@article{BlaettnerDasPaprotkaetal.2016, author = {Bl{\"a}ttner, Sebastian and Das, Sudip and Paprotka, Kerstin and Eilers, Ursula and Krischke, Markus and Kretschmer, Dorothee and Remmele, Christian W. and Dittrich, Marcus and M{\"u}ller, Tobias and Schuelein-Voelk, Christina and Hertlein, Tobias and Mueller, Martin J. and Huettel, Bruno and Reinhardt, Richard and Ohlsen, Knut and Rudel, Thomas and Fraunholz, Martin J.}, title = {Staphylococcus aureus Exploits a Non-ribosomal Cyclic Dipeptide to Modulate Survival within Epithelial Cells and Phagocytes}, series = {PLoS Pathogens}, volume = {12}, journal = {PLoS Pathogens}, number = {9}, doi = {10.1371/journal.ppat.1005857}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-180380}, year = {2016}, abstract = {Community-acquired (CA) Staphylococcus aureus cause various diseases even in healthy individuals. Enhanced virulence of CA-strains is partly attributed to increased production of toxins such as phenol-soluble modulins (PSM). The pathogen is internalized efficiently by mammalian host cells and intracellular S. aureus has recently been shown to contribute to disease. Upon internalization, cytotoxic S. aureus strains can disrupt phagosomal membranes and kill host cells in a PSM-dependent manner. However, PSM are not sufficient for these processes. Here we screened for factors required for intracellular S. aureus virulence. We infected escape reporter host cells with strains from an established transposon mutant library and detected phagosomal escape rates using automated microscopy. We thereby, among other factors, identified a non-ribosomal peptide synthetase (NRPS) to be required for efficient phagosomal escape and intracellular survival of S. aureus as well as induction of host cell death. By genetic complementation as well as supplementation with the synthetic NRPS product, the cyclic dipeptide phevalin, wild-type phenotypes were restored. We further demonstrate that the NRPS is contributing to virulence in a mouse pneumonia model. Together, our data illustrate a hitherto unrecognized function of the S. aureus NRPS and its dipeptide product during S. aureus infection.}, language = {en} } @article{AurastGradlPernesetal.2016, author = {Aurast, Anna and Gradl, Tobias and Pernes, Stefan and Pielstr{\"o}m, Steffen}, title = {Big Data und Smart Data in den Geisteswissenschaften}, series = {Bibliothek Forschung und Praxis}, volume = {40}, journal = {Bibliothek Forschung und Praxis}, number = {2}, issn = {1865-7648}, doi = {10.1515/bfp-2016-0033}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-195237}, pages = {200-206}, year = {2016}, abstract = {Kein Abstract verf{\"u}gbar.}, language = {de} } @article{ElHajjDittrichBoecketal.2016, author = {El Hajj, Nady and Dittrich, Marcus and B{\"o}ck, Julia and Kraus, Theo F. J. and Nanda, Indrajit and M{\"u}ller, Tobias and Seidmann, Larissa and Tralau, Tim and Galetzka, Danuta and Schneider, Eberhard and Haaf, Thomas}, title = {Epigenetic dysregulation in the developing Down syndrome cortex}, series = {Epigenetics}, volume = {11}, journal = {Epigenetics}, number = {8}, doi = {10.1080/15592294.2016.1192736}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191239}, pages = {563-578}, year = {2016}, abstract = {Using Illumina 450K arrays, 1.85\% of all analyzed CpG sites were significantly hypermethylated and 0.31\% hypomethylated in fetal Down syndrome (DS) cortex throughout the genome. The methylation changes on chromosome 21 appeared to be balanced between hypo- and hyper-methylation, whereas, consistent with prior reports, all other chromosomes showed 3-11times more hyper- than hypo-methylated sites. Reduced NRSF/REST expression due to upregulation of DYRK1A (on chromosome 21q22.13) and methylation of REST binding sites during early developmental stages may contribute to this genome-wide excess of hypermethylated sites. Upregulation of DNMT3L (on chromosome 21q22.4) could lead to de novo methylation in neuroprogenitors, which then persists in the fetal DS brain where DNMT3A and DNMT3B become downregulated. The vast majority of differentially methylated promoters and genes was hypermethylated in DS and located outside chromosome 21, including the protocadherin gamma (PCDHG) cluster on chromosome 5q31, which is crucial for neural circuit formation in the developing brain. Bisulfite pyrosequencing and targeted RNA sequencing showed that several genes of PCDHG subfamilies A and B are hypermethylated and transcriptionally downregulated in fetal DS cortex. Decreased PCDHG expression is expected to reduce dendrite arborization and growth in cortical neurons. Since constitutive hypermethylation of PCDHG and other genes affects multiple tissues, including blood, it may provide useful biomarkers for DS brain development and pharmacologic targets for therapeutic interventions.}, language = {en} } @article{DotterweichSchlegelmilchKelleretal.2016, author = {Dotterweich, Julia and Schlegelmilch, Katrin and Keller, Alexander and Geyer, Beate and Schneider, Doris and Zeck, Sabine and Tower, Robert J. J. and Ebert, Regina and Jakob, Franz and Sch{\"u}tze, Norbert}, title = {Contact of myeloma cells induces a characteristic transcriptome signature in skeletal precursor cells-implications for myeloma bone disease}, series = {Bone}, volume = {93}, journal = {Bone}, doi = {10.1016/j.bone.2016.08.006}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-186688}, pages = {155-166}, year = {2016}, abstract = {Physical interaction of skeletal precursors with multiple myeloma cells has been shown to suppress their osteogenic potential while favoring their tumor-promoting features. Although several transcriptome analyses of myeloma patient-derived mesenchymal stem cells have displayed differences compared to their healthy counterparts, these analyses insufficiently reflect the signatures mediated by tumor cell contact, vary due to different methodologies, and lack results in lineage-committed precursors. To determine tumor cell contact-mediated changes on skeletal precursors, we performed transcriptome analyses of mesenchymal stem cells and osteogenic precursor cells cultured in contact with the myeloma cell line INA-6. Comparative analyses confirmed dysregulation of genes which code for known disease-relevant factors and additionally revealed upregulation of genes that are associated with plasma cell homing, adhesion, osteoclastogenesis, and angiogenesis. Osteoclast-derived coupling factors, a dysregulated adipogenic potential, and an imbalance in favor of anti-anabolic factors may play a role in the hampered osteoblast differentiation potential of mesenchymal stem cells. Angiopoietin-Like 4 (ANGPTL4) was selected from a list of differentially expressed genes as a myeloma cell contact-dependent target in skeletal precursor cells which warranted further functional analyses. Adhesion assays with full-length ANGPTL4-coated plates revealed a potential role of this protein in INA6 cell attachment. This study expands knowledge of the myeloma cell contact-induced signature in the stromal compartment of myelomatous bones and thus offers potential targets that may allow detection and treatment of myeloma bone disease at an early stage.}, language = {en} } @article{ScharawIskarOrietal.2016, author = {Scharaw, Sandra and Iskar, Murat and Ori, Alessandro and Boncompain, Gaelle and Laketa, Vibor and Poser, Ina and Lundberg, Emma and Perez, Franck and Beck, Martin and Bork, Peer and Pepperkok, Rainer}, title = {The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR}, series = {Journal of Cell Biology}, volume = {215}, journal = {Journal of Cell Biology}, number = {4}, doi = {10.1083/jcb.201601090}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-186731}, pages = {543-558}, year = {2016}, abstract = {Stimulation of cells with epidermal growth factor (EGF) induces internalization and partial degradation of the EGF receptor (EGFR) by the endo-lysosomal pathway. For continuous cell functioning, EGFR plasma membrane levels are maintained by transporting newly synthesized EGFRs to the cell surface. The regulation of this process is largely unknown. In this study, we find that EGF stimulation specifically increases the transport efficiency of newly synthesized EGFRs from the endoplasmic reticulum to the plasma membrane. This coincides with an up-regulation of the inner coat protein complex II (COP II) components SEC23B, SEC24B, and SEC24D, which we show to be specifically required for EGFR transport. Up-regulation of these COP II components requires the transcriptional regulator RNF11, which localizes to early endosomes and appears additionally in the cell nucleus upon continuous EGF stimulation. Collectively, our work identifies a new regulatory mechanism that integrates the degradation and transport of EGFR in order to maintain its physiological levels at the plasma membrane.}, language = {en} } @article{KaluzaWallaceHeardetal.2016, author = {Kaluza, Benjamin F. and Wallace, Helen and Heard, Tim A. and Klein, Aelxandra-Maria and Leonhardt, Sara D.}, title = {Urban gardens promote bee foraging over natural habitats and plantations}, series = {Ecology and Evolution}, volume = {6}, journal = {Ecology and Evolution}, number = {5}, doi = {10.1002/ece3.1941}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162713}, pages = {1304-1316}, year = {2016}, abstract = {Increasing human land use for agriculture and housing leads to the loss of natural habitat and to widespread declines in wild bees. Bee foraging dynamics and fitness depend on the availability of resources in the surrounding landscape, but how precisely landscape related resource differences affect bee foraging patterns remains unclear. To investigate how landscape and its interaction with season and weather drive foraging and resource intake in social bees, we experimentally compared foraging activity, the allocation of foragers to different resources (pollen, nectar, and resin) and overall resource intake in the Australian stingless bee Tetragonula carbonaria (Apidae, Meliponini). Bee colonies were monitored in different seasons over two years. We compared foraging patterns and resource intake between the bees' natural habitat (forests) and two landscapes differently altered by humans (suburban gardens and agricultural macadamia plantations). We found foraging activity as well as pollen and nectar forager numbers to be highest in suburban gardens, intermediate in forests and low in plantations. Foraging patterns further differed between seasons, but seasonal variations strongly differed between landscapes. Sugar and pollen intake was low in plantations, but contrary with our predictions, it was even higher in gardens than in forests. In contrast, resin intake was similar across landscapes. Consequently, differences in resource availability between natural and altered landscapes strongly affect foraging patterns and thus resource intake in social bees. While agricultural monocultures largely reduce foraging success, suburban gardens can increase resource intake well above rates found in natural habitats of bees, indicating that human activities can both decrease and increase the availability of resources in a landscape and thus reduce or enhance bee fitness.}, language = {en} } @article{VendelovadeLimaLorenzattoetal.2016, author = {Vendelova, Emilia and de Lima, Jeferson Camargo and Lorenzatto, Karina Rodrigues and Monteiro, Karina Mariante and Mueller, Thomas and Veepaschit, Jyotishman and Grimm, Clemens and Brehm, Klaus and Hrčkov{\´a}, Gabriela and Lutz, Manfred B. and Ferreira, Henrique B. and Nono, Justin Komguep}, title = {Proteomic Analysis of Excretory-Secretory Products of Mesocestoides corti Metacestodes Reveals Potential Suppressors of Dendritic Cell Functions}, series = {PLoS Neglected Tropical Diseases}, volume = {10}, journal = {PLoS Neglected Tropical Diseases}, number = {10}, doi = {10.1371/journal.pntd.0005061}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166742}, pages = {e0005061}, year = {2016}, abstract = {Accumulating evidences have assigned a central role to parasite-derived proteins in immunomodulation. Here, we report on the proteomic identification and characterization of immunomodulatory excretory-secretory (ES) products from the metacestode larva (tetrathyridium) of the tapeworm Mesocestoides corti (syn. M. vogae). We demonstrate that ES products but not larval homogenates inhibit the stimuli-driven release of the pro-inflammatory, Th1-inducing cytokine IL-12p70 by murine bone marrow-derived dendritic cells (BMDCs). Within the ES fraction, we biochemically narrowed down the immunosuppressive activity to glycoproteins since active components were lipid-free, but sensitive to heat- and carbohydrate-treatment. Finally, using bioassay-guided chromatographic analyses assisted by comparative proteomics of active and inactive fractions of the ES products, we defined a comprehensive list of candidate proteins released by M. corti tetrathyridia as potential suppressors of DC functions. Our study provides a comprehensive library of somatic and ES products and highlight some candidate parasite factors that might drive the subversion of DC functions to facilitate the persistence of M. corti tetrathyridia in their hosts.}, language = {en} } @article{JonesFrucianoKelleretal.2016, author = {Jones, Julia C. and Fruciano, Carmelo and Keller, Anja and Schartl, Manfred and Meyer, Axel}, title = {Evolution of the elaborate male intromittent organ of Xiphophorus fishes}, series = {Ecology and Evolution}, volume = {6}, journal = {Ecology and Evolution}, number = {20}, doi = {10.1002/ece3.2396}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164956}, pages = {7207-7220}, year = {2016}, abstract = {Internally fertilizing animals show a remarkable diversity in male genital morphology that is associated with sexual selection, and these traits are thought to be evolving particularly rapidly. Male fish in some internally fertilizing species have "gonopodia," highly modified anal fins that are putatively important for sexual selection. However, our understanding of the evolution of genital diversity remains incomplete. Contrary to the prediction that male genital traits evolve more rapidly than other traits, here we show that gonopodial traits and other nongonopodial traits exhibit similar evolutionary rates of trait change and also follow similar evolutionary models in an iconic genus of poeciliid fish (Xiphophorus spp.). Furthermore, we find that both mating and nonmating natural selection mechanisms are unlikely to be driving the diverse Xiphophorus gonopodial morphology. Putative holdfast features of the male genital organ do not appear to be influenced by water flow, a candidate selective force in aquatic habitats. Additionally, interspecific divergence in gonopodial morphology is not significantly higher between sympatric species, than between allopatric species, suggesting that male genitals have not undergone reproductive character displacement. Slower rates of evolution in gonopodial traits compared with a subset of putatively sexually selected nongenital traits suggest that different selection mechanisms may be acting on the different trait types. Further investigations of this elaborate trait are imperative to determine whether it is ultimately an important driver of speciation.}, language = {en} } @article{DrakulićFeldhaarLisičićetal.2016, author = {Drakulić, Sanja and Feldhaar, Heike and Lisičić, Duje and Mioč, Mia and Cizelj, Ivan and Seiler, Michael and Spatz, Theresa and R{\"o}del, Mark-Oliver}, title = {Population-specific effects of developmental temperature on body condition and jumping performance of a widespread European frog}, series = {Ecology and Evolution}, volume = {6}, journal = {Ecology and Evolution}, number = {10}, doi = {10.1002/ece3.2113}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164960}, pages = {3115-3128}, year = {2016}, abstract = {All physiological processes of ectotherms depend on environmental temperature. Thus, adaptation of physiological mechanisms to the thermal environments is important for achieving optimal performance and fitness. The European Common Frog, Rana temporaria, is widely distributed across different thermal habitats. This makes it an exceptional model for studying the adaptations to different thermal conditions. We raised tadpoles from Germany and Croatia at two constant temperature treatments (15°C, 20°C), and under natural temperature fluctuations (in outdoor treatments), and tested how different developmental temperatures affected developmental traits, that is, length of larval development, morphometrics, and body condition, as well as jumping performance of metamorphs. Our results revealed population-specific differences in developmental time, body condition, and jumping performance. Croatian frogs developed faster in all treatments, were heavier, in better body condition, and had longer hind limbs and better jumping abilities than German metamorphs. The populations further differed in thermal sensitivity of jumping performance. While metamorphs from Croatia increased their jumping performance with higher temperatures, German metamorphs reached their performance maximum at lower temperatures. These population-specific differences in common environments indicate local genetic adaptation, with southern populations being better adapted to higher temperatures than those from north of the Alps.}, language = {en} } @article{MenaDiegelmannWegeneretal.2016, author = {Mena, Wilson and Diegelmann, S{\"o}ren and Wegener, Christian and Ewer, John}, title = {Stereotyped responses of Drosophila peptidergic neuronal ensemble depend on downstream neuromodulators}, series = {eLife}, volume = {5}, journal = {eLife}, doi = {10.7554/eLife.19686}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165003}, pages = {e19686}, year = {2016}, abstract = {Neuropeptides play a key role in the regulation of behaviors and physiological responses including alertness, social recognition, and hunger, yet, their mechanism of action is poorly understood. Here, we focus on the endocrine control ecdysis behavior, which is used by arthropods to shed their cuticle at the end of every molt. Ecdysis is triggered by ETH (Ecdysis triggering hormone), and we show that the response of peptidergic neurons that produce CCAP (crustacean cardioactive peptide), which are key targets of ETH and control the onset of ecdysis behavior, depends fundamentally on the actions of neuropeptides produced by other direct targets of ETH and released in a broad paracrine manner within the CNS; by autocrine influences from the CCAP neurons themselves; and by inhibitory actions mediated by GABA. Our findings provide insights into how this critical insect behavior is controlled and general principles for understanding how neuropeptides organize neuronal activity and behaviors.}, language = {en} } @article{KonteTerpitzPlemenitaš2016, author = {Konte, Tilen and Terpitz, Ulrich and Plemenitaš, Ana}, title = {Reconstruction of the High-Osmolarity Glycerol (HOG) Signaling Pathway from the Halophilic Fungus Wallemia ichthyophaga in Saccharomyces cerevisiae}, series = {Frontiers in Microbiology}, journal = {Frontiers in Microbiology}, doi = {10.3389/fmicb.2016.00901}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165214}, year = {2016}, abstract = {The basidiomycetous fungus Wallemia ichthyophaga grows between 1.7 and 5.1 M NaCl and is the most halophilic eukaryote described to date. Like other fungi, W. ichthyophaga detects changes in environmental salinity mainly by the evolutionarily conserved high-osmolarity glycerol (HOG) signaling pathway. In Saccharomyces cerevisiae, the HOG pathway has been extensively studied in connection to osmotic regulation, with a valuable knock-out strain collection established. In the present study, we reconstructed the architecture of the HOG pathway of W. ichthyophaga in suitable S. cerevisiae knock-out strains, through heterologous expression of the W. ichthyophaga HOG pathway proteins. Compared to S. cerevisiae, where the Pbs2 (ScPbs2) kinase of the HOG pathway is activated via the SHO1 and SLN1 branches, the interactions between the W. ichthyophaga Pbs2 (WiPbs2) kinase and the W. ichthyophaga SHO1 branch orthologs are not conserved: as well as evidence of poor interactions between the WiSho1 Src-homology 3 (SH3) domain and the WiPbs2 proline-rich motif, the absence of a considerable part of the osmosensing apparatus in the genome of W. ichthyophaga suggests that the SHO1 branch components are not involved in HOG signaling in this halophilic fungus. In contrast, the conserved activation of WiPbs2 by the S. cerevisiae ScSsk2/ScSsk22 kinase and the sensitivity of W. ichthyophaga cells to fludioxonil, emphasize the significance of two-component (SLN1-like) signaling via Group III histidine kinase. Combined with protein modeling data, our study reveals conserved and non-conserved protein interactions in the HOG signaling pathway of W. ichthyophaga and therefore significantly improves the knowledge of hyperosmotic signal processing in this halophilic fungus.}, language = {en} } @article{HeldBerzHensgenetal.2016, author = {Held, Martina and Berz, Annuska and Hensgen, Ronja and Muenz, Thomas S. and Scholl, Christina and R{\"o}ssler, Wolfgang and Homberg, Uwe and Pfeiffer, Keram}, title = {Microglomerular Synaptic Complexes in the Sky-Compass Network of the Honeybee Connect Parallel Pathways from the Anterior Optic Tubercle to the Central Complex}, series = {Frontiers in Behavioral Neuroscience}, volume = {10}, journal = {Frontiers in Behavioral Neuroscience}, number = {186}, doi = {10.3389/fnbeh.2016.00186}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165080}, year = {2016}, abstract = {While the ability of honeybees to navigate relying on sky-compass information has been investigated in a large number of behavioral studies, the underlying neuronal system has so far received less attention. The sky-compass pathway has recently been described from its input region, the dorsal rim area (DRA) of the compound eye, to the anterior optic tubercle (AOTU). The aim of this study is to reveal the connection from the AOTU to the central complex (CX). For this purpose, we investigated the anatomy of large microglomerular synaptic complexes in the medial and lateral bulbs (MBUs/LBUs) of the lateral complex (LX). The synaptic complexes are formed by tubercle-lateral accessory lobe neuron 1 (TuLAL1) neurons of the AOTU and GABAergic tangential neurons of the central body's (CB) lower division (TL neurons). Both TuLAL1 and TL neurons strongly resemble neurons forming these complexes in other insect species. We further investigated the ultrastructure of these synaptic complexes using transmission electron microscopy. We found that single large presynaptic terminals of TuLAL1 neurons enclose many small profiles (SPs) of TL neurons. The synaptic connections between these neurons are established by two types of synapses: divergent dyads and divergent tetrads. Our data support the assumption that these complexes are a highly conserved feature in the insect brain and play an important role in reliable signal transmission within the sky-compass pathway.}, language = {en} } @article{KunzLiangNillaetal.2016, author = {Kunz, Meik and Liang, Chunguang and Nilla, Santosh and Cecil, Alexander and Dandekar, Thomas}, title = {The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development}, series = {Database}, volume = {2016}, journal = {Database}, doi = {10.1093/database/baw041}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147369}, pages = {baw041}, year = {2016}, abstract = {The drug-minded protein interaction database (DrumPID) has been designed to provide fast, tailored information on drugs and their protein networks including indications, protein targets and side-targets. Starting queries include compound, target and protein interactions and organism-specific protein families. Furthermore, drug name, chemical structures and their SMILES notation, affected proteins (potential drug targets), organisms as well as diseases can be queried including various combinations and refinement of searches. Drugs and protein interactions are analyzed in detail with reference to protein structures and catalytic domains, related compound structures as well as potential targets in other organisms. DrumPID considers drug functionality, compound similarity, target structure, interactome analysis and organismic range for a compound, useful for drug development, predicting drug side-effects and structure-activity relationships.}, language = {en} } @article{BeckerKucharskiRoessleretal.2016, author = {Becker, Nils and Kucharski, Robert and R{\"o}ssler, Wolfgang and Maleszka, Ryszard}, title = {Age-dependent transcriptional and epigenomic responses to light exposure in the honey bee brain}, series = {FEBS Open Bio}, volume = {6}, journal = {FEBS Open Bio}, number = {7}, doi = {10.1002/2211-5463.12084}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147080}, pages = {622-639}, year = {2016}, abstract = {Light is a powerful environmental stimulus of special importance in social honey bees that undergo a behavioral transition from in-hive to outdoor foraging duties. Our previous work has shown that light exposure induces structural neuronal plasticity in the mushroom bodies (MBs), a brain center implicated in processing inputs from sensory modalities. Here, we extended these analyses to the molecular level to unravel light-induced transcriptomic and epigenomic changes in the honey bee brain. We have compared gene expression in brain compartments of 1- and 7-day-old light-exposed honey bees with age-matched dark-kept individuals. We have found a number of differentially expressed genes (DEGs), both novel and conserved, including several genes with reported roles in neuronal plasticity. Most of the DEGs show age-related changes in the amplitude of light-induced expression and are likely to be both developmentally and environmentally regulated. Some of the DEGs are either known to be methylated or are implicated in epigenetic processes suggesting that responses to light exposure are at least partly regulated at the epigenome level. Consistent with this idea light alters the DNA methylation pattern of bgm, one of the DEGs affected by light exposure, and the expression of microRNA miR-932. This confirms the usefulness of our approach to identify candidate genes for neuronal plasticity and provides evidence for the role of epigenetic processes in driving the molecular responses to visual stimulation.}, language = {en} } @article{BrunetVolffSchartl2016, author = {Brunet, Fr{\´e}d{\´e}ric G. and Volff, Jean-Nicolas and Schartl, Manfred}, title = {Whole Genome Duplications Shaped the Receptor Tyrosine Kinase Repertoire of Jawed Vertebrates}, series = {Genome Biology Evolution}, volume = {8}, journal = {Genome Biology Evolution}, number = {15}, doi = {10.1093/gbe/evw103}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146988}, pages = {1600-1613}, year = {2016}, abstract = {The receptor tyrosine kinase (RTK) gene family, involved primarily in cell growth and differentiation, comprises proteins with a common enzymatic tyrosine kinase intracellular domain adjacent to a transmembrane region. The amino-terminal portion of RTKs is extracellular and made of different domains, the combination of which characterizes each of the 20 RTK subfamilies among mammals. We analyzed a total of 7,376 RTK sequences among 143 vertebrate species to provide here the first comprehensive census of the jawed vertebrate repertoire. We ascertained the 58 genes previously described in the human and mouse genomes and established their phylogenetic relationships. We also identified five additional RTKs amounting to a total of 63 genes in jawed vertebrates. We found that the vertebrate RTK gene family has been shaped by the two successive rounds of whole genome duplications (WGD) called 1R and 2R (1R/2R) that occurred at the base of the vertebrates. In addition, the Vegfr and Ephrin receptor subfamilies were expanded by single gene duplications. In teleost fish, 23 additional RTK genes have been retained after another expansion through the fish-specific third round (3R) of WGD. Several lineage-specific gene losses were observed. For instance, birds have lost three RTKs, and different genes are missing in several fish sublineages. The RTK gene family presents an unusual high gene retention rate from the vertebrate WGDs (58.75\% after 1R/2R, 64.4\% after 3R), resulting in an expansion that might be correlated with the evolution of complexity of vertebrate cellular communication and intracellular signaling.}, language = {en} } @phdthesis{Jung2016, author = {Jung, Lisa Anna}, title = {Targeting MYC Function as a Strategy for Tumor Therapy}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146993}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {A large fraction of human tumors exhibits aberrant expression of the oncoprotein MYC. As a transcription factor regulating various cellular processes, MYC is also crucially involved in normal development. Direct targeting of MYC has been a major challenge for molecular cancer drug discovery. The proof of principle that its inhibition is nevertheless feasible came from in vivo studies using a dominant-negative allele of MYC termed OmoMYC. Systemic expression of OmoMYC triggered long-term tumor regression with mild and fully reversible side effects on normal tissues. In this study, OmoMYC's mode of action was investigated combining methods of structural biology and functional genomics to elucidate how it is able to preferentially affect oncogenic functions of MYC. The crystal structure of the OmoMYC homodimer, both in the free and the E-box-bound state, was determined, which revealed that OmoMYC forms a stable homodimer, and as such, recognizes DNA via the same base-specific DNA contacts as the MYC/MAX heterodimer. OmoMYC binds DNA with an equally high affinity as MYC/MAX complexes. RNA-sequencing showed that OmoMYC blunts both MYC-dependent transcriptional activation and repression. Genome-wide DNA-binding studies using chromatin immunoprecipitation followed by high-throughput sequencing revealed that OmoMYC competes with MYC/MAX complexes on chromatin, thereby reducing their occupancy at consensus DNA binding sites. The most prominent decrease in MYC binding was seen at low-affinity promoters, which were invaded by MYC at oncogenic levels. Strikingly, gene set enrichment analyses using OmoMYC-regulated genes enabled the identification of tumor subgroups with high MYC levels in multiple tumor entities. Together with a targeted shRNA screen, this identified novel targets for the eradication of MYC-driven tumors, such as ATAD3A, BOP1, and ADRM1. In summary, the findings suggest that OmoMYC specifically inhibits tumor cell growth by attenuating the expression of rate-limiting proteins in cellular processes that respond to elevated levels of MYC protein using a DNA-competitive mechanism. This opens up novel strategies to target oncogenic MYC functions for tumor therapy.}, subject = {Myc}, language = {en} } @article{FalibeneRocesRoessleretal.2016, author = {Falibene, Augustine and Roces, Flavio and R{\"o}ssler, Wolfgang and Groh, Claudia}, title = {Daily Thermal Fluctuations Experienced by Pupae via Rhythmic Nursing Behavior Increase Numbers of Mushroom Body Microglomeruli in the Adult Ant Brain}, series = {Frontiers in Behavioral Neuroscience}, volume = {10}, journal = {Frontiers in Behavioral Neuroscience}, number = {73}, doi = {10.3389/fnbeh.2016.00073}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146711}, year = {2016}, abstract = {Social insects control brood development by using different thermoregulatory strategies. Camponotus mus ants expose their brood to daily temperature fluctuations by translocating them inside the nest following a circadian rhythm of thermal preferences. At the middle of the photophase brood is moved to locations at 30.8°C; 8 h later, during the night, the brood is transferred back to locations at 27.5°C. We investigated whether daily thermal fluctuations experienced by developing pupae affect the neuroarchitecture in the adult brain, in particular in sensory input regions of the mushroom bodies (MB calyces). The complexity of synaptic microcircuits was estimated by quantifying MB-calyx volumes together with densities of presynaptic boutons of microglomeruli (MG) in the olfactory lip and visual collar regions. We compared young adult workers that were reared either under controlled daily thermal fluctuations of different amplitudes, or at different constant temperatures. Thermal regimes significantly affected the large (non-dense) olfactory lip region of the adult MB calyx, while changes in the dense lip and the visual collar were less evident. Thermal fluctuations mimicking the amplitudes of natural temperature fluctuations via circadian rhythmic translocation of pupae by nurses (amplitude 3.3°C) lead to higher numbers of MG in the MB calyces compared to those in pupae reared at smaller or larger thermal amplitudes (0.0, 1.5, 9.6°C), or at constant temperatures (25.4, 35.0°C). We conclude that rhythmic control of brood temperature by nursing ants optimizes brain development by increasing MG densities and numbers in specific brain areas. Resulting differences in synaptic microcircuits are expected to affect sensory processing and learning abilities in adult ants, and may also promote interindividual behavioral variability within colonies.}, language = {en} } @article{KaltdorfSrivastavaGuptaetal.2016, author = {Kaltdorf, Martin and Srivastava, Mugdha and Gupta, Shishir K. and Liang, Chunguang and Binder, Jasmin and Dietl, Anna-Maria and Meir, Zohar and Haas, Hubertus and Osherov, Nir and Krappmann, Sven and Dandekar, Thomas}, title = {Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach}, series = {Frontiers in Molecular Bioscience}, volume = {3}, journal = {Frontiers in Molecular Bioscience}, doi = {10.3389/fmolb.2016.00022}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147396}, pages = {22}, year = {2016}, abstract = {New antimycotic drugs are challenging to find, as potential target proteins may have close human orthologs. We here focus on identifying metabolic targets that are critical for fungal growth and have minimal similarity to targets among human proteins. We compare and combine here: (I) direct metabolic network modeling using elementary mode analysis and flux estimates approximations using expression data, (II) targeting metabolic genes by transcriptome analysis of condition-specific highly expressed enzymes, and (III) analysis of enzyme structure, enzyme interconnectedness ("hubs"), and identification of pathogen-specific enzymes using orthology relations. We have identified 64 targets including metabolic enzymes involved in vitamin synthesis, lipid, and amino acid biosynthesis including 18 targets validated from the literature, two validated and five currently examined in own genetic experiments, and 38 further promising novel target proteins which are non-orthologous to human proteins, involved in metabolism and are highly ranked drug targets from these pipelines.}, language = {en} } @phdthesis{Ruf2016, author = {Ruf, Franziska}, title = {The circadian regulation of eclosion in \(Drosophila\) \(melanogaster\)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146265}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Eclosion is the emergence of an adult insect from the pupal case at the end of development. In the fruit fly Drosophila melanogaster, eclosion is a circadian clock-gated event and is regulated by various peptides. When studied on the population level, eclosion reveals a clear rhythmicity with a peak at the beginning of the light-phase that persists also under constant conditions. It is a long standing hypothesis that eclosion gating to the morning hours with more humid conditions is an adaption to reduce water loss and increase the survival. Eclosion behavior, including the motor pattern required for the fly to hatch out of the puparium, is orchestrated by a well-characterized cascade of peptides. The main components are ecdysis-triggering hormone (ETH), eclosion hormone (EH) and crustacean cardioactive peptide (CCAP). The molt is initiated by a peak level and pupal ecdysis by a subsequent decline of the ecdysteroid ecdysone. Ecdysteroids are produced by the prothoracic gland (PG), an endocrine tissue that contains a peripheral clock and degenerates shortly after eclosion. Production and release of ecdysteroids are regulated by the prothoracicotropic hormone (PTTH). Although many aspects of the circadian clock and the peptidergic control of the eclosion behavior are known, it still remains unclear how both systems are interconnected. The aim of this dissertation research was to dissect this connection and evaluate the importance of different Zeitgebers on eclosion rhythmicity under natural conditions. Potential interactions between the central clock and the peptides regulating ecdysis motor behavior were evaluated by analyzing the influence of CCAP on eclosion rhythmicity. Ablation and silencing of CCAP neurons, as well as CCAP null-mutation did not affect eclosion rhythmicity under either light or temperature entrainment nor under natural conditions. To dissect the connection between the central and the peripheral clock, PTTH neurons were ablated. Monitoring eclosion under light and temperature entrainment revealed that eclosion became arrhythmic under constant conditions. However, qPCR expression analysis revealed no evidence for cycling of Ptth mRNA in pharate flies. To test for a connection with pigment-dispersing factor (PDF)-expressing neurons, the PDF receptor (PDFR) and short neuropeptide F receptor (sNPFR) were knocked down in the PTTH neurons. Knockdown of sNPFR, but not PDFR, resulted in arrhythmic eclosion under constant darkness conditions. PCR analysis of the PTTH receptor, Torso, revealed its expression in the PG and the gonads, but not in the brain or eyes, of pharate flies. Knockdown of torso in the PG lead to arrhythmicity under constant conditions, which provides strong evidence for the specific effect of PTTH on the PG. These results suggest connections from the PDF positive lateral neurons to the PTTH neurons via sNPF signaling, and to the PG via PTTH and Torso. This interaction presumably couples the period of the peripheral clock in the PG to that of the central clock in the brain. To identify a starting signal for eclosion and possible further candidates in the regulation of eclosion behavior, chemically defined peptidergic and aminergic neurons were optogenetically activated in pharate pupae via ChR2-XXL. This screen approach revealed two candidates for the regulation of eclosion behavior: Dromyosuppressin (DMS) and myo-inhibitory peptides (MIP). However, ablation of DMS neurons did not affect eclosion rhythmicity or success and the exact function of MIP must be evaluated in future studies. To assess the importance of the clock and of possible Zeitgebers in nature, eclosion of the wildtype Canton S and the clock mutant per01 and the PDF signaling mutants pdf01 and han5304 was monitored under natural conditions. For this purpose, the W{\"u}rzburg eclosion monitor (WEclMon) was developed, which is a new open monitoring system that allows direct exposure of pupae to the environment. A general decline of rhythmicity under natural conditions compared to laboratory conditions was observed in all tested strains. While the wildtype and the pdf01 and han5304 mutants stayed weakly rhythmic, the per01 mutant flies eclosed mostly arrhythmic. PDF and its receptor (PDFR encoded by han) are required for the synchronization of the clock network and functional loss can obviously be compensated by a persisting synchronization to external Zeitgebers. The loss of the central clock protein PER, however, lead to a non-functional clock and revealed the absolute importance of the clock for eclosion rhythmicity. To quantitatively analyze the effect of the clock and abiotic factors on eclosion rhythmicity, a statistical model was developed in cooperation with Oliver Mitesser and Thomas Hovestadt. The modelling results confirmed the clock as the most important factor for eclosion rhythmicity. Moreover, temperature was found to have the strongest effect on the actual shape of the daily emergence pattern, while light has only minor effects. Relative humidity could be excluded as Zeitgeber for eclosion and therefore was not further analyzed. Taken together, the present dissertation identified the so far unknown connection between the central and peripheral clock regulating eclosion. Furthermore, a new method for the analysis of eclosion rhythms under natural conditions was established and the necessity of a functional clock for rhythmic eclosion even in the presence of multiple Zeitgebers was shown.}, subject = {Taufliege}, language = {en} } @article{DejungSubotaBuceriusetal.2016, author = {Dejung, Mario and Subota, Ines and Bucerius, Ferdinand and Dindar, G{\"u}lcin and Freiwald, Anja and Engstler, Markus and Boshart, Michael and Butter, Falk and Janzen, Chistian J.}, title = {Quantitative proteomics uncovers novel factors involved in developmental differentiation of Trypanosoma brucei}, series = {PLoS Pathogens}, volume = {12}, journal = {PLoS Pathogens}, number = {2}, doi = {10.1371/journal.ppat.1005439}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146362}, pages = {e1005439}, year = {2016}, abstract = {Developmental differentiation is a universal biological process that allows cells to adapt to different environments to perform specific functions. African trypanosomes progress through a tightly regulated life cycle in order to survive in different host environments when they shuttle between an insect vector and a vertebrate host. Transcriptomics has been useful to gain insight into RNA changes during stage transitions; however, RNA levels are only a moderate proxy for protein abundance in trypanosomes. We quantified 4270 protein groups during stage differentiation from the mammalian-infective to the insect form and provide classification for their expression profiles during development. Our label-free quantitative proteomics study revealed previously unknown components of the differentiation machinery that are involved in essential biological processes such as signaling, posttranslational protein modifications, trafficking and nuclear transport. Furthermore, guided by our proteomic survey, we identified the cause of the previously observed differentiation impairment in the histone methyltransferase DOT1B knock-out strain as it is required for accurate karyokinesis in the first cell division during differentiation. This epigenetic regulator is likely involved in essential chromatin restructuring during developmental differentiation, which might also be important for differentiation in higher eukaryotic cells. Our proteome dataset will serve as a resource for detailed investigations of cell differentiation to shed more light on the molecular mechanisms of this process in trypanosomes and other eukaryotes.}, language = {en} } @phdthesis{Cicova2016, author = {Cicova, Zdenka}, title = {Characterization of a novel putative factor involved in host adaptation in Trypanosoma brucei}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-142462}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Trypanosomes are masters of adaptation to different host environments during their complex life cycle. Large-scale proteomic approaches provide information on changes at the cellular level in a systematic way. However, a detailed work on single components is necessary to understand the adaptation mechanisms on a molecular level. Here we have performed a detailed characterization of a bloodstream form (BSF) stage-specific putative flagellar host adaptation factor (Tb927.11.2400) identified previously in a SILAC-based comparative proteome study. Tb927.11.2400 shares 38\% amino acid identity with TbFlabarin (Tb927.11.2410), a procyclic form (PCF) stage specific flagellar BAR domain protein. We named Tb927.11.2400 TbFlabarin like (TbFlabarinL) and demonstrate that it is a result of a gene duplication event, which occurred in African trypanosomes. TbFlabarinL is not essential for growth of the parasites under cell culture conditions and it is dispensable for developmental differentiation from BSF to the PCF in vitro. We generated a TbFlabarinL-specific antibody and showed that it localizes in the flagellum. The co-immunoprecipitation experiment together with a biochemical cell fractionation indicated a dual association of TbFlabarinL with the flagellar membrane and the components of the paraflagellar rod.}, subject = {Trypanosoma brucei}, language = {en} } @phdthesis{Kupper2016, author = {Kupper, Maria}, title = {The immune transcriptome and proteome of the ant Camponotus floridanus and vertical transmission of its bacterial endosymbiont Blochmannia floridanus}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-142534}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {The evolutionary success of insects is believed to be at least partially facilitated by symbioses between insects and prokaryotes. Bacterial endosymbionts confer various fitness advantages to their hosts, for example by providing nutrients lacking from the insects' diet thereby enabling the inhabitation of new ecological niches. The Florida carpenter ant Camponotus floridanus harbours endosymbiotic bacteria of the genus Blochmannia. These primary endosymbionts mainly reside in the cytoplasm of bacteriocytes, specialised cells interspersed into the midgut tissue, but they were also found in oocytes which allows their vertical transmission. The social lifestyle of C. floridanus may facilitate the rapid spread of infections amongst genetically closely related animals living in huge colonies. Therefore, the ants require an immune system to efficiently combat infections while maintaining a "chronic" infection with their endosymbionts. In order to investigate the immune repertoire of the ants, the Illumina sequencing method was used. The previously published genome sequence of C. floridanus was functionally re-annotated and 0.53\% of C. floridanus proteins were assigned to the gene ontology (GO) term subcategory "immune system process". Based on homology analyses, genes encoding 510 proteins with possible immune function were identified. These genes are involved in microbial recognition and immune signalling pathways but also in cellular defence mechanisms, such as phagocytosis and melanisation. The components of the major signalling pathways appear to be highly conserved and the analysis revealed an overall broad immune repertoire of the ants though the number of identified genes encoding pattern recognition receptors (PRRs) and antimicrobial peptides (AMPs) is comparatively low. Besides three genes coding for homologs of thioester-containing proteins (TEPs), which have been shown to act as opsonins promoting phagocytosis in other insects, six genes encoding the AMPs defesin-1 and defensin-2, hymenoptaecin, two tachystatin-like peptides and one crustin-like peptide are present in the ant genome. Although the low number of known AMPs in comparison to 13 AMPs in the honey bee Apis mellifera and 46 AMPs in the wasp Nasonia vitripennis may indicate a less potent immune system, measures summarised as external or social immunity may enhance the immune repertoire of C. floridanus, as it was discussed for other social insects. Also, the hymenoptaecin multipeptide precursor protein may be processed to yield seven possibly bioactive peptides. In this work, two hymenoptaecin derived peptides were heterologously expressed and purified. The preliminary antimicrobial activity assays indicate varying bacteriostatic effects of different hymenoptaecin derived peptides against Escherichia coli D31 and Staphylococcus aureus which suggests a functional amplification of the immune response further increasing the antimicrobial potency of the ants. Furthermore, 257 genes were differentially expressed upon immune challenge of C. floridanus and most of the immune genes showing differential expression are involved in recognition of microbes or encode immune effectors rather than signalling components. Additionally, genes coding for proteins involved in storage and metabolism were downregulated upon immune challenge suggesting a trade-off between two energy-intensive processes in order to enhance effectiveness of the immune response. The analysis of gene expression via qRT-PCR was used for validation of the transcriptome data and revealed stage-specific immune gene regulation. Though the same tendencies of regulation were observed in larvae and adults, expression of several immune-related genes was generally more strongly induced in larvae. Immune gene expression levels depending on the developmental stage of C. floridanus are in agreement with observations in other insects and might suggest that animals from different stages revert to individual combinations of external and internal immunity upon infection. The haemolymph proteome of immune-challenged ants further established the immune-relevance of several proteins involved in classical immune signalling pathways, e.g. PRRs, extracellularly active proteases of the Toll signalling pathway and effector molecules such as AMPs, lysozymes and TEPs. Additionally, non-canonical proteins with putative immune function were enriched in immune-challenged haemolymph, e.g. Vitellogenins, NPC2-like proteins and Hemocytin. As known from previous studies, septic wounding also leads to the upregulation of genes involved in stress responses. In the haemolymph, proteins implicated in protein stabilisation and in the protection against oxidative stress and insecticides were enriched upon immune challenge. In order to identify additional putative immune effectors, haemolymph peptide samples from immune-challenged larvae and adults were analysed. The analysis in this work focussed on the identification of putative peptides produced via the secretory pathway as previously described for neuropeptides of C. floridanus. 567 regulated peptides derived from 39 proteins were identified in the larval haemolymph, whereas 342 regulated peptides derived from 13 proteins were found in the adult haemolymph. Most of the peptides are derived from hymenoptaecin or from putative uncharacterised proteins. One haemolymph peptide of immune-challenged larvae comprises the complete amino acid sequence of a predicted peptide derived from a Vitellogenin. Though the identified peptide lacks similarities to any known immune-related peptide, it is a suitable candidate for further functional analysis. To establish a stable infection with the endosymbionts, the bacteria have to be transmitted to the next generation of the ants. The vertical transmission of B. floridanus is guaranteed by bacterial infestation of oocytes. This work presents the first comprehensive and detailed description of the localisation of the bacterial endosymbionts in C. floridanus ovaries during oogenesis. Whereas the most apical part of the germarium, which contains the germ-line stem cells, is not infected by the bacteria, small somatic cells in the outer layers of each ovariole were found to be infected in the lower germarium. Only with the beginning of cystocyte differentiation, endosymbionts are exclusively transported from follicle cells into the growing oocytes, while nurse cells were never infected with B. floridanus. This infestation of the oocytes by bacteria very likely involves exocytosis-endocytosis processes between follicle cells and the oocytes. A previous study suggested a down-modulation of the immune response in the midgut tissue which may promote endosymbiont tolerance. Therefore, the expression of several potentially relevant immune genes was analysed in the ovarial tissue by qRT-PCR. The relatively low expression of genes involved in Toll and IMD signalling, and the high expression of genes encoding negative immune regulators, such as PGRP-LB, PGRP-SC2, and tollip, strongly suggest that a down-modulation of the immune response may also facilitate endosymbiont tolerance in the ovaries and thereby contribute to their vertical transmission. Overall, the present thesis improves the knowledge about the immune repertoire of C. floridanus and provides new candidates for further functional analyses. Moreover, the involvement of the host immune system in maintaining a "chronic" infection with symbiotic bacteria was confirmed and extended to the ovaries.}, subject = {Camponotus floridanus}, language = {en} } @phdthesis{Maurus2016, author = {Maurus, Katja}, title = {Melanoma Maintenance by the AP1 Transcription Factor FOSL1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-142995}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Identifying novel driver genes in cancer remains a crucial step towards development of new therapeutic approaches and the basic understanding of the disease. This work describes the impact of the AP1 transcription activator component FOSL1 on melanoma maintenance. FOSL1 is strongly upregulated during the progression of melanoma and the protein abundance is highest in metastases. I found that the regulation of FOSL1 is strongly dependent on ERK1/2- and PI3K- signaling, two pathways frequently activated in melanoma. Moreover, the involvement of p53 in FOSL1 regulation in melanoma was investigated. Elevated levels of the tumor suppressor led to decreased FOSL1 protein levels in a miR34a/miR34c- dependent manner. The benefit of elevated FOSL1 amounts in human melanoma cell lines was analyzed by overexpression of FOSL1 in cell lines with low endogenous FOSL1 levels. Enhanced levels of FOSL1 had several pro-tumorigenic effects in human melanoma cell lines. Besides increased proliferation and migration rates, FOSL1 overexpression induced the colony forming ability of the cells. Additionally, FOSL1 was necessary for anchorage independent growth in 3D cell cultures. Microarray analyses revealed novel downstream effectors of FOSL1. On the one hand, FOSL1 was able to induce the transcription of different neuron-related genes, such as NEFL, NRP1 and TUBB3. On the other hand, FOSL1 influenced the transcription of DCT, a melanocyte specific gene, in dependence of the differentiation of the melanoma cell line, indicating dedifferentiation. Furthermore, FOSL1 induced the transcription of HMGA1, a chromatin remodeling protein with reprogramming ability, which is characteristic for stem cells. Consequently, the influence of HMGA1 on melanoma maintenance was investigated. In addition to decreased proliferation and reduced anoikis resistance, HMGA1 knockdown reduced melanoma cell survival. Interestingly, the FOSL1 induced pro-tumorigenic effects were demonstrated to be dependent on the HMGA1 level. HMGA1 manipulation reversed FOSL1 induced proliferation and colony forming ability, as well as the anchorage independent growth effect. In conclusion, I could show that additional FOSL1 confers a clear growth benefit to melanoma cells. This benefit is attributed to the induction of stem cell determinants, but can be blocked by the inhibition of the ERK1/2 or PI3K signaling pathways.}, subject = {Melanom}, language = {en} } @phdthesis{Schoenwaelder2016, author = {Sch{\"o}nw{\"a}lder, Sina Maria Siglinde}, title = {Entwicklung und Charakterisierung von Gelatine-basierten Hydrogelen und PLGA-basierten Janus-Partikeln}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-142636}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Zusammenfassung In der Regenerativen Medizin sind polymerbasierte Biomaterialien von großer Bedeutung f{\"u}r die Entwicklung und Anwendung verbesserter bzw. neuer Therapien. Die Erforschung der Oberfl{\"a}cheneigenschaften von Biomaterialien, welche als Implantate eingesetzt werden, ist eine grundlegende Voraussetzung f{\"u}r deren erfolgreichen Einsatz. Die Protein-Oberfl{\"a}chen- Interaktion geschieht initial, sobald ein Implantat mit K{\"o}rperfl{\"u}ssigkeiten oder mit Gewebe in Kontakt kommt, und tr{\"a}gt maßgeblich zur direkten Wechselwirkung von Implantat und umgebenden Zellen bei. Dieser Prozess wird in der vorliegenden Arbeit an Gelatine untersucht. Daher bestand ein Ziel darin, stabile, nanometerd{\"u}nne Gelatineoberfl{\"a}chen herzustellen und darauf die Adsorption von humanen Plasmaproteinen und bakteriellen Proteinen zu analysieren. Die Abscheidung der Gelatinefilme in variabler Schichtdicke auf zuvor mit PPX-Amin modifizierten Oberfl{\"a}chen wurde unter Verwendung eines Rotationsbeschichters durchgef{\"u}hrt. Um stabile Hydrogelfilme zu erhalten, wurden die Amingruppen der disaggregierten Gelatinefibrillen untereinander und mit denen der Amin-Modifizierung durch ein biokompatibles Diisocyanat quervernetzt. Dieser Prozess lieferte einen reproduzierbaren und chemisch stabilen Gelatinefilm, welcher durch die substratunabh{\"a}ngige Amin-Modifizierung kovalent auf unterschiedlichste Oberfl{\"a}chen aufgebracht werden konnte. Die durch den Herstellungsprozess pr{\"a}zise eingestellte Schichtdicke (Nano- bzw. Mikrometermaßstab) wurde mittels Ellipsometrie und Rasterkraftmikroskopie ermittelt. Die ebenso bestimmte Rauheit war unabh{\"a}ngig von der Schichtdicke sehr gering. Gelatinefilme, die auf funktionalisierte und strukturierte Proben aufgebracht wurden, konnten durch Elektronenmikroskopie dargestellt werden. Mit Hilfe der Infrarot-Reflexions-Absorptions-Spektroskopie wurden die Gelatinefilme im Hinblick auf ihre Stabilit{\"a}t chemisch charakterisiert. Zur Quantifizierung der Adsorption humaner Plasmaproteine (Einzelproteinl{\"o}sungen) und komplexer Proteingemische aus steril filtrierten Kultur{\"u}berst{\"a}nden des humanpathogenen Bakteriums Pseudomonas aeruginosa wurde die Quarzkristall-Mikrowaage mit Dissipations{\"u}berwachung eingesetzt. Hiermit konnte nicht nur die adsorbierte Menge an Proteinen auf dem Gelatinehydrogel bzw. Referenzoberfl{\"a}chen (Gold, PPX-Amin, Titan), sondern auch die viskoelastischen Eigenschaften des adsorbierten Proteinfilms bestimmt werden. Allgemein adsorbierte auf dem Gelatinehydrogel eine geringere Proteinmasse im Vergleich zu den Referenzoberfl{\"a}chen. Circa ein Viertel der adsorbierten Proteine migrierte in die Poren des gequollenen Gels und ver{\"a}nderte dessen viskoelastische Eigenschaften. Durch anschließende MALDI-ToF/MS- und MS/MS-Analyse konnten die bakteriellen Proteine auf den untersuchten Oberfl{\"a}chen identifiziert und untereinander verglichen werden. Hierbei zeigten sich nur geringf{\"u}gige Unterschiede in der Proteinzusammensetzung. Zudem wurde eine Sekund{\"a}rionenmassenspektrometrie mit Flugzeitanalyse an reinen Gelatinefilmen und an mit humanen Plasmaproteinen beladenen Gelatinefilmen durchgef{\"u}hrt. Durch eine anschließende multivariante Datenanalyse konnte zwischen den untersuchten Proben eindeutig differenziert werden. Dieser Ansatz erm{\"o}glicht es, die Adsorption von unterschiedlichen Proteinen auf proteinbasierten Oberfl{\"a}chen markierungsfrei zu untersuchen und kann zur Aufkl{\"a}rung der in vivo-Situation beitragen. Dar{\"u}ber hinaus bietet dieser Untersuchungsansatz neue Perspektiven f{\"u}r die Gestaltung und das schnelle und effiziente Screening von unterschiedlichen Proteinzusammensetzungen. Biomaterialien k{\"o}nnen jedoch nicht nur als Implantate oder Implantatbeschichtungen eingesetzt werden. Im Bereich des drug delivery und der Depotarzneimittel sind biologisch abbaubare Polymere, aufgrund ihrer variablen Eigenschaften, von großem Interesse. Die Behandlung von bakteriellen und fungalen Pneumonien stellt insbesondere bei Menschen mit Vorerkrankungen wie Cystische Fibrose oder prim{\"a}re Ziliendyskinesie eine große Herausforderung dar. Oral oder intraven{\"o}s applizierte Wirkstoffe erreichen die Erreger aufgrund der erh{\"o}hten Z{\"a}higkeit des Bronchialsekretes oft nicht in ausreichender Konzentration. Daher besteht ein weiteres Ziel der vorliegenden Arbeit darin, mittels electrohydrodynamic cojetting mikrometergroße, inhalierbare, wirkstoffbeladene Partikel mit zwei Kompartimenten (Janus-Partikel) herzustellen und deren Eignung f{\"u}r die therapeutische Anwendung bei Lungeninfektionen zu untersuchen. Durch das in dieser Arbeit entwickelte L{\"o}sungsmittelsystem k{\"o}nnen Janus-Partikel aus biologisch abbaubaren Co-Polymeren der Polymilchs{\"a}ure (Poly(lactid-co-glycolid), PLGA) hergestellt und mit verschiedenen Wirkstoffen beladen werden. Darunter befinden sich ein Antibiotikum (Aztreonam, AZT), ein Antimykotikum (Itraconazol, ICZ), ein Mukolytikum (Acetylcystein, ACC) und ein Antiphlogistikum (Ibuprofen, IBU). Die Freisetzung der eingelagerten Wirkstoffe, mit Ausnahme von ICZ, konnte unter physiologischen Bedingungen mittels Dialyse und anschließender Hochleistungsfl{\"u}ssigkeitschromatographie gemessen werden. Die Freisetzungsrate wird von der Kettenl{\"a}nge des Polymers beeinflusst, wobei eine k{\"u}rzere Kettenl{\"a}nge zu einer schnelleren Freisetzung f{\"u}hrt. Das in die Partikel eingelagerte Antimykotikum zeigte in vitro eine gute Wirksamkeit gegen Aspergillus nidulans. Durch das Einlagern von ICZ in die Partikel ist es m{\"o}glich diesen schlecht wasserl{\"o}slichen Wirkstoff in eine f{\"u}r Patienten zug{\"a}ngliche und wirksame Applikationsform zu bringen. In Interaktion mit P. aeruginosa erzielten die mit Antibiotikum beladenen Partikel in vitro bessere Ergebnisse als der Wirkstoff in L{\"o}sung, was sich in einem in vivo-Infektionsmodell mit der Wachsmotte Galleria mellonella best{\"a}tigte. AZT-beladene Partikel hatten gegen{\"u}ber einer identischen Wirkstoffmenge in L{\"o}sung eine 27,5\% bessere {\"U}berlebensrate der Wachsmotten zur Folge. Des Weiteren hatten die Partikel keinen messbaren negativen Einfluss auf die Wachsmotten. Dreidimensionale Atemwegsschleimhautmodelle, hergestellt mit Methoden des Tissue Engineerings, bildeten die Basis f{\"u}r Untersuchungen der Partikel in Interaktion mit humanen Atemwegszellen. Die Untersuchung von Apoptose- und Entz{\"u}ndungsmarkern im {\"U}berstand der 3D-Modelle zeigte diesbez{\"u}glich keinen negativen Einfluss der Partikel auf die humanen Zellen. Diese gut charakterisierten und standardisierten in vitro-Testsysteme machen es m{\"o}glich, Medikamentenuntersuchungen an menschlichen Zellen durchzuf{\"u}hren. Hinsichtlich der histologischen Architektur und funktionellen Eigenschaften der 3D-Modelle konnte eine hohe in vitro-/in vivo-Korrelation zu menschlichem Gewebe festgestellt werden. Humane Mucine auf den 3D-Modellen dienten zur Untersuchung der schleiml{\"o}senden Wirkung von ACC-beladenen Partikeln. Standen diese in r{\"a}umlichem Kontakt zu den Mucinen, wurde deren Z{\"a}higkeit durch das freigesetzte ACC herabgesetzt, was qualitativ mittels histologischen Methoden best{\"a}tigt werden konnte. Die in dieser Arbeit entwickelten Herstellungsprotokolle dienen als Grundlage und k{\"o}nnen f{\"u}r die Synthese {\"a}hnlicher Systeme, basierend auf anderen Polymeren und Wirkstoffen, modifiziert werden. Gelatine und PLGA erwiesen sich als vielseitig einsetzbare Werkstoffe und bieten eine breite Anwendungsvielfalt in der Regenerativen Medizin, was die erzielten Resultate bekr{\"a}ftigen.}, subject = {Gelatine}, language = {de} } @article{ZhuShabalaCuinetal.2016, author = {Zhu, Min and Shabala, Lana and Cuin, Tracey A and Huang, Xin and Zhou, Meixue and Munns, Rana and Shabala, Sergey}, title = {Nax loci affect SOS1-like Na\(^{+}\)/H\(^{+}\) exchanger expression and activity in wheat}, series = {Journal of Experimental Botany}, volume = {67}, journal = {Journal of Experimental Botany}, number = {3}, doi = {10.1093/jxb/erv493}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-150236}, pages = {835-844}, year = {2016}, abstract = {Salinity stress tolerance in durum wheat is strongly associated with a plant's ability to control Na\(^{+}\) delivery to the shoot. Two loci, termed Nax1 and Nax2, were recently identified as being critical for this process and the sodium transporters HKT1;4 and HKT1;5 were identified as the respective candidate genes. These transporters retrieve Na\(^{+}\) from the xylem, thus limiting the rates of Na\(^{+}\) transport from the root to the shoot. In this work, we show that the Nax loci also affect activity and expression levels of the SOS1-like Na\(^{+}\)/H\(^{+}\) exchanger in both root cortical and stelar tissues. Net Na\(^{+}\) efflux measured in isolated steles from salt-treated plants, using the non-invasive ion flux measuring MIFE technique, decreased in the sequence: Tamaroi (parental line)>Nax1=Nax2>Nax1:Nax2 lines. This efflux was sensitive to amiloride (a known inhibitor of the Na\(^{+}\)/H\(^{+}\) exchanger) and was mirrored by net H\(^{+}\) flux changes. TdSOS1 relative transcript levels were 6-10-fold lower in Nax lines compared with Tamaroi. Thus, it appears that Nax loci confer two highly complementary mechanisms, both of which contribute towards reducing the xylem Na\(^{+}\) content. One enhances the retrieval of Na\(^{+}\) back into the root stele via HKT1;4 or HKT1;5, whilst the other reduces the rate of Na\(^{+}\) loading into the xylem via SOS1. It is suggested that such duality plays an important adaptive role with greater versatility for responding to a changing environment and controlling Na\(^{+}\) delivery to the shoot.}, language = {en} } @article{PeckSchugZhangetal.2016, author = {Peck, Barrie and Schug, Zachary T. and Zhang, Qifeng and Dankworth, Beatrice and Jones, Dylan T. and Smethurst, Elizabeth and Patel, Rachana and Mason, Susan and Jian, Ming and Saunders, Rebecca and Howell, Michael and Mitter, Richard and Spencer-Dene, Bradley and Stamp, Gordon and McGarry, Lynn and James, Daniel and Shanks, Emma and Aboagye, Eric O. and Critchlow, Susan E. and Leung, Hing Y. and Harris, Adrian L. and Wakelam, Michael J. O. and Gottlieb, Eyal and Schulze, Almut}, title = {Inhibition of fatty acid desaturation is detrimental to cancer cell survival in metabolically compromised environments}, series = {Cancer \& Metabolism}, volume = {4}, journal = {Cancer \& Metabolism}, number = {6}, doi = {10.1186/s40170-016-0146-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-145905}, year = {2016}, abstract = {Background Enhanced macromolecule biosynthesis is integral to growth and proliferation of cancer cells. Lipid biosynthesis has been predicted to be an essential process in cancer cells. However, it is unclear which enzymes within this pathway offer the best selectivity for cancer cells and could be suitable therapeutic targets. Results Using functional genomics, we identified stearoyl-CoA desaturase (SCD), an enzyme that controls synthesis of unsaturated fatty acids, as essential in breast and prostate cancer cells. SCD inhibition altered cellular lipid composition and impeded cell viability in the absence of exogenous lipids. SCD inhibition also altered cardiolipin composition, leading to the release of cytochrome C and induction of apoptosis. Furthermore, SCD was required for the generation of poly-unsaturated lipids in cancer cells grown in spheroid cultures, which resemble those found in tumour tissue. We also found that SCD mRNA and protein expression is elevated in human breast cancers and predicts poor survival in high-grade tumours. Finally, silencing of SCD in prostate orthografts efficiently blocked tumour growth and significantly increased animal survival. Conclusions Our data implicate lipid desaturation as an essential process for cancer cell survival and suggest that targeting SCD could efficiently limit tumour expansion, especially under the metabolically compromised conditions of the tumour microenvironment.}, language = {en} } @phdthesis{Mattern2016, author = {Mattern, Felix}, title = {Alterungsbedingte Effekte auf DNA-Methylierungsprofile entwicklungsrelevanter Gene in Eizellen und Embryonen am Modellorganismus Bos taurus}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144562}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Die postovulatorische Alterung sowie die ovarielle Alterung konnten bei der Anwendung assistierter Reproduktionstechniken (ARTs) als entscheidende Faktoren identifiziert werden, die den Reproduktionserfolg nachhaltig beeintr{\"a}chtigen. Die postovulatorische Alterung tritt ein, sobald die reife Eizelle nicht mehr innerhalb ihres physiologischen Zeitfensters befruchtet wird. Die ovarielle Alterung beschreibt hingegen die Abnahme des Follikel-Vorrats mit zunehmendem Alter des weiblichen Individuums bzw. des Ovars. Sowohl die postovulatorische Alterung als auch die ovarielle Alterung f{\"u}hren u.a. zu einer reduzierten Oozytenqualit{\"a}t und einer geringeren Blastozystenrate. Die Zielsetzung dieser Arbeit bestand darin, den Einfluss der postovulatorischen Alterung und der ovariellen Alterung im Holstein-Rind (Bos taurus) auf die DNA-Methylierung entwicklungsrelevanter Gene in Eizellen und Embryonen zu untersuchen. Aus Schlachthof-Ovarien wurden Antralfollikeln unterschiedlicher Gr{\"o}ße (<2 mm, 3-5 mm und >6 mm) isoliert. Eizellen aus Follikeln der Gr{\"o}ße 3-5 mm wurden f{\"u}r 24h (physiologisch) und 48h (gealtert) in vitro gereift (IVM). Die gereiften Oozyten wurden anschließend in vitro fertilisiert und Embryonen im 4-6 Zellstadium generiert. Sowohl in den unreifen Eizellen aus Antralfollikeln unterschiedlicher Gr{\"o}ße als auch in den gereiften Oozyten und den Embryonen wurde die Promotormethylierung der Gene bH19, bSNRPN, bZAR1, bDNMT3A, bOCT4, bDNMT3Lo und bDNMT3Ls analysiert. Zur Untersuchung der ovariellen Alterung wurden mittelgroßen Antralfollikel aus Ovarien lebender Rinder (in vivo) unterschiedlichen Alters (9-12 Monate, 3-7 Jahre und 8-11 Jahre) gewonnen. In den daraus isolierten unreifen Eizellen wurde die DNA-Methylierung der Promotorregionen der Gene bTERF2, bREC8, bBCL-XL, bPISD, bBUB1, bDNMT3Lo, bH19 und bSNRPN bestimmt. Als Methode zur Analyse der Promotormethylierung wurde die Limiting Dilution Bisulfit-Sequenzierung angewendet. In unreifen Eizellen aus Antralfollikeln unterschiedlicher Gr{\"o}ße (<2 mm, 3-5 mm und >6 mm) konnte ein erh{\"o}htes Auftreten abnormal methylierter Allele in den gepr{\"a}gten Genen bH19 und bSNRPN von Eizellen kleiner Follikel (<2 mm) identifiziert werden. Dieses Ergebnis k{\"o}nnte eine m{\"o}gliche Ursache einer bereits bekannten und mehrfach beschriebenen geringeren Entwicklungskompetenz von Eizellen kleiner Follikel (<2 mm) auf epigenetischer Ebene darstellen. Die verl{\"a}ngerte Reifungsdauer der IVM-Eizellen hatte eine signifikante Hypermethylierung in der Promotorregion des Gens DNMT3Lo von 48h-gereiften Eizellen zur Folge. Beim {\"U}bergang von 48h-gereiften Eizellen zum Embryo konnte eine signifikante Hypomethylierung von CpG7 des stammzellspezifischen Transkripts DNMT3Ls beobachtet werden. Diese CpG-Stelle wies ebenfalls einen signifikanten Anstieg von CpGs mit nicht-eindeutigem Methylierungszustand in unreifen Eizellen mit steigender Follikelgr{\"o}ße auf. Da sich die CpG-Position innerhalb eines Sequenz-Motivs einer Bindungsstelle des Transkriptionsfaktors CREB befindet, k{\"o}nnten die Methylierungsdaten auf eine Interaktion zwischen dem Transkriptionsfaktor CREB und der DNA-Methylierung w{\"a}hrend der Entwicklung und Reifung der Eizelle sowie der Transition von der Eizelle zum Embryo hindeuten. Die DNA-Methylierungsprofile der untersuchten Gene in unreifen Eizellen aus K{\"u}hen unterschiedlichen Alters (9-12 Monate, 3-7 Jahre und 8-11 Jahre) wiesen keine signifikanten Unterschiede zwischen den Altersgruppen auf. Die ovarielle Alterung bei Rindern zwischen 9 Monaten und 11 Jahren zeigte damit keinen Effekt auf die DNA-Methylierung der untersuchten Promotorregionen der Gene bTERF2, bREC8, bBCL-XL, bPISD, bBUB1, bDNMT3Lo, bH19 und bSNRPN. Nach einer simulierten postovulatorischen Alterung durch eine in vitro Reifung f{\"u}r 48h konnte eine Ver{\"a}nderung der DNA-Methylierung der Oozyten-spezifischen (DNMT3Lo) und Stammzell-spezifischen (DNMT3Ls) Promotoren des katalytisch inaktiven Cofaktors von DNMT3A, DNMT3L, beobachtet werden. Die ver{\"a}nderte DNA-Methylierung von DNMT3Ls tritt dabei erst im fr{\"u}hen Embryo in Erscheinung und interagiert vermutlich mit dem Transkriptionsfaktor CREB. Die Ver{\"a}nderungen von DNMT3Lo in Eizellen und DNMT3Ls in den daraus generierten Embryonen l{\"a}sst vermuten, dass es sich hierbei um eine dynamische Anpassung des Embryos auf {\"a}ußere Umweltbedingungen der Eizelle {\"u}ber die Methylierung der DNA handelt.}, subject = {Oozyte}, language = {de} } @phdthesis{Sickel2016, author = {Sickel, Wiebke}, title = {High-throughput biodiversity assessment - Powers and limitations of meta-barcoding}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144573}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Traditional species identification based on morphological characters is laborious and requires expert knowledge. It is further complicated in the case of species assemblages or degraded and processed material. DNA-barcoding, species identification based on genetic data, has become a suitable alternative, yet species assemblages are still difficult to study. In the past decade meta-barcoding has widely been adopted for the study of species communities, due to technological advances in modern sequencing platforms and because manual separation of individual specimen is not required. Here, meta-barcoding is put into context and applied to the study of bee-collected pollen as well as bacterial communities. These studies provide the basis for a critical evaluation of the powers and limitations of meta-barcoding. Advantages identified include species identification without the need for expert knowledge as well as the high throughput of samples and sequences. In microbiology, meta-barcoding can facilitate directed cultivation of taxa of interest identified with meta-barcoding data. Disadvantages include insufficient species resolution due to short read lengths and incomplete reference databases, as well as limitations in abundance estimation of taxa and functional profiling. Despite these, meta-barcoding is a powerful method for the analysis of species communities and holds high potential especially for automated biomonitoring.}, subject = {Biodiversit{\"a}t}, language = {en} } @article{GrimmKleinKopeketal.2016, author = {Grimm, Jonathan B. and Klein, Teresa and Kopek, Benjamin G. and Shtengel, Gleb and Hess, Harald F. and Sauer, Markus and Lavis, Luke D.}, title = {Synthesis of a far-red photoactivatable silicon-containing rhodamine for super-resolution microscopy}, series = {Angewandte Chemie International Edition}, volume = {55}, journal = {Angewandte Chemie International Edition}, number = {5}, doi = {10.1002/anie.201509649}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191069}, pages = {1723-1727}, year = {2016}, abstract = {The rhodamine system is a flexible framework for building small-molecule fluorescent probes. Changing N-substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si-containing analogue of Q-rhodamine. This probe is the first example of a "caged" Si-rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red-shifted to allow multicolor imaging. The dye is a useful label for super-resolution imaging and constitutes a new scaffold for far-red fluorogenic molecules.}, language = {en} } @article{HassounaOttWuestefeldetal.2016, author = {Hassouna, I. and Ott, C. and W{\"u}stefeld, L. and Offen, N. and Neher, R. A. and Mitkovski, M. and Winkler, D. and Sperling, S. and Fries, L. and Goebbels, S. and Vreja, I. C. and Hagemeyer, N. and Dittrich, M. and Rossetti, M. F. and Kr{\"o}hnert, K. and Hannke, K. and Boretius, S. and Zeug, A. and H{\"o}schen, C. and Dandekar, T. and Dere, E. and Neher, E. and Rizzoli, S. O. and Nave, K.-A. and Sir{\´e}n, A.-L. and Ehrenreich, H.}, title = {Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus}, series = {Molecular Psychiatry}, volume = {21}, journal = {Molecular Psychiatry}, number = {12}, doi = {10.1038/mp.2015.212}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-186669}, pages = {1752-1767}, year = {2016}, abstract = {Recombinant human erythropoietin (EPO) improves cognitive performance in neuropsychiatric diseases ranging from schizophrenia and multiple sclerosis to major depression and bipolar disease. This consistent EPO effect on cognition is independent of its role in hematopoiesis. The cellular mechanisms of action in brain, however, have remained unclear. Here we studied healthy young mice and observed that 3-week EPO administration was associated with an increased number of pyramidal neurons and oligodendrocytes in the hippocampus of similar to 20\%. Under constant cognitive challenge, neuron numbers remained elevated until >6 months of age. Surprisingly, this increase occurred in absence of altered cell proliferation or apoptosis. After feeding a \(^{15}\)N-leucine diet, we used nanoscopic secondary ion mass spectrometry, and found that in EPO-treated mice, an equivalent number of neurons was defined by elevated \(^{15}\)N-leucine incorporation. In EPO-treated NG2-Cre-ERT2 mice, we confirmed enhanced differentiation of preexisting oligodendrocyte precursors in the absence of elevated DNA synthesis. A corresponding analysis of the neuronal lineage awaits the identification of suitable neuronal markers. In cultured neurospheres, EPO reduced Sox9 and stimulated miR124, associated with advanced neuronal differentiation. We are discussing a resulting working model in which EPO drives the differentiation of non-dividing precursors in both (NG2+) oligodendroglial and neuronal lineages. As endogenous EPO expression is induced by brain injury, such a mechanism of adult neurogenesis may be relevant for central nervous system regeneration.}, language = {en} } @article{SchneiderDittrichBoecketal.2016, author = {Schneider, Eberhard and Dittrich, Marcus and B{\"o}ck, Julia and Nanda, Indrajit and M{\"u}ller, Tobias and Seidmann, Larissa and Tralau, Tim and Galetzka, Danuta and El Hajj, Nady and Haaf, Thomas}, title = {CpG sites with continuously increasing or decreasing methylation from early to late human fetal brain development}, series = {Gene}, volume = {592}, journal = {Gene}, number = {1}, doi = {10.1016/j.gene.2016.07.058}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-186936}, pages = {110-118}, year = {2016}, abstract = {Normal human brain development is dependent on highly dynamic epigenetic processes for spatial and temporal gene regulation. Recent work identified wide-spread changes in DNA methylation during fetal brain development. We profiled CpG methylation in frontal cortex of 27 fetuses from gestational weeks 12-42, using Illumina 450K methylation arrays. Sites showing genome-wide significant correlation with gestational age were compared to a publicly available data set from gestational weeks 3-26. Altogether, we identified 2016 matching developmentally regulated differentially methylated positions (m-dDMPs): 1767 m-dDMPs were hypermethylated and 1149 hypomethylated during fetal development. M-dDMPs are underrepresented in CpG islands and gene promoters, and enriched in gene bodies. They appear to cluster in certain chromosome regions. M-dDMPs are significantly enriched in autism-associated genes and CpGs. Our results promote the idea that reduced methylation dynamics during fetal brain development may predispose to autism. In addition, m-dDMPs are enriched in genes with human-specific brain expression patterns and/or histone modifications. Collectively, we defined a subset of dDMPs exhibiting constant methylation changes from early to late pregnancy. The same epigenetic mechanisms involving methylation changes in cis-regulatory regions may have been adopted for human brain evolution and ontogeny.}, language = {en} } @article{MarkertBritzProppertetal.2016, author = {Markert, Sebastian Matthias and Britz, Sebastian and Proppert, Sven and Lang, Marietta and Witvliet, Daniel and Mulcahy, Ben and Sauer, Markus and Zhen, Mei and Bessereau, Jean-Louis and Stigloher, Christian}, title = {Filling the gap: adding super-resolution to array tomography for correlated ultrastructural and molecular identification of electrical synapses at the C. elegans connectome}, series = {Neurophotonics}, volume = {3}, journal = {Neurophotonics}, number = {4}, doi = {10.1117/1.NPh.3.4.041802}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-187292}, pages = {041802}, year = {2016}, abstract = {Correlating molecular labeling at the ultrastructural level with high confidence remains challenging. Array tomography (AT) allows for a combination of fluorescence and electron microscopy (EM) to visualize subcellular protein localization on serial EM sections. Here, we describe an application for AT that combines near-native tissue preservation via high-pressure freezing and freeze substitution with super-resolution light microscopy and high-resolution scanning electron microscopy (SEM) analysis on the same section. We established protocols that combine SEM with structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). We devised a method for easy, precise, and unbiased correlation of EM images and super-resolution imaging data using endogenous cellular landmarks and freely available image processing software. We demonstrate that these methods allow us to identify and label gap junctions in Caenorhabditis elegans with precision and confidence, and imaging of even smaller structures is feasible. With the emergence of connectomics, these methods will allow us to fill in the gap-acquiring the correlated ultrastructural and molecular identity of electrical synapses.}, language = {en} } @article{KilincEhrigPessianetal.2016, author = {Kilinc, Mehmet Okyay and Ehrig, Klaas and Pessian, Maysam and Minev, Boris R. and Szalay, Aladar A.}, title = {Colonization of xenograft tumors by oncolytic vaccinia virus (VACV) results in enhanced tumor killing due to the involvement of myeloid cells}, series = {Journal of Translational Medicine}, volume = {14}, journal = {Journal of Translational Medicine}, number = {340}, doi = {10.1186/s12967-016-1096-1}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168914}, year = {2016}, abstract = {Background The mechanisms by which vaccinia virus (VACV) interacts with the innate immune components are complex and involve different mechanisms. iNOS-mediated NO production by myeloid cells is one of the central antiviral mechanisms and this study aims to investigate specifically whether iNOS-mediated NO production by myeloid cells, is involved in tumor eradication following the virus treatment. Methods Human colon adenocarcinoma (HCT-116) xenograft tumors were infected by VACV. Infiltration of iNOS\(^{+}\) myeloid cell population into the tumor, and virus titer was monitored following the treatment. Single-cell suspensions were stained for qualitative and quantitative flow analysis. The effect of different myeloid cell subsets on tumor growth and colonization were investigated by depletion studies. Finally, in vitro culture experiments were carried out to study NO production and tumor cell killing. Student's t test was used for comparison between groups in all of the experiments. Results Infection of human colon adenocarcinoma (HCT-116) xenograft tumors by VACV has led to recruitment of many CD11b\(^{+}\) ly6G\(^{+}\) myeloid-derived suppressor cells (MDSCs), with enhanced iNOS expression in the tumors, and to an increased intratumoral virus titer between days 7 and 10 post-VACV therapy. In parallel, both single and multiple rounds of iNOS-producing cell depletions caused very rapid tumor growth within the same period after virus injection, indicating that VACV-induced iNOS\(^{+}\) MDSCs could be an important antitumor effector component. A continuous blockade of iNOS by its specific inhibitor, L-NIL, showed similar tumor growth enhancement 7-10 days post-infection. Finally, spleen-derived iNOS+ MDSCs isolated from virus-injected tumor bearing mice produced higher amounts of NO and effectively killed HCT-116 cells in in vitro transwell experiments. Conclusions We initially hypothesized that NO could be one of the factors that limits active spreading of the virus in the cancerous tissue. In contrast to our initial hypothesis, we observed that PMN-MDSCs were the main producer of NO through iNOS and NO provided a beneficial antitumor effect, The results strongly support an important novel role for VACV infection in the tumor microenvironment. VACV convert tumor-promoting MDSCs into tumor-killing cells by inducing higher NO production.}, language = {en} } @article{VogtmannHuaZelleretal.2016, author = {Vogtmann, Emily and Hua, Xing and Zeller, Georg and Sunagawa, Shinichi and Voigt, Anita Y. and Hercog, Rajna and Goedert, James J. and Shi, Jianxin and Bork, Peer and Sinha, Rashmi}, title = {Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {5}, doi = {10.1371/journal.pone.0155362}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166904}, pages = {e0155362}, year = {2016}, abstract = {Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population. In addition, metagenome-predicted genes, modules, and pathways in the Washington, DC cases and controls were compared to cases and controls recruited in France whose specimens were processed using the same platform. Associations between the presence of fecal Fusobacteria, Fusobacterium, and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by metagenomics, whereas higher relative abundance of Clostridia in cancer cases based on 16S rRNA was merely borderline based on metagenomics. This demonstrated that within the same sample set, most, but not all taxonomic associations were seen with both methods. Considering significant cancer associations with the relative abundance of genes, modules, and pathways in a recently published French metagenomics dataset, statistically significant associations in the Washington, DC population were detected for four out of 10 genes, three out of nine modules, and seven out of 17 pathways. In total, colorectal cancer status in the Washington, DC study was associated with 39\% of the metagenome-predicted genes, modules, and pathways identified in the French study. More within and between population comparisons are needed to identify sources of variation and disease associations that can be reproduced despite these variations. Future studies should have larger sample sizes or pool data across studies to have sufficient power to detect associations that are reproducible and significant after correction for multiple testing.}, language = {en} } @article{Hoelldobler2016, author = {H{\"o}lldobler, Bert}, title = {Queen Specific Exocrine Glands in Legionary Ants and Their Possible Function in Sexual Selection}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {3}, doi = {10.1371/journal.pone.0151604}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167057}, pages = {e0151604}, year = {2016}, abstract = {The colonies of army ants and some other legionary ant species have single, permanently wingless queens with massive post petioles and large gasters. Such highly modified queens are called dichthadiigynes. This paper presents the unusually rich exocrine gland endowment of dichthadiigynes, which is not found in queens of other ant species. It has been suggested these kinds of glands produce secretions that attract and maintain worker retinues around queens, especially during migration. However, large worker retinues also occur in non-legionary species whose queens do not have such an exuberance of exocrine glands. We argue and present evidence in support of our previously proposed hypothesis that the enormous outfit of exocrine glands found in dichthadiigynes is due to sexual selection mediated by workers as the main selecting agents}, language = {en} } @article{JoschinskiBeerHelfrichFoersteretal.2016, author = {Joschinski, Jens and Beer, Katharina and Helfrich-F{\"o}rster, Charlotte and Krauss, Jochen}, title = {Pea Aphids (Hemiptera: Aphididae) Have Diurnal Rhythms When Raised Independently of a Host Plant}, series = {Journal of Insect Science}, volume = {16}, journal = {Journal of Insect Science}, number = {1}, doi = {10.1093/jisesa/iew013}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168783}, pages = {31}, year = {2016}, abstract = {Seasonal timing is assumed to involve the circadian clock, an endogenous mechanism to track time and measure day length. Some debate persists, however, and aphids were among the first organisms for which circadian clock involvement was questioned. Inferences about links to phenology are problematic, as the clock itself is little investigated in aphids. For instance, it is unknown whether aphids possess diurnal rhythms at all. Possibly, the close interaction with host plants prevents independent measurements of rhythmicity. We reared the pea aphid Acyrthosiphon pisum (Harris) on an artificial diet, and recorded survival, moulting, and honeydew excretion. Despite their plant-dependent life style, aphids were independently rhythmic under light-dark conditions. This first demonstration of diurnal aphid rhythms shows that aphids do not simply track the host plant's rhythmicity.}, language = {en} } @phdthesis{Blaettner2016, author = {Bl{\"a}ttner, Sebastian}, title = {The role of the non-ribosomal peptide synthetase AusAB and its product phevalin in intracellular virulence of Staphylococcus aureus}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146662}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Staphylococcus aureus is a prevalent commensal bacterium which represents one of the leading causes in health care-associated bacterial infections worldwide and can cause a variety of different diseases ranging from simple abscesses to severe and life threatening infections including pneumonia, osteomyelitis and sepsis. In recent times multi-resistant strains have emerged, causing severe problems in nosocomial as well as community-acquired (CA) infection settings, especially in the United States (USA). Therefore S. aureus has been termed as a superbug by the WHO, underlining the severe health risk originating from it. Today, infections in the USA are dominated by S. aureus genotypes which are classified as USA300 and USA400, respectively. Strains of genotype USA300 are responsible for about 70\% of the CA infections. The molecular mechanisms which render S. aureus such an effective pathogen are still not understood in its entirety. For decades S. aureus was thought to be a strictly extracellular pathogen relying on pore-forming toxins like α-hemolysin to damage human cells and tissue. Only recently it has been shown that S. aureus can enter non-professional phagocytes, using adhesins like the fibronectin-binding proteins which mediate an endocytotic uptake into the host cells. The bacteria are consequently localized to endosomes, where the degradation of enclosed bacterial cells through phagosome maturation would eventually occur. S. aureus can avoid degradation, and translocate to the cellular cytoplasm, where it can replicate. The ability to cause this so-called phagosomal escape has mainly been attributed to a family of amphiphilic peptides called phenol soluble modulins (PSMs), but as studies have shown, they are not sufficient. In this work I used a transposon mutant library in combination with automated fluorescence microscopy to screen for genes involved in the phagosomal escape process and intracellular survival of S. aureus. I thereby identified a number of genes, including a non-ribosomal peptide synthetase (NRPS). The NRPS, encoded by the genes ausA and ausB, produces two types of small peptides, phevalin and tyrvalin. Mutations in the ausAB genes lead to a drastic decrease in phagosomal escape rates in epithelial cells, which were readily restored by genetic complementation in trans as well as by supplementation of synthetic phevalin. In leukocytes, phevalin interferes with calcium fluxes and activation of neutrophils and promotes cytotoxicity of intracellular bacteria in both, macrophages and neutrophils. Further ausAB is involved in survival and virulence of the bacterium during mouse lung pneumoniae. The here presented data demonstrates the contribution of the bacterial cyclic dipeptide phevalin to S. aureus virulence and suggests, that phevalin directly acts on a host cell target to promote cytotoxicity of intracellular bacteria.}, subject = {Staphylococcus aureus}, language = {en} } @article{HornKellerHildebrandtetal.2016, author = {Horn, Hannes and Keller, Alexander and Hildebrandt, Ulrich and K{\"a}mpfer, Peter and Riederer, Markus and Hentschel, Ute}, title = {Draft genome of the \(Arabidopsis\) \(thaliana\) phyllosphere bacterium, \(Williamsia\) sp. ARP1}, series = {Standards in Genomic Sciences}, volume = {11}, journal = {Standards in Genomic Sciences}, number = {8}, doi = {10.1186/s40793-015-0122-x}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146008}, year = {2016}, abstract = {The Gram-positive actinomycete \(Williamsia\) sp. ARP1 was originally isolated from the \(Arabidopsis\) \(thaliana\) phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus \(Williamsia\) and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.}, language = {en} } @article{OttoHahlbrockEichetal.2016, author = {Otto, Christoph and Hahlbrock, Theresa and Eich, Kilian and Karaaslan, Ferdi and J{\"u}rgens, Constantin and Germer, Christoph-Thomas and Wiegering, Armin and K{\"a}mmerer, Ulrike}, title = {Antiproliferative and antimetabolic effects behind the anticancer property of fermented wheat germ extract}, series = {BMC Complementary and Alternative Medicine}, volume = {16}, journal = {BMC Complementary and Alternative Medicine}, number = {160}, doi = {10.1186/s12906-016-1138-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146013}, year = {2016}, abstract = {Background Fermented wheat germ extract (FWGE) sold under the trade name Avemar exhibits anticancer activity in vitro and in vivo. Its mechanisms of action are divided into antiproliferative and antimetabolic effects. Its influcence on cancer cell metabolism needs further investigation. One objective of this study, therefore, was to further elucidate the antimetabolic action of FWGE. The anticancer compound 2,6-dimethoxy-1,4-benzoquinone (DMBQ) is the major bioactive compound in FWGE and is probably responsible for its anticancer activity. The second objective of this study was to compare the antiproliferative properties in vitro of FWGE and the DMBQ compound. Methods The IC\(_{50}\) values of FWGE were determined for nine human cancer cell lines after 24 h of culture. The DMBQ compound was used at a concentration of 24 μmol/l, which is equal to the molar concentration of DMBQ in FWGE. Cell viability, cell cycle, cellular redox state, glucose consumption, lactic acid production, cellular ATP levels, and the NADH/NAD\(^+\) ratio were measured. Results The mean IC\(_{50}\) value of FWGE for the nine human cancer cell lines tested was 10 mg/ml. Both FWGE (10 mg/ml) and the DMBQ compound (24 μmol/l) induced massive cell damage within 24 h after starting treatment, with changes in the cellular redox state secondary to formation of intracellular reactive oxygen species. Unlike the DMBQ compound, which was only cytotoxic, FWGE exhibited cytostatic and growth delay effects in addition to cytotoxicity. Both cytostatic and growth delay effects were linked to impaired glucose utilization which influenced the cell cycle, cellular ATP levels, and the NADH/NAD\(^+\) ratio. The growth delay effect in response to FWGE treatment led to induction of autophagy. Conclusions FWGE and the DMBQ compound both induced oxidative stress-promoted cytotoxicity. In addition, FWGE exhibited cytostatic and growth delay effects associated with impaired glucose utilization which led to autophagy, a possible previously unknown mechanism behind the influence of FWGE on cancer cell metabolism.}, language = {en} } @article{KneitzMishraChalopinetal.2016, author = {Kneitz, Susanne and Mishra, Rasmi R. and Chalopin, Domitille and Postlethwait, John and Warren, Wesley C. and Walther, Ronald B. and Schartl, Manfred}, title = {Germ cell and tumor associated piRNAs in the medaka and \(Xiphophorus\) melanoma models}, series = {BMC Genomics}, volume = {17}, journal = {BMC Genomics}, number = {357}, doi = {10.1186/s12864-016-2697-z}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146028}, year = {2016}, abstract = {Background A growing number of studies report an abnormal expression of Piwi-interacting RNAs (piRNAs) and the piRNA processing enzyme Piwi in many cancers. Whether this finding is an epiphenomenon of the chaotic molecular biology of the fast dividing, neoplastically transformed cells or is functionally relevant to tumorigenesisis is difficult to discern at present. To better understand the role of piRNAs in cancer development small laboratory fish models can make a valuable contribution. However, little is known about piRNAs in somatic and neoplastic tissues of fish. Results To identify piRNA clusters that might be involved in melanoma pathogenesis, we use several transgenic lines of medaka, and platyfish/swordtail hybrids, which develop various types of melanoma. In these tumors Piwi, is expressed at different levels, depending on tumor type. To quantify piRNA levels, whole piRNA populations of testes and melanomas of different histotypes were sequenced. Because no reference piRNA cluster set for medaka or Xiphophorus was yet available we developed a software pipeline to detect piRNA clusters in our samples and clusters were selected that were enriched in one or more samples. We found several loci to be overexpressed or down-regulated in different melanoma subtypes as compared to hyperpigmented skin. Furthermore, cluster analysis revealed a clear distinction between testes, low-grade and high-grade malignant melanoma in medaka. Conclusions Our data imply that dysregulation of piRNA expression may be associated with development of melanoma. Our results also reinforce the importance of fish as a suitable model system to study the role of piRNAs in tumorigenesis.}, language = {en} } @article{LichthardtKerscherDietzetal.2016, author = {Lichthardt, Sven and Kerscher, Alexander and Dietz, Ulrich A. and Jurowich, Christian and Kunzmann, Volker and von Rahden, Burkhard H. A. and Germer, Christoph-Thomas and Wiegering, Armin}, title = {Original article: role of adjuvant chemotherapy in a perioperative chemotherapy regimen for gastric cancer}, series = {BMC Cancer}, volume = {16}, journal = {BMC Cancer}, number = {650}, doi = {10.1186/s12885-016-2708-0}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147743}, year = {2016}, abstract = {Background Multimodal treatment strategies - perioperative chemotherapy (CTx) and radical surgery - are currently accepted as treatment standard for locally advanced gastric cancer. However, the role of adjuvant postoperative CTx (postCTx) in addition to neoadjuvant preoperative CTx (preCTx) in this setting remains controversial. Methods Between 4/2006 and 12/2013, 116 patients with locally advanced gastric cancer were treated with preCTx. 72 patients (62 \%), in whom complete tumor resection (R0, subtotal/total gastrectomy with D2-lymphadenectomy) was achieved, were divided into two groups, one of which receiving adjuvant therapy (n = 52) and one without (n = 20). These groups were analyzed with regard to survival and exclusion criteria for adjuvant therapy. Results Postoperative complications, as well as their severity grade, did not correlate with fewer postCTx cycles administered (p = n.s.). Long-term survival was shorter in patients receiving postCTx in comparison to patients without postCTx, but did not show statistical significance. In per protocol analysis by excluding two patients with perioperative death, a shorter 3-year survival rate was observed in patients receiving postCTx compared to patients without postCTx (3-year survival: 71.2 \% postCTx group vs. 90.0 \% non-postCTx group; p = 0.038). Conclusion These results appear contradicting to the anticipated outcome. While speculative, they question the value of post-CTx. Prospectively randomized studies are needed to elucidate the role of postCTx.}, language = {en} } @phdthesis{Pischimarov2016, author = {Pischimarov, Jordan Ivanov}, title = {Bioinformatische Methoden zur Identifizierung und Klassifizierung somatischer Mutationen in h{\"a}matologischen Erkrankungen}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147773}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Die Sequenzierungstechnologien entwickeln sich stetig weiter, dies erm{\"o}glicht eine zuvor nicht erreichte Ausbeute an experimentellen Daten und auch an Neuentwicklungen von zuvor nicht realisierbaren Experimenten. Zugleich werden spezifische Datenbanken, Algorithmen und Softwareprogramme entwickelt, um die neu entstandenen Daten zu analysieren. W{\"a}hrend der Untersuchung bioinformatischer Methoden f{\"u}r die Identifizierung und Klassifizierung somatischer Mutationen in h{\"a}matologischen Erkrankungen, zeigte sich eine hohe Vielfalt an alternativen Softwaretools die f{\"u}r die jeweiligen Analyseschritte genutzt werden k{\"o}nnen. Derzeit existiert noch kein Standard zur effizienten Analyse von Mutationen aus Next-Generation-Sequencing (NGS)-Daten. Die unterschiedlichen Methoden und Pipelines generieren Kandidaten, die zum gr{\"o}ßten Anteil in allen Ans{\"a}tzen identifiziert werden k{\"o}nnen, jedoch werden Software spezifische Kandidaten nicht einheitlich detektiert. Um eine einheitliche und effiziente Analyse von NGS-Daten durchzuf{\"u}hren war im Rahmen dieser Arbeit die Entwicklung einer benutzerfreundlichen und einheitlichen Pipeline vorgesehen. Hierf{\"u}r wurden zun{\"a}chst die essentiellen Analysen wie die Identifizierung der Basen, die Alignierung und die Identifizierung der Mutationen untersucht. Des Weiteren wurden unter Ber{\"u}cksichtigung von Effizienz und Performance diverse verf{\"u}gbare Softwaretools getestet, ausgewertet und sowohl m{\"o}gliche Verbesserungen als auch Erleichterungen der bisherigen Analysen vorgestellt und diskutiert. Durch Mitwirken in Konsortien wie der klinischen Forschergruppe 216 (KFO 216) und International Cancer Genome Consortium (ICGC) oder auch bei Haus-internen Projekten wurden Datens{\"a}tze zu den Entit{\"a}ten Multiples Myelom (MM), Burkitt Lymphom (BL) und Follikul{\"a}res Lymphom (FL) erstellt und analysiert. Die Selektion geeigneter Softwaretools und die Generierung der Pipeline basieren auf komparativen Analysen dieser Daten, sowie auf geteilte Ergebnisse und Erfahrungen in der Literatur und auch in Foren. Durch die gezielte Entwicklung von Skripten konnten biologische und klinische Fragestellungen bearbeitet werden. Hierzu z{\"a}hlten eine einheitliche Annotation der Gennamen, sowie die Erstellung von Genmutations-Heatmaps mit nicht Variant-Calling-File (VCF)-Syntax konformen Dateien. Des Weiteren konnten nicht abgedeckte Regionen des Genoms in den NGS-Daten identifiziert und analysiert werden. Neue Projekte zur detaillierten Untersuchung der Verteilung von wiederkehrender Mutationen und Funktionsassays zu einzelnen Mutationskandidaten konnten basierend auf den Ergebnissen initiiert werden. Durch eigens erstellte Python-Skripte konnte somit die Funktionalit{\"a}t der Pipeline erweitert werden und zu wichtigen Erkenntnissen bei der biologischen Interpretation der Sequenzierungsdaten f{\"u}hren, wie beispielsweise zu der Detektion von drei neuen molekularen Subgruppen im MM. Die Erweiterungen, der in dieser Arbeit entwickelten Pipeline verbesserte somit die Effizienz der Analyse und die Vergleichbarkeit unserer Daten. Des Weiteren konnte durch die Erstellung eines eigenen Skripts die Analyse von unbeachteten Regionen in den NGS-Daten erfolgen.}, subject = {Pipeline-Rechner}, language = {de} } @article{SommerlandtSpaetheRoessleretal.2016, author = {Sommerlandt, Frank M. J. and Spaethe, Johannes and R{\"o}ssler, Wolfgang and Dyer, Adrian G.}, title = {Does Fine Color Discrimination Learning in Free-Flying Honeybees Change Mushroom-Body Calyx Neuroarchitecture?}, series = {PLoS One}, volume = {11}, journal = {PLoS One}, number = {10}, doi = {10.1371/journal.pone.0164386}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147932}, pages = {e0164386}, year = {2016}, abstract = {Honeybees learn color information of rewarding flowers and recall these memories in future decisions. For fine color discrimination, bees require differential conditioning with a concurrent presentation of target and distractor stimuli to form a long-term memory. Here we investigated whether the long-term storage of color information shapes the neural network of microglomeruli in the mushroom body calyces and if this depends on the type of conditioning. Free-flying honeybees were individually trained to a pair of perceptually similar colors in either absolute conditioning towards one of the colors or in differential conditioning with both colors. Subsequently, bees of either conditioning groups were tested in non-rewarded discrimination tests with the two colors. Only bees trained with differential conditioning preferred the previously learned color, whereas bees of the absolute conditioning group, and a stimuli-na{\"i}ve group, chose randomly among color stimuli. All bees were then kept individually for three days in the dark to allow for complete long-term memory formation. Whole-mount immunostaining was subsequently used to quantify variation of microglomeruli number and density in the mushroom-body lip and collar. We found no significant differences among groups in neuropil volumes and total microglomeruli numbers, but learning performance was negatively correlated with microglomeruli density in the absolute conditioning group. Based on these findings we aim to promote future research approaches combining behaviorally relevant color learning tests in honeybees under free-flight conditions with neuroimaging analysis; we also discuss possible limitations of this approach.q}, language = {en} } @article{AnkenbrandWeberBeckeretal.2016, author = {Ankenbrand, Markus J. and Weber, Lorenz and Becker, Dirk and F{\"o}rster, Frank and Bemm, Felix}, title = {TBro: visualization and management of de novo transcriptomes}, series = {Database}, volume = {2016}, journal = {Database}, doi = {10.1093/database/baw146}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147954}, pages = {baw146}, year = {2016}, abstract = {RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro's modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers.}, language = {en} } @article{OthmanNaseemAwadetal.2016, author = {Othman, Eman M. and Naseem, Muhammed and Awad, Eman and Dandekar, Thomas and Stopper, Helga}, title = {The Plant Hormone Cytokinin Confers Protection against Oxidative Stress in Mammalian Cells}, series = {PLoS One}, volume = {11}, journal = {PLoS One}, number = {12}, doi = {10.1371/journal.pone.0168386}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147983}, pages = {e0168386}, year = {2016}, abstract = {Modulating key dynamics of plant growth and development, the effects of the plant hormone cytokinin on animal cells gained much attention recently. Most previous studies on cytokinin effects on mammalian cells have been conducted with elevated cytokinin concentration (in the μM range). However, to examine physiologically relevant dose effects of cytokinins on animal cells, we systematically analyzed the impact of kinetin in cultured cells at low and high concentrations (1nM-10μM) and examined cytotoxic and genotoxic conditions. We furthermore measured the intrinsic antioxidant activity of kinetin in a cell-free system using the Ferric Reducing Antioxidant Power assay and in cells using the dihydroethidium staining method. Monitoring viability, we looked at kinetin effects in mammalian cells such as HL60 cells, HaCaT human keratinocyte cells, NRK rat epithelial kidney cells and human peripheral lymphocytes. Kinetin manifests no antioxidant activity in the cell free system and high doses of kinetin (500 nM and higher) reduce cell viability and mediate DNA damage in vitro. In contrast, low doses (concentrations up to 100 nM) of kinetin confer protection in cells against oxidative stress. Moreover, our results show that pretreatment of the cells with kinetin significantly reduces 4-nitroquinoline 1-oxide mediated reactive oxygen species production. Also, pretreatment with kinetin retains cellular GSH levels when they are also treated with the GSH-depleting agent patulin. Our results explicitly show that low kinetin doses reduce apoptosis and protect cells from oxidative stress mediated cell death. Future studies on the interaction between cytokinins and human cellular pathway targets will be intriguing.}, language = {en} } @article{KunzWolfSchulzeetal.2016, author = {Kunz, Meik and Wolf, Beat and Schulze, Harald and Atlan, David and Walles, Thorsten and Walles, Heike and Dandekar, Thomas}, title = {Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools}, series = {Genes}, volume = {8}, journal = {Genes}, number = {1}, doi = {10.3390/genes8010008}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147990}, pages = {8}, year = {2016}, abstract = {Lung cancer is currently the leading cause of cancer related mortality due to late diagnosis and limited treatment intervention. Non-coding RNAs are not translated into proteins and have emerged as fundamental regulators of gene expression. Recent studies reported that microRNAs and long non-coding RNAs are involved in lung cancer development and progression. Moreover, they appear as new promising non-invasive biomarkers for early lung cancer diagnosis. Here, we highlight their potential as biomarker in lung cancer and present how bioinformatics can contribute to the development of non-invasive diagnostic tools. For this, we discuss several bioinformatics algorithms and software tools for a comprehensive understanding and functional characterization of microRNAs and long non-coding RNAs.}, language = {en} } @article{Kramer2016, author = {Kramer, Susanne}, title = {Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution}, series = {Nucleic Acids Research}, journal = {Nucleic Acids Research}, doi = {10.1093/nar/gkw1245}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148002}, pages = {gkw1245}, year = {2016}, abstract = {The detection of mRNAs undergoing transcription or decay is challenging, because both processes are fast. However, the relative proportion of an mRNA in synthesis or decay increases with mRNA size and decreases with mRNA half-life. Based on this rationale, I have exploited a 22 200 nucleotide-long, short-lived endogenous mRNA as a reporter for mRNA metabolism in trypanosomes. The extreme 5΄ and 3΄ ends were labeled with red- and green-fluorescent Affymetrix® single mRNA FISH probes, respectively. In the resulting fluorescence images, yellow spots represent intact mRNAs; red spots are mRNAs in transcription or 3΄-5΄ decay, and green spots are mRNAs in 5΄-3΄ degradation. Most red spots were nuclear and insensitive to transcriptional inhibition and thus likely transcription intermediates. Most green spots were cytoplasmic, confirming that the majority of cytoplasmic decay in trypanosomes is 5΄-3΄. The system showed the expected changes at inhibition of transcription or translation and RNAi depletion of the trypanosome homologue to the 5΄-3΄ exoribonuclease Xrn1. The method allows to monitor changes in mRNA metabolism both on cellular and on population/tissue wide levels, but also to study the subcellular localization of mRNA transcription and decay pathways. I show that the system is applicable to mammalian cells.}, language = {en} } @article{MildnerRoces2016, author = {Mildner, Stephanie and Roces, Flavio}, title = {Plasticity of Daily Behavioral Rhythms in Foragers and Nurses of the Ant Camponotus rufipes: Influence of Social Context and Feeding Times}, series = {PLoS One}, volume = {12}, journal = {PLoS One}, number = {1}, doi = {10.1371/journal.pone.0169244}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148010}, pages = {e0169244}, year = {2016}, abstract = {Daily activities within an ant colony need precise temporal organization, and an endogenous clock appears to be essential for such timing processes. A clock drives locomotor rhythms in isolated workers in a number of ant species, but its involvement in activities displayed in the social context is unknown. We compared locomotor rhythms in isolated individuals and behavioral rhythms in the social context of workers of the ant Camponotus rufipes. Both forager and nurse workers exhibited circadian rhythms in locomotor activity under constant conditions, indicating the involvement of an endogenous clock. Activity was mostly nocturnal and synchronized with the 12:12h light-dark-cycle. To evaluate whether rhythmicity was maintained in the social context and could be synchronized with non-photic zeitgebers such as feeding times, daily behavioral activities of single workers inside and outside the nest were quantified continuously over 24 hours in 1656 hours of video recordings. Food availability was limited to a short time window either at day or at night, thus mimicking natural conditions of temporally restricted food access. Most foragers showed circadian foraging behavior synchronized with food availability, either at day or nighttime. When isolated thereafter in single locomotor activity monitors, foragers mainly displayed arrhythmicity. Here, high mortality suggested potential stressful effects of the former restriction of food availability. In contrast, nurse workers showed high overall activity levels in the social context and performed their tasks all around the clock with no circadian pattern, likely to meet the needs of the brood. In isolation, the same individuals exhibited in turn strong rhythmic activity and nocturnality. Thus, endogenous activity rhythms were inhibited in the social context, and timing of daily behaviors was flexibly adapted to cope with task demands. As a similar socially-mediated plasticity in circadian rhythms was already shown in honey bees, the temporal organization in C. rufipes and honey bees appear to share similar basic features.}, language = {en} } @article{AdolfiHerpinRegensburgeretal.2016, author = {Adolfi, Mateus C. and Herpin, Amaury and Regensburger, Martina and Sacquegno, Jacopo and Waxman, Joshua S. and Schartl, Manfred}, title = {Retinoic acid and meiosis induction in adult versus embryonic gonads of medaka}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, doi = {10.1038/srep34281}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147843}, pages = {34281}, year = {2016}, abstract = {In vertebrates, one of the first recognizable sex differences in embryos is the onset of meiosis, known to be regulated by retinoic acid (RA) in mammals. We investigated in medaka a possible meiotic function of RA during the embryonic sex determination (SD) period and in mature gonads. We found RA mediated transcriptional activation in germ cells of both sexes much earlier than the SD stage, however, no such activity during the critical stages of SD. In adults, expression of the RA metabolizing enzymes indicates sexually dimorphic RA levels. In testis, RA acts directly in Sertoli, Leydig and pre-meiotic germ cells. In ovaries, RA transcriptional activity is highest in meiotic oocytes. Our results show that RA plays an important role in meiosis induction and gametogenesis in adult medaka but contrary to common expectations, not for initiating the first meiosis in female germ cells at the SD stage.}, language = {en} } @article{KrajinovicReimerKudlichetal.2016, author = {Krajinovic, K. and Reimer, S. and Kudlich, T. and Germer, C. T. and Wiegering, A.}, title = {"Rendezvous technique" for intraluminal vacuum therapy of anastomotic leakage of the jejunum}, series = {Surgical Case Reports}, volume = {2}, journal = {Surgical Case Reports}, number = {114}, doi = {10.1186/s40792-016-0243-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147883}, year = {2016}, abstract = {Background Anastomotic leakage (AL) is one of the most common and serious complications following visceral surgery. In recent years, endoluminal vacuum therapy has dramatically changed therapeutic options for AL, but its use has been limited to areas easily accessible by endoscope. Case presentation We describe the first use of endoluminal vacuum therapy in the small intestine employing a combined surgical and endoscopic "rendezvous technique" in which the surgeon assists the endoscopic placement of an endoluminal vacuum therapy sponge in the jejunum by means of a pullback string. This technique led to a completely closed AL after 27 days and 7 changes of the endosponge. Conclusion The combined surgical and endoscopic rendezvous technique can be useful in cases of otherwise difficult endosponge placement.}, language = {en} }