@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} } @article{AmatobiOzbekUnalSchaebleretal.2023, author = {Amatobi, Kelechi M. and Ozbek-Unal, Ayten Gizem and Sch{\"a}bler, Stefan and Deppisch, Peter and Helfrich-F{\"o}rster, Charlotte and Mueller, Martin J. and Wegener, Christian and Fekete, Agnes}, title = {The circadian clock is required for rhythmic lipid transport in Drosophila in interaction with diet and photic condition}, series = {Journal of Lipid Research}, volume = {64}, journal = {Journal of Lipid Research}, number = {10}, doi = {10.1016/j.jlr.2023.100417}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-349961}, pages = {100417}, year = {2023}, abstract = {Modern lifestyle is often at odds with endogenously driven rhythmicity, which can lead to circadian disruption and metabolic syndrome. One signature for circadian disruption is a reduced or altered metabolite cycling in the circulating tissue reflecting the current metabolic status. Drosophila is a well-established model in chronobiology, but day-time dependent variations of transport metabolites in the fly circulation are poorly characterized. Here, we sampled fly hemolymph throughout the day and analyzed diacylglycerols (DGs), phosphoethanolamines (PEs) and phosphocholines (PCs) using LC-MS. In wild-type flies kept on sugar-only medium under a light-dark cycle, all transport lipid species showed a synchronized bimodal oscillation pattern with maxima at the beginning and end of the light phase which were impaired in period01 clock mutants. In wild-type flies under constant dark conditions, the oscillation became monophasic with a maximum in the middle of the subjective day. In strong support of clock-driven oscillations, levels of the targeted lipids peaked once in the middle of the light phase under time-restricted feeding independent of the time of food intake. When wild-type flies were reared on full standard medium, the rhythmic alterations of hemolymph lipid levels were greatly attenuated. Our data suggest that the circadian clock aligns daily oscillations of DGs, PEs, and PCs in the hemolymph to the anabolic siesta phase, with a strong influence of light on phase and modality.}, language = {en} } @article{SchuhmannScheiner2023, author = {Schuhmann, Antonia and Scheiner, Ricarda}, title = {A combination of the frequent fungicides boscalid and dimoxystrobin with the neonicotinoid acetamiprid in field-realistic concentrations does not affect sucrose responsiveness and learning behavior of honeybees}, series = {Ecotoxicology and Environmental Safety}, volume = {256}, journal = {Ecotoxicology and Environmental Safety}, doi = {10.1016/j.ecoenv.2023.114850}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-350047}, year = {2023}, abstract = {The increasing loss of pollinators over the last decades has become more and more evident. Intensive use of plant protection products is one key factor contributing to this decline. Especially the mixture of different plant protection products can pose an increased risk for pollinators as synergistic effects may occur. In this study we investigated the effect of the fungicide Cantus® Gold (boscalid/dimoxystrobin), the neonicotinoid insecticide Mospilan® (acetamiprid) and their mixture on honeybees. Since both plant protection products are frequently applied sequentially to the same plants (e.g. oilseed rape), their combination is a realistic scenario for honeybees. We investigated the mortality, the sucrose responsiveness and the differential olfactory learning performance of honeybees under controlled conditions in the laboratory to reduce environmental noise. Intact sucrose responsiveness and learning performance are of pivotal importance for the survival of individual honeybees as well as for the functioning of the entire colony. Treatment with two sublethal and field relevant concentrations of each plant protection product did not lead to any significant effects on these behaviors but affected the mortality rate. However, our study cannot exclude possible negative sublethal effects of these substances in higher concentrations. In addition, the honeybee seems to be quite robust when it comes to effects of plant protection products, while wild bees might be more sensitive. Highlights • Mix of SBI fungicides and neonicotinoids can lead to synergistic effects for bees. • Combination of non-SBI fungicide and neonicotinoid in field-realistic doses tested. • Synergistic effect on mortality of honeybees. • No effects on sucrose responsiveness and learning performance of honeybees. • Synergistic effects by other pesticide mixtures or on wild bees cannot be excluded.}, 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} } @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{DedukhDaCruzKneitzetal.2022, author = {Dedukh, Dmitrij and Da Cruz, Irene and Kneitz, Susanne and Marta, Anatolie and Ormanns, Jenny and Tichop{\´a}d, Tom{\´a}š and Lu, Yuan and Alsheimer, Manfred and Janko, Karel and Schartl, Manfred}, title = {Achiasmatic meiosis in the unisexual Amazon molly, Poecilia formosa}, series = {Chromosome Research}, volume = {30}, journal = {Chromosome Research}, number = {4}, doi = {10.1007/s10577-022-09708-2}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325128}, pages = {443-457}, year = {2022}, abstract = {Unisexual reproduction, which generates clonal offspring, is an alternative strategy to sexual breeding and occurs even in vertebrates. A wide range of non-sexual reproductive modes have been described, and one of the least understood questions is how such pathways emerged and how they mechanistically proceed. The Amazon molly, Poecilia formosa, needs sperm from males of related species to trigger the parthenogenetic development of diploid eggs. However, the mechanism, of how the unreduced female gametes are produced, remains unclear. Cytological analyses revealed that the chromosomes of primary oocytes initiate pachytene but do not proceed to bivalent formation and meiotic crossovers. Comparing ovary transcriptomes of P. formosa and its sexual parental species revealed expression levels of meiosis-specific genes deviating from P. mexicana but not from P. latipinna. Furthermore, several meiosis genes show biased expression towards one of the two alleles from the parental genomes. We infer from our data that in the Amazon molly diploid oocytes are generated by apomixis due to a failure in the synapsis of homologous chromosomes. The fact that this failure is not reflected in the differential expression of known meiosis genes suggests the underlying molecular mechanism may be dysregulation on the protein level or misexpression of a so far unknown meiosis gene, and/or hybrid dysgenesis because of compromised interaction of proteins from diverged genomes.}, language = {en} } @article{RoesslerGrobFleischmann2023, author = {R{\"o}ssler, Wolfgang and Grob, Robin and Fleischmann, Pauline N.}, title = {The role of learning-walk related multisensory experience in rewiring visual circuits in the desert ant brain}, series = {Journal of Comparative Physiology A}, volume = {209}, journal = {Journal of Comparative Physiology A}, number = {4}, doi = {10.1007/s00359-022-01600-y}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325096}, pages = {605-623}, year = {2023}, abstract = {Efficient spatial orientation in the natural environment is crucial for the survival of most animal species. Cataglyphis desert ants possess excellent navigational skills. After far-ranging foraging excursions, the ants return to their inconspicuous nest entrance using celestial and panoramic cues. This review focuses on the question about how na{\"i}ve ants acquire the necessary spatial information and adjust their visual compass systems. Na{\"i}ve ants perform structured learning walks during their transition from the dark nest interior to foraging under bright sunlight. During initial learning walks, the ants perform rotational movements with nest-directed views using the earth's magnetic field as an earthbound compass reference. Experimental manipulations demonstrate that specific sky compass cues trigger structural neuronal plasticity in visual circuits to integration centers in the central complex and mushroom bodies. During learning walks, rotation of the sky-polarization pattern is required for an increase in volume and synaptic complexes in both integration centers. In contrast, passive light exposure triggers light-spectrum (especially UV light) dependent changes in synaptic complexes upstream of the central complex. We discuss a multisensory circuit model in the ant brain for pathways mediating structural neuroplasticity at different levels following passive light exposure and multisensory experience during the performance of learning walks.}, language = {en} } @article{FrickeRedlichZhangetal.2022, author = {Fricke, Ute and Redlich, Sarah and Zhang, Jie and Tobisch, Cynthia and Rojas-Botero, Sandra and Benjamin, Caryl S. and Englmeier, Jana and Ganuza, Cristina and Riebl, Rebekka and Uhler, Johannes and Uphus, Lars and Ewald, J{\"o}rg and Kollmann, Johannes and Steffan-Dewenter, Ingolf}, title = {Plant richness, land use and temperature differently shape invertebrate leaf-chewing herbivory on plant functional groups}, series = {Oecologia}, volume = {199}, journal = {Oecologia}, number = {2}, doi = {10.1007/s00442-022-05199-4}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325079}, pages = {407-417}, year = {2022}, abstract = {Higher temperatures can increase metabolic rates and carbon demands of invertebrate herbivores, which may shift leaf-chewing herbivory among plant functional groups differing in C:N (carbon:nitrogen) ratios. Biotic factors influencing herbivore species richness may modulate these temperature effects. Yet, systematic studies comparing leaf-chewing herbivory among plant functional groups in different habitats and landscapes along temperature gradients are lacking. This study was conducted on 80 plots covering large gradients of temperature, plant richness and land use in Bavaria, Germany. We investigated proportional leaf area loss by chewing invertebrates ('herbivory') in three plant functional groups on open herbaceous vegetation. As potential drivers, we considered local mean temperature (range 8.4-18.8 °C), multi-annual mean temperature (range 6.5-10.0 °C), local plant richness (species and family level, ranges 10-51 species, 5-25 families), adjacent habitat type (forest, grassland, arable field, settlement), proportion of grassland and landscape diversity (0.2-3 km scale). We observed differential responses of leaf-chewing herbivory among plant functional groups in response to plant richness (family level only) and habitat type, but not to grassland proportion, landscape diversity and temperature—except for multi-annual mean temperature influencing herbivory on grassland plots. Three-way interactions of plant functional group, temperature and predictors of plant richness or land use did not substantially impact herbivory. We conclude that abiotic and biotic factors can assert different effects on leaf-chewing herbivory among plant functional groups. At present, effects of plant richness and habitat type outweigh effects of temperature and landscape-scale land use on herbivory among legumes, forbs and grasses.}, language = {en} } @article{ZupancRoessler2022, author = {Zupanc, G{\"u}nther K. H. and R{\"o}ssler, Wolfgang}, title = {Government funding of research beyond biomedicine: challenges and opportunities for neuroethology}, series = {Journal of Comparative Physiology A}, volume = {208}, journal = {Journal of Comparative Physiology A}, number = {3}, doi = {10.1007/s00359-022-01552-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325113}, pages = {443-456}, year = {2022}, abstract = {Curiosity-driven research is fundamental for neuroethology and depends crucially on governmental funding. Here, we highlight similarities and differences in funding of curiosity-driven research across countries by comparing two major funding agencies—the National Science Foundation (NSF) in the United States and the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG). We interviewed representatives from each of the two agencies, focusing on general funding trends, levels of young investigator support, career-life balance, and international collaborations. While our analysis revealed a negative trend in NSF funding of biological research, including curiosity-driven research, German researchers in these areas have benefited from a robust positive trend in DFG funding. The main reason for the decrease in curiosity-driven research in the US is that the NSF has only partially been able to compensate for the funding gap resulting from the National Institutes of Health restricting their support to biomedical research using select model organisms. Notwithstanding some differences in funding programs, particularly those relevant for scientists in the postdoctoral phase, both the NSF and DFG clearly support curiosity-driven research.}, language = {en} } @article{EnglmeierMitesserBenbowetal.2023, author = {Englmeier, Jana and Mitesser, Oliver and Benbow, M. Eric and Hothorn, Torsten and von Hoermann, Christian and Benjamin, Caryl and Fricke, Ute and Ganuza, Cristina and Haensel, Maria and Redlich, Sarah and Riebl, Rebekka and Rojas Botero, Sandra and Rummler, Thomas and Steffan-Dewenter, Ingolf and Stengel, Elisa and Tobisch, Cynthia and Uhler, Johannes and Uphus, Lars and Zhang, Jie and M{\"u}ller, J{\"o}rg}, title = {Diverse effects of climate, land use, and insects on dung and carrion decomposition}, series = {Ecosystems}, volume = {26}, journal = {Ecosystems}, number = {2}, issn = {1432-9840}, doi = {10.1007/s10021-022-00764-7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325064}, pages = {397-411}, year = {2023}, abstract = {Land-use intensification and climate change threaten ecosystem functions. A fundamental, yet often overlooked, function is decomposition of necromass. The direct and indirect anthropogenic effects on decomposition, however, are poorly understood. We measured decomposition of two contrasting types of necromass, rat carrion and bison dung, on 179 study sites in Central Europe across an elevational climate gradient of 168-1122 m a.s.l. and within both local and regional land uses. Local land-use types included forest, grassland, arable fields, and settlements and were embedded in three regional land-use types (near-natural, agricultural, and urban). The effects of insects on decomposition were quantified by experimental exclusion, while controlling for removal by vertebrates. We used generalized additive mixed models to evaluate dung weight loss and carrion decay rate along elevation and across regional and local land-use types. We observed a unimodal relationship of dung decomposition with elevation, where greatest weight loss occurred between 600 and 700 m, but no effects of local temperature, land use, or insects. In contrast to dung, carrion decomposition was continuously faster with both increasing elevation and local temperature. Carrion reached the final decomposition stage six days earlier when insect access was allowed, and this did not depend on land-use effect. Our experiment identified different major drivers of decomposition on each necromass form. The results show that dung and carrion decomposition are rather robust to local and regional land use, but future climate change and decline of insects could alter decomposition processes and the self-regulation of ecosystems.}, language = {en} } @article{ShirakashiSisarioTabanetal.2023, author = {Shirakashi, Ryo and Sisario, Dmitri and Taban, Danush and Korsa, Tessa and Wanner, Sophia B. and Neubauer, Julia and Djuzenova, Cholpon S. and Zimmermann, Heiko and Sukhorukov, Vladimir L.}, title = {Contraction of the rigor actomyosin complex drives bulk hemoglobin expulsion from hemolyzing erythrocytes}, series = {Biomechanics and Modeling in Mechanobiology}, volume = {22}, journal = {Biomechanics and Modeling in Mechanobiology}, number = {2}, doi = {10.1007/s10237-022-01654-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325107}, pages = {417-432}, year = {2023}, abstract = {Erythrocyte ghost formation via hemolysis is a key event in the physiological clearance of senescent red blood cells (RBCs) in the spleen. The turnover rate of millions of RBCs per second necessitates a rapid efflux of hemoglobin (Hb) from RBCs by a not yet identified mechanism. Using high-speed video-microscopy of isolated RBCs, we show that electroporation-induced efflux of cytosolic ATP and other small solutes leads to transient cell shrinkage and echinocytosis, followed by osmotic swelling to the critical hemolytic volume. The onset of hemolysis coincided with a sudden self-propelled cell motion, accompanied by cell contraction and Hb-jet ejection. Our biomechanical model, which relates the Hb-jet-driven cell motion to the cytosolic pressure generation via elastic contraction of the RBC membrane, showed that the contributions of the bilayer and the bilayer-anchored spectrin cytoskeleton to the hemolytic cell motion are negligible. Consistent with the biomechanical analysis, our biochemical experiments, involving extracellular ATP and the myosin inhibitor blebbistatin, identify the low abundant non-muscle myosin 2A (NM2A) as the key contributor to the Hb-jet emission and fast hemolytic cell motion. Thus, our data reveal a rapid myosin-based mechanism of hemolysis, as opposed to a much slower diffusive Hb efflux.}, language = {en} } @article{MoustafaFouadIbrahimetal.2023, author = {Moustafa, Moataz A. M. and Fouad, Eman A. and Ibrahim, Emad and Erdei, Anna Laura and K{\´a}rp{\´a}ti, Zsolt and F{\´o}nagy, Adrien}, title = {The comparative toxicity, biochemical and physiological impacts of chlorantraniliprole and indoxacarb on Mamestra brassicae (Lepidoptera: Noctuidae)}, series = {Toxics}, volume = {11}, journal = {Toxics}, number = {3}, issn = {2305-6304}, doi = {10.3390/toxics11030212}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-303931}, year = {2023}, abstract = {Background: The cabbage moth, Mamestra brassicae, is a polyphagous pest that attacks several crops. Here, the sublethal and lethal effects of chlorantraniliprole and indoxacarb were investigated on the developmental stages, detoxification enzymes, reproductive activity, calling behavior, peripheral physiology, and pheromone titer of M. brasssicae. Methods: To assess pesticide effects, the second instar larvae were maintained for 24 h on a semi-artificial diet containing insecticides at their LC\(_{10}\), LC\(_{30}\), and LC\(_{50}\) concentrations. Results: M. brassicae was more susceptible to chlorantraniliprole (LC\(_{50}\) = 0.35 mg/L) than indoxacarb (LC\(_{50}\) = 1.71 mg/L). A significantly increased developmental time was observed with both insecticides at all tested concentrations but decreases in pupation rate, pupal weight, and emergence were limited to the LC50 concentration. Reductions in both the total number of eggs laid per female and the egg viability were observed with both insecticides at their LC\(_{30}\) and LC\(_{50}\) concentrations. Both female calling activity and the sex pheromone (Z11-hexadecenyl acetate and hexadecenyl acetate) titer were significantly reduced by chlorantraniliprole in LC\(_{50}\) concentration. Antennal responses of female antennae to benzaldehyde and 3-octanone were significantly weaker than controls after exposure to the indoxocarb LC\(_{50}\) concentration. Significant reductions in the enzymatic activity of glutathione S-transferases, mixed-function oxidases, and carboxylesterases were observed in response to both insecticides.}, language = {en} } @phdthesis{Pitsch2024, author = {Pitsch, Maximilian Jonathan}, title = {Zyklisches Adenosinmonophosphat (cAMP) als {\"A}quivalent akkumulierter neuronaler Evidenz}, doi = {10.25972/OPUS-35129}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-351292}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {Die vier Crz-Neurone des ventralen Nervensystems von Drosophila melanogaster sammeln Evidenz, wann im Rahmen eines Paarungsakts zirka 6 Minuten vergangen sind. Diese Entscheidung ist f{\"u}r die m{\"a}nnliche Fliege von Bedeutung, da das M{\"a}nnchen vor Ablauf dieser ~6 Minuten, welche den Zeitpunkt der Ejakulation darstellen, eher das eigene Leben opfern w{\"u}rde, als dass es die Paarung beenden w{\"u}rde. Nach Ablauf der ~6 Minuten f{\"a}llt die Motivation des M{\"a}nnchens dagegen dramatisch ab. Im Rahmen der vorliegenden Arbeit wurde zun{\"a}chst mittels optogenetischer neuronaler Inhibitionsprotokolle sowie Verhaltensanalysen das Ph{\"a}nomen der Evidenz-akkumulation in den Crz-Neuronen genauer charakterisiert. Dabei zeigte sich, dass die akkumulierte Evidenz auch w{\"a}hrend einer elektrischen Inhibition der Crz-Neurone persistierte. Dieses Ergebnis warf die Hypothese auf, dass das {\"A}quivalent der akkumulierten Evidenz in den Crz-Neuronen biochemischer Natur sein k{\"o}nnte. Es wurde daraufhin ein Hochdurchsatzscreening-Verfahren entwickelt, mittels dessen 1388 genetische Manipulationen der Crz-Neurone durchgef{\"u}hrt und auf eine {\"A}nderung der Evidenzakkumulation getestet wurden. Nur ~30 genetische Manipulationen zeigten eine ver{\"a}nderte Evidenzakkumulation, wobei die meisten dieser Manipulationen den cAMP-Signalweg betrafen. Mittels der optogenetischen Photoadenylatzyklase bPAC, einer Reihe weiterer genetischer Manipulationen des cAMP-Signalwegs sowie der ex vivo Kalzium-Bildgebung und Fluoreszenzlebensdauer-Mikroskopie konnte best{\"a}tigt werden, dass cAMP das {\"A}quivalent der in den Crz-Neuronen spannungsabh{\"a}ngig akkumulierten Evidenz darstellt, wobei die Kombination dieser Methoden nahelegte, dass der Schwellenwert der Evidenzakkumulation durch die cAMP-Bindungsaffinit{\"a}t der regulatorischen PKA-Untereinheiten festgelegt sein k{\"o}nnte. Mittels genetischer Mosaikexperimente sowie bildgebenden Verfahren konnte dar{\"u}ber hinaus gezeigt werden, dass innerhalb des Crz-Netzwerks eine positive R{\"u}ckkopplungsschleife aus rekurrenter Aktivit{\"a}t sowie der cAMP-Akkumulation besteht, welche, sobald die cAMP-Spiegel den Schwellenwert erreichen, zu einem netzwerkweit synchronisierten massiven Kalziumeinstrom f{\"u}hrt, was die Abgabe des Crz-Signals an nachgeschaltete Netzwerke triggert. Dieses Ph{\"a}nomen k{\"o}nnte ein Analogon des Aktionspotenzials auf Netzwerkebene sowie auf Intervallzeitskalen darstellen und wurde als „Eruption" bezeichnet. Genetische, optogenetische sowie Bildgebungsexperimente konnten zeigen, dass die CaMKII derartige Eruptionen durch Niedrighalten der cAMP-Spiegel unterdr{\"u}ckt, was den Zeitmessmechanismus des ersten beschriebenen Intervallzeitmessers CaMKII offenlegt.}, subject = {Evidenz}, language = {de} } @article{RoemerAguilarMeyeretal.2022, author = {R{\"o}mer, Daniela and Aguilar, Gonzalo Pacheco and Meyer, Annika and Roces, Flavio}, title = {Symbiont demand guides resource supply: leaf-cutting ants preferentially deliver their harvested fragments to undernourished fungus gardens}, series = {The Science of Nature}, volume = {109}, journal = {The Science of Nature}, number = {3}, doi = {10.1007/s00114-022-01797-7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-325080}, year = {2022}, abstract = {Leaf-cutting ants are highly successful herbivores in the Neotropics. They forage large amounts of fresh plant material to nourish a symbiotic fungus that sustains the colony. It is unknown how workers organize the intra-nest distribution of resources, and whether they respond to increasing demands in some fungus gardens by adjusting the amount of delivered resources accordingly. In laboratory experiments, we analyzed the spatial distribution of collected leaf fragments among nest chambers in Acromyrmex ambiguus leaf-cutting ants, and how it changed when one of the fungus gardens experienced undernourishment. Plant fragments were evenly distributed among nest chambers when the fungal symbiont was well nourished. That pattern changed when one of the fungus gardens was undernourished and had a higher leaf demand, resulting in more leaf discs delivered to the undernourished fungus garden over at least 2 days after deprivation. Some ants bypassed nourished gardens to directly deliver their resource to the chamber with higher nutritional demand. We hypothesize that cues arising from that chamber might be used for orientation and/or that informed individuals, presumably stemming from the undernourished chamber, may preferentially orient to them.}, language = {en} } @phdthesis{BakariSoale2024, author = {Bakari Soale, Majeed}, title = {Regulation of the Variant Surface Glycoprotein (VSG) Expression and Characterisation of the Nucleolar DExD/H box Protein Hel66 in \(Trypanosoma\) \(brucei\)}, doi = {10.25972/OPUS-25809}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-258090}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {The variant surface glycoprotein (VSG) of African trypanosomes plays an essential role in protecting the parasites from host immune factors. These trypanosomes undergo antigenic variation resulting in the expression of a single VSG isoform out of a repertoire of around 2000 genes. The molecular mechanism central to the expression and regulation of the VSG is however not fully understood. Gene expression in trypanosomes is unusual due to the absence of typical RNA polymerase II promoters and the polycistronic transcription of genes. The regulation of gene expression is therefore mainly post-transcriptional. Regulatory sequences, mostly present in the 3´ UTRs, often serve as key elements in the modulation of the levels of individual mRNAs. In T. brucei VSG genes, a 100 \% conserved 16mer motif within the 3´ UTR has been shown to modulate the stability of VSG transcripts and hence their expression. As a stability-associated sequence element, the absence of nucleotide substitutions in the motif is however unusual. It was therefore hypothesised that the motif is involved in other essential roles/processes besides stability of the VSG transcripts. In this study, it was demonstrated that the 100 \% conservation of the 16mer motif is not essential for cell viability or for the maintenance of functional VSG protein levels. It was further shown that the intact motif in the active VSG 3´ UTR is neither required to promote VSG silencing during switching nor is it needed during differentiation from bloodstream forms to procyclic forms. Crosstalk between the VSG and procyclin genes during differentiation to the insect vector stage is also unaffected in cells with a mutated 16mer motif. Ectopic overexpression of a second VSG however requires the intact motif to trigger silencing and exchange of the active VSG, suggesting a role for the motif in transcriptional VSG switching. The 16mer motif therefore plays a dual role in VSG in situ switching and stability of VSG transcripts. The additional role of the 16mer in the essential process of antigenic variation appears to be the driving force for the 100 \% conservation of this RNA motif. A screen aimed at identifying candidate RNA-binding proteins interacting with the 16mer motif, led to the identification of a DExD/H box protein, Hel66. Although the protein did not appear to have a direct link to the 16mer regulation of VSG expression, the DExD/H family of proteins are important players in the process of ribosome biogenesis. This process is relatively understudied in trypanosomes and so this candidate was singled out for detailed characterisation, given that the 16mer story had reached a natural end point. Ribosome biogenesis is a major cellular process in eukaryotes involving ribosomal RNA, ribosomal proteins and several non-ribosomal trans-acting protein factors. The DExD/H box proteins are the most important trans-acting protein factors involved in the biosynthesis of ribosomes. Several DExD/H box proteins have been directly implicated in this process in yeast. In trypanosomes, very few of this family of proteins have been characterised and therefore little is known about the specific roles they play in RNA metabolism. Here, it was shown that Hel66 is involved in rRNA processing during ribosome biogenesis. Hel66 localises to the nucleolus and depleting the protein led to a severe growth defect. Loss of the protein also resulted in a reduced rate of global translation and accumulation of rRNA processing intermediates of both the small and large ribosomal subunits. Hel66 is therefore an essential nucleolar DExD/H protein involved in rRNA processing during ribosome biogenesis. As very few protein factors involved in the processing of rRNAs have been described in trypanosomes, this finding represents an important platform for future investigation of this topic.}, subject = {Trypanosoma brucei}, language = {en} } @article{MaloukhNazzalKumarappanetal.2023, author = {Maloukh, Lina and Nazzal, Yousef and Kumarappan, Alagappan and Howari, Fares and Ambika, Lakshmi Kesari and Yahmadi, Rihab and Sharma, Manish and Iqbal, Jibran and Al-Taani, Ahmed A. and Salem, Imen Ben and Xavier, Cijo M. and Naseem, Muhamad}, title = {Metagenomic analysis of the outdoor dust microbiomes: a case study from Abu Dhabi, UAE}, series = {Atmosphere}, volume = {14}, journal = {Atmosphere}, number = {2}, issn = {2073-4433}, doi = {10.3390/atmos14020327}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-304391}, year = {2023}, abstract = {Outdoor dust covers a shattered range of microbial agents from land over transportation, human microbial flora, which includes pathogen and commensals, and airborne from the environment. Dust aerosols are rich in bacterial communities that have a major impact on human health and living environments. In this study, outdoor samples from roadside barricades, safety walls, and fences (18 samples) were collected from Abu Dhabi, UAE and bacterial diversity was assessed through a 16S rRNA amplicon next generation sequencing approach. Clean data from HiSeq produced 1,099,892 total reads pairs for 18 samples. For all samples, taxonomic classifications were assigned to the OTUs (operational taxonomic units) representative sequence using the Ribosomal Database Project database. Analysis such as alpha diversity, beta diversity, differential species analysis, and species relative abundance were performed in the clustering of samples and a functional profile heat map was obtained from the OTUs by using bioinformatics tools. A total of 2814 OTUs were identified from those samples with a coverage of more than 99\%. In the phylum, all 18 samples had most of the bacterial groups such as Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Twelve samples had Propionibacteria acnes and were mainly found in RD16 and RD3. Major bacteria species such as Propionibacteria acnes, Bacillus persicus, and Staphylococcus captis were found in all samples. Most of the samples had Streptococcus mitis, Staphylococcus capitis. and Nafulsella turpanensis and Enhydrobacter aerosaccus was part of the normal microbes of the skin. Salinimicrobium sp., Bacillus alkalisediminis, and Bacillus persicus are halophilic bacteria found in sediments. The heat map clustered the samples and species in vertical and horizontal classification, which represents the relationship between the samples and bacterial diversity. The heat map for the functional profile had high properties of amino acids, carbohydrate, and cofactor and vitamin metabolisms of all bacterial species from all samples. Taken together, our analyses are very relevant from the perspective of out-door air quality, airborne diseases, and epidemics, with broader implications for health safety and monitoring.}, language = {en} } @phdthesis{MaierverhHartmann2024, author = {Maier [verh. Hartmann], Carina Ramona}, title = {Regulation of the Mevalonate Pathway by the Deubiquitinase USP28 in Squamous Cancer}, doi = {10.25972/OPUS-34874}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-348740}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2024}, abstract = {The reprogramming of metabolic pathways is a hallmark of cancer: Tumour cells are dependent on the supply with metabolites and building blocks to fulfil their increased need as highly proliferating cells. Especially de novo synthesis pathways are upregulated when the cells of the growing tumours are not able to satisfy the required metabolic levels by uptake from the environment. De novo synthesis pathways are often under the control of master transcription factors which regulate the gene expression of enzymes involved in the synthesis process. The master regulators for de novo fatty acid synthesis and cholesterogenesis are sterol regulatory element-binding proteins (SREBPs). While SREBP1 preferably controls the expression of enzymes involved in fatty acid synthesis, SREBP2 regulates the transcription of the enzymes of the mevalonate pathway and downstream processes namely cholesterol, isoprenoids and building blocks for ubiquinone synthesis. SREBP activity is tightly regulated at different levels: The post-translational modification by ubiquitination decreases the stability of active SREBPs. The attachment of K48-linked ubiquitin chains marks the transcription factors for the proteasomal degradation. In tumour cells, high levels of active SREBPs are essential for the upregulation of the respective metabolic pathways. The increased stability and activity of SREBPs were investigated in this thesis. SREBPs are ubiquitinated by the E3 ligase Fbw7 which leads to the subsequential proteolysis of the transcription factors. The work conducted in this thesis identified the counteracting deubiquitination enzyme USP28 which removes the ubiquitin chains from SREBPs and prevents their proteasomal degradation. It further revealed that the stabilization of SREBP2 by USP28 plays an important role in the context of squamous cancers. Increased USP28 levels are associated with a poor survival in patients with squamous tumour subtypes. It was shown that reduced USP28 levels in cell lines and in vivo result in a decrease of SREBP2 activity and downregulation of the mevalonate pathway. This manipulation led to reduced proliferation and tumour growth. A direct comparison of adenocarcinomas and squamous cell carcinomas in lung cancer patients revealed an upregulation of USP28 as well as SREBP2 and its target genes. Targeting the USP28-SREBP2 regulatory axis in squamous cell lines by inhibitors also reduced cell viability and proliferation. In conclusion, this study reports evidence for the importance of the mevalonate pathway regulated by the USP28-SREBP2 axis in tumour initiation and progression of squamous cancer. The combinatorial inhibitor treatment of USP28 and HMGCR, the rate limiting enzyme of the mevalonate pathway, by statins opens the possibility for a targeted therapeutic treatment of squamous cancer patients.}, subject = {Ubiquitin}, language = {en} } @article{DhillonKuebertFlockDahmsetal.2023, author = {Dhillon, Maninder Singh and K{\"u}bert-Flock, Carina and Dahms, Thorsten and Rummler, Thomas and Arnault, Joel and Steffan-Dewenter, Ingolf and Ullmann, Tobias}, title = {Evaluation of MODIS, Landsat 8 and Sentinel-2 data for accurate crop yield predictions: a case study using STARFM NDVI in Bavaria, Germany}, series = {Remote Sensing}, volume = {15}, journal = {Remote Sensing}, number = {7}, issn = {2072-4292}, doi = {10.3390/rs15071830}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-311132}, year = {2023}, abstract = {The increasing availability and variety of global satellite products and the rapid development of new algorithms has provided great potential to generate a new level of data with different spatial, temporal, and spectral resolutions. However, the ability of these synthetic spatiotemporal datasets to accurately map and monitor our planet on a field or regional scale remains underexplored. This study aimed to support future research efforts in estimating crop yields by identifying the optimal spatial (10 m, 30 m, or 250 m) and temporal (8 or 16 days) resolutions on a regional scale. The current study explored and discussed the suitability of four different synthetic (Landsat (L)-MOD13Q1 (30 m, 8 and 16 days) and Sentinel-2 (S)-MOD13Q1 (10 m, 8 and 16 days)) and two real (MOD13Q1 (250 m, 8 and 16 days)) NDVI products combined separately to two widely used crop growth models (CGMs) (World Food Studies (WOFOST), and the semi-empiric Light Use Efficiency approach (LUE)) for winter wheat (WW) and oil seed rape (OSR) yield forecasts in Bavaria (70,550 km\(^2\)) for the year 2019. For WW and OSR, the synthetic products' high spatial and temporal resolution resulted in higher yield accuracies using LUE and WOFOST. The observations of high temporal resolution (8-day) products of both S-MOD13Q1 and L-MOD13Q1 played a significant role in accurately measuring the yield of WW and OSR. For example, L- and S-MOD13Q1 resulted in an R\(^2\) = 0.82 and 0.85, RMSE = 5.46 and 5.01 dt/ha for WW, R\(^2\) = 0.89 and 0.82, and RMSE = 2.23 and 2.11 dt/ha for OSR using the LUE model, respectively. Similarly, for the 8- and 16-day products, the simple LUE model (R\(^2\) = 0.77 and relative RMSE (RRMSE) = 8.17\%) required fewer input parameters to simulate crop yield and was highly accurate, reliable, and more precise than the complex WOFOST model (R\(^2\) = 0.66 and RRMSE = 11.35\%) with higher input parameters. Conclusively, both S-MOD13Q1 and L-MOD13Q1, in combination with LUE, were more prominent for predicting crop yields on a regional scale than the 16-day products; however, L-MOD13Q1 was advantageous for generating and exploring the long-term yield time series due to the availability of Landsat data since 1982, with a maximum resolution of 30 m. In addition, this study recommended the further use of its findings for implementing and validating the long-term crop yield time series in different regions of the world.}, language = {en} } @article{DhillonDahmsKuebertFlocketal.2023, author = {Dhillon, Maninder Singh and Dahms, Thorsten and K{\"u}bert-Flock, Carina and Liepa, Adomas and Rummler, Thomas and Arnault, Joel and Steffan-Dewenter, Ingolf and Ullmann, Tobias}, title = {Impact of STARFM on crop yield predictions: fusing MODIS with Landsat 5, 7, and 8 NDVIs in Bavaria Germany}, series = {Remote Sensing}, volume = {15}, journal = {Remote Sensing}, number = {6}, issn = {2072-4292}, doi = {10.3390/rs15061651}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-311092}, year = {2023}, abstract = {Rapid and accurate yield estimates at both field and regional levels remain the goal of sustainable agriculture and food security. Hereby, the identification of consistent and reliable methodologies providing accurate yield predictions is one of the hot topics in agricultural research. This study investigated the relationship of spatiotemporal fusion modelling using STRAFM on crop yield prediction for winter wheat (WW) and oil-seed rape (OSR) using a semi-empirical light use efficiency (LUE) model for the Free State of Bavaria (70,550 km\(^2\)), Germany, from 2001 to 2019. A synthetic normalised difference vegetation index (NDVI) time series was generated and validated by fusing the high spatial resolution (30 m, 16 days) Landsat 5 Thematic Mapper (TM) (2001 to 2012), Landsat 7 Enhanced Thematic Mapper Plus (ETM+) (2012), and Landsat 8 Operational Land Imager (OLI) (2013 to 2019) with the coarse resolution of MOD13Q1 (250 m, 16 days) from 2001 to 2019. Except for some temporal periods (i.e., 2001, 2002, and 2012), the study obtained an R\(^2\) of more than 0.65 and a RMSE of less than 0.11, which proves that the Landsat 8 OLI fused products are of higher accuracy than the Landsat 5 TM products. Moreover, the accuracies of the NDVI fusion data have been found to correlate with the total number of available Landsat scenes every year (N), with a correlation coefficient (R) of +0.83 (between R\(^2\) of yearly synthetic NDVIs and N) and -0.84 (between RMSEs and N). For crop yield prediction, the synthetic NDVI time series and climate elements (such as minimum temperature, maximum temperature, relative humidity, evaporation, transpiration, and solar radiation) are inputted to the LUE model, resulting in an average R\(^2\) of 0.75 (WW) and 0.73 (OSR), and RMSEs of 4.33 dt/ha and 2.19 dt/ha. The yield prediction results prove the consistency and stability of the LUE model for yield estimation. Using the LUE model, accurate crop yield predictions were obtained for WW (R\(^2\) = 0.88) and OSR (R\(^2\) = 0.74). Lastly, the study observed a high positive correlation of R = 0.81 and R = 0.77 between the yearly R\(^2\) of synthetic accuracy and modelled yield accuracy for WW and OSR, respectively.}, language = {en} } @article{AupperleLellbachHeidrichKehletal.2023, author = {Aupperle-Lellbach, Heike and Heidrich, Daniela and Kehl, Alexandra and Conrad, David and Brockmann, Maria and T{\"o}rner, Katrin and Beitzinger, Christoph and M{\"u}ller, Tobias}, title = {KITLG copy number germline variations in schnauzer breeds and their relevance in digital squamous cell carcinoma in black giant schnauzers}, series = {Veterinary Sciences}, volume = {10}, journal = {Veterinary Sciences}, number = {2}, issn = {2306-7381}, doi = {10.3390/vetsci10020147}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-303913}, year = {2023}, abstract = {Copy number variations (CNVs) of the KITLG gene seem to be involved in the oncogenesis of digital squamous cell carcinoma (dSCC). The aims of this study were (1) to investigate KITLG CNV in giant (GS), standard (SS), and miniature (MS) schnauzers and (2) to compare KITLG CNV between black GS with and without dSCC. Blood samples from black GS (22 with and 17 without dSCC), black SS (18 with and 4 without dSSC; 5 unknown), and 50 MS (unknown dSSC status and coat colour) were analysed by digital droplet PCR. The results are that (1) most dogs had a copy number (CN) value > 4 (range 2.5-7.6) with no significant differences between GS, SS, and MS, and (2) the CN value in black GS with dSCC was significantly higher than in those without dSCC (p = 0.02). CN values > 5.8 indicate a significantly increased risk for dSCC, while CN values < 4.7 suggest a reduced risk for dSCC (grey area: 4.7-5.8). Diagnostic testing for KITLG CNV may sensitise owners to the individual risk of their black GS for dSCC. Further studies should investigate the relevance of KITLG CNV in SS and the protective effects in MS, who rarely suffer from dSCC.}, language = {en} }