@article{CoelhoKultimaCosteaetal.2018, author = {Coelho, Luis Pedro and Kultima, Jens Roat and Costea, Paul Igor and Fournier, Coralie and Pan, Yuanlong and Czarnecki-Maulden, Gail and Hayward, Matthew Robert and Forslund, Sofia K. and Schmidt, Thomas Sebastian Benedikt and Descombes, Patrick and Jackson, Janet R. and Li, Qinghong and Bork, Peer}, title = {Similarity of the dog and human gut microbiomes in gene content and response to diet}, series = {Microbiome}, volume = {6}, journal = {Microbiome}, doi = {10.1186/s40168-018-0450-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-223177}, year = {2018}, abstract = {Background Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs. Results We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies. Conclusions We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.}, language = {en} } @article{CoelhoAlvesMonteiroetal.2019, author = {Coelho, Luis Pedro and Alves, Renato and Monteiro, Paulo and Huerta-Cepas, Jaime and Freitas, Ana Teresa and Bork, Peer}, title = {NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language}, series = {Microbiome}, volume = {7}, journal = {Microbiome}, number = {84}, doi = {10.1186/s40168-019-0684-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-223161}, year = {2019}, abstract = {Background Shotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community. In order to understand these communities, bioinformatics methods are crucial. A common first step in processing metagenomes is to compute abundance estimates of different taxonomic or functional groups from the raw sequencing data. Given the breadth of the field, computational solutions need to be flexible and extensible, enabling the combination of different tools into a larger pipeline. Results We present NGLess and NG-meta-profiler. NGLess is a domain specific language for describing next-generation sequence processing pipelines. It was developed with the goal of enabling user-friendly computational reproducibility. It provides built-in support for many common operations on sequencing data and is extensible with external tools with configuration files. Using this framework, we developed NG-meta-profiler, a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling (taxonomic and functional). It is significantly faster than either MOCAT2 or htseq-count and (as it builds on NGLess) its results are perfectly reproducible. Conclusions NG-meta-profiler is a high-performance solution for metagenomics processing built on NGLess. It can be used as-is to execute standard analyses or serve as the starting point for customization in a perfectly reproducible fashion. NGLess and NG-meta-profiler are open source software (under the liberal MIT license) and can be downloaded from https://ngless.embl.de or installed through bioconda.}, 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{Classen2021, author = {Claßen, Alexandra}, title = {The ERK-cascade in the pathophysiology of cardiac hypertrophy}, doi = {10.25972/OPUS-22966}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229664}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2021}, abstract = {ERK1/2 are known key players in the pathophysiology of heart failure, but the members of the ERK cascade, in particular Raf1, can also protect the heart from cell death and ischemic injury. An additional autophosphorylation (ERK1 at Thr208, ERK2 at Thr188) empowers ERK1/2 translocation to the nucleus and phosphorylation of nuclear targets which take part in the development of cardiac hypertrophy. Thereby, targeting this additional phosphorylation is a promising pharmacological approach. In this thesis, an in silico model of ERK cascade in the cardiomyocyte is introduced. The model is a semi-quantitive model and its behavior was tested with different softwares (SQUAD and CellNetAnalyzer). Different phosphorylation states of ERK1/2 as well as different stimuli can be reproduced. The different types of stimuli include hypertrophic as well as non-hypertrophic stimuli. With the introduced in-silico model time courses and synergistic as well as antagonistic receptor stimuli combinations can be predicted. The simulated time courses were experimentally validated. SQUAD was mainly used to make predictions about time courses and thresholds, whereas CNA was used to analyze steady states and feedback loops. Furthermore, new targets of ERK1/2 which partially contribute, also in the formation of cardiac hypertrophy, were identified and the most promising of them were illuminated. Important further targets are Caspase 8, GAB2, Mxi-2, SMAD2, FHL2 and SPIN90. Cardiomyocyte gene expression data sets were analyzed to verify involved components and to find further significantly altered genes after induced hypertrophy with TAC (transverse aortic constriction). Changes in the ultrastructure of the cardiomyocyte are the final result of induced hypertrophy.}, subject = {Herzhypertrophie}, language = {en} } @article{ClaussWinklerLohmeyeretal.1990, author = {Clauss, Gerd and Winkler, Christoph and Lohmeyer, J{\"u}rgen and Anders, Fritz and Schartl, Manfred}, title = {Oncofetal antigen in Xiphophorus detected by monoclonal antibodies directed against melanoma-associated antigens}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-61784}, year = {1990}, abstract = {Monoclonal antlbodies (MAbs) directed against Xiphophorus melanoma cells were deve(oped and tested by lndirect immunofluorescence and Immunoperoxidase staining for reactivity with a panel of I 5 allogeneic tissues and 12 allogeneic cell llnes. The reactivity of such MAbs was restricted to melanoma cells from tumor biopsies and melanoma-derived cell lines. ln addition, all embryonie cells of all histiotypes from developmental stages later than mld·organogenesis and from corresponding short term in vitro cultures reacted with these MAbs. ln contrast, normal tissues and organs from adult fish dlsplayed no reactivity, thus implying that the melanoma-associated antigens detected by the MAbs described are oncofetal antigens.}, subject = {Physiologische Chemie}, language = {en} } @article{ClassenEardleyHempetal.2020, author = {Classen, Alice and Eardley, Connal D. and Hemp, Andreas and Peters, Marcell K. and Peters, Ralph S. and Ssymank, Axel and Steffan-Dewenter, Ingolf}, title = {Specialization of plant-pollinator interactions increases with temperature at Mt. Kilimanjaro}, series = {Ecology and Evolution}, volume = {10}, journal = {Ecology and Evolution}, number = {4}, doi = {10.1002/ece3.6056}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-235959}, pages = {2182-2195}, year = {2020}, abstract = {Aim: Species differ in their degree of specialization when interacting with other species, with significant consequences for the function and robustness of ecosystems. In order to better estimate such consequences, we need to improve our understanding of the spatial patterns and drivers of specialization in interaction networks. Methods: Here, we used the extensive environmental gradient of Mt. Kilimanjaro (Tanzania, East Africa) to study patterns and drivers of specialization, and robustness of plant-pollinator interactions against simulated species extinction with standardized sampling methods. We studied specialization, network robustness and other network indices of 67 quantitative plant-pollinator networks consisting of 268 observational hours and 4,380 plant-pollinator interactions along a 3.4 km elevational gradient. Using path analysis, we tested whether resource availability, pollinator richness, visitation rates, temperature, and/or area explain average specialization in pollinator communities. We further linked pollinator specialization to different pollinator taxa, and species traits, that is, proboscis length, body size, and species elevational ranges. Results: We found that specialization decreased with increasing elevation at different levels of biological organization. Among all variables, mean annual temperature was the best predictor of average specialization in pollinator communities. Specialization differed between pollinator taxa, but was not related to pollinator traits. Network robustness against simulated species extinctions of both plants and pollinators was lowest in the most specialized interaction networks, that is, in the lowlands. Conclusions: Our study uncovers patterns in plant-pollinator specialization along elevational gradients. Mean annual temperature was closely linked to pollinator specialization. Energetic constraints, caused by short activity timeframes in cold highlands, may force ectothermic species to broaden their dietary spectrum. Alternatively or in addition, accelerated evolutionary rates might facilitate the establishment of specialization under warm climates. Despite the mechanisms behind the patterns have yet to be fully resolved, our data suggest that temperature shifts in the course of climate change may destabilize pollination networks by affecting network architecture.}, language = {en} } @phdthesis{Claes2003, author = {Claes, Ellen}, title = {Einfluss funktionsloser Photorezeptoren auf die Anatomie der Retina - Eine licht- und elektronenmikroskopische Studie anhand der CNGA3-/-Rho-/- Maus}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-8181}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2003}, abstract = {Netzhauterkrankungen, wie Retinitis pigmentosa, sind in der Bev{\"o}lkerung weit verbreitet (1,5 Millionen weltweit). Gew{\"o}hnlich berichten die Betroffenen {\"u}ber Nachtblindheit und periphere Gesichtsfeldausf{\"a}lle. H{\"a}ufig f{\"u}hrt diese Erkrankung, die durch eine fortschreitende Degeneration von Photorezeptoren verursacht wird, zur vollst{\"a}ndigen Erblindung. Bisher beschrieb man den pathologischen Prozess vor allem an rd-M{\"a}usen. Allerdings setzt bei diesen die Degeneration sehr fr{\"u}h ein. Somit ist die {\"U}bertragbarkeit auf den Menschen erschwert, da abgesehen von wenigen Ausnahmen, der Verlust von Photorezeptoren hier erst im zweiten Lebensabschnitt beginnt. Deshalb war es interessant, im Rahmen dieser Arbeit anhand der CNGA3-/-Rho-/- Maus ein Modell zu untersuchen, das {\"a}hnlich dem menschlichen System, zun{\"a}chst eine intakte Morphologie zeigt. Dadurch war es m{\"o}glich eine genaue zeitliche Abfolge der Degeneration zu dokumentieren. Dies kann medizinisch zur Entwicklung eines Therapieansatzes genutzt werden, der bereits zu Beginn der Degeneration greift, und damit den fortlaufenden Prozess zum Stillstand bringen kann. Die CNGA3-/-Rho-/- Maus repr{\"a}sentiert ein System funktionsloser Photorezeptoren, bei dem der zyklische Nukleotid-Kanal (CNGA3) der Zapfenaußensegmente und das Rhodopsin (Rho) der St{\"a}bchenaußensegmente ausgeschaltet wurde. Best{\"a}tigt wurde dies durch ein Elektroretinogramm mit einer negativen Photoantwort bez{\"u}glich Zapfen und St{\"a}bchen. Die Degeneration f{\"u}hrt zu einem vollst{\"a}ndigen Verlust aller Photorezeptoren nach drei Monaten (Pm3). Zum Zeitpunkt Pw4 konnte, vergleichbar dem Wildtyp, eine intakte {\"a}ußere Retina nachgewiesen werden, bei der lediglich die {\"a}ußeren St{\"a}bchensegmente fehlen. Die synaptischen Kontakte zwischen den Terminalien der Photorezeptoren, der Horizontalzellen und Bipolarzelldendriten waren normal entwickelt und St{\"a}bchenendigungen als auch Zapfenendf{\"u}ßchen bildeten funktionelle Triaden aus. Bei den St{\"a}bchenendigungen konnte mit zunehmender Degeneration (Pw5, Pw6) eine Akkumulation synaptischer B{\"a}nder und postsynaptischer Elemente beobachtet werden. Im Zeitraum Pw4-7 zeigten sowohl die Zapfen, als auch die Horizontalzellen und St{\"a}bchen-Bipolarzellen, eine bemerkenswerte strukturelle Plastizit{\"a}t. Obwohl durch die Photorezeptoren kein Lichtsignal vermittelt wurde, konnten pr{\"a}synaptische Marker (bassoon) und postsynaptische Glutamatrezeptoren (GluR1, mGluR6) an den Photorezeptorterminalien nachgewiesen werden. Dies l{\"a}sst die Vermutung zu, dass eine Transmitterfreisetzung theoretisch m{\"o}glich w{\"a}re. Dar{\"u}ber hinaus konnte im Zeitraum von 12 Monaten keine nennenswerte Auswirkung auf die IPL beobachtet werden: Amakrin- und Zapfen-Bipolarzellen waren normal stratifiziert und die Expression der Transmitter-Rezeptoren zeigte ein charakteristisches Verteilungsmuster. Außerdem war die Ultrastruktur von konventionellen und Bandsynapsen der des Wildtyps vergleichbar. Dar{\"u}ber hinaus bildeten sowohl Amakrinzellen, als auch Bipolar- und Ganglienzellen, Forts{\"a}tze in die INL hinein. Allgemein zeigt die immunhistochemisch und ultrastrukturell untersuchte CNGA3-/-Rho-/- Maus, dass weder funktionell aktive Photorezeptoren noch Licht eine stimulierende Wirkung auf die Ausbildung synaptischer Strukturen und die Expression verschiedener Rezeptoren haben.}, subject = {Netzhaut}, language = {de} } @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} } @article{ChumduriTurco2021, author = {Chumduri, Cindrilla and Turco, Margherita Y.}, title = {Organoids of the female reproductive tract}, series = {Journal of Molecular Medicine}, volume = {99}, journal = {Journal of Molecular Medicine}, number = {4}, doi = {10.1007/s00109-020-02028-0}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-328374}, pages = {531-553}, year = {2021}, abstract = {Healthy functioning of the female reproductive tract (FRT) depends on balanced and dynamic regulation by hormones during the menstrual cycle, pregnancy and childbirth. The mucosal epithelial lining of different regions of the FRT—ovaries, fallopian tubes, uterus, cervix and vagina—facilitates the selective transport of gametes and successful transfer of the zygote to the uterus where it implants and pregnancy takes place. It also prevents pathogen entry. Recent developments in three-dimensional (3D) organoid systems from the FRT now provide crucial experimental models that recapitulate the cellular heterogeneity and physiological, anatomical and functional properties of the organ in vitro. In this review, we summarise the state of the art on organoids generated from different regions of the FRT. We discuss the potential applications of these powerful in vitro models to study normal physiology, fertility, infections, diseases, drug discovery and personalised medicine.}, language = {en} } @article{ChristopherDUgelvigWiesenhoferetal.2018, author = {Christopher D., Pull and Ugelvig, Line V. and Wiesenhofer, Florian and Anna V., Grasse and Tragust, Simon and Schmitt, Thomas and Brown, Mark JF and Cremer, Sylvia}, title = {Destructive disinfection of infected brood prevents systemic disease spread in ant colonies}, series = {eLIFE}, volume = {7}, journal = {eLIFE}, doi = {10.7554/eLife.32073}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-223728}, pages = {e 32073, 1-29}, year = {2018}, abstract = {In social groups, infections have the potential to spread rapidly and cause disease outbreaks. Here, we show that in a social insect, the ant Lasius neglectus, the negative consequences of fungal infections (Metarhizium brunneum) can be mitigated by employing an efficient multicomponent behaviour, termed destructive disinfection, which prevents further spread of the disease through the colony. Ants specifically target infected pupae during the pathogens non-contagious incubation period, utilising chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a metazoan body that specifically targets and eliminates infected cells, ants destroy infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, in an analogous fashion, the same principles of disease defence apply at different levels of biological organisation.}, 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} } @article{ChipperfieldDythamHovestadt2011, author = {Chipperfield, Joseph D. and Dytham, Calvin and Hovestadt, Thomas}, title = {An Updated Algorithm for the Generation of Neutral Landscapes by Spectral Synthesis}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-68938}, year = {2011}, abstract = {Background: Patterns that arise from an ecological process can be driven as much from the landscape over which the process is run as it is by some intrinsic properties of the process itself. The disentanglement of these effects is aided if it possible to run models of the process over artificial landscapes with controllable spatial properties. A number of different methods for the generation of so-called 'neutral landscapes' have been developed to provide just such a tool. Of these methods, a particular class that simulate fractional Brownian motion have shown particular promise. The existing methods of simulating fractional Brownian motion suffer from a number of problems however: they are often not easily generalisable to an arbitrary number of dimensions and produce outputs that can exhibit some undesirable artefacts. Methodology: We describe here an updated algorithm for the generation of neutral landscapes by fractional Brownian motion that do not display such undesirable properties. Using Monte Carlo simulation we assess the anisotropic properties of landscapes generated using the new algorithm described in this paper and compare it against a popular benchmark algorithm. Conclusion/Significance: The results show that the existing algorithm creates landscapes with values strongly correlated in the diagonal direction and that the new algorithm presented here corrects this artefact. A number of extensions of the algorithm described here are also highlighted: we describe how the algorithm can be employed to generate landscapes that display different properties in different dimensions and how they can be combined with an environmental gradient to produce landscapes that combine environmental variation at the local and macro scales.}, subject = {Landschaft}, language = {en} } @article{ChenMishraGlaessetal.2017, author = {Chen, Yi-chun and Mishra, Dushyant and Gl{\"a}ß, Sebastian and Gerber, Bertram}, title = {Behavioral Evidence for Enhanced Processing of the Minor Component of Binary Odor Mixtures in Larval Drosophila}, series = {Frontiers in Psychology}, volume = {8}, journal = {Frontiers in Psychology}, number = {1923}, doi = {10.3389/fpsyg.2017.01923}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170011}, year = {2017}, abstract = {A fundamental problem in deciding between mutually exclusive options is that the decision needs to be categorical although the properties of the options often differ but in grade. We developed an experimental handle to study this aspect of behavior organization. Larval Drosophila were trained such that in one set of animals odor A was rewarded, but odor B was not (A+/B), whereas a second set of animals was trained reciprocally (A/B+). We then measured the preference of the larvae either for A, or for B, or for "morphed" mixtures of A and B, that is for mixtures differing in the ratio of the two components. As expected, the larvae showed higher preference when only the previously rewarded odor was presented than when only the previously unrewarded odor was presented. For mixtures of A and B that differed in the ratio of the two components, the major component dominated preference behavior—but it dominated less than expected from a linear relationship between mixture ratio and preference behavior. This suggests that a minor component can have an enhanced impact in a mixture, relative to such a linear expectation. The current paradigm may prove useful in understanding how nervous systems generate discrete outputs in the face of inputs that differ only gradually.}, language = {en} } @article{ChenGerber2014, author = {Chen, Yi-chun and Gerber, Bertram}, title = {Generalization and discrimination tasks yield concordant measures of perceived distance between odours and their binary mixtures in larval Drosophila}, series = {The Journal of Experimental Biology}, volume = {217}, journal = {The Journal of Experimental Biology}, number = {12}, doi = {10.1242/jeb.100966}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-121625}, pages = {2071-7}, year = {2014}, abstract = {Similarity between odours is notoriously difficult to measure. Widely used behavioural approaches in insect olfaction research are cross-adaptation, masking, as well as associative tasks based on olfactory learning and the subsequent testing for how specific the established memory is. A concern with such memory-based approaches is that the learning process required to establish an odour memory may alter the way the odour is processed, such that measures of perception taken at the test are distorted. The present study was therefore designed to see whether behavioural judgements of perceptual distance are different for two different memory-based tasks, namely generalization and discrimination. We used odour-reward learning in larval Drosophila as a study case. In order to challenge the larvae's olfactory system, we chose to work with binary mixtures and their elements (1-octanol, n-amyl acetate, 3-octanol, benzaldehyde and hexyl acetate). We determined the perceptual distance between each mixture and its elements, first in a generalization task, and then in a discrimination task. It turns out that scores of perceptual distance are correlated between both tasks. A re-analysis of published studies looking at element-to-element perceptual distances in larval reward learning and in adult punishment learning confirms this result. We therefore suggest that across a given set of olfactory stimuli, associative training does not grossly alter the pattern of perceptual distances.}, language = {en} } @phdthesis{Chen2012, author = {Chen, Yi-chun}, title = {Experimental access to the content of an olfactory memory trace in larval Drosophila}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-83705}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2012}, abstract = {Animals need to evaluate their experiences in order to cope with new situations they encounter. This requires the ability of learning and memory. Drosophila melanogaster lends itself as an animal model for such research because elaborate genetic techniques are available. Drosphila larva even saves cellular redundancy in parts of its nervous system. My Thesis has two parts dealing with associative olfactory learning in larval Drosophila. Firstly, I tackle the question of odour processing in respect to odour quality and intensity. Secondly, by focusing on the evolutionarily conserved presynaptic protein Synapsin, olfactory learning on the cellular and molecular level is investigated. Part I.1. provides a behaviour-based estimate of odour similarity in larval Drosophila by using four recognition-type experiments to result in a combined, task-independent estimate of perceived difference between odour-pairs. A further comparison of these combined perceived differences to published calculations of physico-chemical difference reveals a weak correlation between perceptual and physico-chemical similarity. Part I.2. focuses on how odour intensity is interpreted in the process of olfactory learning in larval Drosophila. First, the dose-effect curves of learnability across odour intensities are described in order to choose odour intensities such that larvae are trained at intermediate odour intensity, but tested for retention either with that trained intermediate odour intensity, or with respectively HIGHer or LOWer intensities. A specificity of retention for the trained intensity is observed for all the odours used. Such intensity specificity of learning adds to appreciate the richness in 'content' of olfactory memory traces, and to define the demands on computational models of associative olfactory memory trace formation. In part II.1. of the thesis, the cellular site and molecular mode of Synapsin function is investigated- an evolutionarily conserved, presynaptic vesicular phosphoprotein. On the cellular level, the study shows a Synapsin-dependent memory trace in the mushroom bodies, a third-order "cortical" brain region of the insects; on the molecular level, Synapsin engages as a downstream element of the AC-cAMP-PKA signalling cascade.}, subject = {Taufliege}, language = {en} } @article{ChenReiherHermannLuibletal.2016, author = {Chen, Jiangtian and Reiher, Wencke and Hermann-Luibl, Christiane and Sellami, Azza and Cognigni, Paola and Kondo, Shu and Helfrich-F{\"o}rster, Charlotte and Veenstra, Jan A. and Wegener, Christian}, title = {Allatostatin A Signalling in Drosophila Regulates Feeding and Sleep and Is Modulated by PDF}, series = {PLoS Genetics}, volume = {12}, journal = {PLoS Genetics}, number = {9}, doi = {10.1371/journal.pgen.1006346}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178170}, year = {2016}, abstract = {Feeding and sleep are fundamental behaviours with significant interconnections and cross-modulations. The circadian system and peptidergic signals are important components of this modulation, but still little is known about the mechanisms and networks by which they interact to regulate feeding and sleep. We show that specific thermogenetic activation of peptidergic Allatostatin A (AstA)-expressing PLP neurons and enteroendocrine cells reduces feeding and promotes sleep in the fruit fly Drosophila. The effects of AstA cell activation are mediated by AstA peptides with receptors homolog to galanin receptors subserving similar and apparently conserved functions in vertebrates. We further identify the PLP neurons as a downstream target of the neuropeptide pigment-dispersing factor (PDF), an output factor of the circadian clock. PLP neurons are contacted by PDF-expressing clock neurons, and express a functional PDF receptor demonstrated by cAMP imaging. Silencing of AstA signalling and continuous input to AstA cells by tethered PDF changes the sleep/activity ratio in opposite directions but does not affect rhythmicity. Taken together, our results suggest that pleiotropic AstA signalling by a distinct neuronal and enteroendocrine AstA cell subset adapts the fly to a digestive energy-saving state which can be modulated by PDF.}, language = {en} } @phdthesis{Chen2018, author = {Chen, Jiangtian}, title = {Functions of allatostatin A (AstA) and myoinhibitory peptides (MIPs) in the regulation of food intake and sleep in Drosophila}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156838}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {Neuropeptides and peptide hormones carrying neural or physiological information are intercellular signalling substances. They control most if not all biological processes in vertebrates and invertebrates by acting on specific receptors on the target cell. In mammals, many different neuropeptides and peptide hormones are involved in the regulation of feeding and sleep. In \textit{Drosophila}, allatostatin A (AstA) and myoinhibitory peptides (MIPs) are brain-gut peptides. The AstA receptors are homologues of the mammalian galanin receptors and the amino acid sequences of MIPs are similar to a part of galanin, which has an orexigenic effect and is implicated in the control of sleep behaviour in mammals. I am interested in dissecting pleiotropic functions of AstA and MIPs in the regulation of food intake and sleep in \textit{Drosophila}. \par In the first part of the dissertation the roles of brain-gut peptide allatostatin A are analysed. Due to the genetic and molecular tools available, the fruit fly \textit{Drosophila melanogaster} is chosen to investigate functions of AstA. The aims in this part are to identify pleiotropic functions of AstA and assign specific effects to the activity of certain subsets of AstA expressing cells in \textit{Drosophila} adults. A new and restricted \textit{AstA\textsuperscript{34}-Gal4} line was generated. The confocal imaging result showed that AstA neurons are located in the posterior lateral protocerebrum (PLP), the gnathal ganglia (GNG), the medullae, and thoracic-abdominal ganglion (TAG). AstA producing DLAa neurons in the TAG innervate hindgut and the poterior part of midgut. In addition, AstA are detected in the enteroendocrine cells (EECs).\par Thermogenetic activation and neurogenetic silencing tools with the aid of the \textit{UAS/Gal4} system were employed to manipulate the activity of all or individual subsets of AstA cells and investigate the effects on food intake, locomotor activity and sleep. Our experimental results showed that thermogenetic activation of two pairs of PLP neurons and/or AstA expressing EECs reduced food intake, which can be traced to AstA signalling by using \textit{AstA} mutants. In the locomotor activity, thermogenetic activation of two pairs of PLP neurons and/or AstA expressing EECs resulted in strongly inhibited locomotor activity and promoted sleep without sexual difference, which was most apparent during the morning and evening activity peaks. The experimental and control flies were not impaired in climbing ability. In contrast, conditional silencing of the PLP neurons and/or AstA expressing EECs reduced sleep specifically in the siesta. The arousal experiment was employed to test for the sleep intensity. Thermogenetically activated flies walked significantly slower and a shorter distance than controls for all arousal stimulus intensities. Furthermore, PDF receptor was detected in the PLP neurons and the PLP neurons reacted with an intracellular increase of cAMP upon PDF, only when PDF receptor was present. Constitutive activation of AstA cells by tethered PDF increased sleep and thermogenetic activation of the PDF producing sLNvs promoted sleep specifically in the morning and evening. \par The study shows that the PLP neurons and/or EECs vis AstA signalling subserve an anorexigenic and sleep-regulating function in \textit{Drosophila}. The PLP neurons arborise in the posterior superior protocerebrum, where the sleep relevant dopaminergic neurons are located, and EECs extend themselves to reach the gut lumen. Thus, the PLP neurons are well positioned to regulate sleep and EECs potentially modulate feeding and possibly locomotor activity and sleep during sending the nutritional information from the gut to the brain. The results of imaging, activation of the PDF signalling pathway by tethered PDF and thermoactivation of PDF expressing sLNvs suggest that the PLP neurons are modulated by PDF from sLNv clock neurons and AstA in PLP neurons is the downstream target of the central clock to modulate locomotor activity and sleep. AstA receptors are homologues of galanin receptors and both of them are involved in the regulation of feeding and sleep, which appears to be conserved in evolutionary aspect.\par In the second part of the dissertation, I analysed the role of myoinhibitory peptides. MIPs are brain-gut peptides in insects and polychaeta. Also in \textit{Drosophila}, MIPs are expressed in the CNS and EECs in the gut. Previous studies have demonstrated the functions of MIPs in the regulation of food intake, gut motility and ecdysis in moths and crickets. Yet, the functions of MIPs in the fruit fly are little known. To dissect effects of MIPs regarding feeding, locomotor activity and sleep in \textit{Drosophila melanogater}, I manipulated the activity of MIP\textsuperscript{W{\"U}} cells by using newly generated \textit{Mip\textsuperscript{W{\"U}}-Gal4} lines. Thermogenetical activation or genetical silencing of MIP\textsuperscript{W{\"U}} celles did not affect feeding behaviour and resulted in changes in the sleep status. \par My results are in contradiction to a recent research of Min Soohong and colleagues who demonstrated a role of MIPs in the regulation of food intake and body weight in \textit{Drosophila}. They showed that constitutive silencing of MIP\textsuperscript{KR} cells increased food intake and body weight, whereas thermogenetic activation of MIP\textsuperscript{KR} cells decreased food intake and body weight by using \textit{Mip\textsuperscript{KR}-Gal4} driver. Then I repeated the experiments with the \textit{Mip\textsuperscript{KR}-Gal4} driver, but could not reproduce the results. Interestingly, I just observed the opposite phenotype. When MIP\textsuperscript{KR} cells were silenced by expressing UAS-tetanus toxin (\textit{UAS-TNT}), the \textit{Mip\textsuperscript{KR}\$>\$TNT} flies showed reduced food intake. The thermogenetic activation of MIP\textsuperscript{KR} cells did not affect food intake. Furthermore, I observed that the thermogenetic activation of MIP\textsuperscript{KR} cells strongly reduced the sleep duration.\par In the third part of the dissertation, I adapted and improved a method for metabolic labelling for \textit{Drosophila} peptides to quantify the relative amount of peptides and the released peptides by mass spectrometry under different physiological and behavioural conditions. qRT-PCR is a practical technique to measure the transcription and the corresponding mRNA level of a given peptide. However, this is not the only way to measure the translation and production of peptides. Although the amount of peptides can be quantified by mass spectrometry, it is not possible to distinguish between peptides stored in vesicles and released peptides in CNS extracts. I construct an approach to assess the released peptides, which can be calculated by comparing the relative amount of peptides between two timepoints in combination with the mRNA levels which can be used as semiquantitative proxy reflecting the production of peptides during this period. \par After optimizing the protocol for metabolic labelling, I carried out a quantitative analysis of peptides before and after eclosion as a test. I was able to show that the EH- and SIFa-related peptides were strongly reduced after eclosion. This is in line with the known function and release of EH during eclosion. Since this test was positive, I next used the metabolic labelling in \textit{Drosophila} adult, which were either fed \textit{ad libitum} or starved for 24 hrs, and analysed the effects on the amount of AstA and MIPs. In the mRNA level, my results showed that in the brain \textit{AstA} mRNA level in the 24 hrs starved flies was increased compared to in the \textit{ad libitum} fed flies, whereas in the gut the \textit{AstA} mRNA level was decreased. Starvation induced the reduction of \textit{Mip} mRNA level in the brain and gut. Unfortunately, due to technical problems I was unable to analyse the metabolic labelled peptides during the course of this thesis.\par}, subject = {AstA}, language = {en} } @phdthesis{Chan2002, author = {Chan, Gordon}, title = {The Role of Vav-1, Vav-2 and Lsc in NK T cell development and NK cell cytotoxicity}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-3645}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {The hematopoietic-specific Rho-family GTP exchange factor (GEF) Vav-1 is a regulator of lymphocyte antigen receptor signaling and mediates normal maturation and activation of B and T cells. Recent findings suggest that Vav-1 also forms part of signaling pathways required for natural and antibody dependent cellular cytotoxicity (ADCC) of human NK cells. In this study, I show that Vav-1 is also expressed in murine NK cells. Vav-1-/- mice had normal numbers of splenic NK cells, and these displayed a similar expression profile of NK cell receptors as cells from wild type mice. Unexpectedly, IL-2-activated Vav-1-/- NK cells retained normal ADCC. Fc-receptor mediated activation of ERK, JNK, and p38 was also normal. In contrast, Vav-1-/- NK cells exhibited reduced natural cytotoxicity against EL4, C4.4.25, RMA and RMA/S. Together, these results demonstrate that Vav-1 is dispensable for mainstream NK cell development, but is required for NK cell natural cytotoxicity. Vav-2, a protein homologous to Vav-1 has also been implicated in NK cell functions. However, NK cells from Vav-2-/- mice have normal cytotoxic activities and NK cells that lack both Vav-1 and Vav-2 exhibit similar defect as Vav-1-/- cells. Thus Vav-2 has no apparent function in the development and the activation of NK cells. Although NK cell development is normal in Vav-1-/- mice, their numbers of NKT cells were dramatically diminished. Furthermore, NKT cells from Vav-1 mutant mice failed to produce IL-4 and IFNg following in vivo CD3 stimulation. A similar loss of NKT cells was observed in Vav-1-/-Vav-2-/- mice, but not in Vav-2-/- mice, suggesting that only Vav-1, and not Vav-2, is an essential regulator of NKT cell development and NK cell cytotoxicity. Similar to Vav-1, Lsc is a Rho GEF that is expressed specifically in the hematopoietic system. It contains a regulator of G-protein signaling (RGS) domain which negatively regulates the Ga12 and Ga13 subunits of G-protein coupled receptors (GPCRs). This study shows that NK and NKT cell development are normal in Lsc-/- mice. However, NK cells from mutant mice display enhanced cytotoxic responses towards a panel of tumor cells. These data implicate for the first time a RGS-containing Rho GEF in cytotoxic responses and suggest that Lsc down-modulate NK cell activation.}, subject = {Maus}, language = {en} } @phdthesis{Chaidir2002, author = {Chaidir,}, title = {Insektizide Rocaglamid-Derivate und Verwandte Verbindungen aus Aglaia-Arten (Meliaceae)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-647}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2002}, abstract = {Auf der Suche nach neuen biologisch aktiven Naturstoffe aus der Gattung Aglaia(Meliaceae) wurde die insektizide Wirkung von Methanol-Extrakten verschiedener Aglaia-Arten gegen{\"u}ber frisch geschl{\"u}pften Raupen des Schadinsektes Spodoptera littoralis (Noctuidae) untersucht. Die getesteten Proben stammen aus Vietnam und S{\"u}dchina. Aus den in diesem Bioscreening aufgefallenen Extrakten wurden mit Hilfe von durch Biotests begleiteter Fraktionierung sowie parallel durchgef{\"u}hrten chemisch-physikalischen Analysen insgesamt 29 Naturstoffe isoliert und charakterisiert. Darunter befinden sich sechs bisher nicht beschriebene Benzofurane (Rocaglamide), zwei Benzopyrane (je ein Aglain und ein Aglaforbesin), zwei Benzoxepine (Forbagline) sowie ein Zimts{\"a}ure-Putrescin-Bisamid. Die Strukturaufkl{\"a}rung erfolgte vor allem durch NMR-Spektroskopie (darunter 2D-Experimente wie H-H-COSY, HMQC, HMBC und ROESY) sowie durch Massenspektrometrie. Die Untersuchungen zur Struktur-Wirkungs-Beziehung ergaben f{\"u}r die Rocaglamide V, Z und AA eine starke insektizide Aktivit{\"a}t gegen{\"u}ber Raupen von S. littoralis mit LC50- und EC50-Werten von 2.0 bis 6.6 ppm bzw. 0.1 bis 1.0 ppm, w{\"a}hrend die Rocaglamide X und Y {\"u}berraschenderweise keine Aktivit{\"a}t zeigten. Letztere stellen bisher die ersten Beispiele f{\"u}r biologisch inaktive Rocaglamid-Derivate {\"u}berhaupt dar. Dieser Befund weist darauf hin, daß f{\"u}r die insektizide Aktivit{\"a}t dieser Verbindungs-Klasse der Hydroxyl-Substituent am C-8b neben dem Benzofuran-Grundk{\"o}rper eine entscheidende Rolle spielt, da eine Alkoxylierung an C-8b zum vollst{\"a}ndigen Verlust der Aktivit{\"a}t f{\"u}hrt. In einem Screening mit drei verschiedenen basalen Medien, die mit unterschiedlichen Phytohormonen und organischen Zus{\"a}tzen versetzt worden waren, erwies sich das RW-(Risser und White) Medium mit 1 mg/l 2.4-D, 0.2 mg/l BAP, 0.1 g/l Ascorbins{\"a}ure und 0.5 g/l Caseinhydrolysat als geeignetstes Kulturmedium zur Kalusbildung bei Aglaia-Arten. Die Vorversuche zeigten dar{\"u}ber hinaus deutlich, daß Kalluskulturen von Aglaia elliptica in der Lage sind, relevante Inhaltsstoffe wie das Zimts{\"a}ure-Pyrrolidin-Bisamid- Derivat zu bilden.}, subject = {Aglaia}, language = {de} } @article{ChaianunpornHovestadt2022, author = {Chaianunporn, Thotsapol and Hovestadt, Thomas}, title = {Emergence of spatially structured populations by area-concentrated search}, series = {Ecology and Evolution}, volume = {12}, journal = {Ecology and Evolution}, number = {12}, doi = {10.1002/ece3.9528}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-311939}, year = {2022}, abstract = {The idea that populations are spatially structured has become a very powerful concept in ecology, raising interest in many research areas. However, despite dispersal being a core component of the concept, it typically does not consider the movement behavior underlying any dispersal. Using individual-based simulations in continuous space, we explored the emergence of a spatially structured population in landscapes with spatially heterogeneous resource distribution and with organisms following simple area-concentrated search (ACS); individuals do not, however, perceive or respond to any habitat attributes per se but only to their foraging success. We investigated the effects of different resource clustering pattern in landscapes (single large cluster vs. many small clusters) and different resource density on the spatial structure of populations and movement between resource clusters of individuals. As results, we found that foraging success increased with increasing resource density and decreasing number of resource clusters. In a wide parameter space, the system exhibited attributes of a spatially structured populations with individuals concentrated in areas of high resource density, searching within areas of resources, and "dispersing" in straight line between resource patches. "Emigration" was more likely from patches that were small or of low quality (low resource density), but we observed an interaction effect between these two parameters. With the ACS implemented, individuals tended to move deeper into a resource cluster in scenarios with moderate resource density than in scenarios with high resource density. "Looping" from patches was more likely if patches were large and of high quality. Our simulations demonstrate that spatial structure in populations may emerge if critical resources are heterogeneously distributed and if individuals follow simple movement rules (such as ACS). Neither the perception of habitat nor an explicit decision to emigrate from a patch on the side of acting individuals is necessary for the emergence of such spatial structure.}, language = {en} }