@phdthesis{Hackl2016, author = {Hackl, Thomas}, title = {A draft genome for the Venus flytrap, Dionaea muscipula : Evaluation of assembly strategies for a complex Genome - Development of novel approaches and bioinformatics solutions}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-133149}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {The Venus flytrap, \textit{Dionaea muscipula}, with its carnivorous life-style and its highly specialized snap-traps has fascinated biologist since the days of Charles Darwin. The goal of the \textit{D. muscipula} genome project is to gain comprehensive insights into the genomic landscape of this remarkable plant. The genome of the diploid Venus flytrap with an estimated size between 2.6 Gbp to 3.0 Gbp is comparatively large and comprises more than 70 \% of repetitive regions. Sequencing and assembly of genomes of this scale are even with state-of-the-art technology and software challenging. Initial sequencing and assembly of the genome was performed by the BGI (Beijing Genomics Institute) in 2011 resulting in a 3.7 Gbp draft assembly. I started my work with thorough assessment of the delivered assembly and data. My analysis showed that the BGI assembly is highly fragmented and at the same time artificially inflated due to overassembly of repetitive sequences. Furthermore, it only comprises about on third of the expected genes in full-length, rendering it inadequate for downstream analysis. In the following I sought to optimize the sequencing and assembly strategy to obtain an assembly of higher completeness and contiguity by improving data quality and assembly procedure and by developing tailored bioinformatics tools. Issues with technical biases and high levels of heterogeneity in the original data set were solved by sequencing additional short read libraries from high quality non-polymorphic DNA samples. To address contiguity and heterozygosity I examined numerous alternative assembly software packages and strategies and eventually identified ALLPATHS-LG as the most suited program for assembling the data at hand. Moreover, by utilizing digital normalization to reduce repetitive reads, I was able to substantially reduce computational demands while at the same time significantly increasing contiguity of the assembly. To improve repeat resolution and scaffolding, I started to explore the novel PacBio long read sequencing technology. Raw PacBio reads exhibit high error rates of 15 \% impeding their use for assembly. To overcome this issue, I developed the PacBio hybrid correction pipeline proovread (Hackl et al., 2014). proovread uses high coverage Illumina read data in an iterative mapping-based consensus procedure to identify and remove errors present in raw PacBio reads. In terms of sensitivity and accuracy, proovread outperforms existing software. In contrast to other correction programs, which are incapable of handling data sets of the size of D. muscipula project, proovread's flexible design allows for the efficient distribution of work load on high-performance computing clusters, thus enabling the correction of the Venus flytrap PacBio data set. Next to the assembly process itself, also the assessment of the large de novo draft assemblies, particularly with respect to coverage by available sequencing data, is difficult. While typical evaluation procedures rely on computationally extensive mapping approaches, I developed and implemented a set of tools that utilize k-mer coverage and derived values to efficiently compute coverage landscapes of large-scale assemblies and in addition allow for automated visualization of the of the obtained information in comprehensive plots. Using the developed tools to analyze preliminary assemblies and by combining my findings regarding optimizations of the assembly process, I was ultimately able to generate a high quality draft assembly for D. muscipula. I further refined the assembly by removal of redundant contigs resulting from separate assembly of heterozygous regions and additional scaffolding and gapclosing using corrected PacBio data. The final draft assembly comprises 86 × 10 3 scaffolds and has a total size of 1.45 Gbp. The difference to the estimated genomes size is well explained by collapsed repeats. At the same time, the assembly exhibits high fractions full-length gene models, corroborating the interpretation that the obtained draft assembly provides a complete and comprehensive reference for further exploration of the fascinating biology of the Venus flytrap.}, subject = {Venusfliegenfalle}, language = {en} } @article{BeerSteffanDewenterHaerteletal.2016, author = {Beer, Katharina and Steffan-Dewenter, Ingolf and H{\"a}rtel, Stephan and Helfrich-F{\"o}rster, Charlotte}, title = {A new device for monitoring individual activity rhythms of honey bees reveals critical effects of the social environment on behavior}, series = {Journal of Comparative Physiology A}, volume = {202}, journal = {Journal of Comparative Physiology A}, number = {8}, doi = {10.1007/s00359-016-1103-2}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188030}, pages = {555-565}, year = {2016}, abstract = {Chronobiological studies of individual activity rhythms in social insects can be constrained by the artificial isolation of individuals from their social context. We present a new experimental set-up that simultaneously measures the temperature rhythm in a queen-less but brood raising mini colony and the walking activity rhythms of singly kept honey bees that have indirect social contact with it. Our approach enables monitoring of individual bees in the social context of a mini colony under controlled laboratory conditions. In a pilot experiment, we show that social contact with the mini colony improves the survival of monitored young individuals and affects locomotor activity patterns of young and old bees. When exposed to conflicting Zeitgebers consisting of a light-dark (LD) cycle that is phase-delayed with respect to the mini colony rhythm, rhythms of young and old bees are socially synchronized with the mini colony rhythm, whereas isolated bees synchronize to the LD cycle. We conclude that the social environment is a stronger Zeitgeber than the LD cycle and that our new experimental set-up is well suited for studying the mechanisms of social entrainment in honey bees.}, language = {en} } @article{XuHeKaiseretal.2016, author = {Xu, Li and He, Jianzheng and Kaiser, Andrea and Gr{\"a}ber, Nikolas and Schl{\"a}ger, Laura and Ritze, Yvonne and Scholz, Henrike}, title = {A Single Pair of Serotonergic Neurons Counteracts Serotonergic Inhibition of Ethanol Attraction in Drosophila}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {12}, doi = {10.1371/journal.pone.0167518}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166762}, pages = {e0167518}, year = {2016}, abstract = {Attraction to ethanol is common in both flies and humans, but the neuromodulatory mechanisms underlying this innate attraction are not well understood. Here, we dissect the function of the key regulator of serotonin signaling—the serotonin transporter-in innate olfactory attraction to ethanol in Drosophila melanogaster. We generated a mutated version of the serotonin transporter that prolongs serotonin signaling in the synaptic cleft and is targeted via the Gal4 system to different sets of serotonergic neurons. We identified four serotonergic neurons that inhibit the olfactory attraction to ethanol and two additional neurons that counteract this inhibition by strengthening olfactory information. Our results reveal that compensation can occur on the circuit level and that serotonin has a bidirectional function in modulating the innate attraction to ethanol. Given the evolutionarily conserved nature of the serotonin transporter and serotonin, the bidirectional serotonergic mechanisms delineate a basic principle for how random behavior is switched into targeted approach behavior.}, language = {en} } @article{RosenbaumSchickWollbornetal.2016, author = {Rosenbaum, Corinna and Schick, Martin Alexander and Wollborn, Jakob and Heider, Andreas and Scholz, Claus-J{\"u}rgen and Cecil, Alexander and Niesler, Beate and Hirrlinger, Johannes and Walles, Heike and Metzger, Marco}, title = {Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo}, series = {PLoS One}, volume = {11}, journal = {PLoS One}, number = {3}, doi = {10.1371/journal.pone.0151335}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146544}, pages = {e0151335}, year = {2016}, abstract = {Background Enteric glial cells (EGCs) are the main constituent of the enteric nervous system and share similarities with astrocytes from the central nervous system including their reactivity to an inflammatory microenvironment. Previous studies on EGC pathophysiology have specifically focused on mucosal glia activation and its contribution to mucosal inflammatory processes observed in the gut of inflammatory bowel disease (IBD) patients. In contrast knowledge is scarce on intestinal inflammation not locally restricted to the mucosa but systemically affecting the intestine and its effect on the overall EGC network. Methods and Results In this study, we analyzed the biological effects of a systemic LPS-induced hyperinflammatory insult on overall EGCs in a rat model in vivo, mimicking the clinical situation of systemic inflammation response syndrome (SIRS). Tissues from small and large intestine were removed 4 hours after systemic LPS-injection and analyzed on transcript and protein level. Laser capture microdissection was performed to study plexus-specific gene expression alterations. Upon systemic LPS-injection in vivo we observed a rapid and dramatic activation of Glial Fibrillary Acidic Protein (GFAP)-expressing glia on mRNA level, locally restricted to the myenteric plexus. To study the specific role of the GFAP subpopulation, we established flow cytometry-purified primary glial cell cultures from GFAP promotor-driven EGFP reporter mice. After LPS stimulation, we analyzed cytokine secretion and global gene expression profiles, which were finally implemented in a bioinformatic comparative transcriptome analysis. Enriched GFAP+ glial cells cultured as gliospheres secreted increased levels of prominent inflammatory cytokines upon LPS stimulation. Additionally, a shift in myenteric glial gene expression profile was induced that predominantly affected genes associated with immune response. Conclusion and Significance Our findings identify the myenteric GFAP-expressing glial subpopulation as particularly susceptible and responsive to acute systemic inflammation of the gut wall and complement knowledge on glial involvement in mucosal inflammation of the intestine.}, 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{ChenReiherHermannLuibletal.2016, author = {Chen, Jiangtian and Reiher, Wencke and Hermann-Luibl, Christiane and Sellami, Azza and Cognigni, Paola and Kondo, Shu and Helfrich-F{\"o}rster, Charlotte and Veenstra, Jan A. and Wegener, Christian}, title = {Allatostatin A Signalling in Drosophila Regulates Feeding and Sleep and Is Modulated by PDF}, series = {PLoS Genetics}, volume = {12}, journal = {PLoS Genetics}, number = {9}, doi = {10.1371/journal.pgen.1006346}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178170}, year = {2016}, abstract = {Feeding and sleep are fundamental behaviours with significant interconnections and cross-modulations. The circadian system and peptidergic signals are important components of this modulation, but still little is known about the mechanisms and networks by which they interact to regulate feeding and sleep. We show that specific thermogenetic activation of peptidergic Allatostatin A (AstA)-expressing PLP neurons and enteroendocrine cells reduces feeding and promotes sleep in the fruit fly Drosophila. The effects of AstA cell activation are mediated by AstA peptides with receptors homolog to galanin receptors subserving similar and apparently conserved functions in vertebrates. We further identify the PLP neurons as a downstream target of the neuropeptide pigment-dispersing factor (PDF), an output factor of the circadian clock. PLP neurons are contacted by PDF-expressing clock neurons, and express a functional PDF receptor demonstrated by cAMP imaging. Silencing of AstA signalling and continuous input to AstA cells by tethered PDF changes the sleep/activity ratio in opposite directions but does not affect rhythmicity. Taken together, our results suggest that pleiotropic AstA signalling by a distinct neuronal and enteroendocrine AstA cell subset adapts the fly to a digestive energy-saving state which can be modulated by PDF.}, language = {en} } @phdthesis{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} } @article{SchwarzTamuriKultysetal.2016, author = {Schwarz, Roland F. and Tamuri, Asif U. and Kultys, Marek and King, James and Godwin, James and Florescu, Ana M. and Schultz, J{\"o}rg and Goldman, Nick}, title = {ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments}, series = {Nucleic Acids Research}, volume = {44}, journal = {Nucleic Acids Research}, number = {8}, doi = {10.1093/nar/gkw022}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166374}, pages = {e77}, year = {2016}, abstract = {Sequence Logos and its variants are the most commonly used method for visualization of multiple sequence alignments (MSAs) and sequence motifs. They provide consensus-based summaries of the sequences in the alignment. Consequently, individual sequences cannot be identified in the visualization and covariant sites are not easily discernible. We recently proposed Sequence Bundles, a motif visualization technique that maintains a one-to-one relationship between sequences and their graphical representation and visualizes covariant sites. We here present Alvis, an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the power of the visualization method with an interactive toolkit allowing detection of covariant sites, annotation of trees with synapomorphies and homoplasies, and motif detection. It also offers numerical analysis functionality, such as dimension reduction and classification. Alvis is user-friendly, highly customizable and can export results in publication-quality figures. It is available as a full-featured standalone version (http://www.bitbucket.org/rfs/alvis) and its Sequence Bundles visualization module is further available as a web application (http://science-practice.com/projects/sequence-bundles).}, 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{SerenGrimmFitzetal.2016, author = {Seren, {\"U}mit and Grimm, Dominik and Fitz, Joffrey and Weigel, Detlef and Nordborg, Magnus and Borgwardt, Karsten and Korte, Arthur}, title = {AraPheno: a public database for Arabidopsis thaliana phenotypes}, series = {Nucleic Acids Research}, volume = {45}, journal = {Nucleic Acids Research}, number = {D1}, doi = {10.1093/nar/gkw986}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147909}, pages = {D1054-D1059}, year = {2016}, abstract = {Natural genetic variation makes it possible to discover evolutionary changes that have been maintained in a population because they are advantageous. To understand genotype-phenotype relationships and to investigate trait architecture, the existence of both high-resolution genotypic and phenotypic data is necessary. Arabidopsis thaliana is a prime model for these purposes. This herb naturally occurs across much of the Eurasian continent and North America. Thus, it is exposed to a wide range of environmental factors and has been subject to natural selection under distinct conditions. Full genome sequencing data for more than 1000 different natural inbred lines are available, and this has encouraged the distributed generation of many types of phenotypic data. To leverage these data for meta analyses, AraPheno (https://arapheno.1001genomes.org) provide a central repository of population-scale phenotypes for A. thaliana inbred lines. AraPheno includes various features to easily access, download and visualize the phenotypic data. This will facilitate a comparative analysis of the many different types of phenotypic data, which is the base to further enhance our understanding of the genotype-phenotype map.}, language = {en} } @phdthesis{Imes2016, author = {Imes, Dennis}, title = {Aufkl{\"a}rung der molekularen Struktur und Funktion des R-Typ Anionenkanals QUAC1 in Schließzellen}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-136860}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Zum Gasaustausch mit Ihrer Umgebung besitzen h{\"o}here Pflanzen stomat{\"a}re Komplexe. Die Turgor-getrieben Atmungs{\"o}ffnungen in der Epidermis der Bl{\"a}tter werden von zwei Schließzellen ums{\"a}umt. Um bei Trockenheit einen exzessiven Verlust von Wasser zu verhindern, synthetisieren/importieren Schließzellen das Stresshormon ABA (Abszisins{\"a}ure), das {\"u}ber eine schnelle ABA-Signalkaskade plasmamembrangebundene Ionenkan{\"a}le steuert. Dabei wird der Stomaschluss durch die Aktivit{\"a}t von R-(rapid) und S-(slow)Typ Anionenkan{\"a}len initiiert. Obwohl die R- und S-Typ Anionenstr{\"o}me in Schließzellen seit Jahrzehnten bekannt waren, konnte erst k{\"u}rzlich das Gen identifiziert werden, das f{\"u}r den S-Typ Anionenkanal (SLAC1, Slow activating Anion Channel 1) kodiert. Daraufhin wurde schnell der Zusammenhang zwischen dem Stresshormon ABA, der ABA-Signalkette und der Aktivit{\"a}t des SLAC1 Anionenkanals im heterologen Expressionssystem der X. laevis Oozyten als auch in Schließzellprotoplasten aufgekl{\"a}rt. Es konnte gezeigt werden, dass ABA durch einen zytosolischen Rezeptor/Phosphatasekomplex (RCAR1/ABI1) erkannt wird und die Aktivit{\"a}t von kalziumabh{\"a}ngigen Kinasen (CPK-Familie) sowie kalziumunabh{\"a}ngigen Kinasen der SnRK2-Familie (OST1) steuert. In Anwesenheit von ABA phosphorylieren diese Kinasen SLAC1 und sorgen so f{\"u}r die Aktivierung von Anionenstr{\"o}men und damit f{\"u}r die Initiierung des Stomaschlusses. Die genetische Herkunft der ABA-induzierten R-Typ Str{\"o}me in Schließzellen war zu Beginn der vorliegenden Arbeit noch nicht bekannt. R-Typ Str{\"o}me zeichnen sich durch eine strikte Spannungsabh{\"a}ngigkeit und sehr schnellen Aktivierungs- sowie Deaktivierungskinetiken aus. Die Charakterisierung von Verlustmutanten des Schließzell-exprimierten Gens ALMT12 (Aluminium-aktivierter Malattransporter 12) konnte in Zusammenarbeit mit der Arbeitsgruppe Martinoia (Z{\"u}rich) erste Hinweise auf die Beteiligung dieses Gens an der Stomabewegung demonstrieren. Anschließende Patch-Clamp Untersuchungen an Schließzellprotoplasten aus Wildtyppflanzen und ALMT12-Verlustmutanten zeigten, dass ALMT12 f{\"u}r die Malat-aktivierte R-Typ Anionenstromkomponente verantwortlich ist. Deshalb wurde der Anionenkanal QUAC1 (Quickly activating Anion Channel 1) benannt - in Anlehnung an die Benennung des Anionenkanals SLAC1. Mit der Identifizierung von QUAC1 in planta war es nun meine Aufgabe, die elektrischen Eigenschaften von ALMT12/QUAC1 und dessen Aktivit{\"a}tskontrolle durch die ABA-Signalkaskade im heterologen Expressionssystem der Xenopus Oozyten zu untersuchen. Protein-Protein Interaktionsstudien mit der Hilfe der Bimolekularen Fluoreszenz-Technik, sowie die Beobachtung von markant erh{\"o}hten QUAC1 Anionenstr{\"o}men in Anwesenheit der SnRK2 Kinase OST1 und den Calcium-abh{\"a}ngigen Kinasen CPK2 und CPK20, ließen den Schluss zu, dass QUAC1, ebenso wie SLAC1, unter der Kontrolle des schnellen ABA-Signalwegs steht. Eine zus{\"a}tzliche Expression des negativen Regulators ABI1 unterdr{\"u}ckte die aktivierenden Eigenschaften der QUAC1-aktivierenden Kinasen, was die Hypothese der Koregulation von S- und R-Typ Anionenkan{\"a}len durch die gleiche ABA-Signalkaskade weiter unterst{\"u}tzt. Zur weiteren Aufkl{\"a}rung der elektrischen Eigenschaften von QUAC1 wurden tiefgreifende elektrophysiologische Untersuchungen mit der Zwei-Elektroden-Spannungsklemmen Technik durchgef{\"u}hrt. Durch die Wahl von geschickten Spannungsprotokollen konnte sowohl die schnelle Aktivierungskinetik als auch die schnelle Deaktivierungskinetik von QUAC1 bestimmt und quantifiziert werden. Diese Stromantworten waren sehr {\"a}hnlich zu den R-Typ Str{\"o}men, die man von Patch-Clamp Untersuchungen an Schließzellprotoplasten kannte, was ein weiteres Indiz daf{\"u}r war, dass es sich bei QUAC1 tats{\"a}chlich um eine Komponente des R-Typ Kanals aus Schließzellen handelt. Weiterf{\"u}hrende Untersuchungen bez{\"u}glich der Spannungsabh{\"a}ngigkeit und der Selektivit{\"a}t von QUAC1 charakterisierten das Protein als einen Depolarisations-aktivierten Anionenkanal mit einer starken Pr{\"a}ferenz f{\"u}r Dicarbons{\"a}uren wie Malat und Fumarat. Zudem konnte auch eine Leitf{\"a}higkeit f{\"u}r Sulfat und Chlorid nachgewiesen werden. Interessanterweise erwies sich Malat nicht nur als ein permeierendes Ion, sondern auch als ein regulierendes Ion, welches das spannungsabh{\"a}ngige Schalten von QUAC1 maßgeblich beeinflusst. Extrazellul{\"a}res Malat verschob die Offenwahrscheinlichkeit von QUAC1 sehr stark zu negativeren Membranspannungen, so dass der Anionenkanal bereits bei typischen Ruhespannungen von Schließzellen (ca. -150 mV) aktiviert werden konnte. Eine Beladung von QUAC1-exprimierender Oozyten mit Malat bewirkte zum einen h{\"o}here Anioneneffluxstr{\"o}me, aber auch eine Verschiebung der spannungsabh{\"a}ngigen Offenwahrscheinlichkeit zu negativeren Membranpotentialen. Struktur-Funktionsanalysen sollten die umstrittene Topologie von ALMT-{\"a}hnlichen Proteinen beleuchten und die molekulare Herkunft der Phosphorylierungsaktivierung aufzeigen, sowie die Malatabh{\"a}ngigkeit und die starke Spannungsabh{\"a}ngigkeit von QUAC1 aufkl{\"a}ren. Es zeigte sich jedoch schnell, dass Punktmutationen und Deletionen im C-Terminus von QUAC1 sehr h{\"a}ufig zu nicht-funktionellen Mutanten f{\"u}hrten. Diese Tatsache weist darauf hin, dass es sich um einen hoch-strukturierten und funktionell sehr wichtigen Bereich des Anionenkanals handelt. Auch die Topologie des Anionenkanalproteins wird in der Literatur kontrovers diskutiert. Sowohl die Lage des N- und C-Terminus (extrazellul{\"a}r oder intrazellul{\"a}r), als auch die Anzahl der membrandurchspannenden Dom{\"a}nen war nicht abschließend gekl{\"a}rt. Deshalb wurde in einem Fluoreszenz-basiertem Ansatz die Lage der Termini bestimmt. Im Rahmen meiner Arbeit konnte somit eindeutig gezeigt werden, dass sich beide Termini im Zytosol der Zelle befinden. Auf Grundlage von Modellen aus der Literatur und meiner Topologiebestimmungen konnte schließlich ein erweitertes Modell zur Struktur von QUAC1 entwickelt werden. Dieses Modell kann in Zukunft als Ausgangspunkt f{\"u}r weiterf{\"u}hrende Struktur-Funktionsanalysen dienen. Diese Arbeit hat somit gezeigt, dass das Gen QUAC1 tats{\"a}chlich eine Komponente der R-Typ Str{\"o}me in Schließzellen kodiert. Ebenso wie SLAC1 steht der Malat-induzierte Anionenkanal QUAC1 unter der Kontrolle der schnellen ABA-Signalkaskade. In Zukunft bleibt zu kl{\"a}ren, welche weiteren Gene f{\"u}r die R-Typ Kanalproteine in Schließzellen kodieren und welche strukturelle Grundlage f{\"u}r die besonderen Eigenschaften von QUAC1 hinsichtlich seiner schnellen Kinetiken, seiner Selektivit{\"a}t und Aktivierbarkeit durch Malat.}, subject = {Ackerschmalwand}, language = {de} } @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} } @phdthesis{Bertho2016, author = {Bertho, Sylvain}, title = {Biochemical and molecular characterization of an original master sex determining gene in Salmonids}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139130}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Sexual development is a fundamental and versatile process that shapes animal morphology, physiology and behavior. The underlying developmental process is composed of the sex determination and the sex differentiation. Sex determination mechanisms are extremely labile among taxa. The initial triggers of the sex determination process are often genetics called sex determining genes. These genes are expressed in the bipotential gonad and tilt the balance to a developmental program allowing the differentiation of either a testis or an ovary. Fish represent a large and fascinating vertebrate group to study both sex determination and sex differentiation mechanisms. To date, among the known sex determining genes, three gene families namely sox, dmrt and TGF-β factors govern this developmental program. As exception to this rule, sdY "sexually dimorphic on the Y" does not belong to one of these families as it comes from the duplication / evolution of an ancestor gene related to immunity, i.e., the interferon related factor 9, irf9. sdY is the master sex determining gene in salmonids, a group of fishes that include species such as rainbow trout and Atlantic salmon. The present study was aimed to firstly characterize the features of SdY protein. Results indicate that SdY is predominantly localized in the cytoplasm tested in various fish and mammalian cell lines and confirmed by different methods. Predictive in silico analysis revealed that SdY is composed of a β-sandwich core surrounded by three α-helices as well specific characteristics conferring a putative protein-protein interaction site. Secondly, the study was aimed to understand how SdY could trigger testicular differentiation. SdY is a truncated divergent version of Irf9 that has a conserved protein-protein domain but lost the DNA interaction domain of its ancestor gene. It was then hypothesized that SdY could initiate testicular differentiation by protein-protein interactions. To evaluate this we first conducted a yeast-two-hybrid screen that revealed a high proportion of transcription factors including fox proteins. Using various biochemical and cellular methods we confirm an interaction between SdY and Foxl2, a major transcription factor involved in ovarian differentiation and identity maintenance. Interestingly, the interaction of SdY with Foxl2 leads to nuclear translocation of SdY from the cytoplasm. Furthermore, this SdY translocation mechanism was found to be specific to fish Foxl2 and to a lesser extend Foxl3 and not other Fox proteins or mammalian FoxL2. In addition, we found that this interaction allows the stabilization of SdY and prevents its degradation. Finally, to better decipher SdY action we used as a model a mutated version of SdY that was identified in XY females of Chinook salmon natural population. Results show that this mutation induces a local conformation defect obviously leading to a misfolded protein and a quick degradation. Moreover, the mutated version compromised the interaction with Foxl2 defining a minimal threshold to induce testicular differentiation. Altogether results from my thesis propose that SdY would trigger testicular differentiation in salmonids by preventing Foxl2 to promote ovarian differentiation. Further research should be now carried out on how this interaction of SdY and Foxl2 acts in-vivo.}, subject = {Lachsartige }, language = {en} } @phdthesis{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{GomezHFelipeMedinaSanchezMartinetal.2016, author = {Gom{\´e}z-H, Laura and Felipe-Medina, Natalia and S{\´a}nchez-Mart{\´i}n, Manuel and Davies, Owen R. and Ramos, Isabel and Garc{\´i}a-Tu{\~n}{\´o}n, Ignacio and de Rooij, Dirk G. and Dereli, Ihsan and T{\´o}th, Attila and Barbero, Jos{\´e} Luis and Benavente, Ricardo and Llano, Elena and Pendas, Alberto M.}, title = {C14ORF39/SIX6OS1 is a constituent of the synaptonemal complex and is essential for mouse fertility}, series = {Nature Communications}, volume = {7}, journal = {Nature Communications}, doi = {10.1038/ncomms13298}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-165907}, pages = {13298}, year = {2016}, abstract = {Meiotic recombination generates crossovers between homologous chromosomes that are essential for genome haploidization. The synaptonemal complex is a 'zipper'-like protein assembly that synapses homologue pairs together and provides the structural framework for processing recombination sites into crossovers. Humans show individual differences in the number of crossovers generated across the genome. Recently, an anonymous gene variant in C14ORF39/SIX6OS1 was identified that influences the recombination rate in humans. Here we show that C14ORF39/SIX6OS1 encodes a component of the central element of the synaptonemal complex. Yeast two-hybrid analysis reveals that SIX6OS1 interacts with the well-established protein synaptonemal complex central element 1 (SYCE1). Mice lacking SIX6OS1 are defective in chromosome synapsis at meiotic prophase I, which provokes an arrest at the pachytene-like stage and results in infertility. In accordance with its role as a modifier of the human recombination rate, SIX6OS1 is essential for the appropriate processing of intermediate recombination nodules before crossover formation.}, 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} } @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{BertChmielewskaBergmannetal.2016, author = {Bert, Bettina and Chmielewska, Justyna and Bergmann, Sven and Busch, Maximilian and Driever, Wolfgang and Finger-Baier, Karin and H{\"o}ßler, Johanna and K{\"o}hler, Almut and Leich, Nora and Misgeld, Thomas and N{\"o}ldner, Torsten and Reiher, Annegret and Schartl, Manfred and Seebach-Sproedt, Anja and Thumberger, Thomas and Sch{\"o}nfelder, Gilbert and Grune, Barbara}, title = {Considerations for a European animal welfare standard to evaluate adverse phenotypes in teleost fish}, series = {The EMBO Journal}, volume = {35}, journal = {The EMBO Journal}, number = {11}, doi = {10.15252/embj.201694448}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188783}, pages = {1151-1154}, year = {2016}, abstract = {No abstract available.}, 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{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{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{DeelemanReinholdMillerFloren2016, author = {Deeleman-Reinhold, Christa L. and Miller, Jeremy and Floren, Andreas}, title = {Depreissia decipiens, an enigmatic canopy spider from Borneo revisited (Araneae, Salticidae), with remarks on the distribution and diversity of canopy spiders in Sabah, Borneo}, series = {ZooKeys}, volume = {556}, journal = {ZooKeys}, doi = {10.3897/zookeys.556.6174}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168342}, pages = {1-17}, year = {2016}, abstract = {Depreissia is a little known genus comprising two hymenopteran-mimicking species, one found in Central Africa and one in the north of Borneo. The male of D. decipiens is redescribed, the female is described for the first time. The carapace is elongated, dorsally flattened and rhombus-shaped, the rear of the thorax laterally depressed and transformed, with a pair of deep pits; the pedicel is almost as long as the abdomen. The male palp is unusual, characterized by the transverse deeply split membranous tegulum separating a ventral part which bears a sclerotized tegular apophysis and a large dagger-like retrodirected median apophysis. The female epigyne consists of one pair of large adjacent spermathecae and very long copulatory ducts arising posteriorly and rising laterally alongside the spermathecae continuing in several vertical and horizontal coils over the anterior surface. Relationships within the Salticidae are discussed and an affinity with the Cocalodinae is suggested. Arguments are provided for a hypothesis that D. decipiens is not ant-mimicking as was previously believed, but is a mimic of polistinine wasps. The species was found in the canopy in the Kinabalu area only, in primary and old secondary rainforest at 200-700 m.a.s.l. Overlap of canopy-dwelling spider species with those in the understorey are discussed and examples of species richness and endemism in the canopy are highlighted. Canopy fogging is a very efficient method of collecting for most arthropods. The canopy fauna adds an extra dimension to the known biodiversity of the tropical rainforest. In southeast Asia, canopy research has been neglected, inhibiting evaluation of comparative results of this canopy project with that from other regions. More use of fogging as a collecting method would greatly improve insight into the actual species richness and species distribution in general.}, language = {en} } @article{LorenzinBenaryBaluapurietal.2016, author = {Lorenzin, Francesca and Benary, Uwe and Baluapuri, Apoorva and Walz, Susanne and Jung, Lisa Anna and von Eyss, Bj{\"o}rn and Kisker, Caroline and Wolf, Jana and Eilers, Martin and Wolf, Elmar}, title = {Different promoter affinities account for specificity in MYC-dependent gene regulation}, series = {eLife}, volume = {5}, journal = {eLife}, doi = {10.7554/eLife.15161}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-162913}, pages = {e15161}, year = {2016}, abstract = {Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells.}, language = {en} } @article{KupperStigloherFeldhaaretal.2016, author = {Kupper, Maria and Stigloher, Christian and Feldhaar, Heike and Gross, Roy}, title = {Distribution of the obligate endosymbiont Blochmannia floridanus and expression analysis of putative immune genes in ovaries of the carpenter ant Camponotus floridanus}, series = {Arthropod Structure \& Development}, volume = {45}, journal = {Arthropod Structure \& Development}, number = {5}, doi = {10.1016/j.asd.2016.09.004}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-187482}, pages = {475-487}, year = {2016}, abstract = {The bacterial endosymbiont Blochmannia floridanus of the carpenter ant Camponotus floridanus contributes to its hosts' ontogeny via nutritional upgrading during metamorphosis. This primary endosymbiosis is essential for both partners and vertical transmission of the endosymbionts is guaranteed by bacterial infestation of oocytes. Here we present a detailed analysis of the presence and localisation of B. floridanus in the ants' ovaries obtained by FISH and TEM analyses. The most apical part of the germarium harbouring germ-line stem cells (GSCs) is not infected by the bacteria. The bacteria are detectable for the first time in lower parts of the germarium when cystocytes undergo the 4th and 5th division and B. floridanus infects somatic cells lying under the basal lamina surrounding the ovarioles. With the beginning of cystocyte differentiation, the endosymbionts are exclusively transported from follicle cells into the growing oocytes. This infestation of the oocytes by bacteria very likely involves exocytosis endocytosis processes between follicle cells and the oocytes. Nurse cells were never found to harbour the endosymbionts. Furthermore we present first gene expression data in C floridanus ovaries. These data indicate a modulation of immune gene expression which may facilitate tolerance towards the endosymbionts and thus may contribute to their transovarial transmission.}, language = {en} } @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{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{VazeHelfrichFoerster2016, author = {Vaze, Koustubh M. and Helfrich-F{\"o}rster, Charlotte}, title = {Drosophila ezoana uses an hour-glass or highly damped circadian clock for measuring night length and inducing diapause}, series = {Physiological Entomology}, volume = {41}, journal = {Physiological Entomology}, number = {4}, doi = {10.1111/phen.12165}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-204278}, pages = {378-389}, year = {2016}, abstract = {Insects inhabiting the temperate zones measure seasonal changes in day or night length to enter the overwintering diapause. Diapause induction occurs after the duration of the night exceeds a critical night length (CNL). Our understanding of the time measurement mechanisms is continuously evolving subsequent to B{\"u}nning's proposal that circadian systems play the clock role in photoperiodic time measurement (B{\"u}nning, 1936). Initially, the photoperiodic clocks were considered to be either based on circadian oscillators or on simple hour-glasses, depending on 'positive' or 'negative' responses in Nanda-Hamner and B{\"u}nsow experiments (Nanda \& Hammer, 1958; B{\"u}nsow, 1960). However, there are also species whose responses can be regarded as neither 'positive', nor as 'negative', such as the Northern Drosophila species Drosophila ezoana, which is investigated in the present study. In addition, modelling efforts show that the 'positive' and 'negative' Nanda-Hamner responses can also be provoked by circadian oscillators that are damped to different degrees: animals with highly sustained circadian clocks will respond 'positive' and those with heavily damped circadian clocks will respond 'negative'. In the present study, an experimental assay is proposed that characterizes the photoperiodic oscillators by determining the effects of non-24-h light/dark cycles (T-cycles) on critical night length. It is predicted that there is (i) a change in the critical night length as a function of T-cycle period in sustained-oscillator-based clocks and (ii) a fxed night-length measurement (i.e. no change in critical night length) in damped-oscillator-based clocks. Drosophila ezoana flies show a critical night length of approximately 7 h irrespective of T-cycle period, suggesting a damped-oscillator-based photoperiodic clock. The conclusion is strengthened by activity recordings revealing that the activity rhythm of D. ezoana flies also dampens in constant darkness.}, language = {en} } @article{DjuzenovaFiedlerKatzeretal.2016, author = {Djuzenova, Cholpon S. and Fiedler, Vanessa and Katzer, Astrid and Michel, Konstanze and Deckert, Stefanie and Zimmermann, Heiko and Sukhorukov, Vladimir L. and Flentje, Michael}, title = {Dual PI3K-and mTOR-inhibitor PI-103 can either enhance or reduce the radiosensitizing effect of the Hsp90 inhibitor NVP-AUY922 in tumor cells: The role of drug-irradiation schedule}, series = {Oncotarget}, volume = {7}, journal = {Oncotarget}, number = {25}, doi = {10.18632/oncotarget.9501}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177770}, pages = {38191-38209}, year = {2016}, abstract = {Inhibition of Hsp90 can increase the radiosensitivity of tumor cells. However, inhibition of Hsp90 alone induces the anti-apoptotic Hsp70 and thereby decreases radiosensitivity. Therefore, preventing Hsp70 induction can be a promising strategy for radiosensitization. PI-103, an inhibitor of PI3K and mTOR, has previously been shown to suppress the up-regulation of Hsp70. Here, we explore the impact of combining PI-103 with the Hsp90 inhibitor NVP-AUY922 in irradiated glioblastoma and colon carcinoma cells. We analyzed the cellular response to drug-irradiation treatments by colony-forming assay, expression of several marker proteins, cell cycle progression and induction/repair of DNA damage. Although PI-103, given 24 h prior to irradiation, slightly suppressed the NVP-AUY922-mediated up-regulation of Hsp70, it did not cause radiosensitization and even diminished the radiosensitizing effect of NVP-AUY922. This result can be explained by the activation of PI3K and ERK pathways along with G1-arrest at the time of irradiation. In sharp contrast, PI-103 not only exerted a radiosensitizing effect but also strongly enhanced the radiosensitization by NVP-AUY922 when both inhibitors were added 3 h before irradiation and kept in culture for 24 h. Possible reasons for the observed radiosensitization under this drug-irradiation schedule may be a down-regulation of PI3K and ERK pathways during or directly after irradiation, increased residual DNA damage and strong G2/M arrest 24 h thereafter. We conclude that duration of drug treatment before irradiation plays a key role in the concomitant targeting of PI3K/mTOR and Hsp90 in tumor cells.}, language = {en} } @phdthesis{Beck2016, author = {Beck, Katherina}, title = {Einfluss von RSK auf die Aktivit{\"a}t von ERK, den axonalen Transport und die synaptische Funktion in Motoneuronen von \(Drosophila\) \(melanogaster\)}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-130717}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {In dieser Arbeit sollte die Funktion von RSK in Motoneuronen von Drosophila untersucht werden. Mutationen im RSK2-Gen verursachen das Coffin-Lowry-Syndrom (CLS), das durch mentale Retardierung charakterisiert ist. RSK2 ist haupts{\"a}chlich in Regionen des Gehirns exprimiert, in denen Lernen und Ged{\"a}chtnisbildung stattfinden. In M{\"a}usen und Drosophila, die als Modellorganismen f{\"u}r CLS dienen, konnten auf makroskopischer Ebene keine Ver{\"a}nderungen in den Hirnstrukturen gefunden werden, dennoch wurden in verschiedenen Verhaltensstudien Defekte im Lernen und der Ged{\"a}chtnisbildung beobachtet. Die synaptische Plastizit{\"a}t und die einhergehenden Ver{\"a}nderungen in den Eigenschaften der Synapse sind fundamental f{\"u}r adaptives Verhalten. Zur Analyse der synaptischen Plastizit{\"a}t eignet sich das neuromuskul{\"a}re System von Drosophila als Modell wegen des stereotypen Innervierungsmusters und der Verwendung ionotroper Glutamatrezeptoren, deren Untereinheiten homolog sind zu den Untereinheiten der Glutamatrezeptoren des AMPA-Typs aus S{\"a}ugern, die wesentlich f{\"u}r die Bildung von LTP im Hippocampus sind. Zun{\"a}chst konnte gezeigt werden, dass RSK in den Motoneuronen von Drosophila an der pr{\"a}synaptischen Seite lokalisiert ist, wodurch RSK eine Synapsen-spezifische Funktion aus{\"u}ben k{\"o}nnte. Morphologische Untersuchungen der Struktur der neuromuskul{\"a}ren Synapsen konnten aufzeigen, dass durch den Verlust von RSK die Gr{\"o}ße der neuromuskul{\"a}ren Synapse, der Boutons sowie der Aktiven Zonen und Glutamatrezeptorfelder reduziert ist. Obwohl mehr Boutons gebildet werden, sind weniger Aktive Zonen und Glutamatrezeptorfelder in der neuromuskul{\"a}ren Synapse enthalten. RSK reguliert die synaptische Transmission, indem es die postsynaptische Sensitivit{\"a}t, nicht aber die Freisetzung der Neurotransmitter an der pr{\"a}synaptischen Seite beeinflusst, obwohl in immunhistochemischen Analysen eine postsynaptische Lokalisierung von RSK nicht nachgewiesen werden konnte. RSK ist demnach an der Regulation der synaptischen Plastizit{\"a}t glutamaterger Synapsen beteiligt. Durch immunhistochemische Untersuchungen konnte erstmals gezeigt werden, dass aktiviertes ERK an der pr{\"a}synaptischen Seite lokalisiert ist und diese synaptische Lokalisierung von RSK reguliert wird. Dar{\"u}ber hinaus konnte in dieser Arbeit nachgewiesen werden, dass durch den Verlust von RSK hyperaktiviertes ERK in den Zellk{\"o}rpern der Motoneurone vorliegt. RSK wird durch den ERK/MAPK-Signalweg aktiviert und {\"u}bernimmt eine Funktion sowohl als Effektorkinase als auch in der Negativregulation des Signalwegs. Demnach dient RSK in den Zellk{\"o}rpern der Motoneurone als Negativregulator des ERK/MAPK-Signalwegs. Dar{\"u}ber hinaus k{\"o}nnte RSK die Verteilung von aktivem ERK in den Subkompartimenten der Motoneurone regulieren. Da in vorangegangenen Studien gezeigt werden konnte, dass ERK an der Regulation der synaptischen Plastizit{\"a}t beteiligt ist, indem es die Insertion der AMPA-Rezeptoren zur Bildung der LTP reguliert, sollte in dieser Arbeit aufgekl{\"a}rt werden, ob der Einfluss von RSK auf die synaptische Plastizit{\"a}t durch seine Funktion als Negativregulator von ERK zustande kommt. Untersuchungen der genetischen Interaktion von rsk und rolled, dem Homolog von ERK in Drosophila, zeigten, dass die durch den Verlust von RSK beobachtete reduzierte Gesamtzahl der Aktiven Zonen und Glutamatrezeptorfelder der neuromuskul{\"a}ren Synapse auf die Funktion von RSK als Negativregulator von ERK zur{\"u}ckzuf{\"u}hren ist. Die Gr{\"o}ße der neuromuskul{\"a}ren Synapse sowie die Gr{\"o}ße der Aktiven Zonen und Glutamatrezeptorfelder beeinflusst RSK allerdings durch seine Funktion als Effektorkinase des ERK/MAPK-Signalwegs. Studien des axonalen Transports von Mitochondrien zeigten, dass dieser in vielen neuropathologischen Erkrankungen beeintr{\"a}chtigt ist. Die durchgef{\"u}hrten Untersuchungen des axonalen Transports in Motoneuronen konnten eine neue Funktion von RSK in der Regulation des axonalen Transports aufdecken. In den Axonen der Motoneurone von RSK-Nullmutanten wurden BRP- und CSP-Agglomerate nachgewiesen. RSK k{\"o}nnte an der Regulation des axonalen Transports von pr{\"a}synaptischem Material beteiligt sein. Durch den Verlust von RSK wurden weniger Mitochondrien in anterograder Richtung entlang dem Axon transportiert, daf{\"u}r verweilten mehr Mitochondrien in station{\"a}ren Phasen. Diese Ergebnisse zeigen, dass auch der anterograde Transport von Mitochondrien durch den Verlust von RSK beeintr{\"a}chtigt ist.}, subject = {Taufliege}, language = {de} } @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{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} } @phdthesis{AppeltMenzel2016, author = {Appelt-Menzel, Antje}, title = {Etablierung und Qualifizierung eines humanen Blut-Hirn-Schranken-Modells unter Verwendung von induziert pluripotenten und multipotenten Stammzellen}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134646}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2016}, abstract = {Die Blut-Hirn-Schranke (BHS) stellt eine der dichtesten und wichtigsten Barrieren zwischen Blutzirkulation und Zentralnervensystem (ZNS) dar. Sie besteht aus spezialisierten Endothelzellen, welche die zerebralen Kapillaren auskleiden und durch sehr dichte Tight Junctions (TJs) miteinander verbunden sind. Weitere Komponenten der dynamischen Blut-Hirn-Schrankenbarriere stellen Perizyten, Astrozyten, Neurone und Mikrogliazellen dar, welche zusammen mit der extrazellul{\"a}ren Matrix der Basalmembran der Gehirnkapillaren und den zuvor genannten Endothelzellen ein komplexes regulatorisches System, die so genannte neurovaskul{\"a}re Einheit bilden (Hawkins und Davis 2005). Die Hauptfunktionen der BHS lassen sich in drei Untergruppen untergliedern, die physikalische, metabolische und Transport-Barriere (Neuhaus und Noe 2010). Haupts{\"a}chlich dient die BHS der Aufrechterhaltung der Hom{\"o}ostase des ZNS und dem Schutz vor neurotoxischen Substanzen sowie Pathogenen, wie Bakterien und Viren. Zudem ist sie auch f{\"u}r die Versorgung der Neuronen mit N{\"a}hrstoffen und regulierenden Substanzen sowie den Efflux von Stoffwechselendprodukten des ZNS zur{\"u}ck ins Blut verantwortlich. F{\"u}r die Entwicklung von Medikamenten zur Behandlung von neurodegenerativen Erkrankungen, wie Morbus Alzheimer, Morbus Parkinson und Multiple Sklerose oder Gehirntumoren, stellt die Dichtigkeit der BHS gegen{\"u}ber Substanzen und die hohe metabolische Aktivit{\"a}t der Endothelzellen aber ein großes Problem dar. Viele Medikamente sind nicht in der Lage in ausreichender Konzentration die BHS zu {\"u}berwinden, um an ihren Wirkort zu gelangen oder werden vor dem Transport metabolisiert und die Wirksamkeit dadurch eingeschr{\"a}nkt. Weiterhin spielen auch Defekte der BHS eine entscheidende Rolle in der Beeinflussung der Pathogenese vieler ZNS-Erkrankungen. Aufgrund des hohen Bedarfs an geeigneten Testsystemen in der Grundlagen- sowie pr{\"a}klinischen Forschung f{\"u}r Medikamentenentwicklung und Infektionsstudien wurden eine Vielzahl unterschiedlicher BHS-Modelle entwickelt. Neben in silico-, azellul{\"a}ren in vitro- und in vivo-Modellen sind auch zahlreiche zellbasierte Modelle der BHS entwickelt worden. Standardisierte Modelle auf Basis immortalisierter Zelllinien jedoch weisen nur eine inhomogene TJ-Expression auf und verf{\"u}gen meist {\"u}ber eine geringe Barriereintegrit{\"a}t, erfasst {\"u}ber transendotheliale elektrische Widerst{\"a}nde (TEER) unter 150 · cm2 (Deli et al. 2005). Im Vergleich dazu wurden in Tierexperimenten TEER-Werte von mehr als 1500 · cm2 an der BHS gemessen (Butt et al. 1990; Crone und Olesen 1982). Die Verf{\"u}gbarkeit humaner prim{\"a}rer BHS-Zellen ist sehr limitiert und ihr Einsatz nicht nur im Hinblick auf ethische Aspekte bedenklich. Humane Gehirnzellen k{\"o}nnen z. B. aus Biopsie- oder Autopsiematerial von Patienten mit Epilepsie oder Gehirntumoren isoliert werden. Allerdings besteht hier das Risiko, dass die isolierten Zellen krankheitsbedingt ver{\"a}ndert sind, was die Eigenschaften der BHS-Modelle erheblich beeinflussen kann. Eine Alternative, die diese Probleme umgeht, ist die Verwendung von humanen induziert pluripotenten Stammzellen (hiPSCs), um standardisierte humane BHS-Modelle unter reproduzierbaren Bedingungen bereitzustellen. Im Rahmen dieser Arbeit ist es gelungen, hiPSCs in vitro nach etablierten und standardisierten Methoden in Endothelzellen der BHS, neurale Stammzellen (hiPS-NSCs) sowie Astrozyten (hiPS-A) zu differenzieren (Lippmann et al. 2012; Lippmann et al. 2014; Wilson et al. 2015; Yan et al. 2013;Reinhardt et al. 2013) und zum Aufbau der Modelle einzusetzen. Die Endothelzellen wurden mit Hilfe protein- und genbasierter Nachweismethoden auf das Vorhandensein von endothelzellspezifischen TJ-Markern sowie spezifischen Transportern untersucht und funktionell charakterisiert. Die Kryokonservierung der hiPS-EC-Progenitoren, die im Rahmen der vorliegenden Arbeit entwickelt wurde, erm{\"o}glicht eine gr{\"o}ßere r{\"a}umliche und zeitliche Flexibilit{\"a}t beim Arbeiten mit den stammzellbasierten Modellen sowie das Anlegen standardisierter Zellbanken. Weiterhin wurden multipotente NSCs aus fetalen Gehirnbiopsien isoliert (fNSCs) und als Kontrollkulturen zu den hiPS-NSCs f{\"u}r den Aufbau von BHS-Modellen eingesetzt. Mit dem Ziel die in vivo-BHS bestm{\"o}glich zu imitieren und die Modelleigenschaften zu optimieren, wurde ein Set aus zehn unterschiedlichen BHS-Modellen basierend auf prim{\"a}ren Zellen, hiPSCs und fNSCs analysiert. Der Aufbau der BHS-Modelle erfolgte unter Verwendung von Transwellsystemen. Durch die systematische Untersuchung des Einflusses der unterschiedlichen Zelltypen der neurovaskul{\"a}ren Einheit auf die Barriereintegrit{\"a}t und Genexpression des BHS-Endothels, konnten die Quadrupel-Kulturen mit Perizyten, Astrozyten und hiPS-NSCs als die Kultur mit den physiologischsten Eigenschaften identifiziert werden. Auf Grund der signifikant erh{\"o}hten TEER-Werte von bis zu 2500 · cm2 und einer um mindestens 1,5-fachen Steigerung der Genexpression BHSrelevanter Transporter und TJ-Molek{\"u}le gegen{\"u}ber den Monokulturen, wurden diese Modelle f{\"u}r weiterf{\"u}hrende Studien ausgew{\"a}hlt. Das Vorhandensein eines komplexen, in vivo-{\"a}hnlichen TJ-Netzwerkes, bestehend aus Occludin, Claudin 1, 3, 4 und 5, konnte mittels quantitativer Realtime-PCR, Western Blot sowie ultrastruktureller Analyse in der Gefrierbruch- und Raster-Elektronenmikroskopie nachgewiesen werden. Neben der Begrenzung der parazellul{\"a}ren Permeabilit{\"a}t, welche {\"u}ber die geringe Permeation von FITC-Dextran (4 kDa und 40 kDa), Fluoreszein und Lucifer Yellow nachgewiesen wurde, stellt die BHS ebenfalls eine Barriere f{\"u}r den transzellul{\"a}ren Transport von Substanzen dar. Eine Beurteilung der Modelle hinsichtlich der Qualifikation f{\"u}r die Nutzung im Wirkstoffscreening wurde mit Hilfe von Transportversuchen unter dem Einsatz von BHS-relevanten Referenzsubstanzen durchgef{\"u}hrt. Die Klassifikation der Testsubstanzen erfolgte analog ihrer Permeationsgeschwindigkeiten: Diazepam und Koffein gelten als schnell transportierte Wirkstoffe, Ibuprofen, Celecoxib und Diclofenac werden mit einer mittleren Geschwindigkeit {\"u}ber die BHS transportiert und Loratadin sowie Rhodamin 123 sind langsam permeierende Substanzen. Innerhalb der Versuche mit den Quadrupelkulturen wurde diese Reihenfolge best{\"a}tigt, lediglich f{\"u}r Koffein wurde ein signifikant niedrigerer Permeationskoeffizient verglichen mit der Monokultur erzielt. Der Einsatz der hiPSC-Technologie erm{\"o}glicht es zudem, aus einer Stammzelllinie große Mengen an humanen somatischen Zelltypen zu generieren und f{\"u}r gezielte Anwendungen bereitzustellen. Es konnte im Rahmen dieser Arbeit gezeigt werden, dass mit Hilfe eines eigens f{\"u}r diese Zwecke konstruierten R{\"u}hrreaktorsystems eine reproduzierbare Expansion der hiPSCs unter definierten Bedingungen erm{\"o}glicht wurde. Basierend auf dieser Grundlage ist nun ein Hochdurchsatz-Screening von Medikamenten denkbar. Die in dieser Arbeit pr{\"a}sentierten Daten belegen die Etablierung eines stammzellbasierten in vitro- Quadrupelmodels der humanen BHS, welches {\"u}ber in vivo-{\"a}hnliche Eigenschaften verf{\"u}gt. Die Anforderungen, die an humane BHS-Modelle gestellt werden, wie die Reproduzierbarkeit der Ergebnisse, eine angemessene Charakterisierung, welche die Untersuchung der Permeabilit{\"a}t von Referenzsubstanzen einschließt, die Analyse der Expression von BHS-relevanten Transportermolek{\"u}len sowie die solide und physiologische Morphologie der Zellen, wurden erf{\"u}llt. Das etablierte BHS-Modell kann in der Pharmaindustrie f{\"u}r die Entwicklung von Medikamenten eingesetzt werden. Ausreichend qualifizierte Modelle k{\"o}nnen hier in der pr{\"a}klinischen Forschung genutzt werden, um Toxizit{\"a}ts- und Transportstudien an neu entwickelten Substanzen durchzuf{\"u}hren und eine bessere in vitro-in vivo-Korrelation der Ergebnisse zu erm{\"o}glichen oder Mechanismen zu entwickeln, um die BHS-Barriere gezielt zu {\"u}berwinden.}, subject = {Blut-Hirn-Schranke}, language = {de} } @article{HackerEscalonaEspinosaConsalvoetal.2016, author = {Hacker, Ulrich T. and Escalona-Espinosa, Laura and Consalvo, Nicola and Goede, Valentin and Schiffmann, Lars and Scherer, Stefan J. and Hedge, Priti and Van Cutsem, Eric and Coutelle, Oliver and B{\"u}ning, Hildegard}, title = {Evaluation of Angiopoietin-2 as a biomarker in gastric cancer: results from the randomised phase III AVAGAST trial}, series = {British Journal of Cancer}, volume = {114}, journal = {British Journal of Cancer}, number = {8}, doi = {10.1038/bjc.2016.30}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189578}, pages = {855-862}, year = {2016}, abstract = {Background: In the phase III AVAGAST trial, the addition of bevacizumab to chemotherapy improved progression-free survival (PFS) but not overall survival (OS) in patients with advanced gastric cancer. We studied the role of Angiopoietin-2 (Ang-2), a key driver of tumour angiogenesis, metastasis and resistance to antiangiogenic treatment, as a biomarker. Methods: Previously untreated, advanced gastric cancer patients were randomly assigned to receive bevacizumab (n = 387) or placebo (n = 387) in combination with chemotherapy. Plasma collected at baseline and at progression was analysed by ELISA. The role of Ang-2 as a prognostic and a predictive biomarker of bevacizumab efficacy was studied using a Cox proportional hazards model. Logistic regression analysis was applied for correlations with metastasis. Results: Median baseline plasma Ang-2 levels were lower in Asian (2143 pg ml\(^-\)\(^1\)) vs non-Asian patients (3193 pg ml\(^-\)\(^1\)), P<0.0001. Baseline plasma Ang-2 was identified as an independent prognostic marker for OS but did not predict bevacizumab efficacy alone or in combination with baseline VEGF. Baseline plasma Ang-2 correlated with the frequency of liver metastasis (LM) at any time: Odds ratio per 1000 pg ml\(^-\)\(^1\) increase: 1.19; 95\% CI 1.10-1.29; P<0.0001 (non-Asians) and 1.37; 95\% CI 1.13-1.64; P = 0.0010 (Asians). Conclusions: Baseline plasma Ang-2 is a novel prognostic biomarker for OS in advanced gastric cancer strongly associated with LM. Differences in Ang-2 mediated vascular response may, in part, account for outcome differences between Asian and non-Asian patients; however, data have to be further validated. Ang-2 is a promising drug target in gastric cancer.}, 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{ThormannAhrensArmijosetal.2016, author = {Thormann, Birthe and Ahrens, Dirk and Armijos, Diego Mar{\´i}n and Peters, Marcell K. and Wagner, Thomas and W{\"a}gele, Johann W.}, title = {Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae) of an Ecuadorian Mountain Forest Using DNA Barcoding}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {2}, doi = {10.1371/journal.pone.0148268}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167253}, pages = {e0148268}, year = {2016}, abstract = {Background Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates. Methodology/Principal Findings Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae) of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic) species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs) (n = 284-289). Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2) and 469-481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m) had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation. Conclusions/Significance Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50\% singletons), the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a valuable tool for evaluating biodiversity of hyperdiverse insect communities, especially when exact taxonomic identifications are missing.}, 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{SchlinkertLudwigBataryetal.2016, author = {Schlinkert, Hella and Ludwig, Martin and Bat{\´a}ry, P{\´e}ter and Holzschuh, Andrea and Kov{\´a}cs-Hosty{\´a}nszki, Anik{\´o} and Tscharntke, Teja and Fischer, Christina}, title = {Forest specialist and generalist small mammals in forest edges and hedges}, series = {Wildlife Biology}, volume = {22}, journal = {Wildlife Biology}, number = {3}, doi = {10.2981/wlb.00176}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-168333}, pages = {86-94}, year = {2016}, abstract = {Agricultural intensification often leads to fragmentation of natural habitats, such as forests, and thereby negatively affects forest specialist species. However, human introduced habitats, such as hedges, may counteract negative effects of forest fragmentation and increase dispersal, particularly of forest specialists. We studied effects of habitat type (forest edge versus hedge) and hedge isolation from forests (connected versus isolated hedge) in agricultural landscapes on abundance, species richness and community composition of mice, voles and shrews in forest edges and hedges. Simultaneously to these effects of forest edge/hedge type we analysed impacts of habitat structure, namely percentage of bare ground and forest edge/hedge width, on abundance, species richness and community composition of small mammals. Total abundance and forest specialist abundance (both driven by the most abundant species Myodes glareolus, bank vole) were higher in forest edges than in hedges, while hedge isolation had no effect. In contrast, abundance of habitat generalists was higher in isolated compared to connected hedges, with no effect of habitat type (forest edge versus hedge). Species richness as well as abundance of the most abundant habitat generalist Sorex araneus (common shrew), were not affected by habitat type or hedge isolation. Decreasing percentage of bare ground and increasing forest edge/hedge width was associated with increased abundance of forest specialists, while habitat structure was unrelated to species richness or abundance of any other group. Community composition was driven by forest specialists, which exceeded habitat generalist abundance in forest edges and connected hedges, while abundances were similar to each other in isolated hedges. Our results show that small mammal forest specialists prefer forest edges as habitats over hedges, while habitat generalists are able to use unoccupied ecological niches in isolated hedges. Consequently even isolated hedges can be marginal habitats for forest specialists and habitat generalists and thereby may increase regional farmland biodiversity.}, language = {en} } @article{ChagtaiZillDaineseetal.2016, author = {Chagtai, Tasnim and Zill, Christina and Dainese, Linda and Wegert, Jenny and Savola, Suvi and Popov, Sergey and Mifsud, William and Vujanic, Gordan and Sebire, Neil and Le Bouc, Yves and Ambros, Peter F. and Kager, Leo and O`Sullivan, Maureen J. and Blaise, Annick and Bergeron, Christophe and Holmquist Mengelbier, Linda and Gisselsson, David and Kool, Marcel and Tytgat, Godelieve A.M. and van den Heuvel-Eibrink, Marry M. and Graf, Norbert and van Tinteren, Harm and Coulomb, Aurore and Gessler, Manfred and Williams, Richard Dafydd and Pritchard-Jones, Kathy}, title = {Gain of 1q As a Prognostic Biomarker in Wilms Tumors (WTs) Treated With Preoperative Chemotherapy in the International Society of Paediatric Oncology (SIOP) WT 2001 Trial: a SIOP Renal Tumours Biology Consortium Study}, series = {Journal of Clinical Oncology}, volume = {34}, journal = {Journal of Clinical Oncology}, number = {26}, doi = {10.1200/JCO.2015.66.0001}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-187478}, pages = {3195-3205}, year = {2016}, abstract = {Purpose Wilms tumor (WT) is the most common pediatric renal tumor. Treatment planning under International Society of Paediatric Oncology (SIOP) protocols is based on staging and histologic assessment of response to preoperative chemotherapy. Despite high overall survival (OS), many relapses occur in patients without specific risk factors, and many successfully treated patients are exposed to treatments with significant risks of late effects. To investigate whether molecular biomarkers could improve risk stratification, we assessed 1q status and other potential copy number biomarkers in a large WT series. Materials and Methods WT nephrectomy samples from 586 SIOP WT 2001 patients were analyzed using a multiplex ligation-dependent probe amplification (MLPA) assay that measured the copy number of 1q and other regions of interest. Results One hundred sixty-seven (28\%) of 586 WTs had 1q gain. Five-year event-free survival (EFS) was 75.0\% in patients with 1q gain (95\% CI, 68.5\% to 82.0\%) and 88.2\% in patients without gain (95\% CI, 85.0\% to 91.4\%). OS was 88.4\% with gain (95\% CI, 83.5\% to 93.6\%) and 94.4\% without gain (95\% CI, 92.1\% to 96.7\%). In univariable analysis, 1q gain was associated with poorer EFS (P<.001; hazard ratio, 2.33) and OS (P=.01; hazard ratio, 2.16). The association of 1q gain with poorer EFS retained significance in multivariable analysis adjusted for 1p and 16q loss, sex, stage, age, and histologic risk group. Gain of 1q remained associated with poorer EFS in tumor subsets limited to either intermediate-risk localized disease or nonanaplastic localized disease. Other notable aberrations associated with poorer EFS included MYCN gain and TP53 loss. Conclusion Gain of 1q is a potentially valuable prognostic biomarker in WT, in addition to histologic response to preoperative chemotherapy and tumor stage.}, language = {en} } @article{WidmannArtingerBiesingeretal.2016, author = {Widmann, Annekathrin and Artinger, Marc and Biesinger, Lukas and Boepple, Kathrin and Peters, Christina and Schlechter, Jana and Selcho, Mareike and Thum, Andreas S.}, title = {Genetic Dissection of Aversive Associative Olfactory Learning and Memory in Drosophila Larvae}, series = {PLoS Genetics}, volume = {12}, journal = {PLoS Genetics}, number = {10}, doi = {10.1371/journal.pgen.1006378}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166672}, pages = {e1006378}, year = {2016}, abstract = {Memory formation is a highly complex and dynamic process. It consists of different phases, which depend on various neuronal and molecular mechanisms. In adult Drosophila it was shown that memory formation after aversive Pavlovian conditioning includes—besides other forms—a labile short-term component that consolidates within hours to a longer-lasting memory. Accordingly, memory formation requires the timely controlled action of different neuronal circuits, neurotransmitters, neuromodulators and molecules that were initially identified by classical forward genetic approaches. Compared to adult Drosophila, memory formation was only sporadically analyzed at its larval stage. Here we deconstruct the larval mnemonic organization after aversive olfactory conditioning. We show that after odor-high salt conditioning larvae form two parallel memory phases; a short lasting component that depends on cyclic adenosine 3'5'-monophosphate (cAMP) signaling and synapsin gene function. In addition, we show for the first time for Drosophila larvae an anesthesia resistant component, which relies on radish and bruchpilot gene function, protein kinase C activity, requires presynaptic output of mushroom body Kenyon cells and dopamine function. Given the numerical simplicity of the larval nervous system this work offers a unique prospect for studying memory formation of defined specifications, at full-brain scope with single-cell, and single-synapse resolution.}, 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{FischerHelfrichFoersterPeschel2016, author = {Fischer, Robin and Helfrich-F{\"o}rster, Charlotte and Peschel, Nicolai}, title = {GSK-3 Beta Does Not Stabilize Cryptochrome in the Circadian Clock of Drosophila}, series = {PLoS ONE}, volume = {11}, journal = {PLoS ONE}, number = {1}, doi = {10.1371/journal.pone.0146571}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-180370}, year = {2016}, abstract = {Cryptochrome (CRY) is the primary photoreceptor of Drosophila's circadian clock. It resets the circadian clock by promoting light-induced degradation of the clock protein Timeless (TIM) in the proteasome. Under constant light, the clock stops because TIM is absent, and the flies become arrhythmic. In addition to TIM degradation, light also induces CRY degradation. This depends on the interaction of CRY with several proteins such as the E3 ubiquitin ligases Jetlag (JET) and Ramshackle (BRWD3). However, CRY can seemingly also be stabilized by interaction with the kinase Shaggy (SGG), the GSK-3 beta fly orthologue. Consequently, flies with SGG overexpression in certain dorsal clock neurons are reported to remain rhythmic under constant light. We were interested in the interaction between CRY, Ramshackle and SGG and started to perform protein interaction studies in S2 cells. To our surprise, we were not able to replicate the results, that SGG overexpression does stabilize CRY, neither in S2 cells nor in the relevant clock neurons. SGG rather does the contrary. Furthermore, flies with SGG overexpression in the dorsal clock neurons became arrhythmic as did wild-type flies. Nevertheless, we could reproduce the published interaction of SGG with TIM, since flies with SGG overexpression in the lateral clock neurons shortened their free-running period. We conclude that SGG does not directly interact with CRY but rather with TIM. Furthermore we could demonstrate, that an unspecific antibody explains the observed stabilization effects on CRY.}, language = {en} } @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{WoelflingBeckerUhletal.2016, author = {W{\"o}lfling, Mirko and Becker, Mira C. and Uhl, Britta and Traub, Anja and Fiedler, Konrad}, title = {How differences in the settling behaviour of moths (Lepidoptera) may contribute to sampling bias when using automated light traps}, series = {European Journal of Entomology}, volume = {113}, journal = {European Journal of Entomology}, doi = {10.14411/eje.2016.066}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-191154}, pages = {502-506}, year = {2016}, abstract = {Quantitative community-wide moth surveys frequently employ flight-interception traps equipped with UV-light emitting sources as attractants. It has long been known that moth species differ in their responsiveness to light traps. We studied how the settling behaviour of moths at a light trap may further contribute to sampling bias. We observed the behaviour of 1426 moths at a light tower. Moths were classified as either, settling and remaining still after arrival, or continually moving on the gauze for extended periods of time. Moths that did not move after settling may not end up in the sampling container of the light trap and therefore are under-represented in automated trap samples relative to their true proportions in the community. Our analyses revealed highly significant behavioural differences between moths that differed in body size. Small moths were more likely to remain stationary after settling. As a corollary, representatives of three taxa, which in Europe are predominantly small species (Nolidae, Geometridae: Eupitheciini, Erebidae: Lithosiini), usually settled down immediately, whereas most other moths remained active on or flying around the trap for some time. Moth behaviour was also modulated by ambient temperature. At high temperatures, they were less likely to settle down immediately, but this behavioural difference was most strongly apparent among medium-sized moths. These results indicate the likely extent of the sampling bias when analysing and interpreting automated light-trap samples. Furthermore, to control for temperature modulated sampling bias temperature should always be recorded when sampling moths using flight-interception traps.}, language = {en} } @article{PfeifferKruegerMaierhoferetal.2016, author = {Pfeiffer, Susanne and Kr{\"u}ger, Jacqueline and Maierhofer, Anna and B{\"o}ttcher, Yvonne and Kl{\"o}ting, Nora and El Hajj, Nady and Schleinitz, Dorit and Sch{\"o}n, Michael R. and Dietrich, Arne and Fasshauer, Mathias and Lohmann, Tobias and Dreßler, Miriam and Stumvoll, Michael and Haaf, Thomas and Bl{\"u}her, Matthias and Kovacs, Peter}, title = {Hypoxia-inducible factor 3A gene expression and methylation in adipose tissue is related to adipose tissue dysfunction}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, number = {27969}, doi = {10.1038/srep27969}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-167662}, year = {2016}, abstract = {Recently, a genome-wide analysis identified DNA methylation of the HIF3A (hypoxia-inducible factor 3A) as strongest correlate of BMI. Here we tested the hypothesis that HIF3A mRNA expression and CpG-sites methylation in adipose tissue (AT) and genetic variants in HIF3A are related to parameters of AT distribution and function. In paired samples of subcutaneous AT (SAT) and visceral AT (VAT) from 603 individuals, we measured HIF3A mRNA expression and analyzed its correlation with obesity and related traits. In subgroups of individuals, we investigated the effects on HIF3A genetic variants on its AT expression (N = 603) and methylation of CpG-sites (N = 87). HIF3A expression was significantly higher in SAT compared to VAT and correlated with obesity and parameters of AT dysfunction (including CRP and leucocytes count). HIF3A methylation at cg22891070 was significantly higher in VAT compared to SAT and correlated with BMI, abdominal SAT and VAT area. Rs8102595 showed a nominal significant association with AT HIF3A methylation levels as well as with obesity and fat distribution. HIF3A expression and methylation in AT are fat depot specific, related to obesity and AT dysfunction. Our data support the hypothesis that HIF pathways may play an important role in the development of AT dysfunction in obesity.}, 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} } @article{LetunicBork2016, author = {Letunic, Ivica and Bork, Peer}, title = {Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees}, series = {Nucleic Acids Research}, volume = {44}, journal = {Nucleic Acids Research}, number = {W1}, doi = {10.1093/nar/gkw290}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166181}, pages = {W242-W245}, year = {2016}, abstract = {Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.}, language = {en} } @article{HolzschuhDaineseGonzalezVaroetal.2016, author = {Holzschuh, Andrea and Dainese, Matteo and Gonzalez-Varo, Juan P. and Mudri-Stojnic, Sonja and Riedinger, Verena and Rundl{\"o}f, Maj and Scheper, Jeroen and Wickens, Jennifer B. and Wickens, Victoria J. and Bommarco, Riccardo and Kleijn, David and Potts, Simon G. and Roberts, Stuart P. M. and Smith, Henrik G. and Vil{\`a}, Montserrat and Vujic, Ante and Steffan-Dewenter, Ingolf}, title = {Mass-flowering crops dilute pollinator abundance in agricultural landscapes across Europe}, series = {Ecology Letters}, volume = {19}, journal = {Ecology Letters}, number = {10}, doi = {10.1111/ele.12657}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-187356}, pages = {1228-1236}, year = {2016}, abstract = {Mass-flowering crops (MFCs) are increasingly cultivated and might influence pollinator communities in MFC fields and nearby semi-natural habitats (SNHs). Across six European regions and 2 years, we assessed how landscape-scale cover of MFCs affected pollinator densities in 408 MFC fields and adjacent SNHs. In MFC fields, densities of bumblebees, solitary bees, managed honeybees and hoverflies were negatively related to the cover of MFCs in the landscape. In SNHs, densities of bumblebees declined with increasing cover of MFCs but densities of honeybees increased. The densities of all pollinators were generally unrelated to the cover of SNHs in the landscape. Although MFC fields apparently attracted pollinators from SNHs, in landscapes with large areas of MFCs they became diluted. The resulting lower densities might negatively affect yields of pollinator- dependent crops and the reproductive success of wild plants. An expansion of MFCs needs to be accompanied by pollinator-supporting practices in agricultural landscapes.}, 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} } @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} }