybee prey, bears all the costs. The results of these studies contribute to the understanding of the evolution of cooperative and non-cooperative communication with chemical signals taking into account differential benefits for sender and/or receiver.}, subject = {Hautfl{\"u}gler}, language = {en} } @phdthesis{Arumugam2010, author = {Arumugam, Manimozhiyan}, title = {Comparative metagenomic analysis of the human intestinal microbiota}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-55903}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {The human gut is home for thousands of microbes that are important for human life. As most of these cannot be cultivated, metagenomics is an important means to understand this important community. To perform comparative metagenomic analysis of the human gut microbiome, I have developed SMASH (Simple metagenomic analysis shell), a computational pipeline. SMASH can also be used to assemble and analyze single genomes, and has been successfully applied to the bacterium Mycoplasma pneumoniae and the fungus Chaetomium thermophilum. In the context of the MetaHIT (Metagenomics of the human intestinal tract) consortium our group is participating in, I used SMASH to validate the assembly and to estimate the assembly error rate of 576.7 Gb metagenome sequence obtained using Illumina Solexa technology from fecal DNA of 124 European individuals. I also estimated the completeness of the gene catalogue containing 3.3 million open reading frames obtained from these metagenomes. Finally, I used SMASH to analyze human gut metagenomes of 39 individuals from 6 countries encompassing a wide range of host properties such as age, body mass index and disease states. We find that the variation in the gut microbiome is not continuous but stratified into enterotypes. Enterotypes are complex host-microbial symbiotic states that are not explained by host properties, nutritional habits or possible technical biases. The concept of enterotypes might have far reaching implications, for example, to explain different responses to diet or drug intake. We also find several functional markers in the human gut microbiome that correlate with a number of host properties such as body mass index, highlighting the need for functional analysis and raising hopes for the application of microbial markers as diagnostic or even prognostic tools for microbiota-associated human disorders.}, subject = {Darmflora}, language = {en} } @phdthesis{Batzilla2011, author = {Batzilla, Julia}, title = {Complete genome sequence of Yersinia enterocolitica subspecies palearctica serotype O:3: Identification of novel virulence-associated genes and evolutionary aspects}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-69668}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {Yersinia enterocolitica subsp. palearctica Serobiotyp O:3/4 ist verantwortlich f{\"u}r 80-90 \% aller Yersiniosen beim Menschen in Deutschland und Europa. Y. enterocolitica Infektionen zeigen vielf{\"a}ltige Krankheitsbilder wie Gastroenteritis, Lymphadenitis und verschiedene Sp{\"a}tkomplikationen wie reaktive Arthritis. Das wichtigste Tierreservoir stellt das Hausschwein dar. Rohes Schweinefleisch in Metzgereien in Deutschland und anderen Regionen in Nord-Ost Europa ist h{\"a}ufig mit Yersinien kontaminiert (Bayern: 25 \%). Da sich Serobiotyp O:3/4-St{\"a}mme geografisch und phylogenetisch deutlich von dem bisher sequenzierten Serobiotyp O:8/1B Stamm 8081 unterscheiden, wurde eine komplette Genomsequenzierung des europ{\"a}ischen Serobiotyp O:3/4 DSMZ Referenzstammes Y11 (aus Patientenstuhl isoliert) durchgef{\"u}hrt. Um einen genaueren Einblick in die Y. enterocolitica subsp. palearctica Gruppe zu erhalten, wurden zus{\"a}tzlich zwei weitere Serobiotyp O:3/4 Isolate (Stamm Y8265, Patientenisolat, und Stamm Y5307, mit reaktiver Arthritis assoziiertes Patientenisolat), sowie ein eng verwandtes Y. enterocolitica subsp. palearctica Serobiotyp O:5,27/3 Isolat, Stamm Y527P, und zwei Biotyp 1A Isolate (ein Isolat nosokomialer Herkunft (Serogruppe O:5) und ein Umwelt-Isolat (O:36)) unvollst{\"a}ndig sequenziert. Die nicht mausvirulenten St{\"a}mme wurden mit dem mausvirulenten Y. enterocolitica subsp. enterocolitica Serobiotyp O:8/1B Stamm 8081 verglichen, um genetische Besonderheiten von Stamm Y11 und der Y. enterocolitica subsp. palearctica Gruppe zu identifizieren. Besonderer Fokus lag hierbei auf dem pathogenen Potential von Stamm Y11, um neue potentielle Virulenz Faktoren und Fitnessfaktoren zu identifizieren, darunter vor allem solche, die eine Rolle bei der Wirtsspezifit{\"a}t von Serobiotyp O:3/4 spielen k{\"o}nnten. Y. enterocolitica subsp. palearctica Serobiotyp O:3/4 St{\"a}mmen fehlen einige der Charakteristika der mausvirulenten Gruppe Y. enterocolitica subsp. enterocolitica, beispielsweise die Yersiniabactin kodierende‚ High-Pathogenicity Island (HPI), das Yts1 Typ 2 Sekretionssystem und das Ysa Typ 3 Sekretionssystem. Die Serobiotyp O:3/4-St{\"a}mme haben ein anderes Repertoir von Virulenz Faktoren erworben, darunter Gene bzw. genomische Inseln f{\"u}r das Ysp Typ 3 Sekretionssystem, Rtx-{\"a}hnliches putatives Toxin, Insektizid-Toxine und ein funktionelles PTS System f{\"u}r die Aufnahme von N-acetyl-galactosamin, dem aga-Operon. Nach dem Transfer des aga-Operons in Y. enterocolitica subsp. enterocolitica O:8/1B konnte Wachstum auf N-acetyl-galactosamin festgestellt werden. Neben diesen Genen k{\"o}nnen m{\"o}glicherweise auch zwei Prophagen (PhiYep-2 und PhiYep-3) und eine asn tRNA assoziierte genomische Insel (GIYep-01) zur Pathoadaptation von Y. enterocolitica subsp. palearctica Serobiotyp O:3/4 beitragen. Der PhiYep-3 Prophage und die GIYep-01 Insel weisen Rekombinationsaktivit{\"a}t auf, und PhiYep-3 wurde nicht in allen untersuchten Serobiotyp O:3/4 St{\"a}mmen gefunden. Y. enterocolitica subsp. palearctica Serobiotyp O:5,27/3 Stamm Y527P ist genetisch eng verwandt zu allen Serobiotyp O:3/4 Isolaten, wohingegen die Biotyp 1A Isolate ein mehr Mosaik-artiges Genom aufweisen und potentielle Virulenzgene sowohl mit Serobiotyp O:8/1B als auch O:3/4 gemeinsam haben, was einen gemeinsamen Vorfahren impliziert. Neben dem pYV Virulenz-Plasmid fehlen den Biotyp 1A Isolaten klassische Virulenzmarker wie das Ail Adhesin, das YstA Enterotoxin und das Virulenz-assoziierte Protein C (VapC). Interessanterweise gibt es keine betr{\"a}chtlichen Unterschiede zwischen den bekannten Virulenzfaktoren des nosokomialen Isolats und dem Umweltisolat der Biotyp 1A-Gruppe, abgesehen von einem verk{\"u}rzten Rtx Toxin-{\"a}hnlichem Genkluster und {\"U}berresten eines P2-{\"a}hnlichen Phagen im Krankenhausisolat der Serogruppe O:5.}, subject = {Genanalyse}, language = {en} } @phdthesis{Thakar2006, author = {Thakar, Juilee}, title = {Computational models for the study of responses to infections}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-17266}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {In diesem Jahrhundert haben neue experimentelle Techniken und Computer-Verfahren enorme Mengen an Information erzeugt, die bereits viele biologische R{\"a}tsel enth{\"u}llt haben. Doch die Komplexit{\"a}t biologischer Systeme wirft immer weitere neue Fragen auf. Um ein System zu verstehen, bestand der Hauptansatz bis jetzt darin, es in Komponenten zu zerlegen, die untersucht werden k{\"o}nnen. Ein neues Paradigma verkn{\"u}pft die einzelnen Informationsteile, um sie auf globaler Ebene verstehen zu k{\"o}nnen. In der vorgelegten Doktorarbeit habe ich deshalb versucht, infekti{\"o}se Krankheiten mit globalen Methoden („Systembiologie") bioinformatisch zu untersuchen. Im ersten Teil wird der Apoptose-Signalweg analysiert. Apoptose (Programmierter Zelltod) wird bei verschiedenen Infektionen, zum Beispiel bei Viruserkrankungen, als Abwehrmaßnahme eingesetzt. Die Interaktionen zwischen Proteinen, die ‚death' Dom{\"a}nen beinhalten, wurden untersucht, um folgende Fragen zu kl{\"a}ren: i) wie wird die Spezifit{\"a}t der Interaktionen erzielt? -sie wird durch Adapter erreicht, ii) wie werden Proliferation/ {\"U}berlebenssignale w{\"a}hrend der Aktivierung der Apoptose eingeleitet? - wir fanden Hinweise f{\"u}r eine entscheidende Rolle des RIP Proteins (Rezeptor-Interagierende Serine/Threonine-Proteinkinase 1). Das Modell erlaubte uns, die Interaktions-Oberfl{\"a}chen von RIP vorherzusagen. Der Signalweg wurde anschließend auf globaler Ebene mit Simulationen f{\"u}r verschiedene Zeitpunkte analysiert, um die Evolution der Aktivatoren und Inhibitoren des Signalwegs und seine Struktur besser zu verstehen. Weiterhin wird die Signalverarbeitung f{\"u}r Apoptosis-Signalwege in der Maus detailliert modelliert, um den Konzentrationsverlauf der Effektor-Kaspasen vorherzusagen. Weitere experimentelle Messungen von Kaspase-3 und die {\"U}berlebenskurven von Zellen best{\"a}tigen das Modell. Der zweite Teil der Resultate konzentriert sich auf das Phagosom, eine Organelle, die eine entscheidende Rolle bei der Eliminierung von Krankheitserregern spielt. Dies wird am Beispiel von M. tuberculosis veranschaulicht. Die Fragestellung wird wiederum in zwei Aspekten behandelt: i) Um die Prozesse, die durch M. tuberculosis inhibiert werden zu verstehen, haben wir uns auf das Phospholipid-Netzwerk konzentriert, das bei der Unterdr{\"u}ckung oder Aktivierung der Aktin-Polymerisation eine große Rolle spielt. Wir haben f{\"u}r diese Netzwerkanalyse eine Simulation f{\"u}r verschiedene Zeitpunkte {\"a}hnlich wie in Teil eins angewandt. ii) Es wird vermutet, dass Aktin-Polymere bei der Fusion des Phagosoms mit dem Lysosom eine Rolle spielen. Um diese Hypothese zu untersuchen, wurde ein in silico Modell von uns entwickelt. Wir fanden heraus, dass in der Anwesenheit von Aktin-Polymeren die Suchzeit f{\"u}r das Lysosom um das F{\"u}nffache reduziert wurde. Weiterhin wurden die Effekte der L{\"a}nge der Aktin-Polymere, die Gr{\"o}ße der Lysosomen sowie der Phagosomen und etliche andere Modellparameter analysiert. Nach der Untersuchung eines Signalwegs und einer Organelle f{\"u}hrte der n{\"a}chste Schritt zur Untersuchung eines komplexen biologischen Systems der Infektabwehr. Dies wurde am Beispiel der Wirt-Pathogen Interaktion bei Bordetella pertussis und Bordetella bronchiseptica dargestellt. Die geringe Menge verf{\"u}gbarer quantitativer Daten war der ausschlaggebende Faktor bei unserer Modellwahl. F{\"u}r die dynamische Simulation wurde ein selbst entwickeltes Bool'sches Modell verwendet. Die Ergebnisse sagen wichtige Faktoren bei der Pathologie von Bordetellen hervor, besonders die Bedeutung der Th1 assoziierten Antworten und dagegen nicht der Th2 assoziierten Antworten f{\"u}r die Eliminierung des Pathogens. Einige der quantitativen Vorhersagen wurden durch Experimente wie die Untersuchung des Verlaufs einer Infektion in verschiedenen Mutanten und Wildtyp-M{\"a}usen {\"u}berpr{\"u}ft. Die begrenzte Verf{\"u}gbarkeit kinetischer Daten war der kritische Faktor bei der Auswahl der computer-gest{\"u}tzten Modelle. Der Erfolg unserer Modelle konnte durch den Vergleich mit experimentellen Beobachtungen belegt werden. Die vergleichenden Modelle in Kapitel 6 und 9 k{\"o}nnen zur Untersuchung neuer Wirt-Pathogen Interaktionen verwendet werden. Beispielsweise f{\"u}hrt in Kapitel 6 die Analyse von Inhibitoren und inhibitorischer Signalwege aus drei Organismen zur Identifikation wichtiger regulatorischer Zentren in komplexen Organismen und in Kapitel 9 erm{\"o}glicht die Identifikation von drei Phasen in B. bronchiseptica und der Inhibition von IFN-\&\#947; durch den Faktor TTSS die Untersuchung {\"a}hnlicher Phasen und die Inhibition von IFN-\&\#947; in B. pertussis. Eine weitere wichtige Bedeutung bekommen diese Modelle durch die m{\"o}gliche Identifikation neuer, essentieller Komponenten in Wirt-Pathogen Interaktionen. In silico Modelle der Effekte von Deletionen zeigen solche Komponenten auf, die anschließend durch experimentelle Mutationen weiter untersucht werden k{\"o}nnen.}, subject = {Bordetella pertussis}, language = {en} } @phdthesis{Schmid2010, author = {Schmid, Benjamin}, title = {Computational tools for the segmentation and registration of confocal brain images of Drosophila melanogaster}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51490}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {Neuroanatomical data in fly brain research are mostly available as spatial gene expression patterns of genetically distinct fly strains. The Drosophila standard brain, which was developed in the past to provide a reference coordinate system, can be used to integrate these data. Working with the standard brain requires advanced image processing methods, including visualisation, segmentation and registration. The previously published VIB Protocol addressed the problem of image registration. Unfortunately, its usage was severely limited by the necessity of manually labelling a predefined set of neuropils in the brain images at hand. In this work I present novel tools to facilitate the work with the Drosophila standard brain. These tools are integrated in a well-known open-source image processing framework which can potentially serve as a common platform for image analysis in the neuroanatomical research community: ImageJ. In particular, a hardware-accelerated 3D visualisation framework was developed for ImageJ which extends its limited 3D visualisation capabilities. It is used for the development of a novel semi-automatic segmentation method, which implements automatic surface growing based on user-provided seed points. Template surfaces, incorporated with a modified variant of an active surface model, complement the segmentation. An automatic nonrigid warping algorithm is applied, based on point correspondences established through the extracted surfaces. Finally, I show how the individual steps can be fully automated, and demonstrate its application for the successful registration of fly brain images. The new tools are freely available as ImageJ plugins. I compare the results obtained by the introduced methods with the output of the VIB Protocol and conclude that our methods reduce the required effort five to ten fold. Furthermore, reproducibility and accuracy are enhanced using the proposed tools.}, subject = {Taufliege}, language = {en} } @phdthesis{Englmeier2024, author = {Englmeier, Jana}, title = {Consequences of climate change and land-use intensification for decomposer communities and decomposition processes}, doi = {10.25972/OPUS-31399}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-313994}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {The increase in intensively used areas and climate change are direct and indirect consequences of anthropogenic actions, caused by a growing population and increasing greenhouse gas emissions. The number of research studies, investigating the effects of land use and climate change on ecosystems, including flora, fauna, and ecosystem services, is steadily growing. This thesis contributes to this research area by investigating land-use and climate effects on decomposer communities (arthropods and microbes) and the ecosystem service 'decomposition of dead material'. Chapter II deals with consequences of intensified land use and climate change for the ecosystem service 'decomposition of dead organic material' (necromass). Considering the severe decline in insects, we experimentally excluded insects from half of the study objects. The decomposition of both dung and carrion was robust to land-use changes. Dung decomposition, moreover, was unaffected by temperature and the presence/ absence of insects. Along the altitudinal gradient, however, highest dung decomposition was observed at medium elevation between 600 and 700 m above sea level (although insignificant). As a consequence, we assume that at this elevation there is an ideal precipitation:temperature ratio for decomposing organisms, such as earthworms or collembolans. Carrion decomposition was accelerated by increasing elevation and by the presence of insects, indicating that increasing variability in climate and an ongoing decline in insects could modify decomposition processes and consequently natural nutrient cycles. Moreover, we show that different types of dead organic material respond differently to environmental factors and should be treated separately in future studies. In Chapter III, we investigated land-use and climate effects on dung-visiting beetles and their resource specialization. Here, all beetles that are preferentially found on dung, carrion or other rotten material were included. Both α- and γ-diversity were strongly reduced in agricultural and urban areas. High precipitation reduced dung-visiting beetle abundance, whereas γ-diversity was lowest in the warmest regions. Resource specialization decreased with increasing temperatures. The results give evidence that land use as well as climate can alter dung-visiting beetle diversity and resource specialization and may hence influence the natural balance of beetle communities and their contribution to the ecosystem service 'decomposition of dead material'. The following chapter, Chapter IV, contributes to the findings in Chapter II. Here, carrion decomposition is not only explained by land-use intensity and climate but also by diversity and community composition of two taxonomic groups found on carrion, beetles and bacteria. The results revealed a strong correlation between bacteria diversity and community composition with temperature. Carrion decomposition was to a great extent directed by bacterial community composition and precipitation. The role of beetles was neglectable in carrion decomposition. With this study, I show that microbes, despite their microscopic size, direct carrion decomposition and may not be neglected in future decomposition studies. In Chapter V a third necromass type is investigated, namely deadwood. The aim was to assess climate and land-use effects on deadwood-inhabiting fungi and bacteria. Main driver for microbial richness (measured as number of OTUs) was climate, including temperature and precipitation. Warmer climates promoted the diversity of bacteria, whereas fungi richness was unaffected by temperature. In turn, fungi richness was lower in urban landscapes compared to near-natural landscapes and bacteria richness was higher on meadows than on forest sites. Fungi were extremely specialized on their host tree, independent of land use and climate. Bacteria specialization, however, was strongly directed by land use and climate. These results underpin previous studies showing that fungi are highly specialized in contrast to bacteria and add new insights into the robustness of fungi specialization to climate and land use. I summarize that climate as well as intensive land use influence biodiversity. Temperature and precipitation, however, had positive and negative effects on decomposer diversity, while anthropogenic land use had mostly negative effects on the diversity of decomposers.}, subject = {Mikroorganismus}, language = {en} } @phdthesis{Kurz2020, author = {Kurz, Andreas}, title = {Correlative live and fixed cell superresolution microscopy}, doi = {10.25972/OPUS-19945}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-199455}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2020}, abstract = {Over the last decade life sciences have made an enormous leap forward. The development of complex analytical instruments, in particular in fluorescence microscopy, has played a decisive role in this. Scientist can now rely on a wide range of imaging techniques that offer different advantages in terms of optical resolution, recording speed or living cell compatibility. With the help of these modern microscopy techniques, multi-protein complexes can be resolved, membrane receptors can be counted, cellular pathways analysed or the internalisation of receptors can be tracked. However, there is currently no universal technique for comprehensive experiment execution that includes dynamic process capture and super resolution imaging on the same target object. In this work, I built a microscope that combines two complementary imaging techniques and enables correlative experiments in living and fixed cells. With an image scanning based laser spot confocal microscope, fast dynamics in several colors with low photodamage of the cells can be recorded. This novel system also has an improved resolution of 170 nm and was thoroughly characterized in this work. The complementary technique is based on single molecule localization microscopy, which can achieve a structural resolution down to 20-30 nm. Furthermore I implemented a microfluidic pump that allows direct interaction with the sample placed on the microscope. Numerous processes such as living cell staining, living cell fixation, immunostaining and buffer exchange can be observed and performed directly on the same cell. Thus, dynamic processes of a cell can be frozen and the structures of interest can be stained and analysed with high-resolution microscopy. Furthermore, I have equipped the detection path of the single molecule technique with an adaptive optical element. With the help of a deformable mirror, imaging functions can be shaped and information on the 3D position of the individual molecules can be extracted.}, subject = {Einzelmolek{\"u}lmikroskopie}, language = {en} } @phdthesis{Foeger2000, author = {F{\"o}ger, Niko}, title = {Costimulatory function of CD44}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1186}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2000}, abstract = {T cell activation is supposed to require two signals via engagement of the TCR and a costimulatory molecule. However, the signaling cascade of costimulatory molecules has remained elusive. Here, I provide evidence that CD44 supports proliferation as well as apoptosis mainly, if not exclusively, by enhancing signal transduction via the TCR/CD3 complex. Blockade of CD44 interferes with mounting of an immune response. This has been demonstrated by the significantly decreased IL-2 production of a T helper line, when stimulated in the presence of a competing CD44 receptor globulin. To evaluate the underlying mechanism, CD44 was cross-linked by an immobilized antibody (IM7). Cross-linking of CD44 induces proliferation of peripheral T cells and apoptosis of thymocytes and a T helper line in the presence of subthreshold levels of anti-CD3. CD44-induced proliferation was accompanied by an upregulation of the activation markers CD25 and CD69 and an increased cytokine production. TCR-mediated apoptosis was accompanied by an upregulation of CD95 ligand and CD95 receptor, which could be greatly enhanced by costimulation via CD44. On the level of signal transduction, coligation of CD44 with CD3 resulted in a strong and sustained increase of early tyrosine phosphorylation events and upregulated downstream signal transduction pathways, such as the ras/ERK and the JNK signaling cascades. These pleiotropic effects of CD44 are due to its involvement in the most proximal events in TCR signaling, as demonstrated by a strong increase in the phosphorylation of the TCR z-chain and ZAP-70. Notably, cross-linking of CD44 was binding-site dependent and was only effective when supporting colocalization of the TCR/CD3 complex and CD44. Cross-linking of CD44 via immobilized IM7 also induced profound changes in cell morphology, characterized by strong adhesion, spreading and development of surface extensions, which were dependent on a functional tubulin and actin cytoskeleton. These cytoskeletal rearrangements were mediated by rac1, a small GTPase of the rho subfamily, and src-family kinases, two of which, fyn and lck, were found to be associated with CD44. By cross-linkage of CD44 these kinases were redistributed into so called lipid rafts. It is supposed that for T cell activation a relocation of the TCR/CD3 complex into the same membrane microdomains is required. The data are interpreted in the sense that the costimulatory function of CD44 relies on its cooperativity with the TCR. Most likely by recruitment of phosphokinases CD44 significantly lowers the threshold for the initiation of signaling via the TCR. The requirement for immobilized anti-CD44, the necessity for neighbouring anti-CD3 and the dependence on the binding site of CD44 strongly suggest that the costimulatory mechanism involves cytoskeletal rearrangements, which facilitate recruitment and redirection of src-family protein kinases in glycolipid enriched membrane microdomains.}, subject = {Antigen CD44}, language = {en} } @phdthesis{Roeschard2002, author = {R{\"o}schard, Jacqueline}, title = {Cutter, carriers and bucket brigades ...}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-2240}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {This study investigates the foraging behaviour of grass-cutting ants, Atta vollenweideri, with specific consideration of the following issues: (a) cutting behaviour and the determination of fragment size, (b) the effect of load size on transport economics, (c) division of labour and task-partitioning. Grass-cutting ants, Atta vollenweideri, harvest grass fragments that serve as substrate for the cultivation of a symbiotic fungus. Foragers were observed to cut grass fragments across the blade, thus resulting in longish, rectangular-shaped fragments in contrast to the semicircular fragments of leaf-cutting ants. Cutting was very time-consuming: In tough grasses like the typical grassland species Paspallum intermedium and Cyperus entrerrianus, cutting times lasted up to more than 20 minutes per fragment and roughly half of all initiated cutting attempts were given up by the ants. Foragers harvesting the softer grass Leersia hexandra were smaller than those foraging on the hard grasses. Fragment size determination and the extent of size-matching between ant body size and fragment size was investigated regarding possible effects of tissue toughness on decision-making and as a function of the distance from the nest. Tissue toughness affected decision-making such that fragment width correlated with ant body mass for the hard grass but not for the soft one, suggesting that when cutting is difficult, larger ants tend to select wider grasses to initiate cutting. The length of the fragments cut out of the two grass species differed statistically, but showed a large overlap in their distribution. Distance from the nest affected load size as well as the extent of size-matching: Fragments collected directly after cutting were significantly larger than those carried on the trail. This indicates that fragments were cut once again on their way to the nest. Size-matching depended on the trail sector considered, and was stronger in ants sampled closer to the nest, suggesting that carriers either cut fragments in sizes corresponding to their body mass prior transport, or transferred them to nestmates of different size after a short carrying distance. During transport, a worker takes a fragment with its mandibles at one end and carries it in a more or less vertical position. Thus, load length might particularly affect maneuverability, because of the marked displacement of the gravitational center. Conversely, based on the energetic of cutting, workers might maximise their individual harvesting rate by cutting long grass fragments, since the longer a grass fragment, the larger is the amount of material harvested per unit cutting effort. I therefore investigated the economics of load transport by focusing on the effects of load size (mass and length) on gross material transport rate to the nest. When controlling for fragment mass, both running speed of foragers and gross material transport rate was observed to be higher for short fragments. In contrast, if fragment mass was doubled and length maintained, running speed differed according to the mass of the loads, with the heavier fragments being transported at the lower pace. For the sizes tested, heavy fragments yielded a higher transport rate in spite of the lower speed of transport, as they did not slow down foragers so much that it counterbalanced the positive effects of fragment mass on material transport rate. The sizes of the fragments cut by grass-cutting ants under natural conditions therefore may represent the outcome of an evolutionary trade-off between maximising harvesting rate at the cutting site and minimising the effects of fragment size on material transport rates. I investigated division of labour and task partitioning during foraging by recording the behaviour of marked ants while cutting, and by monitoring the transport of fragments from the cutting until they reached the nest. A. vollenweideri foragers showed division of labour between cutting and carrying, with larger workers cutting the fragments, and smaller ones transporting them. This division was absent for food sources very close to the nest, when no physical trail was present. Along the trail, the transport of fragment was a partitioned task, i.e., workers formed bucket brigades composed of 2 to 5 carriers. This sequential load transport occurred more often on long than on short trails. The first carriers of a bucket brigade covered only short distances before dropping their fragments, turned back and continued foraging at the same food source. The last carriers covered the longest distance. There was no particular location on the trail for load dropping , i.e., fragments were not cached. I tested the predictions of two hypotheses about the causes of bucket brigades: First, bucket brigades might occur because of load-carriage effects: A load that is too big for an ant to be carried is dropped and carried further by nestmates. Second, fragments carried by bucket brigades might reach the nest quicker than if they are transported by a single carrier. Third, bucket brigades might enhance information flow among foragers: By transferring the load a worker may return earlier back to the foraging site and be able to reinforce the chemical trail, thus recruitment. In addition, the dropped fragment itself may contain information for unladen foragers about currently harvested sources and may enable them to choose between sources of different quality. I investigated load-carriage effects and possible time-saving by presenting ants with fragments of different but defined sizes. Load size did not affect frequency of load dropping nor the distance the first carrier covered before dropping, and transport time by bucket brigades was significantly longer than by single carriers. In order to study the information transfer hypothesis, I presented ants with fragments of different attractivity but constant size. Ants carrying high-quality fragments would be expected to drop them more often than workers transporting low-quality fragments, thus increasing the frequency of bucket brigades. My results show that increasing load quality increased the frequency of bucket brigades as well as it decreased the carrying distance of the first carrier. In other words, more attractive loads were dropped more frequently and after a shorter distance than less attractive ones with the first carriers returning to the foraging site to continue foraging. Summing up, neither load-carriage effects nor time-saving caused the occurrence of bucket brigades. Rather, the benefit might be found at colony level in an enhanced information flow.}, subject = {Atta}, language = {en} } @phdthesis{Siegl2014, author = {Siegl, Christine}, title = {Degradation of Tumour Suppressor p53 during Chlamydia trachomatis Infections}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-108679}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {The intracellular pathogen Chlamydia is the causative agent of millions of new infections per year transmitting diseases like trachoma, pelvic inflammatory disease or lymphogranuloma venereum. Undetected or recurrent infections caused by chlamydial persistence are especially likely to provoke severe pathologies. To ensure host cell survival and to facilitate long term infections Chlamydia induces anti-apoptotic pathways, mainly at the level of mitochondria, and restrains activity of pro-apoptotic proteins. Additionally, the pathogen seizes host energy, carbohydrates, amino acids, lipids and nucleotides to facilitate propagation of bacterial progeny and growth of the chlamydial inclusion. At the beginning of this study, Chlamydia-mediated apoptosis resistance to DNA damage induced by the topoisomerase inhibitor etoposide was investigated. In the course of this, a central cellular protein crucial for etoposide-mediated apoptosis, the tumour suppressor p53, was found to be downregulated during Chlamydia infections. Subsequently, different chlamydial strains and serovars were examined and p53 downregulation was ascertained to be a general feature during Chlamydia infections of human cells. Reduction of p53 protein level was established to be mediated by the PI3K-Akt signalling pathway, activation of the E3-ubiquitin ligase HDM2 and final degradation by the proteasome. Additionally, an intriguing discrepancy between infections of human and mouse cells was detected. Both activation of the PI3K-Akt pathway as well as degradation of p53 could not be observed in Chlamydia-infected mouse cells. Recently, production of reactive oxygen species (ROS) and damage to host cell DNA was reported to occur during Chlamydia infection. Thus, degradation of p53 strongly contributes to the anti-apoptotic environment crucial for chlamydial infection. To verify the importance of p53 degradation for chlamydial growth and development, p53 was stabilised and activated by the HDM2-inhibiting drug nutlin-3 and the DNA damage-inducing compound etoposide. Unexpectedly, chlamydial development was severely impaired and inclusion formation was defective. Completion of the chlamydial developmental cycle was prevented resulting in loss of infectivity. Intriguingly, removal of the p53 activating stimulus allowed formation of the bacterial inclusion and recovery of infectivity. A similar observation of growth recovery was made in infected cell lines deficient for p53. As bacterial growth and inclusion formation was strongly delayed in the presence of activated p53, p53-mediated inhibitory regulation of cellular metabolism was suspected to contribute to chlamydial growth defects. To verify this, glycolytic and pentose phosphate pathways were analysed revealing the importance of a functioning PPP for chlamydial growth. In addition, increased expression of glucose-6-phosphate dehydrogenase rescued chlamydial growth inhibition induced by activated p53. The rescuing effect was even more pronounced in p53-deficient cells treated with etoposide or nutlin-3 revealing additional p53-independent aspects of Chlamydia inhibition. Removal of ROS by anti-oxidant compounds was not sufficient to rescue chlamydial infectivity. Apparently, not only the anti-oxidant capacities of the PPP but also provision of precursors for nucleotide synthesis as well as contribution to DNA repair are important for successful chlamydial growth. Modulation of host cell signalling was previously reported for a number of pathogens. As formation of ROS and DNA damage are likely to occur during infections of intracellular bacteria, several strategies to manipulate the host and to inhibit induction of apoptosis were invented. Downregulation of the tumour suppressor p53 is a crucial point during development of Chlamydia, ensuring both host cell survival and metabolic support conducive to chlamydial growth.}, subject = {Chlamydia-trachomatis-Infektion}, language = {en} } @phdthesis{Hauber2011, author = {Hauber, Melanie Erika}, title = {Description and Improvement of the 'Whedo'-Aquaculture-System in Malanville (North of Benin)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-57711}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {This work delves into the recently developed 'Whedo'-aquaculture-system in the rural community of Malanville (North Benin)and aims on providing a closer insight on this - for the area--recent system including the ecological but also the sociological and economical aspects in order to develop this extensive traditional fishery to a more productive semi-intensive aquaculture system. With the retreat of the flood 'Whedos' usually become infested with numerous hydato-and tenagophytes, while the presence and density of the free-floating macrophytes were positively related to the nutrient content of the 'Whedo'. Extensive plant infestation also affects water quality through the decomposition of organic material and its accumulation in thick mud layers on the pond bottom as well as through the nocturnal oxygen consumption. Unfavourable water quality, especially low dissolved oxygen as well as high conductivity and nitrite levels, was identified to be the main factor determining which fish species were able to survive the harsh conditions prevailing in the 'Whedos' during the dry season. With the deteriorating water quality with advancing dry season, fish diversity decreased significantly leaving only species that are highly adapted to such unfavourable conditions. The most abundant species were Clarias gariepinus, Heterotis niloticus, Oreochromis niloticus L., Hemichromis c.f. letourneauxi, Polypterus senegalus and Epiplatys spilargyreius. Besides, the investigations also concentrated on the fish diversity of the rivers Niger and Sota with the results that for three species distribution gaps could be closed and for further three species their already known distribution could be expanded. But otherwise it could also be detected that some economically important species that were abundant in the past. In regard to the 'Whedo'-management, the investigations showed that the owners lack most of the knowledge on appropriate management strategies, e.g. the feeding and stocking regime. The exploitation period depends on the extent of the previous annual flood and the location of the 'Whedo' within the floodplain, but the main season is from February to April. The biomass harvested on a hectare basis separated for each of the 'Whedos' averaged 17 tons/ha in 2008 and 8.6 tons/ha in 2009. However, 72 percent of the total biomass of Clarias only had an average weight of 40 grams. Therefore, two separated feeding trials were conducted and in total 6 supplementary feeds were tested on Clarias gariepinus. Groundnut cake, fish trash, rice bran, blood meal and azolla meal were used in different combination and rations to formulate the experimental diets. Diet containing 19 percent blood meal resulted in the best economical benefits showing that the use of high quality feed ingredients such as groundnut cake is not recommendable because local fish prices are too low to compensate the additional feeding costs. Instead of high quality feed farmers should focus on ingredients that are free of charge and easy to process. The supplementation based on 19 percent blood meal resulted in the doubling of the net profit compared to the income based on feeding only rice bran, thus provided higher additional income, enhancing the livelihood of the fish farmers. Concluding, the 'Whedo'-aquaculture system is still in its infancy but nevertheless is an attractive system for the rural population because of existing knowledge of post-flood wetland fisheries as well as the low investment needed for its installation. Additionally, the local fish supply will increase and hence not only contribute to a better provision of protein-rich food and reduced pressure on the wild fish stocks but might also prevent fish prices to increase in a way that the poor won't be able anymore to afford their most important source of animal protein. But fish farmers need more knowledge on appropriate management strategies and thus should be provided with technical support to guarantee a successful development and not to discourage the owners as a consequence of avoidable failures. Furthermore, the use of supplementary feed offers a cheap and effective means to increase the biomass production and thus enhance the extensive fishery to a semi-intensive aquaculture system.}, subject = {Aquakultur}, language = {en} } @phdthesis{Proppert2014, author = {Proppert, Sven Martin}, title = {Design, implementation and characterization of a microscope capable of three-dimensional two color super-resolution fluorescence imaging}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-107905}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {This thesis reviews the fundamentals of three-dimensional super-resolution localization imaging. In order to infer the axial coordinate of the emission of single fluorophores, the point spread function is engineered following a technique usually referred to as astigmatic imaging by the introduction of a cylindrical lens to the detection path of a microscope. After giving a short introduction to optics and localization microscopy, I outline sources of aberrations as frequently encountered in 3D-localization microscopy and will discuss their respective impact on the precision and accuracy of the localization process. With the knowledge from these considerations, experiments were designed and conducted to verify the validity of the conclusions and to demonstrate the abilities of the proposed microscope to resolve biological structures in the three spatial dimensions. Additionally, it is demonstrated that measurements of huge volumes with virtually no aberrations is in principle feasible. During the course of this thesis, a new method was introduced for inferring axial coordinates. This interpolation method based on cubic B-splines shows superior performance in the calibration of a microscope and the evaluation of subsequent measurement and will therefore be used and explained in this work. Finally, this work is also meant to give future students some guidance for entering the field of 3D localization microscopy and therefore, detailed protocols are provided covering the specific aspects of two color 3D localization imaging.}, subject = {Dimension 3}, language = {en} } @phdthesis{Schneider2011, author = {Schneider, Christof}, title = {Detecting the influence of different potential stress factors on the behavior of the honeybee Apis mellifera using Radiofrequency Identification (RFID)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-71344}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {This study was conducted to determine the influence of different stress factors on the honeybee Apis mellifera. The investigation was motivated by previous experiments that suggested the existence of an unspecific defense mechanism causing a generalized change of flight behavior after the onset of different diseases. This mechanism is thought to impede the ability of flight bees to return to their respective colonies thereby removing the disease from the colony over time. During the last years, the existence of such a "suicidal behavior" was supported by further studies. Thus, an unnoticed, potentially highly effective defense mechanism of social insects was revealed whose spectrum of activity and physiological basics require further investigation. Suggesting that the reaction by the bees is unspecific to different diseases as well as to other potential stress factors, this study was designed to investigate the influence of pathogens, insecticides, and different brood rearing temperatures on different parameters like lifespan, foraging activity, and foraging trip duration of worker bees.}, subject = {Biene}, language = {en} } @phdthesis{Vogel2022, author = {Vogel, Sebastian}, title = {Determinants of saproxylic biodiversity and conclusions for conservation}, doi = {10.25972/OPUS-28926}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-289266}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2022}, abstract = {Over the past centuries, anthropogenic utilization has fundamentally changed the appearance of European forest ecosystems. Constantly growing and changing demands have led to an enormous decline in ecological key elements and a structural homogenization of most forests. These changes have been accompanied by widespread declines of many forest-dwelling and especially saproxylic, i.e. species depending on deadwood. In order to counteract this development, various conservation strategies have been developed, but they primarily focus on a quantitative deadwood enrichment. However, the diversity of saproxylic species is furthermore driven by a variety of abiotic and biotic determinants as well as interactions between organisms. A detailed understanding of these processes has so far been largely lacking. The aim of the present thesis was therefore to improve the existing ecological knowledge of determinants influencing saproxylic species and species communities in order to provide the basis for evidence-based and adapted conservation measures. In chapter II of this thesis, I first investigated the impact of sun exposure, tree species, and their combination on saproxylic beetles, wood-inhabiting fungi, and spiders. Therefore, logs and branches of six tree species were set up under different sun exposures in an experimental approach. The impact of sun exposure and tree species strongly differed among single saproxylic taxa as well as diameters of deadwood. All investigated taxa were affected by sun exposure, whereby sun exposure resulted in a higher alpha-diversity of taxa recorded in logs and a lower alpha-diversity of saproxylic beetles reared from branches compared to shading by canopy. Saproxylic beetles and wood-inhabiting fungi as obligate saproxylic species were additionally affected by tree species. In logs, the respective impact of both determinants also resulted in divergent community compositions. Finally, a rarefaction/extrapolation method was used to evaluate the effectiveness of different combinations of tree species and sun exposure for the conservation of saproxylic species diversity. Based on this procedure, a combination of broadleaved and coniferous as well as hard- and softwood tree species was identified to support preferably high levels of saproxylic species diversity. The aim of chapter III was to evaluate the individual conservational importance of tree species for the protection of saproxylic beetles. For this, the list of tree species sampled for saproxylic beetles was increased to 42 different tree species. The considered tree species represented large parts of taxonomic and phylogenetic diversity native to Central Europe as well as the most important non-native tree species of silvicultural interest. Freshly cut branches were set up for one year and saproxylic beetles were reared afterwards for two subsequent years. The study revealed that some tree species, in particular Quercus sp., host a particular high diversity of saproxylic beetles, but tree species with a comparatively medium or low overall diversity were likewise important for red-listed saproxylic beetle species. Compared to native tree species, non-native tree species hosted a similar overall species diversity of saproxylic beetles but differed in community composition. In chapter IV, I finally analysed the interactions of host beetle diversity and the diversity of associated parasitoids by using experimentally manipulated communities of saproxylic beetles and parasitoid Hymenoptera as a model system. Classical approaches of species identification for saproxylic beetles were combined with DNA-barcoding for parasitoid Hymenoptera. The diversity of the host communities was inferred from their phylogenetic composition as well as differences in seven functional traits. Abundance, species richness, and Shannon-diversity of parasitoid Hymenoptera increased with increasing host abundance. However, the phylogenetic and functional dissimilarity of host communities showed no influence on the species communities of parasitoid Hymenoptera. The results clearly indicate an abundance-driven system in which the general availability, not necessarily the diversity of potential hosts, is decisive. In summary, the present thesis corroborates the general importance of deadwood heterogeneity for the diversity of saproxylic species by combining different experimental approaches. In order to increase their efficiency, conservation strategies for saproxylic species should generally promote deadwood from different tree species under different conditions of sun exposure on landscape-level in addition to the present enrichment of a certain deadwood amount. The most effective combinations of tree species should consider broadleaved and coniferous as well as hard- and softwood tree species. Furthermore, in addition to dominant tree species, special attention should be given to native, subdominant, silviculturally unimportant, and rare tree species.}, 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{Heisig2010, author = {Heisig, Martin}, title = {Development of novel Listeria monocytogenes strains as therapeutic agents for targeted tumor therapy}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48628}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {Despite marked progress in development and improvement of cancer therapies the rate of cancer related death remained stable over the last years. Especially in treating metastases alternative approaches supporting current therapies are required. Bacterial and viral vectors have been advanced from crude tools into highly sophisticated therapeutic agents detecting and treating neoplastic leasions. They might be potent enough to fill in this therapeutic demand. In this thesis Listeria monocytogenes was investigated as carrier for targeted bacterial cancer therapy. One part of the study focussed on modification of a functional bacterial mRNA delivery system. Genomic integration of T7 RNA polymerase driving mRNA production allowed reduction to an one-plasmid-system and thereby partially relieved the growth retardation exerted by mRNA delivery. Importantly the integration allowed metabolic attenuation of the mRNA delivery mutant potentially enabling in vivo applications. Further expansion of the bacterial RNA delivery system for transfer of shRNAs was examined. Bacterial mutants producing high amounts of RNA containing shRNA sequences were constructed, however a functional proof of gene silencing on delivery in eukaryotic cell lines was not achieved. The second part of this thesis focussed on increasing tumor colonization by Listeria monocytogenes in vivo. Coating bacteria with antibodies against receptors overexpressed on distinct tumor cell lines enabled specific bacterial internalization into these cells in vitro. Optimization of the bacterial antibody coating process resulted in an up to 104-fold increase of intracellular bacteria. Combination of this antibody-mediated targeting with the delivery of prodrug-converting enzymes showed a cytotoxic effect in cell lines treated with the corresponding prodrug. Since incubation in murine serum completely abrogated antibodymediated bacterial internalization the antibodies were covalently linked to the bacteria for application in xenografted tumor mice. Bacteria coated and crosslinked in this manner showed enhanced tumor targeting in a murine tumor model demonstrating antibodymediated bacterial tumor targeting in vivo. Independent of antibody-mediated tumor targeting the intrinsic tumor colonization of different Listeria monocytogenes mutants was examined. Listeria monocytogenes \&\#916;aroA \&\#916;inlGHE colonized murine melanoma xenografts highly efficient, reaching up to 108 CFU per gram of tumor mass 7 days post infection. Taken together the presented data shows highly promising aspects for potential bacterial application in future tumor therapies. Combination of the delivery systems with antibodymediated- and intrinsic bacterial tumor targeting might open novel dimensions utilizing Listeria monocytogenes as therapeutic vector in targeted tumor therapy.}, subject = {Krebs }, language = {en} } @phdthesis{Hartmann2024, author = {Hartmann, Oliver}, title = {Development of somatic modified mouse models of Non-Small cell lung cancer}, doi = {10.25972/OPUS-36340}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-363401}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {In 2020, cancer was the leading cause of death worldwide, accounting for nearly 10 million deaths. Lung cancer was the most common cancer, with 2.21 million cases per year in both sexes. This non-homogeneous disease is further subdivided into small cell lung cancer (SCLC, 15\%) and non-small cell lung cancer (NSCLC, 85\%). By 2023, the American Cancer Society estimates that NSCLC will account for 13\% of all new cancer cases and 21\% of all estimated cancer deaths. In recent years, the treatment of patients with NSCLC has improved with the development of new therapeutic interventions and the advent of targeted and personalised therapies. However, these advances have only marginally improved the five-year survival rate, which remains alarmingly low for patients with NSCLC. This observation highlights the importance of having more appropriate experimental and preclinical models to recapitulate, identify and test novel susceptibilities in NSCLC. In recent years, the Trp53fl/fl KRaslsl-G12D/wt mouse model developed by Tuveson, Jacks and Berns has been the main in vivo model used to study NSCLC. This model mimics ADC and SCC to a certain extent. However, it is limited in its ability to reflect the genetic complexity of NSCLC. In this work, we use CRISPR/Cas9 genome editing with targeted mutagenesis and gene deletions to recapitulate the conditional model. By comparing the Trp53fl/fl KRaslsl- G12D/wt with the CRISPR-mediated Trp53mut KRasG12D, we demonstrated that both showed no differences in histopathological features, morphology, and marker expression. Furthermore, next-generation sequencing revealed a very high similarity in their transcriptional profile. Adeno-associated virus-mediated tumour induction and the modular design of the viral vector allow us to introduce additional mutations in a timely manner. CRISPR-mediated mutation of commonly mutated tumour suppressors in NSCLC reliably recapitulated the phenotypes described in patients in the animal model. Lastly, the dual viral approach could induce the formation of lung tumours not only in constitutive Cas9 expressing animals, but also in wildtype animals. Thus, the implementation of CRISPR genome editing can rapidly advance the repertoire of in vivo models for NSCLC research. Furthermore, it can reduce the necessity of extensive breeding.}, subject = {CRISPR/Cas-Methode}, language = {en} } @phdthesis{Schaefer2014, author = {Schaefer, Frauke}, title = {Diagnosis and therapy of malaria under the conditions of a developing country - the example of Burkina Faso}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-102863}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {Malaria is a challenging infection with increasing and wide-spread treatment failure risk due to resistance. With a estimated death toll of 1-3 Million per year, most cases of Malaria affect children under the age of five years in Sub-Saharan Africa. In this thesis, I analyse the current status of malaria control (focussing on diagnosis and therapy) in Burkina Faso to show how this disease burdens public health in endemic countries and to identify possible approaches to improvement. MB is discussed as a therapeutic option under these circumstances. Burkina Faso is used as a representative example for a country in Sub-Saharan Africa with high endemicity for malaria and is here portrayed, its health system characterised and discussed under socioeconomic aspects. More than half of this country's population live in absolute poverty. The burden that malaria, especially treatment cost, poses on these people cannot be under-estimated. A retrospective study of case files from the university pediatric hospital in Burkina Faso's capital, Ouagadougou, shows that the case load is huge, and especially the specific diagnosis of severe malaria is difficult to apply in the hospital's daily routine. Treatment policy as proposed by WHO is not satisfactorily implemented neither in home treatment nor in health services, as data for pretreatment clearly show. In the face of growing resistance in malaria parasites, pharmacological combination therapies are important. Artemisinins currently are the last resort of malaria therapy. As I show with homology models, even this golden bullet is not beyond resistance development. Inconsidered mass use has rendered other drugs virtually useless before. Artemisinins should thus be protected similar to reserve antibiotics against multi-resistant bacteria. There is accumulating evidence that MB is an effective drug against malaria. Here the biological effects of both MB alone and in combination therapy is explored via modeling and experimental data. Several different lines of MB attack on Plasmodium redox defense were identified by analysis of the network effects. Next, CQ resistance based on Pfmdr1 and PfCRT transporters as well as SP resistance were modeled in silico. Further modeling shows that MB has a favorable synergism on antimalarial network effects with these commonly used antimalarial drugs, given their correct application. Also from the economic point of view MB shows great potential: in terms of production price, it can be compared to CQ, which could help to diminuish the costs of malaria treatment to affordable ranges for those most affected and struk by poverty. Malaria control is feasible, but suboptimal diagnosis and treatment are often hindering the achievment of this goal. In order to achieve malaria control, more effort has to be made to implement better adjusted and available primary treatment strategies for uncomplicated malaria that are highly standardised. Unfortunately, campaigns against malaria are chronically underfinanced. In order to maximize the effect of available funds, a cheap treatment option is most important, especially as pharmaceuticals represent the biggest single matter of expense in the fight against malaria.}, subject = {Malaria}, language = {en} } @phdthesis{Pillai2011, author = {Pillai, Deepu}, title = {Differential effects of Pigment epithelium derived factor and epidermal growth factor on Ischemia-reperfusion injury in rats - a magnetic resonance imaging study at 3 tesla}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-57341}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {Stroke, after myocardial infarction and cancer is the third most common cause of death worldwide and 1/6th of all human beings will suffer at least one stroke in their lives. Furthermore, it is the leading cause for adult disability with approximately one third of patients who survive for the next 6 months are dependent on others. Because of its huge socioeconomic burden absorbing 6\% of all health care budgets and with the fact that life expectancy increases globally, one can assume that stroke is already, and will continue to be, the most challenging disease. Ischemic stroke accounts for approximately 80\% of all strokes and results from a thrombotic or embolic occlusion of a major cerebral artery (most often the middle cerebral artery, MCA) or its branches Following acute ischemic stroke, the most worrisome outcome is the rapidly increasing intra-cranial pressure due to the formation of space-occupying vasogenic oedema which can have lethal consequences. Permeability changes at the Blood-Brain Barrier (BBB) usually accompanies the oedematous development and their time course can provide invaluable insight into the nature of the insult, activation of compensatory mechanisms followed by long term repair. Rodent models of focal cerebral ischemia have been developed and optimized to mimic human stroke conditions and serve as indispensable tools in the field of stroke research. The presented work constituting of three separate but complete works by themselves are sequential, where, the first part was dedicated to the establishment of non-invasive small animal imaging strategies on a 3 tesla clinical magnetic resonance scanner. This facilitated the longitudinal monitoring of pathological outcomes following stroke where identical animals can serve as its own control. Tissue relaxometric estimations were carried out initially to derive the transverse (T2), longitudinal (T1) and the transverse relaxation time due to magnetic susceptibility effects (T2*) at the cortical and striatal regions of the rodent brain. Statistically significant differences in T2*-values could be found between the cortex and striatal regions of the rodent brain. The derived tissue relaxation values were considered to modify the existing imaging protocols to facilitate the study of the rodent model of ischemic stroke. The modified sequence protocols adequately characterized all the clinically relevant sequels following acute ischemic stroke, like, the altered perfusion and diffusion characteristics. Subsequent to this, serial magnetic resonance imaging was performed to investigate the temporal and spatial relationship between the biphasic nature of BBB opening and, in parallel, the oedema formation after I/R injury in rats. T2-relaxometry for oedema assessment was performed at 1 h after ischemia, immediately following reperfusion, and at 4, 24 and 48 hours post reperfusion. Post-contrast T1-weighted imaging was performed at the last three time points to assess BBB integrity. The biphasic course of BBB opening with significant reduction in BBB permeability at 24 hours after reperfusion was associated with a progressive expansion of leaky BBB volume, accompanied by a peak ipsilateral oedema formation. At 48 hours, the reduction in T2-value indicated oedema resorption accompanied by a second phase of BBB opening. In addition, at 4 hours after reperfusion, oedema formation could also be detected at the contralateral striatum which persisted to varying degrees throughout the study, indicative of widespread effects of I/R injury. The observations of this study may indicate a dynamic temporal shift in the mechanisms responsible for biphasic BBB permeability changes, with non-linear relations to oedema formation. Two growth factor peptides namely pigment epithelium derived factor (PEDF) and epidermal growth factor (EGF) with widely different trophic properties were considered for their beneficial effects, if any, in the established rodent model of I/R injury and studied up to one week employing magnetic resonance imaging. Both the selected, trophic factors demonstrated significant neuroprotection as demonstrated by a reduction in infarct volume, even though PEDF was found to be the most potent one. PEDF also demonstrated significant attenuation of oedema formation in comparison to both the control and EGF groups, even though EGF could also demonstrate oedema suppression. In the present work, we noticed that interventions with macromolecule protein/peptides by itself could mediate remote oedema at distant sites even though the significance of such an observation is not clear at present. Susceptibility (T2*) weighted tissue relaxometric estimations were considered at the infarct region to detect any metabolic changes arising out of any neuroprotection and/or cellular proliferation / neurogenesis. PEDF group demonstrated a striking reduction of the T2*-values, which is indicative of an increased metabolic activity. Moreover, all the groups (Control, EGF and PEDF) demonstrated significantly elevated T2*-values at the contralateral striatum, which is indicative of widespread metabolic suppression usually associated with a variety of traumatic brain conditions. Moreover, as expected from the properties of PEDF, it demonstrated an extended BBB permeability suppression throughout the duration of the study. This study underlines the merits of considering non-invasive imaging strategies without which it was not possible to study the required parameters in a longitudinal fashion. All the observations are adequately supported by reasonably well defined mechanisms and needs to be further verified and confirmed by an immunohistochemical study. These results also need to be complemented by a functional study to evaluate the behavioural outcome of animals following these treatments. These studies are progressing at our laboratory and the results will be duly published afterwards.}, subject = {Schlaganfall}, language = {en} } @phdthesis{Dietemann2002, author = {Dietemann, Vincent}, title = {Differentiation in reproductive potential and chemical communication of reproductive status in workers and queens of the ant Myrmecia gulosa}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-2202}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {Division of reproductive labour in societies represents a topic of interest in evolutionary biology at least since Darwin. The puzzle of how helpers can be selected for, in spite of their reduced fertility has found an explanation in the kin selection theory: workers can overcome the cost of helping and of forgiving direct reproduction by rearing sufficiently related individuals. However, in the Hymenoptera, little is known on the proximate mechanisms that regulate the division of labour in colonies. Our knowledge is based on several "primitive" ants from the subfamily Ponerinae and two highly eusocial Hymenoptera species. In the former, the dominance hierarchies allowing for the establishment of individuals as reproductives are well understood. In contrast, the pheromonal mechanisms that help maintain their reproductive status are not understood. Similarly in "higher" ants, pheromonal regulation mechanisms of worker reproduction by queens remain largely unknown. The aim of this study is to determine the modalities of production, distribution and action, as well as the identity of the queen pheromones affecting worker reproduction in the ant Myrmecia gulosa. This species belongs to the poorly studied subfamily Myrmeciinae, which is endemic to the Australian region. The subfamily represents, together with the Ponerinae, the most "primitive" ants: their morphology is close to that of the hypothetical ancestor of ants, and the specialisation of queens is weaker than that of "higher" ants. Simple regulation mechanisms were therefore expected to facilitate the investigation. The first step in this study was to characterise the morphological specialisation of queens and workers, and to determine the differences in reproductive potential associated with this specialisation. This study contributes to our understanding of the link between regulation of division of reproductive labour and social complexity. Furthermore, it will help shed light on the reproductive biology in the poorly known subfamily Myrmeciinae. Queens were recognised by workers on the basis of cuticular as well as gland extracts or products. What is the exact function of the multiple pheromones identified and how they interact remains to be determined. This could help understand why queen "signal" in a "primitive" ant with weakly specialised queens such as M. gulosa appears to be as complex as in highly eusocial species. Primer pheromones act on workers? physiology and have long-term effect. Whether workers of M. gulosa reproduce or not is determined by the detection of a queen pheromone of this type. Direct physical contact with the queen is necessary for workers to detect this pheromone. Thus, the colony size of M. gulosa is compatible with a simple system of pheromone perception by workers based on direct physical contact with the queen. When prevented from establishing physical contact with their queen, some workers start to reproduce and are policed by nestmates. The low volatility of the cuticular hydrocarbons (CHCs), their repartition over the entire cuticle and the existence of queen and worker specific CHC profiles suggest that these chemicals constitute a queen pheromone. Importance of HC versus non-HC compounds was confirmed by bioassaying purified fraction of both classes of chemicals. This study demonstrates for the first time that purified HCs indeed are at the basis of the recognition of reproductive status. This supports the idea that they are also at the basis of the recognition of queens by their workers. As CHCs profiles of workers and queens become similar with acquisition of reproductive status, they represent honest fertility markers. These markers could be used as signals of the presence of reproductives in the colonies, and represent the basis of the regulation of division of reproductive labour.}, subject = {Myrmecia gulosa}, language = {en} } @phdthesis{Thoma2011, author = {Thoma, Eva Christina}, title = {Directed differentiation of pluripotent stem cells induced by single genes}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-54706}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2011}, abstract = {Pluripotency describes the ability of stem cells to form every cell type of the body.. Pluripotent stem cells are e.g. embryonic stem cells (ESCs), but also the so called induced pluripotent stem cells (IPS cells), that are generated by reprogramming differentiated somatic cells into a pluripotent state. Furthermore, it has been shown that spermatogonia (SG) derived from adult testes of mouse or human are pluripotent. Because of their ability to differentiate into every somatic cell type, pluripotent stem cells have a unique status in research and regenerative medicine. For the latter, they offer a valuable opportunity to replace destroyed tissues or organs. For basic research, stem cells represent a useful system to study differentiation or developmental processes that are difficult to access in the physiological situation e.g. during embryogenesis. Both applications, however, require methods that allow efficient and directed differentiation of stem cells into defined specialized cell types. This study first aims to investigate the differentiation potential of SG derived from the teleost fish medaka (Oryzias latipes). My results demonstrate that medaka SG are able to form different somatic cell types, namely adipocytes, melanocytes, osteoblasts, and neurons. This indicates that medake SG have retained a broad differentiation potential suggesting that pluripotency is not restricted to mouse and human SG but might be conserved among vertebrates. Next, I wanted to establish a differentiation method that is solely based on ectopic expression of genes known to be essential for the formation of certain somatic cell types - so called master regulators (MRs). My findings show that ectopic expression of the melanocyte-specific transcription factor mitf-m that has previously been shown to induce differentiation of medaka ESCs into pigment cells resulted in the formation of the same cell type in medaka SG. This approach could be used to generate other somatic cell types. Thus, ectopic expression of the MRs cbfa1 and mash1 in MF-SG was sufficient to induce differentiation into osteoblasts and neurons, respectively. Interestingly, these differentiation processes included the activation of genes that are expressed earlier during embryogenesis than the differentiation-inducing MR. Furthermore, my findings show that the approach of MR-induced differentiation can be transferred to mammalian stem cell systems. Ectopic expression of the neural transcription factor ngn2 was sufficient to induce efficient and rapid differentiation of neurons in mouse ESCs. This differentiation process also included the induction of genes that in vivo are activated at earlier stages that ngn2. By generating a transgenic cell line allowing induction of ectopic ngn2 expression, it was possible to obtain a relatively pure culture of functional neurons. Ngn2-induced differentiation did not require any additional signals and occurred even under pluripotency promoting conditions. Moreover, ectopic expression of ngn2 did also induce the formation of cells with neuronal morphology in IPS cells indicating that MR-induced differentiation is operative in different stem cell types. Furthermore, protein transduction of Ngn2 into mouse ESCs also resulted in a neuronal differentiation process up to the appearance of neural precursor cells. Last, my results show that MR-induced differentiation can also be used to generate other cell types than neurons from mouse ESCs. Myoblasts and macrophage-like cells were generated by ectopic expression of the MRs myoD and cebpa, respectively. Using transgenic cell lines enabling induction of MR expression it was possible to obtain mixed cultures with two different differentiation processes occurring in parallel. Altogether this study shows that ectopic expression of single genes is sufficient to induce directed differentiation of stem cells into defined cell types. The feasibility of this approach was demonstrated for different MRs and consequently different somatic cell types. Furthermore, MR induced differentiation was operative in different stem cell types from fish and mouse. Thus, one can conclude that certain genes are able to define cell fates in in vitro stem cell systems and that this cell fate defining potential appears to be a conserved feature in vertebrates. These findings therefore provide new insights in the role of MRs in cell commitment and differentiation processes. Furthermore, this study presents a new method to induce directed differentiation of stem cells that offers several advantages regarding efficiency, rapidness, and reproducibility. MR-induced differentiation therefore represents a promising tool for both stem cell research and regenerative medicine.}, subject = {Stammzelle}, language = {en} } @phdthesis{Aso2010, author = {Aso, Yoshinori}, title = {Dissecting the neuronal circuit for olfactory learning in Drosophila}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-55483}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {This thesis consists of three major chapters, each of which has been separately published or under the process for publication. The first chapter is about anatomical characterization of the mushroom body of adult Drosophila melanogaster. The mushroom body is the center for olfactory learning and many other functions in the insect brains. The functions of the mushroom body have been studied by utilizing the GAL4/UAS gene expression system. The present study characterized the expression patterns of the commonly used GAL4 drivers for the mushroom body intrinsic neurons, Kenyon cells. Thereby, we revealed the numerical composition of the different types of Kenyon cells and found one subtype of the Kenyon cells that have not been described. The second and third chapters together demonstrate that the multiple types of dopaminergic neurons mediate the aversive reinforcement signals to the mushroom body. They induce the parallel memory traces that constitute the different temporal domains of the aversive odor memory. In prior to these chapters, "General introduction and discussion" section reviews and discuss about the current understanding of neuronal circuit for olfactory learning in Drosophila.}, subject = {Taufliege}, language = {en} } @phdthesis{Ott2013, author = {Ott, Christine Kornelia}, title = {Diverse Aspects of the Sorting and Assembly Machinery in Human Mitochondria}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-85462}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2013}, abstract = {Mitochondria are organelles of endosymbiotic origin, which play many important roles in eukaryotic cells. Mitochondria are surrounded by two membranes and, considering that most of the mitochondrial proteins are produced in the cytosol, possess import machineries, which transport mitochondria-targeted proteins to their designated location. A special class of outer mitochondrial membrane (OMM) proteins, the β-barrel proteins, require the sorting and assembly machinery (SAM) for their OMM integration. Both mitochondrial β-barrel proteins and the central component of the SAM complex, Sam50, have homologs in gram-negative bacteria. In yeast mitochondria, bacterial β-barrel proteins can be imported and assembled into the OMM. Our group demonstrated that this, however, is not the case for human mitochondria, which import only neisserial β barrel proteins, but not those of Escherichia coli and Salmonella enterica. As a part of this study, I could demonstrate that β-barrel proteins such as Omp85 and PorB of different Neisseria species are targeted to human mitochondria. Interestingly, only proteins belonging to the neisserial Omp85 family were integrated into the OMM, whereas PorB was imported into mitochondria but not assembled. By exchanging parts of homologous neisserial Omp85 and E. coli BamA and, similarly, of neisserial PorB and E. coli OmpC, it could be demonstrated in this work that the mitochondrial import signal of bacterial β barrel proteins cannot be limited to one short linear sequence, but rather secondary structure and protein charge seem to play an important role, as well as specific residues in the last β-strand of Omp85. Omp85 possesses five conserved POTRA domains in its amino-terminal part. This work additionally demonstrated that in human mitochondria, at least two POTRA domains of Omp85 are necessary for membrane integration and functionality of Omp85. In the second part of this work, the influence of Sam50 on the mitochondrial cristae structure was investigated. This work contributed to a study performed by our group in which it was confirmed that Sam50 is present in a high molecular weight complex together with mitofilin, CHCHD3, CHCHD6, DnaJC11, metaxin 1 and metaxin 2. This connection between the inner and outer mitochondrial membrane was shown to be crucial for the maintenance of the mitochondrial cristae structure. In addition, a role of Sam50 in respiratory complex assembly, suggested by a SILAC experiment conducted in our group, could be confirmed by in vitro import studies. An influence of Sam50 not only on respiratory complexes but also on the recently described respiratory complex assembly factor TTC19 was demonstrated. It was shown that TTC19 not only plays a role in complex III assembly as published, but also influences the assembly of respiratory complex IV. Thus, in this part of the work a connection between the OMM protein Sam50 and maintenance of cristae structure, respiratory complex assembly and an assembly factor could be established.}, subject = {Mitochondrien}, language = {en} } @phdthesis{Wende2014, author = {Wende, Beate}, title = {Diversity of saproxylic beetles and host tree specialisation in differently managed forests across Germany}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-107049}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {Chapter I The gradual turnover of dead organic material into mineral nutrients is a key ecological function, linking decomposition and primary production, the essential parts of the nutrient-energy cycle. However, disturbances in terms of species or resource losses might impair the equilibrium between production and decomposition. Humanity has converted large proportions of natural landscapes and intensified land-use activity for food production. Globally, only very few areas are totally unaffected by human activity today. To ensure the maintenance of both essential ecosystem services, knowledge about the interplay of biodiversity and ecosystem functioning as well as effects of intensified management on both is crucial. The vast majority of terrestrial biomass production as well as decomposition take place in forest ecosystems. Though forestry has a long sustainable history in Europe, its intensification during the last century has caused severe impacts on forest features and, consequently, on the associated biota, especially deadwood dependent organisms. Among these, saproxylic beetles are the most diverse group in terms of species numbers and functional diversity, but also most endangered due to habitat loss. These features classify them as ideal research organisms to study effects of intensified forestry on ecosystem services. The BELONGDEAD project located in Germany aimed to investigate deadwood decay and functional consequences of diversity changes in the associated fauna on the decomposition process from the initialisation of deadwood decay to complete degradation. As part of the BeLongDead project, this dissertation focussed on saproxylic beetle species, thereby evaluating (1) regionally effects of tree species identity of fresh deadwood and (2) forest management of varying intensities on the diversity, abundance and community composition of saproxylic beetles (chapter II); (3) the specialisation degree of different trophic guilds of saproxylic beetles, and thus the stability and robustness of their interaction networks against disturbances (chapter III); (4) the impact of environmental features of local to regional spatial scales on species richness of saproxylic beetles differing in their habitat niche in terms of deadwood decay stages (chapter IV). Chapter II The vast majority of European forest ecosystems have been anthropogenically affected, leaving less than 1\% of the about 1 milliard hectare as natural forests. A long history of forestry and especially the technological progress during the last century have caused massive habitat fragmentation as well as substantial loss of essential resources in European forest ecosystems. Due to this, the substrate-dependent group of saproxylic beetles has experienced severe species losses. Thus, investigations concerning saproxylic diversity and deadwood volume were badly needed. However, the importance of different deadwood in terms of tree species identity for the colonization by saproxylic beetles under different local and regional management regimes is poorly understood. Therefore, we studied possible regional differences in colonization patterns of saproxylic beetle species in a total of 688 fresh deadwood logs of 13 tree species in 9 sites of managed conifer and beech forests, and unmanaged beech forests, respectively. We found that tree species identity was an important driver in determining saproxylic species composition and abundance within fresh deadwood. However, saproxylic species showed different colonization patterns of deadwood items of the same tree species among the study regions. Regionally consistent, conifer forests were most diverse. We attribute the latter result to the historically adaption of saproxylic beetle species to semi-open forests, which conditions are actually best reflected by conifer forests. To preserve a diverse local species pool of early successional saproxylic beetles, we suggest an equal high degree of deadwood diversity in a tree species context in due consideration of regional differences. Chapter III The extinction risk of a particular species corresponds with its species-specific requirements on resources and habitat conditions, in other words with the width of the species` ecological niche. Species with a narrow ecological niche are defined as specialists. Members of this group experience higher extinction risk by resource limitation than generalists, which are able to utilize a variety of resources. For the classification of species as specialists or generalists, thus evaluating possible extinction risks, ecologists use the concept of interaction networks. This method has often been applied for mutualistic or antagonistic plant-animal interactions, but information for networks of detritivores is scarce. Therefore, saproxylic beetle species sampled as described in chapter II were categorised according to their larval diet; additionally their interaction networks (N=108) with 13 dead host tree species were analysed. Specialisation degree was highest for wood-digesting beetles and decreased with increasing trophic level. Also the network indices evaluating robustness and generality indicated a higher susceptibility to species extinctions for xylophagous than for mycetophagous and predatory beetles. The specialisation of xylophagous species on specific tree species might be an adaption to tree species specific ingredients stored for defence against pathogens and pests. However, we conclude that the high specialisation degree of xylophages and thus their higher extinction risk by resource loss harbours certain dangers for ecosystem function and stability as species diversity is positively linked to both. Chapter IV Populations depend on individual emigration and immigration events to ensure genetic exchange. For successful migration it is of utmost importance that spatially separated populations are obtainable by specimen. Migratory success depends on the one hand on the species dispersal abilities and on the other on the availability of suitable habitats in the surrounding landscape in which the distinct host populations exist. However, consequences of intensive forest management correspond not only to severe reduction of local deadwood amount, but, among others, also a change in tree species composition and high levels of fragmentation in the surrounding forest area. Saproxylic beetle species differ in their dispersal behaviour according to the temporal availability of their preferred habitat. Generally, early successional saproxylic beetles are able to disperse over large distances, whereas beetles inhabiting advanced decayed wood often remain close to their larval habitat. Due to this, environmental factors might affect saproxylic beetle guilds differently. We classified the saproxylic beetles sampled as described in chapter II according to their calculated habitat niche as early, intermediate or late successional saproxylic beetles. For the different guilds the effects of 14 environmental factors on different spatial scales (stand factors at 0.1 km radius, landscape composition at 2 km radius, and regionally differing abiotic factors in 400 km to 700 km distance) were investigated. Consistently for all guilds, species richness decreased with fragmentation at local and landscape scale, and increased in warmer climate. However, we found contradictory results between the guilds to some extent. We relate this to guild specific habitat requirements of the saproxylic beetles. Therefore, for the development of appropriate conservation practices guild-specific requirements saproxylic beetles have to be considered not only locally but on larger spatial scales. Chapter V In conclusion, this dissertation identified main drivers of early successional saproxylic beetle species richness on various spatial scales. Our results emphasize the importance to develop management schemes meeting species-specific and guild-specific habitat requirements of the saproxylic beetle fauna at relevant spatial and temporal scales. Therefore, short-term actions suggested for sustainable forest management should be the focus on a diverse tree species composition consisting of indigenous tree species with respect to regional differences. Moreover, senescent trees, fallen and standing deadwood should remain in the forests, and some tree individuals should be allowed to grow old. Long-term actions should involve the reduction of forest fragmentation and the connection of spatial widely separated forest fragments. Furthermore, to fully understand the effects of forest management long-term research should be conducted to compare habitat requirements of intermediate and late successional beetles with the results presented in this dissertation.}, subject = {Saproxylophage}, language = {en} } @phdthesis{Classen2014, author = {Claßen, Alice}, title = {Diversity, traits and ecosystem services of pollinators along climate and land use gradients on Mount Kilimanjaro}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-101292}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {Since more than two centuries naturalists are fascinated by the profound changes in biodiversity observed along climatic gradients. Although the theories explaining changes in the diversity and the shape of organisms along climatic gradients belong to the foundations of modern ecology, our picture on the spatial patterns and drivers of biodiversity is far from being complete. Ambiguities in theory and data are common and past work has been strongly concentrated on plants and vertebrates. In the last two decades, interest in the fundamental processes structuring diversity along climatic gradients gained new impetus as they are expected to improve our understanding about how ecosystems will respond to global environmental changes. Global temperatures are rising faster than ever before; natural habitats are transformed into agricultural land and existing land use systems get more and more intensified to meet the demands of growing human populations. The fundamental shifts in the abiotic and biotic environment are proclaimed to affect ecosystems all over the world; however, precise predictions about how ecosystems respond to global changes are still lacking. We investigated diversity, traits and ecosystem services of wild bees along climate and land use gradients on Mount Kilimanjaro (Tanzania, East Africa). Wild bees play a major role in ecosystems, as they contribute to the reproduction and performance of wild and crop plants. Their responsiveness to environmental changes is therefore of high ecological and economic importance. Temperature and energy resources have often been suggested to be the main determinants of global and local species richness, but the mechanisms behind remain poorly understood. In the study described in chapter II we analyzed species richness patterns of wild bees along climate and land use gradients on Mount Kilimanjaro and disentangled the factors explaining most of the changes in bee richness. We found that floral resources had a weak but significant effect on pollinator abundance, which in turn was positively related to species richness. However, temperature was the strongest predictor of species richness, affecting species richness both directly and indirectly by positively influencing bee abundances. We observed higher levels of bee-flower-interactions at higher temperatures, independently of flower and bee abundances. This suggests that temperature restricts species richness by constraining the exploitation of resources by ectotherms. Current land use did not negatively affect species richness. We conclude that the richness of bees is explained by both temperature and resource availability, whereas temperature plays the dominant role as it limits the access of ectotherms to floral resources and may accelerate ecological and evolutionary processes that drive the maintenance and origination of diversity. Not only species numbers, but also morphological traits like body size are expected to be shaped by both physiological and energetic constraints along elevational gradients. Paradoxically, Bergmann´s rule predicts increases of body sizes in cooler climates resulting from physiological constraints, while species-energy theory suggests declines in the mean body size of species caused by increased extinction probabilities for large-bodied species in low-energy habitats. In chapter III we confronted this ambiguity with field data by studying community-wide body size variation of wild bees on Mt. Kilimanjaro. We found that along a 3680 m elevational gradient bee individuals became on average larger within species, while large species were increasingly absent from high-elevational communities. This demonstrates, on the one hand, how well-established, but apparently contrasting ecological theories can be merged through the parallel consideration of different levels of biological organization. On the other hand it signals that the extinction risk in the course of environmental change is not equally distributed among species within a community. Land use intensification is known to threaten biodiversity, but the consequences for ecosystem services are still a matter of debate. In chapter IV, we experimentally tested the single and combined contributions of pest predators and pollinators to coffee production along a land use intensification gradient on Mount Kilimanjaro. We found that pest predation increased fruit set by on average 9\%, while pollination increased fruit weight of coffee by on average 7.4\%. Land use had no significant effect on both ecosystem services. However, we found that in coffee plantations with most intensified land use, pollination services were virtually exclusively provided by the honey bee (Apis mellifera). The reliance on a single pollinator species is risky, as possible declines of that species may directly lower pollination services, resulting in yield losses. In contrast, pollination services in structurally complex homegardens were found to be provided by a diverse pollinator community, increasing the stability of pollination services in a long term. We showed that on Mount Kilimanjaro pollinator communities changed along elevational gradients in terms of species richness (chapter II) and trait composition (chapter III). Temperature and the temperature-mediated accessibility of resources were identified as important predictors of these patterns, which contributes to our fundamental understanding about the factors that shape ectothermic insect communities along climatic gradients. The strong temperature-dependence of pollinators suggests that temperature shifts in the course of global change are likely to affect pollinator communities. Pollinators might either profit from rising temperatures, or shift to higher elevations, which could result in related biotic attrition in the lowland with consequences for the provision of ecosystem services in cropping systems. Up to now, land use intensification had no significant impact on the diversity of pollinator communities and their ecosystem services. Pollinators might profit from the strong landscape heterogeneity in the region and from the amount of flower resources in the understory of cropping systems. However,progressing homogenization of the landscape and the pronounced application of pesticides could result in reduced diversity and dominance of single species, as we already found in sun coffee plantations. Such shifts in community compositions could threaten the stability of ecosystem services within cropping and natural systems in a long term.}, subject = {Kilimandscharo}, language = {en} } @phdthesis{Engelmann2008, author = {Engelmann, Julia Cath{\´e}rine}, title = {DNA microarrays: applications and novel approaches for analysis and interpretation}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-29747}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {In der vorliegenden Dissertation wird die Entwicklung eines phylogenetischen DNA Microarrays, die Analyse von mehreren Microarray-Genexpressionsdatens{\"a}tzen und neue Ans{\"a}tze f{\"u}r die Datenanalyse und Interpretation der Ergebnisse vorgestellt. Die Entwicklung und Analyse der Daten eines phylogenetischen DNA Microarrays wird in der ersten Publikation dargestellt. Ich konnte zeigen, dass die Spezies-Detektion mit phylogenetischen Microarrays durch die Datenanalyse mit einem linearen Regressionsansatz signifikant verbessert werden kann. Standard-Methoden haben bislang nur Signalintensit{\"a}ten betrachtet und eine Spezies als an- oder abwesend bezeichnet, wenn die Signalintensit{\"a}t ihres Messpunktes oberhalb eines willk{\"u}rlich gesetzten Schwellenwertes lag. Dieses Verfahren ist allerdings aufgrund von Kreuz-Hybridisierungen nicht auf sehr nah verwandte Spezies mit hoher Sequenzidentit{\"a}t anwendbar. Durch die Modellierung des Hybridisierungs und Kreuz-Hybridisierungsverhaltens mit einem linearen Regressionsmodell konnte ich zeigen, dass Spezies mit einer Sequenz{\"a}hnlichkeit von 97\% im Markergen immer noch unterschieden werden k{\"o}nnen. Ein weiterer Vorteil der Modellierung ist, dass auch Mischungen verschiedener Spezies zuverl{\"a}ssig vorhergesagt werden k{\"o}nnen. Theoretisch sind auch quantitative Vorhersagen mit diesem Modell m{\"o}glich. Um die großen Datenmengen, die in {\"o}ffentlichen Microarray-Datenbanken abgelegt sind besser nutzen zu k{\"o}nnen, bieten sich Meta-Analysen an. In der zweiten Publikation wird eine explorative Meta-Analyse auf Arabidopsis thaliana-Datens{\"a}tzen vorgestellt. Mit der Analyse verschiedener Datens{\"a}tze, die den Einfluss von Pflanzenhormonen, Pathogenen oder verschiedenen Mutationen auf die Genexpression untersucht haben, konnten die Datens{\"a}tze anhand ihrer Genexpressionsprofile in drei große Gruppen eingeordnet werden: Experimente mit Indol-3-Essigs{\"a}ure (IAA), mit Pathogenen und andere Experimente. Gene, die charakteristisch f{\"u}r die Gruppe der IAA-Datens{\"a}tze beziehungsweise f{\"u}r die Gruppe der Pathogen-Datens{\"a}tze sind, wurden n{\"a}her betrachtet. Diese Gene hatten Funktionen, die bereits mit Pathogenbefall bzw. dem Einfluss von IAA in Verbindung gebracht wurden. Außerdem wurden Hypothesen {\"u}ber die Funktionen von bislang nicht annotierten Genen aufgestellt. In dieser Arbeit werden auch Prim{\"a}ranalysen von einzelnen Arabidopsis thaliana Genexpressions-Datens{\"a}tzen vorgestellt. In der dritten Publikation wird ein Experiment beschrieben, das durchgef{\"u}hrt wurde um herauszufinden ob Mikrowellen-Strahlung einen Einfluss auf die Genexpression einer Zellkultur hat. Dazu wurden explorative Analysemethoden angewendet. Es wurden geringe aber signifikante Ver{\"a}nderungen in einer sehr kleinen Anzahl von Genen beobachtet, die experimentell best{\"a}tigt werden konnten. Die Funktionen der regulierten Gene und eine Meta-Analyse mit {\"o}ffentlich zug{\"a}nglichen Datens{\"a}tzen einer Datenbank deuten darauf hin, dass die pflanzliche Zellkultur die Strahlung als eine Art Energiequelle {\"a}hnlich dem Licht wahrnimmt. Des weiteren wird in der vierten Publikation die funktionelle Analyse eines Arabidopsis thaliana Genexpressionsdatensatzes beschrieben. Die Analyse der Genexpressions eines pflanzlichen Tumores zeigte, dass er seinen Stoffwechsel von aerob und auxotroph auf anaerob und heterotroph umstellt. Gene der Photosynthese werden im Tumorgewebe reprimiert, Gene des Aminos{\"a}ure- und Fettstoffwechsels, der Zellwand und Transportkan{\"a}le werden so reguliert, dass Wachstum und Entwicklung des Tumors gef{\"o}rdert werden. In der f{\"u}nften Publikation in dieser Arbeit wird GEPAT (Genome Expression Pathway Analysis Tool) beschrieben. Es besteht aus einer Internet- Anwendung und einer Datenbank, die das einfache Hochladen von Datens{\"a}tzen in die Datenbank und viele M{\"o}glichkeiten der Datenanalyse und die Integration anderer Datentypen erlaubt. In den folgenden zwei Publikationen (Publikation 6 und Publikation 7) wird GEPAT auf humane Microarray-Datens{\"a}tze angewendet um Genexpressionsdaten mit weiteren Datentypen zu verkn{\"u}pfen. Genexpressionsdaten und Daten aus vergleichender Genom-Hybridisierung (CGH) von prim{\"a}ren Tumoren von 71 Mantel-Zell-Lymphom (MCL) Patienten erm{\"o}glichte die Ermittlung eines Pr{\"a}diktors, der die Vorhersage der {\"U}berlebensdauer von Patienten gegen{\"u}ber herk{\"o}mmlichen Methoden verbessert. Die Analyse der CGH Daten zeigte, dass auch diese f{\"u}r die Vorhersage der {\"U}berlebensdauer geeignet sind. F{\"u}r den Datensatz von Patienten mit großzellig diffusem B-Zell-Lymphom DLBCL konnte aus den Genexpressionsdaten ebenfalls ein neuer Pr{\"a}diktor vorgeschlagen werden. Mit den zwischen lang und kurz {\"u}berlebenden Patienten differentiell exprimierten Genen der MCL Patienten und mit den Genen, die zwischen den beiden Untergruppen von DLBCL reguliert sind, wurden Interaktionsnetzwerke gebildet. Diese zeigen, dass bei beiden Krebstypen Gene des Zellzyklus und der Proliferation zwischen Patienten mit kurzer und langer {\"U}berlebensdauer unterschiedlich reguliert sind.}, subject = {Microarray}, language = {en} } @phdthesis{Li2009, author = {Li, Naixin}, title = {Dorso-ventral Differentiation and Specification of the Mesencephalon in Early Chick Embryos}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-32950}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2009}, abstract = {The chick midbrain is subdivided into functionally distinct ventral and dorsal domains, tegmentum and optic tectum. In the mature tectum, neurons are organized in layers, while they form discrete nuclei in the tegmentum. An interesting characteristic of the embryonic brain is the development of a large optic tectum, of which the growth becomes obvious at embryonic day 3 (E3). Dorsoventral (DV) specification of the early midbrain should thus play a crucial role for the organization of the neuronal circuitry in optic tectum and tegmentum. In the first part of my thesis, I investigated regional commitment and establishment of cellular differences along the midbrain DV axis. I examined the commitment of gene expression patterns in isolated ventral and dorsal tissue in vivo and in vitro, and studied their cell mixing properties. Explant cultures, and grafting of dorsal midbrain into a ventral environment or vice versa, revealed a gradual increase in the autonomy of region-specific gene regulation between, which was accompanied by a gradual increase in differential adhesive properties from E2 to E3, once the DV axis polarity was fixed. These events happened at a time-point when the majority of midbrain cells are not yet differentiated. Long-term transplantation (6 - 9 days) using quail cells from ventral midbrain as grafts showed the same result. Hence, the results suggest that progressive specification of the midbrain DV axis is accompanied by progressively reduced cell mixing between dorsal and ventral precursors, leading to a partial regionalization of midbrain tissue into autonomous units of precursor cell populations. In the second part I investigated the genes that might be involved in regulating the growth of the tectum. In particular, I focused on the role of Pax7 transcription factor, a paired domain protein. The results suggested that Pax7 was involved in regulating the medial-lateral extension of the tectum. Over expression of Pax7 in dorsal midbrain led to an enlarged tectum accompanied by a raise in cell division, while Pax7 knockdown by shrank caused a reduction in tectum. The overall pattern of neuronal differentiation was not disturbed by an up or down regulation of Pax7. Pax7 also positively regulated Pax3, another pair-ruled gene expressed dorsally. These results suggest that Pax7 very likely together with Pax3 could facilitate or maintain neural cell proliferation in the midbrain at early stages and that a regulation of the size in that region does not influence the neuronal patterning of the developmental field. I further checked the expression and function of a GFPase Rab 23, that was suggested to be involved in the DV patterning in mouse neural tube as a negative regulator of Shh signaling. Overexpression of Rab23 indicated that it facilitated the expression of Pax7 and Pax3 in the neural tube and suppressed ventral genes like Nkx6.1 cell autonomously, however, it did not disturb neuronal patterning. Interestingly, a thorough expression study of Rab 23 during chick early development revealed that Rab23 is already expressed very early and asymmetrically during gastrulation, suggesting a possible role of Rab23 on the left-right determination of Hensen's node. In combination with the result that Rab23 is expressed in the notochord early in development, I assume that both Rab23 and Shh exist in all neural progenitor cells initially, and when their expression patterns separate gradually the neural cells adopt a ventral or dorsal fate according to their location along the dorsoventral axis. The avian embryo is a classic system used widely to investigate questions of vertebrate development. The easy and cheap accessibility of the embryo for in ovo or ex ovo experiments all around the year make it an ideal animal model to work with. The only recently developed method of over expressing genes in specific cells or regions in the chick embryo by electroporation enabled me to study different ways of gene suppression using this way of gene transfection. Thus, I compared the effect of long-hairpin and short hairpin dsRNA in different vectors and antisense morpholino oligonucleotides. The results revealed that all hairpin dsRNA constructs did reduce gene and protein expression often accompanied by morphological changes. Most efficiently were shRNAi constructs cloned into a siRNA-specific vector - pSilencer 1.0-U6. Gene silencing was already well observed 36 hours after transfection. In comparison antisense morpholino oligonucleotides did not show such big gene reduction as the shRNA in pSilencer. Taken together, this methodical research proposes that the shRNA in the pSilencer vector was a good and effective tool to reduce gene and protein expression locally.}, subject = {Differenzierung}, language = {en} } @phdthesis{Banaszek2013, author = {Banaszek, Agnes}, title = {Dual Antigen-Restricted Complementation of a Two-Part Trispecific Antibody for Targeted Immunotherapy of Blood Cancer}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-90174}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2013}, abstract = {Cancer cells frequently escape from immune surveillance by down-regulating two important components of the immune defence: antigen-presenting MHC and costimulatory molecules. Therefore several novel anti-tumour compounds that aim to assist the immune system in recognising and fighting cancer are currently under development. Recombinant bispecific antibodies represent one group of such novel therapeutics. They target two different antigens and recruit cytotoxic effector cells to tumour cells. For cancer immunotherapy, bispecific T cell-engaging antibodies are already well characterised. These antibodies target a tumour-associated antigen and CD3ε, the constant molecule of the T cell receptor complex. On the one hand, this study presents the development of a bispecific antibody targeting CD3ε and the rhabdomyosarcoma-associated fetal acetylcholine receptor. On the other hand, it describes a novel two-part trispecific antibody format for the treatment of leukaemia and other haematological malignancies in the context of haematopoietic stem cell transplantation (HSCT). For HSCT, an HLA-identical donor is preferred, but very rarely available. In an HLA-mismatched setting, the HLA disparity could be exploited for targeted cancer treatment. In the present study, a two-part trispecific HLA-A2 × CD45 × CD3 antibody was developed for potential cases in which the patient is HLA-A2-positive, but the donor is not. This holds true for about half the cases in Germany, since HLA-A2 is the most common HLA molecule found here. Combinatorial targeting of HLA-A2 and the leucocyte-common antigen CD45 allows for highly specific dual-antigen restricted tumour targeting. More precisely, two single-chain antibody constructs were developed: i) a single-chain variable fragment (scFv) specific for HLA-A2, and ii) a scFv against CD45, both linked to the VL and the VH domain of a CD3ε-specific antibody, respectively. It turned out that, after the concomitant binding of these constructs to the same HLA-A2- and CD45-expressing cell, the unpaired variable domains of a CD3ε-specific antibody assembled to a functional scFv. In a therapeutic situation, this assembly should exclusively occur on the recipient's blood cancer cells, leading to T cell-mediated cancer cell destruction. In this way, a relapse of disease might be prevented, and standard therapy (radiation and chemotherapy) might be omitted. For both approaches, the antibody constructs were periplasmically expressed in E. coli, purified via His tag, and biochemically characterised. Their binding to the respective targets was proven by flow cytometry. The stimulatory properties of the antibodies were assayed by measuring IL-2 release after incubation with T cells and antigen-expressing target cells. Both the bispecific antibody against rhabdomyosarcoma and the assembled trispecific antibody against blood cancer mediated T-cell activation in a concentration-dependent manner at nanomolar concentrations. For the trispecific antibody, this effect indeed proved to be dual antigen-restricted, as it could be blocked by prior incubation of either HLA-A2- or CD45-specific scFv and did not occur on single-positive (CD45+) or double-negative (HLA-A2- CD45-) target cells. Furthermore, antibodies from both approaches recruited T cells for tumour cell destruction in vitro.}, subject = {Immuntherapie}, language = {en} } @phdthesis{Liu2022, author = {Liu, Ruiqi}, title = {Dynamic regulation of the melanocortin 4 receptor system in body weight homeostasis and reproductive maturation in fish}, doi = {10.25972/OPUS-20653}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-206536}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2022}, abstract = {Puberty is an important period of life with physiological changes to enable animals to reproduce. Xiphophorus fish exhibit polymorphism in body size, puberty timing, and reproductive tactics. These phenotypical polymorphisms are controlled by the Puberty (P) locus. In X. nigrensis and X. multilineatus, the P locus encodes the melanocortin 4 receptor (Mc4r) with high genetic polymorphisms. Mc4r is a member of the melanocortin receptors, belonging to class A G-protein coupled receptors. The Mc4r signaling system consists of Mc4r, the agonist Pomc (precursor of various MSH and of ACTH), the antagonist Agrp and accessory protein Mrap2. In humans, MC4R has a role in energy homeostasis. MC4R and MRAP2 mutations are linked to human obesity but not to puberty. Mc4rs in X. nigrensis and X. multilineatus are present in three allele classes, A, B1 and B2, of which the X-linked A alleles express functional receptors and the male-specific Y-linked B alleles encode defective receptors. Male body sizes are correlated with B allele type and B allele copy numbers. Late-maturing large males carry B alleles in high copy number while early-maturing small males carry B alleles in low copy number or only A alleles. Cell culture co-expression experiments indicated that B alleles may act as dominant negative receptor mutants on A alleles. In this study, the main aim was to biochemically characterize the mechanism of puberty regulation by Mc4r in X. nigrensis and X. multilineatus, whether it is by Mc4r dimerization and/or Mrap2 interaction with Mc4r or other mechanisms. Furthermore, Mc4r in X. hellerii (another swordtail species) and medaka (a model organism phylogenetically close to Xiphophorus) were investigated to understand if the investigated mechanisms are conserved in other species. In medaka, the Mc4r signaling system genes (mc4r, mrap2, pomc, agrp1) are expressed before hatching, with agrp1 being highly upregulated during hatching and first feeding. These genes are mainly expressed in adult brain, and the transcripts of mrap2 co-localize with mc4r indicating a function in modulating Mc4r signaling. Functional comparison between wild-type and mc4r knockout medaka showed that Mc4r knockout does not affect puberty timing but significantly delays hatching due to the retarded embryonic development of knockout medaka. Hence, the Mc4r system in medaka is involved in regulation of growth rather than puberty. In Xiphophorus, expression co-localization of mc4r and mrap2 in X. nigrensis and X. hellerii fish adult brains was characterized by in situ hybridization. In both species, large males exhibit strikingly high expression of mc4r while mrap2 shows similar expression level in the large and small male and female. Differently, X. hellerii has only A-type alleles indicating that the puberty regulation mechanisms evolved independently in Xiphophorus genus. Functional analysis of Mrap2 and Mc4r A/B1/B2 alleles of X. multilineatus showed that increased Mrap2 amounts induce higher cAMP response but EC50 values do not change much upon Mrap2 co-expression with Mc4r (expressing only A allele or A and B1 alleles). A and B1 alleles were expressed higher in large male brains, while B2 alleles were only barely expressed. Mc4r A-B1 cells have lower cAMP production than Mc4r A cells. Together, this indicates a role of Mc4r alleles, but not Mrap2, in puberty onset regulation signaling. Interaction studies by FRET approach evidenced that Mc4r A and B alleles can form heterodimers and homodimers in vitro, but only for a certain fraction of the expressed receptors. Single-molecule colocalization study using super-resolution microscope dSTORM confirmed that only few Mc4r A and B1 receptors co-localized on the membrane. Altogether, the species-specific puberty onset regulation in X. nigrensis and X. multilineatus is linked to the presence of Mc4r B alleles and to some extent to its interaction with A allele gene products. This is reasoned to result in certain levels of cAMP signaling which reaches the dynamic or static threshold to permit late puberty in large males. In summary, puberty onset regulation by dominant negative effect of Mc4r mutant alleles is a special mechanism that is found so far only in X. nigrensis and X. multilineatus. Other Xiphophorus species obviously evolved the same function of the pathway by diverse mechanisms. Mc4r in other fish (medaka) has a role in regulation of growth, reminiscent of its role in energy homeostasis in humans. The results of this study will contribute to better understand the biochemical and physiological functions of the Mc4r system in vertebrates including human.}, subject = {Japank{\"a}rpfling}, language = {en} } @phdthesis{Thom2002, author = {Thom, Corinna}, title = {Dynamics and Communication Structures of Nectar Foraging in Honey Bees (Apis mellifera)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-3601}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {In this thesis, I examined honey bee nectar foraging with emphasis on the communication system. To document how a honey bee colony adjusts its daily nectar foraging effort, I observed a random sample of individually marked workers during the entire day, and then estimated the number and activity of all nectar foragers in the colony. The total number of active nectar foragers in a colony changed frequently between days. Foraging activity did not usually change between days. A honey bee colony adjusts its daily foraging effort by changing the number of its nectar foragers rather than their activity. I tested whether volatiles produced by a foraging colony activated nectar foragers of a non-foraging colony by connecting with a glass tube two colonies. Each colony had access to a different green house. In 50\% of all experiments, volatile substances from the foraging colony stimulated nectar foragers of the non-foraging colony to fly to an empty feeder. The results of this study show that honey bees can produce a chemical signal or cue that activates nectar foragers. However, more experiments are needed to establish the significance of the activating volatiles for the foraging communication system. The brief piping signal of nectar foragers inhibits forager recruitment by stopping waggle dances (Nieh 1993, Kirchner 1993). However, I observed that many piping signals (approximately 43\%) were produced off the dance floor, a restricted area in the hive where most waggle dances are performed. If the inhibition of waggle dances would be the only function of the brief piping signal, tremble dancers should produce piping signals mainly on the dance floor, where the probability to encounter waggle dancers is highest. To therefore investigate the piping signal in more detail, I experimentally established the foraging context of the brief piping signal, characterized its acoustic properties, and documented for the first time the unique behavior of piping nectar foragers by observing foragers throughout their entire stay in the hive. Piping nectar foragers usually began to tremble dance immediately upon their return into the hive, spent more time in the hive, more time dancing, had longer unloading latencies, and were the only foragers that sometimes unloaded their nectar directly into cells instead of giving it to a nectar receiver bee. Most of the brief piping signals (approximately 99\%) were produced by tremble dancers, yet not all tremble dancers (approximately 48\%) piped. This suggests that piping and tremble dancing have related, but not identical functions in the foraging system. Thus, the brief piping signals may not only inhibit forager recruitment, but have an additional function both on and off the dance floor. In particular, the piping signal might function 1. to stop the recruitment of additional nectar foragers, and 2. as a modulatory signal to alter the response threshold of signal receivers to the tremble dance. The observation that piping tremble dancers often did not experience long unloading delays before they started to dance gave rise to a question. A forager's unloading delay provides reliable information about the relative work capacities of nectar foragers and nectar receivers, because each returning forager unloads her nectar to a nectar receiver before she takes off for the next foraging trip. Queuing delays for either foragers or receivers lower foraging efficiency and can be eliminated by recruiting workers to the group in shortage. Short unloading delays indicate to the nectar forager a shortage of foragers and stimulate waggle dancing which recruits nectar foragers. Long unloading delays indicate a shortage of nectar receivers and stimulate tremble dancing which recruits nectar receivers (Seeley 1992, Seeley et al. 1996). Because the short unloading delays of piping tremble dancers indicated that tremble dancing can be elicited by other factors than long unloading delays, I tested whether a hive-external stimulus, the density of foragers at the food source, stimulated tremble dancing directly. The experiments show that tremble dancing can be caused directly by a high density of foragers at the food source and suggest that tremble dancing can be elicited by a decrease of foraging efficiency either inside (e.g. shortage of receiver bees) or outside (e.g. difficulty of loading nectar) the hive. Tremble dancing as a reaction to hive-external stimuli seems to occur under natural conditions and can thus be expected to have some adaptive significance. The results imply that if the hive-external factors that elicit tremble dancing do not indicate a shortage of nectar receiver bees in the hive, the function of the tremble dance may not be restricted to the recruitment of additional nectar receivers, but might be the inhibition or re-organization of nectar foraging.}, subject = {Bienen }, language = {en} } @phdthesis{Christensen2003, author = {Christensen, Morten Overby}, title = {Dynamics of human DNA Topoisomerases I and II}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-4927}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2003}, abstract = {The first goal of this study was to develop cell lines with a stable expression of bio-fluorescent topo II and topo I. This was successfully achieved using a bicistronic vector system. Control experiments showed that proteins of expected size were expressed, and that GFP-tagged topos I, IIa, and IIb were active in the cells and fully integrated in the endogenous pools of the enzymes. These cell-lines provided a novel tool for investigating the cell biology of human DNA topoisomerases. Our most important finding was, that both types of mammalian topoisomerases are entirely mobile proteins that are in continuous and rapid flux between all compartments of the nucleus and between the cytososl and the chromosomes of mitotic cells. This was particularly surprising with regard to topo II, which is considered to be a structural component of the nuclear matrix and the chromosome scaffold. We must conclude that if this was the case, then these architectural structures appear to be much more dynamic than believed until now. In this context it should also be mentioned, that the alignment of topo II with the central axes of the chromosome arms, which has until now been considered a hall-mark of the enzyme's association with the chromosomal scaffold, is not seen in vivo and can be demonstrated to be to some extent an artefact of immunohistochemistry. Furthermore, we show that the two isoforms of topo II (a and b) have a different localisation during mitotic cell division, supporting the general concept that topo II functions at mitosis are exclusively assigned to the a-form, whereas at interphase the two isoenzymes work in concert. Despite unrestricted mobility within the entire nuclear space, topoisomerases I and II impose as mostly nucleolar proteins. We show that this is due to the fact that in the nucleoli they are moving slower than in the nucleoplasm. The decreased nucleolar mobility cannot be due to DNA-interactions, because compounds that fix topoisomerases to the DNA deplete them from the nucleoli. Interestingly, the subnucleolar distribution of topoisomerases I and II was complementary. The type II enzyme filled the entire nucleolar space, but excluded the fibrial centers, whereas topo I accumulated at the fibrial centers, an allocation directed by the enzyme's N-terminus. During mitosis, it also mediates association with the nucleolar organising regions of the acrocentric chromosomes. Thus, topo I stays associated with the rDNA during the entire cell-cycle and consistently colocalizes there with RNA-polymerase I. Finally, we show that certain cancer drugs believed to act by stabilising covalent catalytic DNA-intermediates of topoisomerases, do indeed immobilize the enzymes in living cells. Interestingly, these drugs do not target topoisomerases in the nucleoli but only in the nucleoplasm.}, subject = {Mensch}, language = {en} }